Biology subjects

Kiselyov, K.

Publications and source records attributed to Kiselyov, K..

7 recordsLinked to original sources

bioRxiv2024

Epidrug Screening Identifies Type I PRMT Inhibitors as Modulators of Lysosomal Exocytosis and Drug Sensitivity in Cancers

Epigenetic changes drive differential gene expression, contributing to oncogenic transformation and drug resistance. Lysosomes are crucial in cell signaling and the sequestration of toxins and chemotherapeutic agents. This sequestration followed by expulsion through lysosomal exocytosis is a factor in drug resistance. The epigenetic regulation of lysosomal exocytosis remains poorly understood. Our research focuses on this regulation, hypothesizing that epigenetic modifier drugs (epidrugs) capable of inhibiting lysosomal exocytosis and could serve as potential therapeutics. Additionally, we investigate their potential synergy with drugs known to be sequestered in lysosomes. To examine this concept, we screened approximately 150 epigenetic drugs targeting various reader, writer, or eraser proteins. These drugs were assessed for their combined cytotoxic effects with cisplatin, their impact on lysosomal exocytosis, and on lysosomal biogenesis. Our findings reveal that among the epidrugs showing synergy with cisplatin and further reducing cell viability in combination, two type I PRMT inhibitors, MS023 and GSK3368715, inhibited lysosomal exocytosis. Notably, neither of these drugs altered the expression of the CLEAR lysosomal biogenesis network of genes, suggesting the involvement of novel regulators in lysosomal functions. To explore the specific components of the trafficking machinery affected by PRMT inhibitors, we conducted an RNA-seq analysis, uncovering several differentially expressed genes (DEGs). In addition to previously described functions such as methylation activity, or DNA repair; these DEGs included those involved in vesicular trafficking, lysosomal enzyme activity and lysosome dynamics, offering potential insights into the mechanism of reduced exocytosis and identifying a novel mode for its regulation. Additionally, both inhibitors exhibited synergy with other drugs known to be sequestered in lysosomes, such as carboplatin, oxaliplatin, sunitinib, and doxorubicin, indicating that inhibition of lysosomal exocytosis may be a common phenomenon for such drugs. These findings underscore the potential of Type I PRMT inhibitors as therapeutic agents in cancer treatment. Consistently, analysis on the publicly available patient data revealed that lower levels of type I PRMTs (PRMT1 and 6) were associated with better patient response to these drugs, further suggesting their potential as drug candidates for combination therapy to enhance chemotherapy efficacy and improve cancer patient survival rates.

cancer biology↗

bioRxiv2023

Lysosomal mitochondrial interaction promotes tumor growth in squamous cell carcinoma of the head and neck

Tumor growth and proliferation are regulated by numerous mechanisms. Communication between intracellular organelles has recently been shown to regulate cellular proliferation and fitness. The way lysosomes and mitochondria communicate with each other (lysosomal/mitochondrial interaction) is emerging as a major determinant of tumor proliferation and growth. About 30% of squamous carcinomas (including squamous cell carcinoma of the head and neck, SCCHN) overexpress TMEM16A, a calcium-activated chloride channel, which promotes cellular growth and negatively correlates with patient survival. TMEM16A has recently been shown to drive lysosomal biogenesis, but its impact on mitochondrial function is unclear. Here, we show that (1) patients with high TMEM16A SCCHN display increased mitochondrial content specifically complex I; (2) In vitro and in vivo models uniquely depend on mitochondrial complex I activity for growth and survival; (3) {beta}-catenin/NRF2 signaling is a critical linchpin that drives mitochondrial biogenesis, and (4) mitochondrial complex I and lysosomal function are codependent for proliferation. Taken together, our data demonstrate that LMI drives tumor proliferation and facilitates a functional interaction between lysosomes and mitochondria. Therefore, inhibition of LMI may serve as a therapeutic strategy for patients with SCCHN.

cancer biology↗

bioRxiv2023

Missense mutations in the calcium-activated chloride channel TMEM16A promote tumor growth by activating oncogenic signaling in Human Cancer.

The calcium-activated chloride channel TMEM16A is overexpressed in several tumors. This condition is associated with a poor survival prognosis but highlights TMEM16As potential as a biomarker and target for anti-cancer therapies. Numerous somatic mutations of TMEM16A have been reported; however, their potential and molecular mechanism of oncogenesis are unknown. Here, we investigate the function and oncogenicity of nine-point mutations found in human cancerous tissues (R451P, R455Q, M546I, R557W, F604L, D902N, K913E, D914H, and Q917K). These mutations are located on the extracellular side and near the third Ca2+-binding site, near a PtdIns(4,5)P2 site in the human TMEM16A channel. Our findings reveal that these mutations affected gating, Ca2+ sensitivity, phosphorylation of essential signaling proteins, cell proliferation, and tumor growth. Notably, R451P and D902N exhibit low Ca2+ sensitivity, yet their overexpression promotes phosphorylation of EGFR and AKT, as well as in vivo tumorigenesis, without Ca2+-enhancing stimuli. Conversely, the charged-neutralizing mutation R451Q and the conservative mutation D902E restored Ca2+ sensitivity and altered cell proliferation and tumor growth as wild-type did. Thus, we conclude that the oncogenic phenotype of TMEM16A missense mutations is independent of chloride flux but involves the differential activation of cell signaling components associated with cell proliferation.

cancer biology↗

bioRxiv2023

Impairment of autophagy-lysosomal activity near the chronically implanted microelectrodes

Intracortical microelectrodes that can record and stimulate brain activity have become a valuable technique for basic science research and clinical applications. However, long-term implantation of these microelectrodes can lead to progressive neurodegeneration in the surrounding microenvironment, characterized by elevation in disease-associated markers. Dysregulation of autophagy-lysosomal degradation, a major intracellular waste removal process, is considered a key factor in the onset and progression of neurodegenerative diseases. It is plausible that similar dysfunctions in autophagy-lysosomal degradation contribute to tissue degeneration following implantation-induced focal brain injury, ultimately impacting recording performance. To understand how the focal, persistent brain injury caused by long-term microelectrode implantation impairs the autophagy-lysosomal pathway, we employed two-photon microscopy and immunohistology. This investigation focused on the spatiotemporal characterization of autophagy-lysosomal activity near the chronically implanted microelectrode. We observed an aberrant accumulation of immature autophagy vesicles near the microelectrode over the chronic implantation period. Additionally, we found deficits in autophagy-lysosomal clearance proximal to the chronic implant, which was associated with an accumulation of autophagy cargo and a reduction in lysosomal protease level during the chronic period. Furthermore, our evidence suggests astrocytes contribute to the clearance of myelin debris via autophagy-lysosomal degradation near the implanted microelectrode. Together, this study sheds light on the process of brain tissue degeneration caused by long-term microelectrode implantation, with a specific focus on impaired intracellular waste degradation.

bioengineering↗

bioRxiv2022

GDAP1 binds 4-hydroxynonenal, the toxic end-product of lipid peroxidation, using its GST-like binding pocket

GDAP1 (Ganglioside-induced differentiation-associated protein 1) is a novel member of the GST superfamily of detoxifying enzymes that is anchored to the outer mitochondrial membrane. GDAP1 mutations and changes in expression levels result in the inherited neuropathy Charcot-Marie-Tooth (CMT) disease, types 2K, 4A and 4H. GDAP1 activity has been associated with many mitochondrial functions however direct molecular interactions underpinning these connections have remained elusive. Here we establish that GDAP1 can bind 4-hydroxynonenal (4HNE), a toxic end-product of lipid peroxidation. 4HNE binding requires the -loop, a large sequence motif that is inserted within the substrate recognition domain and is unique to GDAP1. In human cells, GDAP1 overexpression plays a cytoprotective role against oxidative stress. This effect is lost upon deletion of the -loop. Lastly, we demonstrate that a CMT-causing mutant that destabilizes -loop positioning also results in a decrease in 4HNE binding affinity. Together these results establish 4HNE as the biological ligand for GDAP1, provide mechanistic insight into 4HNE binding, and demonstrate that altered 4HNE recognition is the likely mechanism underlying CMT-causing mutants such as T157P near the 4HNE binding site.

biochemistry↗

bioRxiv2021

Evolutionary rate covariation identifies SLC30A9 (ZnT9) as a mitochondrial zinc transporter.

Recent advances in genome sequencing have led to the identification of new ion and metabolite transporters, many of which have not been characterized. Due to the variety of subcellular localizations, cargo and transport mechanisms, such characterization is a daunting task, and predictive approaches focused on the functional context of transporters are very much needed. Here we present a case for identifying a transporter localization using evolutionary rate covariation (ERC), a computational approach based on pairwise correlations of amino acid sequence evolutionary rates across the mammalian phylogeny. As a case study, we find that poorly characterized transporter SLC30A9 (ZnT9) uniquely and prominently coevolves with several components of the mitochondrial oxidative phosphorylation chain, suggesting mitochondrial localization. We confirmed this computational finding experimentally using recombinant human SLC30A9. SLC30A9 loss caused zinc mishandling in the mitochondria, suggesting that under normal conditions it acts as a zinc exporter. We therefore propose that ERC can be used to predict the functional context of novel transporters and other poorly characterized proteins.

evolutionary biology↗

bioRxiv2017

Whole-cell scale dynamic organization of lysosomes revealed by spatial statistical analysis

In eukaryotic cells, lysosomes are distributed in the cytoplasm as individual membrane-bound compartments to degrade macromolecules and to control cellular metabolism. A fundamental yet unanswered question is whether and, if so, how individual lysosomes are spatially organized so that their functions can be coordinated and integrated to meet changing needs of cells. To address this question, we analyze their collective behavior in cultured cells using spatial statistical techniques. We find that in single cells, lysosomes maintain nonrandom, stable, yet distinct spatial distributions, which are mediated by the coordinated effects of the cytoskeleton and lysosomal biogenesis on different lysosomal subpopulations. Furthermore, we find that throughout the intracellular space, lysosomes form dynamic clusters that substantially increase their interactions with endosomes. Together, our findings reveal the spatial organization of lysosomes at the whole-cell scale and provide new insights into how organelle interactions are mediated and regulated over the entire intracellular space.\n\nHighlightsO_LILysosomes maintain stable yet distinct spatial distributions in single cells\nC_LIO_LIThe cytoskeleton and lysosomal biogenesis mediate stable lysosomal distributions\nC_LIO_LILysosomes form dynamic clusters that promote their interactions with endosomes\nC_LIO_LITwo subpopulations of lysosomes jointly mediate formation of lysosomal clusters\nC_LI\n\neTOC BlurbLysosomes are spatially organized at the whole-cell scale and form dynamic clusters that promote their interactions with endosomes.

systems biology↗