Sarthak Sahoo

MHC-I downregulation is associated with immune-evasion in breast cancers with heterogeneous activation of epithelial-mesenchymal plasticity

The paper shows that in mixed E-qM breast tumors, qM cancer cells create immunosuppressive niches leading to MHC-I downregulation and immune evasion.

Cyclic Hypoxia drives Wnt5a-ROR1 stroma-tumor crosstalk promoting breast cancer growth

This study shows cyclic hypoxia promotes breast cancer growth through WNT5A-ROR1 signaling between stromal and tumor cells in a co-culture model.

A Nanomechanical Fingerprint of Centromeric Methylation Co-Localization in TNBC Chromosomal Instability

This study maps 5mC and H3K9me3 co-localization on individual chromosomes using AFM, revealing mechanical stiffness differences between cancer and non-tumorigenic cells.

Spatially Organized Tertiary Lymphoid Structures Emerge in Small Cell Lung Cancer and Associate with Improved Survival

The paper identifies spatially organized tertiary lymphoid structures in small cell lung cancer and links their presence to improved patient survival.

Hepatobiliary Progenitor-like Reprogramming in Liver Metastases

This study identifies hepatobiliary progenitor-like reprogramming in liver metastases, driven by TGF-β and hypoxia, and shows its association with poor survival.

Systems-level analysis identifies IRF6 as an inhibitor of epithelial-mesenchymal transition

The paper identifies IRF6 as an inhibitor of epithelial-mesenchymal transition (EMT) through integrated computational and experimental analysis.

Endocrine therapy-specific lineage and partial epithelial-mesenchymal reprogramming defines divergent resistant cell-states in ER+ breast cancer

This study identifies drug-specific resistance mechanisms in ER+ breast cancer by analyzing multi-omic data, revealing distinct transcriptional and chromatin states associated with SERM, SERD, and ESR1 mutant resistance.

CD4+ T-cells sensitize quasi-mesenchymal breast tumors lacking CD73 to anti-CTLA4 immune checkpoint blockade therapy

This study shows that targeting CD73 in quasi-mesenchymal breast tumors enhances their response to anti-CTLA4 therapy through CD4+ T-cell dependence.

Translation of a four-codon ORF in the 3'UTR of MAP3K10 regulates its expression

The paper identifies a conserved four-codon dORF in the 3'UTR of MAP3K10 regulated by an RNA G-quadruplex, which modulates MAP3K10 expression.

Regulatory network and spatial modeling reveal cooperative mechanisms of resistance and immune escape in ER+ breast cancer

This study models regulatory networks and spatial dynamics in ER+ breast cancer to show how resistance and immune escape co-occur and how combination therapies can counteract these mechanisms.

Multi-omics investigation reveals molecular determinants of cancer cell evolution on soft extracellular matrix

The paper investigates how cancer cells adapt to soft extracellular matrix by analyzing multi-omics data to identify molecular mechanisms underlying fitness differences.

An integrative molecular systems approach unravels mechanisms underlying biphasic nitrate uptake by plant nitrate transporter NRT1.1

The paper identifies mechanisms of NRT1.1 phosphorylation switch in plants, showing how phosphorylation and conformational changes regulate nitrate uptake modes.

Metastatic organotropism in small cell lung cancer

This study identifies key cellular programs and pathways driving metastatic organotropism in small cell lung cancer using preclinical models and multiomic profiling.

Bioenergetic reprogramming of macrophages reduces drug tolerance in Mycobacterium tuberculosis

This study shows that altering macrophage metabolism can reduce drug tolerance in Mycobacterium tuberculosis by affecting bacterial redox states.

Multi-modal transcriptomic analysis unravels enrichment of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer

The paper uses multi-modal transcriptomic data to show basal breast cancer exhibits hybrid epithelial/mesenchymal states and higher phenotypic heterogeneity compared to luminal breast cancer.

Prognostic association of immunoproteasome expression in solid tumours is governed by the immediate immune environment

The paper examines the prognostic role of immunoproteasome expression in solid tumours, finding it correlates with immune infiltration and survival outcomes, but varies by tumour type and immune context.

Dynamics of a hepatocyte-cholangiocyte decision-making gene regulatory network during liver development and regeneration

The paper identifies a gene regulatory network governing hepatocyte-cholangiocyte fate decisions during liver development and regeneration, revealing its multistable dynamics and ability to predict cell-state transitions.

Emergent dynamics of a three-node regulatory network explain phenotypic switching and heterogeneity: a case study of Th1/Th2/Th17 cell differentiation

The paper models a three-node regulatory network to explain phenotypic switching and heterogeneity in Th1/Th2/Th17 cell differentiation, showing how epigenetic repression influences transition rates between phenotypes.

Lhx2 in germ cells suppresses endothelial cell migration in the developing ovary

This study shows that Lhx2 in germ cells suppresses endothelial cell migration in developing ovaries, leading to increased angiogenesis.

Transcriptomic-based quantification of the epithelial-hybrid-mesenchymal spectrum across biological contexts

The paper compares three transcriptomic metrics to quantify epithelial-mesenchymal plasticity across cancer and non-cancer contexts, finding high concordance and applicability beyond cancer.

Prioritizing and characterizing functionally relevant genes across human tissues

This paper introduces FUGUE, a machine learning model that predicts tissue-relevant genes across 30 human tissues using transcriptional and network features, outperforming conventional metrics and providing prioritized gene lists.

Multistability in cellular differentiation enabled by a network of three mutually repressing master regulators

The paper investigates a network of three mutually repressing master regulators, showing it can lead to multiple stable cell states and applies this to understand T cell differentiation.

Mechanistic modeling of the SARS-CoV-2 and immune system interplay unravels design principles for diverse clinicopathological outcomes

This paper develops a mechanistic model of SARS-CoV-2 and immune system interactions to explain diverse clinical outcomes and guide drug combination strategies.

Emergent properties of HNF4α-PPARγ network may drive consequent phenotypic plasticity in NAFLD

The paper develops a mathematical model of the HNF4α-PPARγ network to show how it enables phenotypic plasticity in NAFLD by allowing hepatocytes to adopt adipocyte-like states.