Biology subjects

Choudhury, A.

Publications and source records attributed to Choudhury, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Spatially-resolved multimodal profiling identifies functionally-heterogeneous cancer-associated fibroblasts associated with poor radiotherapy outcomes in muscle-invasive bladder cancer.

Background: Cancer-associated fibroblasts (CAFs) contribute to systemic therapy resistance in muscle-invasive bladder cancer (MIBC), but their functional heterogeneity and relevance to curative bladder-preserving radiotherapy, are poorly understood. Methods: Transcriptomic analysis was performed on 279 tumours from BC2001, a phase 3 radiotherapy clinical trial. To study CAF heterogeneity, we integrated bulk RNA-seq, single-cell spatial analysis of multiplex immunofluorescence images and quantification of extracellular matrix (ECM) features in 155 MIBC biopsies. The functional heterogeneity of distinct CAF populations was evaluated by single-nuclear RNA-seq. Spatial interactions between CAF populations and CD8+ T-cells was assessed and the relevance of lymphocytes to radiation responses was evaluated in a CAF-enriched murine bladder cancer model (BBN963). Results: BC2001 patients with CAF-enriched tumours had worse overall survival (HR=1.671, 95% CI 1.221-2.287, Log-rank p=0.0012). CAF abundance and antigen expression was highly heterogenous. Podoplanin (PDPN) was expressed on the majority of CAFs and was associated with inflammatory pathways. Enrichment of CAF gene signatures was associated with a significant increase in CAFs expressing fibroblast activation protein (FAP) (p=0.004) and dense ECM features (p=0.0004). Fifty-three percent of tumours exhibited stromal CD8+ T-cell exclusion with significant enrichment in FAP-dominant neighbourhoods (p<0.001). In vivo, lymphocytes were critical for radiation-induced tumour control, indicating that immune cold or excluded tumours may have limited radiotherapy responses. Conclusion: In MIBC, CAFs are associated with poor radiotherapy outcomes. Multiple mechanisms are deployed by functionally-heterogeneous CAFs, including promotion of chronic inflammation by PDPN+ CAFs and ECM remodelling by FAP+ CAFs which impact CD8+ T-cell distribution and radiation responses.

cancer biology↗

bioRxiv2026

High-resolution lineage tracking maps the multi-phase evolution and adaptive potential of biofilms

Although biofilms represent the dominant bacterial lifestyle and are major contributors to recalcitrant, treatment-resistant infections, their evolutionary dynamics at the individual lineage resolution remain poorly understood. We combine DNA barcoding-mediated lineage tracking and spatial sampling of > 100,000 lineages of Escherichia coli to characterize sequential phases of biofilm evolution quantitatively. Severe founder effects during surface colonization initially reduce the effective population size by nearly three orders of magnitude, establishing significant spatial segregation. This structure is subsequently eroded by a previously underappreciated secondary migration phase, during which cells released upon perturbation recolonize biofilms with a rate 103-fold higher than naive planktonic cells. Adaptive evolution subsequently drives specialization through mutations targeting these distinct stages of the biofilm life cycle. Under severe antibiotic bottlenecks, active secondary migration continuously resuscitates local lineage diversity, enabling the parallel emergence of resistance across hundreds of independent lineages. Once locally established, migration drives a rapid spatial spread of resistant mutants. Together, these findings reveal how spatial segregation and secondary migration shape biofilm dynamics, coupling short-term ecological resilience with long-term adaptive potential.

microbiology↗

bioRxiv2026

Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation

In the past few years, we have seen a veritable surge in single-cell (e.g., RNA sequencing) techniques and datasets, enabling increasingly detailed characterization of cellular heterogeneity across tissues and conditions. This surge in single-cell techniques has been complemented by a large number of analysis frameworks and pipelines, and a large parameter space and researcher degrees of freedom to use them. Many neutral benchmarks have been presented for various computational tasks, but most make design decisions that render them incompatible with each other, e.g., different datasets and metrics, or parameter sets used. In this work, we showcase a recently developed framework, Omnibenchmark, to build reproducible, extensible and standardized method comparisons. This not only facilitates the broad investigation of pipelines used in single-cell data analysis, but also highlights how the process of building benchmarks can be streamlined and unified. We do this as an initial proof-of-principle for an arms-length benchmark that evaluates five single-cell RNA sequencing pipelines (filtering to normalization to dimensionality reduction to clustering) on three datasets. This standardization enables benchmarks to be easily extended in several directions, including broader parameter sweeps, comparisons across software versions and architectures, isolation of pipeline steps, and integration of additional pipelines, datasets, and metrics.

bioinformatics↗

bioRxiv2026

Whole-genome pre-amplification as a viable approach for genomic screening of FFPE-derived DNA samples

Whole-genome sequencing (WGS) enables comprehensive analysis of tumour genomes, but its use in formalin-fixed paraffin-embedded (FFPE) samples is limited by DNA fragmentation and low yields. Whole-genome amplification (WGA) methods such as multiple displacement amplification (MDA) can boost DNA availability but distort copy-number alteration (CNA) profiles. DNA ligation-mediated MDA (DLMDA) mitigates this bias by reconstituting fragmented templates, yet its performance in FFPE-derived DNA remains uncertain. We compared paired DLMDA pre-amplified (2h, 8h) and non-pre-amplified FFPE prostate tumour samples from 22 archival blocks (5, 15 and 20 years old). DLMDA increased DNA yield by 42- to 86-fold, with global CNA patterns largely preserved. However, DLMDA significantly reduced the number of detected CNA deletions and amplifications. These effects were independent of both block age and reaction time. CNA dropouts were randomly distributed across the genome, indicating that DLMDA does not introduce regional bias. Our results show that DLMDA enables robust DNA yield recovery and avoids false-positive CNA artefacts, but at the cost of reduced CNA sensitivity. While suitable for CNA screening pipelines through WGS, further improvements are required to minimise the false-negative risk and improve the techniques sensitivity for FFPE-based genomics.

molecular biology↗

bioRxiv2026

Mechanism of O2 Activation for Conversion of Fatty Acids into Terminal Alkenes in a Membrane-bound Metalloenzyme UndB

Multinuclear metal centers catalyze some of the most challenging oxidative transformations in biological and chemical catalysis, yet the molecular principles controlling oxygen activation in non-heme diiron enzymes remain unclear. Structural studies of desaturase-like diiron enzymes frequently reveal elongated Fe-Fe separations lacking canonical bridging motifs, whereas spectroscopic measurements indicate substantial metal-metal coupling during catalysis, creating a longstanding mechanistic paradox between structural and spectroscopic observations. Here we show that oxygen activation can be dynamically regulated by fluctuations in metal-metal distance through extensive multiscale simulations of the membrane-bound fatty-acid decarboxylase UndB. UndB catalyses the conversion of naturally abundant free fatty acids into terminal 1-alkenes-valuable hydrocarbon precursors for sustainable biofuels, and exhibits unusual hydrogen peroxide formation that has led to conflicting mechanistic proposals. Combining quantum mechanics/molecular mechanics (QM/MM) simulations with free energy analysis and quantum chemical calculations, we identify a catalytically competent ensemble in which transient Fe-Fe contraction establishes effective metal-metal coupling and enables formation of a peroxodiiron(III/III) intermediate despite elongated resting-state structures and the absence of canonical bridging motifs. The computed free-energy landscape quantitatively reproduces experimentally inferred catalytic barriers and accounts for the substantial H2O2 formation observed during catalysis. The reactive state resembles a P-like intermediate rather than the canonical diamond-core Q species commonly invoked for related diiron enzymes. Comparison with magnetic coupling and mechanistic features reported for related non-heme diiron enzymes, including Alkane monooxygenase AlkB, Stearoyl-CoA Desaturase 1 (SCD1) and the soluble decarboxylase UndA, suggests that dynamic metal-metal distance modulation represents a general mechanism governing oxygen activation across diverse diiron enzyme families. These findings establish metal-metal distance modulation as a previously unrecognized control parameter for oxygen activation in diiron and related multinuclear metalloenzymes, reconciling structural and spectroscopic observations and revealing how protein conformational dynamics regulate electronic coupling to control oxidative catalysis, thereby suggesting a general principle for tuning reactivity in multinuclear catalysts.

biophysics↗

bioRxiv2025

WSB-1 regulates DNA repair and the response to DNA damage response inhibitors in breast cancer

Tumour hypoxia is a poor prognostic factor and linked with metastatic spread and treatment resistance in most solid tumours, including breast cancer. We previously showed hypoxia-regulated E3 ligase WSB-1s association with poor prognosis in breast cancer. Here, we evaluated the role of WSB-1 in DNA repair regulation in breast cancer, and whether these phenotypes can be exploited therapeutically. WSB-1 knockdown led to transcriptome-wide DNA repair factor upregulation, including homologous recombination (HR) factors BRCA1and RAD51. Reciprocally, WSB-1 overexpression led to downregulation of these repair factors and decreased DNA repair capacity. Patient gene expression datasets analyses also showed an inverse correlation between WSB1 expression vs DNA repair and HR pathways. HR-deficient cancers, including BRCA1/2-deficient breast cancers, are extremely sensitive to PARP inhibitors, a phenotype described as BRCAness. We therefore hypothesised if high WSB-1 expression could be similarly exploited therapeutically. WSB-1 overexpression alone radiosensitised cells and led to increased Olaparib (PARP inhibitor) and Berzosertib (ATR inhibitor) sensitivity in vitro. Our study indicates that WSB-1 expression in breast cancer is associated with modulation of HR factor expression, and we propose that elevated WSB-1 expression could be considered as a potential BRCAness biomarker and promote increased sensitivity to DNA repair targeted therapy in these patients.

cancer biology↗

bioRxiv2025

Comparative Analysis of Indole Derivative Production Among Clinical Isolates of Fusobacterium nucleatum

Pathogenic bacteria adapt to distinct disease environments, but whether these adaptations create therapeutic vulnerabilities remains unclear. Fusobacterium nucleatum has emerged as a key microbial player in colorectal cancer (CRC), yet its strain-specific virulence mechanisms remain poorly defined. In this pilot study of 16 clinical F. nucleatum isolates from CRC patients (n=6), Crohns disease patients (n=6), colon of healthy individuals (n=3), and an oral lesion (n=1), a subset of CRC-derived strains produced 3-4-fold higher levels of endogenous indole. Exogenous indole treatment differentially affected growth and biofilm formation, with some strains increasing biofilm despite growth inhibition. Notably, sensitivity to exogenous indole was independent of endogenous production and revealed that isolate 7-1 (EAVG002), a member of the tumorigenic Fna C2 clade, was uniquely hypersensitive to I3CA- and IPA-mediated stress. Invasion assays further showed that indole and its derivatives (I3A, I3CA) reduced invasion of a highly indole-tolerant CRC-derived isolate (SB-CTX3Tcol3) into CRC cells by [~]50%, comparable to antibiotic treatment. Furthermore, in two CRC cell lines, exposure to indole or indole derivatives resulted in substantial variability in adherens junction and tight junction transcript levels, with I3A having the strongest effect on tight junction (CLDN1, CLDN7) transcripts. Collectively, these findings reveal profound strain-level heterogeneity and indole derivative effects, highlighting vulnerabilities that could enable precision therapeutic targeting of pathogenic F. nucleatum populations within the host environment while preserving beneficial commensals.

microbiology↗

bioRxiv2025

Pathological Mechanisms of Motor Dysfunction in Familial Danish Dementia: Insights from a Knock-In Rat Model

Familial Danish Dementia (FDD) is a rare autosomal dominant neurodegenerative disorder caused by a mutation in the integral membrane protein 2B (ITM2b) gene. Clinically, FDD is characterized by cerebral amyloid angiopathy (CAA), cerebellar ataxia, and dementia. Notably, FDD shares several neuropathological features with Alzheimers disease (AD), including CAA, neuroinflammation, and neurofibrillary tangles. In this study, we investigate the pathological mechanisms linking CAA, white matter damage, and motor dysfunction using a recently developed FDD knock-in (FDD-KI) rat model. This model harbors the Danish mutation in the endogenous rat Itm2b gene, along with an App gene encoding humanized amyloid-{beta} (A{beta}). Our analysis revealed substantial vascular Danish amyloid (ADan) deposition in the cerebellar subpial and leptomeningeal vessels of FDD-KI rats, showing an age-related increase comparable to that observed in human FDD patients. Additionally, vascular A{beta} deposits (A{beta}-CAA) were present in FDD-KI rats, but A{beta}-CAA patterns showed some differences between species. Motor function assessments in FDD-KI rats demonstrated age-accelerated motor deficits and gait abnormalities, mirroring the clinical characteristics of FDD patients. To further explore the mechanisms underlying these deficits, we examined cerebellar pathology and found age-related myelin disruption and axonal fiber loss, consistent with postmortem human FDD pathology. Cerebellar demyelination appeared to be driven by neuroinflammation, marked by increased microglial/macrophage activation in response to vascular amyloid deposition. Additionally, we observed extravascular fibrinogen leakage, indicating widespread vascular permeability in both white and gray matter, with fibrinogen deposits surrounding amyloid-positive vessels in aged FDD-KI rats and postmortem FDD cerebellum. These findings suggest that this FDD-KI rat model is the first animal model to recapitulate key neuropathological features of human FDD patients, including both ADan- and A{beta}-type CAA, neuroinflammation, and white matter lesions--pathologies that may underlie the motor and gait impairments seen in the disease.

neuroscience↗

bioRxiv2025

Fractionated radiation alters the extracellular matrix produced by muscle-invasive bladder cancer cells

Muscle-invasive bladder cancer (MIBC) is a prevalent disease that can be treated with radiotherapy, but has a poor prognosis. Radiation-induced extracellular matrix (ECM) remodelling and fibrosis can induce tumour resistance and recurrence, but has not been studied in MIBC. Here we aimed to characterise the impact of radiation on the ECM composition of MIBC. Materials and MethodsThree MIBC cell lines (T24, UMUC3, J82) were treated with fractionated radiation. We used proteomics to analyse the ECM composition produced by surviving cancer cells and immunofluorescence to investigate changes in the morphology and number of ECM fibres. We evaluated the RNA expression of identified ECM proteins (FN1, COL5A1, COL1A1, TNF6AIP6, FLG) in one cystectomy (TCGA-BLCA, n=397) and two radiotherapy (BC2001, n=313; BCON, n=151) cohorts. ResultsThere were 613 proteins affected by radiation (padj<0.05, fold change >2 or <-2), 68 of which were ECM-associated proteins. There was a general increase in proteases and protease regulators but heterogeneity across cell lines. Enrichment analysis showed ECM organisation was the primary pathway affected. Immunofluorescence confirmed radiation affected ECM structure, generally, reducing the number, length and width of fibres. High FN1, COL5A1, COL1A1, TNF6AIP6 and FLG mRNA levels were adverse prognostic markers in clinical cohorts. ConclusionRadiation alters the composition and structure of the ECM produced by MIBC. As a proof-of-concept, we showed the expression of radiation-affected ECM genes are prognostic markers in MIBC. Future studies should validate these radiation-induced ECM changes in clinical samples.

cancer biology↗

bioRxiv2025

Hypoxia-induced extracellular matrix changes are conserved in cancer and directly impact radiotherapy benefit

Our overarching aim was to determine how hypoxia affects the extracellular matrix (ECM). Transcriptomic analysis (21,941 patients; 10 cancer types) identified ECM remodelling as the predominant pathway affected by hypoxia. Multi-omics confirmed that hypoxia impacts ECM organisation and collagen degradation; 53 ECM genes were affected, of which 74% were HIF1/HIF2-regulated. Spatial transcriptomics highlighted different hypoxia remodelling processes in tumour and stroma. Five ECM genes commonly affected in tumour and in vitro constituted a signature. This signature was independently prognostic and independently predictive of radiotherapy benefit in multiple malignancies. Patients within either high or low hypoxic-ECM score tertiles benefited from radiotherapy versus surgery. Hypoxic ECMs generated in vitro increased adhesion and decreased migration of cancer cells, an effect enhanced by irradiation. Immunofluorescence demonstrated that hypoxia decreased collagen fibre number, and irradiation decreased cell-ECM interactions. Taken together, these findings demonstrate hypoxia induces pan-cancer ECM changes, directly impacting radiotherapy benefit.

cancer biology↗

bioRxiv2025

High-Throughput Conjugation Reveals Strain Specific Recombination Patterns Enabling Precise Trait Mapping in Escherichia coli

Genetic exchange is a cornerstone of evolutionary biology and genomics, driving adaptation and enabling the identification of genetic determinants underlying phenotypic traits. In Escherichia coli, horizontal gene transfer via conjugation and transduction not only promotes diversification and adaptation but has also been instrumental in mapping genetic traits. However, the dynamics and variability of bacterial recombination remain poorly understood, particularly concerning the patterns of recombined DNA fragments. To elucidate these patterns and simultaneously develop a tool for trait mapping, we designed a high-throughput conjugation method to generate recombinant libraries. Recombination profiles were inferred through whole-genome sequencing of individual clones and populations after selection of a marker from the donor strain in the recipient. This analysis revealed an extraordinary range of recombined fragment sizes, spanning less than ten kilobases to over a megabase--a pattern that varied across the three tested strains. Mathematical modelling indicated that this diversity in recombined fragment size enables precise identification of selected loci following genetic crosses. Consistently, population sequencing pinpointed a selected marker at kilobase-scale accuracy, offering a robust tool for identifying subtle genetic determinants that could include point mutations in core genes. These findings challenge the conventional view that conjugation always transfers large fragments, suggesting that even short recombined segments, traditionally attributed to transduction, may originate from conjugation.

microbiology↗

bioRxiv2024

Caveolin-1 and Aquaporin-4 as Mediators of Fibrinogen-Driven Cerebrovascular Pathology in Hereditary Cerebral Amyloid Angiopathy

Cerebral Amyloid Angiopathy (CAA), characterized by amyloid-{beta} (A{beta}) accumulation within perivascular spaces (PVS), contributes to vascular damage and inflammation in Alzheimers disease (AD). Despite its significance, the mechanisms driving A{beta} deposition in PVS and the resulting vascular pathology remain poorly understood. Growing evidence suggests that fibrinogen, the main component in blood clots, interacts with A{beta} and exacerbates inflammation in AD. Fibrinogen also co-deposits with A{beta} in the PVS of CAA-positive vessels in the brains of hereditary CAA patients. However, the mechanisms by which fibrinogen contributes to cerebrovascular impairment remain poorly understood. To investigate this, we used TgSwDI transgenic mice, which develop robust CAA pathology, and observed a significant increase in fibrin(ogen) extravasation and colocalization with A{beta} in the PVS. Moreover, we observed a significant aquaporin-4 (AQP4) depolarization in CAA-laden blood vessels of TgSwDI mice, which correlated with fibrin(ogen)-A{beta} colocalization. Given AQP4 crucial role in A{beta} clearance through glymphatic pathway, its depolarization may disrupt critical A{beta} clearance, thereby exacerbating CAA pathology. Additionally, Caveolin-1, a protein involved in non-specific transcytosis across the endothelium, significantly increased with age in TgSwDI mice and correlated with fibrin(ogen) extravasation. To further explore the relationship between fibrin(ogen) and these cerebrovascular alterations, we depleted fibrinogen in TgSwDI mice using siRNA approach. This intervention resulted in decreased CAA, restored polarized expression of AQP4, reduced caveolin-1 levels, attenuated microglial activation, and improved spatial memory in fibrinogen-depleted TgSwDI mice. These findings suggest that targeting fibrinogen could be a promising strategy for mitigating CAA pathology and its associated cerebrovascular pathology. Significance StatementOur study uncovers the mechanism by which fibrin(ogen)-A{beta} colocalization exacerbates CAA pathology. Our findings highlight the potential link between fibrinogen/ fibrin(ogen)-A{beta} colocalization and AQP4 depolarization thereby exacerbating CAA pathology. The age-dependent increase of endothelial caveolin-1 could facilitate fibrin(ogen) extravasation, assisting the later to binds to A{beta} in the perivascular space which ultimately induce microglial neuroinflammation and AQP4 depolarization, thus exacerbating CAA pathology. Furthermore, fibrinogen depletion could mitigate CAA severity, reduce microglial activation, restore AQP4 polarization and memory impairment. These results suggest that targeting fibrinogen and caveolin-1-mediated transcytosis may offer new strategies to address CAA-associated cerebrovascular pathology.

neuroscience↗

bioRxiv2024

Targeted therapy of oncomicrobe F. nucleatum with bioengineered probiotic expressing guided antimicrobial peptide (gAMP)

Colorectal cancer (CRC) is a leading cause of cancer-related mortality, with Fusobacterium nucleatum (F. nucleatum) identified as a key contributor to its progression. This study explores a novel targeted therapy using bioengineered probiotics expressing guided antimicrobial peptides (gAMPs) to selectively inhibit F. nucleatum. We engineered Lactococcus lactis MG1363 to express gAMPs derived from Ovispirin and Cathelin-related peptide SCF, linked to a Statherin-derived guide peptide (YQPVPE) that binds specifically to the F. nucleatum membrane porin FomA. Our results demonstrate that the Statherin-derived guide peptide enhances the binding affinity to F. nucleatum, significantly increasing the preferential attachment compared to control peptides. In vitro assays revealed that both unguided and guided AMPs effectively inhibited biofilm formation in F. nucleatum, with gAMPs showing reduced toxicity against non-target bacteria (Bacteroides fragilis and Escherichia coli). The gAMPs were also more effective in modulating growth kinetics, exhibiting selective toxicity towards F. nucleatum at lower concentrations. Co-culture experiments in a simulated human gut microbiome demonstrated that the gAMP probiotic maintained microbial diversity while effectively reducing F. nucleatum abundance. Quantitative PCR and 16S rRNA sequencing confirmed that gAMP treatment preserved the richness of the microbiota, contrasting with significant dysbiosis observed in control samples. These findings support the potential of engineered probiotics as a targeted therapeutic approach to combat F. nucleatum-associated CRC. By leveraging the specificity of Statherin-derived peptides, this strategy not only addresses the pathogenicity of F. nucleatum but also mitigates the adverse effects of traditional antimicrobial therapies on beneficial gut microbiota. Future studies will explore the clinical applicability of this approach in CRC management and its impact on overall gut health.

microbiology↗

bioRxiv2024

Investigating the impact of the interstitial fluid flow and hypoxia interface on cancer biology using a spheroid-on-chip perfusion system

Solid tumours are complex and heterogeneous systems, which exist in a dynamic biophysical microenvironment. Conventional cancer research methods have long relied on two-dimensional (2D) static cultures which neglect the dynamic, three-dimensional (3D) nature of the biophysical tumour microenvironment (TME), especially the role and impact of interstitial fluid flow (IFF). To address this, we undertook a transcriptome-wide analysis of the impact of IFF-like perfusion flow using a spheroid-on-chip microfluidic platform, which allows 3D cancer spheroids to be integrated into extracellular matrices (ECM)-like hydrogels and exposed to continuous perfusion, to mimic IFF in the TME. Importantly, we have performed these studies both in experimental (normoxia) and pathophysiological (hypoxia) oxygen conditions. Our data indicated that gene expression was altered by flow when compared to static conditions, and for the first time showed that these gene expression patterns differed in different oxygen tensions, reflecting a differential role of spheroid perfusion in IFF-like flow in tumour-relevant hypoxic conditions in the biophysical TME. We were also able to identify factors primarily linked with IFF-like conditions which are linked with prognostic value in cancer patients and therefore could correspond to a potential novel biomarker of IFF in cancer. This study therefore highlights the need to consider relevant oxygen conditions when studying the impact of flow in cancer biology, as well as demonstrating the potential of microfluidic models of flow to identify IFF-relevant tumour biomarkers.

cancer biology↗

bioRxiv2024

Blood-based detection of MMP11 as a marker of prostate cancer progression regulated by the ALDH1A1-TGF-β1 signaling mechanism

BackgroundProstate cancer (PCa) is the second most common type of tumor diagnosed in men and the fifth leading cause of cancer-related death in male patients. The response of metastatic disease to standard treatment is heterogeneous. As for now, there is no curative treatment option available for metastatic PCa, and the clinical tests capable of predicting metastatic dissemination and metastatic response to the therapies are lacking. Our recent study identifies aldehyde dehydrogenases ALDH1A1 and ALDH1A3 as critical regulators of PCa metastases. Still, the exact mechanisms mediating the role of these proteins in PCa metastatic dissemination remain not fully understood, and plasma-based biomarkers of these metastatic mechanisms are also not available. MethodsGenetic silencing, gene overexpression, or treatment with different doses of the retinoic acid (RA) isomers, which are the products of ALDH catalytic activity, were used to modulate the interplay between retinoic acid receptors (RARs) and androgen receptor (AR). RNA sequencing (RNAseq), reporter assays, and chromatin immunoprecipitation (ChIP) analysis were employed to validate the role of RARs and AR in the regulation of the transforming growth factor-beta 1 (TGFB1) expression. Gene expression levels of ALDH1A1, ALDH1A3, and the matrix metalloproteinase 11 (MMP11) and their correlation with pathological parameters and clinical outcomes were analyzed by mining several publicly available patient datasets as well as our multi-center transcriptomic dataset from patients with high-risk and locally advanced PCa. The levels of MMP11 protein were analyzed by enzyme-linked immunosorbent assay (ELISA) in independent cohorts of plasma samples from patients with localized or metastatic PCa and healthy donors, while plasma proteome profiles were obtained for selected subsets of PCa patients. ResultsWe could show that ALDH1A1 and ALDH1A3 genes differently regulate TGFB1 expression in a RAR-and AR-dependent manner. We further observed that the TGF-{beta}1 pathway contributes to the regulation of the MMPs, including MMP11. We have confirmed the relevance of MMP11 as a promising clinical marker for PCa using several independent gene expression datasets. Further, we have validated plasma MMP11 levels as a prognostic biomarker in patients with metastatic PCa. Finally, we proposed a hypothetical ALDH1A1/MMP11-related plasma proteome-based prognostic signature. ConclusionsTGFB1/MMP11 signaling contributes to the ALDH1A1-driven PCa metastases. MMP11 is a promising blood-based biomarker of PCa progression.

cancer biology↗

bioRxiv2023

Glioma-neuronal circuit remodeling induces regional immunosuppression

Neuronal activity-driven mechanisms impact glioblastoma cell proliferation and invasion1-7, and glioblastoma remodels neuronal circuits8,9. Distinct intratumoral regions maintain functional connectivity via a subpopulation of malignant cells that mediate tumor-intrinsic neuronal connectivity and synaptogenesis through their transcriptional programs8. However, the effects of tumor-intrinsic neuronal activity on other cells, such as immune cells, remain unknown. Here we show that regions within glioblastomas with elevated connectivity are characterized by regional immunosuppression. This was accompanied by different cell compositions and inflammatory status of tumor-associated macrophages (TAMs) in the tumor microenvironment. In preclinical intracerebral syngeneic glioblastoma models, CRISPR/Cas9 gene knockout of Thrombospondin-1 (TSP-1/Thbs1), a synaptogenic factor critical for glioma-induced neuronal circuit remodeling, in glioblastoma cells suppressed synaptogenesis and glutamatergic neuronal hyperexcitability, while simultaneously restoring antigen-presentation and pro-inflammatory responses. Moreover, TSP-1 knockout prolonged survival of immunocompetent mice harboring intracerebral syngeneic glioblastoma, but not of immunocompromised mice, and promoted infiltrations of pro-inflammatory TAMs and CD8+ T-cells in the tumor microenvironment. Notably, pharmacological inhibition of glutamatergic excitatory signals redirected tumor-associated macrophages toward a less immunosuppressive phenotype, resulting in prolonged survival. Altogether, our results demonstrate previously unrecognized immunosuppression mechanisms resulting from glioma-neuronal circuit remodeling and suggest future strategies targeting glioma-neuron-immune crosstalk may open up new avenues for immunotherapy.

cancer biology↗

bioRxiv2023

NOTCH3 drives meningioma tumorigenesis and resistance to radiotherapy

Meningiomas are the most common primary intracranial tumors1-3. Treatments for patients with meningiomas are limited to surgery and radiotherapy, and systemic therapies remain ineffective or experimental4,5. Resistance to radiotherapy is common in high-grade meningiomas6, and the cell types and signaling mechanisms driving meningioma tumorigenesis or resistance to radiotherapy are incompletely understood. Here we report NOTCH3 drives meningioma tumorigenesis and resistance to radiotherapy and find NOTCH3+ meningioma mural cells are conserved across meningiomas from humans, dogs, and mice. NOTCH3+ cells are restricted to the perivascular niche during meningeal development and homeostasis and in low-grade meningiomas but are expressed throughout high-grade meningiomas that are resistant to radiotherapy. Integrating single-cell transcriptomics with lineage tracing and imaging approaches across mouse genetic and xenograft models, we show NOTCH3 drives tumor initiating capacity, cell proliferation, angiogenesis, and resistance to radiotherapy to increase meningioma growth and reduce survival. An antibody stabilizing the extracellular negative regulatory region of NOTCH37,8 blocks meningioma tumorigenesis and sensitizes meningiomas to radiotherapy, reducing tumor growth and improving survival in preclinical models. In summary, our results identify a conserved cell type and signaling mechanism that underlie meningioma tumorigenesis and resistance to radiotherapy, revealing a new therapeutic vulnerability to treat meningiomas that are resistant to standard interventions.

cancer biology↗

bioRxiv2023

Co-enrichment of cancer-associated bacterial taxa is correlated with immune cell infiltrates in esophageal tumor tissue

Esophageal carcinoma (ESCA) is a leading cause of cancer-related death worldwide, and Barretts esophagus (BE) is a strong risk factor along with smoking. Smoking is well-known to induce microbial dysbiosis and we asked if BE and esophageal microbiomes had shared microbial alterations that could provide novel biomarkers. We extracted DNA from BE tissues (n=5) and tumors of 158 patients in the NCI-MD case control study and sequenced the 16S rRNA gene (V3-4), with TCGA ESCA RNAseq (n = 173) and WGS (n = 139) non-human reads used as validation. We identified four taxa, Campylobacter, Prevotella, Streptococcus, and Fusobacterium as highly enriched in esophageal cancer across all cohorts. Using SparCC, we discovered that Fusobacterium and Prevotella were also co-enriched across all cohorts. We then analyzed immune cell infiltration to determine if these dysbiotic taxa were associated with immune signatures. Using xCell to obtain predicted immune infiltrates, we identified a depletion of megakaryocyte-erythroid progenitor (MEP) cells in tumors with presence of any of the four taxa, along with enrichment of platelets in tumors with Campylobactor or Fusobacterium. Taken together, our results suggest that intratumoral presence of these co-occurring bacterial genera may confer tumor promoting immune alternations that allow disease progression in esophageal cancer.

cancer biology↗