S. Sinha

Bilateral cellular flows display asymmetry prior to left-right organizer formation in amniote gastrulation

The paper shows that left-right asymmetry in chick embryos begins before the formation of the left-right organizer, detected through biophysical analysis of cellular flows.

Stretching the structural envelope of isomeric imatinib analogs that reduce β-amyloid production by modulating both β- and γ-secretase cleavages of APP

The paper investigates how structurally diverse imatinib analogs affect APP metabolism similarly, identifying potent isomers for further development.

Unveiling Cas8 Dynamics and Regulation within a transposon-encoded Cascade-TniQ Complex

This study reveals the conformational dynamics of the Cas8 protein in the Cascade-TniQ complex, showing how it transitions between open and closed states to facilitate DNA binding and transposition.

A chemically defined and xeno-free hydrogel system for regenerative medicine.

The paper develops a chemically defined, xeno-free hydrogel system that supports hPSC differentiation into multiple tissue types and improves hepatocyte retention in vivo.

BUTYRATE AMELIORATES INFLAMMATION IN COLON BIOPSY SAMPLES OF IBD PATIENTS AND EXPERIMENTAL COLITIS IN MICE INVOLVING RNA BINDING PROTEIN, AUF1-IL-27 AXIS AND ACCELERATING B1a TO B10 POLARIZATION

This paper shows butyrate enhances B10 cell generation via the AUF1-IL-27 axis in IBD patients and mice, reducing inflammation.

Proliferation-driven mechanical feedback regulates cell dynamics in growing tissues

This study uses agent-based simulations to show that mechanical feedback from cell division and proliferation influences cell dynamics in growing tissues, with distinct diffusion behaviors depending on feedback strength and growth rate.

H2O2 mediated MAPK-mTOR crosstalk determines the XIAP and FLIP degradation pathways and development of resistance to Imatinib

This study shows H2O2-mediated mTOR activation determines protein degradation pathway and Imatinib resistance in K562 cells.

Structure, motion, and multiscale search of traveling networks

This paper introduces traveling networks, analyzes their structure and motion through a tree-based model, and demonstrates their application to real-world systems.

IL6 mediated cFLIP downregulation increases the migratory and invasive potential of triple negative breast cancer cells

The paper shows that IL6-mediated cFLIP downregulation enhances metastasis in triple negative breast cancer by reducing autophagy.

Mechanical feedback drives asynchronous cell divisions during embryogenesis

The paper models biomechanical feedback during zebrafish embryogenesis to predict the transition from synchronous to asynchronous cell divisions and explains the resulting cell cycle lengthening.

Charting the transcriptomic landscape of primary and metastatic cancers in relation to their origin and target normal tissues

The paper compares gene expression in primary and metastatic tumors to their origin and target tissues, finding metastases more resemble target tissues and show reduced cancer hallmark activity.

Lethal COVID-19 Associates With RAAS-Induced Inflammation For Multiple Organ Damage Including Mediastinal Lymph Nodes

This study identifies non-canonical genes linked to RAAS overactivation in lethal COVID-19, causing multi-organ damage and mediastinal lymph node dysfunction.

The atypical cadherin FAT1 is a novel regulator of STAT1, driving its pro-tumorigenic effect via the STAT1/PDCD4 axis in glioblastoma

This study identifies STAT1 as a downstream mediator of FAT1, showing it suppresses PDCD4 to drive pro-tumorigenic effects in glioblastoma.

Machine Learning Guided Differentiation Therapy Targets Cancer Stem Cells in Colorectal Cancers

This paper introduces a machine learning framework to identify and target transcriptomic vulnerabilities in colorectal cancer, demonstrating that differentiation therapy selectively eliminates cancer stem cells and reduces recurrence risk.

High-Fidelity, Hyper-Accurate, and Evolved Mutants Rewire Atomic Level Communication in CRISPR-Cas9

The paper investigates how specific mutations in the Rec3 domain of CRISPR-Cas9 variants affect structural dynamics and allosteric communication to enhance specificity.

RNA-mediated Allosteric Activation in CRISPR-Cas13a

This study elucidates the allosteric activation mechanism of CRISPR-Cas13a using molecular dynamics simulations and experiments, revealing key residues critical for RNA cleavage selectivity.

A conformationally constrained synthetic peptide efficiently inhibits malaria parasite entry into human red blood cells

The paper describes a synthetic cyclic peptide that inhibits malaria parasite entry into human red blood cells by enhancing receptor binding affinity.

Ets1 and IL17RA cooperate to regulate autoimmune responses as well as skin immunity to Staphylococcus aureus

This study shows that Ets1 and IL17RA deficiencies together worsen autoimmune disease and impair skin immunity to Staphylococcus aureus.

Single-cell transcriptomic and TCR analysis of human Cytomegalovirus (hCMV)-specific memory T cells reveals effector and pre-effectors of CD8+- and CD4+-cytotoxic T cells

The paper characterizes hCMV-specific memory T cells using single-cell transcriptomics and TCR analysis, identifying distinct functional subsets and their roles in immunity.

Differentiation and quality control of smooth muscle cells from human pluripotent stem cells via the neural crest lineage

This paper describes a protocol to differentiate human pluripotent stem cells into vascular smooth muscle cells via the neural crest lineage and outlines quality control steps.

Oncometabolite lactate enhances breast cancer progression by orchestrating histone lactylation-dependent c-Myc expression

This study identifies lactate-driven histone lactylation as a mechanism enhancing c-Myc expression and promoting breast cancer progression through SRSF10-mediated alternative splicing.

Hemin-driven chromatin remodelling by atherosclerotic risk gene SMARCA4 switches human blood-derived macrophages from leukocyte disposal to erythrocyte disposal

This study shows SMARCA4 drives hemin-induced chromatin changes in macrophages, switching their phagocytic target from leukocytes to erythrocytes, contributing to atherosclerosis.

Rational development of a small-molecule activator of CK1γ2 that decreases C99 and beta-amyloid levels

This study identifies CK1γ2 as a therapeutic target for Alzheimer's disease by showing its activation reduces C99 and beta-amyloid levels through increased PS1-Ser367 phosphorylation.

Diverse Gut Pathogens Exploit the Host Engulfment Pathway via a Conserved Mechanism

The paper identifies a conserved molecular interface between WxxxE-effector proteins from gut pathogens and the host protein ELMO1, showing how pathogens exploit the host's engulfment pathway.

A Multiomic Analysis Reveals How Breast Cancers Disseminated to the Bone Marrow Acquire Aggressive Phenotypes through Tumor-Stroma Tunnels

This study identifies GIV as a key protein transferred from mesenchymal stromal cells to ER+ breast cancer cells via tunnelling nanotubes, driving aggressive tumor phenotypes.

A novel human iPSC model of COL4A1/A2 small vessel disease unveils a key pathogenic role of matrix metalloproteinases in extracellular matrix abnormalities

This paper develops a human iPSC model of COL4A1/A2 small vessel disease, showing that MMP inhibition rescues ECM abnormalities and mural cell defects.

Broad-spectrum antiviral inhibitors targeting pandemic potential RNA viruses

This study identifies broad-spectrum antiviral agents effective against multiple RNA virus families, including arboviruses and respiratory pathogens.

Growth Signaling Autonomy in Circulating Tumor Cells Aids Metastatic Seeding

This study defines the transcriptome, proteome, and phenome of growth signaling autonomy in breast cancer cells and shows its role in metastatic progression and drug resistance.

Free volume theory explains the unusual behavior of viscosity in a non-confluent tissue during morphogenesis

The paper uses simulations to show that cell size polydispersity and deformability explain the viscosity plateau in non-confluent zebrafish tissue beyond a critical packing fraction.

Topological transitions, turbulent-like motion and long-time-tails driven by cell division in biological tissues

The paper shows that cell division and apoptosis in epithelial monolayers generate turbulent-like flows with energy spectra and velocity correlations similar to inertial turbulence.