Biology subjects

Hariharan, A.

Publications and source records attributed to Hariharan, A..

10 recordsLinked to original sources

bioRxiv2026

PBF/PTTG1IP coordinates focal adhesion formation, polarity and cell motility

Directional cell migration requires cells to sense extracellular cues and coordinate adhesion, cytoskeletal remodelling and polarity, yet the molecular regulators that integrate these events remain incompletely defined. PTTG1-binding factor (PBF/PTTG1IP) is a transmembrane glycoprotein extensively characterised in pathological overexpression and cancer models, where elevated expression promotes tumourigenic cellular phenotypes. However, its endogenous physiological function remains poorly understood. Here, separate enrichment analyses of transcriptomic and phosphoproteomic profiles from PBF-overexpressing cells collectively highlighted cell adhesion, extracellular matrix organisation, cytoskeletal regulation and cell motility as major PBF-associated programmes. Using a novel Pbf knockout mouse model, we show that primary Pbf-KO mouse embryonic fibroblasts exhibit impaired migration and invasion. PBF loss reduced fibronectin adhesion, disrupted focal adhesion number, size and distribution, attenuated FAK Tyr397 phosphorylation and delayed early adhesion formation. Live-cell imaging and Golgi orientation assays further revealed altered actin organisation and impaired front-rear polarity in Pbf-KO cells. Key phenotypes were conserved in CRISPR-Cas9 PBF-KO human thyroid cancer cells, while targeted PBF re-expression restored migration in Pbf-KO MEFs. We thus identify PBF as an endogenous regulator of cell adhesion, polarity and directional motility, providing a framework for understanding how pathological PBF overexpression may promote invasive behaviour in cancer.

cell biology↗

bioRxiv2025

Unraveling Genomic Signatures of lncRNA Expression in Zebrafish Caudal Fin Regeneration: Bridging Regenerative Potential and Positional Memory.

Zebrafish (Danio rerio) is an essential model organism for tissue regeneration, but the function of long non-coding RNAs (lncRNAs) in tissue regeneration is not well understood. Identifying important regeneration-associated lncRNAs may allow for cross-species applications, improving tissue repair in other organisms. However, few studies and a lack of functional validation complicate our understanding of their mechanistic functions. This research explores novel lncRNAs associated with caudal fin regeneration and positional memory, aiming to identify those that are evolutionarily important across species and may hold universal significance. RNA-seq data deposited in the NCBI database were compared at various important time points (0h post-amputation (hpa), 12 hpa, 1 day post-amputation (dpa), two dpa, three dpa, and seven dpa) and fin parts (proximal, middle, and distal) to uncover major regulatory lncRNAs. Using HISAT2, StringTie, FEELnc, Conservation Analysis and WGCNA (Weighted Gene Co-expression Network Analysis), we found 107 lncRNAs related to regeneration time points and 229 about positional memory during regeneration. Overlapping analysis identified 13 common genomic regions that are complete or partial lncRNAs, indicating a functional connection between regeneration and positional identity and expressed differently in each time point and each position. Additionally, a comparison with regeneration-associated mRNAs revealed that these 13 regions play critical roles in both processes, providing insights into the molecular mechanisms of regenerative precision. Following validation by RT-PCR, the results further suggest that these overlapping regions are differentially expressed across distinct positions within the same tissue, despite a consistent injury pattern. This positional variation in expression may indicate potential roles in both evolutionary adaptation and the regulation of regenerative processes across multiple tissues.

genomics↗

bioRxiv2024

Determination of permissive and restraining cancer-associated fibroblast (DeCAF) subtypes

Cancer-associated fibroblast (CAF) subpopulations in pancreatic ductal adenocarcinoma (PDAC) have been identified using single-cell RNA sequencing (scRNAseq) with divergent characteristics, but their clinical relevance remains unclear. We translate scRNAseq-derived CAF cell-subpopulation-specific marker genes to bulk RNAseq data, and develop a single- sample classifier, DeCAF, for the classification of clinically restraining and permissive CAF subtypes. We validate DeCAF in 19 independent bulk transcriptomic datasets across four tumor types (PDAC, mesothelioma, bladder and renal cell carcinoma). DeCAF subtypes have distinct histology features, immune landscapes, and are prognostic and predict response to therapy across cancer types. We demonstrate that DeCAF is clinically replicable and robust for the classification of CAF subtypes in patients for multiple tumor types, providing a better framework for the future development and translation of therapies against permissive CAF subtypes and preservation of restraining CAF subtypes. SignificanceWe introduce a replicable and robust classifier, DeCAF, that delineates the significance of the role of permissive and restraining CAF subtypes in cancer patients. DeCAF is clinically tractable, prognostic and predictive of treatment response in multiple cancer types and lays the translational groundwork for the preclinical and clinical development of CAF subtype specific therapies.

genomics↗

bioRxiv2023

A latent cardiomyocyte regeneration potential in the human heart

Cardiomyocytes in the adult human heart show a regenerative capacity, with an annual renewal rate around 0.5%. Whether this regenerative capacity of human cardiomyocytes is employed in heart failure has been controversial. Using retrospective 14C birth dating we analyzed cardiomyocyte renewal in patients with end-stage heart failure. We show that cardiomyocyte generation is minimal in end-stage heart failure patients at rates 18-50 times lower compared to the healthy heart. However, patients receiving left ventricle support device therapy, who showed significant functional and structural cardiac improvement, had a >6-fold increase in cardiomyocyte renewal relative to the healthy heart. Our findings reveal a substantial cardiomyocyte regeneration potential in human heart disease, which could be exploited therapeutically.

cell biology↗

bioRxiv2022

Heterogeneity of RNA editing in mesothelioma and how RNA editing enzyme ADAR2 affects mesothelioma cell growth, response to chemotherapy and tumor microenvironment

We previously observed increased levels of adenosine-deaminase-acting-on-dsRNA (Adar)-dependent RNA editing during mesothelioma development in mice exposed to asbestos. The aim of this study was to characterize and assess the role of ADAR-dependent RNA editing in mesothelioma. Tumors and mesothelioma primary cultures have higher ADAR-mediated RNA editing compared to mesothelial cells. Unsupervised clustering of editing in different genomic regions revealed heterogeneity between tumor samples as well as mesothelioma primary cultures. ADAR2 expression levels are higher in BRCA1-associated protein 1 wild-type tumors, with corresponding changes in RNA editing in transcripts and 3UTR. ADAR2 knockdown and rescue models indicated a role in cell proliferation, altered cell cycle, increased sensitivity to antifolate treatment and type-1 interferon signaling upregulation, leading to changes in the microenvironment in vivo. Our data indicate that RNA editing contributes to mesothelioma heterogeneity and highlights an important role of ADAR2 not only in growth regulation in mesothelioma but also chemotherapy response, in addition to regulating inflammatory response downstream of sensing nucleic acid structures.

cancer biology↗

bioRxiv2022

Brain Capillary Pericytes are Metabolic Sentinels that Control Blood Flow through KATP Channel Activity

Capillary pericytes and their processes cover [~]90% of the total length of the brains capillary bed. Despite their abundance, little is known of pericyte function, and their contributions to the control of brain hemodynamics remain unclear. Here, we report that deep capillary pericytes possess a mechanistic energy switch that, when activated by a decrease in glucose, elicits robust KATP channel activation to increase blood flow and protect energy substrate availability. We demonstrate that pharmacological activation of KATP channels profoundly hyperpolarizes capillary pericytes and leads to dilation of upstream penetrating arterioles and arteriole-proximate capillaries covered with contractile pericytes, leading to an increase in local capillary blood flow. Stimulation of a single capillary pericyte with a KATP channel agonist is sufficient to evoke this response, which is mediated via KIR channel-dependent retrograde propagation of hyperpolarizing electrical signals. Genetic inactivation of pericyte KATP channels via expression of a dominant-negative version of KIR6.1 eliminates these effects. Critically, we show that lowering extracellular glucose below 1 mM evokes dramatic KATP channel-mediated pericyte hyperpolarization. Inhibiting glucose uptake by blocking GLUT1 transporters in vivo also activates this energy switch to increase pericyte KATP channel activity, dilate arterioles and increase blood flow. Together, our findings recast capillary pericytes as metabolic sentinels that respond to local energy deficits by robustly increasing blood flow to protect metabolic substrate delivery to neurons and prevent energetic shortfalls.

neuroscience↗

bioRxiv2020

Ultrasound-mediated mechanical forces selectively kill tumor cells

Ultrasound has been used to target tumors either through local heating or local nanobubbles but these methods damage surrounding normal cells in the target area. Recent studies show that tumor cells are susceptible to mechanical stresses and undergo calcium-dependent apoptosis under conditions that promote normal cell growth. Here we report that low-frequency ultrasound causes apoptosis of tumor cells by activating a calpain-dependent mitochondrial pathway that depends upon calcium entry through the mechanosensitive Piezo1 channels. This is a general property of all tumor cell lines tested so far irrespective of tissue origin. In animals, ultrasound irradiation causes tumor killing in the chick chorioallantoic membrane (CAM) model with relatively little damage to the chick embryos. Further, patient-derived pancreatic tumor organoids are killed by ultrasound treatment. Because low-level ultrasound causes apoptosis of tumor cells from many different tissues in different microenvironments, it may offer a safe non-invasive approach to augment tumor treatments.

cancer biology↗

bioRxiv2020

Force-dependent Piezo1 recruitment to focal adhesions regulates adhesion maturation and turnover specifically in non-transformed cells

Mechanosensing is an integral part of many physiological processes including stem cell differentiation, fibrosis, and cancer progression. Two major mechanosensing systems - focal adhesions and mechanosensitive ion channels, can convert mechanical features of the microenvironment into biochemical signals. We report here surprisingly that the mechanosensitive Ca2+-channel Piezo1, previously perceived to be diffusive on plasma membranes, binds to matrix adhesions in a force-dependent manner, promoting adhesion maturation and cell spreading in normal but not in tumor cells. In the absence of Piezo1, matrix adhesions are smaller in normal cells mimicking transformed cells where adhesions do not change with or without Piezo1. A novel adhesion-targeted calcium sensor shows robust Piezo1-dependent, calcium influx at adhesions in normal cells; but not in transformed cells. A linker domain in Piezo1 is needed for binding to adhesions and overexpression of the domain blocks Piezo1 binding to adhesions decreasing adhesion size and cell spread area. Thus, we suggest that Piezo1 is a novel component of focal adhesions in non-transformed cells that catalyzes adhesion maturation and growth through force-dependent calcium signaling, but this function is absent in most cancer cells.

cell biology↗

bioRxiv2020

Both DNA binding domains of p53 are required for its ultra rapid recruitment to sites of UV damage

p53 concentrates at DNA damage sites within two seconds upon UV laser micro-irradiation. Structural analysis shows that this very rapid response requires both the DNA binding and C-terminal domains of p53. This early recruitment response is also PARP-dependent. As mutations within the DNA binding domain of p53, that are commonly associated with cancer also inhibit this rapid binding, we suggest that this is an important initial step for p53 function as a tumor suppressor. One Sentence Summaryp53 is an early responder to DNA damage

cell biology↗

bioRxiv2018

Mechanical Stretch Kills Transformed Cancer Cells

Transformed cancer cells differ from normal cells in several important features like anchorage independence, Warburg effect and mechanosensing. Consequently, transformed cancer cells develop an anaplastic morphology and respond aberrantly to external mechanical forces. Consistent with altered mechano-responsiveness, here we show that transformed cancer cells from many different tissues have reduced growth and become apoptotic upon cyclic stretch as do normal cells after the transformation. When matrix rigidity sensing is restored in transformed cancer cells, they survive and grow faster on soft surface upon cyclic stretch like normal cells but undergo anoikis without stretch by activation of death associated protein kinase1 (DAPK1). In contrast, stretch-dependent apoptosis (mechanoptosis) of transformed cells is driven by stretch-mediated calcium influx and calcium-dependent calpain 2 protease activation on both collagen and fibronectin matrices. Further, mechanosensitive calcium channel, Piezo1 is needed for mechanoptosis. Thus, cyclic stretching of transformed cells from different tissues activates apoptosis, whereas similar stretching of normal cells stimulates growth.

cell biology↗