Biology subjects

Dutta, D.

Publications and source records attributed to Dutta, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Integrated Clinical and Proteomic Precision Subgrouping for Severe Dengue Endotype Signature

BackgroundSevere dengue remains difficult to predict because patients with different clinical trajectories may present with overlapping features, and conventional severity classifications may not fully capture underlying biological heterogeneity. In this study, we applied an integrated clinical and proteomic endotyping approach to dissect dengue disease heterogeneity and identify molecular signatures associated with severity. MethodsPlasma proteomic profiles were analyzed together with detailed clinical, biochemical, hematological, coagulation, and immunological parameters from healthy controls and dengue patients classified according to WHO 2009 severity criteria. High-throughput proteomic analysis, unsupervised clustering, pathway enrichment, and machine-learning-based classification were used to identify dengue endotypes and define molecular features associated with predicted severe disease. ResultsIncreasing dengue severity was associated with progressive abnormalities in liver function, coagulation parameters, hematological indices, and inflammatory mediators, including IL-6, IL-15, HGF, and MUC-16. However, proteomic profiling revealed substantial overlap across conventional severity categories, indicating that clinical classification alone does not fully resolve dengue host-response heterogeneity. Integrated clinical-proteomic clustering identified distinct dengue endotypes, including a predicted severe endotype enriched for inflammatory, antiviral, and cytotoxic lymphocyte-associated pathways. This high-risk endotype was characterized by elevated IL-15, IFN-{gamma}, and granzymes, consistent with coordinated activation of cytotoxic lymphocyte-associated antiviral responses. Machine-learning analysis further showed that proteomic features were strong discriminators of this endotype, supporting their potential utility as biomarkers of severe host-response states. ConclusionIntegrated clinical-proteomic endotyping provides molecular resolution beyond conventional severity grading and identifies immune pathways associated with severe dengue. This framework may improve biological understanding of dengue progression and support future risk stratification and biomarker development.

systems biology↗

bioRxiv2026

HIV Infection in Humanized Microglial Mice Disrupts Feeding Behavior and Circadian Rhythms with Cortical Neuroinflammation

Although effective antiretroviral therapy (ART) has substantially reduced the severity of human immunodeficiency virus (HIV)-associated neurocognitive disorders (HAND), the condition remains highly prevalent. Understanding HAND has been a challenge due to the lack of small animal models capable of supporting productive HIV infection in the brain. Recent advances in humanized mouse models with engrafted human glial cells now enable systemic HIV infection that extends to the central nervous system, offering a powerful platform to study HAND pathogenesis. In this study, we investigated behavioral alterations and neuropathological changes associated with HIV infection. Using home-cage monitoring, we observed that HIV-infected mice exhibited reduced feeding efficiency, consuming less food despite spending more time at the feeder, compared to uninfected controls. Additionally, infected animals displayed disrupted circadian rhythms, with a significant correlation between central nervous system viral load and increased locomotor activity during the light cycle. Neuropathological analyses revealed region-specific vulnerability, with the cortex exhibiting pronounced inflammatory and neurodegenerative changes. These findings were supported by transcriptomic profiling, which demonstrated heightened inflammatory and antiviral gene expression in the cortex, along with differentially expressed genes associated with neuropathology and behavioral deficits. Together, these results highlight distinct region-specific responses to HIV infection in the brain and establish this humanized mouse model as a valuable tool for elucidating the mechanisms underlying HAND and its associated behavioral deficits.

neuroscience↗

bioRxiv2026

The Urinary Tract Commensal Peptoniphilus spp. Encodes a Novel 17β-Hydroxysteroid Dehydrogenase

Microbial steroid metabolism represents an underappreciated extension of the vertebrate endocrine system, with growing evidence that host-associated microbes contribute to the diversity and bioavailability of sex steroids within human tissues. Emerging studies have linked microbial androgen metabolism to urinary microbiome composition and to resistance to androgen deprivation therapy (ADT) in prostate cancer. While microbial pathways capable of converting steroid precursors such as cortisol to androgens, via the steroid-17,20-desmolase pathway, such as DesG-mediated interconversion of androstenedione to testosterone have been reported, the diversity of enzymes mediating downstream androgen interconversion remains incompletely defined. Here, we investigate the androgen-forming capabilities of anaerobic bacteria from the male genitourinary microbiome, focusing on NADPH-dependent 17{beta}-hydroxysteroid dehydrogenases (17{beta}-HSDHs) that catalyze interconversion of androstenedione and testosterone. We isolated androgen-forming bacterial strains from human male urine and identified a previously uncharacterized 17{beta}-HSDH encoded by Peptoniphilus obesi, demonstrated that this enzyme catalyzes the NADPH-dependent reduction of androstenedione to testosterone and the reverse oxidation reaction. Sequence similarity searches further identified a homologous 17{beta}-HSDH in Anaerococcus, which was synthesized and functionally validated, revealing conserved activity despite low sequence identity to the previously characterized urinary tract enzyme DesG. The enzymes were found to have broad substrate specificity for C19 and C18 17keto- and 17{beta}-hydroxysteroids. Together, these findings expand the known diversity of microbial 17{beta}-HSDHs and identify previously unrecognized androgen-forming activities within the genitourinary microbiome. ImportanceMicrobial steroid-transforming pathways may provide a mechanism by which commensal anaerobes contribute to androgen availability in the genitourinary tract. By identifying novel 17{beta}-hydroxysteroid dehydrogenases from Peptoniphilus and Anaerococcus, genera repeatedly associated with prostate cancer, this study provides mechanistic insight into how microbial steroid metabolism may influence hormone-driven disease.

microbiology↗

bioRxiv2025

Width of Range Overlap in Congeneric Bird Species Pairs Along An Elevational Gradient In The Eastern Himalayas

We investigated the distribution of range overlap between contiguous pairs of congeneric bird species along a 200-2800 m elevational gradient in the eastern Himalayas. Over a 3-year field survey between from 2012 to 2014 we recorded 15867 birds comprising 245 species in elevational intervals of 50 m. From this data set, we selected 107 congeneric pairs and fit a logistic curve to the abundance ratio versus elevation data to estimate the width of transition zone over which the species ratio changes from 90% to 10%. We found that the distribution of the transition widths range from < 50 m (about a quarter of the pairs) to more than 500 m. This lack of physical exclusion suggests that there is considerable niche separation between closely related species. For a smaller subset of species pairs with better quality data and model fit we investigated the correlation between the degree of range overlap (transition width) on the one hand, and phylogenetic distance and morphological trait difference on the other. We found a significant correlation with mass, beak width and wing size, but not with tarsus length, beak length and phylogenetic distance. This suggests that mass beak width and wing size may play an important role in niche differentiation in the area.

ecology↗

bioRxiv2025

The urinary pathobiont Actinobaculum massiliense generates androgens via the dirAB pathway

While overlooked during the Human Microbiome Project, characterizing the urinary microbiota in health and disease is a new frontier in microbiome science. Recent studies have associated differential abundance of bacterial taxa including Propionimicrobium lymphophilum and Actinobaculum/Actinotignum spp. with prostate cancer. In this study, we collected urine from subjects prior to prostate biopsy and applied a novel Human Sterolbiome Discovery High-throughput (HSDH) assay to identify culturable urinary bacteria with the ability to generate androgens. Application of the HSDH assay to urine samples led to the isolation of eight P. lymphophilum strains positive for cortisol side-chain cleavage (steroid-17,20-desmolase), 17{beta}-HSDH activity, or both. In addition, we isolated three strains of Actinobaculum massiliense that encode DHEA isomerase reductase (dir) genes. The dirA gene encodes a novel 3{beta}/17{beta}-hydroxysteroid dehydrogenase/{Delta}4,5-isomerase and the dirB gene encodes a novel 17{beta}-hydroxysteroid dehydrogenase isoform. Structural prediction and molecular dynamics reveal probable catalytic mechanisms based on the shared catalytic triad but distinct binding pocket geometries of the DirA and DirB that describe their respective reactions. Phylogenetic analysis of DirA and DirB revealed homologs in urinary tract commensals as well as bacteria associated with steroid degradation found in aquatic and terrestrial environments. Taken together, the development of the HSDH assay and the identification of the dir pathway genes is a significant advance in microbial endocrinology, laying the methodological foundation and providing the molecular basis for understanding the role of urinary tract bacteria in host endocrine physiology.

microbiology↗

bioRxiv2025

Integrative multi-omic analysis identifies key transcription factors and target proteins in renal cell carcinoma and its subtypes

To characterize key transcription factors (TFs) whose differential DNA binding can be altered by genetic variants associated with risk for renal cell carcinoma (RCC), we conducted a series of mixed model-based analyses integrating 449 TF ChIP-seq profiles across 9 kidney-related cell lines and summary statistics from a multi-ancestry genome-wide association study of RCC. We identified 96 unique TFs for which presence of SNPs in a neighborhood of TF ChIP-seq peaks are significantly associated (p-value <1x10-4) with their effect on RCC, including EPAS1, ARNT, PAX8 and PBRM1, previously implicated in RCC pathogenesis. Most TFs overlapped active promoters/enhancers in RCC tumors but remained significant after adjusting for tumor chromatin accessibility. Further, we found the co-occupancy of 220 pairs of RCC-related TFs to be associated with RCC risk (FDR<5%) beyond effects of individual TFs, highlighting synergistic regulation between pairs of TFs. To further investigate distal (trans) regulation of TF-binding disruption at RCC associated loci on the proteome, we used a set-based regression to aggregate the trans-effects of multiple loci overlapping with TF binding sites. Across 2,732 proteins profiled in UKB-PPP, identified 169 trans-associated (p-value<1.6x10-7) proteins, nominating specific targets for each TF. For example, we identified TLR3 and ZP3 to be associated with EPAS1, ARNT, and PBRM1, indicating these proteins are likely affected by RCC-related variants disrupting binding sites of the corresponding TFs. These results characterize the landscape of RCC-related TFs and implicate TF-mediated proteomic mechanisms in RCC pathogenesis, nominating testable targets for laboratory studies.

genetics↗

bioRxiv2025

In silico reconstruction of primary and metastatic tumor architecture using GIS-augmented spatial transcriptomics

The tumor microenvironment (TME) comprises different cell populations that interact, contributing to tumor heterogeneity and therapy response. Spatial transcriptomics offers valuable insights into transcriptional complexity and heterogeneity of the TME. We established Geographic Information System (GIS)-augmented In-Silico Reconstruction of Tumor Architecture (GIS-ROTA), a biologically informed analytic framework that integrates pathway or cell type-based enrichment analysis with local Morans I to uncover functional spatial domains. In our Visium dataset of primary and metastatic estrogen receptor-positive breast tumor samples, GIS-ROTA revealed extensive co-localization of estrogen response with metabolic pathway gene sets and mutual exclusivity with metastasis-related and specific immune-related pathway gene sets. The novelty of our approach lies in considering biological functions prior to identifying any spatial domains, providing direct interpretability and minimizing the subjectivity of interpreting clusters observed from conventional analytic methods. Overall, our GIS-ROTA framework integrates biological knowledge first, yielding spatial patterns with functional relevance and enabling identification of novel targets for development of therapeutic strategies.

cancer biology↗

bioRxiv2025

QuickStainer: a rapid negative staining device for improved preservation of molecular structure

Negative staining is a widely used technique for observing macromolecules and their assemblies by transmission electron microscopy. It is commonly employed to optimize specimens for cryo-EM. The stain, typically a uranyl salt, surrounds the structure, providing an outline view at about 20 [A] resolution. Many macromolecules are relatively stable and rigid, and negative stain images provide a good representation of their structure. However, some are labile or flexible and their structure or assembly state is altered by binding to the carbon substrate on the grid before specimen staining. In these cases, the negatively stained appearance does not faithfully represent the structure in solution. This problem is reduced when samples are incubated on the carbon surface for short times (5 s) rather than typical times (30-60 s) before staining. To reduce disruption to a minimum, we have developed a rapid negative staining device (QuickStainer) using 3D-printed components, a stepper motor for precisely timed movements, and an Arduino-controlled interface to execute commands. QuickStainer produces consistent, reproducible results, achieving sample incubation times as low as 10 ms before staining. Tests show rapid adherence of molecules to the grid and greatly improved structural preservation of labile specimens compared with standard preparation protocols. The design of QuickStainer can accommodate inclusion of additional steps, such as timed incubation with enzyme substrate, before staining.

biophysics↗

bioRxiv2025

Thick filament molecular interfaces play a critical role in pathogenesis of hypertrophic and dilated cardiomyopathy

Hypertrophic (HCM) and dilated (DCM) cardiomyopathy variants in genes encoding the myosin heavy chain (MYH7), myosin light chains (MYL2 and MYL3), and cardiac myosin binding protein-C (cMyBP-C, MYBPC3) lead to cardiac hypertrophy or dilatation, with abnormal contractility, relaxation, and energy consumption. Here we defined the structural consequences of >200 pathogenic and benign missense variants in these genes by mapping variants onto a cryo-EM-based atomic model of the human cardiac thick filament. We identified HCM variants residing in 31 molecular interfaces of the complex thick filament interactome, including the two main interfaces of the myosin interacting-heads motif (IHM), and interfaces involving the myosin heavy chain, essential and regulatory light chains, and cMyBP-C. Pathogenic DCM missense variants are rare, and altered only interfaces involving the myosin IHM and tails. None of the 21 variants classified as benign were within interfaces. We demonstrate earlier disease onset and adverse outcomes in HCM patients with pathogenic variants within versus outside of molecular interfaces, emphasizing their importance in normal thick filament function and improving risk stratification of patients. The dissimilar distribution of DCM and HCM variants could explain the different features of the two phenotypes.

biophysics↗

bioRxiv2025

Dengue NS1 Antibodies drive Immune Complex Formation, Hyperglycaemia and systemic pathology in a murine NS1 plasmid challenge model

Dengue virus (DV) NS1, a secreted virotoxin and key pathogenic factor, can trigger immune responses with poorly understood long-term effects. This study assessed immunopathology in mice administered with DV NS1 plasmid DNA via intraperitoneal (IP), intramuscular (IM), or intravenous (IV) route for DV serotypes 1-4. IP delivery caused the most pronounced effects, including elevated AST/ALT and GRP78 levels, hyperglycemia, and altered organ weights, with DV4 NS1 showing the strongest hepatic damage. Despite serum NS1 antigen being undetectable, mice developed strong NS1-specific antibodies (Abs) and immune complexes. Liver histology revealed degeneration and immune cell depletion. DV NS1 plasmid DNA was detected in liver tissue, but not RNA. DV could infect and replicate in murine pancreatic beta cells. In liver cells, DV increased GAPDH expression, while NS1-Ab-positive serums reduced it. Findings indicated that NS1-specific Abs, not the antigen, drove immune-metabolic dysfunctions, emphasizing the need to evaluate Ab-mediated effects in dengue pathogenesis. Significance StatementDengue virus (DV) remains a leading tropical pathogen, yet the long-term effects of its secreted virotoxin NS1 are incompletely understood. Using a murine model, we demonstrated that NS1 plasmid DNA administration drove systemic and organ-specific pathology. Serotype-specific differences in immune responses, biochemical alterations, and histopathological changes underscored NS1s complex role in disease severity. Elevated immune complexes and liver enzyme profiles highlighted mechanisms of immune modulation and hepatic injury, key features of dengue, while increased serum glucose and GRP78 levels pointed to early markers of diabetes onset. These findings provide foundational evidence that NS1- and NS1 antibody-mediated pathways link dengue pathogenesis with metabolic dysfunction, offering critical insights into host-pathogen interactions and comorbidity development.

microbiology↗

bioRxiv2025

ACSS2-Mediated Metabolic-Epigenetic Crosstalk Drives Fulvestrant Resistance and Represents a Novel Therapeutic Target

1.Endocrine therapies target hormone-dependent cancer cells, primarily through estrogen receptor alpha (ER), expressed in [~]70% of breast cancers (ER+). Despite treatment advances, 30-40% of ER+ breast cancer patients experience recurrence and metastasis, with 5-year survival rates of only 31.9%. We validated poor outcomes for liver metastasis patients treated with Fulvestrant (Fulv) using the local Carle Foundation Hospital cohort and examined metabolic pathways in liver metastatic patient-derived xenograft (PDX) models, revealing upregulated lipid and acetyl-CoA production. Our previous work demonstrated that combining Fulv with acetyl-CoA synthase inhibitor (ACSI) targeting Acyl-CoA Synthetase Short Chain Family Member 2 (ACSS2), synergistically reduced ER+ metastatic breast cancer (MBC) cell viability in vitro. Using multiple analytical approaches-isotope tracing, CUT&RUN sequencing, immunofluorescence, western blot, and RNA sequencing-we characterized the effects of acetyl-CoA synthesis inhibition on Fulv-induced alterations. Fulv treatment of MBC cells increased ACSS2 expression and acetate utilization. Isotope tracing revealed that Fulv decreased acetate flux to the TCA cycle while promoting fatty acid synthesis. Importantly, ACSS2 was predominantly nuclear and CUT&RUN sequencing showed that Fulv treatment increased ACSS2 chromatin occupancy and ER/ACSS2/H3K27ac overlapping sites near genes associated with tumor progression, which was eliminated by combination of ACSI and Fulv. RNA sequencing revealed reduction of Fulv-induced expression of genes involved in cancer cell metabolism and key signaling pathways in cancer with the Fulv+ACSI combination. In a therapy-resistant xenograft model, combining Fulv and ACSI reduced Fulv-dependent increase in metastatic burden. Our findings indicate ACSS2 contributes to endocrine therapy resistance through nuclear acetyl-CoA provision for epigenetic alterations. Targeting these cancer cell adaptations represents a novel therapeutic approach potentially reducing metastasis-related mortality and improving breast cancer treatment outcomes.

cancer biology↗

bioRxiv2025

Annotating the X-ray diffraction pattern of vertebrate striated muscle

Low-angle X-ray diffraction is a powerful technique for analyzing the molecular structure of the myofilaments of striated muscle in situ. It has contributed greatly to our understanding of the relaxed, 430-[A]-repeating organization of myosin heads in thick filaments in skeletal and cardiac muscle. Using X-ray diffraction, changes in filament structure can be detected on the [A] length scale and millisecond time scale, leading to models that are the foundation of our understanding of the structural basis of contraction. As with all X-ray fiber diffraction studies, interpretation requires modeling, which has previously been based on low-resolution knowledge of thick filament structure and is complicated by the contributions of multiple filament components to most X-ray reflections. Here, we use an atomic model of the human cardiac thick filament C-zone, derived from cryo-EM, to compute objectively the contributions of myosin heads, tails, titin, and cMyBP-C to the diffraction pattern, by including/excluding these components in the calculations. Our results support some previous interpretations but contradict others. We confirm that the myosin heads are responsible for most of the intensity on the myosin layer-lines, including the M3 meridional. Contrary to expectation, we find that myosin tails contribute little to the pattern, including the M6 meridional; this reflection arises mainly from heads and other components. The M11 layer line (39 [A] spacing) arises mostly from the curved and kinked structure of titin, which allows eleven [~]42-[A]-long domains to fit into the 430 [A] repeat. The M11 spacing can be used as a measure of strain in the myosin filament backbone as there is negligible head contribution. These insights should aid future understanding of the X-ray pattern of intact muscle in different conditions such as contraction and drug treatment. Significance statementX-ray diffraction is widely used to study the structure of striated muscle, revealing the molecular organization of the thick and thin filaments in situ. Changes in the X-ray pattern during contraction provide insights into contractile mechanisms on the [A] length scale and millisecond timescale. Interpretation of X-ray patterns is based on modeling, which is complicated by contributions of multiple filament components to different reflections and the lack of a reliable thick filament model. Here, we use a cryo-EM-based atomic model of the thick filament to compute contributions of different filament components to the diffraction pattern, by including/excluding these components in the calculations. The insights gained will aid interpretation of the X-ray pattern in relaxation and contraction and following drug treatment.

biophysics↗

bioRxiv2025

Hyperglycemic state and fluid shear stress affect metastatic breast cancer cell migration via focal adhesion kinase

We tested how the diabetes-related hyperglycemic condition affects the migration of highly metastatic triple-negative breast cancer (TNBC) cells, MDA-MB-231, under a physiological fluid shear environment. MDA-MB-231 cells displayed a significantly enhanced migratory behavior under a high glucose condition (25 mM) specifically when exposed to flow at 15 dyne/cm2 shear stress. In contrast, the effect of fluid shear was marginal under low glucose (5 mM). Normal epithelial MCF-10A cells, on the other hand, showed increased migration by fluid shear under both low and high glucose conditions. The fluid shear-triggered MDA-MB-231 cell migration under high glucose was significantly abrogated by a focal adhesion kinase (FAK) inhibitor, supporting the mediatory role of FAK in MDA-MB-231 TNBC cell sensing of the high glucose-fluid shear environment during migration. The role of FAK was further demonstrated by the effects of FAK inhibitor on MDA-MB-231 cell migration in scratch wound healing and Boyden chamber migration assays. Our studies provide evidence that high glucose and fluid shear could jointly trigger MDA-MB-231 TNBC cell migration that requires FAK activity. These may provide improved mechanistic insights into how concurrent diabetes may impact the pro-metastatic behavior of breast cancer and suggest the impact of exploring FAK as a relevant therapeutic target.

bioengineering↗

bioRxiv2024

HIRA-SETDB1-H3K9me3 axis regulate chromatin architecture in chronic myeloid leukemia cells

Histone cell cycle regulator A (HIRA) confers chromatin accessibility and regulates developmental hematopoiesis. But whether HIRA displays similar role in leukemia, a condition caused by abnormalities during hematopoiesis, remain elusive. Here we show that HIRA interact with heterochromatin cluster in Chronic Myeloid Leukemia, K562, cells. FRAP, FLIM-FRET and ATAC-sequencing analysis revealed increased chromatin compaction, altered spatial distribution of chromatin towards nuclear periphery and loss in chromatin accessibility at the promoter and gene bodies upon downregulation of HIRA in K562 cells. Enhanced chromatin compaction was attributed to increased histone H3K9me3 level mediated by histone methyltransferase SETDB1. Incorporation of histone H3.3 within the SETDB1 promoter in HIRA-knockdown cells induced SETDB1 expression. HIRA-SETDB1-H3K9me3 axis regulate the chromatin architecture in CML cells leading to inhibition of proliferation while induction in differentiation. We anticipate that the exploration of this axis would introduce new paradigm in understanding and targeting molecules that could influence CML disease progression.

cancer biology↗

bioRxiv2024

Wag31, a membrane tether, is crucial for lipid homeostasis in mycobacteria

The mycobacterial cytoskeletal protein Wag31 is necessary for maintaining cell shape and directing cellular growth and elongation. Wag31 has a characteristic N-terminal DivIVA-domain and a C-terminal coiled-coil domain. While the role of Wag31 in polar elongation is known, there is limited mechanistic insight on how it orchestrates growth and elongation. In this report, we delineate roles of the N- and C-terminal domains of Wag31 using genetics, state-of-the-art multi-omics, biochemical, and imaging approaches. We show that Wag31 predominantly interacts with several membrane-associated proteins involved in lipid metabolism, cell wall synthesis and division. Native levels of Wag31 are critical for the maintenance and distribution of membrane lipids. Both depletion and overexpression of Wag31 perturbs lipid homeostasis, leading to the formation of intracellular lipid inclusions (ILIs). Protein-lipid crosslinking and imaging studies reveal that purified Wag31 can bind and effectively tether Cardiolipin (CL)-containing liposomes. We further show that the tethering activity lies in the DivIVA-domain containing N-terminal of Wag31 while the C-terminal mediates protein-protein interactions of Wag31. Despite retaining its ability to interact with partner proteins, the DivIVA domain-deleted Wag31 mutant shows defects in liposome tethering in vitro and non-polar localization of CL in vivo, which eventually causes lethality. Our study suggests that membrane tethering licenses Wag31 to form scaffolds that help orchestrate protein-lipid and protein-protein interactions necessary for mycobacterial growth and survival.

microbiology↗

bioRxiv2024

SARS-CoV-2 protein ORF3a induces Atg8ylation of lysosomal membranes

Atg8ylation is an autophagy associated response to membrane damage that recruits mammalian ATG8 proteins (mATG8s) to damaged membranes to promote their repair or removal. Here, we show that the SARS-CoV-2 protein ORF3a induces lysosomal membrane atg8ylation and that this response protects cells from death. mATG8s interact with ORF3a and are required for lysosomal damage induced by ORF3a. ORF3a targets mTOR in an Atg8ylation dependent manner and promotes lysophagy through mATG8 mediated coordination of TRIM16 and Galectin-3. ORF3a triggers apoptosis, necroptosis, and pyroptosis, whereas atg8ylation limits ORF3a- induced cell death. Together, our findings identify mATG8s and the autophagy conjugation machinery as key regulators of lysosomal atg8ylation and lysophagy in response to the SARS-CoV-2 virulence factor ORF3a.

cell biology↗

bioRxiv2024

De-biased sparse canonical correlation for identifying cancer-related trans-regulated genes

SO_SCPLOWUMMARYC_SCPLOWIn cancer multi-omic studies, identifying the effects of somatic copy number aberrations (CNA) on physically distal gene expressions (trans-associations) can potentially uncover genes critical for cancer pathogenesis. Sparse canonical correlation analysis (SCCA) has emerged as a promising method for identifying associations in high-dimensional settings, owing to its ability to aggregate weaker associations and its improved interpretability. Traditional SCCA lacks hypothesis testing capabilities, which are critical for controlling false discoveries. This limitation has recently been addressed through a bias correction technique that enables calibrated hypothesis testing. In this article, we leverage the theoretical advancements in de-biased SCCA to present a computationally efficient pipeline for multi-omics analysis. This pipeline identifies and tests associations between multi-omics data modalities in biomedical settings, such as the trans-effects of CNA on gene expression. We propose a detailed algorithm to choose the tuning parameters of de-biased SCCA. Applying this pipeline to data on estrogen receptor (ER)-associated CNAs and 10,756 gene expressions from 1,904 breast cancer patients in the METABRIC study, we identified 456 CNAs trans-associated with 256 genes. Among these, 5 genes were identified only through de-biased SCCA and not by the standard pairwise regression approach. Downstream analysis with the 256 genes revealed that these genes were overrepresented in pathways relevant to breast cancer.

genetics↗

bioRxiv2024

An expanded metabolic pathway for androgen production by host-associated bacteria

A growing body of literature implicates host-associated microbiota in the modulation of circulating androgen levels in the host, which could have far-reaching implications for androgen-mediated diseases. However, the microbial genetic pathways involved in androgen production remain unknown. Here, we report the first host-associated microbial gene (desF) encoding an enzyme that catalyzes conversion of androstenedione to epitestosterone (epiT) in the gut bacterium, Clostridium scindens. Despite current dogma that epiT is a nuclear androgen-receptor (AR) antagonist, we demonstrate that epiT is a potent androgen, as assessed by its ability to promote prostate cancer cell growth and expression of prostate specific antigen (PSA). We then quantified the desF gene in fecal samples collected from individuals with advanced prostate cancer (rising blood PSA) undergoing androgen deprivation therapy combined with abiraterone acetate and prednisone (AA/P). Strikingly, fecal desF levels were elevated in a subset of individuals progressing on AA/P versus samples taken during AA/P response (stable). Importantly, we observed that AA does not inhibit the bacterial desmolase enzyme that is analogous to the human drug target of AA. We then determined that bacterial isolates from urine or prostatectomy tissue are capable of androgen production. From these isolates we detected 17{beta}-hydroxysteroid dehydrogenase (17{beta}-HSDH) activity, which has not been previously reported in urinary tract bacteria, and discovered the desG gene in urinary isolates encoding 17{beta}-HSDH that catalyzed conversion of androstenedione to testosterone. Applying advanced artificial intelligence and molecular dynamics, we predict the structures and ligand binding to DesF and DesG. Using a novel bioengineered microencapsulation technique, we demonstrate that urinary androgen-producing bacterial strains can also promote prostate cancer cell growth through steroid metabolism. Taken together, our results are a significant advance for steroid microbiology in humans and suggest that these microbial biotransformations should be further studied in the context of androgen-mediated physiological processes and diseases.

microbiology↗