Biology subjects

Kishore, A.

Publications and source records attributed to Kishore, A..

5 recordsLinked to original sources

bioRxiv2025

Cracking the code of co-authorship networks geo-temporally using interpretable machine learning

An exponential growth in the scientific literature necessitates the development of highly scalable computational tools that can effectively analyze and distill insights from complex, interconnected research landscapes. We introduce Distributed, Interpretable, and Scalable computing for Co-authorship Networks (DISCo-Net), a robust and scalable tool engineered to curate and examine large-scale co-authorship networks by harnessing the power of distributed computing and advanced relational database queries. We use DISCo-Net to analyze co-authorship networks derived from millions of papers in the life sciences and physical sciences over more than two decades. Using a range of deep learning approaches, we surprisingly found that pre-trained zero-shot embeddings from a sentence transformer better captured global co-authorship relationships than a complex graphical attention transformer. Even more surprisingly, a simple interpretable Term Frequency-Inverse Document Frequency (TF-IDF) model performed as well as the Bidirectional Encoder Representations from Transformers (BERT) model. Through topic modeling on TF-IDF document descriptors, we identified nine major research areas prevalent globally over the past 24 years and captured topic-specific shifting trends in scientific output. Our study draws an innovative parallel between collaborative research networks and genomic regulatory structures, applying genomics data analysis methodologies to uncover patterns in global scientific collaboration. This approach reveals interpretable alignments between research interests and human developmental stages, while also identifying emerging influential players in the global research landscape. The findings highlight potential far-reaching consequences of current funding challenges, particularly in the U.S., and offer actionable insights for optimizing resource allocation and fostering innovation in an interconnected global scientific community.

scientific communication and education↗

bioRxiv2025

CDKN2ALow cancer cells outcompete macrophages for microenvironmental zinc to drive immunotherapy resistance

Anti-PD1 therapies are primarily thought to rely on functional T cell responses; yet tumors with limited T cell infiltration can still benefit, suggesting alternative mechanisms contribute to therapeutic efficacy. Indeed, we found that myeloid-rich, T cell-poor tumor models respond to anti-Pd1, and this is dependent on a cancer cell-macrophage crosstalk mediated by cancer cell Cdkn2a expression. Mechanistically, we found that cancer cells with decreased Cdkn2a expression (Cdkn2aLow), which occurs in [~]50% of all human cancers, reorganize zinc compartmentalization by upregulating the zinc importer Slc39a9 at the plasma membrane. Increased cancer cell plasma membrane Slc39a9 leads to intracellular zinc accumulation in cancer cells and depletion of zinc in the tumor microenvironment (TME), resulting in zinc-starved tumor-associated macrophages (TAMs) with reduced phagocytic activity. Restoring zinc availability in TAMs--via dietary supplementation or Slc39a9 knockdown in cancer cells--reprograms TAMs to a pro-phagocytic state and sensitizes Cdkn2aLow tumors to anti-Pd1 therapy. Remarkably, Slc39a9 knockdown tumors respond to anti-Pd1 in Rag1-/- mice, and co-injection of zinc-replete macrophages is sufficient to drive an anti-Pd1 response in immunodeficient mice, demonstrating the T cell-independent nature of this response. Clinically, TAMs from CDKN2ALow cancer patients show reduced zinc and phagocytosis gene signatures. Moreover, patients with lower circulating zinc levels have significantly worse time-to-event outcomes than those with higher levels. Together, these findings uncover a previously unrecognized mechanism by which Cdkn2aLow cancer cells outcompete TAMs for zinc, impairing their function and limiting anti-Pd1 efficacy. They also provide evidence that macrophages alone, without T cells, can enhance anti-PD1 response through zinc-mediated reprogramming of phagocytosis.

cancer biology↗

bioRxiv2023

A kinome-wide synthetic lethal CRISPR/Cas9 screen reveals that mTOR inhibition prevents adaptive resistance to CDK4/CDK6 blockade in HNSCC

The comprehensive genomic analysis of the head and neck cancer (HNSCC) oncogenome revealed frequent loss of p16INK4A (CDKN2A) in most HPV negative HNSCC lesions, often concomitant with amplification of the cyclin D1 (CCND1) gene locus. However, cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors as single agents have shown modest effect in the clinic, even when combined with cetuximab. The aberrant activation of PI3K/mTOR pathway is highly prevalent in HNSCC, and recent clinical trials targeting mTOR showed promising results in terms of objective responses and progression free survival. However, the clinical efficacy of mTOR inhibitors (mTORi) for advanced HNSCC patients may be limited due to intrinsic or acquired resistance. By a kinome-wide CRISPR/Cas9 screen, we identified cell cycle inhibition as a synthetic lethal target for mTORi. Combination of mTORi and palbociclib, a CDK4/6 specific inhibitor, showed strong synergism in HNSCC-derived cells in vitro and in vivo. Remarkably, we found that adaptive increase in cyclin E1 (CCNE1) expression upon palbociclib treatment underlies the rapid acquired resistance to this CDK4/6 inhibitor in HNSCC. Mechanistically, mTORi inhibits the formation of eIF4G-CCNE1 mRNA complexes, with the consequent reduction in mRNA translation and CCNE1 protein expression. Our findings suggest that concomitant mTOR blockade reverts the adaptive resistance to palbociclib, thereby providing a novel multimodal therapeutic option for HNSCC patients by co-targeting mTOR and CDK4/6. Our findings may have broad implications to halt the emergence of palbociclib resistance.

cancer biology↗

bioRxiv2023

Semiconducting carbon nanotubes decrease neuronal bursting in a network of rat hippocampal neurons in vitro while increasing intrinsic excitability of single neurons

The diverse electrical, chemical and structural properties of the functional derivatives of carbon nanotubes (CNTs) have shown biomedical possibilities for neuroprosthesis or neural interfaces. However, the studies have been generally confined to metallic CNTs that affect cell viability unless chemically functionalized for biocompatibility. Here, we explored the effects of semiconducting single-walled carbon nanotubes (ssw-CNT), on the active electrical properties of dissociated hippocampal neurons in-vitro using multielectrode array, calcium imaging and whole-cell patch clamp recordings. The findings show that ssw-CNT treatment regulates neural network excitability from burst to tonic firing by changing the calcium dynamics. However, at a single neuronal level, ssw-CNT increases neuronal excitability.

neuroscience↗

bioRxiv2021

Immunosuppressive traits of the hybrid epithelial/mesenchymal phenotype

Recent preclinical and clinical data suggests enhanced metastatic fitness of hybrid epithelial/ mesenchymal (E/M) phenotypes, but mechanistic details regarding their survival strategies during metastasis remain unclear. Here, we investigate immune-evasive strategies of hybrid E/M states. We construct and simulate the dynamics of a minimalistic regulatory network encompassing the known associations among regulators of EMT (epithelial-mesenchymal transition) and PD-L1, an established immune-suppressor. Our model simulations, integrated with single-cell and bulk RNA-seq data analysis, elucidate that hybrid E/M cells can have high levels of PD-L1, similar to those seen in cells with a full EMT phenotype, thus obviating the need for cancer cells to undergo a full EMT to be immune-evasive. Specifically, in breast cancer, we show the co-existence of hybrid E/M phenotypes, enhanced resistance to anti-estrogen therapy and increased PD-L1 levels. Our results underscore how the emergent dynamics of interconnected regulatory networks can coordinate different axes of cellular fitness during metastasis.

cancer biology↗