Biology subjects

Kale, A.

Publications and source records attributed to Kale, A..

5 recordsLinked to original sources

bioRxiv2025

Cirrhosis severity modulates proteomic and immune landscapes in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) most often arises in cirrhotic livers, yet the biological impact of cirrhosis severity on the tumor proteome remains poorly understood. Here, we performed a comprehensive quantitative proteomic analysis of 141 HCC tumors stratified by the degree of cirrhosis to delineate fibrosis-related molecular heterogeneity. Principal component analysis revealed substantial overlap between groups, indicating that increasing cirrhosis severity produces incremental rather than global proteomic shifts. Nevertheless, 295 proteins showed significant differential abundance (Hedges g > 0.3, p < 0.05), including upregulation of HMOX1 and LRSAM1 and downregulation of CYP27A1 in Medium/High cirrhosis. Pathway enrichment highlighted alterations in organelle assembly, heme metabolism, and extracellular-matrix disassembly, alongside reduced cytoskeletal and focal-adhesion integrity. Proteome-based immune deconvolution suggested proportional remodeling of natural-killer and B-cell subsets with advancing cirrhosis. A five-gene signature derived from the most upregulated proteins (HMOX1, LRSAM1, MAP2, EDEM3, RFC3) was associated with significantly worse overall survival in the TCGA-LIHC cohort (Hazard ratio 1.7, p = 0.0033). Together, these findings demonstrate that cirrhosis severity subtly but measurably reshapes the tumor proteome and immune landscape in HCC, reflecting a continuum of biological remodeling rather than discrete molecular states. Incorporating cirrhosis gradation into molecular classification may improve risk stratification, biomarker discovery, and the design of precision therapies for HCC.

cancer biology↗

bioRxiv2022

Novel metabolic role for CD47 in pancreatic β-cell insulin secretion and islet transplant outcomes

Diabetes is a global public health burden and is characterized clinically by a relative or absolute insulin deficiency. Therapeutic agents that stimulate and improve insulin secretion and insulin sensitivity are in high demand as diabetic treatment. CD47 is a cell surface glycoprotein implicated in multiple cellular functions, including recognition of self, angiogenesis, and nitric oxide signaling, however its role in the regulation of insulin secretion remains unknown. For the first time we demonstrate that CD47 receptor signaling inhibits insulin release from {beta}-cells and that it can be pharmacologically exploited to boost insulin secretion. CD47 depletion stimulates insulin granule exocytosis via activation of the Rho GTPase Cdc42. CD47 deficiency improved glucose clearance and insulin sensitivity in mice. CD47 blockade enhanced islet transplantation efficiency and improved outcomes. Further, anti-CD47 antibody treatment delayed the onset of diabetes in non-obese diabetic mice and protected them from overt diabetes. Our findings identify CD47 as a previously unrecognized regulator of insulin secretion and its manipulation in {beta}-cells offers a novel therapeutic opportunity for diabetes and islet transplantation by correcting insulin deficiency. One Sentence SummaryCD47 limits insulin secretion and islet transplant outcomes

physiology↗

bioRxiv2019

Aging-related inflammation driven by cellular senescence enhances NAD consumption via activation of CD38+ macrophages

Decline in tissue NAD levels during aging is linked to aging and its associated diseases. However, the mechanism for aging-associated NAD decline remains unclear. Here we report that pro-inflammatory M1-like macrophages, but not naive or M2 macrophages, accumulate in metabolic tissues including visceral white adipose tissue and the liver during aging. Remarkably, these M1-like macrophages highly express the NAD consuming enzyme CD38 and have enhanced CD38-dependent NADase activity. We also find that senescent cells progressively accumulate in visceral white adipose tissue during aging and that inflammatory cytokines found in the supernatant from senescent cells (Senescence associated secretory proteins, SASP) induce macrophages to proliferate and to express CD38. These results highlight a new causal link between visceral tissue senescence and tissue NAD decline during aging and represent a novel therapeutic opportunity targeting maintenance of NAD levels during aging.

immunology↗

bioRxiv2019

A Proteomic Atlas of Senescence-Associated Secretomes for Aging Biomarker Development

The senescence-associated secretory phenotype (SASP) has recently emerged as a driver of, and promising therapeutic target for, multiple age-related conditions, ranging from neurodegeneration to cancer. The complexity of the SASP, typically assessed by a few dozen secreted proteins, has been greatly underestimated, and a small set of factors cannot explain the diverse phenotypes it produces in vivo. Here, we present the SASP Atlas, a comprehensive proteomic database of soluble and exosome SASP factors originating from multiple senescence inducers and cell types. Each profile consists of hundreds of largely distinct proteins, but also includes a subset of proteins elevated in all SASPs. Our analyses identify several candidate biomarkers of cellular senescence that overlap with aging markers in human plasma, including GDF15, STC1 and SERPINs, which significantly correlated with age in plasma from a human cohort, the Baltimore Longitudinal Study of Aging. Our findings will facilitate the identification of proteins characteristic of senescence-associated phenotypes and catalog potential senescence biomarkers to assess the burden, originating stimulus and tissue of origin of senescent cells in vivo.\n\nAbbreviationsATV, atazanavir treatment; BLSA, Baltimore Longitudinal Study of Aging; CTL, control; DDA, data-dependent acquisition; DAMP, damage-associated molecular pattern; DIA, data-independent acquisition; eSASP, extracellular vesicle senescence associated secretory phenotype; EVs, extracellular vesicles; IR, X-irradiation; MS, mass spectrometry; RAS, inducible RAS overexpression; SA-{beta}-Gal, senescence-associated {beta}-galactosidase; SEN, senescent; sSASP, soluble senescence associated secretory phenotype.

cell biology↗

bioRxiv2018

Mathematical Modelling of Actin treadmill in Apicomplexans

Plasmodium parasite, a representative member of phylum Apicomplexa is a causative agent of malaria in human as well as other animals. To infect host cells, Plasmodium first finds receptors on the host cell surface, then binds specifically, and finally penetrates host cell membrane to acquire the host cellular resources. The motility for moving on the cell surface is equipped by the precise and tight control of actin treadmill. Several regulators are required to achieve precision and robustness in the control of actin treadmill. However, the mechanistic detail of the treadmill regulatory network and the cross-talk among regulators are not well understood. We developed a stochastic model of treadmill regulation and explored the dynamics of filament growth, nucleation time, and elongation time. Our study mainly highlighted on how and what helps cells to maintain an average size of the actin filaments within a species. This is particularly important, since, excessive growth of filament can lead to cell lysis. Moreover, we also explore how the regulators interact to fine-tune the control elements in the actin treadmill.

systems biology↗