Vijayanand Lab

Vijayanand Lab

— Pandurangan Vijayanand, M.D. Ph.D. // Associate Professor
William K. Bowes Distinguished Professor

Overview

Dr. Vijayanand lab employs genomics tools to understand, diagnose and treat pulmonary disease such as asthma, lung cancer and infectious disease.

His laboratory has developed a number of techniques to study the molecular profiles of circulating and airway immune cells from patients with asthma and other diseases, using fewer cells than was possible previously.

Dr. Vijayanand also oversees a large-scale effort to map epigenomic modifications in more than a dozen different types of human immune cells from normal individuals to understand how epigenetic variations cause susceptibility to disease. For many human diseases, large-scale genomic studies have identified common genetic variants that occur more frequently in people with cardiovascular, autoimmune, inflammatory and infectious diseases, diabetes and asthma than in those without these diseases. However, it has been difficult to pinpoint which genetic changes are truly relevant to disease, or in what specific cell types the genetic variation has the largest effect on one’s health. Mapping the epigenome will allow Vijay and his team to zoom in on those genes with the greatest likelihood to contribute to disease, and the cell types in which they act, and therefore will help identify novel therapeutic targets.

From The Lab

Jun 21, 2019 // Journal of Experimental Medicine

To kill tumors, activate this elite group of T cells

Nov 15, 2018 // Cell

DICE: Immune cell atlas goes live

Jan 19, 2018 // Science Immunology

Novel genomic tools provide new insight into human immune system

Dec 6, 2017

San Diego Team wins $ 6.9 million grant to establish PrecISE Network Clinical Center

Jun 19, 2017

Tumor immune fitness determines survival of lung cancer patients

Vijayanand Lab

Publications

Nat Commun

Identification of significant chromatin contacts from HiChIP data by FitHiChIP

2019-09
Bhattacharyya S, Chandra V, Vijayanand P, Ay F
J Immunol

Human eosinophils express a distinct gene expression program in response to IL-3 compared with common β-chain cytokines IL-5 and GM-CSF

2019-07
Nelson RK, Brickner H, Panwar B, Ramírez-Suástegui C, Herrera-de la Mata S, Liu N, Diaz D, Alexander LEC, Ay F,…
Elife

Circulating T cell-monocyte complexes are markers of immune perturbations

2019-06
Burel JG, Pomaznoy M, Lindestam Arlehamn CS, Weiskopf D, da Silva Antunes R, Jung Y, Babor M, Schulten V, Seumois G,…
J Exp Med

Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer

2019-06
Clarke J, Panwar B, Madrigal A, Singh D, Gujar R, Wood O, Chee SJ, Eschweiler S, King EV, Awad AS, Hanley CJ, McCann…
J Clin Invest

Dengue-specific CD8+ T cell subsets display specialized transcriptomic and TCR profiles

2019-03
Tian Y, Babor M, Lane J, Seumois G, Liang S, Goonawardhana NDS, De Silva, AD, Phillips E, Mallal SA, da Silva Antunes…
J Clin Invest

Reduced expression of phosphatase PTPN2 promotes pathogenic conversion of Tregs in autoimmunity

2019-03
Svensson MN, Doody KM, Schmiedel BJ, Bhattacharyya S, Panwar B, Wiede F, Yang S, Santelli E, Wu DJ, Sacchetti C, Gujar…
Sci Transl Med

Recurrent group A Streptococcus tonsillitis is an immunosusceptibility disease involving antibody deficiency and aberrant TFH cells

2019-02
Dan JM, Havenar-Daughton C, Kendric K, Al-Kolla R, Rosales SL, Anderson EL, LaRock CN, Vijayanand P, Seumois G,…
J Immunol

Cutting edge: transcriptional profiling reveals multifunctional and cytotoxic antiviral responses of zika virus-specific CD8+ T cells

2018-12
Grifoni A, Costa-Ramos P, Pham J, Tian Y, Rosales SL, Seumois G, Sidney J, de Silva AD, Premkumar L, Collins MH, Stone…
Cell

Impact of genetic polymorphisms on human immune cell gene expression

2018-11
Schmiedel BJ, Singh D, Madrigal A, Valdovino-Gonzalez AG, White BM, Zaperdiel-Gonzalo J, Ha B, Altay G, Greenbaum JA,…
J Clin Invest

Th1/Th17 polarization persists following whole-cell pertussis vaccination despite repeated acellular boosters

2018-08
da Silva Antunes R, Babor M, Carpenter C, Khalil N, Cortese M, Mentzer AJ, Seumois G, Petro CD, Purcell LA, Vijayanand…
Cell Rep

Identification of an early unipotent neutrophil progenitor with pro-tumoral activity in mouse and human bone marrow

2018-08
Zhu YP, Padgett L, Dinh HQ, Marcovecchio P, Blatchley A, Wu R, Ehinger E, Kim C, Mikulski Z, Seumois G, Madrigal A,…
J Immunol

Transcriptomic analysis of CD4+ T cells reveals novel immune signatures of latent tuberculosis

2018-05
Burel JG, Lindestam Arlehamn CS, Khan N, Seumois G, Greenbaum JA, Taplitz R, Gilman RH, Saito M, Vijayand P, Sette A,…
J Allergy Clin Immunol

Allergen-specific immunotherapy modulates the balance of circulating Tfh and Tfr cells

2018-02
Schulten V, Tripple V, Seumois G, Qian Y, Scheuemann RH, Fu Z, Locci M, Rosales S, Vijayanand P, Sette A, Alam R,…
Sci Immunol

Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis

2018-01
Patil VS, Madrigal A, Schmiedel BJ, Clarke J, O'Rourke P, de Silva AD, Harris E, Peters B, Seumois G, Weiskopf D, Sette…
J Natl Cancer Inst

Targeting the myofibroblastic cancer-associated fibroblast phenotype through inhibition of NOX4

2018-01
Hanley CJ, Mellone M, Ford K, Thirdborough SM, Mellows T, Frampton SJ, Smith DM, Harden E, Szyndralewiez C, Bullock M,…
Methods Mol Biol

An integrated and semiautomated microscaled approach to profile cis-regulatory elements by histone modification ChIP-Seq for large-scale epigenetic studies

2018-01
Youhanna Jankeel D, Cayford J, Schmiedel BJ, Vijayanand P, Seumois G
Methods Mol Biol

A sensitive and integrated approach to profile messenger RNA from samples with low cell numbers

2018-01
Rosales SL, Liang S, Engel I, Schmiedel BJ, Kronenberg M, Vijayanand P, Seumois G
Clin Cancer Res

Head and neck squamous cell carcinomas are characterized by a stable immune signature within the primary tumor over time and space

2017-12
Wood O, Clarke J, Woo J, Mirza AH, Woelk CH, Thomas GJ, Vijayanand P, King EV, Ottensmeier CH
Nat Commun

Unique phenotypes and clonal expansions of human CD4 effector memory T cell re-expressing CD45RA

2017-11
Tian Y, Babor M, Lane J, Schulten V, Patil VS, Seumois G, Rosales SL, Fu Z, Picarda G, Burel J, Zapardiel-Gonzalo J,…
Br J Cancer

Evaluating the effect of immune cells on the outcome of patients with mesothelioma

2017-10
Chee SJ, Lopez M, Mellows T, Gankande S, Moutasim KA, Harris S, Clarke J, Vijayanand P, Thomas GJ, Ottensmeier CH
Am J Respir Crit Care Med

Differential recognition of mycobacterium tuberculosis-specific epitopes as a function of tuberculosis disease history

2017-09
Scriba TJ, Carpenter C, Carrasco Pro S, Sidney J, Musvosvi M, Rozot V, Seumois G, Rosales SL, Vijayanand P, Goletti D,…
Nat Immunol

Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer

2017-08
Ganesan AP, Clarke J, Wood O, Garrido-Martin EM, Chee SJ, Mellows T, Samaniego-Castruita D, Singh D, Seumois…
J Immunol

An integrated workflow to assess technical and biological variability of cell population frequencies in human peripheral blood by flow cytometry

2017-02
Burel JG, Qian Y, Lindestam Arlehamn C, Weiskopf D, Zapardiel-Gonzalo J, Taplitz R, Gilman RH, Saito M, de Silva AD,…
Nature Communications

17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells.

2016-11
Schmiedel BJ, Seumois G, Samaniego-Castruita D, (...) Sette A, Peters B, Vijayanand P*.
Oncotarget

Gene expression analysis of TIL rich HPV-driven head and neck tumors reveals a distinct B-cell signature when compared to HPV independent tumors.

2016-07
Wood O, Woo J, Seumois G, (...) Vijayanand P*, Woelk CH, King E, Ottensmeier C.
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…
Nat Immunol

Innate-like functions of natural killer T cell subsets result from highly divergent programs

2016-06
Engel I, Seumois G, Chavez L, Samaniego-Castruita D, White B, Chawla A, Mock D, Vijayanand P, Kronenberg M
Journal of Experimental Medicine

Control of Foxp3 stability through modulation of TET activity.

2016-03
Yue X, Trifari S, Äijö T, Tsagaratou A, Pastor WA, Zepeda-Martínez JA, Lio CW, Li X, Huang Y, Vijayanand P*, …
Journal of Experimental Medicine

Identification of a novel cis-regulatory element essential for immune tolerance

2015-11
LaFlam TN, Seumois G, Miller CN, Lwin W, Fasano KJ, Waterfield M, Proekt I, Vijayanand P*, Anderson MS
Clin Exp Allergy

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

2015-05
Hinz, D, Seumois, G, (...), Peters, B, Vijayanand, P*, Sette, A
Journal of Immunology

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

2014-09
Arlehamn, C.L., Seumois, G., Gerasimova, A., Huang, C., Fu, Z., Yue, X., Rao, A., Sette, A., Vijayanand, P*, Peters, B*
PLOS One

Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data

2013-01
Gerasimova, A, Chavez, L, Li, B, Seumois, G, Greenbaum, J, Rao, A, Vijayanand, P*, Peters, B.
Am J Clin Exp Immunol

An integrated nano-scale approach to profile miRNAs in limited clinical samples

2012-11
Seumois, G.*, Vijayanand, P*., Eisley, C.J., Omran, N., Kalinke, L., North, M., Ganesan, A.P., Simpson, L.J.,…
Immunity

Interleukin-4 Production by Follicular Helper T Cells Requires the Conserved Il4 Enhancer Hypersensitivity Site V.

2012-02
Vijayanand, P*, Seumois, G, Simpson, LJ, Abdul-Wajid, S, Baumjohann, D, Panduro, M, Huang, X, Interlandi, J, Djuretic,…
Thorax

Sputum IL-6 concentrations in severe asthma and its relationship with FEV1

2011-06
Morjaria, J.B., Babu, K.S., Vijayanand, P.*, Chauhan, A.J., Davies, D.E., and Holgate, S.T.
Journal of Immunology

Chemokine receptor 4 plays a key role in T cell recruitment into the airways of asthmatic patients

2010-04
Vijayanand, P.*, Durkin, K., Hartmann, G., Morjaria, J., Seumois, G., Staples, K.J., Hall, D., Bessant, C.,…
The New England Journal of Medicine

Invariant natural killer T cells in asthma and chronic obstructive pulmonary disease

2007-04
Vijayanand, P.*, Seumois, G., Pickard, C., Powell, R.M., Angco, G., Sammut, D., Gadola, S.D., Friedmann, P.S., and…

Principal Investigator

Pandurangan Vijayanand, M.D. Ph.D.

Associate Professor

Dr. Vijayanand was appointed an Associate Professor in 2015. He is the inaugural holder of the William K. Bowes Distinguished Professorship

Dr. Vijayanand received his M.D. from the MGR Medical University in Chennai, India, and completed his residency in Internal Medicine followed by a Pulmonary Fellowship in the United Kingdom. In 2008, he obtained his Ph.D. from the University of Southampton, United Kingdom, where he studied the mechanisms of accumulation and activation of T cells in human asthma. Since then, Dr. Vijayanand has split his time between laboratory research and seeing patients at the University of Southampton, where he currently holds an appointment as an Associate Professor in the School of Medicine. In 2007, he was awarded a prestigious National Career Development Fellowship to undertake translational studies in the epigenetic regulation of the immune cell signaling molecules in human asthma at UC San Francisco, where he was appointed adjunct assistant professor in the Department of Medicine in 2009. Two years later, Vijay joined the La Jolla Institute for Immunology as an adjunct assistant professor.

Lab Members

Praveen Akuthota

Clinical Associate Professor

Dr. Akuthota’s research efforts range from basic scientific investigations of human eosinophil biology and eosinophilic inflammation to clinical and translational efforts in asthma and eosinophilic pulmonary disease. He is the corresponding Principal Investigator for the UCSD Clinical Center in the National Heart, Lung, and Blood Institute’s PrecISE Network that will be studying precision interventions in severe asthma. He is a co-investigator on a study published in the New England Journal of Medicine showing the efficacy of anti-IL-5 therapy in the treatment of the eosinophilic disease EGPA (Churg Strauss syndrome). His research group is involved in other multicenter studies in eosinophilic disease and asthma. He is a Clinical Affiliate at the La Jolla Institute for Allergy and Immunology, working with them in developing joint efforts in asthma research (www.togetherforasthma.org). Basic science investigations from Dr. Akuthota focus on ex vivo studies of human eosinophils and include published work studying eosinophil trafficking and work studying microparticle release by eosinophils. He has written several reviews and chapters discussing eosinophil immunobiology and clinical considerations in eosinophilic diseases. Dr. Akuthota is an At-Large Member of the Board of Directors of the International Eosinophil Society.

Justin Cayford

Graduate Student

Vivek Chandra

Instructor

Biosketch:
I did PhD from ICGEB, New Delhi component, India. My studies characterized several pathways modulated by the Hepatitis E Virus that are major contributors to viral pathogenesis. To study how lncRNA and chromatin biology is revolutionizing our understanding of complex biological problems, I joined the laboratory of Cornelis Murre at University of California, San Diego in September 2010 as a Postdoctoral fellow. Recently from September 2017, I joined Vijay’s group at LJI as an Instructor.

Research Focus & Career Goals:
Recent work, to which I have also contributed, and from some other laboratories has established that global regulation of cellular differentiation is the result of the coordinated interplay of dynamic changes in the organization of chromatin, epigenetic modifications, lncRNAs and transcription factors. I will continuously look for ways to incorporate new features into the construction of a more complete regulatory-network map. I am convinced that the growing molecular toolbox at our disposal necessitates a quantitative systems approach to answer biological problems. By comparing the regulatory networks of pathologic conditions, I expect to gain new insights into the central question: how do regulatory networks instruct cellular behavior under diseased condition and can we discover drugs that can alter these regulatory networks.

James Clarke

Visiting Scientist

Simon Eschweiler

Postdoctoral Fellow

Biosketch:
During my MSc in Molecular Biotechnology (2013 – RWTH Aachen, Germany) I found my calling in studying the immune system and hence went on to obtain my PhD in Immunology (2017 – University of Luebeck). During my graduate work, I investigated the regulatory pathway and microenvironmental cues that guide antibody glycosylation and placed special emphasis on the regulation of the germinal center reaction by stimulatory T follicular helper and suppressive T follicular regulatory cells. In late 2017 I joined Vijay’s lab to investigate tumor-infiltrating lymphocyte subsets and their contribution to an efficacious anti-tumor immune response.

Research Focus:
I am implementing my expertise into a specific disease-focused perspective in cancer research to elucidate pathways of tumor evasion and the identification of novel immunotherapy targets.

Career Goals:
Improve cancer treatment efficacy by unraveling novel drug targets and rationally combining existing immunotherapy drugs

Anusha Preethi Ganesan

MD, PhD

Biosketch:
I obtained my MD from Madras Medical College and completed my pediatric residency in the UK. Fascinated by the concept of cancer vaccines, I undertook my PhD in tumor immunology jointly at the University of Southampton (Ottensmeier Lab) and University of California, San Francisco (Coussens Lab). As part of the UCSD pediatric hematology oncology fellowship program, I am currently pursuing subspecialty training and postdoctoral research.

Research Focus:
The immune system plays a critical role in regulating tumor growth and progression. My research is focused on elucidating the molecular mechanisms underlying a protective anti-tumor immune response with the goal of identifying novel immunotherapeutic targets.

Career Goals:
As a physician scientist, my goal is to undertake translational research into pediatric cancers, particularly, relapsed leukemia and harness the immune system to provide durable immunity against this disease.

Cristian Gonzalez-Colin

Research Technician I

I will get my bachelor’s degree in Genomic Sciences in September 2020 from National Autonomous University of Mexico. I did some tool development focused on text mining and machine learning algorithms before I was given the opportunity to join Vijay’s lab as a research technician in June 2019.

Research Focus:
Currently, I analyze transcriptomic and epigenomic data in several types of human immune cells looking for non-coding variants that give rise to susceptibility to diseases.

Career goals:
My goal is to become a researcher focused on developing bioinformatics software to understand the mechanisms that control the genomic regulation, especially how these mechanisms interact with non-coding variants in response to human diseases.

Ravindra Gujar, Ph.D.

Postdoctoral Fellow

Biosketch:
I got my Masters degree in Biotechnology from Madurai Kamaraj University, India. Thereafter I did my PhD from Jawaharlal Nehru University, India. My Doctoral work focused on innate immunity in context to immunosuppressive receptors on Dendritic cells. Soon after completing my PhD, I was given the opportunity to join Vijay’s lab.

Research Focus & Career Goals
My primary focus was to develop low cell number Epigenetics assay like ATAC-seq or Chip-seq. I am investigating the origins of asthma by studying children from birth till they develop asthma later in life. I am working on various aspects in project which include genome sequencing, epigenetic assays, and functional studies in human immune cells and further validation of key molecule(s) in mouse asthma models. My goal is to become scientific researcher in understanding and unraveling molecular mechanism of Asthma.

Richard Harris

Visiting Scientist

Anthony Kusnadi, Ph.D.

Postdoc Fellow

Born in Indonesia, I obtained my B.Sc. degree in Life Science and Biotechnology (2012) from Underwood International College, Yonsei University in Seoul, South Korea. In 2010, I traveled to the USA to participate in a study abroad program for one academic year in University of Washington, Seattle. In 2018, I graduated from Weill Cornell Medicine with a Ph.D. degree in Immunology and Microbial Pathogenesis. During my graduate education, I investigated the effects and consequences of long term TNF exposure in human macrophages, a condition that is especially relevant in several auto-inflammatory disorders, including Rheumatoid Arthritis. I identified that transcription factor SREBP2 plays an unexpected, yet important role in shaping macrophages response to chronic TNF stimulation. In the spring 2019, I decided to join Vijayanand’s laboratory as a postdoctoral fellow.

Research Focus:
Currently, I am involved in the Cooperative Centers on Human Immunology (CCHI) consortium at La Jolla Institute for Immunology. Within the consortium, my research focuses on elucidating the characteristic of epitope-specific CD4 T cells in human lung and how this particular heterogeneous subset of T cells plays roles in maintaining lung homeostasis and driving protective immunity after vaccination.

Career Goal:
My future career goal is to become an independent scientist who can lead a research group that investigate the immune system and its relationship with diseases and disorders.

Shu Liang

Lab Manager/Research Technician II

Biosketch:
I got my B.S. degree from Shanghai Jiao Tong University in Laboratory Medicine, then my M.S. from University of Washington in the same major. I did some web development work before I realized how much I like working in a lab. Lucky enough, I was given the opportunity to join Vijay’s lab.

I’ve been working on NGS library preparation since I joined, and got familiar with more aspects of NGS technology as I grow. After getting promoted as the lab manager, I took on more responsibilities on supporting the smooth performance of the whole lab.

Research Focus:
Currently, the majority of my work goes to NGS library preparation protocol optimization in two major ways: developing highly sensitive and cost-effective RNA sequencing protocols that are suitable for our lab’s research subjects; optimizing the protocols to increase the throughput.

Career Goal:
My interests lie in new technologies. I plan to become an assay or instrument developer that push the limits restraining scientists from achieving their research goals.

Ariel Madrigal

Research Technician II

Biosketch:
Born in Mexico City, I obtained my bachelor’s degree in Genomic Sciences (2017) from National Autonomous University of Mexico. This program combines different disciplines, mainly biology, computer science and mathematics. I joined Vijay’s lab in June 2016 as a research technician focused on analyzing transcriptomic and epigenomic data.

Research Focus:
My main focus is to understand immune cell populations through the development and employment of computational algorithms. I enjoy analyzing vast amounts of data derived from techniques such as single cell RNA-Seq, ChIP-Seq, ATAC-Seq, etc. I found fascinating how all these data allow us to comprehend better the function of a cell. Lately, I’ve been interested in understanding how genetic variation affects the phenotype of diverse cell populations, and how this translates into predisposition to disease.

Career goals:
My short-term goal is to continue my education obtaining a Ph.D. in Bioinformatics. In the future, I see myself as a researcher focused on understanding genomic regulation, especially the role of non-coding genetic variation in human disease.

Sara Herrera de la Mata

Research Technician I

Biosketch:
Born in Madrid, Spain, I obtained my B.S. Double Degree in Pharmacology (2016) and Biotechnology (2017) from the European University of Madrid in Spain. In 2016, I travelled to the USA to finish my degree at the University of California Riverside (UCR), where I also obtained a Postgraduate in Bioengineering Management and joined an on-campus laboratory working in immunology and cancer. In 2017, I had the great opportunity to join the Vijayanand Laboratory as a Research Technician focused on the development of high-throughput sequencing technologies such as single cell transcriptomic and RNA-seq, and being involved in some of the projects carried out in the laboratory, like asthma and infectious diseases. Joining Vijay´s Lab and La Jolla Institute for Immunology is being a great experience for me and I believe this opportunity is boosting and adding enormous value to my career development.

Research Focus:
Currently, I am involved in multiple projects performing highly complex genomics assays in human samples which consist of micro-scaled sample processing, preparation of sequencing libraries, the performance of sequencing runs, and the posterior analysis of the obtained sequencing data. Moreover, I provide sequencing input to other lab members and collaborators regarding their sequencing-based projects.

Career Goal:
My future career goal is to obtain a PhD in Immunology, a field of study in science which fascinates me, and, ultimately, to pursue a career in scientific research of immunological diseases.

Benjamin Meckiff, Ph.D.

Postdoctoral Fellow

I obtained an MSci in Biochemistry and Biological Chemistry from the University of Nottingham (UK) in 2009 but it was during my time working in the biotechnology industry that I became captivated with human immunology. I subsequently returned to academia in 2013, earning an MRes in Cancer Sciences, followed by a PhD, both at the University of Birmingham (UK).

My graduate work focused on investigating the CD4+ T cell response to the Epstein-Barr virus including the characterization of a hitherto poorly described cytotoxic population detectable during acute infection.

In the summer of 2019 I joined Vijay’s lab to try and further understand the biology of cytotoxic CD4+ T cells (CD4-CTLs) in the context of viral infections.

Research Focus
My current work is focused on determining the functional and phenotypic properties of pathogen-specific CD4-CTLs as well as identifying the molecular mechanisms that drive CD4-CTL differentiation.

Heena Mistry, Ph.D.

Postdoctoral Fellow

Originally from United Kingdom, I obtained a BSc Honours in Physiology and Pharmacology (2002) and subsequently a Bachelor of Medicine degree (2006) from the University of Southampton, UK. I have always been fascinated in Respiratory Medicine throughout my clinical training and obtained a Respiratory Specialist Registrar National Training Number to ultimately fulfil my career ambition of becoming a Consultant Respiratory Physician. I first developed my subspecialty interest in ‘Severe Asthma’ through my clinical training and actively pursued the opportunity of being a Junior Clinical Research Fellow at Portsmouth Hospitals NHS Trust, UK to enhance my knowledge of this field and gain clinical research experience. I am especially fascinated by the complexities and challenges faced both in managing ‘Severe Asthma’ clinically and in forming a greater understanding of the physiological, pathophysiological, immunological and genetic mechanisms involved in this disease. As a consequence, I became a Clinical Research Fellow in ‘Severe Asthma’ and am currently undertaking a PhD in Infection, Inflammation and Immunity at University of Southampton, UK. I joined the Vijayanand Lab in 2019 as a part of my pre-doctoral fellowship.

Research Focus:
As a Visiting Research Fellow, I aim to acquire specific skills in flow cytometry, immune cell sorting, cutting-edge genomic assays (bulk-RNA-Seq, single-cell RNA Seq) and bioinformatics/statistical data analysis, as well as clinical translation and application of findings. The ‘Severe Asthma’ project will provide me with specialist training in Human Immunology, CD4+ Cell Biology, Transcriptomics, Genomics and Bioinformatics. Ultimately, enhancing my knowledge of the immunological, genetic and molecular basis of asthma.

Career Goals:
I hope to obtain a PhD in Infection, Inflammation and Immunity during my fellowship and the experience gained will equip me with the core vital skills to fulfil my aspiration of becoming a Clinician Scientist/Academic Researcher.

Monalisa Mondal

Research Technician I

I did my Masters in Microbiology from University of Kalyani, India in 2009. In 2010, I was awarded a research fellowship from the Council of Scientific and Industrial Research (CSIR), India. Since then, I am associated with different labs and have experience in different molecular biological projects. In 2018, I got a great opportunity to join Vijay’s Lab to expand my knowledge in immunology and get trained in Next-generation sequencing (NGS) and its application in understanding both the genetic and epigenetic basis of immunological diseases.

Research Focus:
Currently, I am involved in different NGS related experiments, as well as Genomic Assays mainly associated with different projects in the lab. I also lend my hands on other sequencing activities with collaborators.

Career Goal:
My interest lies in learning the ever-expanding techniques associated with NGS and their implication to understand the hidden patterns of gene regulation and other genetic/epigenetic factors observed in different complex diseases like Asthma and Cancer.

Bharat Panwar, Ph.D.

Bioinformatics Scientist

Biosketch:
I obtained my PhD in Bioinformatics from Institute of Microbial Technology (under Jawaharlal Nehru University), India. I have contributed several open-source prediction methods and web-servers to the global scientific community. I am currently working with Dr. Vijayanand and Dr. Ay at LJI.

Research Focus: 
I work in a dynamic and highly collaborative environment and analyze different datasets include epigenomic, transcriptomics, 3D genome organization and single-cell experiments of different immune cells in health and disease (asthma, cancer). I have developed a generic bioinformatics system for prioritizing potential therapeutics target for SLE pathogenesis and providing Bioinformatics assistance to Kyowa Kirin Pharmaceutical Research, Inc. (KKR) for SLE project. I am also analyzing transcriptome profiles of different immune cells (CD8, CD4, B-cell, Macrophage, and NK-cells) for a cancer-immunotherapy project.

Career Goals: 
As a Bioinformatics scientist, my goal is to help experimental biologists to find cure for human diseases by designing and developing analysis systems to extract meaning from large scale genomic data.

Sengjun Park, Ph.D.

Postdoctoral Fellow

Born in Seoul, South Korea, I obtained my PhD in molecular immunology (2017) from Pohang University of Science and Technology (POSTECH, Yoontae Lee’s lab). During my PhD course, I tried to unravel the novel pathway that governing the development of follicular helper T cells. After graduation, I kept studying T cell-mediated autoimmune diseases and placed my special interest on tissue-resident CD8 T cells. Recently from May 2019, I joined Vijay’s group at LJI as a postdoctoral fellow.

Research Focus:
The immune system can suppress tumor development. My research is focused on understanding the molecular mechanisms that initiate tissue-resident memory T cell development in terms of anti-tumor immunity against tumor progression.

Career Goal:
I am very interested in a protective anti-tumor immune response with the goal of applying new therapeutic targets into translational research.

Vicente Fajardo Rosas

Research Technician I

Born in the State of Mexico, Mexico, I am a student of the Undergraduate Program on Genomic Sciences of the National Autonomous University of Mexico. This program’s main focus is to provide to its students a multidisciplinary knowledge involving molecular and cell biology, maths and computer sciences. In order to obtain my last credits and graduate, I am working as a member of Vijay’s lab in the LJI. As part of this wonderful team, I work in the analysis of single cell RNA sequencing (scRNA-seq) data of diverse immune cell types. Moreover, I am mainly interested in the application of bioinformatics to the discovery and understanding of new immune cell populations, as well as the translation of this knowledge into new therapies against common immune diseases and cancers.

Benjamin Schmiedel, Ph.D.

Instructor

I obtained my Diploma in Biochemistry in 2006 from the Martin-Luther-University of Halle-Wittenberg, Germany, and graduated in 2011 with a PhD degree from the Eberhard Karls University of Tübingen, Germany. I joined the La Jolla Institute for Allergy and Immunology (LJI) in July 2012, and got appointed as Instructor in the Division of Vaccine Discovery in December 2016.

Research Focus:
In several projects, my research is focused on epigenetic mechanisms modulating the expression of candidate genes which are implicated in the susceptibility and development of asthma and other autoimmune diseases. In addition, I’m managing and conducting the DICE project (Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics; http://dice-database.org), a large-scale genome-wide study which provides datasets on gene expression, eQTLs and epigenetic marks in human immune cells, and defines the cell type-specific three-dimensional architecture of the genome. The DICE project aids to reveal the effects of disease risk-associated genetic polymorphisms on gene expression in specific immune cell types, providing mechanistic insights into how they influence disease development and pathogenesis.

Career Goals:
I’m pursuing a career in translational research to better the understanding of molecular mechanisms and underlying processes of genetic variations affecting the function of immune cells, aiming to discover new drug targets and improving treatment options for autoimmune diseases and cancer.

Greg Seumois

Core Director, Sequencing & Instructor

Biosketch:
Born and bred in Belgium, I obtained an MSc in Biology (1998 -University of Mons) and a PhD in Immunology (2007 – University of Liege). In 2006, I crossed the English Channel to go learn more about human immunology and translational research in Southampton (Pr. Djukanovitch Lab, UK). It’s in UK I met Vijay with who I started to work on an ambitious program of research on T cells epigenetics in asthma. Part of our epigenetic post-doc training, we joined Mark Ansel’s team at UCSF, in San Francisco. In 2010 we accepted the opportunity to be part of Anjana Rao’s research group here in LJI. In 2012, I got promoted LJI-Instructor. Recently I took Vijay’s challenge to be part, on his side, to the development of a laboratory of Immuno-genomics in LJI. Finally, involved in the development and day-to-day management since its creation in 2013, I’m Core Director of the LJI – Next Generation Sequencing Facility.

Research Focus:
I dedicate my time and effort to develop high-throughput sequencing technologies such as single cell transcriptomic, ChIP-Seq, ChIA-PET, and many more… The scientific rational is to understand better and with a different angle, the mechanisms of epigenetic regulation of gene expression in (rare) immune cells, pathologically relevant in many diseases such as asthma, SLE, tuberculosis…

Career Goals:
As an independent research group leader, I aim to develop innovative ways to investigate, understand and, ultimately, cure human diseases.

Hayley Simon

Research Technician I

My work in research began while obtaining a BS in Biological Sciences from the University of California, Santa Barbara. Using immunological tools like immunohistochemistry, I assisted a team studying vascular senescence in the star ascidian Botryllus schlosseri. Following graduation, I was given the opportunity to expand my knowledge and skill set in immunology through a position as a Research Technician in the Vijay Lab. The majority of my work at La Jolla Institute involves single-cell RNA sequencing projects, including integrating new methods to increase the lab’s single-cell throughput.

I continue my study of the Science of Life outside of work through my love of cooking, surfing, hiking, and camping.

Ciro Ramirez Suastegui

Research Technician I

I graduated in September 2018 with a bachelor in Genomic Sciences from the National Autonomous University of Mexico. This is an interdisciplinary program which combines mainly biology, computer science, and mathematics. I joined La Jolla Institute for Allergy and Immunology in June of 2017.

Reasearch Focus:
I have worked on sexual chromosomes evolution in mammals and reptiles using bioinformatics. At LJI, I am involved in the analysis of transcriptomic data in various types of human immune cells and in different diseases. My main focus is single-cell analysis in the context of disease aimed to the discovery of new target for therapy.

Career Goals:
My goal is to become a bioinformatic tools developer and help the scientific community with the software I create. I would focus on Single Cell software development, but I am open to explore other fields, given than bioinformatics is so flexible.

Alice Wang

Research Tech I

Biosketch:
I obtained my M.S. Degree in Physiology 2017 in a joint program from George Mason University and Georgetown University. As a native San Diegan I really missed the beautiful weather here, so shortly after graduation, I came back to San Diego and joined the Vijayanand Lab. As a research technician, I assist with various activities including RNA sequencing projects for other lab members and collaborators. Every day, I continue to apply my knowledge in human physiology to further understand how the immune system responds to infectious and respiratory diseases.

Career Goal:
My goal is to become a scientific researcher focused on understanding how the immune system responds to human diseases in order to develop potential vaccines and novel treatments.

Adrian von Witzleben

Visiting Scientist

Vijayanand Lab

Research Projects

Asthma

The Vijayanand lab employs genomic and epigenomic tools to understand the molecular basis of asthma.

Selected References

Selected References

Seumois G, Chavez L, Gerasimova A, Lienhard M, Omran N, Kalinke L, Vedanayagam M, Ganesan AP, Chawla A, Djukanović R, Ansel KM, Peters B, Rao A, Vijayanand P. (2014). Epigenomic analysis of primary human T cells reveals novel enhancers associated with Th2 memory differentiation and asthma susceptibility. Nature Immunology 15(8):777-88. PMCID: PMC4140783

Schmiedel BJ, Seumois G, Samaniego-Castruita D, Cayford J, Schulten V, Chavez L, Ay F, Sette A, Peters B, Vijayanand P. (2016). 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells. Nature Communications. 7:13426. PMCID: PMC5116091.

Engel, I., Seumois, G., Chavez, L., Chawla, A., Castruita, D.S., White, B., Mock, D., Vijayanand, P*., Kronenberg, M*. (*joint senior authors) (2016). Innate-like functions of natural killer T cell subsets result from highly divergent gene programs. Nature Immunology. 17(6):728-39. PMCID: PMC4944658.

Seumois, G., Zapardiel-Gonzalo, J., White, B., Singh, D., Schulten, V., Dillon, M., Hinz, D., Broide, D.H, Sette, A., Peters, B., Vijayanand, P (2016). Transcriptional profiling of Th2 cells identifies pathogenic features associated with asthma. Journal of Immunology. PMCID: PMC4936908

Grants

NIH/NIAID, R01AI121426
Epigenome-wide association study of childhood asthma
Objective: Investigate the epigenetic basis of childhood asthma.
Role: Contact PI (P. Vijayanand)

NIH/NHLBI, R01HL114093
Epigenetics of severe asthma
Objective: To identify molecules that drive the pathogenesis of severe asthma.
Role: Contact PI (P. Vijayanand)

NIH/NHLBI, UG1HL139117
San Diego Team Asthma Management using Phenotypes (STAMP)
Objective: To develop personalized therapies for patients with severe asthma
Role: Multiple PI (P.Vijayanand, P. Akuthota, S. Jain)

NIH/NIAID U19AI135731
LJI Epitope Validation Center: Characterization of epitope-specific T cells responding to food, fungal and inner city allergens
Objective: Molecular characterization of fungal-allergen-epitope specific T cells in asthma.
Role: PI of Project 3

GENETICS OF HUMAN DISEASES (https://www.dice-database.org)

Selected References

Selected References

Benjamin J. Schmiedel, D. S., Ariel Madrigal, Alan G. Valdovino-Gonzalez, Brandie M. White, Jose Zapardiel-Gonzalo, Brendan Ha, Gokmen Altay, Jason A. Greenbaum, Graham McVicker, Grégory Seumois, Anjana Rao, Mitchell Kronenberg, Bjoern Peters, Vijayanand P. Impact of genetic polymorphisms on human immune cell gene expression. 2018 CELL (in press)

Schmiedel BJ, Seumois G, Samaniego-Castruita D, Cayford J, Schulten V, Chavez L, Ay F, Sette A, Peters B, Vijayanand P. (2016). 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells. Nature Communications. 7:13426. PMCID: PMC5116091.

Grants

NIH/NIAID, R24AI108564
Research resources: epigenomic and transcriptomic profiles of human immune

CANCER IMMUNOLOGY, TISSUE RESIDENT MEMORY T CELLS, CYTOTOXIC CD4 T CELLS

Selected References

Selected References

Ganesan AP, Clarke J, Wood O, Garrido-Martin E, Chee S, Mellows T, Samaniego-Castruita D, Singh D, Seumois G, Alzetani A, Woo E, Friedmann PS, King E, Thomas GJ, Sanchez-Elsner T, Vijayanand, P* & Ottensmeier, C. (*corresponding author) (2017). Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer. Nature Immunology. 18 (8):940-950. PMID: 28628092

Patil V, Madrigal A, Schmiedel B, Clarke J, O’Rourke P, Silva A, Harris E, Peters B, Seumois G, Weiskopf D, Sette A, Vijayanand P. Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis. Science Immunology. 2018 Jan 19; 3(19): eaan8664 PMID: 29352091

Cancer Research UK Network Accelerator Award

Molecular analysis of the success determinants and mechanisms of solid tumour immunotherapy