Biology subjects

Santharam, M. A.

Publications and source records attributed to Santharam, M. A..

3 recordsLinked to original sources

bioRxiv2020

Cytokine priming of naive CD8+ T lymphocytes modulates chromatin accessibility that partially overlaps with changes induced by antigen simulation

BackgroundNaive CD8+ T lymphocytes undergo antigen non-specific proliferation following exposure to certain synergistic combination of inflammatory (IL-6, IL-21) and homeostatic (IL-7, IL-15) cytokines. Such cytokine-stimulated naive CD8+ T cells display increased T cell antigen receptor (TCR) sensitivity, allowing them to respond to limiting concentrations of cognate antigenic peptides and altered peptide ligands of lower affinity towards the TCR. The purpose of this study is to gain insight into the molecular mechanisms of such cytokine priming. MethodsNaive CD8+ T lymphocytes expressing the PMEL-1 transgenic TCR were stimulated with IL-15 and IL-21, and chromatin accessibility was assessed using the assay for transposase-accessible chromatin (ATAC) sequencing. Cells stimulated by the cognate antigenic peptide mgp10025-33 were used as controls. ResultsCompared to naive cells, cytokine-primed cells showed 212 opening and 484 closing peaks, whereas antigen-stimulated cells showed 12087 opening and 6982 closing peaks. However, a significant fraction of the opening (33%) and closing (63%) peaks of cytokine-primed cells overlapped with those of the antigenic stimulated cells. Chromatin accessibility peaks modulated in cytokine-primed cells were strongly represented in gene ontology pathways for T cell signaling, activation, regulation and effector functions. Many of the transcription factor binding motifs located close to the opening and closing peaks of cytokine-primed cells also occurred in antigen-stimulated cells. ConclusionsOur data suggest that by modulating the gene expression programs involved in TCR signaling, cytokine priming induces a poised state that lowers the TCR signaling threshold in naive CD8+ T cells and increases their antigen responsiveness.

immunology↗

bioRxiv2020

SILAC proteomics implicates the ubiquitin conjugating enzyme UBE2D in SOCS1-mediated downmodulation of the MET receptor in hepatocytes

Suppressor of Cytokine Signaling 1 (SOCS1) functions as a tumor suppressor in hepatocellular carcinoma (HCC) and many other types of cancers. SOCS1 mediates its functions by inhibiting tyrosine kinases, promoting ubiquitination and proteasomal degradation of signal transducing proteins, and by modulating transcription factors. Here, we studied the impact of SOCS1 on the hepatocyte proteome using Stable Isotopic Labelling of Amino acids in Cell culture (SILAC)-based mass spectrometry on the Hepa1-6 murine HCC cell line stably expressing wildtype SOCS1 or a mutant SOCS1 with impaired SH2 domain. As SOCS1 regulates the hepatocyte growth factor (HGF) receptor MET, the SILAC-labelled cells were stimulated or not with HGF. Following mass spectrometry analysis, differentially modulated proteins were identified, quantified and analyzed for pathway enrichment. Of the 3440 proteins identified in Hepa-SOCS1 cells at steady state, 181 proteins were significantly modulated compared to control cells. The SH2 domain mutation and HGF increased the number of differentially modulated proteins. Protein interaction network analysis revealed enrichment of SOCS1-modulated proteins within multiprotein complexes such as ubiquitin conjugating enzymes, proteasome, mRNA spliceosome, mRNA exosome and mitochondrial ribosome. These findings suggest that SOCS1, induced by cytokines, growth factors and diverse other stimuli, may dynamically modulate of large macromolecular regulatory complexes to help maintain cellular homeostasis. Notably, the expression of UBE2D ubiquitin conjugating enzyme, which is implicated in the control of growth factor receptor tyrosine kinase signaling, was found to be regulated by SOCS1.

molecular biology↗

bioRxiv2020

Prognostic significance of SOCS1 and SOCS3 tumor suppressors in hepatocellular carcinoma and its correlation to key oncogenic signaling pathways

Suppressor of cytokine signaling (SOCS) proteins SOCS1 and SOCS3 are considered tumor suppressors in liver hepatocellular carcinoma (LIHC). To gain insight into the underlying molecular mechanisms, the expression of SOCS1/ SOCS3 was evaluated in The Cancer Genome Atlas LIHC dataset along with key oncogenic signaling pathway genes. SOCS1 expression was not significantly reduced in HCC yet higher expression predicted favorable prognosis, whereas SOCS3 lacked predictive potential despite lower expression. Only a small proportion of the cell cycle, receptor tyrosine kinase, growth factor and RAS-RAF-MEK-MAPK signaling genes negatively correlated with SOCS1 or SOCS3, of which even fewer showed elevated expression in HCC and predicted survival. However, many PI3K-AKT-MTOR pathway genes showed mutual exclusivity with SOCS1/SOCS3 and displayed independent predictive ability. Among genes that negatively correlated with SOCS1/SOCS3, CDK2, MLST8, AURKA, MAP3K4 and RPTOR showed corresponding modulations in the livers of mice lacking Socs1 or Socs3 during liver regeneration and in experimental HCC, and in Hepa1-6 murine HCC cells overexpressing SOCS1/SOCS3. However, Cox proportional hazards model identified CXCL8, DAB2 and PIK3R1 as highly predictive in combination with SOCS1 or SOCS3. These data suggest that developing prognostic biomarkers and precision treatment strategies based on SOCS1/SOCS3 expression need careful testing in different patient cohorts.

cancer biology↗