Biology subjects

Kumar, A.

Publications and source records attributed to Kumar, A..

At least 235 records · Page 13Linked to original sources

bioRxiv2025

R allele of ACTN3 R577X gene polymorphism is associated with Elite Indian Boxer Status

Genetic variations are considered important for athletic performance. In this regard, polymorphisms in angiotensin I-converting enzyme (ACE) and -actinin-3 genes are widely studied for their association with elite athlete status. The ACE gene regulates circulatory homeostasis, with the I variant of the ACE insertion/deletion (ACE I/D) gene polymorphism being associated with endurance performance, while the R allele of the R577X polymorphism of the ACTN3 gene, crucial for fast glycolytic muscle fibers, has been associated with speed and power performances. The present study investigated the association of these genetic variants with elite boxer (N=57) status and compared it with elite power/speed athletes (N=40), endurance athletes (N=44) and nonathletes (N=98) in the Indian population. The R allele frequency was found significantly higher in boxers than the nonathletes (p < 0.05). The allele and genotype frequencies of boxers, endurance and power/speed athletes did not differ significantly (p > 0.05). After analyzing overall athletic cohort on the basis of their level of performance, the frequency of RR genotype (24.1%) and R allele (47.7%) in national level athletes was found significantly higher than in nonathletes (8.7% and 34.2%, respectively), with the significant difference (p < 0.05) between national level endurance athletes and nonathletes only. The ACE I/D gene polymorphism was not found associated with any of the athletic cohorts (p > 0.05). Taken altogether, our study showed that the R allele of ACTN3 gene polymorphism is associated with elite boxer status as compared to the nonathletes. HighlightsO_LIBoxers had a higher ACTN3 gene R allele frequency than nonathletes; genotype did not differ. C_LIO_LIBoxers with RR genotype had more than 3x higher odds versus nonathletes (p = 0.02) in the X dominant model (RR vs RX+XX). C_LIO_LIACTN3 gene allele and genotype frequencies differed between overall athletic cohort and nonathletes. C_LIO_LIACE gene frequencies showed no difference or association across athletic cohorts. C_LI

genetics↗

bioRxiv2025

Multifaceted Actions of Neurosteroids

Background and purposeNeurosteroids modulate neuronal function and are promising therapeutic agents for neuropsychiatric disorders. Neurosteroid analogues are approved for treating postpartum depression and are of interest in other disorders. GABA-A receptors are well characterized targets of natural neurosteroids, but other biological pathways are likely relevant to therapeutic mechanisms and/or to off-target effects. We performed hypothesis-generating in silico analyses and broad in vitro biological screens to assess the range of actions of neurosteroids analogues of varying structural attributes. Key ResultsWe employed in silico molecular similarity analysis and network pharmacology to elucidate likely targets. This analysis confirmed likely targets beyond GABA-A receptors. We then functionally screened 19 distinct neurosteroid structures across 78 targets representing interconnected signaling pathways, complemented with a limited screen of kinase activation. Results revealed unanticipated modulation of targets by neurosteroids with some structural selectivity. Many compounds-initiated androgen receptor translocation with little or no enantioselectivity. Modulation of multiple G-protein receptors was also unexpected. Conclusions and implicationsNeurosteroids are ascendant treatments in neuropsychiatry, but their full spectrum of actions remains unclear. This virtual and biological screening discovery approach opens new vistas for exploring mechanism of neurosteroids analogues. The multifaceted approach provides an unbiased, holistic exploration of the potential effects of neurosteroids across various molecular targets and provides a platform for future validation studies to aid drug discovery.

neuroscience↗

bioRxiv2025

Multimodal Neuroimaging Reveals Distinct Characteristics of Levodopa-Induced Dyskinesias in de novo Parkinsons Disease Patients

Levodopa-induced dyskinesia (LID) is a significant treatment complication that affects a substantial proportion of Parkinsons disease (PD) patients. Our understanding of the neural basis of LID remains limited, partly due to the small sample sizes in existing neuroimaging studies. In this study, we utilized structural MRI data from the Parkinsons Progression Markers Initiative (PPMI) database, including de novo PD patients (104 non-dyskinetic for a least 3 years after diagnosis and 120 who developed dyskinesia) and 100 age- and sex-matched healthy controls. Additionally, we analyzed resting-state functional MRI data from a subset of these participants to investigate connectivity differences among the groups. Our analysis revealed no significant baseline volumetric differences between dyskinetic and non-dyskinetic PD patients. However, the thickness of frontal and sensorimotor cortices were significantly greater in dyskinetic patients. In the subcortical regions, vertex-based shape analysis identified localized surface growth in the left caudate and left pallidum, as well as surface morphology changes in the bilateral pallidum in dyskinetics. Resting-state functional connectivity analysis revealed stronger connectivity between the putamen, inferior frontal gyrus, and sensory cortex in dyskinetic PD patients compared to non-dyskinetics. These findings suggest that specific morphological and functional changes in the motor cortical-basal ganglia circuitry of de novo PD patients may predispose them to LID over time. Additionally, the altered functional connectivity patterns reinstate the role of the inferior frontal gyrus in the pathophysiology of dyskinesia and suggest that it might be a suitable target for neuromodulatory interventions, consistent with previous reports.

neuroscience↗

bioRxiv2025

Epigenetic Modulation of Host Immunity related genes in Pulmonary Tuberculosis: A Comprehensive Analysis of DNA Methylation Profiles in Peripheral Blood Mononuclear Cells

BackgroundIn the last few years, there has been increasing evidence in the literature for promoter hypermethylation of various host genes following infection with various pathogens. Therefore, in the present study, the role of epigenetic reprogramming of host cells through DNA methylation was evaluated which indicates that the disease progression takes place through changes in host immune response related genes. ObjectiveTo elucidate the differential genome-wide DNA methylation profile of peripheral blood mononuclear cells in pulmonary tuberculosis (PTB) patients. Materials and methodsTo decipher the methylation profile of PBMCs in PTB patients whole genome bisulphite sequencing was performed using 4 DNA samples from each study group i.e. PTB, healthy controls and diseased controls. Briefly, the samples were subjected to bisulphite conversion followed by library preparation and whole genome bisulphite sequencing. The data then were analysed for differential methylation analysis followed by gene set enrichment analysis to select DMRs for validation by sanger sequencing. Further the GEOR2 online server was used to investigate the mRNA expression of selected genes associated with hypermethylated DMRs in promoter region. ResultsDifferential methylation region analysis was performed for the following comparisons. TB v/s Diseased (Hypermethylated=1756; Hypomethylated=1886), TB v/s Healthy( Hypermethylated=2203; Hypomethylated=2466), Diseased v/s Healthy ( Hypermethylated=1656; Hypomethylated=3936). Further gene set enrichment analysis showed that the hypermetylated regions belonged to genes that are involved in immune responses mainly T cell functioning and T cell mediated immune processes. There were 8 DMR belonging to TAF8,FZD5, HLA-DRB, MIR483, PVRIG, SH2B2, ZAP70, TNFRSF13C simultaneously (n=10 from each study group). mRNA expression analysis with GEOR2 (Datasets used n= 12) revealed significant downregulation of TNFRSF13C, ZAP70, PVRIG Among the selected genes associated with hypermethylated DMRs in promoter region. (e) ConclusionThe altered differential methylation profile of PBMCs from TB patients shows that on onset the active disease there occurs aberrant methylation of expression regulating regions that in turn results in decreased T cell functions and hence suboptimal immune responses in TB

molecular biology↗

bioRxiv2025

Unveiling BPDE Induced Carcinogenic Signaling: Computational Insights into NF-κB, MAPK, and PI3K/Akt Pathway Activation

AbstractThe Carcinogen benzo[a]pyran-7, 8 dihydrodiol 9, 10 epoxide(BaP-DNP) the active metabolite of benzo[a]pyrene has been postulated to induce carcinogenesis through formation of adduct with DNA and through alteration of critical pathways involved in signaling. Besides genotoxicity, BPDE has more recently been reported to alter the NF-{kappa}B, MAPK, and PI3K/Akt, that are involved in inflammation, cell survival and cell proliferation. From the above molecular docking analysis of BPDE binding to the potential proteins of these pathways, the mechanism of action of the compound is examined. The studies conducted on docking reveal moderate binding affinity of BPDE with NF-{kappa}B, that is, -6.11 kcal/mol, which points out its role in inflammation and oncogenic signaling. In addition, BPDE has more protein-binding affinities within the MAPK and PI3K/Akt pathway for CDK1 (-7.46 kcal/mol), LOX (-7.47 kcal/mol), and CDK6 (-6.84 kcal/mol). These indicate that influence of BPDE in tumour progression should not be only through the activation of NF-{kappa}B but would rather be supported by significant inputs of pathways that include PI3K/Akt and MAPK. This interaction would seem to favor cell survival, proliferation, and apoptosis resistance. Broader analysis of the data presented allows defining NF-{kappa}B as one of the key molecules contributing to BPDE-induced carcinogenesis; however, the data also point to the significant participation of the MAPK and PI3K/Akt pathways in this process. Future work should also more fully detail how these pathways interconnect and also evaluate the effectiveness of inhibiting NF-{kappa}B and related pathways in preventing BPDEs carcinogenic action. This study adds to understanding of molecular mechanisms and therapeutic targets of BPDE. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/631754v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@d157e0org.highwire.dtl.DTLVardef@1e061b4org.highwire.dtl.DTLVardef@2ea4acorg.highwire.dtl.DTLVardef@3d50b7_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Biopolymers can be used for consolidation of lunar and Martian regoliths

Creating long-term extraterrestrial habitats to support continuous human occupation requires structures that can bear load, while remaining resilient to large temperature fluctuations. Exploiting locally available regolith is part of a paradigm termed in situ resource utilization (ISRU) that advocates minimal dependence on terrestrial supplies via local resource exploitation for construction. In this work, we report on a consolidation method for making load-bearing structures out of lunar and Martian regolith simulants using biopolymer binders. We quantify the compressive and tensile strength of the final brick-like structures, termed biopolymer regolith composites, and investigate their dependence on biopolymer concentration and chemistry. A pressure-assisted die casting process is developed that can produce bricks with compressive strengths of [~] 15 MPa and tensile strengths of around 2 MPa, from regolith simulants. We finally report on the performance of these bricks under large temperature and pressure variations and find that their strengths remain unchanged. We believe that this makes biopolymer regolith composite bricks suitable candidates for use in harsh extraterrestrial environments, while adhering to the guidelines of the ISRU paradigm. Keyword: Lunar regolith; Martian regolith; Space habitation; Extraterrestrial construction; Biopolymers; Regolith simulant

bioengineering↗

bioRxiv2025

NF-κB mediates transactivation of HNRNPD, resulting in PTEN destabilization and constitutive activation of the PI3K-AKT pathway in oral cancer cells

Heterogeneous Ribonucleoprotein D (hnRNPD), an RNA binding protein transcriptionally upregulated by NF-{kappa}B transcription factor, is associated with poor outcome of Oral Squamous Cell Carcinoma (OSCC). However, the role of hnRNPD in OSCC remains elusive. This study reveals that hnRNPD positively affects the proliferation, migration, invasion, and survival of OSCC cells. Transcriptome profiling in hnRNPD knockout cells identified significant upregulation of PTEN and inhibition of the PI3K/AKT/mTOR axis. HnRNPD mediates the destabilization of PTEN mRNA by binding to the class II AU-Rich Element (ARE) in 3UTR of PTEN. The expression of hnRNPD and PTEN are strongly negatively correlated in OSCC tissue specimens, further corroborating hnRNPD-mediated PTEN destabilization. The hnRNPD knockout inhibited autophagy, evident by an accumulation of autophagic vesicles and decreased autophagic flux. Mechanistically, the hnRNPD knockout reduced the expression of NF-{kappa}B, eventually downregulating its transcriptional target LC3b, a key mediator of autophagy. SA-{beta}-Galactosidase staining in hnRNPD KO cells conclusively demonstrated the onset of cellular senescence. The present study demonstrates hnRNPD-driven positive modulation of autophagy via NF-{kappa}B, independent of the PI3K/AKT/mTOR axis, highlighting it as a novel therapeutic target for treating oral cancer. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/631360v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@11f6844org.highwire.dtl.DTLVardef@f65124org.highwire.dtl.DTLVardef@1492571org.highwire.dtl.DTLVardef@13931dd_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIHnRNPD mediates oral cancer cell proliferation, migration, invasion, and survival. C_LIO_LIHnRNPD acts as a novel regulator of the PI3K/AKT/mTOR axis by destabilization of PTEN. C_LIO_LINF-{kappa}B/RelA downregulated on knockout of HNRNPD, inhibiting autophagy through downregulating its transcriptional target LCB-II. C_LIO_LIHnRNPD mediates cellular senescence in oral cancer cells. C_LI

cancer biology↗

bioRxiv2025

Changes in free-roaming dog population demographics and health associated with a catch-neuter-vaccinate-release program in Jamshedpur, India

Indias large free-roaming dog populations contribute to significant human health, environmental, and social challenges. Population management strategies, such as capture-neuter-vaccinate-return (CNVR), aim to reduce dog numbers, improve their welfare, and reduce human-animal conflict. The Humane Society International, in partnership with the Animal Health Foundation, implemented a CNVR program in Jamshedpur, neutering and vaccinating over 20,000 dogs. This study evaluates the impact of this program on dog health, population structure and size. The study areas encompassed 10 sites within the Jamshedpur Metropolitan Region, including both intervention sites where CNVR was directly applied and sites without direct intervention. Data was collected from May 2014 until December 2018, including bi-annual street surveys, as well as clinical data from the dogs captured and treated. We fit logistic regression, negative binomial, and binomial mixed effects models to assess changes in dog population characteristics, health, and reproductive conditions over time in relation to the CNVR intervention. We found that, over time, the CNVR program significantly reduced the probability of dogs entering the clinic with mange, transmissible venereal tumours, and pregnant. Street surveys showed an increase in sterilised dogs, with higher proportions observed in CNVR-treated sites, although the counts of dogs observed increased overall. The age-structure of free-roaming dogs remained stable over time. In CNVR-treated areas, the probability of observing lactating female dogs decreased, whereas it increased in untreated sites. This work contributes to the growing body of knowledge investigating the impact of dog population management interventions. Continued monitoring and evaluation of CNVR programs are required to identify optimal coverage required to reduce population size effectively.

ecology↗

bioRxiv2024

Can we infer excitation-inhibition balance from the spectrum of population activity?

Networks in the brain operate in an excitation-inhibition (EI) balanced state. Altered EI balance underlies aberrant dynamics and impaired information processing. Given its importance, it is crucial to establish non-invasive measures of the EI balances. Previous studies have suggested that relative EI balance can be inferred from the spectrum of the population signals such as Local Field Potentials, Electroencephalogram and Magnetoencephalography. This idea exploits the fact that in most cases excitatory and inhibitory synapses have quite different time constants. However, it is not clear to what extent spectral slope of population activity is related to the network parameters that define the EI balance e.g. excitatory and inhibitory conductance. To address this question we simulated two different types of recurrent networks and measured spectral slope for a wide range of parameters. Our results show that the slope of the spectrum cannot predict the ratio of excitatory and inhibitory synaptic conductance. Only in a small set of simulations a change in the spectral slope was consistent with the corresponding change in the synaptic weights or inputs to the network. Thus, our results show that we should be careful in interpreting the change in the slope of the population activity spectrum. Significant statementNon-invasive signals such as electroencephalogram (EEG) and magneto-encephalogram (MEG) are routine acquired from human subjects in different functional and dysfunctional states. It is of great interest to relate properties of EEG/MEG to the underlying physiology and network properties. In this regard, recently it was proposed that the slope of the EEG/MEG spectrum can be related to excitation-inhibition balance: steeper slopes indicate higher inhibition. Here we show that such an explanation holds only for a small set of conditions. In most cases spectral slope is not informative of underlying excitation-inhibition balance. Thus, we argue that while spectral slope may be a good biomarker of brain state, it is not informative about the underlying excitation-inhibition balance or network parameters.

neuroscience↗

bioRxiv2024

PAX2 is Transcriptionally Silenced by a Distinct Mechanism of Epigenetic Reprogramming to Initiate Endometrial Carcinogenesis

In most cancers, including endometrial cancer, tumor suppressor genes harboring inactivating mutations have been systematically cataloged. However, locus-specific epigenetic alterations contributing to cancer initiation and progression remain only partly described, creating knowledge gaps about functionally significant tumor suppressors and underlying mechanisms associated with their inactivation. Here, we show that PAX2 is an endometrial tumor suppressor recurrently inactivated by a distinct epigenetic reprogramming event not associated with promoter hypermethylation. PAX2 is expressed throughout normal endometrial glands; however, microscopic clones with PAX2 protein loss arise spontaneously in adulthood and progress to endometrial precancers and cancers. Here we show that PAX2 protein loss occurs via transcriptional silencing in 80% of endometrial cancers. Mechanistically, transcriptomic, epigenomic, 3D genomic, and machine learning analyses showed that silencing is associated with replacement of open/active chromatin features (H3K27ac/H3K4me3) with inaccessible/repressive features (H3K27me3). The spread of the H3K27me3 signal is restrained by cohesin loops, preventing transcriptional dysregulation of neighboring genes. Functionally, PAX2 loss promoted endometrial carcinogenesis by rewiring the transcriptional landscape via global enhancer reprogramming. Genetically engineered mouse models together with organoid and human cell line studies established Pax2 as an in vivo endometrial tumor suppressor that cooperates with Pten to produce lethal cancers. Our discovery of a specific and recurring epigenetic alteration that transcriptionally silences PAX2 to initiate most endometrial cancers opens new lines of investigation into the origins of endometrial cancer with diverse implications for its diagnosis and treatment. One Sentence SummaryWe demonstrate that PAX2 is silenced by a highly recurrent epigenetic mechanism to initiate most endometrial cancers, establishing a novel mechanism of tumor suppressor inactivation.

cancer biology↗

bioRxiv2024

In Silico Toxicity Assessment of Organophosphates: A DFT and Molecular Docking Study on Their Interaction with Human Serum Albumin (HSA)

This study presents an in silico analysis of the toxicity of Organophosphates (OPs) through their interaction with Human Serum Albumin (HSA) protein using density functional theory (DFT) and molecular docking approaches. Organophosphates, known for their widespread use as pesticides, have raised significant concerns due to their potential toxicological effects. To investigate the molecular mechanisms underlying OP toxicity, we conducted DFT calculations to determine the electronic properties and reactivity of selective OP compounds. Molecular docking simulations were performed to explore the binding affinity, interaction sites, and conformational changes of HSA upon exposure to OPs. The DFT analysis revealed key electronic descriptors, such as HOMO-LUMO gap and electrostatic potential, that indicate high reactivity of OPs with biological molecules. Docking results showed strong binding affinities between OPs and HSA, particularly at sites involved in metabolite and drug transport, suggesting potential interference with the proteins native function. The interaction of OPs with HSA was further supported by molecular dynamics simulations, which confirmed the stability of the OP-HSA complex over time. These findings provide critical insights into the molecular basis of organophosphate toxicity, emphasizing the importance of their interaction with HSA. The combined DFT and molecular docking approach offers a valuable framework for predicting the toxicological behavior of OPs and lays the foundation for further in vitro and in vivo studies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/628551v3_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@881814org.highwire.dtl.DTLVardef@e4cb5forg.highwire.dtl.DTLVardef@e3cb74org.highwire.dtl.DTLVardef@1426bb4_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

The impact of fold-dilution and diluent volume on the estimation of colony forming units in a bacterial culture

Considering the non-uniform distribution of bacteria in a liquid culture, accurate enumeration of bacteria by serial dilution is important yet challenging in microbiological research. The deviation of estimated population size from the actual population size is anticipated in view of the sampling error arising at dilution, which is known to increase at each successive dilution; and the sampling error associated with the sample volume, where it is inversely proportional. In the dilution process of such population following a Poisson distribution, the relation of sampling error with the sequentially diluted suspensions is yet to be empirically demonstrated. Also, as a given-fold dilution can be achieved by passaging of either a higher or a lower sample volume, the sampling error associated in this case with the volume being passaged also remains to be evaluated. In view of that, the current experimental study was undertaken to further understand bacterial distribution and the underlying sampling error in dimensions previously not demonstrated. We demonstrated that sampling error in the enumeration process is independent of the bacterial cell densities of the diluted suspensions, which was on contrary to the theoretical assumptions. Moreover, sampling error is also not dependent on the number of passages in the dilution process. Importantly, we also demonstrated that passaging either a higher or lower sample volumes during serial dilution yielded similar enumeration, which was exceptional with regards to the statistical fluctuations inherent to a Poisson distribution.

microbiology↗

bioRxiv2024

Shroom3-Rock interaction and profibrotic function: Resolving mechanism of an intronic CKD risk allele.

Common intronic enhancer SNPs in Shroom3 associate with CKD in GWAS, although there is paucity of detailed mechanism. Previously, we reported a role for Shroom3 in mediating crosstalk between TGF{beta}1- & Wnt/Ctnnb1 pathways promoting renal fibrosis (TIF). However, beneficial roles for Shroom3 in proteinuria have also been reported suggesting pleiotropic effects. Here we focused on identifying the specific profibrotic Shroom3 motif. Given known therapeutic roles for Rho-kinase inhibitors in experimental CKD, and the established interaction between Shroom3 and Rock via its ASD2 domain, we hypothesized that Shroom3-mediated ROCK activation played a crucial role in its profibrotic function in high expressors. To test this hypothesis, we developed transgenic mice and cell lines that inducibly overexpressed wild-type- (WT-Sh3) or ASD2-domain deletion- Shroom3 (ASD2{Delta}-Sh3). Prior scRNAseq data showed that during TIF, Shroom3 and Rock co-expression occurred in injured tubular cells and fibroblasts, highlighting cell-types where this mechanism could be involved. Using HEK293T cells, we first confirmed absent ROCK binding and inhibited TGF{beta}1-signaling with ASD2{Delta}-Sh3-overexpression vs WT-Sh3. In mIMCD cells, ASD2{Delta}-Sh3 overexpression, reduced Rock activation (phospho-MYPT1), pro-fibrotic and pro-inflammatory transcripts vs WT-Sh3. Fibroblast proliferation (3T3) was also reduced with ASD2{Delta}-Sh3. In vivo, we studied ureteric obstruction (UUO) and Aristolochic nephropathy (AAN) as TIF models. In AAN, inducible global-, or Pan-tubular specific-, WTSh3-overexpression showed increased azotemia, and TIF vs ASD2{Delta}-Sh3 mice. WT-Sh3 mice consistently showed significant enrichment of Rho-GTPase, TGF{beta}1- and Wnt/CtnnB1- signaling in kidney transcriptome, paralleling Shroom3-coexpressed genes in tubulo-interstitial transcriptomes from human CKD. In UUO, again WT-Sh3 mice recapitulated increased fibrosis vs ASD2{Delta}-Sh3. Importantly, ASD2{Delta}-Sh3 did not develop albuminuria vs WT-Sh3, while mutating a disparate Fyn-binding Shroom3 motif induced albuminuria in mice, suggesting motif-specific roles for Shroom3 in the kidney. Hence, our data show a critical role for the Rock-binding, ASD2-domain in mediating TIF in milieu of Shroom3 excess, with relevance to human CKD.

systems biology↗

bioRxiv2024

Arginyltransferase1 drives a mitochondria-dependent program to induce cell death

Cell death regulation is essential for stress adaptation and/or signal response. Past studies have shown that eukaryotic cell death is mediated by an evolutionarily conserved enzyme, arginyltransferase1 (Ate1). The downregulation of Ate1, as seen in many types of cancer, prominently increases cellular tolerance to a variety of stressing conditions. Conversely, in yeast and mammalian cells, Ate1 is elevated under acute oxidative stress conditions and this change appears to be essential for triggering cell death. However, studies of Ate1 were conventionally focused on its function in inducing protein degradation via the N-end rule pathway in the cytosol, leading to an incomplete understanding of the role of Ate1 in cell death. Our recent investigation shows that Ate1 dually exists in the cytosol and mitochondria, the latter of which has an established role in cell death initiation. Here, by using budding yeast as a model organism, we found that mitochondrial translocation of Ate1 is promoted by the presence of oxidative stressors and is essential for inducing cell death with characteristics of apoptosis. Also, we found that Ate1-induced cell death is dependent on the formation of the mitochondrial permeability pore and at least partly dependent on the action of mitochondria-contained factors including the apoptosis-inducing factor, but is not directly dependent on mitochondrial electron transport chain activity or its derived reactive oxygen species (ROS). Furthermore, our evidence suggests that, contrary to widespread assumptions, the cytosolic protein degradation pathways including ubiquitin-proteasome, autophagy, or endoplasmic reticulum (ER) stress response has little or negligible impacts on Ate1-induced cell death. We conclude that Ate1 controls the mitochondria-dependent cell death pathway.

biochemistry↗

bioRxiv2024

ALDH1 subtype-specific inhibitor targets key cell populations in triple negative breast cancer

Aggressive breast cancer subtypes, particularly triple-negative breast cancer (TNBC), lack effective targeted therapies, requiring novel approaches. This study focuses on the aldehyde dehydrogenase 1A (ALDH1A) subfamily, comprising ALDH1A1, ALDH1A2, and ALDH1A3, and their roles in tumor biology and the tumor microenvironment. Comprehensive transcriptomic and single-cell analyses revealed subtype- and cell-specific expression patterns of ALDH1A isoforms, with ALDH1A3 predominantly expressed in epithelial cancer cells of basal-like tumors, while ALDH1A1 and ALDH1A2 were expressed in stromal and immune-associated subpopulations. Guided by these findings, we developed ABD0171, a selective ALDH1A3 inhibitor that demonstrated potent isoform-specific activity. ABD0171 effectively disrupted key pathways in TNBC cells in vitro, including IL6/JAK/STAT3, tPA and Src/FAK, and exhibited superior selectivity, robust antitumor and antimetastatic effects, and a favorable safety profile in vivo. These results establish ALDH1A3 as a promising therapeutic target and validate ABD0171 as a candidate to address current challenges in aggressive breast cancers.

cancer biology↗

bioRxiv2024

HP1a promotes chromatin liquidity and drives spontaneous heterochromatin compartmentalization

Compartmentalization of the nucleus into heterochromatin and euchromatin is highly conserved across eukaryotes. Constitutive heterochromatin (C-Het) constitutes a liquid-like condensate that packages the repetitive regions of the genome through the enrichment of histone modification H3K9me3 and recruitment of its cognate reader protein Heterochromatin Protein-1 (HP1a). The ability for well-ordered nucleosome arrays and HP1a to independently form biomolecular condensates suggests that the emergent material properties of C-Het compartments may contribute to its functions such as force-buffering, dosage-dependent gene silencing, and selective permeability. Using an in vitro reconstitution system we directly assess the contributions of H3K9me3 and HP1a on the biophysical properties of C-Het. In the presence of HP1a, H3K9me3 (Me-) and unmodified (U-) chromatin form co-condensates composed of distinct, immiscible domains. These chromatin domains form spontaneously and are reversible. Independently of HP1a, H3K9me3 modifications are sufficient to increase linker-DNA length within chromatin arrays and slow chromatin condensate growth. HP1a increases the liquidity of chromatin condensates while dramatically differentiating the viscoelastic properties of Me-chromatin versus U-chromatin. Mutating key residues in HP1a show that HP1a interactions with itself and chromatin determine the relative interfacial tension between chromatin compartments, however the formation of condensates is driven by the underlying chromatin. These direct measurements map the energetic landscape that determines C-Het compartmentalization, demonstrating that nuclear compartmentalization is a spontaneous and energetically favorable process in which HP1a plays a critical role in establishing a hierarchy of affinities between H3K9me3-chromatin and unmodified-chromatin. Highlights HP1a is necessary and sufficient for heterochromatin compartmentalization. Heterochromatin compartmentalization is reversible and proceeds through microphase-separation. H3K9me3 is sufficient to change nucleosome-array dynamics and mesoscale material properties. HP1a increases chromatin liquidity. HP1a-chromatin interaction modes tune the interfacial tensions and morphologies of heterochromatin compartments.

biophysics↗

bioRxiv2024

The TWEAK/Fn14 signaling promotes skeletal muscle wasting during cancer cachexia

Cachexia is an involuntary loss of body weight mostly due to skeletal muscle wasting. The proinflammatory cytokine TWEAK and its receptor Fn14 constitute a major signaling system that regulates skeletal muscle mass in diverse conditions. However, the role of TWEAK/Fn14 system in the regulation of skeletal muscle mass during cancer-induced cachexia remains poorly understood. In this study, we demonstrate that the levels of Fn14, but not TWEAK, are induced in skeletal muscle of multiple mouse models of cancer cachexia. Targeted deletion of Fn14 inhibits muscle wasting and gene expression of multiple components of the ER stress-induced unfolded protein response (UPR) in the KPC mouse model of pancreatic ductal adenocarcinoma (PDAC) cancer cachexia. The TWEAK/Fn14 signaling activates PERK and IRE1 arm of the UPR and inhibits protein synthesis in cultured primary myotubes. Inhibition of PERK using pharmacological or molecular approaches improves protein synthesis and inhibits atrophy in TWEAK-treated cultured myotubes. Silencing of Fn14 in KPC cells prior to their inoculation in pancreas of mice also attenuates tumor growth without having any significant effect on muscle atrophy. The knockdown of Fn14 inhibits proliferation, migration, and invasion of cultured KPC cells. Finally, our results demonstrate that targeted ablation of Fn14 also attenuates muscle atrophy in the Lewis lung carcinoma model of cancer cachexia. Altogether, our study provides initial evidence that the inhibition of TWEAK/Fn14 signaling can prevent tumor growth and skeletal muscle wasting during cancer-induced cachexia.

cell biology↗

bioRxiv2024

Fn14 signaling regulates satellite cell self-renewal and expansion during adult skeletal muscle repair

Skeletal muscle regeneration in adults is predominantly driven by satellite cells. Loss of satellite cell pool and function leads to skeletal muscle wasting in many conditions and disease states. Here, we demonstrate that the levels of fibroblast growth factor-inducible 14 (Fn14) are increased in satellite cells after muscle injury. Conditional ablation of Fn14 in Pax7-expressing satellite cells drastically reduces their expansion and skeletal muscle regeneration following injury. Fn14 is required for satellite cell self-renewal and proliferation as well as to prevent precocious differentiation. Targeted deletion of Fn14 inhibits Notch signaling but leads to the spurious activation of STAT3 signaling in regenerating skeletal muscle and in cultured muscle progenitor cells. Silencing of STAT3 improves proliferation and inhibits premature differentiation of Fn14-deficient satellite cells. Furthermore, conditional ablation of Fn14 in satellite cells exacerbates myopathy in the mdx mouse model of Duchenne muscular dystrophy (DMD) whereas its overexpression improves the engraftment of exogenous muscle progenitor cells into the dystrophic muscle of mdx mice. Altogether, our study highlights the crucial role of Fn14 in the regulation of satellite cell fate and function and suggests that Fn14 can be a potential molecular target to improve muscle regeneration in muscular disorders.

cell biology↗