Sivasankaran M Ponnan

Dedicated Clinical Immunologist and Flow Cytometry Specialist with 13 years of expertise, driving high-dimensional (46-color spectral) flow cytometry, cell sorting, and instrument optimization in GCLP-compliant settings. Proven ability in immune assay development and validation, supporting cutting-edge immunotherapy (CAR T, Treg), vaccine, infectious disease, and autoimmune research. Proficient in advanced imaging flow and dedicated to regulatory excellence (RAPS Certified), with ASCP SCYM certification in progress.

Lupus Research Alliance: 

2024 / Co-Investigator 

Topic: Correlative Biomarkers in the REACT-01 Pediatric Lupus CD19 CAR Trial. 

Department of Health Research-Indian Council of Medical Research: 

2015 / Principal Investigator 

Topic: Mucosal immune responses among HIV discordant couples. 

International AIDS Vaccine Initiative (IAVI) and United States Agency for International Development (USAID):    

2014 / Co-Investigator 

Topic: Analysis of protective humoral and cell-mediated immunity in HIV-1-vaccinated individuals from the IAVI-Phase I clinical trial.

• Affiliate member of Seattle Children's Invent postdoctoral program. (2023-Till date)
• Vaccine Ambassador-THSTI and International Vaccine Access Health Center at the Johns Hopkins Bloomberg School of Public Health. (2020)
• Young Scientist Fellowship- HRD Fellowship– ICMR - Govt. of India (2015-2019).
• Student membership Award - International Society of Advancement in Cytometry (ISAC)
• Summer Training Fellowships at Serum Institute of India, Pune-(2009)
• Undergraduate - University 3rd Rank- University of Madras-(2007)

• CAR T-Cell Therapy in Lupus: Hope for a Cure, Science Insights Day, 10/02/24, Seattle Children’s Hospitals
• Basics and advancement in flow cytometry, Chettinad Medical College and Hospital, 2022
• GCLP training, Division of AIDS, National Institute of Health, USA
• Vaccinology course, Institut Pasteur, Paris, France, 2018
• Viral Inhibition Assay Training, Imperial College of London, London, 2017

• Basics of Flow Cytometry, 11/02/17
• Polychromatic Flow Cytometry and Cell Sorting, 09/10/18
• IAVI-Viral Inhibition Assay training and workshop, 04/23/18

• Directed Flow Cytometry Core Facility (IISc): Spearheaded operations as Senior Research Scientist, supervising 3 technicians. Managed QC, optimized cell sorting, maintenance, user training, calibration protocols, and experimental design consultation, ensuring high data quality standards.
• Led Clinical Immunology Team (Fred Hutch): Progressed to Staff Scientist, directing 15 technicians as lead T cell immunologist for HVTN trials. Drove endpoint analysis/reporting of T-cell responses for vaccine efficacy, implemented standardized assays, and ensured regulatory compliance.
• Pioneered 46-Color SLE CAR-T Biomarker Panel: Developed a novel spectral flow panel for the REACT01 trial, enabling simultaneous detection of autoreactive B/T cells and analysis of immune dysregulation. Collaborated with BD Biosciences and Seattle Children’s Correlative Science Lab.

Invited lightning talk: CAR T-Cell Therapy in Lupus: Hope for a Cure- the importance of 46 colors spectral panel for the endpoints. “Science Insights Day” Oct 2, 2024. Settle Children’s Hospitals.

 Invited Talk: Basics and advancement in flow cytometry, Chettinad Medical College and Hospital, Chennai 2022.

Poster Presentation: Optimizing the 46-color full spectrum deep immunophenotyping flow cytometry panel for childhood-onset Systemic Lupus Erythematosus (cSLE) REACT-01 Phase 1 anti-CD19 CAR T clinical trial. “Science Insights Day” Oct 2, 2024. Settle Children’s Hospitals.

Poster Presentation: Induction and maintenance of T memory stem cells (Tscm) by a subtype c prophylactic vaccine in a phase I trial, India. International Vaccine Conference, Conducted by ICGEB, New Delhi. (2017),

1. Sivasankaran.M.P, Kannan T, Hemalatha B, Sujitha K, Luke E H. Role of stem cell like memory T cells (TSCM) and memory T cell subsets in the host immune response to HIV. BMC Infectious Diseases, 2019 (Suppl1):324. [original work].

2. Muthuraman M, Manikannan M, Krupakar P, Sivasankarn.M.P, Luke E H. Effects of marine extracts on augmenting cytokine production and its anti-tumor activity. BMC Infectious Diseases, 2019 (Suppl 1):324. [original work].

3. Swathirajan, C.R., Nandagopal, P., Vignesh, R, Sivasankaran, M.P. and Singla, N. Association of Circulatory Tfh-like Cells with Neutralizing Antibody Responses among Chronic HIV-1 Subtype C Infected LTNP and Progressors. AIDS Research and Human Retroviruses, 2018, Vol. 34, pp. 117-117. [original work]

2025:

1. Munusamy Ponnan S, Stephanie Rhea, Sowmya Pattabhi, and Shaun W Jackson. Optimizing the 46-color full spectrum deep immunophenotyping flow cytometry panel for childhood-onset Systemic Lupus Erythematosus (cSLE) REACT-01 Phase 1 anti-CD19 CAR T clinical trial. (In Preparation)

2. Munusamy Ponnan S, Sebastien Lewis, Stephanie Rhea, David J. Rawlings, Eric J. Allenspach, and Shaun W Jackson. Enrichment and Dysregulation of Autoreactive B and T cells drive the immunopathogenesis of STAT1 Gain-of-Function (GOF) Syndrome. (In Preparation)

3. Munusamy Ponnan S, Shaun W Jackson. Review on Mechanisms of B cell Tolerance in Health and Autoimmunity. Arthritis and Rheumatology (In Press)

4. Munusamy Ponnan S, Sakthivel Govindaraj, Vijayakumar Velu. Role of follicular homing natural killer cells in HIV infection. Current Opin HIV AIDS. 2025 Mar 1;20(2):154-158.

5. Christopher D. Thouvenel, Chris Tipton, Yasuhiro Yamazaki, Munusamy Ponnan S, et al., Hypomorphic RAG2 deficiency promotes selection of self-reactive B cells. Journal of Clinical Immunology, 2025 Jan 15;45(1):66

2024:

6. Selvavinayagam ST, Suvaithenamudhan S, Yong YK, Hemashree K, Rajeshkumar M, Kumaresan A, Arthydevi P, Kannan M, Gopalan N, Vignesh R, Murugesan A, Sivasankaran MP, et al., Genomic surveillance of omicron B.1.1.529 SARS-CoV-2 and its variants between December 2021 and March 2023 in Tamil Nadu, India-A state-wide prospective longitudinal study. J Med Virol. 2024 Feb;96(2):e29456. doi: 10.1002/jmv.29456. PMID: 38329187.

2023:

7. Selvavinayagam ST, Aswathy B, Yong YK, Frederick A, Murali L, Kalaivani V, Karishma SJ, Rajeshkumar M, Anusree A, Kannan M, Gopalan N, Vignesh R, Murugesan A, Tan HY, Zhang Y, Chandramathi S, Sivasankaran MP, et al., Plasma CXCL8 and MCP-1 as surrogate plasma biomarkers of latent tuberculosis infection among household contacts-A cross-sectional study. PLOS Glob Public Health. 2023 Nov 22;3(11):e0002327. doi: 10.1371/journal.pgph.0002327. PMID: 37992019.

8. Svensson Akusjärvi, Sara; Krishnan, Shuba; Ambikan, Anoop T.; Mikaeloff, Flora; Munusamy Ponnan, Sivasankaran, et al., Role of myeloid cells in system-level immunometabolic dysregulation during prolonged successful HIV-1 treatment. AIDS. 2023 Feb 9. doi: 10.1097/QAD.0000000000003512. Epub ahead of print. PMID: 36779490.

2022:

9. Ambikan AT, Yang H, Krishnan S, Svensson Akusjärvi S, Gupta S, Lourda M, Sperk M, Arif M, Zhang C, Nordqvist H, Ponnan SM, et al., Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity. Cell Syst. 2022 Jul 8: S2405-4712(22)00276-9. doi: 10.1016/j.cels.2022.06.006. Epub ahead of print. PMID: 35933992; PMCID: PMC9263811.

10. Svensson Akusjärvi S, Ambikan AT, Mikaeloff F, Ponnan SM et al., Monocyte driven system-level inflammatory and immunometabolic dysregulation during prolonged successful HIV-1 treatment. Research Square; 2022. DOI: 10.21203/rs.3.rs-1574216/v1.

2021:

11. Krishnan S, Nordqvist H, Ambikan AT, Gupta S, Sperk M, Svensson-Akusjärvi S, Mikaeloff F, Benfeitas R, Saccon E, Ponnan SM, et al., Metabolic Perturbation Associated With COVID-19 Disease Severity and SARS-CoV-2 Replication. Mol Cell Proteomics. 2021; 20:100159. doi: 10.1016/j.mcpro.2021.100159. Epub 2021 Oct 5. PMID: 34619366; PMCID: PMC8490130.

12. Sperk M, Mikaeloff F, Svensson-Akusjärvi S, Krishnan S, Ponnan SM, et al. Distinct lipid profile, low-level inflammation, and increased antioxidant defense signature in HIV-1 elite control status. iScience. 2021 Jan 28;24(2):102111. doi: 10.1016/j.isci.2021.102111. PMID: 33659876; PMCID: PMC7892918. [original work]

13. Ponnan SM, Vidyavijayan KK, et al., Role of Circulating T Follicular Helper Cells and Stem-Like Memory CD4+ T Cells in the Pathogenesis of HIV-2 Infection and Disease Progression. Front Immunol. 2021Apr 16; 12:666388. doi: 10.3389/fimmu.2021.666388. PMID: 33936106; PMCID: PMC8085399. [original work]

14. Munusamy Ponnan S, Thiruvengadam K, et al., Elevated Numbers of HIV-Specific Poly-Functional CD8+ T Cells with Stem Cell-Like and Follicular Homing Phenotypes in HIV-Exposed Seronegative Individuals. Front Immunol. 2021 Mar 15; 12:638144. doi: 10.3389/fimmu.2021.638144. PMID: 33889151; PMCID: PMC8056154. [original work]

15. Munusamy Ponnan S, Thiruvengadam K, et al., Deciphering the Role of Mucosal Immune Responses and the Cervicovaginal Microbiome in Resistance to HIV Infection in HIV-Exposed Seronegative (HESN) Women. Microbiol Spectr. 2021 Oct 31;9(2):e0047021. doi: 10.1128/Spectrum.00470-21. Epub 2021 Oct 27. PMID: 34704803; PMCID: PMC8549735. [original work]

2020:

16. Munusamy Ponnan S, Hayes P, et al., Evaluation of antiviral T cell responses and TSCM cells in volunteers enrolled in a phase I HIV-1 subtype C prophylactic vaccine trial in India. PLoS One. 2020Feb 25;15(2): e0229461. doi: 10.1371/journal.pone.0229461. PMID: 32097435; PMCID: PMC7041807. [original work]

17. Kathirvel S, Mani M, Gopala Krishnan GK, Sethumadhavan A, Vijayalakshmi T, Ponnan SM, Hanna LE, Mathaiyan M. Molecular characterization of Enterococcus faecalis isolates from urinary tract infection and interaction between Enterococcus faecalis encountered Dendritic and Natural Killer cells. Microb Pathog. 2020Mar; 140:103944. doi: 10.1016/j.micpath.2019.103944. Epub 2019 Dec 23. PMID: 31877329. [original work]

2019:

18. Swathirajan CR, Nandagopal P, et al., Association of circulatory Tfh-like cells with neutralizing antibody responses among chronic HIV-1 subtype C infected long-term nonprogressors and progressors. Pathog Dis. 2019 Jun 1;77(4): ftz044. doi: 10.1093/femspd/ftz044. PMID: 31505637. [original work]

19. Munusamy Ponnan S, Pattabiram S, et al.,Induction and maintenance of bi-functional (IFN-γ + IL-2+ and IL-2+ TNF-α+) T cell responses by DNA prime MVA boosted subtype C prophylactic vaccine tested in a Phase I trial in India. PLoS One. 2019 Mar 28;14(3):e0213911. doi: 10.1371/journal.pone.0213911. PMID: 30921340; PMCID: PMC6438518. [original work]

2018:

20. Munusamy Ponnan S, Swaminathan S, et al., Induction of circulating T follicular helper cells and regulatory T cells correlating with HIV-1 gp120 variable loop antibodies by a subtype C prophylactic vaccine tested in a Phase I trial in India. PLoS One. 2018Aug 29;13(8):e0203037. doi: 10.1371/journal.pone.0203037. [original work]

2013:

21. Sivasankaran M P, K Sujitha, Asgar Ali, Detection of resistance determinants by molecular analysis among the quinolone resistant Salmonella enterica serovar Typhi isolates from Kanchipuram. International Journal of Medical Research” (IJMR) Jan 2013: 1(2):8-1.

22. Asgar Ali, Sujitha K, Devika T, Sivasankaran M P, Balan K, Praveen Kumar G S, Saleem M, Joseph P Innocent, Vijayalakshmi TS, A Study on Paederus Dermatitis Outbreak in a Suburban Teaching Research Hospital, Kanchipuram, India. Medicine Science 2013;2(3):764-9.

1. Lee Sunho , Lee Jueun , Lyoo Kwang-Soo , et al., Hwang Geum-Sook Unraveling metabolic signatures in SARS-CoV-2 variant infections using multiomics analysis. Front Immunol. 2024,15. [Invited review].

2. Zhang X, Shen J, Huang M, Li R. Efficacy and safety of adding immune checkpoint inhibitors to first-line standard therapy for recurrent or advanced cervical cancer: a phase 3 clinical trials meta-analysis. Front Immunol. 2024;15. [Invited review].

3. Chandrika Bhattacharyya,a Diganta Barman,b et al., The influence 1 of maternal Breast milk and Vaginal microbiome on Neonatal gut microbiome succession: A longitudinal study over/through for the first year of birth. Microbial Spectrum. Feb 2023. [Invited review-In Press].

4. Pulvirenti F, Garzi G, Milito C, et al., SARS-CoV-2 pre-exposure prophylaxis with tixagevimab/cilgavimab (AZD7442) provides protection in inborn errors of immunity with antibody defects: a real-world experience. Front Immunol. 2023, 26.[Invited review].

5. Kurmyshkina OV, Dobrynin PV, Kovchur PI, Volkova TO. Sequencing-based transcriptome analysis reveals diversification of immune response- and angiogenesis-related expression patterns of early-stage cervical carcinoma as compared with high-grade CIN. Front Immunol. 2023 Sep 4; 14:1215607. [Invited review].

6. Lucile DUMOLARD, CAROLINE ASPORD, et al., Immune checkpoints on T and NK cells in the context of HBV infection: landscape, pathophysiology, and therapeutic exploitation. Front Immunol. 2023. [Invited review].

7. Alan Messala A. Britto, Juliana D. Siqueira, et al., Microbiome analysis of Brazilian women’s cervix reveals specific bacterial abundance correlation to RIG-like receptor gene expression. Front Immunol. 2023. [Invited review].

8. Wang Y, Guan Y, Hu Y, Li Y, Lu N, Zhang C. Murine CXCR3+CXCR6+γδT Cells Reside in the Liver and Provide Protection Against HBV Infection. Front Immunol. 2022 Jan 21; 12:757379. doi: 10.3389/fimmu.2021.757379. [Invited review].

9. Gilbert C, Lefeuvre C, et al.,Age-Related Expression of IFN-λ1 Versus IFN-I and Beta-Defensins in the Nasopharynx of SARS-CoV-2-Infected Individuals. Front Immunol. 2021 Nov 10; 12:750279. doi: 10.3389/fimmu.2021.750279. [Invited review].

10. de Armas LR, Gavegnano C et al., The Effect of JAK1/2 Inhibitors on HIV Reservoir Using Primary Lymphoid Cell Model of HIV Latency. Front Immunol. 2021Aug 31; 12:720697. doi: 10.3389/fimmu.2021.720697. [Invited review].

11. Okoye I, Xu L, Oyegbami O, et al., Plasma Extracellular Vesicles Enhance HIV-1 Infection of Activated CD4+ T Cells and Promote the Activation of Latently Infected J-Lat10.6 Cells via miR-139-5p Transfer. Front Immunol. 2021Jun 24; 12:697604. doi: 10.3389/fimmu.2021.697604. [Invited review].