Siva Kasinathan, MD, PhD

Instructor

Pediatric Rheumatology

Mary L. Johnson Specialty Services

Pediatric Rheumatology

730 Welch Road

Palo Alto, CA 94304

Maps, Directions & Parking

Phone: (650) 723-3877

Fax: (650) 736-4344

Locations

Mary L. Johnson Specialty Services

Pediatric Rheumatology

730 Welch Road

Palo Alto, CA 94304

Maps, Directions & Parking

Phone : (650) 723-3877 723-3877)

Fax : (650) 736-4344

Services

Rheumatology

Work and Education

Professional Education

University of Washington School of Medicine, Seattle, WA, 06/14/2019

Residency

Stanford University Pediatric Residency at Lucile Packard Children's Hospital, Palo Alto, CA, 06/24/2022

Fellowship

Stanford University Pediatric Rheumatology Fellowship, Stanford, CA, 07/06/2025

Board Certifications

Pediatrics, American Board of Pediatrics, 2022

Publications

Synthetic transcription factors designed by domain recombination enhance CAR T cell antitumor function. _Cell_Takacsi-Nagy, O., Kasinathan, S., Hartman, A., Yin, Y., Wu, L., Chen, A. Y., Moser, L. M., May, A. P., Reeder, G. C., Celallos Fuentes, E., Kernick, C., Lu, J., McClellan, A. K., Raposo, C. J., Terrall, B., Theberath, N. E., Yan, P. K., Xu, P., Sotillo, E., Eyquem, J., Mackall, C. L., Roth, T. L., Satpathy, A. T.2026

Abstract

Human protein-coding genes evolved via rearrangement of domains from ancestral genes. We develop a scalable, evolutionarily guided method to assemble novel genes from constituent domains within a protein family, termed DESynR (domain engineered via synthesis and recombination) genes. In primary human T cells, DESynR activator protein-1 (AP-1) transcription factors (TFs) significantly outperform natural AP-1 TFs across in vitro and in vivo antitumor assays. DESynR AP-1 TFs induce broad transcriptional and epigenetic reprogramming and establish non-natural T cell states that optimize features of exhaustion, effector and cytotoxic function, and persistence-sometimes co-opting gene modules from disparate cell types. Reprogramming is primarily driven by differential regulation of established AP-1-bound regulatory elements rather than unique binding. Finally, we screen DESynR erythroblast transformation-specific (ETS) and forkhead box (FOX) TFs to support generalizability across protein families. Overall, we demonstrate that reconfiguring existing protein domains may uncover non-evolved genes that program therapeutically relevant cell states.

View details for DOI 10.1016/j.cell.2026.07.054

View details for PubMedID 42617595

DNASE1L3 Deficiency With Novel Missense Variant: Enzymatic and Plasma Fragmentomic Evidence of Pathogenicity and Partial Response to JAK Blockade _ACR OPEN RHEUMATOLOGY_Tenorio, A., Sugio, T., Cheng, J., Bonner, D. E., Esfahani, M., Kasinathan, S., Hsu, J. J., Moyer, A., Vera, L., Carter, J., Reuter, C. M., Marwaha, S., Balboni, I., Wheeler, M. T., Bernstein, J. A., Alizadeh, A., Gomez-Ospina, N.2026; 8 (2)

View details for DOI 10.1002/acr2.70184

View details for Web of Science ID 001697626100001

FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry. _Immunity_Umhoefer, J. M., Arce, M. M., Kasinathan, S., Whalen, S., Dajani, R., Subramanya, S., Goudy, L., Belk, J. A., Zhou, R., Pham, M. T., Zhang, W., Hernandez, R., Tran, C., Kirthivasan, N., Freimer, J. W., Mowery, C. T., Nguyen, V., Ota, M., Gowen, B. G., Simeonov, D. R., Curie, G. L., Li, Z., Chen, A. Y., Corn, J. E., Chang, H. Y., Tang, Q., Gilbert, L. A., Satpathy, A. T., Pollard, K. S., Marson, A.2025

Abstract

FOXP3 is a lineage-defining transcription factor (TF) for immune-suppressive regulatory T cells (Treg cells). Although mice exclusively express FOXP3 in Treg cells, stimulated conventional CD4+ T cells (Tconv cells) also transiently express FOXP3 in humans. Mechanisms governing these distinct expression patterns need elucidation. Here, we performed CRISPR screens tiling the FOXP3 locus and targeting TFs in human Treg and Tconv cells to identify cis-regulatory elements (CREs) and trans-regulators of FOXP3. Tconv cell FOXP3 expression depended on a subset of Treg cell CREs, as well as Tconv-cell-selective positive (NS+) and negative (NS-) CREs. Combinatorial silencing of Tconv cell CREs revealed their epistatic logic. These CREs are occupied and regulated by TFs that we identified as FOXP3 regulators. Finally, mutagenesis of murine NS- CRE revealed its essentiality for restricting FOXP3 expression to Treg cells. We map CRE and TF circuitry to reveal distinct cell- and species-specific regulation of FOXP3 expression.

View details for DOI 10.1016/j.immuni.2025.10.020

View details for PubMedID 41237776

Central control of dynamic gene circuits governs T cell rest and activation. _Nature_Arce, M. M., Umhoefer, J. M., Arang, N., Kasinathan, S., Freimer, J. W., Steinhart, Z., Shen, H., Pham, M. T., Ota, M., Wadhera, A., Dajani, R., Dorovskyi, D., Chen, Y. Y., Liu, Q., Zhou, Y., Swaney, D. L., Obernier, K., Shy, B. R., Carnevale, J., Satpathy, A. T., Krogan, N. J., Pritchard, J. K., Marson, A.2024

Abstract

The ability of cells to maintain distinct identities and respond to transient environmental signals requires tightly controlled regulation of gene networks1-3. These dynamic regulatory circuits that respond to extracellular cues in primary human cells remain poorly defined. The need for context-dependent regulation is prominent in T cells, where distinct lineages must respond to diverse signals to mount effective immune responses and maintain homeostasis4-8. Here we performed CRISPR screens in multiple primary human CD4+ T cell contexts to identify regulators that control expression of IL-2Rα, a canonical marker of T cell activation transiently expressed by pro-inflammatory effector T cells and constitutively expressed by anti-inflammatory regulatory T cells where it is required for fitness9-11. Approximately 90% of identified regulators of IL-2Rα had effects that varied across cell types and/or stimulation states, including a subset that even had opposite effects across conditions. Using single-cell transcriptomics after pooled perturbation of context-specific screen hits, we characterized specific factors as regulators of overall rest or activation and constructed state-specific regulatory networks. MED12 - a component of the Mediator complex - serves as a dynamic orchestrator of key regulators, controlling expression of distinct sets of regulators in different T cell contexts. Immunoprecipitation-mass spectrometry revealed that MED12 interacts with the histone methylating COMPASS complex. MED12 was required for histone methylation and expression of genes encoding key context-specific regulators, including the rest maintenance factor KLF2 and the versatile regulator MYC. CRISPR ablation of MED12 blunted the cell-state transitions between rest and activation and protected from activation-induced cell death. Overall, this work leverages CRISPR screens performed across conditions to define dynamic gene circuits required to establish resting and activated T cell states.

View details for DOI 10.1038/s41586-024-08314-y

View details for PubMedID 39663454

Transposition enables low-input single-molecule concurrent genomics and epigenomics _NATURE GENETICS_Kasinathan, S., Ramani, V.2024

View details for DOI 10.1038/s41588-024-01753-3

View details for Web of Science ID 001230115600002

View details for PubMedID 38783121

View details for PubMedCentralID 7735760

Direct transposition of native DNA for sensitive multimodal single-molecule sequencing. _Nature genetics_Nanda, A. S., Wu, K., Irkliyenko, I., Woo, B., Ostrowski, M. S., Clugston, A. S., Sayles, L. C., Xu, L., Satpathy, A. T., Nguyen, H. G., Alejandro Sweet-Cordero, E., Goodarzi, H., Kasinathan, S., Ramani, V.2024

Abstract

Concurrent readout of sequence and base modifications from long unamplified DNA templates by Pacific Biosciences of California (PacBio) single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules. We developed two methods that implement tagmentation and use 90-99% less input than current protocols: (1) single-molecule real-time sequencing by tagmentation (SMRT-Tag), which allows detection of genetic variation and CpG methylation; and (2) single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which uses exogenous adenine methylation to add a third channel for probing chromatin accessibility. SMRT-Tag of 40 ng or more human DNA (approximately 7,000 cell equivalents) yielded data comparable to gold standard whole-genome and bisulfite sequencing. SAMOSA-Tag of 30,000-50,000 nuclei resolved single-fiber chromatin structure, CTCF binding and DNA methylation in patient-derived prostate cancer xenografts and uncovered metastasis-associated global epigenome disorganization. Tagmentation thus promises to enable sensitive, scalable and multimodal single-molecule genomics for diverse basic and clinical applications.

View details for DOI 10.1038/s41588-024-01748-0

View details for PubMedID 38724748

View details for PubMedCentralID 7877196

Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler. _Nature structural & molecular biology_Abdulhay, N. J., Hsieh, L. J., McNally, C. P., Ostrowski, M. S., Moore, C. M., Ketavarapu, M., Kasinathan, S., Nanda, A. S., Wu, K., Chio, U. S., Zhou, Z., Goodarzi, H., Narlikar, G. J., Ramani, V.2023

Abstract

Nearly all essential nuclear processes act on DNA packaged into arrays of nucleosomes. However, our understanding of how these processes (for example, DNA replication, RNA transcription, chromatin extrusion and nucleosome remodeling) occur on individual chromatin arrays remains unresolved. Here, to address this deficit, we present SAMOSA-ChAAT: a massively multiplex single-molecule footprinting approach to map the primary structure of individual, reconstituted chromatin templates subject to virtually any chromatin-associated reaction. We apply this method to distinguish between competing models for chromatin remodeling by the essential imitation switch (ISWI) ATPase SNF2h: nucleosome-density-dependent spacing versus fixed-linker-length nucleosome clamping. First, we perform in vivo single-molecule nucleosome footprinting in murine embryonic stem cells, to discover that ISWI-catalyzed nucleosome spacing correlates with the underlying nucleosome density of specific epigenomic domains. To establish causality, we apply SAMOSA-ChAAT to quantify the activities of ISWI ATPase SNF2h and its parent complex ACF on reconstituted nucleosomal arrays of varying nucleosome density, at single-molecule resolution. We demonstrate that ISWI remodelers operate as density-dependent, length-sensing nucleosome sliders, whose ability to program DNA accessibility is dictated by single-molecule nucleosome density. We propose that the long-observed, context-specific regulatory effects of ISWI complexes can be explained in part by the sensing of nucleosome density within epigenomic domains. More generally, our approach promises molecule-precise views of the essential processes that shape nuclear physiology.

View details for DOI 10.1038/s41594-023-01093-6

View details for PubMedID 37696956

View details for PubMedCentralID 3647478

The glucose-sensing transcription factor MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis. _PLoS biology_Carroll, P. A., Freie, B. W., Cheng, P. F., Kasinathan, S., Gu, H., Hedrich, T., Dowdle, J. A., Venkataramani, V., Ramani, V., Wu, X., Raftery, D., Shendure, J., Ayer, D. E., Muller, C. H., Eisenman, R. N.2021; 19 (10): e3001085

Abstract

Male germ cell (GC) production is a metabolically driven and apoptosis-prone process. Here, we show that the glucose-sensing transcription factor (TF) MAX-Like protein X (MLX) and its binding partner MondoA are both required for male fertility in the mouse, as well as survival of human tumor cells derived from the male germ line. Loss of Mlx results in altered metabolism as well as activation of multiple stress pathways and GC apoptosis in the testes. This is concomitant with dysregulation of the expression of male-specific GC transcripts and proteins. Our genomic and functional analyses identify loci directly bound by MLX involved in these processes, including metabolic targets, obligate components of male-specific GC development, and apoptotic effectors. These in vivo and in vitro studies implicate MLX and other members of the proximal MYC network, such as MNT, in regulation of metabolism and differentiation, as well as in suppression of intrinsic and extrinsic death signaling pathways in both spermatogenesis and male germ cell tumors (MGCTs).

View details for DOI 10.1371/journal.pbio.3001085

View details for PubMedID 34669700

Massively multiplex single-molecule oligonucleosome footprinting. _eLife_Abdulhay, N. J., McNally, C. P., Hsieh, L. J., Kasinathan, S., Keith, A., Estes, L. S., Karimzadeh, M., Underwood, J. G., Goodarzi, H., Narlikar, G. J., Ramani, V.2020; 9

Abstract

Our understanding of the beads-on-a-string arrangement of nucleosomes has been built largely on high-resolution sequence-agnostic imaging methods and sequence-resolved bulk biochemical techniques. To bridge the divide between these approaches, we present the single-molecule adenine methylated oligonucleosome sequencing assay (SAMOSA). SAMOSA is a high-throughput single-molecule sequencing method that combines adenine methyltransferase footprinting and single-molecule real-time DNA sequencing to natively and nondestructively measure nucleosome positions on individual chromatin fibres. SAMOSA data allows unbiased classification of single-molecular 'states' of nucleosome occupancy on individual chromatin fibres. We leverage this to estimate nucleosome regularity and spacing on single chromatin fibres genome-wide, at predicted transcription factor binding motifs, and across both active and silent human epigenomic domains. Our analyses suggest that chromatin is comprised of a diverse array of both regular and irregular single-molecular oligonucleosome patterns that differ subtly in their relative abundance across epigenomic domains. This irregularity is particularly striking in constitutive heterochromatin, which has typically been viewed as a conformationally static entity. Our proof-of-concept study provides a powerful new methodology for studying nucleosome organization at a previously intractable resolution, and offers up new avenues for modeling and visualizing higher-order chromatin structure.

View details for DOI 10.7554/eLife.59404

View details for PubMedID 33263279

Non-B-Form DNA Is Enriched at Centromeres. _Molecular biology and evolution_Kasinathan, S. n., Henikoff, S. n.2018; 35 (4): 949–62

Abstract

Animal and plant centromeres are embedded in repetitive "satellite" DNA, but are thought to be epigenetically specified. To define genetic characteristics of centromeres, we surveyed satellite DNA from diverse eukaryotes and identified variation in <10-bp dyad symmetries predicted to adopt non-B-form conformations. Organisms lacking centromeric dyad symmetries had binding sites for sequence-specific DNA-binding proteins with DNA-bending activity. For example, human and mouse centromeres are depleted for dyad symmetries, but are enriched for non-B-form DNA and are associated with binding sites for the conserved DNA-binding protein CENP-B, which is required for artificial centromere function but is paradoxically nonessential. We also detected dyad symmetries and predicted non-B-form DNA structures at neocentromeres, which form at ectopic loci. We propose that centromeres form at non-B-form DNA because of dyad symmetries or are strengthened by sequence-specific DNA binding proteins. This may resolve the CENP-B paradox and provide a general basis for centromere specification.

View details for DOI 10.1093/molbev/msy010

View details for PubMedID 29365169

View details for PubMedCentralID PMC5889037