Sette Lab

Sette Lab

"New infectious agents originate all the time dating back to the plague in the siege of Athens in the 7th century to the endemic flu in 1918 that killed 20 million people. For medical science, it’s a perennial race between new infectious diseases coming up and society reacting to them, understanding them and ultimately defeating them." — Alessandro Sette, Dr. Biol.Sci. // Center Head, Division Head, and Professor
Center for Infectious Disease

Overview

Dr. Alessandro Sette has devoted more than 30 years of study towards understanding the immune response, measuring immune activity, and developing disease intervention strategies against cancer, autoimmunity, allergy, and infectious diseases. The laboratory is defining in chemical terms the specific structures (epitopes) that the immune system recognizes, and uses this knowledge to measure and understand immune responses.

The Sette lab’s approach uses epitopes as specific probes to define the immune signatures associated with productive/protective immunity versus deficient immunity/immunopathology. This research will improve understanding of how the body successfully battles infection, and conversely, how pathogens escape the immune system, causing the individual to succumb to disease. Because of the laboratory’s success in its study of immune response, Sette and his team believe their research will lead to development of new therapeutic and prophylactic approaches to fighting infectious diseases. In this area, Sette’s disease focus has shifted over the years from HIV, HBV and HCV to emerging diseases and diseases of potential biodefense concern to, most recently, diseases and pathogens relevant to worldwide global health, including dengue viruses, malaria, tuberculosis, and trypanosome infections.

Furthermore, Dr. Sette’s team has adapted the methods and techniques developed in the context of infectious disease to understand the T cell response to common allergens. These efforts have resulted in the discovery of previously unknown human T cell epitopes that may be key in the initiation of allergic responses, and to the development of biochemical and bioinformatic tools that have been used to map the human T cell response to a large panel of common allergens.

Finally, Dr. Sette has overseen the design and curation efforts of the national Immune Epitope Database (IEDB), a freely available, widely used bioinformatics resource, since its inception in the early 2000s. The IEDB catalogs all epitopes for humans, non-human primates, rodents, and other vertebrates, from allergens, infectious diseases, autoantigens and transplants, and includes epitope prediction tools to accelerate immunology research around the world.

From The Lab

Jun 21, 2017 // Nature

Parkinson's is partly an autoimmune disease, study finds

Apr 14, 2017

LJI research lab wins Best Academic Research Team Award

Jun 16, 2016

La Jolla Institute receives research grant from The Michael J. Fox Foundation

Apr 8, 2016

Mapping T cells

Dec 17, 2015

La Jolla Institute for Allergy and Immunology team receives $18 million consortium grant

Sette Lab

Publications

Gut

T cell neoepitope discovery in colorectal cancer by high throughput profiling of somantic mutations in expressed genes

2016-12
Mennonna D, Maccalli C, Romano MC, Garavaglia C, Capocefalo F, Bordoni R, Severgnini M, De Bellis G, Sidney J, Sette A,…
J Allergy Clin Immunol

Reply

2016-10
Westernberg L, Schulten V, Sette A, Peters B
EBioMedicine

Protective role of cross-reactive CD8 T cells against dengue virus infection

2016-10
Elong Ngono A, Chen HW, Tang WW, Joo Y, King K, Weiskopf D, Sidney J, Sette A, Shresta S
Am J Pathol

HIV interferes with mycobacterium tuberculosis antigen presentation in human dendritic cells

2016-10
J Exp Med

Preventing tumor escape by targeting a post-proteasomal trimming independent epitope

2016-10
Textor A, Schimidt K, Kloetzel PM, Wei_brich B, Perez C, Charo J, Anders K, Sidney J, Sette A, Schumacher TN, Keller C,…
J Immunol

Response to comment on "A cytokine-independent approach to identify antigen-specific human germinal center T follicular helper cells and rare antigen-specific CD4+ T cells in blood

2016-10
Dan JM, Havenar-Daughton C, Silvestri G, Sette A, Crotty S
J Infect Dis

HLA-DRB1 alleles are associated with different magnitudes of engue virus-specific CD4+ T-cell responses

2016-10
Weiskopf D, Angelo MA, Grifoni A, O'Rourke PH, Sidney J, Paul S, De Silva AD, Phillips E, Mallal S, Premawansa S,…
Clin Exp Allergy

Immunoproteomic analysis of house dust mite antigens reveals distinct classes of dominant T cell antigens according to function and serological reactivity

2016-09
JCI Insight

Adjuvanted multi-epitope vaccines protect HLA-A*11:01 transgenic mice against toxoplasma gondii

2016-09
El Bissati K, Chentoufi AA, Krishack PA, Zhou Y, Woods S, Dubey JP, Vang J, Lykins J, Broderick KE, Mui E, Suzuki Y, Sa…
Clin Exp Allergy

Sequence conservation predicts T cell reactivity against ragweed allergens

2016-09
Pham J, Oseroff C, Hinz D, Sidney J, Paul S, Greenbaum J, Vita R, Philips E, Mallal S, Peters B, Sette A
J Allergy Clin Immunol

T-cell epitope conservation across allergen species is a major determinant of immunogenicity

2016-08
Westernberg L, Schulten V, Greenbaum JA, Natali S, Tripple V, McKinney DM, Frazier A, Hofer H, Wallner M, Sallusto F,…
J Immunol

A cytokine-independent approach to identify antigen-specific human germinal center T follicular helper cells and rare antigen-specific CD4+ T cells in blood

2016-08
Dan JM, Lindestam Arlehamn CS, Weiskopf D, de Silva Antunes R, Havenar-Daughton C, Reiss SM, Brigger M, Bothwell M,…
Curr Protoc Immunol

TepiTool: a pipeline for computational prediction T cell epitope candidates

2016-08
Paul S, Sidney J, Sette A, Peters B
J Immunol

Transcriptional profiling of Th2 cells identifies pathogenic features associated with asthma

2016-07
Seumois G, Zapardiel-Gonzalo J, White B, Singh D, Shulten V, Dillon M, Hinz D, Broide DH, Sette A, Peters B, Vijayanand…
PLoS Pathog

A quantitative analysis of complexity of human pathogen-specific CD4 T cell responses in healthy M. tuberculosis infected south africans

2016-07
Lindestam Arlehamn CS, McKinney DM, Carpenter C, Paul S, Rozot V, Makgotlho E, Gregg Y, van Rooyen M, ernst JD,…
Cell Immunol

Th1 versus Th2 T cell polarization by whole-cell and acellular childhood pertussis vaccines persists upon re-immunication in adolescence and adulthood

2016-06
Bancroft T, Dillon MB, de Silva Antunes R, Paul S, Peters B, Crotty S, Lindestam Arlehamn CS, Sette A
Immunology

T-cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome

2016-05
Bresciani A, Paul S, Schommer N, Dillon MB, Bancroft T, Greenbaum J, Sette A, Nielsen M, Peters B
Clin Exp Allergy

Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with allergen-specific modulation of immune reactivity

2016-05
Hinz D, Seumois G, Gholami AM, Greenbaum JA, Lane J, White B, Broide DH, Schulten V, Sidney J, Bakhru P, Oseroff C,…
J Virol

Immunodominant dengue virus specific CD8+ T cells responses are associated with a memory PD-1+ phenotype

2016-04
de Alwis R, Bangs DJ, Angelo MA, Cerpas C, Fernando A, Sidney J, Peters B, Gresh L, Balmaseda A, de Silva AD, Harris E,…
Clin Exp Allergy

Distinct modulation of allergic T cell responses by subcutaneous vs. sublingual allergen-specific immunotherapy

2016-03
Immunogenetics

Characterization of the peptide binding specificity of the HLA class I alleles B*38:01 and B*39:06

2016-03
Sidney J, Schloss J, Moore C, Lindvall M, Wriston A, Hunt DF, Shabanowitz TP, Sette A
Immunology

Reproducibility and conflicts in immune epitope data

2016-03
Vita R, Vasilevsky N, Bandrowski A, Haendel M, Sette A, Peters B
Immunology

Reproducibility and conflicts in immune epitope data

2016-03
Vita R, Vasilevsky N, Bandrowski A, Haendel M, Sette A, Peters B
Clin Exp Allergy

Distinct modulation of allergic T cell responses by subcutaneous vs. sublingual allergen-specific immunotherapy

2016-03
Immunogenetics

Characterization of the peptide binding specificity of the HLA class I alleles B*38:01 and B*39:06

2016-03
Sidney J, Schloss J, Moore C, Lindvall M, Wriston A, Hunt DF, Shabanowitz TP, Sette A
J Virol

Immunodominant dengue virus specific CD8+ T cells responses are associated with a memory PD-1+ phenotype

2016-02
de Alwis R, Bangs DJ, Angelo MA, Cerpas C, Fernando A, Sidney J, Peters B, Gresh L, Balmaseda A, De Silva AD, Harris E,…
Expert Rev Vaccines

Deciphering the human antigenome

2016-02
Sette A, Schenkelberg TR, Koff WC
J Infect Dis

Apoptotic epitope-specific CD8+ T cells and interferon signaling intersect in chronic hepatitis C virus infection

2016-02
Martini H, Citro A, Martire C, D'Ettorre G, Labbadia G, Accapezzato D, Piconese S, De Marzio P, Cavallari EN, Calvo L,…
Expert Rev Vaccines

Deciphering the human antigenome

2016-02
Sette A, Schenkelberg TR, Koff WC
J Immunol

The length distribution of class I-restricted T cell epitopes is determined by both peptide supply and MHC allele-specific binding preference

2016-02
Trolle T, McMurtrey CP, Sidney J, Bardet W, Osborn SC, Kaever T, Sette A, Hildebrand WH, Nielsen M, Peters B
J Infect Dis

Apoptotic epitope-specific CD8+ T cells and interferon signaling intersect in chronic hepatitis C virus infection

2016-02
Martini H, Citro A, Martire C, D'Ettorre G, Labbadia G, Accapezzato D, Piconese S, De Marzio P, Cavallari EN, Calvo L,…
J Immunol

The length distribution of class I-restricted T cell epitopes is determined by both peptide supply and MHC allele-specific binding preference

2016-02
Trolle T, McMurtrey CP, Sidney J, Bardet W, Osborn SC, Kaever T, Sette A, Hildebrand WH, Nielsen M, Peters B
J Allergy Clin Immunol

T-cell epitope conservation across allergen species is a major determinant of immunogenicity

2016-02
Westernberg L, Schulten V, Greenbaum JA, Natali S, Tripple V, McKinney DM, Frazier A, Hofer H, Wallner M, Sallusto F,…
eLIFE

Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove

2016-01
McMurtrey C, Trolle T, Sansom T, Remesh SG, Kaever T, Bardet W, Jackson K, McLeod R, Sette A, Nielsen M, Zajonc DM,…
eLIFE

Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove

2016-01
McMurtrey C, Trolle T, Sansom T, Remesh SG, Kaever T, Bardet W, Jackson K, McLeod R, Sette A, Nielsen M, Zajonc DM,…
Immunology

T cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome

2016-01
Bresciani A, Paul S, Schommer N, Dillon MB, Bancroft T, Greenbaum J, Sette A, Nielsen M, Peters B
J Biomed Semantics

An ontology for major histocompatibility restriction

2016-01
Vita R, Overton JA, Seymour E, Sidney J, Kaufman J, Tallmadge RL, Ellis S, Hammond J, Butcher GW, Sette A, Peters B
J Biomed Semantics

An ontology for major histocompatibility restriction

2016-01
Vita R, Overton JA, Seymour E, Sidney J, Kaufman J, Tallmadge RL, Ellis S, Hammond J, Butcher GW, Sette A, Peters B
OncoImmunology

Cripto-1 vaccination elicits protective immunity against metastatic melanoma

2016-01
Ligtenberg MA, Witt K, Galvez-Cancino F, Sette A, Liadser A, Klessling R
OncoImmunology

Cripto-1 vaccination elicits protective immunity against metastatic melanoma

2016-01
Ligtenberg MA, Witt K, Galvez-Cancino F, Sette A, Lundqvist A, Lladser A, Kiessling R
Gut

T cell neoepitope discovery in colorectal cancer by high throughput profiling of somantic mutations in expressed genes

2015-12
Mennonna D, Maccalli C, Romano MC, Garavaglia C, Capocefalo F, Bordoni R, Severgnini M, De Bellis G, Sidney J, Sette A,…
Clin Exp Allergy

Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with allergen-specific modulation of immune reactivity

2015-12
Hinz D, Seumois G, Gholami AM, Greenbaum JA, Lane J, White B, Broide DH, Schulten V, Sidney J, Bakhru P, Oseroff C,…
Tuberculosis

A side-by-side comparison of T cell reactivity to fifty-nine mycobacterium tuberculosis antigens in diverse populations from five continents

2015-12
Carpenter C, Sidney J, Kolla R, Nayak K, Tomiyama H, Tomiyaya C, Padilla OA, Rozot V, Ahamed SF, Ponte C, Rolla V,…
Clinical and Experimental Allergy

Different Bla-g T cell antigens dominate responses in asthma versus rhinitis subjects

2015-12
Dillon MB, Schulten V, Oseroff C, Paul S, Dullanty LM, Frazier A, Belles X, Piulachs MD, Visness C, Bacharier L,…
Nature Communications

RSV-specific airway resident memory CD8+ T cells and differential disease severity after experimental human infection

2015-12
Jozwik A, Habibi MS, Paras A, Zhu J, Guvenel A, Dhariwal J, Almond M, Wong EH, Sykes A, Maybeno M, Del Rosario J,…
Human Immunology

Development and validation of a sample sparing strategy for HLA typing utilizing next generation sequencing

2015-12
McKinney DM, Fu Z, Le L, Greenbaum JA, Peters B, Sette A
Tuberculosis

The TB-specific CD4(+) T cell immune repertoire in both cynomolgus and rhesus macaques largely overlap with humans

2015-12
Mothé BR, Lindestam Arlehamn CS, Dow C, Dillon MB, Wiseman RQ, Bohn P, Karl J, Golden NA, Gilpil T, Foreman TW,…
Journal of Biological Chemistry

The T210M substitution in the HLA-a*02:01 gp100 epitope strongly affects overall proteasomal cleavage site usage and antigen processing

2015-12
Textoris-Taube K, Keller C, Liepe J, Henklein P, Sidney J, Sette A, Kloetzel PM, Mishto M
Journal of Infectious Disease

Human CD8+ T-cell responses against the 4 dengue virus serotypes are associated with distinct patterns of protein targets

2015-12
Weiskopf D, Cerpas C, Angelo MA, Bangs DJ, Sidney J, Paul S, Peters B, Sanches FP, Silvera CG, Costa PR, Kallas EG,…
Journal of Investigative Dertamology Symposium Proceedings

The use of the immune epitope database to study autoimmune epitope data related to alopecia areata

2015-11
Sette A, Paul S, Vaughan K, Peters B
Clinical and Experimental Allergy

Definition of a pool of epitopes that recapitulates the T cell reactivity against major house dust mite allergens

2015-10
Hinz D, Oseroff C, Pham J, Sidney J, Peters B, Sette A
Journal of Virology

Cytomeglaovirus-specific CD4 T cells are cytolytic and mediate vaccine protection

2015-10
Verma S, Weiskopf D, Gupta A, McDonald B, Peters B, Sette A, Benedict CA
Immunogenetics

The common equine class I molecule Eqca-1*00101 (ELA-A3.1) is characterized by narrow peptide binding and T cell epitope repertoires

2015-09
Bergmann T, Moore C, Sidney J, Miller D, Tallmadge R, Harman RM, Oseroff C, Wriston A, Shabanowitz J, Hunt DF,…
Clinical and Experimental Allergy

HLA-DQ allele-restricted activation of nitroso sulfamethoxazole-specific CD4-positive T lymphocytes from patients with cystic fibrosis

2015-08
Ogese MO, Saide K, Faulkner L, Whitaker P, Peckham D, Alfirevic A, Baker DM, Sette A, Pirmohamed M, Park BK, Naisbitt DJ
Science

IMMUNODEFICIENCIES. Impairment of immunity to candida and mycobacterium in humans with bi-allelic RORC mutations

2015-08
Okada S, Markle JG, Deenick EK, Mele F, Averbuch D, Lagos M, Alzahrani M, Al-Muhsen S, Halwani R, Ma CS, Wong N,…
Proceedings of the National Academy of Sciences of the United States of America

Dengue virus infection elicits highly polarized CX3CR1+ cytotoxic CD4+ T cells associated with portective immunity

2015-08
Weiskopf D, Bangs DJ, Sidney J, Kolla RV, De Silva AD, de Silva AM, Crotty S, Peters B, Sette A
eLife

An open-source computational and data resource to analyze digital maps of immunopeptidomes

2015-07
Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpízar A, Schittenhelm RB, Ramarthinam SH, Lindestam…
Journal of Immunological Methods

Development and validation of a broad scheme for predition of HLA class II restricted T cell epitopes

2015-07
Paul S, Lindestam Arlenhamn CS, Scriba TJ, Dillon MB, Oseroff C, Hinz D, McKinney DM, Pro SC, Sidney J, Peters B, Sette…
Bioinformatics

Automated benchmarking of peptide-MHC class I binding predictions

2015-07
Trolle T, Metushi IG, Greenbaum JA, Kim Y, Sidney J, Lund O, Sette A, Peters B, Nielsen M
PLoS One

CD8+ T cells specific to apoptosis-associated antigens predict the response to tumor necrosis factor inhibitor therapy in rhermatoid arthritis

2015-06
Citro A, Scrivo R, Martini H, Martire C, DeMarzio P, Vestri AR, Sideny J, Sette A, Barnaba V, Valesini G
Journal of Immunology

A population response analysis approach to assign class II HLA-epitope restrictions

2015-06
Paul S, Dillon MB, Lindestam Arlehamn CS, Huang H, Davis MM, McKinney DM, Scriba TJ, Sidney J, Peters B, Sette A
Autoimmunity

Fine specificities of natural regulatory T cells after IVIG therapy in patients with Kawasaki disease

2015-05
Burns JC, Touma R, Song Y, Padilla RL, Tremoulet AH, Sidney J, Sette A, Franco A
Autoimmunity

Vaccination to modulate atherosclerosis

2015-05
Kimura T, Tse K, Sette A, Ley K
PLoS One

Analysis of human RSV immunity at the molecular level: learning from the past and present

2015-05
Vaughan K, Ponomarenko J, Peters B, Sette A
Proceedings of the National Academy of Sciences of the United States of America

Human ebola virus infection results in substantial immune activation

2015-04
McElroy AK, Akondy RS, Davis CW, Ellebedy AH, Mehta AK, Kraft CS, Lyon GM, Ribner BS, Varkey J, Sidney J, Sette A,…
ACS Chemical Biology

Consequences of periodic α-to-β(3) residue replacement for immunological recognition of peptide epitopes

2015-03
Cheloha RW, Sullivan JA, Wang T, Sand JM, Sidney J, Sette A, Cook ME, Suresh M, Gellman SH
Journal of Allergy and Clinical Immunology

Immunoproteomic analysis of German cockroach (Blattella germanica) reveals antigens differentially recognized as a function of disease severity

2015-02
Dillon MB, Schulten VM, Hinz D, Oseroff C, Dullanty L, Tripple V, Pham J, Paul S, Frazier A, Sidney J, Peters B, Sette A
PLoS One

Identification of immunodominany CD4-restricted epitopes co-located with antibody binding sites in individuals vaccinated with ALVAC-HIV and AIDSVAX B/E

2015-02
Ratto-Kim S, deSouza MS, Currier JR, Krasavvas N, Sidney J, Rolland M, Valencia-Micolta A, Madnote S, Sette A,…
Journal of Allergy and Clinical Immunology

Characterization of the T cell response targeting Timothy grass antigens in allergic, healthy and specific immunotherapy-treated patients

2015-02
Schulten VM, Tripple V, Frazier A, Alam R, Broide D, Sette A, Peters B
Journal of Allergy and Clinical Immunology

A systematic analysis of pollen transcriptomes from plant allergens reveals conserved targets of immune responses

2015-02
Sternberg L, Greenbaum J, Schulten VM, Tripple V, Baker D, Frazier A, Hofer H, Wallner M, Sette A, Peters B
Proceedings of the National Academy of Sciences of the United States of America

Immunological consequences of intragenus conservation of mycobacterium tuberculosis T-cell epitopes

2015-01
Lindestam Arlehamn CS, Paul S, Mele F, Huang C, Greenbaum JA, Vita R, Sidney J, Peters B, Sallusto F, Sette A
Nucleic Acids Research

The immune epitope database (IEDB) 3.0

2015-01
Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, Cantrell JR, Wheeler DK, Gabbard JL, Hix D, Sette A, Peters B
Journal of Virology

The human CD8+ T cell responses induced by a live attenuated tetravalent dengue vaccine are directed against highly conserved epitopes

2015-01
Weiskopf D, Angelo MA, Bangs DJ, Sidney J, Paul S, Peters B, de Silva AD, Lindow JC, Diehl SA, Whitehead S, Durbin A,…
Journal of Immunology

CD4 T cells specific for a latency-associated γ-herpesvirus epitope are polyfunctional and cytotoxic

2014-12
Freeman ML, Burkum CE, Cookenham T, Roberts AD, Lanzer KG, Huston GE, Jensen MK, Sidney J, Peters B, Kohlmeier JE,…
International Archives of Allergy and Immunology

New strategies for allergen T cell epitope identification: going beyond IgE

2014-11
Schulten V, Peters B, Sette A
Journal of Allergy and Clinical Immunology

Association between specific timothy grass antigens and changes in TH1- and TH2-cell responses following specific immunotherapy

2014-11
Schulten V, Tripple V, Sidney J, Greenbaum J, Frazier A, Alam R, Broide D, Peters B, Sette A
Journal of Experimental Medicine

Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity

2014-10
Duan F, Duitama J, Al Seesi S, Ayres CM, Corcelli SA, Pawashe AP, Blanchard T, McMahon D, Sidney J, Sette A, Baker BM,…
World Allergy Organization Journal

Allergy-associated T cell epitope repertoiries are surprisingly diverse and include non-IgE reactive antigens

2014-10
Frazier A, Schulten V, Hinz D, Oseroff C, Sidney J, Peters B, Sette A
Journal of Immunology

Bispecificity for myelin and neuronal self-antigens is a common feature of CD3 T cells in C57BL/6 mice

2014-10
Lucca LE, Desbois S, Ramadan A, Ben-Nun A, Eisenstein M, Carrié N, Guéry JC, Sette A, Nguyen P, Geiger TL, Mars LT,…
Journal of Virology

Immunodominance changes as a function of the infecting dengue virus serotype and primary versus secondard infection

2014-10
Weiskopf D, Angelo MA, Sidney J, Peters B, Shresta S, Sette A
Journal of Immunology

Transcriptional profile of tuberculosis antigen-specific T cells reveals novel multifunctional features

2014-09
Arlehamn CL, Seumois G, Gerasimova A, Huang C, Fu Z, Yue X, Sette A, Vijayanand P, Peters B
PLoS One

Sterile immunity to malaria after DNA prime/adenovirus boost immunization is associated with effector memory CD8+T cells targeting AMA1 class I epitopes

2014-09
Sedegah M, Hollingdale MR, Farooq F, Ganeshan H, Belmonte M, Kim Y, Peters B, Sette A, Huang J, McGrath S, Abot E,…
Journal of Virology

Impact of distinct poxvirus infections on the specificities and functionalities of CD4+ T cell responses

2014-09
Siciliano NA, Hersperger AR, Lacuanan AM, Xu RH, Sidney J, Sette A, Sigal LJ, Eisenlohr LC
Journal of Virology

Analysis of HLA A*02 association with vaccine efficacy in RV144 HIV-1 vaccine trial

2014-08
Gartland AJ, Li S, McNevin J, Tomaras GD, Gottardo R, Janes H, Fong Y, Morris D, Geraghty DE, Kijak GH, Edelfsen PT,…
BMC Bioinformatics

Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions

2014-07
Kim Y, Sidney J, Buus S, Sette A, Nielsen M, Peters B
Cold Spring Harbor Perspectives in Medicine

Antigens for CD4 and CD8 T cells in tuberculosis

2014-05
Lindestam Arlehamn CS, Lewinsohn D, Sette A, Lewinsohn D
Human Immunology

Substantial gaps in knowledge of bordetella pertussis antibody and T cell epitopes relevant for natural immunity and vaccine efficacy

2014-05
Vaughan K, Seymour E, Peters B, Sette A
PLoS Pathogens

Broadly reactive human CD8 T cells that recognize an epitope conserved between VZV, HSZ and EBV

2014-03
Chiu C, McCausland M, Sidney J, Duh FM, Rouphael N, Mehta A, Mulligan M, Carrington M, Wieland A, Sullivan NL, Weinburg…
Frontiers in Immunology

Definition of CD4 immunosignatures associated with MTB

2014-03
Lindestam Arlehamn CS, Sette A
Frontiers in Immunology

T-cell immunity to infection with dengue virus in humans

2014-03
Weiskopf D, Sette A
Journal of Neuroimmunology

A molecular view of multiple sclerosis and experimental autoimmune encephalitis: what can we learn from the epitope data?

2014-02
Vaughan K, Peters B, O'Connor KC, Martin R, Sette A
Infection and Immunity

Brucella melitensis T cell epitope recognition by humans recovered from brucellosis in Peru

2014-01
Cannella AP, Lindestam Arlehamn CS, Sidney J, Patra KP, Torres K, Tsolis RM, Liang L, Felgner PL, Saito M, Gotuzzo E,…
Journal of Hepatology

HLA-B*27 subtype specificity determines targeting and viral exolution of hepatitis C virus-specific CD8+ T-cell epitope

2014-01
Nitschke K, Barriga A, Schmidt J, Timm J, Viazov S, Kuntzen T, Kim AY, Lauer GM, Allen TM, Gaudleri S, Rauch A, Lange…
Journal of Immunology

HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity

2013-12
Paul S, Weiskopf D, Angelo MA, Sidney J, Peters B, Sette A
Virology

Characterizing monkeypox virus specific CD8+ T cell epitopes in rhesus macaques

2013-12
Song H, Sidney J, Wiserman RW, Josleyn N, Cohen M, Blaney JE, Jahrling PB, Sette A
Frontiers in Immunology

Atheroprotective vaccination with MHC-II restricted peptides from ApoB-100

2013-12
Tse K, Gonen A, Sidney J, Ouyang H, Witztum JL, Sette A, Tse H, Ley K
Journal of Immunology

Structure-based design of altered MHC class II-restricted peptide ligands with heterogeneous immunogenicity

2013-11
Chen S, Li Y, Depontieu FR, McMiller TL, English AM, Shabanowitz J, Kos F, Sidney J, Sette A, Rosenberg SA, Hunt DF,…
Journal of Immunology

Asymptomatic HLA-A*02:01-restricted epitopes from herpes simplex virus glycoprotein B preferentially recall polyfunctional CD8+ T cells from seropositive asymptomatic individuals and protect HLA transgenic mice against ocular herpes

2013-11
Dervillez X, Qureshi H, Chentoufi AA, Khan AA, Kritzer E, Yu DC, Diaz OR, Gottimukkala C, Kalantari M, Villacres MC,…
International Immunology

T cells in atherosclerosis

2013-11
Tse K, Tse H, Sidney J, Sette A, Ley K
PLoS Computational Biology

Properties of MHC class I presented peptides that enhance immunogenicity

2013-10
Calis JJ, Maybeno M, Greenbaum JA, Weiskopf D, De Silva AD, Sette A, Keşmir C, Peters B
Immunity

Human circulating PD-1+CXCR3-CXCR5+ memory Tfh cells are highly functional and correlate with broadly neutralizing HIN antibody responses

2013-10
Locci M, Havenar_Daughton C, Landais E, Wu J, Kroenke MA, Arlehamn, CL, Su LF, Cubas R, Davis MM, Sette A, Haddad EK,…
PLoS Neglected Tropical Diseases

Identification of conserved and HLA promiscuous DENV3 T-cell epitopes

2013-10
Nascimento EJ, Mailliard RB, Khan AM, Sidney J, Sette A, Guzman N, Paulaitis M, de Melo AB, Cordeiro MT, Gil LV,…
Autoimmunity Reviews

HLA shared epitope and ACPA: just a marker or an active player?

2013-10
Pratesi F, Petit Teixeira E, Sidney J, Michou L, Puxeddu I, Sette A, Cornelis F, Migliorini P
Infection and Immunity

Immunisation with apical membrane antigen 1 confers sterile infection-blocking immunity against plasmodium sporozoite challenge in a rodent model

2013-10
Schussek S, Trieu A, Apte SH, Sidney J, Sette A, Doolan DL
Immunology

CD4(+) T cell inhibitory ligands: a tool for characterizing dysfunctional CD4(+) T cells during chronic infection

2013-09
Dow C, Henderson R, Sette A, Mothé BR
PLoS One

Correction: unexpected diversity of cellular immune responses against Nef and Vif in HIV-1-infected patients who spontaneously control viral replication

2013-09
Tarosso LF, Sauer MM, Sanabanni S, Giret MT, Tomiyama HI, Sidney J, Piaskowski SM, Diaz RS, Sabino EC, Sette A,…
Journal of Virology

CE8+ T-cell epitope mapping for pneumonia viurs of mice in H-2b mice

2013-09
Walsh KB, Sidney J, Welch M, Fremgen DM, Sette A, Oldstone MB
PLoS Pathogens

Local CD4 and CD8 T-cell reactivity to HSV-1 antigens documents broad viral protein expression and immune competence in latently infected human trigeminal ganglia

2013-08
van Velzen M, Jing L, Osterhaus AD, Sette A, Koelle DM, Verjans GM
Genes and Immunity

Relation of HLA class I and II supertypes with spontaneous clearance of hepatitis C virus

2013-07
Kuniholm MH, Anastos K, Kovacs A, Gao X, Marti D, Sette A, Greenblatt RM, Peters M, Cohen MH, Minkoff H, Gange SJ, Thio…
Journal of Neuroinflammation

Increased CD8+ T cell responses to apoptotic T cell-associated antigens in multiple sclerosis

2013-07
Lolli F, Martini H, Citro A, Franceschini D, Portaccio E, Amato MP, Mechelli R, Annibali V, Sidney J, Sette A, Salvetti…
Nature Medicine

Association of HLA-DRB1-restricted CD4(+) T cell responses with HIV immune control

2013-07
Ranasinghe S, Cutler S, Davis I, Lu R, Soghoian DZ, Qi Y, Sidney J, Kranias G, Flanders MD, Lindqvist M, Kuhl B. Alter…
Malaria Journal

Identification of minimal human MHC-restricted CD8+ T-cell epitopes within the plasmodium falciparum circumsporozoite protein (CSP)

2013-06
Sedegah M, Kim Y, Ganeshan H, Huang J, Belmonte M, Abot E, Banania JG, Farooq F, McGrath S, Peters B, Sette A, Soisson…
Journal of Clinical Investigation

Discovering natrually processed antigenic determinants that confer protective T cell immunity

2013-05
Gilchuk P, Spencer CT, Conant SB, Hill T, Gray JJ, Niu X, Zheng M, Erickson JJ, Boyd KL, McAfee KJ, Oseroff C, Hadrup…
Immunogenetics

A strategy to determine HLA class II restriction broadly covering the DR, DP, and DQ allelic variants most commonly expressed in the general population

2013-05
McKinney DM, Southwood S, Hinz D, Oseroff C, Arlenhamn CS, Schulten V, Taplitz R, Broide D, Hanekom WA, Scriba TJ, Wood…
Immunogenetics

Peptide-binding motifs associated with MHC molecules common in Chinese rhesus macaques are analogous to those of human HLA supertypes and include HLA-B27-like alleles

2013-05
Mothé BR, Southwood S, Sidney J, English AM, Wriston A, Hoof I, Shabanowitz J, Hunt DF, Sette A
Proceedings of the National Academy of Sciences of the United States of America

Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells

2013-05
Weiskopf D, Angelo MA, de Azeredo EL, Sidney J, Greenbaum JA, Fernando AN, Broadwater A, Kolla RA, De Silva AD, de…
Cancer Cell

Relapse or eradication of cancer is predicted by peptide-major histocompatibility complex affinity

2013-04
Engels B, Engelhard VH, Sidney J, Sette A, Binder DC, Liu RB, Kranz DM, Meredith SC, Rowley DA, Schreiber H
European Journal of Immunology

Sculpting MHC class II-restricted self and non-self peptidome by the class I Ag-processing machinery and its impact of Th-cell responses

2013-04
Spencer CT, Dragovic SM, Conant SB, Gray JJ, Zheng M, Samir P, Niu X, Moutaftsi M, Van Kaer L, Sette A, Link AJ, Joyce S
Journal of Biomedical Semantics

Query enhancement through the practical application of ontology: the IEDB and OBI

2013-04
Vita R, Overton JA, Greenbaum JA, Sette A, OBI consortium, Peters B
Proceedings of the National Academy of Sciences of the United States of America

Previously undescribed grass pollen antigens are the major inducers of T helper 2 cytokine-producing T cells in allergic individuals

2013-02
Schulten V, Greenbaum JA, Hauser M, McKinney DM, Sidney J, Kolla R, Lindestam Arlehamn CS, Oseroff C, Alam R, Broide…
Current Protocols in Immunology

Measurement of MHC/peptide interactions by gel filtration or monoclonal antibody capture

2013-02
Sidney J, Southwood S, Moore C, Oseroff C, Pinilla C, Grey HM, Sette A
PLoS Neglected Tropical Diseases

T-cell memory responses elicited by yellow fever vaccine are targeted to overlapping epitopes containing multiple HLA-I and -II binding motifs

2013-01
de Melo AB, Nascimento EJ, Braga-Neto U, Dhalia R, Silva AM, Oelke M, Schneck JP, Sidney J, Sette A, Montenegro SM,…
PLoS Computational Biology

Positional bias of MHC class I restricted T-cell epitopes in viral antigens is likely due to a bias in conservation

2013-01
Kim Y, Yewdell JW, Sette A, Peters B
PLoS Pathogens

Memory T cells in latent Mycobacterium tuberculosis infection are directed against three antigenic islands and largely contained in a CXCR3+CCR6+ Th1 subset

2013-01
Lindestam Arlehamn CS, Gerasimova A, Mele F, Henderson R, Swann J, Greenbaum JA, Kim Y, Sidney J, James EA, Taplitz R,…
Journal of Agricultural and Food Chemistry

Immunogenic peptides can be detected in whole gluten by transamidating highly susceptible glutamine residues: implication in the search for gluten-free cereals

2013-01
Mamone G, Camarca A, Fierro O, Sidney J, Mazzarella G, Addeo F, Auricchio S, Troncone R, Sette A, Gianfranci C
Annals of Allergy Asthma & Immunology

The identification of potentially pathogenic and therapeutic epitopes from common human allergens

2013-01
Schulten V, Oseroff C. Alam R, Broide D, Vijayanand P, Peters B, Sette A
Immunology

The immune epitope database: a historical retrospective of the first decade

2012-10
Salimi N, Fleri W, Peters B, Sette A
Journal of Virology

Memory CD8+ T cells specific for a single immunodominant or subdominant determinant induced by peptide-dendritic cell immunization protect from an acute lethal viral disease

2012-09
Remakus S, Rubio D, Ma X, Sette A, Sigal LJ
Journal of Immunology

T cell responses to known allergen proteins are differently polarized and account for a variable fraction of total response to allergen extracts

2012-08
Oseroff C, Sidney J, Tripple V, McKinney DM, Southwood S, Brodie TM, Sallusto F, Grey H, Alam R, Broide D, Greenbaum…
Journal of Immunology

Analysis of T cell responses to the major allergens from german cockroack: epitope specificity and relationship to IgE production

2012-07
Oseroff C, Sidney J, Tripple V, Grey H, Wood R, Broide DH, Greenbaum J, Kolla R, Peters B, Pomés A, Sette A
Nucleic Acids Research

Immune epitope database analysis resource

2012-07
Kim Y, Ponomarenko J, Tamang D, Wang P, Greenbaum J, Lundegaard C, Sette A, Lund O, Bourne PE, Nielsen M, Peters B
Proceedings of the National Academy of Sciences of the United States of America

Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire

2012-06
Ostrov DA, Grant BJ, Pompeu YA, Sidney J, Harndahi M, Southwood S, Oseroff C, Lu S, Jakoncic J, de Oliveira CA, Yang L,…
Journal of Immunology

Beyond HLA-A*0201: new HLA-transgenic nonobese diabetic mouse models of type 1 diabetes identify the insulin C-peptide as a rich source of CD8+ T cell epitopes

2012-06
Antal Z, Baker, JC, Smith C, Jarchum I, Babad J, Mukherjee G, Yang Y, Sidney J, Sette A, Santamaria P, Dilorenzo TP
PLoS Pathogens

Polyfunctional type-1, -2, and -17 DC8(+) T cell responses to apopototic self-antigens correlate with the chronic evolution of hepatitis C virus infection

2012-06
Franceschini D, Del porto P, Piconese S, Trella E, Accapezzato D, Paroli M, Morrone S, Piccolella E, Spada E, Mele A,…
Immunogenetics

Identification of the peptide-binding motif recognized by the pigtail macaque class I MHC molecule Mane-A1*082:01 (Mane A*0301)

2012-06
Moore C, Sidney J, English AM, Wriston A, Hunt DF, Shabanowitz J, Southwood S, Bradley K, Lafont BA, Mothe BR, Sette A
Journal of Rheumatology

Effect of rheumatoid arthritis (RA) susceptibility genes on the immune response to viral citrullinated peptides in RA

2012-06
Pratesi F, Petit-Teixeira E, Sidney J, Teixeira VH, Puzeddu I, Sette A, Cornelis F, Migliorini P
Immunogenetics

A shared MHC supertype motif emerges by convergent evolution in macaques and mice, but is totally absent in human MHC molecules

2012-06
Sette A, Sidney J, Southwood S, Moore C, Berry J, Dow C, Bradley K, Hoof I, Lewis MG, Hildebrand WH, McMurtey CP,…
Journal of Immunology

Dissecting mechanisms of immunodominance to the common tuberculosis antigens ESAT-6, CFP1-, Rv2031c (hspX), Rv2654c (TB7.7), and Rv1038c (EsxJ)

2012-05
Arkegan CS, Sidney J, Henderson R, Greenbaum JA, James EA, Moutaftsi M, Coler R, McKinney DM, Park D, Taplitz R, Kwok…
Journal of Immunology

Immunogenicity and cross-reactivity of a representative ancestral sequence in hepatitis C virus infection

2012-05
Burke KP, Munshaw S, Osburn WO, Levine J, Liu L, Sidney J, Sette A, Ray SC, Cox A
Clinical Cancer Research

Spleen cells from young but not old immunized mice eradicate large established cancers

2012-05
Schreibe, K, Arin, A, Engels B, Spiotto MT, Sidney J, Sette A, Karrison TG, Weichselbaum RR, Rowley DA, Schreiber H
Proceedings of the National Academy of Sciences of the United States of America

Detection of an autoreactive T-cell population within the polyclonal repertoire that undergoes distinct autoimmune regulator (Aire)-mediated selection

2012-05
Taniguchi RT, Devoss JJ, Moon JJ, Sidney J, Sette A, Jenkins MK, Anderson MS
Human Immunology

Toxoplasma gondii HLA-B*0702-restricted GRA7 (20-28) peptide with adjuvants and a universal helper T cell epitope elicits CD8(+) T cells prodicing interferon-γ and resuces parasite burden in HLA-B*0702 mice

2012-01
Cong H, Mui EJ, Witola WH, Sidney J, Alexander J, Sette A, Maewal A, El Bissati K, Zhou Y Suzuki Y, Lee D, Woods S,…
Clinical and Experimental Immunology

Immunology in the clinic review series; focus on host responses: T cell responses to herpes simplex viruses

2012-01
Laing KJ, Dong L, Sidney J, Sette A, Koelle DM
BMC Bioinformatics

Cost sensitive hierarchial document classification to triage Pubmed abstracts for manual curation

2011-12
Seymour E, Damale R, Sette A, Peters B
Immunogenetics

The role of MHC class I allele manu-A*07 during SIV(mac)239 infection

2011-12
Reed JS, Sindet J, Piaskowski SM, Gidden CE, Leon EJ, Burwitz BJ, Kolar HL, Eemissee CM, Furlott JR, Maness NJ, Walsh…
Journal of Immunological Methods

Applications for T-cell epitope queries and tools in the Immune Epitope Database and Anaylsis Resource

2011-11
Kim Y, Sette A, Peters B
Journal of Virology

Human CD8+ and CD4+ T cell memort to LCMV infection

2011-11
Kotturi M, Swann JA, Peters B, Arlehamn CL, Sidney J, Kolla RV, James EA, Akondy RS, Ahmen R, Kwok WW, Buchmeier MJ,…
Immunome Research

A computational pipeline to generate MHC binding motifs

2011-11
Wang P, Sidney J, Sette A, Peters B
Journal of Immunology

Insights into HLA-restricted T cell responses in a novel mouse model of dengue virus infection point toward new implications for vaccine design

2011-10
Weiskopf D, Yauch LE, Angelo MA, John DV, Greenbaum JA, Sidney J, Kolla RV, De Silva AD, de Silva AM, Grey H, Peters B,…
Hepatology

Human leukocyte antigen B27 selects for rare escape mutations that significantly impair hepatitis C virus replication and require compensatory mutations

2011-10
Neumann-Haefelin C, Oniangue-Ndza C, Kuntzen T, Schmidt J, Nitschke K, Sidney J, Caillet-Saaguy C, Binder M, Kersting…
Journal of Virology

Targeting OX40 promotes lung resident memory CD8 T cell populations that protect against respiratory poxvirus infection

2011-09
Salek-Ardakani S, Moutaftsi M, Sette A, Croft M
Journal of Virology

High-functional-avidity cytotoxic T lymphocyte responses to HLA-B-restricted gad-derived epitopes associated with relative HIV control

2011-09
Berger CT, Frahm N, Price DA, Mothe B, Ghebremichael M, Hartman KL, Kenry LM, Brenchley JM, Ruff LE, Venturi V, Pereyra…
Journal of Medical Primatology

SIV-infected Chinese-origin rhesus macaques express specific MHC class I alleles in either elite controllers or normal progressors

2011-08
Wambua D, Henderson R, Solomon C, Hunter M, Marx P, Sette A, Mothe BR
Immunogenetics

Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes

2011-06
Greenbaum J, Sidney J, Chung J, Brander C, Peters B, Sette A
Immunogenetics

Functional analysis of frequently expressed Chinese rhesus macaque MHC class I molecules Mamu-A1*02601 and Mamu-B*08301 reveals HLA-A2 and HLA-A3 supertypic specificities

2011-05
Southwood S, Solomon C, Hoof I, Rudersdorf R, Sidney J, Peters B, Wahl A, Hawkins O, Hildebrand W, Mothé BR, Sette A
Journal of Immunology

Defining the herpes simplex virus-specific CD8+ T cell repertoire in C57BL/6 mice

2011-04
St Leger AJ, Peters B, Sidney J, Sette A, Hendricks RL
Immunome Research

A model for collaborative curation, the IEDB and CHEBI curation of non-peptidic epitopes

2011-04
Vita R, Peters B, Josephs Z, de Matos P, Ennis M, Turner S, Steinbeck C, Seymour E, Zarbski L, Sette A
Clinical and Experimental Immunology

CD4+ T cells from HIV-1-infected patients recognize wild-type and mutant human immunodeficiency virus-1 protease epitopes

2011-04
Muller NG, Alencar R, Jamal L, Hammer J, Sidney J, Sette A, Brindeiro RM, Kalil J, Cunha-Neto E, Moraes SL
Journal of Allergy

Towards defining molecular determinants recognized by adaptive immunity in allergic disease: an inventory of the available data

2011-02
Vaughan K, Greenbaum J, Kim Y, Vita R, Chung J, Peters B, Broide D, Goodman R, Grey H, Sette A
Nucleic Acids Research

IEDB-3D: structural data within the immune epitope database

2011-01
Ponomarenko J, Papangelopoulos N, Zajonc DM, Peters B, Sette A, Bourne PE
Vaccine

Towards an immunosense vaccine to prevent toxoplasmosis: protective Toxoplasma gondii epitopes restricted by HLA-A*0201

2011-01
Cong H, Mui EJ, Witola WH, Sidney J, Alexander J, Sette A, Maewal A, McLeod R
Cell Immunol

Th1 versus Th2 T cell polarization by whole-cell and acellular childhood pertussis vaccines persists upon re-immunication in adolescence and adulthood

2016-06
Bancroft T, Dillon MB, de Silva Antunes R, Paul S, Peters B, Crotty S, Lindestam Arlehamn CS, Sette A
Immunology

T cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome

2016-05
Bresciani A, Paul S, Schommer N, Dillon MB, Bancroft T, Greenbaum J, Sette A, Nielsen M, Peters B
Clin Exp Allergy

Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with allergen-specific modulation of immune reactivity

2016-05
Hinz D, Seumois G, Gholami AM, Greenbaum JA, Lane J, White B, Broide DH, Schulten V, Sidney J, Bakhru P, Oseroff C,…
Clinical & Developmental Immunology

Evaluating the immunogenicity of protein drugs by applyinng in vitro MHC binding data and the immune epitope database and analysis resource

2017-06
Paul S, Kolla RV, Sidney J, Weiskopf D, Fleri W, Kim Y, Peters B, Sette A
International Archives of Allergy and Immunology

Strategies to query and display allergy-derived epitope data from the immune epitope database

2017-06
Vaughan K, Peters B, Larche M, Pomes A, Broide D, Sette A
PLoS One

The nucleocapsid protein of rift valley fever virus is a ptent human CD8(+) T cell antigen and elicits memory responses

2017-06
Xu W, Watts DM, Costanzo MC, Tang X, Venegas LA, Jiao F, Sette A, Sidney J, Sewell AK, Wooldridge L, Makino S, Morrill…
Journal of Immunology

Cutting edge: prolonged exposure to HIV reinforces a poised epigenetic program for PD-1 expression in virus-specific CD8 T cells

1969-12
Youngblood B, Noto A, Porichis F, Akondy RS, Ndhlovu ZM, Austin JW, Bordi R, Porcopio FA, Miura T, Allen TM, Sidney J,…
PLoS One

Polyfunctional CD4(+) T cell responses to immunodominant epitopes correlate with disease activity of virulent salmonella

2017-06
Maybeno M, Redeker A, Welten SP, Peters B, Loughhead SM, Schoenberger SP, Sette A, Arens R
PLoS One

A meta-analysis of the existing knowledge of immunoreactivity against hepatitis C virus (HCV)

2017-06
Kim Y, Vaughan K, Greenbaum J, Peters B, Law M, Sette A
PLoS One

Broad and cross-clade CD4(+) T-cell responses elicited by a DNA vaccine encoding highly conserved and promiscuous HIV-1 M-group consensus peptides

2017-06
Almeida RR, Rosa DS, Ribeiro SP, Santana VC, Kallas EG, Sidney J, Sette A, Kalil J, Cunha-Neto E
Frontiers in Cellular and Infection Microbiology

Antigen-specific acquired immunity in human brucellosis: implications for diagnosis, prognosis, and vaccine development

2017-06
Cannella AP, Tsolis RM, Liang L, Felgner PL, Saito M, Sette A, Gotuzzo E, Vinetz JM
Autoimmune Diseases

A comparison of epitope repertoires associated with myasthenia gravis in humans and nonhuman hosts

2017-06
Vaughan K, Kim Y, Sette A
J Immunol

A cytokine-independent approach to identify antigen-specific human germinal center T follicular helper cells and rare antigen-specific CD4+ T cells in blood

2016-06
Dan JM, Lindestam Arlehamn CS, Weiskopf D, da Silva Antunes R, Havenar-Daughton C, Reiss SM, Brigger M, Bothwell M,…
J Virol

Immunodominant dengue virus specific CD8+ T cells responses are associated with a memory PD-1+ phenotype

2016-04
de Alwis R, Bangs DJ, Angelo MA, Cerpas C, Fernando A, Sidney J, Peters B, Gresh L, Balmaseda A, de Silva AD, Harris E,…
PLoS Pathog

A quantitative analysis of complexity of human pathogen-specific CD4 T cell responses in healthy M. tuberculosis infected south africans

2016-07
Lindestam Arlehamn CS, McKinney DM, Carpenter C, Paul S, Rozot V, Makgotlho E, Gregg Y, van Rooyen M, ernst JD,…
Clin Exp Allergy

Sequence conservation predicts T cell reactivity against ragweed allergens

2016-06
Pham J, Oseroff C, Hinz D, Sidney J, Paul S, Greenbaum J, Vita R, Philips E, Mallal S, Peters B, Sette A

Principal Investigator

Alessandro Sette, Dr. Biol.Sci.

Center Head, Division Head, and Professor

Dr. Sette is currently a Member and Head of LJI’s Division of Vaccine Discovery as well as chair of the Institute’s Center for Infectious Diseases. Dr. Sette has a doctorate in Biological Sciences from the University of Rome and did postdoctoral work at the National Jewish Center for Immunology and Respiratory Medicine in Denver, Colorado. In 1988, Dr. Sette joined Howard Grey, M.D. at the newly founded Cytel, in La Jolla, and was also appointed as an adjunct assistant professor at The Scripps Research Institute. He founded Epimmune in 1997, where he served both as Vice President of Research and Chief Scientific Officer until 2002, when he joined LJI.

Dr Sette is a leader in the field of T cell epitope-MHC interactions, beginning with his contribution to the discovery of the biological function of MHC in the mid 80s to mid 90s. From those studies he and his collaborators further developed the notion that different MHCs have distinct binding specificities that can be used to predict epitopes. The Sette group also discovered and characterized how MHC variants can be grouped according to broad common functional specificities (MHC supertypes), greatly facilitating epitope classification, characterization and understanding the basic rules of epitope-MHC interactions. At the same time, several studies have outlined the fine specificity of different closely related alleles, in some cases clearly associated with predisposition to disease resistance or susceptibility.

Lab Members

Eddy His Chun Wang

Visiting Scientist

Michael Angelo

Research Technician III

Biosketch:
I graduated from the University of California, San Diego in 2010 with a Bachelor of Science degree in Human Biology. I began working as a Research Technician for Dr. Daniela Weiskopf in the Sette laboratory at the La Jolla Institute for Allergy and Immunology in November of 2010.

Research Focus:

For the past several years my research has been focused on the study of the role of T-cells in the context of infection with Dengue virus. Working with Dr. Weiskopf, we established a model of human dengue disease using HLA transgenic mouse strains, and characterized human dengue-specific CD8+ and CD4+ T-cell responses in natural infection as well as following vaccination.

Career Goals:

I plan to pursue a career in scientific research primarily focused on characterization of the immune response associated with viral infections and human disease.

Ricardo Da Silva Antunes, Ph.D.

Postdoctoral Fellow

Dr. da Silva Antunes earned his PhD in Biomedical Sciences at University of Porto, Portugal in 2010. He further joined St George’s, University of London for a postdoc position in the field of atherosclerosis. In 2012 he moved to La Jolla Institute for Allergy and Immunology under Michael Croft supervision and handled a project focused in the innate immune cells of the lung and development of asthma in collaboration with JanssenTM. Upon joining the Sette’s lab in January of 2016, he took over a project exploring how differences in T cell response contribute to the time-dependent decline in protection by the acellular pertussis vaccine.

His motivation to gain broad experience in several immunological methods and to understand the vast immunological scenarios, in combination with the deep expertise in T cell characterization is paving the road for him to chase a career in scientific research focused on understanding and developing better strategies to efficiently tackle human diseases.

Cecilia Lindestam Arlehamn, Ph.D.

Instructor

Biosketch:
I graduated from University of Kalmar, Sweden in 2005 with a M.S. degree in Biomedicine. I then obtained my Ph.D. in Immunology and Microbiology from the University of Glasgow, Scotland, UK in 2009. I began working as a postdoc in the Sette laboratory at the La Jolla Institute for Allergy and Immunology in January 2010 and was promoted to the Instructor position in January 2014.

Research Focus:
My research projects are focused on defining the T cell responses against Mycobacterium tuberculosis, the causative agent of tuberculosis disease. I am interested in understanding the specific T cell responses mounted against MTB during latent or active infection and following vaccination, as well as the role of environmental exposure to other Mycobacterium species.

Alexandra Backlund

Intern

Tobias Bergmann

Visiting Scientist

Giovanni Birrueta

Research Technician I

Chelsea Carpenter

Research Technician I

Biosketch:
I graduated from University of California, Santa Barbara in 2014 with a B.S. degree in Pharmacology. I began working as a research technician in the Sette laboratory under Cecilia Lindestam Arlehamn at the La Jolla Institute for Allergy and Immunology in September 2014.

Research Focus:
My research project focuses on the T cell response of mycobacterium tuberculosis to further understand how the current BCG vaccine can be improved.

Career Goal:
I plan to continue my career in infectious disease and pursue my research focus on vaccines, treatment, and drug development.

Kenneth Chan

Senior Curator

Gabriele Foos

Senior Curator

April Frazier, Ph.D.

Senior Project Manager

As senior project manager for the Sette and Peters laboratories, I draw on more than seven years of experience managing large, multi-subcontractor grants and research projects in academia and industry. Currently, I keep on track a number of different research programs (including allergy, infectious disease, and Parkinson’s disease) and oversee several large contracts and grants from NIH and commercial companies.

I received a BS degree in Applied Chemistry from Harvey Mudd College in Claremont, CA, and a PhD in Chemistry (Biophysics) from the University of Virginia in 2003. After a two-year stint as a postdoctoral research fellow in Pharmacology in the laboratory of Dawn Quelle at the University of Iowa, where I studied the molecular mechanisms of tumorigenesis, I made the switch to industry. I moved to Vancouver, BC, Canada to join the biophysical characterization department of Celator Pharmaceuticals (a spin-off company from the BC Cancer Agency) as a research scientist before my next position took me to York, England. There, I held a dual position as a Commercial Operations Manager and Research Scientist at Pro-Cure Therapeutics before I returned to the U.S. in 2012 to join the La Jolla Institute.

Alba Grifoni, Ph.D.

Postdoctoral Fellow

Biosketch:
I graduated from University of Rome “Tor Vergata” Italy in 2007, with a Bachelor degree in human biology. I then obtained in the same university my master degree in human and evolutionary biology in 2010. I have accomplished my Ph.D in Immunology and applied biotechnology from University of Rome “Tor Vergata” in 2014. During my PhD, i have performed two years (from 2012 to 2014) of training period for acknowledgment in immune-informatics tools in Proxagen Ltd. Sofia, Bulgaria. In the same agency, I have worked as Junior Researcher from April 2014 to December 2015. I began working as a postdoc in the Sette laboratory at the La Jolla Institute for Allergy and Immunology in February 2016.

Research Focus:
My research project is focused on the characterization of human T cell immune responses against Dengue virus. I am interested in understanding the characteristics of human immune response against infectious agents and the role of HLA molecules.

Career Goals:

I plan to pursue a career in scientific research focused on understanding the human immune response to various infectious agents for diagnostic and vaccine design purpose.

Christian de Groot

Visiting Scientist

Kristen Jensen

Intern

Natalie Khalil

Intern

Mikaela Lindvall

Research Technician II

Biosketch:
I graduated with a degree in Cell and Molecular Biology B.S. from San Diego State University in 2014, and I began working in the Sette lab under John Sidney in January 2015. During my college years, I was a lab assistant at White Labs, Inc., assisting with yeast culture and quality control.

Research Focus:
I work with the “Binding Team” in the Sette lab. We use radiolabeled peptides, mostly derived from autoimmune conditions and pathogens, to determine binding motifs and affinities to a large assortment of MHC Class I and II alleles. We work with a variety of collaborators from both industry and academic institutions.

Career Goals:
In the future, I would like to continue my education and get a masters degree. Eventually, I would like to work in industry and learn more about the business side of science.

Sheridan Martini

Project Assistant

I graduated from Northern Arizona University (Flagstaff, Arizona) in 2014 with a B.S. degree in Chemistry. I then returned to San Diego, California where I briefly worked in a veterinary hospital until joining the research team at La Jolla Institute. I am now a project assistant in the Sette/Peters laboratories.

Alexander Mentzer

Visiting Scientist

Eugene L. Moore, Ph.D.

Scientific Associate

Biosketch:
B.S. Microbiology from University of Arkansas, Fayetteville. Worked in poultry and chemical industries for a while until the self-realization that my talents were being wasted became unbearable. I returned to graduate school where I obtained a Ph.D. in Biochemistry and Molecular Biology from UC Riverside in 2004. The principal focus of my doctoral and post-doctoral research has been studying the biochemistry and neurophysiological mechanisms of novel animal neurotoxins.

Research Focus:
Currently assist the binding group in HLA binding studies.

Career Goals:
Currently the CSO of my first startup, Amplicon Diagnostics. My goals include the development of novel molecular diagnostic methods in companion animal cancer and infectious disease. Working on creation of point-of-care molecular testing platform.

Erin Moore

Lab Assistant

Bianca Mothe, Ph.D.

Adjunct Professor

Patrick O’Rourke

Research Technician I

Biosketch:
I graduated from UC Santa Barbara in 2013 with a B.S. degree in Pharmacology. I began working as a Research Technician in the Sette laboratory at the La Jolla Institute for Allergy and Immunology in May 2015.

Research Focus:
Under Daniela Weiskopf, Ph.D. our research characterizes human DENV-specific CD8+ and CD4+ T cell responses in both, samples from areas with endemic dengue infection and following vaccination.

Career Plans:
I plan on going back to school to achieve either a Ph.D. or Masters and currently I’m interested in staying in an immunological specialization.

John Pham

Research Technician I

Nima Salimi

IEDB Database/Curation Manager

Heidi Schultz

Postdoctoral Fellow

Deborah Shackelford

Senior Curator

John Sidney

Scientific Associate

Yuan Tian

Postdoctoral Fellow

Kerrie Vaughan

IEDB Manager of Data Analyses

Randi Vita, M.D.

IEDB Data Quality Control

Biosketch:
I graduated from The University of Texas at Austin in 1991 with a degree in biology. I then worked in a rheumatology lab under Dr. Peter Lipsky at The University of Texas Southwestern Medical Center. I continued a research career in the allergy laboratory of Rafeul Alam throughout my training at The University of Texas Medical Branch, School of Medicine, graduating with an M.D. and special honors in immunology in 1988. After a clinical research fellowship at the Shriners Burns Institute, Surgery Department, Galveston, Texas, I came to The La Jolla Institute for Allergy and Immunology to complete a basic research fellowship in the laboratory of Amnon Altman. I have been working on the Immune Epitope Database and Analysis Project (IEDB) since 2005.

Research Focus:
My interests include data management, ontology development, and ontology integration into databases in order to allow interoperability and sophisticated reasoning. Additionally, I am interested in data accuracy and reproducibility, as well as transparency and free access to data and scholarly communications.

Career Goals:
I hope to facilitate the integration of formal ontologies into many public scientific resources, like the IEDB, to bring about more accurate data, interoperable data sets, and new scientific conclusions.

Daniela Weiskopf, Ph.D.

Instructor

I have devoted my career to understanding the T cell response to viral infection. In 2009, I received my PhD in Immunology from Innsbruck Medical University, Austria, where I performed research analyzing post-translational modifications of CMV-derived epitopes and modulation of the T cell immune response during aging. Following my PhD, I obtained post-doctoral training under Dr. Alessandro Sette where my efforts were dedicated to characterizing human dengue virus-specific CD8+ and CD4+ T cell in blood samples from areas with endemic dengue infection and following vaccination. Since January 2014 I’m an instructor at the La Jolla Institute and continue to focus on characterizing T cell immunity against dengue virus and other flaviviruses.

Leora Zalman, Ph.D.

Senior Scientific Curator

Biosketch:
I graduated from UCLA with a B.S. in Biochemistry, and then from UC Berkeley with a Ph.D. in Microbiology and Immunology. I did postdoctoral fellowships at UCLA and at Scripps Clinic, and then worked at Scripps as an Assistant Member in the Department of Immunology. Subsequently, I worked at Pfizer for a number of years in the Pharmacology and Virology Departments on drug development of anti-rhinoviral compounds. I have been at La Jolla Institute for Allergy and Immunology since 2006 as a Senior Curator, responsible for compiling immunology data from the scientific literature with specific emphasis on extracting information about B and T cell epitopes into an NIAID-funded database, the Immune Epitope Database (IEDB). In addition, I have been initiating an effort to submit data derived from our lab into ImmPort, a biomedical research data site also funded by NIAID.

Sette Lab

Research Projects

Human Immune Profiling Consortium

The aim of this work, in collaboration with Bjoern Peters and Pandurangan Vijayanand, is to characterize the immune response to dengue virus (DENV) and Mycobacterium tuberculosis (MTB), both of which represent major global health challenges. Specifically, the consortium will apply unbiased methods to identify T cell signatures associated with protection from or susceptibility to the two diseases. This open-ended approach relies heavily on RNA sequencing, a cutting-edge technique to identify genes whose expression is enhanced or diminished by a particular condition.

Selected References

Arlehamn CL, Seumois G, Gerasimova A, Huang C, Fu Z, Yue X, Sette A, Vijayanand P, Peters B. Transcriptional profile of tuberculosis antigen-specific T cells reveals novel multifunctional features. J Immunol. 2014 Sep;193(6):2931-40.

T cell responses to DENV infection and vaccination

The Sette lab’s research on DENV encompasses large-scale epitope identification (supported by an HHS contract) and diverse studies towards understanding the role of T cells and HLA variants in the development of (or protection from) DENV disease (supported in part by a consortium grant led by Eva Harris at UC Berkeley). The latter work addresses questions including whether infection with different serotypes is associated with distinct types of T cell responses, whether any HLA alleles are associated with pathogenesis or protection, and whether vaccination with a formulation in clinical trials is associated with T cell responses similar to those following infection that might serve as correlates of protection.

Selected References

Weiskopf D, Angelo MA, de Azeredo EL, Sidney J, Greenbaum JA, Fernando AN, Broadwater A, Kolla RV, De Silva AD, de Silva AM, Mattia KA, Doranz BJ, Grey HM, Shresta S, Peters B, Sette A. Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells. Proc Natl Acad Sci. 2013 May 28;110(22):E2046-53.

T cell responses to MTB infection and vaccination

Following completion of a massive epitope discovery effort (also supported by an HHS contract), current work on MTB includes development of tools to isolate MTB-specific T cells (supported by the Gates Foundation) and identifying T cell signatures that distinguish three possible infection states: cleared infection, stable latent infection, and latent infection with high risk of progression to disease (in conjunction with a large consortium led by Henry Blumberg at Emory University).

Selected References

Lindestam Arlehamn CS, Gerasimova A, Mele F, Henderson R, Swann J, Greenbaum JA, Kim Y, Sidney J, James EA, Taplitz R, McKinney DM, Kwok WW, Grey H, Sallusto F, Peters B, Sette A. Memory T cells in latent Mycobacterium tuberculosis infection are directed against three antigenic islands and largely contained in a CXCR3+CCR6+ Th1 subset. PLoS Pathog. 2013 Jan;9(1):e1003130.

Immunological basis of differences in protection between pertussis vaccines

The recent increase in cases of whooping cough among teenagers in the US suggests that the protection conferred by the acellular Bordetella pertussis vaccine (aP) that became standard in the mid 1990s is of shorter duration than that conferred by the whole-bacteria formulation (wP) used since the 1950s. To understand the potential basis for this differential efficacy, we are comparing epitope repertoires and exploring the molecular basis for differences in T cell responses between aP- and wP-primed individuals.

Allergy seasonality: In a large effort supported by a consortium grant from NIAID, the Sette group is collaborating with the Peters and Vijayanand labs to test the hypothesis that different stages (in-season versus out-of-season), types (rhinitis versus asthma), and severities of allergic disease are associated with not only differential magnitude of T cell responses, but also distinctive patterns in terms of the T cell subsets involved and their interactions. This work focuses on three important allergens, namely timothy grass), house dust mite (HDM), and cat dander. One set of these studies is characterizing responses in moderate/severe and mild asthmatics, and contrast them with those observed in non-asthmatic individuals suffering from allergic rhinitis. To examine the effect of seasonality, we are comparing T cell responses both in- and out-of-season between allergic and non-allergic individuals.

Selected References

Schulten V, Tripple V, Sidney J, Greenbaum J, Frazier A, Alam R, Broide D, Peters B, Sette A. Association between specific timothy grass antigens and changes in TH1- and TH2-cell responses following specific immunotherapy. J Allergy Clin Immunol. 2014 Nov;134(5):1076-83.

Cockroach allergy

Though cockroach allergy is a major contributor to asthma development in urban settings, the role of T cells in that setting has been understudied until recently. As part of a large NIH-funded effort to develop immunotherapies for this allergy (the Inner City Asthma Consortium, or ICAC), the Sette lab has thus identified dominant epitopes to characterize T cell responses in allergic individuals before and after immunotherapy.

Selected References

Oseroff C, Sidney J, Tripple V, Grey H, Wood R, Broide DH, Greenbaum J, Kolla R, Peters B, Pomés A, Sette A. Analysis of T cell responses to the major allergens from German cockroach: epitope specificity and relationship to IgE production. J Immunol. 2012 Jul;189(2):679-88.