Biology subjects

Joseph, S.

Publications and source records attributed to Joseph, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Molecular anatomy of the entorhinal cortex

The entorhinal cortex (EC) is critical for episodic memory formation and is the epicenter of neurofibrillary tangle formation in Alzheimer's disease. Its cytoarchitectonic and functional heterogeneity has been recognized for decades, but the molecular underpinnings of this heterogeneity are still relatively uncharted. While many features of the region appear to be conserved between rodents and primates, very little is known about the conservation of the molecular identity of EC neurons. Here we perform single-nucleus RNAseq (snRNAseq) of the mouse EC and use in situ hybridization, as well as publicly available transcriptomics data, to enhance the understanding of the heterogeneity of neuron types present in the area. While the well-known dichotomy between lateral and medial EC is evident in superficial layers of EC, we highlight that the medioventral region of EC forms a different population from the caudomedial section. We identify molecular correlates for the previously described parcellation of lateral EC, and show that, at least in layer IIa, subterritories of EC are not separated by abrupt borders but rather form smooth gradients. Lastly, we show that both lateral vs. medial ECIIa markers, and markers that reveal finer grain heterogeneity within ECIIa have conserved patterns of expression in macaque, highlighting the high degree of homology between the two species. Overall this molecular atlas of the mouse EC with some comparative elements is a resource for anatomically-informed molecular studies of the EC and lays the groundwork for mechanistic studies of selective neuronal vulnerability of the region in the context of AD.

neuroscience↗

bioRxiv2026

An endonuclease V protects Bacillus subtilis against a deaminase toxin and a uracil-containing phage

Bacteria deploy polymorphic toxins to inhibit competitors and rely on cognate immunity proteins to prevent self-intoxication. Immunity determinants act by binding and neutralizing incoming toxins, and in the rare cases where toxin-induced damage is also reversed, that activity resides within the immunity protein itself. Whether a conflict system can instead dedicate a separate gene to repairing the damage is unknown. Here we report that an operon in Bacillus subtilis encodes the toxin YwqJ, its cognate immunity protein YwqK, and EndoV an endonuclease that incises DNA at the lesion the toxin creates. YwqJ is a single-stranded DNA cytidine deaminase translocated by the type VIIb secretion system (T7SSb) to mediate contact-dependent interbacterial antagonism. Unexpectedly, EndoV exhibits a preference for uracil over the canonical hypoxanthine, processing genomic uracil in cells and protecting against YwqJ when immunity is absent. Because EndoV acts on the chemical lesion rather than the effector, its protection is indifferent to the source of deamination. EndoVBs accordingly restricts replication of PBS1, a bacteriophage whose genome naturally substitutes uracil for thymine. These findings establish DNA repair as a novel layer of defense within toxin-immunity loci and reveal a DNA repair mechanism that unifies interbacterial antagonism and antiviral immunity.

microbiology↗

bioRxiv2026

An INF2-dependent actin-mediated step in Inositol 1,4,5-trisphosphate receptor cluster formation and activity

Intracellular calcium signaling plays a vital role in regulating various cellular processes including gene regulation, motility, metabolism and cell death. Inositol 1,4,5-trisphosphate receptors (IP3R) on the Endoplasmic Reticulum (ER) are a major cation channel that regulates stimulus-induced calcium release from the ER. While several molecular players regulate activity of IP3R, its regulation by actin filaments were uncharacterized. Here we show that actin filaments polymerized by a specific actin nucleator INF2 facilitates agonist-induced IP3R activity. Our results demonstrate that INF2-mediated actin filaments regulate formation and/or stability of IP3R clusters on the ER that have been previously shown to be hotspots of ER calcium release. Using cell-biological and biochemical techniques we further show that INF2 physically interacts with IP3R isoforms, often at IP3R clusters. While INF2-IP3R interaction is independent of INF2-activity, the ability of INF2 to mediate IP3R clusters is dependent on its actin polymerization activity. Finally, we demonstrate that in addition to its calcium mobilization activity, INF2 on ER specifically regulates IP3R cluster positioning to mediate ER-mitochondrial contacts and facilitate ER to mitochondrial calcium transfer. Overall, these results reveal an actin-dependent step in regulation of IP3R activity both in terms of ER calcium release and modulation of ER-mitochondrial contacts. HighlightsO_LIINF2-mediated actin filaments potentiate agonist-induced IP3R-mediated ER calcium release without affecting the ER calcium stores per se. C_LIO_LIER-localization of INF2 is dispensable for its role on IP3R activity. Moreover INF2-mediated actin filaments affect the activity of all IP3R isoforms. C_LIO_LIINF2 interacts with IP3R in an activity and actin filament independent manner through its C-terminal region. C_LIO_LIINF2 regulates IP3R cluster formation in actin-filament dependent manner and thereby regulates IP3R activity. C_LIO_LIFurther we show that ER-localized INF2 specifically regulate IP3R cluster positioning thereby promoting ER to mitochondrial contact and calcium transfer. C_LI

cell biology↗

bioRxiv2026

Vancomycin tolerance and dispersion of dual species biofilms of Clostridioides difficile and Vancomycin-resistant Enterococcus faecium

ObjectivesBiofilms are the dominant mode of bacterial life. The gut microbiota itself has characteristics of a biofilm that grows on the intestinal mucosa. C. difficile and VRE are commonly co-isolated from patients but biofilm formation has not been studied in a multi-species context. Here we study the interactions between C. difficile and VRE in surface adherent community. ResultsWe found that VRE inhibits C. difficile biofilm formation in dual-species culture in the presence of excess glucose. Robust dual-species biofilms were produced when the carbon source was changed to a non-fermentable sugar such as fucose and xylose. We observed a high level of vancomycin tolerance in C. difficile biofilms that was not affected by the presence of VRE. Finally we also found that a nutrient step-change is sufficient to induce dispersion of single and dual-species biofilms. ConclusionsVRE can inhibit the development of C. difficile biofilms in the presence of a fermentable carbon source. VRE does not appear to affect vancomycin tolerance or nutrient-induced dispersion of C. difficile biofilms. Highlights- VRE inhibits C. difficile biofilm formation in the presence of fermentable glucose. - Stable VRE - C. difficile biofilms are formed by managing the available carbon source. - VRE does not affect C. difficile vancomycin tolerance in this model. - A 10-fold increase in available nutrients is sufficient to induce biofilm dispersion in C. difficile and VRE.

microbiology↗

bioRxiv2026

A two-membrane gateway for monocarboxylates couples host glycolysis to Toxoplasma mitochondrial fitness and virulence

Intracellular pathogens must coordinate their metabolism with nutrient supplies from the host cell, yet the specific metabolites and transport pathways that sustain parasite bioenergetics remain incompletely defined. In the apicomplexan parasite Toxoplasma gondii, infection increases host glycolytic flux and elevates cytosolic lactate and pyruvate, suggesting that these intermediates are co-opted as carbon and energy sources. Here, we show that T. gondii imports host-derived lactate and pyruvate across both the parasitophorous vacuole membrane and the parasite plasma membrane to maintain mitochondrial function, extracellular survival, and acute virulence. Using a hexokinase knockout ({Delta}hk) to abolish endogenous pyruvate production, we find that parasites preserve basal oxygen consumption but become strictly dependent on exogenous monocarboxylates to stimulate mitochondrial respiration. By disrupting the parasite formate-nitrite transporters TgFNT1-3, we identify TgFNT1 and TgFNT2 as the principal monocarboxylate transporters required for lactate- and pyruvate-driven respiratory responses. Furthermore, genetic ablation of TgGRA17, a parasitophorous vacuole pore protein, compromises the growth advantage conferred by elevated exogenous lactate, implicating this pore as the entry route for host-derived monocarboxylates into the vacuole. Conversely, host cells lacking the monocarboxylate exporter MCT1 accumulate cytosolic lactate/pyruvate and enhance parasite growth, linking host monocarboxylate export to parasite fitness. When both endogenous pyruvate production and exogenous uptake are disrupted, parasites display severely reduced mitochondrial basal respiratory capacity, membrane potential, ATP levels, extracellular survival, and virulence in mice. Collectively, these findings define a dual-step pyruvate acquisition pathway in T. gondii and reveal host monocarboxylates as critical fuels that buffer parasite bioenergetic stress during infection. Significance StatementIntracellular parasites rely on host nutrients to power their metabolism, yet the routes by which these metabolites cross the membranes between host cytosol and parasite mitochondria are not well defined. Here, we show that Toxoplasma gondii exploits host glycolysis by importing lactate and pyruvate to sustain mitochondrial function and virulence. We identify a two-step pathway in which these monocarboxylates cross the parasitophorous vacuole via the pore GRA17 and then enter the parasite through the formate-nitrite transporters TgFNT1/2. Blocking both endogenous glycolysis and this exogenous pyruvate supply disables parasite mitochondrial fitness, extracellular survival, and virulence. These findings reveal a fundamental strategy of metabolic plasticity in apicomplexan parasites using a multi-membrane nutrient gateway that couples host glycolysis to parasite bioenergetics.

microbiology↗

bioRxiv2025

Capturing Translation in Action with Protein Synthesis Profiling

Translation is a central control point of gene expression, linking nucleotide sequences to functional proteins. Dysregulated translation contributes to diverse diseases, underscoring the need for methods that can directly reveal which transcripts are actively translated. Ribosome profiling, the current gold standard, provides nucleotide-resolution maps of ribosome occupancy but requires laborious purification and sacrifices information on mRNA isoforms and mRNA modifications by restricting analysis to short ribosome-protected fragments. Here, we introduce Protein Synthesis Profiling (PSP), a proximity-labeling strategy for the transcriptome-wide identification of actively translated mRNAs without the need for ribosome isolation. PSP exploits a fusion of the enzyme APEX2 with the elongation factor eEF2, which transiently associates with ribosomes during elongation, to catalyze selective tagging of mRNAs engaged in translation. When applied to Saccharomyces cerevisiae, PSP captures condition-specific translational programs, recapitulates known stress responses, and expands the detectable repertoire of regulated genes beyond that of existing methods. By preserving full-length transcript features, PSP is scalable, isoform-aware, and broadly adaptable, providing a versatile platform to dissect translational regulation in health and disease.

biochemistry↗

bioRxiv2025

Mapping RNA-Binding Proteins on the Ribosome by Tethered Micrococcal Nuclease

RNA-binding proteins (RBPs) are essential regulators of post-transcriptional gene expression, influencing mRNA processing, translation, and stability. Defining their binding sites on RNA is key to understanding how they assemble into functional ribonucleoprotein (RNP) complexes, but existing footprinting and crosslinking approaches often yield low signal-to-noise, variable efficiency, or require highly purified complexes. To address these limitations, we developed Tethered Micrococcal Nuclease Mapping (TM-map), a sequencing-based strategy that determines the three-dimensional binding sites of RBPs on RNA. In TM-map, the RBP is fused to micrococcal nuclease (MNase), which upon Ca{superscript 2} activation cleaves proximal RNA regions, producing fragments whose 3' termini report the spatial proximity of the fusion. We first validated TM-map using the bacteriophage MS2 coat protein bound to its cognate RNA stem-loop engineered into the Escherichia coli ribosome. Cleavage sites mapped within [~]15 [A] of the stem-loop, confirming that tethered MNase accurately reports local structure on the ribosome surface. We then applied TM-map to the Drosophila Fragile X Mental Retardation Protein (FMRP), a translational regulator with an unresolved ribosome-binding site. Both N-and C-terminal MNase-FMRP fusions produced reproducible cleavage clusters on the 18S rRNA localized to the body and head of the 40S subunit. The similar profiles suggest that FMRPs termini are conformationally flexible and sample multiple orientations relative to the ribosome, consistent with a dynamic interaction rather than a fixed binding mode. TM-map thus provides a simple, high-resolution, and generalizable approach for visualizing RBP-RNA interactions within native RNP assemblies. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/684434v1_ufig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@159d7bcorg.highwire.dtl.DTLVardef@16289c5org.highwire.dtl.DTLVardef@43156forg.highwire.dtl.DTLVardef@344a58_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Cohesin sumoylation is required for repression of subtelomeric gene expression in Saccharomyces cerevisiae.

Cohesin is an evolutionary conserved protein complex first described for its role in sister chromatid cohesion, that impacts several chromosomal processes. The functions of budding yeast cohesin in chromosome segregation, replication and repair are regulated by its post-translational processing and modifications. Cohesin associates with centromeres, pericentric regions and discrete sites along chromosome arms till the end. Near chromosome ends, telomeres exist in a heterochromatin-like configuration and exert SIR-complex mediated telomere position effect resulting in repression of sub-telomeric gene transcription. Previously, we reported that cohesin has a SIR-independent role in subtelomeric gene silencing (Kothiwal and Laloraya, 2019). Here, we investigated the requirement of cohesin sumoylation in subtelomeric repression. We created a sumoylation-deficient cohesin complex by fusing the catalytic domain of a SUMO protease, ULP1, to the C-terminus of Mcd1/Scc1 (Mcd1-UD), a cohesin subunit. We show that cohesin sumoylation is required for repression of sub-telomeric genes. In agreement with our earlier observations of a SIR-independent role of cohesin in telomere silencing, SIR-proteins remained bound to a de-repressed subtelomeric gene in MCD1-UD and its expression further increased upon deletion of SIR2. Interestingly, we did not observe a cohesion defect in this mutant suggesting that sister chromatid cohesion and regulation of sub-telomere gene silencing are separable functions of cohesin. Telomere tethering to the nuclear envelope and telomere compaction are defective in MCD1-UD, indicating that sumoylation contributes to cohesins role in subtelomeric chromosome organization. Our data establish the relevance of cohesin sumoylation in subtelomeric repression, a function independent of cohesins role in sister chromatid cohesion.

genetics↗

bioRxiv2025

Structural evidence for metal ion catalysis in the ribosome

Ribosomes synthesize proteins with an RNA-only active site across all domains of life, yet the details of the catalytic mechanism have remained elusive despite decades of high-resolution ribosome structures. Here, we provide structural evidence for the involvement of two metal ions in peptide bond formation, drawn from ribosome structures spanning bacteria, archaea, and eukaryotes. These metal ions reside in the peptidyl transferase center, one of them adjacent to a universally conserved stack of three base triples, reminiscent of the catalytic triplex in group I/II introns and the spliceosome, which catalyze pre-mRNA splicing. The second metal ion is positioned to stabilize the oxyanion of the tetrahedral intermediate. Metal ion catalysis thus emerges as a recurring mechanistic theme across the central dogma spanning protein synthesis, RNA splicing, and nucleic acid replication.

biochemistry↗

bioRxiv2025

Mesenchymal WNT2B is Required for the Development and Function of the Human Intestine

Background and AimsWNT2B mutations result in Diarrhea-9 (DIAR9), a congenital diarrhea syndrome with an extreme phenotype and unique histological defects. Attempts to model DIAR9 in rodents and study patient epithelial tissue have not been able to fully reproduce the human phenotype, making understanding this condition challenging. Here, we aimed to interrogate the mechanisms and the specific cellular compartment contributing to DIAR9 using a human intestinal organoid model. MethodsHuman intestinal organoids (HIOs) generated from both a patient-derived WNT2BR69*iPSC line and a control line were transplanted into immunocompromised mice for 10 weeks. Grafts were harvested and histologically compared. Bulk RNA sequencing was performed on both organoid groups and on patient-biopsy derived enteroids. In vitro recombination experiments were performed to describe the causative cellular compartment. ResultsLive and histological imaging revealed partial epithelial delamination in WNT2BR69*HIOs, which was absent in controls. A significant number of crypts in WNT2BR69* HIOs lacked OLFM4, a surrogate marker of stem cell activity. Key transcriptomic pathways altered between groups included trafficking of apical digestion proteins, which was confirmed via immunofluorescence. Patient derived enteroid proteomic analysis revealed similar results. Recombination experiments in HIOs revealed that while both epithelial and mesenchymal WNT2B are important for stem cell function, lack of mesenchymal WNT2B was sufficient to elicit the phenotype. ConclusionWe demonstrated that mesenchymal WNT2B is critical for supporting human intestinal epithelial development and function.

developmental biology↗

bioRxiv2025

TRIP13 protects pancreatic cancer cells against intrinsic and therapy-induced DNA replication stress

Oncogene activation in normal untransformed cells induces DNA replication stress and creates a dependency on DNA Damage Response (DDR) mechanisms for cell survival. Different oncogenic stimuli signal via distinct mechanisms in every cancer setting. The DDR is also pathologically re-programmed and deployed in diverse ways in different cancers. Because mutant KRAS is the driver oncogene in 90% of Pancreatic Ductal Adenocarcinomas (PDAC), here we have investigated DDR mechanisms by which KRAS-induced DNA replication stress is tolerated in normal human pancreatic epithelial cells (HPNE). Using a candidate screening approach, we identify TRIP13 as a KRASG12V-induced mRNA that is also expressed at high levels in PDAC relative to normal tissues. Using genetic and pharmacological tools, we show that TRIP13 is necessary to sustain ongoing DNA synthesis and viability specifically in KRASG12V-expressing cells. TRIP13 promotes survival of KRASG12V-expressing HPNE cells in a Homologous Recombination (HR)-dependent manner. KRASG12V-expressing HPNE cells lacking TRIP13 acquire hallmark HR-deficiency (HRD) phenotypes including sensitivity to inhibitors of Trans-Lesion Synthesis (TLS) and Poly-ADP Ribose Polymerase (PARP). Established PDAC cell lines are also sensitized to intrinsic DNA damage and therapy-induced genotoxicity following TRIP13-depletion. Taken together our results expose TRIP13 as an attractive new and therapeutically-tractable vulnerability of KRAS-mutant PDAC.

cancer biology↗

bioRxiv2024

MAPK14/p38α Shapes the Molecular Landscape of Endometrial Cancer and promotes Tumorigenic Characteristics

The molecular underpinnings of High Grade Endometrial Carcinoma (HGEC) metastatic growth and survival are poorly understood. Here we show that ascites-derived and primary tumor HGEC cell lines in 3D spheroid culture faithfully recapitulate key features of malignant peritoneal effusion and exhibit fundamentally distinct transcriptomic, proteomic and metabolomic landscapes when compared with conventional 2D monolayers. Using genetic screening platform we identify MAPK14 (which encodes the protein kinase p38) as a specific requirement for HGEC in spheroid culture. MAPK14/p38 has broad roles in programing the phosphoproteome, transcriptome and metabolome of HGEC spheroids, yet has negligible impact on monolayer cultures. MAPK14 promotes tumorigenicity in vivo and is specifically required to sustain a sub-population of spheroid cells that is enriched in cancer stemness markers. Therefore, spheroid growth of HGEC activates unique biological programs, including p38 signaling, that cannot be captured using 2D culture models and are highly relevant to malignant disease pathology.

cancer biology↗

bioRxiv2024

History of recurrent short and long-term coral bleaching events in Indian coral reefs: a a systematic review of contrasting bleaching patterns, lessons learned, and future directions

Climate change has intensified coral bleaching events, leading to widespread coral mortality and threatening the coral reef survival worldwide. However, species susceptibility patterns to bleaching differ spatially and temporally, making it crucial to understand bleaching impact and species susceptibility patterns across latitudinal ranges, particularly from understudied locations. We critically reviewed 23 years of bleaching episodes on Indian coral reefs (four major reefs and other patch reefs) reported from 1998 to 2020 to understand the geographical footprint of bleaching patterns, species susceptibility differences, and their impact. We found that all four major Indian reef systems (Gulf of Kachchh, Gulf of Mannar, Lakshadweep, and the Andaman Islands) have experienced three major bleaching episodes (1998, 2010, and 2016) and multiple short-term bleaching events. Short-term bleaching events (DHWs> four weeks) created differences in species susceptibility, but the disparity among species diminished to long-term bleaching events (DHWs <4 weeks) in all reef sites. Acropora, Porites, Pocillopora, Montipora, and Turninaria in the Gulf of Mannar, Porites, and Favia in the Gulf of Kachchh, and Acropora in the Andaman and Lakshadweep were the most vulnerable genera during all the bleaching events. In terms of recovery, Porites and other massive forms recovered better than branching forms. Furthermore, species susceptibility pattern analysis (winners vs. losers) to 2016 long-term bleaching events found conflicting results from studies (one-time surveys) in the same area. This result indicates that a one-time survey (survey timing) influences results as bleaching events lengthen, necessitating repeated surveys to determine winners and losers. Although inconsistent data from different study sites makes it difficult to create predictive models, data collected over the past 23 years provides critical insight into coral community susceptibility patterns and bleaching impacts, underscoring the need for systematic, uniform surveys in the future.

ecology↗

bioRxiv2024

Transcriptional regulation in the absence of inositol trisphosphate receptor calcium signaling

The activation of IP3 receptor (IP3R) Ca2+ channels generates agonist-mediated Ca2+ signals that regulate a wide range of biological processes. It is therefore surprising that CRISPR induced loss of all three IP3R isoforms (TKO) in HEK293 and HeLa cell lines yields cells that can survive, grow and divide, albeit more slowly than wild-type cells. In an effort to understand the adaptive mechanisms involved, we have examined the activity of key Ca2+ dependent transcription factors (NFAT, CREB, AP-1 and NF{kappa}b) and signaling pathways using luciferase-reporter assays, phosphoprotein immunoblots and whole genome transcriptomic studies. In addition the role of protein kinase C (PKC) was investigated with inhibitors and siRNA knockdown. The data showed that agonist-mediated NFAT activation was lost but CREB activation was maintained in IP3R TKO cells. Under base-line conditions transcriptome analysis indicated the differential expression (DEG) of 828 and 311 genes in IP3R TKO HEK293 or HeLa cells, respectively, with only 18 genes being in common. In summary three main adaptations in TKO cells are identified in this study: 1) increased basal activity of NFAT, CREB, AP-1 and NF{kappa}b; 2) an increased reliance on Ca2+-insensitive PKC isoforms; and 3) increased production of reactive oxygen species and upregulation of antioxidant defense enzymes. We suggest that whereas wild-type cells rely on a Ca2+ and DAG signal to respond to stimuli, the TKO cells utilize the adaptations to allow key signaling pathways (e.g. PKC, Ras/MAPK, CREB) to transition to the activated state using a DAG signal alone.

cell biology↗

bioRxiv2023

Identification of a short, single site matriglycan that maintains neuromuscular function in the mouse

Matriglycan (-1,3-{beta}-glucuronic acid-1,3--xylose-) is a polysaccharide that is synthesized on -dystroglycan, where it functions as a high-affinity glycan receptor for extracellular proteins, such as laminin, perlecan and agrin, thus anchoring the plasma membrane to the extracellular matrix. This biological activity is closely associated with the size of matriglycan. Using high-resolution mass spectrometry and site-specific mutant mice, we show for the first time that matriglycan on the T317/T319 and T379 sites of -dystroglycan are not identical. T379-linked matriglycan is shorter than the previously characterized T317/T319-linked matriglycan, although it maintains its laminin binding capacity. Transgenic mice with only the shorter T379-linked matriglycan exhibited mild embryonic lethality, but those that survived were healthy. The shorter T379-linked matriglycan exists in multiple tissues and maintains neuromuscular function in adult mice. In addition, the genetic transfer of -dystroglycan carrying just the short matriglycan restored grip strength and protected skeletal muscle from eccentric contraction-induced damage in muscle-specific dystroglycan knock-out mice. Due to the effects that matriglycan imparts on the extracellular proteome and its ability to modulate cell-matrix interactions, our work suggests that differential regulation of matriglycan length in various tissues optimizes the extracellular environment for unique cell types.

biochemistry↗

bioRxiv2023

The DNA Damage Response (DDR) landscape of endometrial cancer defines discrete disease subtypes and reveals therapeutic opportunities.

Genome maintenance is an enabling characteristic that allows neoplastic cells to tolerate the inherent stresses of tumorigenesis and evade therapy-induced genotoxicity. Neoplastic cells also deploy mis-expressed germ cell proteins termed Cancer Testes Antigens (CTAs) to promote genome maintenance and survival. Here, we present the first comprehensive characterization of the DNA Damage Response (DDR) and CTA transcriptional landscapes of endometrial cancer in relation to conventional histological and molecular subtypes. We show endometrial serous carcinoma (ESC), an aggressive endometrial cancer subtype, is defined by gene expression signatures comprising members of the Replication Fork Protection Complex (RFPC) and Fanconi Anemia (FA) pathway and CTAs with mitotic functions. DDR and CTA- based profiling also defines a subset of highly aggressive endometrioid endometrial carcinomas (EEC) with poor clinical outcomes that share similar profiles to ESC yet have distinct characteristics based on conventional histological and genomic features. Using an unbiased CRISPR-based genetic screen and a candidate gene approach, we confirm that DDR and CTA genes that constitute the ESC and related EEC gene signatures are required for proliferation and therapy-resistance of cultured endometrial cancer cells. Our study validates the use of DDR and CTA-based tumor classifiers and reveals new vulnerabilities of aggressive endometrial cancer where none currently exist.

cancer biology↗

bioRxiv2023

Elevated epigenetic age in wild compared to lab-raised house mice

Age is a key parameter in population ecology, with a myriad of biological processes changing with age as organisms develop in early life then later senesce. As age is often hard to accurately measure with non-lethal methods, epigenetic methods of age estimation (epigenetic clocks) have become a popular tool in animal ecology, and are often developed or calibrated using captive animals of known age. However, studies typically rely on invasive blood or tissue samples, which limits their application in more sensitive or elusive species. Moreover, few studies have directly assessed how methylation patterns and epigenetic age estimates compare across environmental contexts (e.g., captive or lab-based vs. wild animals). Here, we built a targeted epigenetic clock from laboratory house mice (strain C57BL/6, Mus musculus) using DNA from non-invasive faecal samples, and then used it to estimate age in a population of wild mice (Mus musculus domesticus) of unknown age. This lab mouse-derived epigenetic clock accurately predicted adult wild mice to be older than juveniles, and showed that wild mice typically increased in epigenetic age over time, but with wide variation in epigenetic ageing rate among individuals. Our results also suggested that, for a given body mass, wild mice had higher methylation across targeted CpG sites than lab mice (and consistently higher epigenetic age estimates as a result), even among the smallest, juvenile mice. This suggests wild and lab mice may display different CpG methylation levels from very early in life, and indicates caution is needed when developing epigenetic clocks on lab animals and applying them in the wild.

molecular biology↗

bioRxiv2023

Schisandrin B suppresses colon cancer growth by inducing cell cycle arrest and apoptosis via the CHOP signalling pathway

Colon cancer is among the most lethal and prevalent malignant tumours in the world, and the lack of effective therapies highlights the need for novel therapeutic approaches. Schisandrin B (Sch B), a lignan extracted from the fruit Schisandra chinensis, has been reported for its anti-cancer properties. However, no studies to date have been done to characterise the exact molecular mechanisms regarding the anti-tumorigenic effect of Sch B in colon cancer. A comprehensive analysis of the molecular mechanism for the anti-tumorigenic effect of Sch B on human colon cancer cells was performed using combination of Raman spectroscopy, RNA-seq, computational docking and molecular biological experiments. The in vivo efficacy was evaluated by a mouse xenograft model. Sch B reduced cell proliferation and triggered apoptosis in human colon cancer cell lines. Raman spectroscopy, computational, RNA-seq, molecular and cellular studies revealed that Sch B activated unfolded protein responses by interacting with CHOP and upregulating CHOP, which thereby induced apoptosis. CHOP knockdown alleviated the Sch B-induced reduction in cell viability and apoptosis. Sch B reduced colon tumour growth in vivo. Our findings provide essential background for clinical trials examining the effects of Sch B in patients with colon cancer.

pharmacology and toxicology↗