Vijayanand Lab

Vijayanand Lab

— Pandurangan Vijayanand, M.D. Ph.D. // Associate Professor, Division of Vaccine Discovery
William K. Bowes Distinguished Professor


A pioneering physician-scientist, Dr. Vijayanand 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. This makes it easier to obtain sufficient material for detailed genetic studies.

In a pioneering study, he applied these tools to a genome-wide study of disease-related changes in the epigenome—the layer atop the genome that controls gene activity and is altered by the environment—of immune cells isolated from patients with asthma. The first of its kind, the study provided specific markers to distinguish different disease states in asthma and paved the way for investigating the role of epigenetic mechanisms in other immune-mediated disorders and infectious diseases.

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

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

Oct 12, 2015

La Jolla Institute welcomes new faculty member

Jul 8, 2014

La Jolla Institute develops new approach to identify genes poised to respond in asthma patients

Vijayanand Lab


Clin Cancer Res

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

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

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

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

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

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

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

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

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

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.

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

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

Wood O, Woo J, Seumois G, (...) Vijayanand P*, Woelk CH, King E, Ottensmeier C.
Journal of Experimental Medicine

Control of Foxp3 stability through modulation of TET activity.

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

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

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

Arlehamn, C.L., Seumois, G., Gerasimova, A., Huang, C., Fu, Z., Yue, X., Rao, A., Sette, A., Vijayanand, P*, Peters, B*
Nature Immunology

Epigenomic analysis of primary human T cells reveals novel enhancers associated with Th2 memory differentiation and asthma susceptibility

Seumois, G, Chavez, L, Gerasimova, A, (...), Peters, B, Rao, A, Vijayanand, P*.

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

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

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

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

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

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

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

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

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, Division of Vaccine Discovery

Dr. Vijayanand was appointed an Associate Professor in the Division of Vaccine Discovery 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 Allergy and Immunology as an adjunct assistant professor in the Division of Signaling and Gene Expression.

Lab Members

Praveen Akuthota

Clinical Associate Professor

Sourya Bhattacharyya

Bioinformatics Postdoctoral Fellow

I did the masters (M.S.) and Ph.D from the department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, India. My PhD research was based on algorithms in Computational Phylogenetics, especially constructing species trees from topologically incongruent gene trees. During masters, I have worked on neonatal EEG signal and video processing for epileptic seizure detection. I joined LJI in April 2017.

Research Focus:
Developement of computational algorithms for analyzing NGS data, especially Hi-C, HiChIP, and ChIP-seq.

Career goals:
Being a computer scientist, I want to understand NGS data and genome regulation for different diseases, and work on the development of their computational models.

Howard Brickner

Visiting Scientist

Vivek Chandra


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

Anusha Preethi Ganesan


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.

Ravindra Gujar

Postdoctoral Fellow

Seka Lazare

Postdoctoral Fellow

Shu Liang

Research Technician I

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. I consider myself pretty lucky to get a chance to get into Vijay’s lab and work with cutting edge technologies.

Career Goal:
My interests lie in new technologies. My goal is to become a researcher/scientist who develop assays to serve my fellow researchers’ research purpose.

Ariel Madrigal

Research Technician II

I obtained my bachelors in genomic sciences from National Autonomous University of Mexico. This program combines different disciplines, mainly mathematics, computer sciences and biology. I joined La Jolla Institute for Allergy and Immunology in June 2016.

Research Focus:
I am involved in the analysis of transcriptomic and epigenomic data in various types of human immune cells and in different diseases.

Career goals:
My goal is to become a scientific researcher focused on the understanding of genomic regulation in different diseases.

Sreeganesh Manoharan


Sara Herrera de la Mata

Research Technician I

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 Allergy and 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.

Ryan Nelson

Visiting Scientist

Bharat Panwar

Postdoctoral Fellow

Veena Shivagouda Patil


I obtained MS in Genetics and Plant Breeding from UAS, Dharwad, India. Went to Temasek Life Sciences Laboratory (TLL), Singapore to do my Doctoral research with Dr Toshie Kai. Obtained my PhD (Biological Sciences) from SBS, NTU, Singapore in 2011. During doctoral research thesis, I worked on piRNAs in the Drosophila germline. I worked with Dr Tariq Rana (SBMRI/UCSD) for Postdoctoral research from 2011 to 2015. While I was in his lab, I worked to understand the role(s) of lncRNAs in innate immunity. In another project, I studies the role(s) of kinases in induced pluripotent stem cell (iPSC) generation. I joined Vijay’s group at LJI in 2015 to understand immunological responses in various infectious diseases such as Dengue and Tuberculosis using genomics and cell biological tools.

Daniela Samaniego

Visiting Scientist

I graduated from the National Autonomous University of Mexico in 2014, with a BS in Genomics Sciences (Integrative Biology). As part of my undergrad, I worked for 18 months in an epigenetics oriented project before joining Dr. Vijayanand’s lab in June 2015. I am currently supporting the lab by performing some computational biology tasks.

Research Focus:
I became interested in epigenetics when I worked with lncRNAs involved in the X-chromosome inactivation for my bachelor’s thesis.

Career Goals:
One of my career goals is to get a Ph.D. in Genomics/Epigenetics. I would like to research how chromatin modulation alters gene expression during early stages of differentiation using computational biology and experimental approaches.

Benjamin Schmiedel


I obtained my Diploma in Biochemistry from University in Halle-Wittenberg (Germany) in 2006. Fascinated by human immunology and translational research, I undertook my PhD in tumor immunology at the University of Tuebingen (Germany). I joined the La Jolla Institute for Allergy and Immunology (LJI) as a Postdoc in July 2012, and got appointed as Instructor in December 2016.

Research Focus:
In a pilot study, I focused on epigenetic mechanisms that modulate the expression of genes implicated in susceptibility and development of asthma, as well as the role of these genes for the function of human T cells. Subsequently, I’m managing a large-scale, genome-wide study on gene expression and epigenetic markers in various types of human immune cells, which will aid the understanding of epigenetic variations that cause the susceptibility to disease.

Career Goals:
I plan to pursue a career in scientific research focusing on the discovery of drug targets to improve the treatment options of human immunological diseases and cancer.

Greg Seumois

Core Director, Sequencing & Instructor

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.

Divya Singh

Research Technician II

I graduated from Johns Hopkins University, Baltimore with a Master’s degree in Biotechnology. I joined LJI in 2013 as a Research Technician. I am currently involved in RNA sequencing for two projects focused on transcriptome analysis of immune cells in various immunological diseases and cancer.

Career goals:
My goal is to become a scientific researcher involved in the genetic and functional studies of human diseases.

Ciro Ramirez Suastegui

Research Technician I

Alice Wang

Research Tech I

Diana Youhanna

Research Tech I

I will obtain my bachelors in human biology from U.C. San
Diego, and then I will be continuing my masters in plant genomics for the
upcoming year.

Career Goal:
My future goal is to obtain PhD and have a career in
scientific research that involves immunology.

Vijayanand Lab

Research Projects


The Vijayanand lab's main objectives in asthma research are to identify enhancers and genes associated with severe asthma and test the function of severe asthma-associated enhancers and their target genes. They have made key contributions in understanding the immunological basis of asthma, including identifying CCR4 as a key chemokine receptor that regulates recruitment of T cells to the human asthmatic airways. Thus, targeting this chemokine receptor in patients with asthma might reduce Th2 cell-driven airway inflammation; therefore, CCR4 antagonists could be an effective new therapy for asthma. This study also provides a wider proof-of-concept for using tissue explants to study immunomodulatory drugs for asthma. Additionally, we clarified the role of iNKT cells in human asthma by carefully enumerating cell numbers in airway samples from asthma and COPD patients.

Selected References

Vijayanand P, Durkin K, Hartmann G, Morjaria J, Seumois G, Staples KJ, Hall D, Bessant C, Bartholomew M, Howarth PH, Friedmann PS, Djukanovic R. (2010). Chemokine receptor 4 plays a key role in T cell recruitment into the airways of asthmatic patients. J Immunol 184, 4568-4574.

Vijayanand P, Seumois G, Pickard C, Powell RM, Angco G, Sammut D, Gadola SD, Friedmann PS, Djukanovic R. (2007). Invariant natural killer T cells in asthma and chronic obstructive pulmonary disease. New Engl J Med 356, 1410-1422.

Hinz, D., Seumois, G., Gholami, A.M., Greenbaum, J.A., Lane, J., White, B., Broide, D.H., Schulten, V., Sidney, J., Bakhru, P., Oseroff, C., Wambre, E., James, E.A., Kwok, W.W., Peters, B., Vijayanand, P., Sette, A. (2015). Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with allergen-specific modulation of immune reactivity. Clin Exp Allergy.

Schulten V, Oseroff C, Alam R, Broide D, Vijayanand P, Peters B, Sette A. (2013). The identification of potentially pathogenic and therapeutic epitopes from common human allergens. Ann Allergy Asthma Immunol, 110 (1):7-10. PMCID: PMC3547526

Genomics: Epigenomic and Transcriptomic Profiles of Human Immune Cells

Genome-wide association studies (GWAS) have yielded increasing numbers of disease-associated candidates in recent years. Our objective is to generate a resource that facilitates research into human immune-related diseases by creating a comprehensive database of cell type- and allele-specific epigenomic and transcriptomic data for the immunology community. The Vijayanand lab has developed a number of genomics (transcriptomic, single-cell and epigenomic) and immunological assays to enable research with small numbers of cells and small-volume clinical samples. These assays are aiding researchers to answer fundamental questions by analyzing rare cell populations and samples from patients whose condition or age limits the volume of blood that may be drawn.

Selected References

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 (accepted for publication).

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. Nat Immunol 15(8):777-88. PMCID:PMC4140783

Arlehamn CL, Seumois G, Gerasimova A, Huang C, Fu Z, Yue X, Rao A, Sette A, Vijayanand P*, Peters B*. (*joint senior authors) (2014). Transcriptional profile of tuberculosis antigen-specific T cells reveals novel multifunctional features. J Immunol 193(6):2931-40. PMCID:PMC4157075

Seumois G*, Vijayanand P*, Eisley CJ, Omran N, Kalinke L, North M, Ganesan AP, Simpson LJ, Hunkapiller N, Moltzahn F, Woodruff PG, Fahy JV, Erle DJ, Djukanovic R, Blelloch R, Ansel KM. (*co-first authors) (2012). An integrated nano-scale approach to profile miRNAs in limited clinical samples. Am J Clin Exp Immunol 1(2):70-89. PMCID: PMC3538381


The aim of this work, in collaboration with Bjoern Peters and Alessandro Sette, 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. The fundamental impact of this research will be greater insight into whether infection and vaccination lead to expansion or contraction of subsets already present within the individual’s T cell pool that maintain their phenotype, and/or lead to differentiation or activation of T cells into states uniquely associated with those conditions. Dr. Vijayanand’s primary project focuses on Epigenomics of DENV and MTB.

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.

Cancer Research UK Network Accelerator Award

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