Biology subjects

Sharma, J.

Publications and source records attributed to Sharma, J..

At least 19 recordsLinked to original sources

bioRxiv2026

An integrated database of ion channels

Ion channels play critical roles in a wide range of physiological processes, including the propagation of nerve impulses, insulin secretion and regulation of heart rate. Alterations in ion-channels function or expression can contribute to the development of various diseases, including cancers, genetic disorders, and infectious diseases. Ion channels represent the second-largest class of membrane proteins considered potential targets for therapeutic intervention. However, a comprehensive data resource integrating information on human ion channels and their associations with diseases has been limited. Therefore, the Integrated Database of Ion Channels (IDIC) was developed, comprising information on 493 human ion channels. The database contains a broad range of ion-channel annotations, including gene and protein information, structural details, protein signature sequences, protein domains, nuclear localization signals, and signal peptides. It also provides cross-references to several established biological resources, including the Human Genome Organization Gene Nomenclature Committee (HGNC), National Center for Biotechnology Information (NCBI) Gene, Vertebrate Genome Annotation (VEGA), Ensembl, and the Protein Data Bank (PDB). Furthermore, IDIC incorporates genomic variations identified in various tumors and disease associations involving ion channels, which have been systematically curated from published literature. Through concise search methods and user-friendly browsing functionalities, IDIC serves as an integrated resource for exploring human ion channels and investigating their structural, functional, genetic, and disease-related characteristics. Thus, the database can facilitate a better understanding of ion channels and their potential involvement in diverse human diseases.

bioinformatics↗

bioRxiv2026

A low-androgen environment sustains redox-active sGC states required to restrain castration-resistant prostate cancer growth via elevated cGMP levels

Castration-resistant prostate cancer (CRPC) remains incurable and fatal, creating a dire need for new safe and effective treatment strategies. We recently reported that the soluble guanylyl cyclase (sGC) stimulator, riociguat, cooperates with standard-of-care androgen deprivation (AD) to inhibit castration-resistant tumor burden by oxygenating hypoxic tumor niches and inducing tumor apoptosis. We further found that AD restores the sensitivity of CRPC cells to riociguat, which requires a redox-active functional sGC complex to stimulate cyclic GMP (cGMP) production. As redox reprogramming is a feature of the low-androgen PC milieu, to better establish the parameters of riociguat efficacy, we wished to determine whether redox-inactive forms of sGC persist in the castrate setting. To do so, we treated CRPC LNAI tumor-bearing animals with cinaciguat, an sGC activator which preferentially acts on the oxidized sGC complex. We found that, compared to riociguat, cinaciguat did not significantly increase intratumoral or systemic cGMP levels in the castrate setting. Nor did cinaciguat treatment significantly decrease tumor burden or oxygenate the hypoxic CRPC tumors. Given the preferential activity of cinaciguat on the redox-inactive sGC complex, our results indicate that the low-androgen castrate setting maintains the sGC complex in its functionally reduced state, affirming the critical benefit of AD for riociguat efficacy in the lethal castration-resistant disease stage.

cancer biology↗

bioRxiv2026

Genetic and structural interpretation of NLRP1 FIIND domain variants in glioma in an Indian cohort: a pilot study

Gliomas, particularly glioblastoma (GBM), are aggressive primary brain tumors associated with dysregulated NLR signaling, a pathway central to innate immunity and inflammation. NLRP1 triggers proinflammatory cytokine release and pyroptotic cell death via autoproteolytic cleavage. The FIIND missense variant rs11651270 (M1184V) may modulate this cleavage process. While NLRP1 polymorphisms are associated with various diseases and cancers, their specific impact on glioma remains to be investigated. In our study, five FIIND-domain single-nucleotide polymorphisms (SNPs) of NLRP1 rs371579423, rs58604457, rs57636751, rs11651270, and rs2301583, were investigated by Sanger sequencing in a clinical cohort of glioma patients and compared against population-matched controls from the GenomeIndia dataset (Rajasthan cohort) using genetic association models. Molecular dynamics simulations were performed to evaluate the structural effects of the missense variant rs11651270 (M1184V) in NLRP1 during pre- and post-cleavage states. The linked variants rs58604457 (G>A) and rs57636751 (C>T) exhibited complete linkage disequilibrium (r2=1.00) and were significantly associated with lower odds of glioma (odds ratio ~0.5). The missense variant rs11651270 (T>C) showed no association with glioma risk. Notably, the SNP rs2301583 had a higher allelic frequency in glioma cases despite being absent in the GenomeIndia population-based control catalogue. Molecular dynamics simulations revealed that the M1184V substitution stabilizes local FIIND architecture by preserving {beta}-strand organization through persistent interactions with neighboring residues. This study provides the first combined genetic and structural analysis of NLRP1 FIIND-domain variants in an Indian glioma cohort. These findings illustrate the potential value of integrating population-based genetic association with structural modelling to generate hypotheses and uncover potential functional mechanisms of inflammasome-gene variants in neuro-oncology.

cancer biology↗

bioRxiv2026

An extended N-terminus restrains the plant cell death-inducing ability of the catalytically competent ribonuclease domain in a pea powdery mildew RALPH effector

RALPH (RNase-like proteins associated with haustoria) effectors, which are preferentially expressed in haustoria and structurally resemble fungal T1/F1 RNases, constitute one of the largest effector families in powdery mildew (PM) fungi, yet their functions in dicot-adapted PM species remain poorly understood. Unlike cereal PM RALPHs, which lack the catalytic residues required for RNase activity, some dicot PM RALPHs retain these residues. Here, we performed a comprehensive structural and expression-based characterization of the pea PM Erysiphe pisi RALPH (EpRALPH) repertoire and functionally characterized EpRALPH11, a RALPH effector with partial conservation of the catalytic residues of T1/F1 fungal RNases. Comparative analyses identified multi-RNase-domain RALPHs as a conserved feature of the Erysiphe lineage, while expression profiling showed that many EpRALPHs are preferentially expressed in haustoria during early host colonization. AlphaFold 3-based structural analyses revealed a conserved T1/F1 RNase-like fold despite substantial sequence and surface charge divergence, indicating functional diversification among EpRALPHs. EpRALPH11 enhanced susceptibility to E. pisi in Medicago truncatula, localized to the nucleolus, and induced nucleolar fragmentation when heterologously expressed in Nicotiana benthamiana leaves. Its RNase domain exhibited T1 RNase activity in vitro, supporting the retention of a catalytically competent RNase domain and, together with its nucleolar localization, suggesting that EpRALPH11 targets plant rRNA and disrupts nucleolar functions. The RNase domain induced cell death in N. benthamiana, whereas the full-length protein and catalytic mutants did not. Cell death induction required exclusive nucleolar localization of the RNase domain, and an extended N-terminal intrinsically disordered region suppressed this activity in the full-length protein. Together, our findings reveal a previously unrecognized mechanis regulating RNase activity in a dicot PM RALPH effector and provide new insights into the functional diversification of RALPHs and their adaptation to obligate biotrophy.

plant biology↗

bioRxiv2026

Recommendations for the ethical and accurate use of population descriptors: a trainee-led survey of early-career researchers

Despite the importance of population descriptors in human genomics research, many scientists struggle to translate evolving ethical guidelines into their computational workflows. To characterize this gap between recommendations and implementation, we conducted a mixed-methods survey of early-career researchers to assess how they understand and implement the landmark 2023 NASEM report on the use of population descriptors in human genetics research. We show that while exposure to the report fosters ethical awareness, fundamental misconceptions about race and ancestry persist across academic disciplines, and trainees face structural bottlenecks, including legacy data constraints and a lack of technical confidence. To address this gap, we offer actionable, stakeholder-specific recommendations across the research lifecycle ranging from decision-support tools to "bring-your-own-data" workshops to leadership from academic journals, scientific societies, and trainee mentors. Ultimately, we argue that to promote scientific rigor and reduce bias in genetic discoveries, the scientific ecosystem must invest in the infrastructure necessary to empower the next generation of researchers.

genetics↗

bioRxiv2026

Trichomonas vaginalis targets Lactobacillus jensenii via pseudopodia-independent phagocytosis and secreted lysozyme TvGH25

A low abundance or absence of protective lactobacilli during acute trichomoniasis is a well-known phenomenon that is associated with T. vaginalis (TV) infection. However, a crucial question that remains unanswered is whether alterations in the lactobacilli population precede TV infection or whether the parasite plays an active role in lactobacilli disappearance. Our findings showed that TV efficiently phagocytosed one of the dominant Lactobacillus species L. jensenii (LJ). Phagocytosis proceeds via a pseudopodia-independent mechanism reminiscent of sinking with a preference for viable cells. The presence of viable LJ leads to an increase in secretion of 27 TV proteins, including TvGH25 lysozyme. This enzyme cleaves peptidoglycan, a major component of the bacterial cell wall. TV overexpressing TvGH25 effectively lowers the bacterial cell count, evidencing the enzymes antimicrobial potential. These data support the notion that TV cells can suppress the Lactobacillus population through a combination of targeted secretory response and phagocytic activity, revealing novel potential targets for developing alternative therapeutic strategies against trichomoniasis. Significance StatementTrichomonas vaginalis (TV) is a sexually transmitted parasite that causes trichomoniasis and is connected to the disruption of the healthy vaginal microbiome, dominated by Lactobacillus species. However, the nature of the interactions between TV and Lactobacillus is poorly understood. In this study, we show that TV uses an unusual form of pseudopodia-independent phagocytosis to engulf L. jensenii alongside a targeted secretory response to the bacterial encounter, involving TvGH25 lysozyme. We found that TV acquired this enzyme by lateral gene transfer from bacteria and repurposed it against bacteria to degrade the major bacterial cell wall component peptidoglycan. TvGH25 thus represents an effective component of TVs antibacterial arsenal. Our findings provide new insights into the mechanistic disruption of the protective Lactobacillus microbiota.

microbiology↗

bioRxiv2026

Identification of Altered Potassium Channels for Drug Repurposing in Long COVID Patients

Long COVID (LC) is a complex condition characterized by persistent, chronic multisystem manifestations, with a significant proportion of patients exhibiting neurological symptoms. Human ion channels (HICs), particularly potassium channels, are abundantly expressed in the nervous system and linked to key metabolic processes, making them potential candidates for understanding LC pathophysiology and drug repurposing. Meta-analysis of RNA-Seq datasets from COVID-19-recovered and LC patients was performed to identify altered HICs in LC. Differential gene expression analysis, functional enrichment analysis, and weighted gene co-expression network analysis were performed to uncover key genes, pathways, and co-expression modules consisting of HICs, lipid metabolism-, and immune signaling-related genes. A total of 715 dysregulated genes, including eighteen HICs were identified, among which seven were potassium channels. Three significant modules containing HICs, lipid metabolism-, and immune signaling-related genes were identified and found to be associated with antigen processing and presentation, complement and coagulation cascades, and cytokine-related pathways. Additionally, drug-gene interaction analysis led to identification of approved drugs targeting KCNA6, KCNJ10, KCNN3, and KCNH4 that might provide opportunities for drug repurposing in neurological manifestations in LC. Further experimental validation is required to establish their efficacy and assess their potential for translation into clinical applications for patients with LC.

bioinformatics↗

bioRxiv2026

Ferroptosis links α-synuclein pathology across brain and skeletal muscle in Parkinsons disease

Parkinsons disease (PD) is increasingly recognized as a multisystem disorder, yet the mechanisms linking neurodegeneration with muscle dysfunction remain largely unknown. In this study, using an A53T -synuclein (Syn) transgenic mouse model, we demonstrate coordinated pathological changes across the brain-muscle organs characterized by systemic inflammation, iron accumulation, oxidative stress, and ferroptosis-associated lipid peroxidation. Our quantitative proteomics data revealed dysregulated iron metabolism and ferroptosis in the brain and skeletal muscle. Biochemical validation confirmed increased expression of Transferrin receptor 1 (TFRC), elevated lipid peroxidation, and suppression of antioxidant defenses, including SLC7A11 and GPX4, indicating enhanced ferroptotic susceptibility. Cell-surface proteomics and biophysical assays further revealed that pathological Syn directly interacts with TFRC, promoting iron accumulation and ferroptosis-associated oxidative damage in neuronal and muscle cells. Together, our findings identify ferroptosis as a shared pathological mechanism across the brain and muscle, mediated by the Syn-TFRC interaction, thus linking neurodegeneration and peripheral muscle pathology in PD.

neuroscience↗

bioRxiv2025

ONCOchannelome: A computational framework to investigate altered ion channels across tumor types

Conventional approaches for analyzing ion channels in cancer primarily focus on the detection of membrane potential to record the polarization states of the cellular membrane. Although these approaches provide meaningful insights during validation, they face challenges in discovery, especially in identifying the ion channels that govern the membrane potential. Moreover, ion channels are known to exhibit context-dependent activity that often depends on the cancer type and metabolic state of the tumor. Here, we developed a computational framework, ONCOchannelome, that allows the identification of potential ion channels via transcriptomic datasets. We collected publicly available RNA-Seq datasets corresponding to 2421 normal, 5442 primary tumor and 588 metastatic samples of 15 tumor types. Using the data, we designed a computational strategy to merge the datasets, identifying differentially expressed ion channels in the tumor and metastatic states and aiding in the determination of ion channels in different tumor states. We subsequently developed strategies to determine the correlation of altered ion channels with epithelial-to-mesenchymal transition and to identify differentially coexpressed ion channel networks along with their possible transcription factors. The ONCOchannelome allows visualization of altered ion channels in the tumor and metastatic states in addition to revealing changes resulting in changes in biological processes and molecular functions as the tumor progresses. The ONCOchannelome enhances our understanding of the dependence of ion channels in different tumors in addition to revealing their observed alterations in progressing from the primary tumor state to the metastatic state.

bioinformatics↗

bioRxiv2025

Encoded cell-material interactions to reroute cytokine signaling for regenerative medicine

Regenerative engineering harnesses materials science and stem cell biology to develop strategies to repair damaged and diseased tissue. Despite advances in designer materials, few techniques effectively provide auto-regulated feedback mechanisms that govern how cells sense and respond to discrete microenvironmental changes. Here, we demonstrate that the artificial, juxtacrine-like receptor synthetic Notch (synNotch) can be activated by endogenous multimeric cytokines in solution, without immobilizing materials, revealing a previously unreported activation modality and yielding up to 24-fold dynamic range. To broaden synNotch sensing to monomeric cytokines, we developed nMATRIX, a co-engineered material-cell platform that detects endogenous, soluble ligands and routes them to programmed gene circuits with spatially confined effects. nMATRIX can be tuned to recognize the interleukins IL-1{beta} and IL-6 using synNotch receptors plus cognate biomaterials, yielding up to 68-fold dynamic range and converting these inflammatory inputs into orthogonal outputs that reprogram nearby cell phenotypes. nMATRIX functions across multiple cell types and can incorporate the synNotch-related SNIPR synthetic receptor platform. nMATRIX repurposed inflammatory signals and converted them into anti-inflammatory cues to polarize macrophages (increased CD163, CD206; decreased CD86). Thus, nMATRIX couples native soluble cues to customized cellular responses with tunable sensitivity, offering a flexible materials-based approach for self-regulating regenerative therapies.

bioengineering↗

bioRxiv2025

Selective targeting of Plasmodium falciparum hexose transporter by phytochemical Ginsenoside Rg1 disrupts glucose metabolism and block development of parasite

The emergence of resistance to first-line antimalarial therapies highlights the critical need for next-generation drugs that target distinct molecular pathways and employ novel mechanisms of action. Notably, the intra-erythrocytic parasite development is highly dependent on a sustained glucose supply as their fundamental energy source. Therefore, exploiting a "selective starvation" strategy, by targeting the parasites reliance on glucose metabolism, particularly through the Plasmodium falciparum hexose transporter (PfHT1), which is critical for parasite survival can serve as a promising therapeutic approach to combat multidrug-resistant Plasmodium parasites. Through molecular docking and structure-based drug design approach, we identified a natural compound, Ginsenoside Rg1 (G-Rg1) from drug bank database library, as a potential PfHT1 inhibitor. The PfHT1 specificity of G-Rg1 was validated using yeast complementation model. Subsequently, to investigate the role of PfHT1 in drug resistant Pf parasites we investigated the stage-specific expression of PfHT1 in both artemisinin (ART)-sensitive and resistant Pf parasites and reported its elevated expression in resistant parasites, predicting its role in their survival. Notably, in vitro growth inhibition studies demonstrated that G-Rg1 effectively suppressed the growth of both ART-sensitive and resistant Pf parasites. Additionally, G-Rg1 potentiated the efficacy of dihydroartemisinin in combination and ring survival assays, indicating its potential to circumvent resistance mechanisms. G-Rg1 administration alone and in combination with ART, in P. berghei ANKA-infected mice reduced parasite multiplication and increased mean survival time. Our findings support G-Rg1 as a promising candidate for drug development against malaria, highlighting the potential of targeting PfHT1 to combat drug-resistant malaria.

pharmacology and toxicology↗

bioRxiv2025

Transcriptional Roadmap of the Human Airway Epithelium Identifying HLF as a Novel Regulator of Basal Stem Cell Function

RationaleThe human airway epithelium depends on a coordinated hierarchy of stem-and differentiated cells to maintain tissue integrity and respond to injury. Defining the transcriptional and translational programs that govern these processes is critical for understanding airway disease and advancing regenerative therapies. ObjectivesTo map the transcriptional landscape of the human airway epithelium and identify regulatory factors controlling basal stem cell function and epithelial differentiation. MethodsWe performed single-cell RNA sequencing on bronchial biopsies from nine healthy never-smokers, categorized into young (<40 years) and aged (>60 years) cohorts. Unbiased cell type annotation and pseudotime trajectory analysis were used to define cell states and transcription factor dynamics. Measurements and Main ResultsAll major airway epithelial cell types were identified, with conserved composition and transcriptional programs across age groups. Basal stem cells (BSCs) exhibited elevated ribosomal gene expression, indicating increased translational readiness. Pseudotime analysis revealed transitions from basal to differentiated states, with MYC, JUN, and FOS upregulated in proliferative suprabasal cells. HLF emerged as a BSC-enriched transcription factor downregulated upon differentiation. Functional assays showed that HLF overexpression suppresses proliferation in airway BSC and in lung squamous carcinoma cells, while Hlf-deficient mice display basal cell hyperplasia and deficient differentiation. In lung cancer datasets, low HLF expression correlated with worse patient survival. ConclusionsThis study defines conserved gene programs in the human airway epithelium and identifies HLF as a novel regulator of BSC proliferation and potential tumor suppressor. These findings may inform the development of regenerative therapies and contribute to improved understanding and treatment of lung disease.

molecular biology↗

bioRxiv2025

Identifying and treating CLN3 disease outside the central nervous system

Background and aimsSevere gastrointestinal (GI) symptoms occur in people with CLN3 disease, a neurodegenerative disorder. If left untreated these GI symptoms compromise life quality and may contribute to death. We hypothesized GI symptoms in CLN3 disease are at least partially due to neurodegeneration in the enteric nervous system (ENS), the master regulator of bowel function. MethodsWe examined the integrity of the ENS in human CLN3 autopsy small bowel and colon, and in CLN3 deficient (Cln3{Delta}ex7/8) mice. We performed detailed immunohistological analyses of enteric neurons and glia and assessed bowel transit times at multiple disease stages. We then tested the therapeutic potential of neonatal intravenous gene therapy (AAV9-hCLN3) to prevent bowel phenotypes in Cln3{Delta}ex7/8 mice. ResultsHuman CLN3 bowel displayed a profound loss of enteric neurons and their neurites, with pathological effects upon enteric glia. Cln3{Delta}ex7/8 mice had normal appearing ENS at 1 month of age, but then experienced progressive loss of both enteric neurons and glia accompanied by marked bowel distention, resembling the human CLN3 phenotype. Degenerative changes in Cln3{Delta}ex7/8 mouse enteric neurons and glia were largely prevented by systemic neonatal delivery of AAV9-hCLN3 gene therapy, preventing bowel distention at disease endstage. ConclusionsOur findings demonstrate that CLN3 deficiency profoundly damages enteric neurons and glia in both murine and human CLN3 disease, contributing to GI dysfunction. This study provides preclinical evidence that systemic gene therapy may effectively treat multiple aspects of bowel pathology, expanding the therapeutic landscape beyond the CNS. What you need to know: Background and ContextSignificant gastrointestinal (GI) symptoms are evident in many pediatric neurological conditions. We hypothesized that, in addition to central nervous system (CNS) effects, defects in the enteric nervous system (ENS) may underlie these GI symptoms in some neurodegenerative diseases. Revealing such defects would open up new opportunities for treating these life-limiting and debilitating symptoms. New FindingsThe enteric nervous system is significantly impacted in human CLN3 disease, a feature that is recapitulated in CLN3 mice. Progressive enteric neurodegeneration in these mice follows a similar time course to neuron loss in the brain, resulting in severe bowel distention. Nevertheless, bowel distention and the majority of the pathology within the enteric nervous system can be mitigated via neonatal gene therapy. LimitationsOur human data will need to be replicated in larger numbers of CLN3 cases, and methods will need to be developed to treat the human bowel, avoiding the risk of liver tumors. ImpactThese results reveal that a neurodegenerative disease previously thought to primarily affect the CNS, damages the bowels enteric nervous system and that ENS degeneration can be prevented in mice by gene therapy. These data provide a new perspective on this pediatric disorder and may have relevance to other pediatric neurologic diseases. Lay SummaryThe progressive loss of neurons in CLN3 disease is not confined to the brain but also occurs in the bowel enteric nervous system, contributing directly to GI dysfunction. Neurodegeneration in the enteric nervous system can be prevented by treating the bowel with gene therapy.

neuroscience↗

bioRxiv2024

Functional Dichotomy of Orbitofrontal Cortex and Anterior Cingulate Cortex Subregions in Decision-Making and Brain-Body Regulation

Mood disorders are associated with complex disruptions in brain networks, including those associated with the orbitofrontal cortex (OFC) and pregenual anterior cingulate cortex (pACC). The functional contribution of the caudal OFC (cOFC) has remained largely unexplored. We investigated the functions of the cOFC and pACC in macaques performing an approach-avoidance task by the combination of multimodal recordings and electrical microstimulation (EMS) of the cOFC. We assessed neural, autonomic and behavioral responses. We found the cOFC to be sensitive to both positive and negative stimuli, whereas the pACC was singificantly more active during aversive outcomes. EMS of the cOFC increased avoidance behavior, suggesting a causal role for the OFC subdivision in cost-benefit decision-making. Physiological measurements were positively correlated with behavioral patterns, emphasizing body-brain synchronization during emotionally significant decision-making. We suggest that the cOFC contributes to inducing pessimistic states, thereby making its dysfunction a potential contributor to the etiology of mood disorders.

neuroscience↗

bioRxiv2024

FungAMR: A comprehensive portrait of antimicrobial resistance mutations in fungi

Antimicrobial resistance (AMR) is a global threat. To optimize the use of our antifungal arsenal, we need rapid detection and monitoring tools that rely on high-quality AMR mutation data. Here, we performed a thorough manual curation of published AMR mutations in fungal pathogens to produce the FungAMR reference dataset. A total of 501 papers were curated, leading to 35,792 mutation entries all classified with the degree of evidence that supports their role in resistance. FungAMR covers 95 species, 246 genes and 208 drugs. We combined variant effect predictors with FungAMR resistance mutations and showed that these tools could be used to help predict the potential impact of mutations on AMR. Additionally, a comparative analysis among species revealed a high level of convergence in the molecular basis of resistance, highlighting some potentially universal resistance mutations. The analysis also showed that a significant number of resistance mutations lead to cross-resistance within antifungals of a class, as well as between classes for certain mutated genes. The acquisition of fungal resistance in the clinic and the field is an urging concern. Finally, we provide a computational tool, ChroQueTas, that leverages FungAMR to screen fungal genomes for AMR mutations. These resources are anticipated to have great utility for researchers in the fight against antifungal resistance.

microbiology↗

bioRxiv2024

CYP3A5 inhibition causes G1/S blockade and synergizes with CDK4/6 inhibitor to suppress prostate cancer cell growth: Implications in reducing health disparity

Prostate cancer (PC) is a leading cause of death in men because of the high incidence and long-term inefficacy of the existing treatment options. Furthermore, it exhibits significant health disparities that affect African-American (AA) men more adversely than others do. Previously, we established CYP3A5, a highly expressed protein in AAs PC, as a positive regulator of androgen receptor (AR) signaling. We examined the impact of CYP3A5 depletion on genome-wide transcriptional output using RNA sequencing to gain deeper mechanistic insights. The data revealed that 561 genes were downregulated and 263 were upregulated upon silencing of CYP3A5 in PC cells. Furthermore, in silico pathway analyses of differentially expressed genes suggested that the cell cycle regulation pathway was most significantly affected by CYP3A5 inhibition. Cell cycle analysis of CYP3A5-silenced cells and those treated with clobetasol, a specific CYP3A5 pharmacological inhibitor, showed G1/S phase blockade. Both CYP3A5-depletion and pharmacological inhibition resulted in the downregulation of cyclin D, cyclin B, and CDK2, along with the upregulation of p27kip1 but had minimal effects on CDK4/6 levels. Combination treatment with clobetasol and the CDK4/6 inhibitor palbociclib exhibited synergy with combination index (CI) values ranging from 0.28-0.78. Our findings support the utility of CYP3A5 as a druggable therapeutic target that works more effectively in combination with CDK4/6 inhibition to limit the progression of PC, especially for AA patients with AA. This combination addresses CDK4/6 inhibitor resistance, which is often linked to CDK2 overexpression, and can potentially be useful in reducing disparities in the clinical outcomes of PC. SignificanceOur study highlights CYP3A5 as a key regulator of the cell cycle in prostate cancer (PC). Its overexpression in African American (AA) patients may be a key molecular driver of disparities in outcomes. The combination of CYP3A5 and CDK4/6 inhibitors shows a synergistic effect on therapeutic outcomes and addresses CDK2-mediated resistance. Thus, targeting both CYP3A5 and CDK4/6 could improve treatment outcomes, especially in AA PC patients.

cancer biology↗

bioRxiv2024

Epigenetic adaptation drives monocyte differentiation into microglia-like cells upon engraftment into the retina

The identification of specific markers to distinguish resident microglia from infiltrating monocytes has been a long-standing challenge in neuroscience. Recently, proteins such as P2RY12, TMEM119, and FCRLS have been proposed as microglia-specific and are now widely used to define microglial populations in health and disease. The specificity of these markers was predicated on the assumption that circulating monocytes retain their distinct signatures after entering the central nervous system (CNS). Here, we challenge this paradigm. Using a combination of bone marrow chimeras, single-cell RNA sequencing, ATAC-seq, flow cytometry, and immunohistochemistry, we demonstrate that monocytes engrafting into the CNS acquire de novo expression of these established microglia markers. This phenotypic conversion is driven by profound epigenetic reprogramming, characterized by dynamic changes in chromatin accessibility at key gene loci, including P2ry12, Tmem119, and Aif1 (Iba1), and a shift in transcription factor binding motifs toward a microglial profile. We show this process occurs in the retina following injury and, remarkably, under physiological conditions in the brain and spinal cord, where blood-derived monocytes progressively contribute to the resident myeloid pool. Furthermore, engrafted monocytes downregulate canonical monocyte markers (Ly6C, CD45), eventually becoming indistinguishable from embryonic microglia based on conventional phenotyping. Our findings reveal that infiltrating monocytes undergo extensive epigenetic and transcriptional remodeling to adopt a microglia-like fate, challenging the specificity of current markers and necessitating a re-evaluation of the distinct roles of these two cell populations in CNS pathology. Significance StatementDistinguishing resident CNS microglia from infiltrating monocytes is fundamental to understanding neuro-inflammation. This study reveals that widely used "microglia-specific" markers are not exclusive, as monocytes entering the central nervous system are epigenetically reprogrammed to express them. This mimicry invalidates long-held assumptions about microglial identity and demonstrates that many cells previously identified as microglia may have a peripheral origin. Our work underscores the critical need for more reliable methods to differentiate these populations to accurately define their respective contributions to CNS health and disease.

immunology↗

bioRxiv2024

Di-HAMP domains of a cytoplasmic chemoreceptor modulate nucleoid array formation and downstream signalling

In bacterial chemosensing, environmental cues are typically sensed by bacterial transmembrane receptors known as methyl accepting chemotaxis proteins (MCPs). MCPs form highly organized arrays using the bacterial membrane as a scaffold, which amplify the signals and transduce them into a cellular response. The FrzCD cytoplasmic receptor from Myxococcus xanthus is unique due to its ability to bind DNA and use the nucleoid as a scaffold to form arrays. In this study, we identified two HAMP (histidine kinase, adenylyl cyclase, MCP and phosphatase) domains located between the DNA binding and signaling domains of FrzCD. In vitro experiments demonstrate that these HAMP domains restrict FrzCD to a dimeric form in solution and modulate FrzCDs affinity for DNA, whereas the signaling domain stabilizes higher-order oligomeric assemblies upon DNA binding. Through fluorescence microscopy and analyses on Myxococcus social behavior, we demonstrate that the impact of FrzCD HAMP domains on DNA binding and oligomerization significantly influences group motility and development. Our results suggest that HAMP domains might have roles not only in signal transduction but also in the plasticity of chemosensory arrays. These observations illustrate mechanisms of regulation of a DNA-bound cytoplasmic array formed by a diffusible MCP. Significance StatementOur study identifies the presence of tandem HAMP domains in a cytoplasmic chemoreceptor, FrzCD, from Myxococcus xanthus, and highlights their role in dynamic receptor oligomerization on a DNA scaffold. By controlling receptor oligomerization and subsequently the array formation on the nucleoid, the tandem HAMP domains impart plasticity to the receptor arrays. Such plasticity governs cellular responses to external signals and dictate bacterial social behavior in group motility and multicellular structure formation.

microbiology↗