@article{jeong_tollison_brochu_chou_huntress_yount_zheng_darville_o'connell_peng_2024, title={Cervicovaginal microbial features predict Chlamydia trachomatis spread to the upper genital tract of infected women}, url={https://doi.org/10.1101/2024.11.26.625070}, DOI={10.1101/2024.11.26.625070}, abstractNote={Introduction: Chlamydia trachomatis (CT) infection can lead to pelvic inflammatory disease, infertility and other reproductive sequelae when it ascends to the upper genital tract. Factors including chlamydial burden, co-infection with other sexually-transmitted bacterial pathogens and oral contraceptive use influence risk for upper genital tract spread. Cervicovaginal microbiome composition influences CT susceptibility and we investigated if it contributes to spread by analyzing amplicon sequence variants (ASVs) derived from the V4 region of 16S rRNA genes in vaginal samples collected from women at high risk for CT infection and for whom endometrial infection had been determined. Results: Participants were classified as CT negative (CT-, n=77), CT positive at the cervix (Endo-, n=77), or CT positive at both cervix and endometrium (Endo+, n=66). Although we were unable to identify many significant differences between CT infected and uninfected women, differences in abundance of ASVs representing Lactobacillus iners and L. crispatus subspecies but not dominant lactobacilli were detected. Twelve informative ASVs predicted endometrial chlamydial infection (AUC=0.74), with CT ASV abundance emerging as a key predictor. We also observed a positive correlation between levels of cervically secreted cytokines previously associated with CT ascension and abundance of the informative ASVs. Conclusion: Our findings suggest that vaginal microbial community members may influence chlamydial spread directly by nutrient limitation and/or disrupting endocervical epithelial integrity and indirectly by modulating pro-inflammatory signaling and/or homeostasis of adaptive immunity. Further investigation of these predictive microbial factors may lead to cervicovaginal microbiome biomarkers useful for identifying women at increased risk for disease.}, author={Jeong, Sangmi and Tollison, Tammy S and Brochu, Hayden and Chou, Hsuan and Huntress, Ian and Yount, Kacy S and Zheng, Xiaojing and Darville, Toni and O'Connell, Catherine M. and Peng, Xinxia}, year={2024}, month={Nov} } @article{john_huntress_smith_chou_tollison_covarrubias_crisci_carpenter_peng_2024, title={Human long noncoding RNA,VILMIR,is induced by major respiratory viral infections and modulates the host interferon response}, url={https://doi.org/10.1101/2024.03.25.586578}, DOI={10.1101/2024.03.25.586578}, abstractNote={ABSTRACTLong noncoding RNAs (lncRNAs) are a newer class of noncoding transcripts identified as key regulators of biological processes. Here we aimed to identify novel lncRNA targets that play critical roles in major human respiratory viral infections by systematically mining large-scale transcriptomic datasets. Using bulk RNA-sequencing (RNA-seq) analysis, we identified a previously uncharacterized lncRNA, named virus inducible lncRNA modulator of interferon response (VILMIR), that was consistently upregulated afterin vitroinfluenza infection across multiple human epithelial cell lines and influenza A virus subtypes.VILMIRwas also upregulated after SARS-CoV-2 and RSV infectionsin vitro. We experimentally confirmed the response ofVILMIRto influenza infection and interferon-beta (IFN-β) treatment in the A549 human epithelial cell line and found the expression ofVILMIRwas robustly induced by IFN-β treatment in a dose and time-specific manner. Single cell RNA-seq analysis of bronchoalveolar lavage fluid (BALF) samples from COVID-19 patients uncovered thatVILMIRwas upregulated across various cell types including at least five immune cells. The upregulation ofVILMIRin immune cells was further confirmed in the human T cell and monocyte cell lines, SUP-T1 and THP-1, after IFN-β treatment. Finally, we found that knockdown ofVILMIRexpression reduced the magnitude of host transcriptional responses to IFN-β treatment in A549 cells. Together, our results show thatVILMIRis a novel interferon-stimulated gene (ISG) that regulates the host interferon response and may be a potential therapeutic target for human respiratory viral infections upon further mechanistic investigation.IMPORTANCEIdentifying host factors that regulate the immune response to human respiratory viral infection is critical to developing new therapeutics. Human long noncoding RNAs (lncRNAs) have been found to play key regulatory roles during biological processes, however the majority of lncRNA functions within the host antiviral response remain unknown. In this study, we identified that a previously uncharacterized lncRNA,VILMIR, is upregulated after major respiratory viral infections including influenza, SARS-CoV-2, and RSV. We demonstrated thatVILMIRis an interferon-stimulated gene that is upregulated after interferon-beta (IFN-β) in several human cell types. We also found that knockdown ofVILMIRreduced the magnitude of host transcriptional responses to IFN-β treatment in human epithelial cells. Our results reveal thatVILMIRregulates the host interferon response and may present a new therapeutic target during human respiratory viral infections.}, author={John, Kristen and Huntress, Ian and Smith, Ethan and Chou, Hsuan and Tollison, Tammy S. and Covarrubias, Sergio and Crisci, Elisa and Carpenter, Susan and Peng, Xinxia}, year={2024}, month={Mar} } @article{brochu_smith_jeong_carlson_hansen_tisoncik-go_law_picker_gale_peng_2024, title={Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques}, url={https://doi.org/10.1101/2024.02.27.582186}, DOI={10.1101/2024.02.27.582186}, abstractNote={ABSTRACTBackgroundRhCMV/SIV vaccines protect ∼59% of vaccinated rhesus macaques against repeated limiting-dose intra-rectal exposure with highly pathogenic SIVmac239M, but the exact mechanism responsible for the vaccine efficacy is not known. It is becoming evident that complex interactions exist between gut microbiota and the host immune system. Here we aimed to investigate if the rhesus gut microbiome impacts RhCMV/SIV vaccine-induced protection.MethodsThree groups of 15 rhesus macaques naturally pre-exposed to RhCMV were vaccinated with RhCMV/SIV vaccines. Rectal swabs were collected longitudinally both before SIV challenge (after vaccination) and post challenge and were profiled using 16S rRNA based microbiome analysis.ResultsWe identified ∼2,400 16S rRNA amplicon sequence variants (ASVs), representing potential bacterial species/strains. Global gut microbial profiles were strongly associated with each of the three vaccination groups, and all animals tended to maintain consistent profiles throughout the pre-challenge phase. Despite vaccination group differences, using newly developed compositional data analysis techniques we identified a common gut microbial signature predictive of vaccine protection outcome across the three vaccination groups. Part of this microbial signature persisted even after SIV challenge. We also observed a strong correlation between this microbial signature and an early signature derived from whole blood transcriptomes in the same animals.ConclusionsOur findings indicate that changes in gut microbiomes are associated with RhCMV/SIV vaccine-induced protection and early host response to vaccination in rhesus macaques.}, author={Brochu, Hayden N. and Smith, Elise and Jeong, Sangmi and Carlson, Michelle and Hansen, Scott G. and Tisoncik-Go, Jennifer and Law, Lynn and Picker, Louis J. and Gale, Michael, Jr. and Peng, Xinxia}, year={2024}, month={Feb} } @article{brochu_smith_jeong_carlson_hansen_tisoncik-go_law_picker_gale jr_peng_2024, title={Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques}, volume={9}, ISSN={["2165-0497"]}, url={https://doi.org/10.1128/spectrum.01285-24}, DOI={10.1128/spectrum.01285-24}, abstractNote={ABSTRACT Rhesus cytomegalovirus expressing simian immunodeficiency virus (RhCMV/SIV) vaccines protect ~59% of vaccinated rhesus macaques against repeated limiting-dose intra-rectal exposure with highly pathogenic SIVmac239M, but the exact mechanism responsible for the vaccine efficacy is unknown. It is becoming evident that complex interactions exist between gut microbiota and the host immune system. Here, we aimed to investigate if the rhesus gut microbiome impacts RhCMV/SIV vaccine-induced protection. Three groups of 15 rhesus macaques naturally pre-exposed to RhCMV were vaccinated with RhCMV/SIV vaccines. Rectal swabs were collected longitudinally both before SIV challenge (after vaccination) and post-challenge and were profiled using 16S rRNA based microbiome analysis. We identified ~2,400 16S rRNA amplicon sequence variants (ASVs), representing potential bacterial species/strains. Global gut microbial profiles were strongly associated with each of the three vaccination groups, and all animals tended to maintain consistent profiles throughout the pre-challenge phase. Despite vaccination group differences, by using newly developed compositional data analysis techniques, we identified a common gut microbial signature predictive of vaccine protection outcome across the three vaccination groups. Part of this microbial signature persisted even after SIV challenge. We also observed a strong correlation between this microbial signature and an early signature derived from whole blood transcriptomes in the same animals. Our findings indicate that changes in gut microbiomes are associated with RhCMV/SIV vaccine-induced protection and early host response to vaccination in rhesus macaques. IMPORTANCE The human immunodeficiency virus (HIV) has infected millions of people worldwide. Unfortunately, still there is no vaccine that can prevent or treat HIV infection. A promising pre-clinical HIV vaccine based on rhesus cytomegalovirus (RhCMV) expressing simian immunodeficiency virus (SIV) antigens (RhCMV/SIV) provides sustained, durable protection against SIV challenge in ~59% of vaccinated rhesus macaques. There is an urgent need to understand the cause of this protection vs non-protection outcome. In this study, we profiled the gut microbiomes of 45 RhCMV/SIV vaccinated rhesus macaques and identified gut microbial signatures that were predictive of RhCMV/SIV vaccination groups and vaccine protection outcomes. These vaccine protection-associated microbial features were significantly correlated with early vaccine-induced host immune signatures in whole blood from the same animals. These findings show that the gut microbiome may be involved in RhCMV/SIV vaccine-induced protection, warranting further research into the impact of the gut microbiome in human vaccine trials.}, journal={MICROBIOLOGY SPECTRUM}, author={Brochu, Hayden N. and Smith, Elise and Jeong, Sangmi and Carlson, Michelle and Hansen, Scott G. and Tisoncik-Go, Jennifer and Law, Lynn and Picker, Louis J. and Gale Jr, Michael and Peng, Xinxia}, editor={Stamatatos, LeonidasEditor}, year={2024}, month={Sep} } @article{diveley_tollison_adams_li_peng_2024, title={Using High-Throughput Approaches To Identify Functional Fc Gamma Receptor SNPs}, volume={212}, ISSN={["1550-6606"]}, DOI={10.4049/jimmunol.212.supp.0207.4264}, number={1}, journal={JOURNAL OF IMMUNOLOGY}, author={Diveley, Kayleigh and Tollison, Tammy and Adams, Nicole and Li, Gang and Peng, Xinxia}, year={2024}, month={May} } @article{brochu_wang_tollison_pyo_thomas_tseng_law_picker_gale_geraghty_et al._2022, title={Alternative splicing and genetic variation of mhc-e: implications for rhesus cytomegalovirus-based vaccines}, volume={5}, ISSN={["2399-3642"]}, url={https://doi.org/10.1038/s42003-022-04344-2}, DOI={10.1038/s42003-022-04344-2}, abstractNote={AbstractRhesus cytomegalovirus (RhCMV)-based vaccination against Simian Immunodeficiency virus (SIV) elicits MHC-E-restricted CD8+ T cells that stringently control SIV infection in ~55% of vaccinated rhesus macaques (RM). However, it is unclear how accurately the RM model reflectsHLA-Eimmunobiology in humans. Using long-read sequencing, we identified 16Mamu-Eisoforms and allMamu-Esplicing junctions were detected amongHLA-Eisoforms in humans. We also obtained the completeMamu-Egenomic sequences covering the full coding regions of 59 RM from a RhCMV/SIV vaccine study. TheMamu-Egene was duplicated in 32 (54%) of 59 RM. Among four groups ofMamu-Ealleles: three ~5% divergent full-length allele groups (G1, G2, G2_LTR) and a fourth monomorphic group (G3) with a deletion encompassing the canonicalMamu-Eexon 6, the presence of G2_LTR alleles was significantly (p = 0.02) associated with the lack of RhCMV/SIV vaccine protection. These genomic resources will facilitate additionalMHC-Etargeted translational research.}, number={1}, journal={COMMUNICATIONS BIOLOGY}, author={Brochu, Hayden and Wang, Ruihan and Tollison, Tammy and Pyo, Chul-Woo and Thomas, Alexander and Tseng, Elizabeth and Law, Lynn and Picker, Louis J. and Gale, Michael and Geraghty, Daniel E. and et al.}, year={2022}, month={Dec} } @article{huang_callahan_wu_holloway_brochu_lu_peng_tzeng_2022, title={Phylogeny-guided microbiome OTU-specific association test (POST)}, volume={10}, ISSN={["2049-2618"]}, url={https://doi.org/10.1186/s40168-022-01266-3}, DOI={10.1186/s40168-022-01266-3}, abstractNote={AbstractBackgroundThe relationship between host conditions and microbiome profiles, typically characterized by operational taxonomic units (OTUs), contains important information about the microbial role in human health. Traditional association testing frameworks are challenged by the high dimensionality and sparsity of typical microbiome profiles. Phylogenetic information is often incorporated to address these challenges with the assumption that evolutionarily similar taxa tend to behave similarly. However, this assumption may not always be valid due to the complex effects of microbes, and phylogenetic information should be incorporated in adata-supervisedfashion.ResultsIn this work, we propose a local collapsing test called phylogeny-guided microbiome OTU-specific association test (POST). In POST, whether or not to borrow information and how much information to borrow from the neighboring OTUs in the phylogenetic tree are supervised by phylogenetic distance and the outcome-OTU association. POST is constructed under the kernel machine framework to accommodate complex OTU effects and extends kernel machine microbiome tests from community level to OTU level. Using simulation studies, we show that when the phylogenetic tree is informative, POST has better performance than existing OTU-level association tests. When the phylogenetic tree is not informative, POST achieves similar performance as existing methods. Finally, in real data applications on bacterial vaginosis and on preterm birth, we find that POST can identify similar or more outcome-associated OTUs that are of biological relevance compared to existing methods.ConclusionsUsing POST, we show that adaptively leveraging the phylogenetic information can enhance the selection performance of associated microbiome features by improving the overall true-positive and false-positive detection. We developed a user friendly R packagePOSTmwhich is freely available on CRAN (https://CRAN.R-project.org/package=POSTm).}, number={1}, journal={MICROBIOME}, author={Huang, Caizhi and Callahan, Benjamin John and Wu, Michael C. and Holloway, Shannon T. and Brochu, Hayden and Lu, Wenbin and Peng, Xinxia and Tzeng, Jung-Ying}, year={2022}, month={Jun} } @article{walsh_tollison_brochu_shaw_diveley_chou_law_kirk_gale_peng_2022, title={Single-Cell-Based High-Throughput Ig and TCR Repertoire Sequencing Analysis in Rhesus Macaques}, volume={208}, ISSN={["1550-6606"]}, url={https://doi.org/10.4049/jimmunol.2100824}, DOI={10.4049/jimmunol.2100824}, abstractNote={Abstract Recent advancements in microfluidics and high-throughput sequencing technologies have enabled recovery of paired H and L chains of Igs and VDJ and VJ chains of TCRs from thousands of single cells simultaneously in humans and mice. Despite rhesus macaques being one of the most well-studied model organisms for the human adaptive immune response, high-throughput single-cell immune repertoire sequencing assays are not yet available due to the complexity of these polyclonal receptors. We used custom primers that capture all known rhesus macaque Ig and TCR isotypes and chains that are fully compatible with a commercial solution for single-cell immune repertoire profiling. Using these rhesus-specific assays, we sequenced Ig and TCR repertoires in >60,000 cells from cryopreserved rhesus PBMCs, splenocytes, and FACS-sorted B and T cells. We were able to recover every Ig isotype and TCR chain, measure clonal expansion in proliferating T cells, and pair Ig and TCR repertoires with gene expression profiles of the same single cells. Our results establish the ability to perform high-throughput immune repertoire analysis in rhesus macaques at the single-cell level.}, number={3}, journal={JOURNAL OF IMMUNOLOGY}, author={Walsh, Evan S. and Tollison, Tammy S. and Brochu, Hayden N. and Shaw, Brian I and Diveley, Kayleigh R. and Chou, Hsuan and Law, Lynn and Kirk, Allan D. and Gale, Michael, Jr. and Peng, Xinxia}, year={2022}, month={Feb}, pages={762–771} } @article{wu_jiang_zou_sun_wu_cui_huntress_peng_li_2022, title={Coupling high-throughput mapping with proteomics analysis delineates cis-regulatory elements at high resolution}, volume={50}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkab890}, abstractNote={Abstract Growing evidence suggests that functional cis-regulatory elements (cis-REs) not only exist in epigenetically marked but also in unmarked sites of the human genome. While it is already difficult to identify cis-REs in the epigenetically marked sites, interrogating cis-REs residing within the unmarked sites is even more challenging. Here, we report adapting Reel-seq, an in vitro high-throughput (HTP) technique, to fine-map cis-REs at high resolution over a large region of the human genome in a systematic and continuous manner. Using Reel-seq, as a proof-of-principle, we identified 408 candidate cis-REs by mapping a 58 kb core region on the aging-related CDKN2A/B locus that harbors p16INK4a. By coupling Reel-seq with FREP-MS, a proteomics analysis technique, we characterized two cis-REs, one in an epigenetically marked site and the other in an epigenetically unmarked site. These elements are shown to regulate the p16INK4a expression over an ∼100 kb distance by recruiting the poly(A) binding protein PABPC1 and the transcription factor FOXC2. Downregulation of either PABPC1 or FOXC2 in human endothelial cells (ECs) can induce the p16INK4a-dependent cellular senescence. Thus, we confirmed the utility of Reel-seq and FREP-MS analyses for the systematic identification of cis-REs at high resolution over a large region of the human genome.}, number={1}, journal={NUCLEIC ACIDS RESEARCH}, author={Wu, Ting and Jiang, Danli and Zou, Meijuan and Sun, Wei and Wu, Di and Cui, Jing and Huntress, Ian and Peng, Xinxia and Li, Gang}, year={2022}, month={Jan} } @article{dawson_rasmussen_peng_lanzas_2021, title={Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen}, volume={18}, ISSN={1742-5662}, url={http://dx.doi.org/10.1098/rsif.2021.0041}, DOI={10.1098/rsif.2021.0041}, abstractNote={Indirect (environmental) and direct (host–host) transmission pathways cannot easily be distinguished when they co-occur in epidemics, particularly when they occur on similar time scales. Phylodynamic reconstruction is a potential approach to this problem that combines epidemiological information (temporal, spatial information) with pathogen whole-genome sequencing data to infer transmission trees of epidemics. However, factors such as differences in mutation and transmission rates between host and non-host environments may obscure phylogenetic inference from these methods. In this study, we used a network-based transmission model that explicitly models pathogen evolution to simulate epidemics with both direct and indirect transmission. Epidemics were simulated according to factorial combinations of direct/indirect transmission proportions, host mutation rates and conditions of environmental pathogen growth. Transmission trees were then reconstructed using the phylodynamic approach SCOTTI (structured coalescent transmission tree inference) and evaluated. We found that although insufficient diversity sets a lower bound on when accurate phylodynamic inferences can be made, transmission routes and assumed pathogen lifestyle affected pathogen population structure and subsequently influenced both reconstruction success and the likelihood of direct versus indirect pathways being reconstructed. We conclude that prior knowledge of the likely ecology and population structure of pathogens in host and non-host environments is critical to fully using phylodynamic techniques.}, number={179}, journal={Journal of The Royal Society Interface}, publisher={The Royal Society}, author={Dawson, Daniel and Rasmussen, David and Peng, Xinxia and Lanzas, Cristina}, year={2021}, month={Jun}, pages={20210041} } @article{barrenas_hansen_law_driscoll_green_smith_chang_golez_urion_peng_et al._2021, title={Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy}, volume={17}, ISSN={["1553-7374"]}, url={https://doi.org/10.1371/journal.ppat.1009278}, DOI={10.1371/journal.ppat.1009278}, abstractNote={Simian immunodeficiency virus (SIV) challenge of rhesus macaques (RMs) vaccinated with strain 68–1 Rhesus Cytomegalovirus (RhCMV) vectors expressing SIV proteins (RhCMV/SIV) results in a binary outcome: stringent control and subsequent clearance of highly pathogenic SIV in ~55% of vaccinated RMs with no protection in the remaining 45%. Although previous work indicates that unconventionally restricted, SIV-specific, effector-memory (EM)-biased CD8+ T cell responses are necessary for efficacy, the magnitude of these responses does not predict efficacy, and the basis of protection vs. non-protection in 68–1 RhCMV/SIV vector-vaccinated RMs has not been elucidated. Here, we report that 68–1 RhCMV/SIV vector administration strikingly alters the whole blood transcriptome of vaccinated RMs, with the sustained induction of specific immune-related pathways, including immune cell, toll-like receptor (TLR), inflammasome/cell death, and interleukin-15 (IL-15) signaling, significantly correlating with subsequent vaccine efficacy. Treatment of a separate RM cohort with IL-15 confirmed the central involvement of this cytokine in the protection signature, linking the major innate and adaptive immune gene expression networks that correlate with RhCMV/SIV vaccine efficacy. This change-from-baseline IL-15 response signature was also demonstrated to significantly correlate with vaccine efficacy in an independent validation cohort of vaccinated and challenged RMs. The differential IL-15 gene set response to vaccination strongly correlated with the pre-vaccination activity of this pathway, with reduced baseline expression of IL-15 response genes significantly correlating with higher vaccine-induced induction of IL-15 signaling and subsequent vaccine protection, suggesting that a robust de novo vaccine-induced IL-15 signaling response is needed to program vaccine efficacy. Thus, the RhCMV/SIV vaccine imparts a coordinated and persistent induction of innate and adaptive immune pathways featuring IL-15, a known regulator of CD8+ T cell function, that support the ability of vaccine-elicited unconventionally restricted CD8+ T cells to mediate protection against SIV challenge.}, number={7}, journal={PLOS PATHOGENS}, publisher={Public Library of Science (PLoS)}, author={Barrenas, Fredrik and Hansen, Scott G. and Law, Lynn and Driscoll, Connor and Green, Richard R. and Smith, Elise and Chang, Jean and Golez, Inah and Urion, Taryn and Peng, Xinxia and et al.}, editor={Silvestri, GuidoEditor}, year={2021}, month={Jul} } @article{liu_hufnagel_catherine m. o'connell_goonetilleke_mokashi_waterboer_tollison_peng_wiesenfeld_hillier_et al._2022, title={Reduced Endometrial Ascension and Enhanced Reinfection Associated With Immunoglobulin G Antibodies to Specific Chlamydia trachomatis Proteins in Women at Risk for Chlamydia}, volume={225}, ISSN={["1537-6613"]}, DOI={10.1093/infdis/jiab496}, abstractNote={Abstract Background Previous research revealed antibodies targeting Chlamydia trachomatis elementary bodies was not associated with reduced endometrial or incident infection in C. trachomatis–exposed women. However, data on the role of C. trachomatis protein–specific antibodies in protection are limited. Methods A whole-proteome C. trachomatis array screening serum pools from C. trachomatis–exposed women identified 121 immunoprevalent proteins. Individual serum samples were probed using a focused array. Immunoglobulin (Ig) G antibody frequencies and endometrial or incident infection relationships were examined using Wilcoxon rank sum test. The impact of the breadth and magnitude of protein-specific IgGs on ascension and incident infection were examined using multivariable stepwise logistic regression. Complementary RNA sequencing quantified C. trachomatis gene transcripts in cervical swab samples from infected women. Results IgG to pGP3 and CT_005 were associated with reduced endometrial infection; anti-CT_443, anti–CT_486, and anti–CT_123 were associated with increased incident infection. Increased breadth of protein recognition did not however predict protection from endometrial or incident infection. Messenger RNAs for immunoprevalent C. trachomatis proteins were highly abundant in the cervix. Conclusions Protein-specific C. trachomatis antibodies are not sufficient to protect against ascending or incident infection. However, cervical C. trachomatis gene transcript abundance positively correlates with C. trachomatis protein immunogenicity. These abundant and broadly recognized antigens are viable vaccine candidates. }, number={5}, journal={JOURNAL OF INFECTIOUS DISEASES}, author={Liu, Chuwen and Hufnagel, Katrin and Catherine M. O'Connell and Goonetilleke, Nilu and Mokashi, Neha and Waterboer, Tim and Tollison, Tammy S. and Peng, Xinxia and Wiesenfeld, Harold C. and Hillier, Sharon L. and et al.}, year={2022}, month={Mar}, pages={846–855} } @article{barrenäs_hansen_law_driscoll_green_smith_chang_golez_urion_peng_et al._2021, title={Sustained IL-15 response signature predicts RhCMV/SIV vaccine efficacy}, url={https://doi.org/10.1101/2021.01.11.426199}, DOI={10.1101/2021.01.11.426199}, abstractNote={AbstractSimian immunodeficiency virus (SIV) challenge of rhesus macaques (RMs) vaccinated with Rhesus Cytomegalovirus (RhCMV) vectors expressing SIV proteins (RhCMV/SIV) results in a binary outcome: stringent control and subsequent clearance of highly pathogenic SIV in ~55% of vaccinated RMs with no protection in the remaining 45%. Although previous work suggests that unconventionally restricted, SIV-specific, effector-memory (EM)-biased CD8+ T cell responses are necessary for efficacy, the magnitude of these responses does not predict efficacy, and the basis of protection vs. non-protection in RhCMV/SIV vector-vaccinated RMs has not been elucidated. Here, we report that RhCMV/SIV vector administration strikingly alters the whole blood transcriptome of vaccinated RMs, with the sustained induction of specific immune-related pathways, including non-canonical T cell receptor (TCR), toll-lie receptor (TLR), inflammasome/cell death, and interleukin-15 (IL-15) signaling, significantly predicting protection. The IL-15 gene expression signature was further evaluated in an independent RM IL-15 treatment cohort, revealing that in whole blood the response to IL-15 is inclusive of innate and adaptive immune gene expression networks that link with RhCMV/SIV vaccine efficacy. We also show that this IL-15 response signature similarly tracks with vaccine protection in an independent RhCMV/SIV vaccination/SIV challenge RM validation cohort. Thus, the RhCMV/SIV vaccine imparts a coordinated and persistent induction of innate and adaptive immune pathways featuring IL-15, a known regulator of CD8+ T cell function, that enable vaccine-elicited CD8+ T cells to mediate protection against highly pathogenic SIV challenge.Author SummarySIV insert-expressing vaccine vectors based on strain 68-1 RhCMV elicit robust, highly effector-memory-biased T cell responses that are associated with an unprecedented level of SIV control after challenge (replication arrest leading to clearance) in slightly over half of vaccinated monkeys. Since efficacy is not predicted by standard measures of immunogenicity, we used functional genomics analysis of RhCMV/SIV vaccinated monkeys with known challenge outcomes to identify immune correlates of protection. We found that arrest of viral replication after challenge significantly correlates with a vaccine-induced response to IL-15 that includes modulation of T cell, inflammation, TLR signaling, and cell death programming. These data suggest that RhCMV/SIV efficacy is not based on chance, but rather, results from a coordinated and sustained vaccine-mediated induction of innate and adaptive immune pathways featuring IL-15, a known regulator of CD8+ effector-memory T cell function, that enable vaccine-elicited CD8+ T cells to mediate efficacy.}, author={Barrenäs, Fredrik and Hansen, Scott G. and Law, Lynn and Driscoll, Connor and Green, Richard R. and Smith, Elise and Chang, Jean and Golez, Inah and Urion, Taryn and Peng, Xinxia and et al.}, year={2021}, month={Jan} } @article{nagarajan_cho_gyorke_nagarajan_ezzell_brochu_huntress_harrell_peng_2021, title={Tumor Necrosis Factor Alpha-Induced Interleukin-1 Alpha Synthesis and Cell Death Is Increased in Mouse Epithelial Cells Infected With Chlamydia muridarum}, volume={224}, ISSN={["1537-6613"]}, DOI={10.1093/infdis/jiab168}, abstractNote={Abstract Chlamydia trachomatis-genital infection in women can be modeled in mice using Chlamydia muridarum. Using this model, it has been shown that the cytokines tumor necrosis factor (TNF)α and interleukin (IL)-1α lead to irreversible tissue damage in the oviducts. In this study, we investigated the contribution of TNFα on IL-1α synthesis in infected epithelial cells. We show that C muridarum infection enhanced TNFα-induced IL-1α expression and release in a mouse epithelial cell line. In addition to IL-1α, several TNFα-induced inflammatory genes were also highly induced, and infection enhanced TNF-induced cell death. In the mouse model of genital infection, oviducts from mice lacking the TNFα receptor displayed minimal staining for IL-1α compared with wild-type oviducts. Our results suggest TNFα and IL-1α enhance each other’s downstream effects resulting in a hyperinflammatory response to chlamydial infection. We propose that biologics targeting TNF-induced IL-1α synthesis could be used to mitigate tissue damage during chlamydial infection.}, journal={JOURNAL OF INFECTIOUS DISEASES}, author={Nagarajan, Uma M. and Cho, Crescentia and Gyorke, Clare E. and Nagarajan, Shanmugam and Ezzell, J. Ashley and Brochu, Hayden and Huntress, Ian and Harrell, Erin and Peng, Xinxia}, year={2021}, month={Aug}, pages={S47–S55} } @article{dinh_paudel_brochu_popowski_gracieux_cores_huang_hensley_harrell_vandergriff_et al._2020, title={Inhalation of lung spheroid cell secretome and exosomes promotes lung repair in pulmonary fibrosis}, volume={11}, ISSN={["2041-1723"]}, url={http://dx.doi.org/10.1038/s41467-020-14344-7}, DOI={10.1038/s41467-020-14344-7}, abstractNote={AbstractIdiopathic pulmonary fibrosis (IPF) is a fatal and incurable form of interstitial lung disease in which persistent injury results in scar tissue formation. As fibrosis thickens, the lung tissue loses the ability to facilitate gas exchange and provide cells with needed oxygen. Currently, IPF has few treatment options and no effective therapies, aside from lung transplant. Here we present a series of studies utilizing lung spheroid cell-secretome (LSC-Sec) and exosomes (LSC-Exo) by inhalation to treat different models of lung injury and fibrosis. Analysis reveals that LSC-Sec and LSC-Exo treatments could attenuate and resolve bleomycin- and silica-induced fibrosis by reestablishing normal alveolar structure and decreasing both collagen accumulation and myofibroblast proliferation. Additionally, LSC-Sec and LSC-Exo exhibit superior therapeutic benefits than their counterparts derived from mesenchymal stem cells in some measures. We showed that an inhalation treatment of secretome and exosome exhibited therapeutic potential for lung regeneration in two experimental models of pulmonary fibrosis.}, number={1}, journal={NATURE COMMUNICATIONS}, publisher={Springer Science and Business Media LLC}, author={Dinh, Phuong-Uyen C. and Paudel, Dipti and Brochu, Hayden and Popowski, Kristen D. and Gracieux, M. Cyndell and Cores, Jhon and Huang, Ke and Hensley, M. Taylor and Harrell, Erin and Vandergriff, Adam C. and et al.}, year={2020}, month={Feb} } @article{brochu_tseng_smith_thomas_jones_diveley_law_hansen_picker_gale_et al._2020, title={Systematic Profiling of Full-Length Ig and TCR Repertoire Diversity in Rhesus Macaque through Long Read Transcriptome Sequencing}, volume={204}, ISSN={["1550-6606"]}, DOI={10.4049/jimmunol.1901256}, abstractNote={Abstract The diversity of Ig and TCR repertoires is a focal point of immunological studies. Rhesus macaques (Macaca mulatta) are key for modeling human immune responses, placing critical importance on the accurate annotation and quantification of their Ig and TCR repertoires. However, because of incomplete reference resources, the coverage and accuracy of the traditional targeted amplification strategies for profiling rhesus Ig and TCR repertoires are largely unknown. In this study, using long read sequencing, we sequenced four Indian-origin rhesus macaque tissues and obtained high-quality, full-length sequences for over 6000 unique Ig and TCR transcripts, without the need for sequence assembly. We constructed, to our knowledge, the first complete reference set for the constant regions of all known isotypes and chain types of rhesus Ig and TCR repertoires. We show that sequence diversity exists across the entire variable regions of rhesus Ig and TCR transcripts. Consequently, existing strategies using targeted amplification of rearranged variable regions comprised of V(D)J gene segments miss a significant fraction (27–53% and 42–49%) of rhesus Ig/TCR diversity. To overcome these limitations, we designed new rhesus-specific assays that remove the need for primers conventionally targeting variable regions and allow single cell level Ig and TCR repertoire analysis. Our improved approach will enable future studies to fully capture rhesus Ig and TCR repertoire diversity and is applicable for improving annotations in any model organism.}, number={12}, journal={JOURNAL OF IMMUNOLOGY}, author={Brochu, Hayden N. and Tseng, Elizabeth and Smith, Elise and Thomas, Matthew J. and Jones, Aiden M. and Diveley, Kayleigh R. and Law, Lynn and Hansen, Scott G. and Picker, Louis J. and Gale, Michael, Jr. and et al.}, year={2020}, month={Jun}, pages={3434–3444} } @article{martinez_fong_li_yang_jennewein_weiner_harrell_mangold_goswami_seage_et al._2019, title={Fc Characteristics Mediate Selective Placental Transfer of IgG in HIV-Infected Women}, volume={178}, ISSN={["1097-4172"]}, DOI={10.1016/j.cell.2019.05.046}, abstractNote={The placental transfer of maternal IgG is critical for infant protection against infectious pathogens. However, factors that modulate the placental transfer of IgG remain largely undefined. HIV-infected women have impaired placental IgG transfer, presenting a unique "disruption model" to define factors that modulate placental IgG transfer. We measured the placental transfer efficiency of maternal HIV and pathogen-specific IgG in US and Malawian HIV-infected mothers and their HIV-exposed uninfected and infected infants. We examined the role of maternal HIV disease progression, infant factors, placental Fc receptor expression, IgG subclass, and glycan signatures and their association with placental IgG transfer efficiency. Maternal IgG characteristics, such as binding to placentally expressed Fc receptors FcγRIIa and FcγRIIIa, and Fc region glycan profiles were associated with placental IgG transfer efficiency. Our findings suggest that Fc region characteristics modulate the selective placental transfer of IgG, with implications for maternal vaccine design and infant health.}, number={1}, journal={CELL}, author={Martinez, David R. and Fong, Youyi and Li, Shuk Hang and Yang, Fang and Jennewein, Madeleine F. and Weiner, Joshua A. and Harrell, Erin A. and Mangold, Jesse F. and Goswami, Ria and Seage, George R., III and et al.}, year={2019}, month={Jun}, pages={190-+} } @article{li_gilbert_carpp_pyo_janes_fong_shen_neidich_goodman_decamp_et al._2019, title={Fc Gamma Receptor Polymorphisms Modulated the Vaccine Effect on HIV-1 Risk in the HVTN 505 HIV Vaccine Trial}, volume={93}, ISSN={["1098-5514"]}, DOI={10.1128/JVI.02041-18}, abstractNote={By analyzing data from the HVTN 505 efficacy trial of a DNA/recombinant adenovirus 5 (rAd5) vaccine regimen, we found that host genetics, specifically Fc gamma receptor genetic variations, influenced whether receiving the DNA/rAd5 regimen was beneficial, neutral, or detrimental to an individual with respect to HIV-1 acquisition risk. Moreover, Fc gamma receptor genetic variations influenced immune responses to the DNA/rAd5 vaccine regimen. Thus, Fc gamma receptor genetic variations should be considered in the analysis of future HIV vaccine trials and the development of HIV vaccines.}, number={21}, journal={JOURNAL OF VIROLOGY}, author={Li, Shuying S. and Gilbert, Peter B. and Carpp, Lindsay N. and Pyo, Chul-Woo and Janes, Holly and Fong, Youyi and Shen, Xiaoying and Neidich, Scott D. and Goodman, Derrick and deCamp, Allan and et al.}, year={2019}, month={Nov} } @article{barrenas_raehtz_xu_law_green_silvestri_bosinger_nishida_li_lu_et al._2019, title={Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control}, volume={10}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-019-12987-9}, abstractNote={AbstractNatural hosts of simian immunodeficiency virus (SIV) avoid AIDS despite lifelong infection. Here, we examined how this outcome is achieved by comparing a natural SIV host, African green monkey (AGM) to an AIDS susceptible species, rhesus macaque (RM). To asses gene expression profiles from acutely SIV infected AGMs and RMs, we developed a systems biology approach termed Conserved Gene Signature Analysis (CGSA), which compared RNA sequencing data from rectal AGM and RM tissues to various other species. We found that AGMs rapidly activate, and then maintain, evolutionarily conserved regenerative wound healing mechanisms in mucosal tissue. The wound healing protein fibronectin shows distinct tissue distribution and abundance kinetics in AGMs. Furthermore, AGM monocytes exhibit an embryonic development and repair/regeneration signature featuring TGF-β and concomitant reduced expression of inflammatory genes compared to RMs. This regenerative wound healing process likely preserves mucosal integrity and prevents inflammatory insults that underlie immune exhaustion in RMs.}, journal={NATURE COMMUNICATIONS}, author={Barrenas, Fredrik and Raehtz, Kevin and Xu, Cuiling and Law, Lynn and Green, Richard R. and Silvestri, Guido and Bosinger, Steven E. and Nishida, Andrew and Li, Qingsheng and Lu, Wuxun and et al.}, year={2019}, month={Nov} } @article{catherine m. o'connell_brochu_girardi_harrell_jones_darville_sena_peng_2019, title={Simultaneous profiling of sexually transmitted bacterial pathogens, microbiome, and concordant host response in cervical samples using whole transcriptome sequencing analysis}, volume={6}, ISSN={["2311-2638"]}, DOI={10.15698/mic2019.03.672}, abstractNote={Pelvic inflammatory disease (PID) is a female upper genital tract inflammatory disorder that arises after sexually transmitted bacterial infections (STI). Factors modulating risk for reproductive sequelae include co-infection, microbiota, host genetics and physiology. In a pilot study of cervical samples obtained from women at high risk for STIs, we examined the potential for unbiased characterization of host, pathogen and microbiome interactions using whole transcriptome sequencing analysis of ribosomal RNA-depleted total RNAs (Total RNA-Seq). Only samples from women with STI infection contained pathogen-specific sequences (3 to 38% transcriptome coverage). Simultaneously, we identified and quantified their active microbial communities. After integration with host-derived reads from the same data, we detected clustering of host transcriptional profiles that reflected microbiome differences and STI infection. Together, our study suggests that total RNA profiling will advance understanding of the interplay of pathogen, host and microbiota during natural infection and may reveal novel, outcome-relevant biomarkers.}, number={3}, journal={MICROBIAL CELL}, author={Catherine M. O'Connell and Brochu, Hayden and Girardi, Jenna and Harrell, Erin and Jones, Aiden and Darville, Toni and Sena, Arlene C. and Peng, Xinxia}, year={2019}, month={Mar}, pages={177–183} } @article{martinez_fouda_peng_ackerman_permar_2018, title={Noncanonical placental Fc receptors: What is their role in modulating transplacental transfer of maternal IgG?}, volume={14}, ISSN={1553-7374}, url={http://dx.doi.org/10.1371/journal.ppat.1007161}, DOI={10.1371/journal.ppat.1007161}, abstractNote={The transplacental transfer of maternal Immunoglobulin G (IgG) to the fetus is critical for protection against infectious diseases in the first year of life [1]. Maternal protective IgG is transferred from the maternal to the fetal circulatory system via the placenta, and this process begins in the first trimester of pregnancy [2]. By 37–40 weeks of gestation, maternal passively acquired IgG concentrations in newborns can exceed maternal IgG serum levels in normal pregnancies [3–7]. Yet, the molecular mechanisms of transplacental transfer of maternal IgG remain poorly understood. In order to reach the fetal circulatory system, maternal IgG must traverse three distinct placental anatomical barriers: (1) the syncytiotrophoblast cell barrier, (2) the villous stroma containing placental fibroblasts and Hofbauer cells, and (3) fetal endothelial cells. It is well established that IgG crosses the syncytiotrophoblast by binding to the canonical IgG shuttle receptor: Fragment crystallizable (Fc) receptor neonatal (FcRn) [2, 8]. However, how maternal IgG traverses the subsequent placental barriers is not completely understood, as they do not express FcRn, yet recent RNAseq analyses have shown that Fcγ receptors, including FcγRIIIa, FcγRIIa, FcγRIIb, and FcγRI, are expressed in term placentas [9]. However, it should be cautioned that it is not yet known if these noncanonical placental FcRs play a role, if at all, in the transplacental transfer of maternal IgG. A deeper understanding of the molecular mechanism(s) of IgG binding to placentally expressed Fc receptors could be important (1) for the design of novel maternal IgG-based therapeutics and vaccines with optimal transplacental transfer efficiency, with the ultimate goal of increasing infant protection against congenital and neonatal infectious diseases, and (2) to optimize the Fc region of immunomodulatory IgG monoclonal antibody therapeutics for blunted transplacental transfer to potentially reduce the transplacental transport of maternal self-reactive IgG in women with autoimmune disorders.}, number={8}, journal={PLOS Pathogens}, publisher={Public Library of Science (PLoS)}, author={Martinez, David R. and Fouda, Genevieve G. and Peng, Xinxia and Ackerman, Margaret E. and Permar, Sallie R.}, editor={Sheppard, Donald C.Editor}, year={2018}, month={Aug}, pages={e1007161} } @misc{lemler_brochu_yang_harrell_peng_2017, title={Elucidating the role of host long non-coding RNA during viral infection: Challenges and paths forward}, volume={5}, number={4}, journal={Vaccines}, author={Lemler, D. J. and Brochu, H. N. and Yang, F. and Harrell, E. A. and Peng, X. X.}, year={2017} } @article{forero_fenstermacher_wohlgemuth_nishida_carter_smith_peng_hayes_francis_treanor_et al._2017, title={Evaluation of the innate immune responses to influenza and live-attenuated influenza vaccine infection in primary differentiated human nasal epithelial cells}, volume={35}, ISSN={0264-410X}, url={http://dx.doi.org/10.1016/j.vaccine.2017.09.058}, DOI={10.1016/j.vaccine.2017.09.058}, abstractNote={The host innate immune response to influenza virus is a key determinant of pathogenic outcomes and long-term protective immune responses against subsequent exposures. Here, we present a direct contrast of the host responses in primary differentiated human nasal epithelial cell (hNEC) cultures following infection with either a seasonal H3N2 influenza virus (WT) or the antigenically-matched live-attenuated vaccine (LAIV) strain. Comparison of the transcriptional profiles obtained 24 and 36h post-infection showed that the magnitude of gene expression was greater in LAIV infected relative to that observed in WT infected hNEC cultures. Functional enrichment analysis revealed that the antiviral and inflammatory responses were largely driven by type III IFN induction in both WT and LAIV infected cells. However, the enrichment of biological pathways involved in the recruitment of mononuclear leukocytes, antigen-presenting cells, and T lymphocytes was uniquely observed in LAIV infected cells. These observations were reflective of the host innate immune responses observed in individuals acutely infected with influenza viruses. These findings indicate that cell-intrinsic type III IFN-mediated innate immune responses in the nasal epithelium are not only crucial for viral clearance and attenuation, but may also play an important role in the induction of protective immune responses with live-attenuated vaccines.}, number={45}, journal={Vaccine}, publisher={Elsevier BV}, author={Forero, Adriana and Fenstermacher, Katherine and Wohlgemuth, Nicholas and Nishida, Andrew and Carter, Victoria and Smith, Elise A. and Peng, Xinxia and Hayes, Melissa and Francis, Doreen and Treanor, John and et al.}, year={2017}, month={Oct}, pages={6112–6121} } @article{peng_li_gilbert_geraghty_katze_2016, title={FCGR2C Polymorphisms Associated with HIV-1 Vaccine Protection Are Linked to Altered Gene Expression of Fc-γ Receptors in Human B Cells}, volume={11}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0152425}, DOI={10.1371/journal.pone.0152425}, abstractNote={The phase III Thai RV144 vaccine trial showed an estimated vaccine efficacy (VE) to prevent HIV-1 infection of 31.2%, which has motivated the search for immune correlates of vaccine protection. In a recent report, several single nucleotide polymorphisms (SNPs) in FCGR2C were identified to associate with the level of VE in the RV144 trial. To investigate the functional significance of these SNPs, we utilized a large scale B cell RNA sequencing database of 462 individuals from the 1000 Genomes Project to examine associations between FCGR2C SNPs and gene expression. We found that the FCGR2C SNPs that associated with vaccine efficacy in RV144 also strongly associated with the expression of FCGR2A/C and one of them also associated with the expression of Fc receptor-like A (FCRLA), another Fc-γ receptor (FcγR) gene that was not examined in the previous report. These results suggest that the expression of FcγR genes is influenced by these SNPs either directly or in linkage with other causal variants. More importantly, these results motivate further investigations into the potential for a causal association of expression and alternative splicing of FCGR2C and other FcγR genes with the HIV-1 vaccine protection in the RV144 trial and other similar studies.}, number={3}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Peng, Xinxia and Li, Shuying S. and Gilbert, Peter B. and Geraghty, Daniel E. and Katze, Michael G.}, editor={Tang, JianmingEditor}, year={2016}, month={Mar}, pages={e0152425} } @article{tisoncik-go_gasper_kyle_eisfeld_selinger_hatta_morrison_korth_zink_kim_et al._2016, title={Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism}, volume={19}, ISSN={1931-3128}, url={http://dx.doi.org/10.1016/j.chom.2016.01.002}, DOI={10.1016/j.chom.2016.01.002}, abstractNote={Pandemic influenza viruses modulate proinflammatory responses that can lead to immunopathogenesis. We present an extensive and systematic profiling of lipids, metabolites, and proteins in respiratory compartments of ferrets infected with either 1918 or 2009 human pandemic H1N1 influenza viruses. Integrative analysis of high-throughput omics data with virologic and histopathologic data uncovered relationships between host responses and phenotypic outcomes of viral infection. Proinflammatory lipid precursors in the trachea following 1918 infection correlated with severe tracheal lesions. Using an algorithm to infer cell quantity changes from gene expression data, we found enrichment of distinct T cell subpopulations in the trachea. There was also a predicted increase in inflammatory monocytes in the lung of 1918 virus-infected animals that was sustained throughout infection. This study presents a unique resource to the influenza research community and demonstrates the utility of an integrative systems approach for characterization of lipid metabolism alterations underlying respiratory responses to viruses.}, number={2}, journal={Cell Host & Microbe}, publisher={Elsevier BV}, author={Tisoncik-Go, Jennifer and Gasper, David J. and Kyle, Jennifer E. and Eisfeld, Amie J. and Selinger, Christian and Hatta, Masato and Morrison, Juliet and Korth, Marcus J. and Zink, Erika M. and Kim, Young-Mo and et al.}, year={2016}, month={Feb}, pages={254–266} } @article{peng_pyo_thomas_pyon_law_wang_geraghty_katze_2015, place={New Orleans}, title={Quantitative expression analysis of rhesus macaque MHC alleles}, volume={194}, number={113}, journal={Journal of Immunology}, author={Peng, X. and Pyo, C. and Thomas, M. and Pyon, Y. and Law, L. and Wang, R. and Geraghty, D. and Katze, M.}, year={2015} } @article{josset_tchitchek_gralinski_ferris_eisfeld_green_thomas_tisoncik-go_schroth_kawaoka_et al._2014, title={Annotation of long non-coding RNAs expressed in Collaborative Cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts}, volume={11}, ISSN={1547-6286 1555-8584}, url={http://dx.doi.org/10.4161/rna.29442}, DOI={10.4161/rna.29442}, abstractNote={The outcome of respiratory virus infection is determined by a complex interplay of viral and host factors. Some potentially important host factors for the antiviral response, whose functions remain largely unexplored, are long non-coding RNAs (lncRNAs). Here we systematically inferred the regulatory functions of host lncRNAs in response to influenza A virus and severe acute respiratory syndrome coronavirus (SARS-CoV) based on their similarity in expression with genes of known function. We performed total RNA-Seq on viral-infected lungs from eight mouse strains, yielding a large data set of transcriptional responses. Overall 5,329 lncRNAs were differentially expressed after infection. Most of the lncRNAs were co-expressed with coding genes in modules enriched in genes associated with lung homeostasis pathways or immune response processes. Each lncRNA was further individually annotated using a rank-based method, enabling us to associate 5,295 lncRNAs to at least one gene set and to predict their potential cis effects. We validated the lncRNAs predicted to be interferon-stimulated by profiling mouse responses after interferon-α treatment. Altogether, these results provide a broad categorization of potential lncRNA functions and identify subsets of lncRNAs with likely key roles in respiratory virus pathogenesis. These data are fully accessible through the MOuse NOn-Code Lung interactive database (MONOCLdb).}, number={7}, journal={RNA Biology}, publisher={Informa UK Limited}, author={Josset, Laurence and Tchitchek, Nicolas and Gralinski, Lisa E and Ferris, Martin T and Eisfeld, Amie J and Green, Richard R and Thomas, Matthew J and Tisoncik-Go, Jennifer and Schroth, Gary P and Kawaoka, Yoshihiro and et al.}, year={2014}, month={Jun}, pages={875–890} } @article{peng_pipes_xiong_green_jones_ruzzo_schroth_mason_palermo_katze_2014, title={Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data}, volume={43}, ISSN={0047-2565}, url={http://dx.doi.org/10.1111/jmp.12125}, DOI={10.1111/jmp.12125}, abstractNote={AbstractBackgroundThe genome annotations of rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques, two of the most common non‐human primate animal models, are limited.MethodsWe analyzed large‐scale macaque RNA‐based next‐generation sequencing (RNAseq) data to identify un‐annotated macaque transcripts.ResultsFor both macaque species, we uncovered thousands of novel isoforms for annotated genes and thousands of un‐annotated intergenic transcripts enriched with non‐coding RNAs. We also identified thousands of transcript sequences which are partially or completely ‘missing’ from current macaque genome assemblies. We showed that many newly identified transcripts were differentially expressed during SIV infection of rhesus macaques or during Ebola virus infection of cynomolgus macaques.ConclusionsFor two important macaque species, we uncovered thousands of novel isoforms and un‐annotated intergenic transcripts including coding and non‐coding RNAs, polyadenylated and non‐polyadenylated transcripts. This resource will greatly improve future macaque studies, as demonstrated by their applications in infectious disease studies.}, number={5}, journal={Journal of Medical Primatology}, publisher={Wiley}, author={Peng, Xinxia and Pipes, Lenore and Xiong, Hao and Green, Richard R. and Jones, Daniel C. and Ruzzo, Walter L. and Schroth, Gary P. and Mason, Christopher E. and Palermo, Robert E. and Katze, Michael G.}, year={2014}, month={May}, pages={317–328} } @article{peng_sova_green_thomas_korth_proll_xu_cheng_yi_chen_et al._2014, title={Deep Sequencing of HIV-Infected Cells: Insights into Nascent Transcription and Host-Directed Therapy}, volume={88}, ISSN={0022-538X 1098-5514}, url={http://dx.doi.org/10.1128/jvi.00768-14}, DOI={10.1128/jvi.00768-14}, abstractNote={ABSTRACT Polyadenylated mature mRNAs are the focus of standard transcriptome analyses. However, the profiling of nascent transcripts, which often include nonpolyadenylated RNAs, can unveil novel insights into transcriptional regulation. Here, we separately sequenced total RNAs (Total RNAseq) and mRNAs (mRNAseq) from the same HIV-1-infected human CD4 + T cells. We found that many nonpolyadenylated RNAs were differentially expressed upon HIV-1 infection, and we identified 8 times more differentially expressed genes at 12 h postinfection by Total RNAseq than by mRNAseq. These expression changes were also evident by concurrent changes in introns and were recapitulated by later mRNA changes, revealing an unexpectedly significant delay between transcriptional initiation and mature mRNA production early after HIV-1 infection. We computationally derived and validated the underlying regulatory programs, and we predicted drugs capable of reversing these HIV-1-induced expression changes followed by experimental confirmation. Our results show that combined total and mRNA transcriptome analysis is essential for fully capturing the early host response to virus infection and provide a framework for identifying candidate drugs for host-directed therapy against HIV/AIDS. IMPORTANCE In this study, we used mass sequencing to identify genes differentially expressed in CD4 + T cells during HIV-1 infection. To our surprise, we found many differentially expressed genes early after infection by analyzing both newly transcribed unprocessed pre-mRNAs and fully processed mRNAs, but not by analyzing mRNAs alone, indicating a significant delay between transcription initiation and mRNA production early after HIV-1 infection. These results also show that important findings could be missed by the standard practice of analyzing mRNAs alone. We then derived the regulatory mechanisms driving the observed expression changes using integrative computational analyses. Further, we predicted drugs that could reverse the observed expression changes induced by HIV-1 infection and showed that one of the predicted drugs indeed potently inhibited HIV-1 infection. This shows that it is possible to identify candidate drugs for host-directed therapy against HIV/AIDS using our genomics-based approach. }, number={16}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Peng, X. and Sova, P. and Green, R. R. and Thomas, M. J. and Korth, M. J. and Proll, S. and Xu, J. and Cheng, Y. and Yi, K. and Chen, L. and et al.}, year={2014}, month={May}, pages={8768–8782} } @article{barrenas_palermo_agricola_agy_aicher_carter_flanary_green_mclain_li_et al._2014, title={Deep Transcriptional Sequencing of Mucosal Challenge Compartment from Rhesus Macaques Acutely Infected with Simian Immunodeficiency Virus Implicates Loss of Cell Adhesion Preceding Immune Activation}, volume={88}, ISSN={0022-538X 1098-5514}, url={http://dx.doi.org/10.1128/jvi.00543-14}, DOI={10.1128/jvi.00543-14}, abstractNote={ABSTRACTPathology resulting from human immunodeficiency virus (HIV) infection is driven by protracted inflammation; the primary loss of CD4+T cells is caused by activation-driven apoptosis. Recent studies of nonhuman primates (NHPs) have suggested that during the acute phase of infection, antiviral mucosal immunity restricts viral replication in the primary infection compartment. These studies imply that HIV achieves systemic infection as a consequence of a failure in host antiviral immunity. Here, we used high-dose intrarectal inoculation of rhesus macaques with simian immunodeficiency virus (SIV) SIVmac251to examine how the mucosal immune system is overcome by SIV during acute infection. The host response in rectal mucosa was characterized by deep mRNA sequencing (mRNA-seq) at 3 and 12 days postinoculation (dpi) in 4 animals for each time point. While we observed a strong host transcriptional response at 3 dpi, functions relating to antiviral immunity were absent. Instead, we observed a significant number of differentially expressed genes relating to cell adhesion and reorganization of the cytoskeleton. We also observed downregulation of genes encoding members of the claudin family of cell adhesion molecules, which are coexpressed with genes associated with pathology in the colorectal mucosa, and a large number of noncoding transcripts. In contrast, at 12 dpi the differentially expressed genes were enriched in those involved with immune system functions, in particular, functions relating to T cells, B cells, and NK cells. Our findings indicate that host responses that negatively affect mucosal integrity occur before inflammation. Consequently, when inflammation is activated at peak viremia, mucosal integrity is already compromised, potentially enabling rapid tissue damage, driving further inflammation.IMPORTANCEThe HIV pandemic is one of the major threats to human health, causing over a million deaths per year. Recent studies have suggested that mucosal antiviral immune responses play an important role in preventing systemic infection after exposure to the virus. Yet, despite their potential role in decreasing transmission rates between individuals, these antiviral mechanisms are poorly understood. Here, we carried out the first deep mRNA sequencing analysis of mucosal host responses in the primary infection compartment during acute SIV infection. We found that during acute infection, a significant host response was mounted in the mucosa before inflammation was triggered. Our analysis indicated that the response has a detrimental effect on tissue integrity, causing increased permeability, tissue damage, and recruitment of SIV target cells. These results emphasize the importance of mucosal host responses preceding immune activation in preventing systemic SIV infection.}, number={14}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Barrenas, Fredrik and Palermo, Robert E. and Agricola, Brian and Agy, Michael B. and Aicher, Lauri and Carter, Victoria and Flanary, Leon and Green, Richard R. and McLain, Randy and Li, Qingsheng and et al.}, editor={Silvestri, G.Editor}, year={2014}, month={May}, pages={7962–7972} } @article{xiong_morrison_ferris_gralinski_whitmore_green_thomas_tisoncik-go_schroth_pardo-manuel de villena_et al._2014, title={Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression}, volume={4}, ISSN={2160-1836}, url={http://dx.doi.org/10.1534/g3.114.011759}, DOI={10.1534/g3.114.011759}, abstractNote={AbstractGenetic variation between diverse mouse species is well-characterized, yet existing knowledge of the mouse transcriptome comes largely from one mouse strain (C57BL/6J). As such, it is unlikely to reflect the transcriptional complexity of the mouse species. Gene transcription is dynamic and condition-specific; therefore, to better understand the mouse transcriptional response to respiratory virus infection, we infected the eight founder strains of the Collaborative Cross with either influenza A virus or severe acute respiratory syndrome coronavirus and sequenced lung RNA samples at 2 and 4 days after infection. We found numerous instances of transcripts that were not present in the C57BL/6J reference annotation, indicating that a nontrivial proportion of the mouse genome is transcribed but poorly annotated. Of these novel transcripts, 2150 could be aligned to human or rat genomes, but not to existing mouse genomes, suggesting functionally conserved sequences not yet recorded in mouse genomes. We also found that respiratory virus infection induced differential expression of 4287 splicing junctions, resulting in strain-specific isoform expression. Of these, 59 were influenced by strain-specific mutations within 2 base pairs of key intron–exon boundaries, suggesting cis-regulated expression. Our results reveal the complexity of the transcriptional response to viral infection, previously undocumented genomic elements, and extensive diversity in the response across mouse strains. These findings identify hitherto unexplored transcriptional patterns and undocumented transcripts in genetically diverse mice. Host genetic variation drives the complexity and diversity of the host response by eliciting starkly different transcriptional profiles in response to a viral infection.}, number={8}, journal={G3: Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Xiong, Hao and Morrison, Juliet and Ferris, Martin T. and Gralinski, Lisa E. and Whitmore, Alan C. and Green, Richard and Thomas, Matthew J. and Tisoncik-Go, Jennifer and Schroth, Gary P. and Pardo-Manuel de Villena, Fernando and et al.}, year={2014}, month={Jun}, pages={1429–1444} } @article{falzarano_de wit_feldmann_rasmussen_okumura_peng_thomas_van doremalen_haddock_nagy_et al._2014, title={Infection with MERS-CoV Causes Lethal Pneumonia in the Common Marmoset}, volume={10}, ISSN={1553-7374}, url={http://dx.doi.org/10.1371/journal.ppat.1004250}, DOI={10.1371/journal.ppat.1004250}, abstractNote={The availability of a robust disease model is essential for the development of countermeasures for Middle East respiratory syndrome coronavirus (MERS-CoV). While a rhesus macaque model of MERS-CoV has been established, the lack of uniform, severe disease in this model complicates the analysis of countermeasure studies. Modeling of the interaction between the MERS-CoV spike glycoprotein and its receptor dipeptidyl peptidase 4 predicted comparable interaction energies in common marmosets and humans. The suitability of the marmoset as a MERS-CoV model was tested by inoculation via combined intratracheal, intranasal, oral and ocular routes. Most of the marmosets developed a progressive severe pneumonia leading to euthanasia of some animals. Extensive lesions were evident in the lungs of all animals necropsied at different time points post inoculation. Some animals were also viremic; high viral loads were detected in the lungs of all infected animals, and total RNAseq demonstrated the induction of immune and inflammatory pathways. This is the first description of a severe, partially lethal, disease model of MERS-CoV, and as such will have a major impact on the ability to assess the efficacy of vaccines and treatment strategies as well as allowing more detailed pathogenesis studies.}, number={8}, journal={PLoS Pathogens}, publisher={Public Library of Science (PLoS)}, author={Falzarano, Darryl and de Wit, Emmie and Feldmann, Friederike and Rasmussen, Angela L. and Okumura, Atsushi and Peng, Xinxia and Thomas, Matthew J. and van Doremalen, Neeltje and Haddock, Elaine and Nagy, Lee and et al.}, editor={Denison, Mark R.Editor}, year={2014}, month={Aug}, pages={e1004250} } @article{peng_alföldi_gori_eisfeld_tyler_tisoncik-go_brawand_law_skunca_hatta_et al._2014, title={The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease}, volume={32}, ISSN={1087-0156 1546-1696}, url={http://dx.doi.org/10.1038/nbt.3079}, DOI={10.1038/nbt.3079}, abstractNote={The genome sequence of the ferret, a model of human respiratory disease, enables research on influenza and cystic fibrosis. The domestic ferret (Mustela putorius furo) is an important animal model for multiple human respiratory diseases. It is considered the 'gold standard' for modeling human influenza virus infection and transmission1,2,3,4. Here we describe the 2.41 Gb draft genome assembly of the domestic ferret, constituting 2.28 Gb of sequence plus gaps. We annotated 19,910 protein-coding genes on this assembly using RNA-seq data from 21 ferret tissues. We characterized the ferret host response to two influenza virus infections by RNA-seq analysis of 42 ferret samples from influenza time-course data and showed distinct signatures in ferret trachea and lung tissues specific to 1918 or 2009 human pandemic influenza virus infections. Using microarray data from 16 ferret samples reflecting cystic fibrosis disease progression, we showed that transcriptional changes in the CFTR-knockout ferret lung reflect pathways of early disease that cannot be readily studied in human infants with cystic fibrosis disease.}, number={12}, journal={Nature Biotechnology}, publisher={Springer Nature}, author={Peng, Xinxia and Alföldi, Jessica and Gori, Kevin and Eisfeld, Amie J and Tyler, Scott R and Tisoncik-Go, Jennifer and Brawand, David and Law, G Lynn and Skunca, Nives and Hatta, Masato and et al.}, year={2014}, month={Nov}, pages={1250–1255} } @article{peng_thierry-mieg_thierry-mieg_nishida_pipes_bozinoski_thomas_kelly_weiss_raveendran_et al._2014, title={Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR)}, volume={43}, ISSN={1362-4962 0305-1048}, url={http://dx.doi.org/10.1093/nar/gku1110}, DOI={10.1093/nar/gku1110}, abstractNote={The non-human primate reference transcriptome resource (NHPRTR, available online at http://nhprtr.org/) aims to generate comprehensive RNA-seq data from a wide variety of non-human primates (NHPs), from lemurs to hominids. In the 2012 Phase I of the NHPRTR project, 19 billion fragments or 3.8 terabases of transcriptome sequences were collected from pools of ∼20 tissues in 15 species and subspecies. Here we describe a major expansion of NHPRTR by adding 10.1 billion fragments of tissue-specific RNA-seq data. For this effort, we selected 11 of the original 15 NHP species and subspecies and constructed total RNA libraries for the same ∼15 tissues in each. The sequence quality is such that 88% of the reads align to human reference sequences, allowing us to compute the full list of expression abundance across all tissues for each species, using the reads mapped to human genes. This update also includes improved transcript annotations derived from RNA-seq data for rhesus and cynomolgus macaques, two of the most commonly used NHP models and additional RNA-seq data compiled from related projects. Together, these comprehensive reference transcriptomes from multiple primates serve as a valuable community resource for genome annotation, gene dynamics and comparative functional analysis.}, number={D1}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Peng, Xinxia and Thierry-Mieg, Jean and Thierry-Mieg, Danielle and Nishida, Andrew and Pipes, Lenore and Bozinoski, Marjan and Thomas, Matthew J. and Kelly, Sara and Weiss, Jeffrey M. and Raveendran, Muthuswamy and et al.}, year={2014}, month={Nov}, pages={D737–D742} } @article{bruce_ryan_thomas_peng_grundhoff_tsai_rose_2013, title={Next-Generation Sequence Analysis of the Genome of RFHVMn, the Macaque Homolog of Kaposi's Sarcoma (KS)-Associated Herpesvirus, from a KS-Like Tumor of a Pig-Tailed Macaque}, volume={87}, ISSN={0022-538X}, url={http://dx.doi.org/10.1128/jvi.02331-13}, DOI={10.1128/jvi.02331-13}, abstractNote={ABSTRACT The complete sequence of retroperitoneal fibromatosis-associated herpesvirus Macaca nemestrina (RFHVMn), the pig-tailed macaque homolog of Kaposi's sarcoma-associated herpesvirus (KSHV), was determined by next-generation sequence analysis of a Kaposi's sarcoma (KS)-like macaque tumor. Colinearity of genes was observed with the KSHV genome, and the core herpesvirus genes had strong sequence homology to the corresponding KSHV genes. RFHVMn lacked homologs of open reading frame 11 (ORF11) and KSHV ORFs K5 and K6, which appear to have been generated by duplication of ORFs K3 and K4 after the divergence of KSHV and RFHV. RFHVMn contained positional homologs of all other unique KSHV genes, although some showed limited sequence similarity. RFHVMn contained a number of candidate microRNA genes. Although there was little sequence similarity with KSHV microRNAs, one candidate contained the same seed sequence as the positional homolog, kshv-miR-K12-10a, suggesting functional overlap. RNA transcript splicing was highly conserved between RFHVMn and KSHV, and strong sequence conservation was noted in specific promoters and putative origins of replication, predicting important functional similarities. Sequence comparisons indicated that RFHVMn and KSHV developed in long-term synchrony with the evolution of their hosts, and both viruses phylogenetically group within the RV1 lineage of Old World primate rhadinoviruses. RFHVMn is the closest homolog of KSHV to be completely sequenced and the first sequenced RV1 rhadinovirus homolog of KSHV from a nonhuman Old World primate. The strong genetic and sequence similarity between RFHVMn and KSHV, coupled with similarities in biology and pathology, demonstrate that RFHVMn infection in macaques offers an important and relevant model for the study of KSHV in humans. }, number={24}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Bruce, A. G. and Ryan, J. T. and Thomas, M. J. and Peng, X. and Grundhoff, A. and Tsai, C.-C. and Rose, T. M.}, year={2013}, month={Oct}, pages={13676–13693} } @article{jones_ruzzo_peng_katze_2012, title={A new approach to bias correction in RNA-Seq}, volume={28}, ISSN={1460-2059 1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/bts055}, DOI={10.1093/bioinformatics/bts055}, abstractNote={Abstract Motivation: Quantification of sequence abundance in RNA-Seq experiments is often conflated by protocol-specific sequence bias. The exact sources of the bias are unknown, but may be influenced by polymerase chain reaction amplification, or differing primer affinities and mixtures, for example. The result is decreased accuracy in many applications, such as de novo gene annotation and transcript quantification. Results: We present a new method to measure and correct for these influences using a simple graphical model. Our model does not rely on existing gene annotations, and model selection is performed automatically making it applicable with few assumptions. We evaluate our method on several datasets, and by multiple criteria, demonstrating that it effectively decreases bias and increases uniformity. Additionally, we provide theoretical and empirical results showing that the method is unlikely to have any effect on unbiased data, suggesting it can be applied with little risk of spurious adjustment. Availability: The method is implemented in the seqbias R/Bioconductor package, available freely under the LGPL license from http://bioconductor.org Contact:  dcjones@cs.washington.edu Supplementary information:  Supplementary data are available at Bioinformatics online.}, number={7}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Jones, Daniel C. and Ruzzo, Walter L. and Peng, Xinxia and Katze, Michael G.}, year={2012}, month={Jan}, pages={921–928} } @article{jones_ruzzo_peng_katze_2012, title={Compression of next-generation sequencing reads aided by highly efficient de novo assembly}, volume={40}, ISSN={1362-4962 0305-1048}, url={http://dx.doi.org/10.1093/nar/gks754}, DOI={10.1093/nar/gks754}, abstractNote={We present Quip, a lossless compression algorithm for next-generation sequencing data in the FASTQ and SAM/BAM formats. In addition to implementing reference-based compression, we have developed, to our knowledge, the first assembly-based compressor, using a novel de novo assembly algorithm. A probabilistic data structure is used to dramatically reduce the memory required by traditional de Bruijn graph assemblers, allowing millions of reads to be assembled very efficiently. Read sequences are then stored as positions within the assembled contigs. This is combined with statistical compression of read identifiers, quality scores, alignment information and sequences, effectively collapsing very large data sets to <15% of their original size with no loss of information. Availability: Quip is freely available under the 3-clause BSD license from http://cs.washington.edu/homes/dcjones/quip.}, number={22}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Jones, Daniel C. and Ruzzo, Walter L. and Peng, Xinxia and Katze, Michael G.}, year={2012}, month={Aug}, pages={e171–e171} } @article{pipes_li_bozinoski_palermo_peng_blood_kelly_weiss_thierry-mieg_thierry-mieg_et al._2012, title={The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics}, volume={41}, ISSN={0305-1048 1362-4962}, url={http://dx.doi.org/10.1093/nar/gks1268}, DOI={10.1093/nar/gks1268}, abstractNote={RNA-based next-generation sequencing (RNA-Seq) provides a tremendous amount of new information regarding gene and transcript structure, expression and regulation. This is particularly true for non-coding RNAs where whole transcriptome analyses have revealed that the much of the genome is transcribed and that many non-coding transcripts have widespread functionality. However, uniform resources for raw, cleaned and processed RNA-Seq data are sparse for most organisms and this is especially true for non-human primates (NHPs). Here, we describe a large-scale RNA-Seq data and analysis infrastructure, the NHP reference transcriptome resource (http://nhprtr.org); it presently hosts data from12 species of primates, to be expanded to 15 species/subspecies spanning great apes, old world monkeys, new world monkeys and prosimians. Data are collected for each species using pools of RNA from comparable tissues. We provide data access in advance of its deposition at NCBI, as well as browsable tracks of alignments against the human genome using the UCSC genome browser. This resource will continue to host additional RNA-Seq data, alignments and assemblies as they are generated over the coming years and provide a key resource for the annotation of NHP genomes as well as informing primate studies on evolution, reproduction, infection, immunity and pharmacology.}, number={D1}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Pipes, Lenore and Li, Sheng and Bozinoski, Marjan and Palermo, Robert and Peng, Xinxia and Blood, Phillip and Kelly, Sara and Weiss, Jeffrey M. and Thierry-Mieg, Jean and Thierry-Mieg, Danielle and et al.}, year={2012}, month={Nov}, pages={D906–D914} } @article{peng_gralinski_ferris_frieman_thomas_proll_korth_tisoncik_heise_luo_et al._2011, title={Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection}, volume={2}, ISSN={2150-7511}, url={http://dx.doi.org/10.1128/mbio.00198-11}, DOI={10.1128/mbio.00198-11}, abstractNote={ABSTRACT We previously reported widespread differential expression of long non-protein-coding RNAs (ncRNAs) in response to virus infection. Here, we expanded the study through small RNA transcriptome sequencing analysis of the host response to both severe acute respiratory syndrome coronavirus (SARS-CoV) and influenza virus infections across four founder mouse strains of the Collaborative Cross, a recombinant inbred mouse resource for mapping complex traits. We observed differential expression of over 200 small RNAs of diverse classes during infection. A majority of identified microRNAs (miRNAs) showed divergent changes in expression across mouse strains with respect to SARS-CoV and influenza virus infections and responded differently to a highly pathogenic reconstructed 1918 virus compared to a minimally pathogenic seasonal influenza virus isolate. Novel insights into miRNA expression changes, including the association with pathogenic outcomes and large differences between in vivo and in vitro experimental systems, were further elucidated by a survey of selected miRNAs across diverse virus infections. The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. These findings represent the first integrated sequencing analysis of the response of host small RNAs to virus infection and show that small RNAs are an integrated component of complex networks involved in regulating the host response to infection. IMPORTANCE Most studies examining the host transcriptional response to infection focus only on protein-coding genes. However, mammalian genomes transcribe many short and long non-protein-coding RNAs (ncRNAs). With the advent of deep-sequencing technologies, systematic transcriptome analysis of the host response, including analysis of ncRNAs of different sizes, is now possible. Using this approach, we recently discovered widespread differential expression of host long (>200 nucleotide [nt]) ncRNAs in response to virus infection. Here, the samples described in the previous report were again used, but we sequenced another fraction of the transcriptome to study very short (about 20 to 30 nt) ncRNAs. We demonstrated that virus infection also altered expression of many short ncRNAs of diverse classes. Putting the results of the two studies together, we show that small RNAs may also play an important role in regulating the host response to virus infection. }, number={6}, journal={mBio}, publisher={American Society for Microbiology}, author={Peng, Xinxia and Gralinski, Lisa and Ferris, Martin T. and Frieman, Matthew B. and Thomas, Matthew J. and Proll, Sean and Korth, Marcus J. and Tisoncik, Jennifer R. and Heise, Mark and Luo, Shujun and et al.}, editor={Cullen, Bryan and Dermody, Terence S.Editors}, year={2011}, month={Nov} } @article{chang_sova_peng_weiss_law_palermo_katze_2011, title={Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4+ T Cell Line}, volume={2}, ISSN={2150-7511}, url={http://dx.doi.org/10.1128/mbio.00134-11}, DOI={10.1128/mbio.00134-11}, abstractNote={ABSTRACT Next-generation sequencing (NGS) enables the highly sensitive measurement of whole transcriptomes. We report the first application to our knowledge of this technology to the analysis of RNA from a CD4 + T cell line infected with intact HIV. We sequenced the total mRNA from infected cells and detected differences in the expression of both host and viral mRNA. Viral reads represented a large portion of the total mapped sequencing reads: approximately 20% at 12 h postinfection (hpi) and 40% at 24 hpi. We also detected a small but significant suppression of T cell activation-related genes at 12 hpi. This suppression persisted and expanded by 24 hpi, providing new possible markers of virus-induced T cell cytopathology. By 24 hpi, the expression of over 50% of detectable host loci was also altered, indicating widespread alteration of host processes, including RNA processing, splicing, and transport to an extent not previously reported. In addition, next-generation sequencing provided insights into alternative viral RNA splice events and the expression of noncoding RNAs, including microRNA host genes. IMPORTANCE Recent advances in sequencing technology now allow the measurement of effectively all the RNA in a cell. This approach is especially useful for studying models of virus infection, as it allows the simultaneous measurement of both host and viral RNA. Using next-generation sequencing (NGS), we measured changes in total mRNA from a HIV-infected T cell line. To our knowledge, this is the first application of this technology to the investigation of HIV-host interactions involving intact HIV. We directly measured the amount of viral mRNA in infected cells and detected novel viral RNA splice variants and changes in the host expression of noncoding RNA species. We also detected small changes in T cell activation and other host processes during the early stages of viral replication that increased near the peak of viral replication, providing new candidate biomarkers of T cell death. }, number={5}, journal={mBio}, publisher={American Society for Microbiology}, author={Chang, Stewart T. and Sova, Pavel and Peng, Xinxia and Weiss, Jeffrey and Law, G. Lynn and Palermo, Robert E. and Katze, Michael G.}, editor={Unutmaz, Derya and Dermody, Terence S.Editors}, year={2011}, month={Sep} } @article{cilloniz_pantin-jackwood_ni_goodman_peng_proll_carter_rosenzweig_szretter_katz_et al._2010, title={Lethal Dissemination of H5N1 Influenza Virus Is Associated with Dysregulation of Inflammation and Lipoxin Signaling in a Mouse Model of Infection}, volume={84}, ISSN={0022-538X}, url={http://dx.doi.org/10.1128/jvi.00553-10}, DOI={10.1128/jvi.00553-10}, abstractNote={ABSTRACT Periodic outbreaks of highly pathogenic avian H5N1 influenza viruses and the current H1N1 pandemic highlight the need for a more detailed understanding of influenza virus pathogenesis. To investigate the host transcriptional response induced by pathogenic influenza viruses, we used a functional-genomics approach to compare gene expression profiles in lungs from 129S6/SvEv mice infected with either the fully reconstructed H1N1 1918 pandemic virus (1918) or the highly pathogenic avian H5N1 virus Vietnam/1203/04 (VN/1203). Although the viruses reached similar titers in the lung and caused lethal infections, the mean time of death was 6 days for VN/1203-infected animals and 9 days for mice infected with the 1918 virus. VN/1203-infected animals also exhibited an earlier and more potent inflammatory response. This response included induction of genes encoding components of the inflammasome. VN/1203 was also able to disseminate to multiple organs, including the brain, which correlated with changes in the expression of genes associated with hematological functions and lipoxin biogenesis and signaling. Both viruses elicited expression of type I interferon (IFN)-regulated genes in wild-type mice and to a lesser extent in mice lacking the type I IFN receptor, suggesting alternative or redundant pathways for IFN signaling. Our findings suggest that VN/1203 is more pathogenic in mice as a consequence of several factors, including the early and sustained induction of the inflammatory response, the additive or synergistic effects of upregulated components of the immune response, and inhibition of lipoxin-mediated anti-inflammatory responses, which correlated with the ability of VN/1203 to disseminate to extrapulmonary organs.}, number={15}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Cilloniz, C. and Pantin-Jackwood, M. J. and Ni, C. and Goodman, A. G. and Peng, X. and Proll, S. C. and Carter, V. S. and Rosenzweig, E. R. and Szretter, K. J. and Katz, J. M. and et al.}, year={2010}, month={May}, pages={7613–7624} } @article{li_chan_li_ni_peng_rosenzweig_tumpey_katze_2010, title={MicroRNA Expression and Virulence in Pandemic Influenza Virus-Infected Mice}, volume={84}, ISSN={0022-538X}, url={http://dx.doi.org/10.1128/jvi.02203-09}, DOI={10.1128/jvi.02203-09}, abstractNote={ABSTRACT The worst known H1N1 influenza pandemic in history resulted in more than 20 million deaths in 1918 and 1919. Although the underlying mechanism causing the extreme virulence of the 1918 influenza virus is still obscure, our previous functional genomics analyses revealed a correlation between the lethality of the reconstructed 1918 influenza virus (r1918) in mice and a unique gene expression pattern associated with severe immune responses in the lungs. Lately, microRNAs have emerged as a class of crucial regulators for gene expression. To determine whether differential expression of cellular microRNAs plays a role in the host response to r1918 infection, we compared the lung cellular “microRNAome” of mice infected by r1918 virus with that of mice infected by a nonlethal seasonal influenza virus, A/Texas/36/91. We found that a group of microRNAs, including miR-200a and miR-223, were differentially expressed in response to influenza virus infection and that r1918 and A/Texas/36/91 infection induced distinct microRNA expression profiles. Moreover, we observed significant enrichment in the number of predicted cellular target mRNAs whose expression was inversely correlated with the expression of these microRNAs. Intriguingly, gene ontology analysis revealed that many of these mRNAs play roles in immune response and cell death pathways, which are known to be associated with the extreme virulence of r1918. This is the first demonstration that cellular gene expression patterns in influenza virus-infected mice may be attributed in part to microRNA regulation and that such regulation may be a contributing factor to the extreme virulence of the r1918.}, number={6}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Li, Y. and Chan, E. Y. and Li, J. and Ni, C. and Peng, X. and Rosenzweig, E. and Tumpey, T. M. and Katze, M. G.}, year={2010}, month={Jan}, pages={3023–3032} } @article{aly_lindner_mackellar_peng_kappe_2010, title={SAP1 is a critical post-transcriptional regulator of infectivity in malaria parasite sporozoite stages}, volume={79}, ISSN={0950-382X}, url={http://dx.doi.org/10.1111/j.1365-2958.2010.07497.x}, DOI={10.1111/j.1365-2958.2010.07497.x}, abstractNote={Summary Plasmodium salivary gland sporozoites upregulate expression of a unique subset of genes, collectively called the UIS (upregulated in infectious sporozoites). Many UIS were shown to be essential for early liver stage development, although little is known about their regulation. We previously identified a conserved sporozoite‐specific protein, SAP1, which has an essential role in Plasmodium liver infection. Targeted deletion of SAP1 in Plasmodium yoelii caused the depletion of a number of selectively tested UIS transcripts in sporozoites, resulting in a complete early liver stage arrest. Here, we use a global gene expression survey to more comprehensively identify transcripts that are affected by SAP1 deletion. We find an effect upon both the transcript abundance of UIS genes, as well as of select genes previously not grouped as UIS. Importantly, we show that the lack of SAP1 causes the specific degradation of these transcripts. Collectively, our data suggest that SAP1 is involved in a selective post‐transcriptional mechanism to regulate the abundance of transcripts critical to the infectivity of sporozoites. Although Pysap1‐ sporozoites are depleted of many of these important transcripts, they confer long‐lasting sterile protection against wild‐type sporozoite challenge in mice. SAP1 is therefore an appealing candidate locus for attenuation of Plasmodium falciparum.}, number={4}, journal={Molecular Microbiology}, publisher={Wiley}, author={Aly, Ahmed S. I. and Lindner, Scott E. and MacKellar, Drew C. and Peng, Xinxia and Kappe, Stefan H. I.}, year={2010}, month={Dec}, pages={929–939} } @article{peng_gralinski_armour_ferris_thomas_proll_bradel-tretheway_korth_castle_biery_et al._2010, title={Unique Signatures of Long Noncoding RNA Expression in Response to Virus Infection and Altered Innate Immune Signaling}, volume={1}, ISSN={2150-7511}, url={http://dx.doi.org/10.1128/mbio.00206-10}, DOI={10.1128/mbio.00206-10}, abstractNote={ABSTRACT Studies of the host response to virus infection typically focus on protein-coding genes. However, non-protein-coding RNAs (ncRNAs) are transcribed in mammalian cells, and the roles of many of these ncRNAs remain enigmas. Using next-generation sequencing, we performed a whole-transcriptome analysis of the host response to severe acute respiratory syndrome coronavirus (SARS-CoV) infection across four founder mouse strains of the Collaborative Cross. We observed differential expression of approximately 500 annotated, long ncRNAs and 1,000 nonannotated genomic regions during infection. Moreover, studies of a subset of these ncRNAs and genomic regions showed the following. (i) Most were similarly regulated in response to influenza virus infection. (ii) They had distinctive kinetic expression profiles in type I interferon receptor and STAT1 knockout mice during SARS-CoV infection, including unique signatures of ncRNA expression associated with lethal infection. (iii) Over 40% were similarly regulated in vitro in response to both influenza virus infection and interferon treatment. These findings represent the first discovery of the widespread differential expression of long ncRNAs in response to virus infection and suggest that ncRNAs are involved in regulating the host response, including innate immunity. At the same time, virus infection models provide a unique platform for studying the biology and regulation of ncRNAs. IMPORTANCE Most studies examining the host transcriptional response to infection focus only on protein-coding genes. However, there is growing evidence that thousands of non-protein-coding RNAs (ncRNAs) are transcribed from mammalian genomes. While most attention to the involvement of ncRNAs in virus-host interactions has been on small ncRNAs such as microRNAs, it is becoming apparent that many long ncRNAs (>200 nucleotides [nt]) are also biologically important. These long ncRNAs have been found to have widespread functionality, including chromatin modification and transcriptional regulation and serving as the precursors of small RNAs. With the advent of next-generation sequencing technologies, whole-transcriptome analysis of the host response, including long ncRNAs, is now possible. Using this approach, we demonstrated that virus infection alters the expression of numerous long ncRNAs, suggesting that these RNAs may be a new class of regulatory molecules that play a role in determining the outcome of infection. }, number={5}, journal={mBio}, publisher={American Society for Microbiology}, author={Peng, Xinxia and Gralinski, Lisa and Armour, Christopher D. and Ferris, Martin T. and Thomas, Matthew J. and Proll, Sean and Bradel-Tretheway, Birgit G. and Korth, Marcus J. and Castle, John C. and Biery, Matthew C. and et al.}, editor={Sonenberg, Nahum and Dermody, Terence S.Editors}, year={2010}, month={Oct} } @article{peng_li_walters_rosenzweig_lederer_aicher_proll_katze_2009, title={Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers}, volume={10}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/1471-2164-10-373}, DOI={10.1186/1471-2164-10-373}, abstractNote={Abstract Background Hepatitis C virus (HCV) is a major cause of chronic liver disease by infecting over 170 million people worldwide. Recent studies have shown that microRNAs (miRNAs), a class of small non-coding regulatory RNAs, are involved in the regulation of HCV infection, but their functions have not been systematically studied. We propose an integrative strategy for identifying the miRNA-mRNA regulatory modules that are associated with HCV infection. This strategy combines paired expression profiles of miRNAs and mRNAs and computational target predictions. A miRNA-mRNA regulatory module consists of a set of miRNAs and their targets, in which the miRNAs are predicted to coordinately regulate the level of the target mRNA. Results We simultaneously profiled the expression of cellular miRNAs and mRNAs across 30 HCV positive or negative human liver biopsy samples using microarray technology. We constructed a miRNA-mRNA regulatory network, and using a graph theoretical approach, identified 38 miRNA-mRNA regulatory modules in the network that were associated with HCV infection. We evaluated the direct miRNA regulation of the mRNA levels of targets in regulatory modules using previously published miRNA transfection data. We analyzed the functional roles of individual modules at the systems level by integrating a large-scale protein interaction network. We found that various biological processes, including some HCV infection related canonical pathways, were regulated at the miRNA level during HCV infection. Conclusion Our regulatory modules provide a framework for future experimental analyses. This report demonstrates the utility of our approach to obtain new insights into post-transcriptional gene regulation at the miRNA level in complex human diseases. }, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Peng, Xinxia and Li, Yu and Walters, Kathie-Anne and Rosenzweig, Elizabeth R and Lederer, Sharon L and Aicher, Lauri D and Proll, Sean and Katze, Michael G}, year={2009}, pages={373} } @article{albuquerque_carret_grosso_tarun_peng_kappe_prudêncio_mota_2009, title={Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events}, volume={10}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/1471-2164-10-270}, DOI={10.1186/1471-2164-10-270}, abstractNote={Abstract Background Plasmodium sporozoites migrate to the liver where they traverse several hepatocytes before invading the one inside which they will develop and multiply into thousands of merozoites. Although this constitutes an essential step of malaria infection, the requirements of Plasmodium parasites in liver cells and how they use the host cell for their own survival and development are poorly understood. Results To gain new insights into the molecular host-parasite interactions that take place during malaria liver infection, we have used high-throughput microarray technology to determine the transcriptional profile of P. berghei-infected hepatoma cells. The data analysis shows differential expression patterns for 1064 host genes starting at 6 h and up to 24 h post infection, with the largest proportion correlating specifically with the early stages of the infection process. A considerable proportion of those genes were also found to be modulated in liver cells collected from P. yoelii- infected mice 24 and 40 h after infection, strengthening the data obtained with the in vitro model and highlighting genes and pathways involved in the host response to rodent Plasmodium parasites. Conclusion Our data reveal that host cell infection by Plasmodium sporozoites leads to a coordinated and sequential set of biological events, ranging from the initial stage of stress response up to the engagement of host metabolic processes and the maintenance of cell viability throughout infection. }, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Albuquerque, Sónia S and Carret, Céline and Grosso, Ana and Tarun, Alice S and Peng, Xinxia and Kappe, Stefan HI and Prudêncio, Miguel and Mota, Maria M}, year={2009}, pages={270} } @article{cillóniz_shinya_peng_korth_proll_aicher_carter_chang_kobasa_feldmann_et al._2009, title={Lethal Influenza Virus Infection in Macaques Is Associated with Early Dysregulation of Inflammatory Related Genes}, volume={5}, ISSN={1553-7374}, url={http://dx.doi.org/10.1371/journal.ppat.1000604}, DOI={10.1371/journal.ppat.1000604}, abstractNote={The enormous toll on human life during the 1918–1919 Spanish influenza pandemic is a constant reminder of the potential lethality of influenza viruses. With the declaration by the World Health Organization of a new H1N1 influenza virus pandemic, and with continued human cases of highly pathogenic H5N1 avian influenza virus infection, a better understanding of the host response to highly pathogenic influenza viruses is essential. To this end, we compared pathology and global gene expression profiles in bronchial tissue from macaques infected with either the reconstructed 1918 pandemic virus or the highly pathogenic avian H5N1 virus A/Vietnam/1203/04. Severe pathology was observed in respiratory tissues from 1918 virus-infected animals as early as 12 hours after infection, and pathology steadily increased at later time points. Although tissues from animals infected with A/Vietnam/1203/04 also showed clear signs of pathology early on, less pathology was observed at later time points, and there was evidence of tissue repair. Global transcriptional profiles revealed that specific groups of genes associated with inflammation and cell death were up-regulated in bronchial tissues from animals infected with the 1918 virus but down-regulated in animals infected with A/Vietnam/1203/04. Importantly, the 1918 virus up-regulated key components of the inflammasome, NLRP3 and IL-1β, whereas these genes were down-regulated by A/Vietnam/1203/04 early after infection. TUNEL assays revealed that both viruses elicited an apoptotic response in lungs and bronchi, although the response occurred earlier during 1918 virus infection. Our findings suggest that the severity of disease in 1918 virus-infected macaques is a consequence of the early up-regulation of cell death and inflammatory related genes, in which additive or synergistic effects likely dictate the severity of tissue damage.}, number={10}, journal={PLoS Pathogens}, publisher={Public Library of Science (PLoS)}, author={Cillóniz, Cristian and Shinya, Kyoko and Peng, Xinxia and Korth, Marcus J. and Proll, Sean C. and Aicher, Lauri D. and Carter, Victoria S. and Chang, Jean H. and Kobasa, Darwyn and Feldmann, Friedericke and et al.}, editor={Diamond, Michael S.Editor}, year={2009}, month={Oct}, pages={e1000604} } @article{goodman_fornek_medigeshi_perrone_peng_dyer_proll_knoblaugh_carter_korth_et al._2009, title={P58IPK: A Novel “CIHD” Member of the Host Innate Defense Response against Pathogenic Virus Infection}, volume={5}, ISSN={1553-7374}, url={http://dx.doi.org/10.1371/journal.ppat.1000438}, DOI={10.1371/journal.ppat.1000438}, abstractNote={To support their replication, viruses take advantage of numerous cellular factors and processes. Recent large-scale screens have identified hundreds of such factors, yet little is known about how viruses exploit any of these. Influenza virus infection post-translationally activates P58IPK, a cellular inhibitor of the interferon-induced, dsRNA-activated eIF2α kinase, PKR. Here, we report that infection of P58IPK knockout mice with influenza virus resulted in increased lung pathology, immune cell apoptosis, PKR activation, and mortality. Analysis of lung transcriptional profiles, including those induced by the reconstructed 1918 pandemic virus, revealed increased expression of genes associated with the cell death, immune, and inflammatory responses. These experiments represent the first use of a mammalian infection model to demonstrate the role of P58IPK in the antiviral response. Our results suggest that P58IPK represents a new class of molecule, a cellular inhibitor of the host defense (CIHD), as P58IPK is activated during virus infection to inhibit virus-induced apoptosis and inflammation to prolong host survival, even while prolonging viral replication.}, number={5}, journal={PLoS Pathogens}, publisher={Public Library of Science (PLoS)}, author={Goodman, Alan G. and Fornek, Jamie L. and Medigeshi, Guruprasad R. and Perrone, Lucy A. and Peng, Xinxia and Dyer, Matthew D. and Proll, Sean C. and Knoblaugh, Sue E. and Carter, Victoria S. and Korth, Marcus J. and et al.}, editor={Andino, RaulEditor}, year={2009}, month={May}, pages={e1000438} } @article{goodman_zeng_proll_peng_cilloniz_carter_korth_tumpey_katze_2009, title={The Alpha/Beta Interferon Receptor Provides Protection against Influenza Virus Replication but Is Dispensable for Inflammatory Response Signaling}, volume={84}, ISSN={0022-538X}, url={http://dx.doi.org/10.1128/jvi.01595-09}, DOI={10.1128/jvi.01595-09}, abstractNote={ABSTRACT The innate immune response provides the first line of defense against foreign pathogens by responding to molecules that are a signature of a pathogenic infection. Certain RNA viruses, such as influenza virus, produce double-stranded RNA as an intermediate during the replication life cycle, which activates pathogen recognition receptors capable of inducing interferon production. By engaging interferon receptors, interferon activates the JAK-STAT pathway and results in the positive feedback of interferon production, amplifying the response to viral infection. To examine how deficiencies in interferon signaling affect the cellular response to infection, we performed influenza virus infections of mouse embryonic fibroblasts lacking the alpha/beta interferon receptor, the gamma interferon receptor, or both. In the absence of the alpha/beta interferon receptor, we observed increased viral replication but decreased activation of PKR, Stat1, and NF-κB; the presence or absence of the gamma interferon receptor did not exhibit discernible differences in these readouts. Analysis of gene expression profiles showed that while cells lacking the alpha/beta interferon receptor exhibited decreased levels of transcription of antiviral genes, genes related to inflammatory and apoptotic responses were transcribed to levels similar to those of cells containing the receptor. These results indicate that while the alpha/beta interferon receptor is needed to curb viral replication, it is dispensable for the induction of certain inflammatory and apoptotic genes. We have identified potential pathways, via interferon regulatory factor 3 (IRF3) activation or Hoxa13 , Polr2a , Nr4a1 , or Ing1 induction, that contribute to this redundancy. This study illustrates another way in which the host has evolved to establish several overlapping mechanisms to respond to viral infections. }, number={4}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Goodman, A. G. and Zeng, H. and Proll, S. C. and Peng, X. and Cilloniz, C. and Carter, V. S. and Korth, M. J. and Tumpey, T. M. and Katze, M. G.}, year={2009}, month={Nov}, pages={2027–2037} } @article{goodman_zeng_cilloniz_carter_peng_proll_tumpey_katze_2009, title={The Type I interferon receptor protects against influenza virus replication while the Type II receptor is dispensible}, volume={48}, ISSN={1043-4666}, url={http://dx.doi.org/10.1016/j.cyto.2009.07.294}, DOI={10.1016/j.cyto.2009.07.294}, number={1-2}, journal={Cytokine}, publisher={Elsevier BV}, author={Goodman, Alan G. and Zeng, Hui and Cilloniz, Cristian and Carter, Victoria S. and Peng, Xinxia and Proll, Sean C. and Tumpey, Terrence M. and Katze, Michael G.}, year={2009}, month={Oct}, pages={83} } @article{peng_chan_li_diamond_korth_katze_2009, title={Virus–host interactions: from systems biology to translational research}, volume={12}, ISSN={1369-5274}, url={http://dx.doi.org/10.1016/j.mib.2009.06.003}, DOI={10.1016/j.mib.2009.06.003}, abstractNote={Research embracing systems biology approaches and careful analysis of the critical host response has greatly expanded our understanding of infectious diseases. First-generation studies based on genomics and proteomics have made significant progress in establishing the foundation for network-based investigations on virus-host interactions. More recently, data from complementary high-throughput technologies, such as siRNA and microRNA screens and next-generation sequencing, are augmenting systems level analyses and are providing a more detailed and insightful multidimensional view of virus-host networks. Together with advances in data integration, systems biology approaches now have the potential to provide profound impacts on translational research, leading to the more rapid development of new therapeutics and vaccines for infectious diseases. In this review, we highlight new high-throughput technologies, a new philosophy for studying virus-host interactions, and discuss the potential of systems biology to facilitate bench-to-bedside research and create novel strategies to combat disease. Can we save the world using these approaches? Read on.}, number={4}, journal={Current Opinion in Microbiology}, publisher={Elsevier BV}, author={Peng, Xinxia and Chan, Eric Y and Li, Yu and Diamond, Deborah L and Korth, Marcus J and Katze, Michael G}, year={2009}, month={Aug}, pages={432–438} } @article{tarun_peng_dumpit_ogata_silva-rivera_camargo_daly_bergman_kappe_2008, title={A combined transcriptome and proteome survey of malaria parasite liver stages}, volume={105}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.0710780104}, DOI={10.1073/pnas.0710780104}, abstractNote={ For 50 years since their discovery, the malaria parasite liver stages (LS) have been difficult to analyze, impeding their utilization as a critical target for antiinfection vaccines and drugs. We have undertaken a comprehensive transcriptome analysis in combination with a proteomic survey of LS. Green fluorescent protein-tagged Plasmodium yoelii (PyGFP) was used to efficiently isolate LS-infected hepatocytes from the rodent host. Genome-wide LS gene expression was profiled and compared with other parasite life cycle stages. The analysis revealed ≈2,000 genes active during LS development, and proteomic analysis identified 816 proteins. A subset of proteins appeared to be expressed in LS only. The data revealed exported parasite proteins and LS metabolic pathways including expression of FASII pathway enzymes. The FASII inhibitor hexachlorophene and the antibiotics, tetracycline and rifampicin, that target the apicoplast inhibited LS development, identifying FASII and other pathways localized in the apicoplast as potential drug targets to prevent malaria infection. }, number={1}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Tarun, A. S. and Peng, X. and Dumpit, R. F. and Ogata, Y. and Silva-Rivera, H. and Camargo, N. and Daly, T. M. and Bergman, L. W. and Kappe, S. H. I.}, year={2008}, month={Jan}, pages={305–310} } @article{vaughan_chiu_ramasamy_li_gardner_tarun_kappe_peng_2008, title={Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis}, volume={24}, ISSN={1460-2059 1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btn140}, DOI={10.1093/bioinformatics/btn140}, abstractNote={Abstract Motivation: The sequencing of the Plasmodium yoelii genome, a model rodent malaria parasite, has greatly facilitated research for the development of new drug and vaccine candidates against malaria. Unfortunately, only preliminary gene models were annotated on the partially sequenced genome, mostly by in silico gene prediction, and there has been no major improvement of the annotation since 2002. Results: Here we report on a systematic assessment of the accuracy of the genome annotation based on a detailed analysis of a comprehensive set of cDNA sequences and proteomics data. We found that the coverage of the current annotation tends to be biased toward genes expressed in the blood stages of the parasite life cycle. Based on our proteomic analysis, we estimate that about 15% of the liver stage proteome data we have generated is absent from the current annotation. Through comparative analysis we identified and manually curated a further 510 P. yoelii genes which have clear orthologs in the P. falciparum genome, but were not present or incorrectly annotated in the current annotation. This study suggests that improvements of the current P. yoelii genome annotation should focus on genes expressed in stages other than blood stages. Comparative analysis will be critically helpful for this re-annotation. The addition of newly annotated genes will facilitate the use of P. yoelii as a model system for studying human malaria. Contact:  xinxia.peng@sbri.org; stefan.kappe@sbri.org Supplementary information:  Supplementary data are available at Bioinformatics online.}, number={13}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Vaughan, Ashley and Chiu, Sum-Ying and Ramasamy, Gowthaman and Li, Ling and Gardner, Malcolm J. and Tarun, Alice S. and Kappe, Stefan H.I. and Peng, Xinxia}, year={2008}, month={Jul}, pages={i383–i389} } @article{mikolajczak_silva-rivera_peng_tarun_camargo_jacobs-lorena_daly_bergman_de la vega_williams_et al._2008, title={Distinct Malaria Parasite Sporozoites Reveal Transcriptional Changes That Cause Differential Tissue Infection Competence in the Mosquito Vector and Mammalian Host}, volume={28}, ISSN={0270-7306}, url={http://dx.doi.org/10.1128/mcb.00553-08}, DOI={10.1128/mcb.00553-08}, abstractNote={ABSTRACT The malaria parasite sporozoite transmission stage develops and differentiates within parasite oocysts on the Anopheles mosquito midgut. Successful inoculation of the parasite into a mammalian host is critically dependent on the sporozoite's ability to first infect the mosquito salivary glands. Remarkable changes in tissue infection competence are observed as the sporozoites transit from the midgut oocysts to the salivary glands. Our microarray analysis shows that compared to oocyst sporozoites, salivary gland sporozoites upregulate expression of at least 124 unique genes. Conversely, oocyst sporozoites show upregulation of at least 47 genes (upregulated in oocyst sporozoites [UOS genes]) before they infect the salivary glands. Targeted gene deletion of UOS3, encoding a putative transmembrane protein with a thrombospondin repeat that localizes to the sporozoite secretory organelles, rendered oocyst sporozoites unable to infect the mosquito salivary glands but maintained the parasites' liver infection competence. This phenotype demonstrates the significance of differential UOS expression. Thus, the UIS-UOS gene classification provides a framework to elucidate the infectivity and transmission success of Plasmodium sporozoites on a whole-genome scale. Genes identified herein might represent targets for vector-based transmission blocking strategies (UOS genes), as well as strategies that prevent mammalian host infection (UIS genes).}, number={20}, journal={Molecular and Cellular Biology}, publisher={American Society for Microbiology}, author={Mikolajczak, S. A. and Silva-Rivera, H. and Peng, X. and Tarun, A. S. and Camargo, N. and Jacobs-Lorena, V. and Daly, T. M. and Bergman, L. W. and de la Vega, P. and Williams, J. and et al.}, year={2008}, month={Aug}, pages={6196–6207} } @inbook{peng_langston_saxton_baldwin_snoddy_2007, title={Detecting Network Motifs in Gene Co-expression Networks Through Integration of Protein Domain Information}, ISBN={9780387345680}, url={http://dx.doi.org/10.1007/978-0-387-34569-7_7}, DOI={10.1007/978-0-387-34569-7_7}, booktitle={Methods of Microarray Data Analysis V}, publisher={Springer US}, author={Peng, Xinxia and Langston, Michael A. and Saxton, Arnold M. and Baldwin, Nicole E. and Snoddy, Jay R.}, year={2007}, month={Feb}, pages={89–102} } @article{kirov_peng_baker_schmoyer_zhang_snoddy_2005, title={GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments}, volume={6}, ISSN={1471-2105}, url={http://dx.doi.org/10.1186/1471-2105-6-72}, DOI={10.1186/1471-2105-6-72}, abstractNote={Abstract Background The analysis of biological data is greatly enhanced by existing or emerging databases. Most existing databases, with few exceptions are not designed to easily support large scale computational analysis, but rather offer exclusively a web interface to the resource. We have recognized the growing need for a database which can be used successfully as a backend to computational analysis tools and pipelines. Such database should be sufficiently versatile to allow easy system integration. Results GeneKeyDB is a gene-centered relational database developed to enhance data mining in biological data sets. The system provides an underlying data layer for computational analysis tools and visualization tools. GeneKeyDB relies primarily on existing database identifiers derived from community databases (NCBI, GO, Ensembl, et al.) as well as the known relationships among those identifiers. It is a lightweight, portable, and extensible platform for integration with computational tools and analysis environments. Conclusion GeneKeyDB can enable analysis tools and users to manipulate the intersections, unions, and differences among different data sets.}, number={1}, journal={BMC Bioinformatics}, publisher={Springer Nature}, author={Kirov, SA and Peng, X and Baker, E and Schmoyer, D and Zhang, B and Snoddy, J}, year={2005}, pages={72} }