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Author

Hong Gao

Other affiliations: Harvard University
Bio: Hong Gao is an academic researcher from Stanford University. The author has contributed to research in topics: Acquired immune system & Chronic lymphocytic leukemia. The author has an hindex of 5, co-authored 6 publications receiving 3226 citations. Previous affiliations of Hong Gao include Harvard University.

Papers
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Journal ArticleDOI
TL;DR: This study shows that, although acute inflammatory stresses from different etiologies result in highly similar genomic responses in humans, the responses in corresponding mouse models correlate poorly with the human conditions and also, one another.
Abstract: A cornerstone of modern biomedical research is the use of mouse models to explore basic pathophysiological mechanisms, evaluate new therapeutic approaches, and make go or no-go decisions to carry new drug candidates forward into clinical trials. Systematic studies evaluating how well murine models mimic human inflammatory diseases are nonexistent. Here, we show that, although acute inflammatory stresses from different etiologies result in highly similar genomic responses in humans, the responses in corresponding mouse models correlate poorly with the human conditions and also, one another. Among genes changed significantly in humans, the murine orthologs are close to random in matching their human counterparts (e.g., R2 between 0.0 and 0.1). In addition to improvements in the current animal model systems, our study supports higher priority for translational medical research to focus on the more complex human conditions rather than relying on mouse models to study human inflammatory diseases.

2,438 citations

Journal ArticleDOI
Wenzhong Xiao1, Wenzhong Xiao2, Michael N. Mindrinos2, Junhee Seok2, Joseph Cuschieri3, Alex G. Cuenca4, Hong Gao2, Douglas L. Hayden5, Laura Hennessy3, Ernest E. Moore6, Joseph P. Minei7, Paul E. Bankey8, Jeffrey L. Johnson6, Jason L. Sperry9, Avery B. Nathens10, Timothy R. Billiar9, Michael West11, Bernard H. Brownstein12, Philip H. Mason, Henry V. Baker4, Celeste C. Finnerty13, Marc G. Jeschke10, M. Cecilia Lopez4, Matthew B. Klein3, Richard L. Gamelli14, Nicole S. Gibran3, Brett D. Arnoldo7, Weihong Xu2, Yuping Zhang2, Steven E. Calvano15, Grace P. McDonald-Smith, David A. Schoenfeld1, John D. Storey16, J. Perren Cobb1, H. Shaw Warren1, Lyle L. Moldawer4, David N. Herndon13, Stephen F. Lowry15, Ronald V. Maier3, Ronald W. Davis2, Ronald G. Tompkins1, W. Xiao1, M. Mindrinos1, J. Seok1, J. Cuschieri1, R. Tompkins1, Roger J. Davis1, R. Maier1, L. Moldawer1, L. Hennessy1, E. Moore1, J. Minei1, P. Bankey1, J. Johnson1, J. Sperry1, A. Nathens1, T. Billiar1, M. West1, B. Brownstein1, D. Herndon1, H. Baker1, C. Finnerty1, M. Jeschke1, M. Lopez1, M. Klein1, R. Gamelli1, N. Gibran1, B. Arnoldo1, G. McDonald-Smith1, D. Schoenfeld1, J. P. Cobb1, Shaw Warren1, A. Cuenca1, S. Lowry1, S. Calvano1, Doug Hayden1, P. Mason1, H. Gao1, J. Storey1, Lily L. Altstein1, Ulysses J. Balis1, David G. Camp1, K. De Asit1, Brian G. Harbrecht1, Shari Honari1, Bruce A. McKinley1, Carol L. Miller-Graziano1, Frederick A. Moore1, Grant E. O'Keefe1, Laurence G. Rahme1, Daniel G. Remick1, Michael B. Shapiro1, Richard D. Smith1, Robert Tibshirani1, Mehmet Toner1, Bram Wispelwey1, Wing Hung Wong1 
TL;DR: It is shown that critical injury in humans induces a genomic storm with simultaneous changes in expression of innate and adaptive immunity genes that alter the status of these genes in the immune system.
Abstract: Human survival from injury requires an appropriate inflammatory and immune response. We describe the circulating leukocyte transcriptome after severe trauma and burn injury, as well as in healthy subjects receiving low-dose bacterial endotoxin, and show that these severe stresses produce a global reprioritization affecting >80% of the cellular functions and pathways, a truly unexpected “genomic storm.” In severe blunt trauma, the early leukocyte genomic response is consistent with simultaneously increased expression of genes involved in the systemic inflammatory, innate immune, and compensatory antiinflammatory responses, as well as in the suppression of genes involved in adaptive immunity. Furthermore, complications like nosocomial infections and organ failure are not associated with any genomic evidence of a second hit and differ only in the magnitude and duration of this genomic reprioritization. The similarities in gene expression patterns between different injuries reveal an apparently fundamental human response to severe inflammatory stress, with genomic signatures that are surprisingly far more common than different. Based on these transcriptional data, we propose a new paradigm for the human immunological response to severe injury.

958 citations

Journal ArticleDOI
TL;DR: IGH-HTS using consensus primers will broaden the availability of MRD quantification in CLL and other B cell malignancies, and this approach has potential for quantitative evaluation of immune diversification following transplant and nontransplant therapies.
Abstract: The primary cause of poor outcome following allogeneic hematopoietic cell transplantation (HCT) for chronic lymphocytic leukemia (CLL) is disease recurrence. Detection of increasing minimal residual disease (MRD) following HCT may permit early intervention to prevent clinical relapse; however, MRD quantification remains an uncommon diagnostic test because of logistical and financial barriers to widespread use. Here we describe a method for quantifying CLL MRD using widely available consensus primers for amplification of all Ig heavy chain (IGH) genes in a mixture of peripheral blood mononuclear cells, followed by high-throughput sequencing (HTS) for disease-specific IGH sequence quantification. To achieve accurate MRD quantification, we developed a systematic bioinformatic methodology to aggregate cancer clone sequence variants arising from systematic and random artifacts occurring during IGH-HTS. We then compared the sensitivity of IGH-HTS, flow cytometry, and allele-specific oligonucleotide PCR for MRD quantification in 28 samples collected from 6 CLL patients following allogeneic HCT. Using amplimer libraries generated with consensus primers from patient blood samples, we demonstrate the sensitivity of IGH-HTS with 454 pyrosequencing to be 10(-5), with a high correlation between quantification by allele-specific oligonucleotide PCR and IGH-HTS (r = 0.85). From the same dataset used to quantify MRD, IGH-HTS also allowed us to profile IGH repertoire reconstitution after HCT-information not provided by the other MRD methods. IGH-HTS using consensus primers will broaden the availability of MRD quantification in CLL and other B cell malignancies, and this approach has potential for quantitative evaluation of immune diversification following transplant and nontransplant therapies.

188 citations

Journal ArticleDOI
Junhee Seok1, Weihong Xu1, Hong Gao1, Ronald W. Davis1, Wenzhong Xiao1 
TL;DR: JETTA is introduced, an integrated software package for the calculation of gene expression indices as well as the identification and visualization of alternative splicing events for high-throughput genome-wide studies of alternatively spliced mRNA transcripts.
Abstract: Summary: High-throughput genome-wide studies of alternatively spliced mRNA transcripts have become increasingly important in clinical research. Consequently, easy-to-use software tools are required to process data from these studies, for example, using exon and junction arrays. Here, we introduce JETTA, an integrated software package for the calculation of gene expression indices as well as the identification and visualization of alternative splicing events. We demonstrate the software using data of human liver and muscle samples hybridized on an exon–junction array. Availability: JETTA and its demonstrations are freely available at http://igenomed.stanford.edu/~junhee/JETTA/index.html Contacts: gro.srentrap@1oaixw

24 citations

Journal ArticleDOI
TL;DR: Polymorphonuclear neutrophils play an important role in mediating the innate immune response after severe traumatic injury; however, the cellular proteome response to traumatic condition is still largely unknown.
Abstract: PURPOSE Polymorphonuclear neutrophils (PMNs) play an important role in mediating the innate immune response after severe traumatic injury; however, the cellular proteome response to traumatic condition is still largely unknown.

17 citations


Cited by
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Journal ArticleDOI
TL;DR: A review of the basis, diagnosis, and current treatment of Sepsis in patients with this disorder is examined.
Abstract: Morbidity and mortality from sepsis remains unacceptably high. Large variability in clinical practice, plus the increasing awareness that certain processes of care associated with improved critical...

2,927 citations

Journal ArticleDOI
TL;DR: This study shows that, although acute inflammatory stresses from different etiologies result in highly similar genomic responses in humans, the responses in corresponding mouse models correlate poorly with the human conditions and also, one another.
Abstract: A cornerstone of modern biomedical research is the use of mouse models to explore basic pathophysiological mechanisms, evaluate new therapeutic approaches, and make go or no-go decisions to carry new drug candidates forward into clinical trials. Systematic studies evaluating how well murine models mimic human inflammatory diseases are nonexistent. Here, we show that, although acute inflammatory stresses from different etiologies result in highly similar genomic responses in humans, the responses in corresponding mouse models correlate poorly with the human conditions and also, one another. Among genes changed significantly in humans, the murine orthologs are close to random in matching their human counterparts (e.g., R2 between 0.0 and 0.1). In addition to improvements in the current animal model systems, our study supports higher priority for translational medical research to focus on the more complex human conditions rather than relying on mouse models to study human inflammatory diseases.

2,438 citations

Journal ArticleDOI
TL;DR: Biomarker-guided immunotherapy that is administered to patients at the proper immune phase of sepsis is potentially a major advance in the treatment of septicaemia and in the field of infectious disease.
Abstract: Sepsis - which is a severe life-threatening infection with organ dysfunction - initiates a complex interplay of host pro-inflammatory and anti-inflammatory processes. Sepsis can be considered a race to the death between the pathogens and the host immune system, and it is the proper balance between the often competing pro- and anti-inflammatory pathways that determines the fate of the individual. Although the field of sepsis research has witnessed the failure of many highly touted clinical trials, a better understanding of the pathophysiological basis of the disorder and the mechanisms responsible for the associated pro- and anti-inflammatory responses provides a novel approach for treating this highly lethal condition. Biomarker-guided immunotherapy that is administered to patients at the proper immune phase of sepsis is potentially a major advance in the treatment of sepsis and in the field of infectious disease.

1,719 citations

Journal ArticleDOI
Feng Yue1, Feng Yue2, Yong Cheng3, Alessandra Breschi, Jeff Vierstra4, Weisheng Wu5, Weisheng Wu1, Tyrone Ryba6, Tyrone Ryba7, Richard Sandstrom4, Zhihai Ma3, Carrie A. Davis8, Benjamin D. Pope6, Yin Shen2, Dmitri D. Pervouchine, Sarah Djebali, Robert E. Thurman4, Rajinder Kaul4, Eric Rynes4, Anthony Kirilusha9, Georgi K. Marinov9, Brian A. Williams9, Diane Trout9, Henry Amrhein9, Katherine I. Fisher-Aylor9, Igor Antoshechkin9, Gilberto DeSalvo9, Lei Hoon See8, Meagan Fastuca8, Jorg Drenkow8, Chris Zaleski8, Alexander Dobin8, Pablo Prieto, Julien Lagarde, Giovanni Bussotti, Andrea Tanzer10, Olgert Denas11, Kanwei Li11, M. A. Bender4, M. A. Bender12, Miaohua Zhang12, Rachel Byron12, Mark Groudine12, Mark Groudine4, David McCleary2, Long Pham2, Zhen Ye2, Samantha Kuan2, Lee Edsall2, Yi-Chieh Wu13, Matthew D. Rasmussen13, Mukul S. Bansal13, Manolis Kellis14, Manolis Kellis13, Cheryl A. Keller1, Christapher S. Morrissey1, Tejaswini Mishra1, Deepti Jain1, Nergiz Dogan1, Robert S. Harris1, Philip Cayting3, Trupti Kawli3, Alan P. Boyle3, Alan P. Boyle5, Ghia Euskirchen3, Anshul Kundaje3, Shin Lin3, Yiing Lin3, Camden Jansen15, Venkat S. Malladi3, Melissa S. Cline16, Drew T. Erickson3, Vanessa M. Kirkup16, Katrina Learned16, Cricket A. Sloan3, Kate R. Rosenbloom16, Beatriz Lacerda de Sousa17, Kathryn Beal, Miguel Pignatelli, Paul Flicek, Jin Lian18, Tamer Kahveci19, Dongwon Lee20, W. James Kent16, Miguel Santos17, Javier Herrero21, Cedric Notredame, Audra K. Johnson4, Shinny Vong4, Kristen Lee4, Daniel Bates4, Fidencio Neri4, Morgan Diegel4, Theresa K. Canfield4, Peter J. Sabo4, Matthew S. Wilken4, Thomas A. Reh4, Erika Giste4, Anthony Shafer4, Tanya Kutyavin4, Eric Haugen4, Douglas Dunn4, Alex Reynolds4, Shane Neph4, Richard Humbert4, R. Scott Hansen4, Marella F. T. R. de Bruijn22, Licia Selleri23, Alexander Y. Rudensky24, Steven Z. Josefowicz24, Robert M. Samstein24, Evan E. Eichler4, Stuart H. Orkin25, Dana N. Levasseur26, Thalia Papayannopoulou4, Kai Hsin Chang4, Arthur I. Skoultchi27, Srikanta Gosh27, Christine M. Disteche4, Piper M. Treuting4, Yanli Wang1, Mitchell J. Weiss, Gerd A. Blobel28, Xiaoyi Cao2, Sheng Zhong2, Ting Wang29, Peter J. Good30, Rebecca F. Lowdon30, Rebecca F. Lowdon29, Leslie B. Adams31, Leslie B. Adams30, Xiao Qiao Zhou30, Michael J. Pazin30, Elise A. Feingold30, Barbara J. Wold9, James Taylor11, Ali Mortazavi15, Sherman M. Weissman18, John A. Stamatoyannopoulos4, Michael Snyder3, Roderic Guigó, Thomas R. Gingeras8, David M. Gilbert6, Ross C. Hardison1, Michael A. Beer20, Bing Ren2 
20 Nov 2014-Nature
TL;DR: The mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types as mentioned in this paper.
Abstract: The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases

1,335 citations

Journal ArticleDOI
TL;DR: It is hypothesised that immunoadjuvant therapy represents the next major advance in sepsis, and explains why many previous sepsi trials which were directed at blocking inflammatory mediators or pathogen recognition signalling pathways failed.
Abstract: Summary Failures of highly touted trials have caused experts to call for re-evaluation of the current approach toward sepsis. New research has revealed key pathogenic mechanisms; autopsy results have shown that most patients admitted to intensive care units for treatment of sepsis had unresolved septic foci at post mortem, suggesting that patients were unable to eradicate invading pathogens and were more susceptible to nosocomial organisms, or both. These results suggest that therapies that improve host immunity might increase survival. Additional work showed that cytokine production by splenocytes taken post mortem from patients who died of sepsis is profoundly suppressed, possibly because of so-called T-cell exhaustion—a newly recognised immunosuppressive mechanism that occurs with chronic antigenic stimulation. Results from two clinical trials of biomarker-guided therapeutic drugs that boosted immunity showed promising findings in sepsis. Collectively, these studies emphasise the degree of immunosuppression that occurs in sepsis, and explain why many previous sepsis trials which were directed at blocking inflammatory mediators or pathogen recognition signalling pathways failed. Finally, highly encouraging results from use of the new immunomodulatory molecules interleukin 7 and anti-programmed cell death 1 in infectious disease point the way for possible use in sepsis. We hypothesise that immunoadjuvant therapy represents the next major advance in sepsis.

1,109 citations