Biology subjects

James, C.

Publications and source records attributed to James, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Epigenetic evolution of colorectal cancer and its microenvironment reveals new vulnerabilities

Epigenetics is central to tumorigenesis, but the co-evolution of the cancer epigenome and its microenvironment is severely understudied. Here, we measure chromatin accessibility and transcriptome, at single cell resolution, of a set of normal colon, primary colorectal cancers and metastases, and identify recurrent epigenetic alterations in tumour cells. We also found that the normal epithelium adjacent to the cancer had recurrent epigenetic alterations associated with inflammatory programs that were partially shared with tumour cells. Distinct tumour-intrinsic transcription factor binding programs were associated with differential abundance of malignant stroma cell identities. We then leveraged matched patient-derived organoids, to assess the functional impact of the most recurrent epigenetic alterations on cancer cell viability, using CRISPR interference. We found a set of epigenetic-driven cancer dependencies, related to developmental reprogramming and cellular stress resilience, representing new potential therapeutic targets.

cancer biology↗

bioRxiv2026

Organoid-like Functional Adrenal Gland Cortex Derived From Human Pluripotent Stem Cells

The adrenal cortex is a critical for life endocrine system. It manages metabolic homeostasis, electrolyte balance, stress response, and sex development. This is accomplished through the release of various steroids from a dynamically changing landscape of concentric cellular zones/layers. Adrenocortical dysfunction is implicated in pathologies ranging from adrenal insufficiency to hypertension. The in-depth investigation of adrenal gland biology, pathology and drug discovery has been hampered by a lack of human, experimentally tractable models. Particularly missing are models that recapitulate the cellular diversity of the adrenal cortex with representation of all fetal and adult cell layers and the capsule. Here, we employ human pluripotent stem cells (hPSCs) to generate cells of all three cortex zones alongside capsular cells in a single 2D platform. This platform mimics the cellular diversity expected from an organoid, yet it provides the simplicity of monolayer cultures, that are better suited for drug discovery and high-throughput settings. These cultures secrete zone-specific steroids (cortisol, aldosterone, and DHEA-S) and exhibit robust, physiologically relevant ACTH stimulation responses. Transcriptomic analysis revealed sequential acquisition of profiles consistent with adrenocortical development, zonation, and signaling programs consistent with zone maintenance. Our platform is validated by a literature meta-analysis that defines transcriptomic signatures for each human cortical cell type, spanning fetal and adult stages. Together, this novel adrenocortical platform enables investigation of adrenal development, disease mechanisms, and therapeutic strategies. Significance StatementWe describe a hPSC-based 2D differentiation strategy with the cell type complexity of an organoid and the technical simplicity necessary for high-throughput assays. The platform contains all cortical subtypes that mediate electrolyte regulation, stress response, sex development and self-maintenance of the tissue. This co-differentiation offers a unique opportunity to study human adrenal development, biology, pathology and enables drug discovery.

developmental biology↗

bioRxiv2026

Molecular determinants of Bcl-xL membrane insertion - Structural plasticity exploration in solution and in nanodiscs identifies IsoAsp deamidation as a loss-of function mechanism in vivo.

Multi-domain Bcl-2 family proteins share the ability to form dimers and oligomers, regardless of their pro- or anti-apoptotic activity. Homotypic interactions (pro-pro and anti-anti) and heterotypic interactions (pro-anti) are well-documented, but the role of higher-order organization in their survival/death functions and membrane interactions remains largely unresolved. Looking into anti-apoptotic Bcl-xL, essentially engineered/truncated proteoforms lacking the disordered loop and/or the hydrophobic C-terminal helix, have been used as proxies of the full-length (FL) protein, to elaborate on structural transitions and intermediate states between monomers and homooligomers prior to membrane insertion. Using a minimalist approach with recombinant FL-Bcl-xL (aa 1-233) and artificial nano-membranes, we demonstrate that both the loop and the C-terminal helix are potent contributors to Bcl-xL structural plasticity. Unlike 3D domain swapping (3DDS) dimers resolved with the C-terminal truncated protein, FL-Bcl-xL organized in solution as dimers bridging the unique Cys151 from two monomers. This spontaneous fold indicates that the C-terminal helix drives FL-Bcl-xL to explore different conformations than truncated Bcl-xL. Yet, dimerization was not a prerequisite for membrane insertion into nanodiscs and Cys151 did not contribute to Bcl-xL survival functions in cells. These data support monomeric Bcl-xL as the minimal functional unit in membranes. Further exploring the frequently deleted disordered loop, we discovered that deamidation of Asn52 and Asn66 in IsoAsp, but not in Asp, impairs membrane insertion into nanodiscs. Thus, this reductionist biochemical approach clarifies the loss of tumorigenic function we observed for deamidated Bcl-xL in xenograft experiments in vivo.

biochemistry↗

bioRxiv2026

The React & Rebound Model: Capturing Emotion Regulation Dynamics from Passive Wearable Data

BackgroundEmotion regulation--the ability to respond to and restore equilibrium after emotional perturbations--is central to mental health. Yet objective measurement remains limited to lab-based studies with group-level results, while consumer wearables focus on physical activity-related metrics rather than emotional dynamics. ObjectiveWe aimed to develop computational models that extract personalized, interpretable emotion regulation parameters from continuous heart rate variability (HRV) data collected via consumer wearables during everyday life, and validate these parameters against self-reported anxiety symptoms. MethodsWe analyzed 4 weeks of continuous HRV data from N = 49 healthy adults wearing Samsung Galaxy Active 2 smartwatches. We derived a continuous autonomic balance signal and developed three computational modeling approaches of increasing sophistication: (1) a static sympathetic load metric, (2) an Ornstein-Uhlenbeck (OU) dynamical systems model capturing continuous restoration dynamics, and (3) a discrete-state Markov transition model--the React & Rebound model-- capturing reactivity and rebound dynamics. All models were estimated using joint hierarchical Bayesian models that simultaneously extract subject-specific parameters from HRV time series and estimate their association with Generalized Anxiety Disorder 7-item scale (GAD-7) scores. The validity of extracted parameters was evaluated against anxiety symptom severity. ResultsStatic sympathetic load correlated modestly with GAD-7 (r = 0.39, R2 = 0.16). The OU model captured 69% of variance (R2 = 0.69), and the React & Rebound model captured 60% (R2 = 0.60) with substantially fewer parameters. Both models revealed that anxiety symptom severity is associated with the interaction between activation and restoration parameters--not either alone. Fast rebound appeared protective even for highly reactive individuals, who scored comparably to low-reactivity groups when restoration was rapid (Cohens d = 1.17 between highest- and lowest-risk quadrants). In the OU model, the interaction effect was specific to GAD-7 scores versus PHQ-9 and ISI scores; in the React & Rebound model, the interaction was credible across all three symptom measures. Both models were unchanged after controlling for physical activity ({Delta}R2 < 0.002). ConclusionsComputational models can extract interpretable emotion regulation parameters from naturalistic wearable data. The React & Rebound model yields two personalized parameters--reactivity and rebound--that are strongly associated with anxiety symptoms and define meaningful autonomic profiles. These parameters bridge autonomic dynamics measurable via consumer devices to neural circuit models of emotion regulation, with implications for characterizing individual autonomic profiles via consumer wearables.

neuroscience↗

bioRxiv2026

Rational design of synthetic proteins using a genome-scale CRISPR screen

Protein structure prediction using deep learning has revolutionized protein design. Yet, our understanding of protein function remains a key limitation for designing novel proteins that perform complex biological tasks. Here, we adopt a massively-parallel, function-first approach to rationally design synthetic proteins. Using genome-scale CRISPR activation, we overexpress [~]19,000 human proteins and measure their impact on precise gene editing. We identify over 800 native proteins that promote homology-directed repair. Using top candidates, we then design synthetic genome editors -- Targeted Repair fUsion Editors (TruEditors) -- by fusing full-length proteins or smaller core domains to the Cas9 nuclease. We develop 12 unique TruEditors that improve precise gene editing in diverse cell types and at genomic loci where existing methods for precise gene editing fail. Using affinity proteomics, we show that these synthetic proteins work by coordinating with endogenous DNA repair complexes. The delivery of TruEditors via mRNA more than doubles the rate of chimeric antigen receptor (CAR) insertion into the TRAC locus of primary human T cells, enhancing CAR T cell-directed tumor cell killing, and improves precise editing in human pluripotent stem cells more than three-fold. Overall, our study demonstrates that genome-wide protein overexpression screens can guide the rational design of synthetic proteins for specific biological tasks.

bioengineering↗

bioRxiv2026

Integrating temporal genomic and transcriptomic analyses to decipher genetic basis of feed intake in dairy cattle

BackgroundFood intake is a complex trait in living organisms, where the genetics of food intake have been widely studied in humans, mice, Drosophila, cattle, pigs, chicken, and fish. In dairy cattle, intake of feed is highly linked to individuals energy balance, health, production, efficiency, and the environmental footprint of the individual to the society. Recent studies have provided solid evidence of the genetic variation of feed intake (FI) in dairy cattle population, but the genetic basis and molecular mechanism of dairy feed intake is still far from clear especially considering the lactation cycles of dairy cattle. This study aims to integrate stage-dependent genome-wide association (GWA) analyses, regional heritability mapping (RHM), and RNA-seq gene expression analyses to identify temporal functional variants associated with cattle dry matter intake (DMI) across multiple stages in lactation cycles. A total of 750,000 daily DMI records from 7,500 lactations of 2,300 cows were available with animals genotype and pedigree information. Total RNA-seq from blood were generated for 121 individuals in this population from 2 lactation stages. Data were split into multiple lactations stages for GWA, RHM, and transcriptomic analyses. ResultsStage-dependent GWAS and RHM identified 21 significant loci associated with DMI across multiple lactation stages. A total of 45 candidate genes were identified from GWA and RHM. Among all the 45 genes, six genes were later found significantly differently expressed between high and low feed intake animal groups using gene expression information from RNA-seq data. These genes show links to sugar and adipose metabolism, milk production, body weight, dopamine-reward pathways and immune functions. ConclusionsOur multi-omics analyses provide molecular evidence that the genetic basis of cattle DMI across lactation is not static. Temporal genomic variants associated with FI were identified with their transcriptomic patterns investigated, decoding the molecular mechanisms underlying DMI. Overall, the associated variants and candidate genes uncovered herein decoded genetic architecture of dairy feed intake on a temporal and multi-omics basis, enhancing the understanding of basic biology of dairy feed intake and informing breeding strategies aimed at improving dairy feed efficiency.

genomics↗

bioRxiv2025

Angiogenic CD8 T cells from PWH induce Granzymes-dependent PAR1 activation promoting endothelial inflammation

In people with HIV (PWH), T cell immune activation and endothelial inflammation are contributors of the increased cardiovascular risk, however the mechanisms remain poorly understood. PAR1 connects the coagulation cascade, endothelial cells and CD8 T cells at the site of endothelial inflammation and we hypothesized that HIV driven CD8 T cell immune activation alters endothelial repair mechanisms. Endothelial repair is partially mediated by angiogenic T (Tang) cells that facilitate proliferation of endothelial cells, and differentiation of endothelial progenitor cells at site of vascular injury. During LCMV infection, we identified a subset of CD31highCD8 T cells that exhibited a long-lived memory precursor phenotype (CD127+KLRG1-) and secreted the proangiogenic cytokine vascular endothelial growth factor (VEGF) after viral control. Furthermore, in PWH, the frequencies of CD8 Tang cells were reduced and showed an activated phenotype and expression of granzymes. GZMA+GZMB+CD8 Tang cells correlated with atherosclerotic cardiovascular disease (ASCVD) risk. In vitro, granzyme dependent PAR1 activation led to calcium mobilization and secretion of proinflammatory cytokines IL-6, IL-8 and angiopoietin-2 by primary human endothelial cells. Altogether, these findings suggest that CD8 T cells are involved in immunity against viruses and endothelial homeostasis and HIV driven immune activation alters these functions.

immunology↗

bioRxiv2025

p38 blockade reverses the immune suppressive tumor microenvironment in metastatic breast cancer

Metastatic breast cancer (MBC) is a life-threatening disease with limited therapeutic options. The immune suppressive tumor microenvironment (TME) limits the potency of the antitumor immune response and facilitates disease progression and metastasis. Our current study demonstrates that p38 is a druggable target in the TME that regulates the outcome of the immune-tumor interaction. The study revealed that systemic blockade of p38 reduces metastasis, and this anti-metastatic response is negated by depletion of CD8+ T cells. Single-cell transcriptomic analysis of the immune-TME showed that pharmacological p38 inhibition (p38i) or tumor-specific inactivation of p38 by CRISPR/Cas9 (p38KO) resulted in a less exhausted and more activated CD8+ T cell phenotype. Immunophenotyping analyses demonstrated that p38 blockade reduced the expression of multiple inhibitory receptors on CD8+ T cells (i.e., PD-1, LAG-3, CTLA-4), indicating a reversal of immune exhaustion and enhanced immune activation systemically and in the TME. In contrast, p38 blockade did not exhibit inhibitory effects on T cells in proliferation assays in vitro and did not affect the proportion of regulatory T cells in vivo. The major negative impact of p38 blockade in vivo was on the myeloid populations, such as myeloid-derived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs). Further, tumor p38 activity was required for the expression of cytokines/chemokines and tumor-derived exosomes with high chemotactic capacity for myeloid cells. Altogether, this study highlights a previously unrecognized p38-driven pathway that promotes an immune suppressive TME and metastasis, and that therapeutic blockade of p38 has important implications for improving antitumor immunity and patient outcomes. STATEMENT OF SIGNIFICANCEThis study highlights a previously unrecognized p38-driven tumor pathway that promotes an immune suppressive microenvironment and metastasis, and that therapeutic blockade of p38 has important implications for improving antitumor immunity and patient outcomes.

cancer biology↗

bioRxiv2025

TNF-α disrupts the malate-aspartate shuttle, driving metabolic rewiring in iPSC-derived enteric neural lineages from Parkinson's Disease patients

Gastrointestinal (GI) dysfunction emerges years before motor symptoms in Parkinsons disease (PD), implicating the enteric nervous system (ENS) in early disease progression. However, the mechanisms linking the PD hallmark protein, -synuclein (-syn), to ENS dysfunction - and whether these mechanisms are influenced by inflammation - remains elusive. Using iPSC-derived enteric neural lineages from patients with -syn triplications, we reveal that TNF- increases mitochondrial--syn interactions, disrupts the malate-aspartate shuttle, and forces a metabolic shift toward glutamine oxidation. These alterations drive mitochondrial dysfunction, characterizing metabolic impairment under cytokine stress. Interestingly, targeting glutamate metabolism with Chicago Sky Blue 6B restores mitochondrial function, reversing TNF--driven metabolic disruption. Our findings position the ENS as a central player in PD pathogenesis, establishing a direct link between cytokines, -syn accumulation, metabolic stress and mitochondrial dysfunction. By uncovering a previously unrecognized metabolic vulnerability in the ENS, we highlight its potential as a therapeutic target for early PD intervention.

neuroscience↗

bioRxiv2024

Laminin β4 is required for the development of human peripheral sensory neurons

The extracellular matrix (ECM) is a mixture of glycoproteins and fibrous proteins that provide the biophysical properties necessary to maintain cellular homeostasis. ECM integrity is of particular importance during development, where it allows proper migration and cellular differentiation. Laminins are ECM heterotrimeric proteins consisting of , {beta}, and {gamma} chains. There are five known chains, four {beta} chains, and three {gamma} chains. Thus, there are 60 potential combinations for laminin trimers, however only 16 laminin trimers have been identified to date. Furthermore, none of them contain laminin {beta}4 and its function is unknown. Here, we sought to characterize the role of LAMB4 (the gene encoding laminin {beta}4) during human embryonic development of the peripheral sensory nervous system. Using human pluripotent stem cells (hPSCs), we found that LAMB4 is expressed in the ectoderm in the early stages of sensory neuron (SN) specification. SNs, part of the peripheral nervous system, are specialized neurons that detect pain, temperature, and touch. Surprisingly, more than 20 million people in the US have some form of peripheral nerve damage (including SNs), however there are very few treatment options available. Learning about the biology of peripheral neurons will uncover potential new therapeutic targets, thus we focused on understanding the effects of LAMB4 in SNs. First, we knocked out LAMB4 in hPSCs, using CRISPR/Cas9, and found that loss of LAMB4 impairs the migration of the SN progenitors neural crest cells (NCCs) and harms SN development and survival. To assess if LAMB4 has clinical relevance, we studied the genetic disorder Familial Dysautonomia (FD), which specifically affects the peripheral nervous system. FD is caused by a mutation in ELP1 (a component of the Elongator complex) leading to developmental and degenerative defects in SNs. A previous report showed that patients with severe FD harbor additional single nucleotide variants in LAMB4. We found that these variants sharply downregulate the expression of LAMB4 and laminin {beta}4 levels in SNs differentiated from induced pluripotent stem cells (iPSCs) reprogramed from patients with severe FD. Moreover, a healthy ECM is sufficient to rescue the developmental phenotypes of FD, further confirming that ECM defects contribute significantly to the etiology of FD. Finally, we found that LAMB4/laminin {beta}4 is necessary for actin filament accumulation and it interacts with laminin 4 and laminin {gamma}3, forming the laminin-443, a previously unreported laminin trimer. Together, these results show that LAMB4 is a critical, but largely unknown gene required for SN development and survival.

cell biology↗

bioRxiv2024

The over-activated peritoneal immune environment in endometriosis is characterised by a lack of PD-1 inhibition.

BackgroundEndometriosis is characterised by chronic inflammation in the peritoneal cavity causing acute and chronic pelvic pain, largely explained by dysregulation in the immune environment within peritoneal fluid. The activation status of the peritoneal immune cells is unclear. In addition, a comparison with the status of the systemic immune system is desirable to explore avenues of diagnosis and treatment of endometriosis-related inflammation and pain. Objective(s)To investigate the immune environment in endometriosis in peritoneal fluid and blood by full-spectrum flow cytometry with a focus on activation and inhibition of immune cells. Study DesignThis was an observational study in patients undergoing laparoscopy for diagnosis or treatment of peritoneal endometriosis or for unrelated conditions; PF was collected from n=5 endometriosis patients and n=4 controls, blood from n=4 endometriosis patients and n=3 controls. Data were analysed for statistical significance using ANOVA, the Kruskal-Wallis or Mann-Whitney U test, with a p-value below 0.05 considered significant. ResultsWe observed a prevailing of myeloid immune cells in the peritoneal fluid as opposed to lymphoid cells in the blood. The main differences between endometriosis and control samples, however, were found in the smaller compartments, i.e., in lymphoid populations in peritoneal fluid and myeloid populations in blood. PD-1 levels in peritoneal fluid endometriosis samples were significantly lower than in controls (p<0.05). Conclusion(s)The immune checkpoint PD-1 could be a new angle of treating endometriosis-related inflammation and pain in women suffering from this chronic and intractable condition. TweetableLack of PD-1 plays a role in endometriosis-related inflammation. AJOG at a glanceO_LIThe inflammatoru immune environment in endometriosis needs investigating as it iis causative of the pain, i.e., the predominant symptom. C_LIO_LIWe found a lack of PD-1 expression on peritoneal fluid cells in endometriosis compared to controls. C_LIO_LIThis could explain the persistent inflammation and open avenues of treatment. C_LI

immunology↗

bioRxiv2024

Evaluating regional heritability mapping methods for identifying QTLs in a wild population of Soay sheep

Regional heritability mapping (RHM) is a method that estimates the heritability of genomic segments that may contain both common and rare variants affecting a complex trait. We compared three RHM methods: SNP-RHM, which uses genomic relationship matrices (GRMs) based on SNP genotypes; Hap-RHM, which uses GRMs based on haplotypes; and SNHap-RHM, which uses both SNP-based and haplotype-based GRMs jointly. We applied these methods to data from a wild population of sheep, analysed eleven polygenic morphometric traits and compared the results with previous genome wide association analyses (GWAS). We found that whilst the inclusion of the regional matrix did not explain significant variation for all regions that were associated with trait variation using GWAS, it did for several regions that were not previously associated with trait variation.

genomics↗

bioRxiv2024

Fluorescence Lifetime Imaging for quantification of targeted drug delivery in varying tumor microenvironments

RationaleTrastuzumab (TZM) is a monoclonal antibody that targets the human epidermal growth factor receptor (HER2) and is clinically used for the treatment of HER2-positive breast tumors. However, the tumor microenvironment can limit the access of TZM to the HER2 targets across the whole tumor and thereby compromise TZMs therapeutic efficacy. An imaging methodology that can non-invasively quantify the binding of TZM-HER2, which is required for therapeutic action, and distribution within tumors with varying tumor microenvironments is much needed. MethodsWe performed near-infrared (NIR) fluorescence lifetime (FLI) Forster Resonance Energy Transfer (FRET) to measure TZM-HER2 binding, using in vitro microscopy and in vivo widefield macroscopy, in HER2 overexpressing breast and ovarian cancer cells and tumor xenografts, respectively. Immunohistochemistry was used to validate in vivo imaging results. ResultsNIR FLI FRET in vitro microscopy data show variations in intracellular distribution of bound TZM in HER2-positive breast AU565 and AU565 tumor-passaged XTM cell lines in comparison to SKOV-3 ovarian cancer cells. Macroscopy FLI (MFLI) FRET in vivo imaging data show that SKOV-3 tumors display reduced TZM binding compared to AU565 and XTM tumors, as validated by ex vivo immunohistochemistry. Moreover, AU565/XTM and SKOV-3 tumor xenografts display different amounts and distributions of TME components, such as collagen and vascularity. Therefore, these results suggest that SKOV-3 tumors are refractory to TZM delivery due to their disrupted vasculature and increased collagen content. ConclusionOur study demonstrates that FLI is a powerful analytical tool to monitor the delivery of antibody drug tumor both in cell cultures and in vivo live systems. Especially, MFLI FRET is a unique imaging modality that can directly quantify target engagement with potential to elucidate the role of the TME in drug delivery efficacy in intact live tumor xenografts.

cancer biology↗

bioRxiv2023

Epigenetic heritability of cell plasticity drives cancer drug resistance through one-to-many genotype to phenotype mapping

Cancer drug resistance is multi-factorial, driven by heritable (epi)genetic changes but also phenotypic plasticity. Here we dissect it by perturbing colorectal cancer patient-derived organoids longitudinally with drugs in sequence. Combining longitudinal tracking, single cell omics, evolutionary modelling, and machine leaning, we found that different targeted drugs select for distinct subclones, supporting rationally designed drug sequences. The cellular memory was encoded as a heritable epigenetic configuration, from which multiple transcriptional programmes could run, supporting a one-to-many (epi)genotype-to- phenotype map that explains how clonal expansions and plasticity manifest together. This may ensure drug resistance subclones can exhibit distinct phenotypes in changing environments while still preserving the cellular memory encoding for their selective advantage. Chemotherapies resistance was instead entirely driven by plasticity. Inducing further chromosomal instability before drug application changed clonal evolution but not convergent transcriptional programmes. Collectively, our data show how genetic and epigenetic alterations are selected to "permissive epigenome" enabling phenotypic plasticity.

cancer biology↗

bioRxiv2023

High Resolution Biological and Physical Sampling Reveals Expression of Domoic Acid Biosynthetic Genes at Frontal Zones

Ocean microbes are the foundation of marine food webs, regulating carbon cycling and ecosystem dynamics. How they proliferate, die, move, and interact is regulated by physical, chemical, and biological factors that are dynamic and challenging to quantify in the natural environment. A significant limitation in many marine field studies is the inability to continuously sample the ever-changing ocean environment over space and time. In this study, we integrated spatiotemporal and multi-omic sample collection in an intensive sampling effort of phytoplankton ecology in Monterey Bay, California during the spring of 2021. Sampling methods coupled: (1) manual shipboard CTD sampling, (2) autonomous sampling using a Long-Range Autonomous Underwater Vehicle (LRAUV) equipped with an Environmental Sampling Processor (ESP), and (3) high-resolution physical measurements by an autonomous vertical profiler (Wirewalker). Sampling occurred as upwelling waned alongside declining domoic acid (DA) and low abundances of toxigenic Pseudo-nitzschia. Conditions needed to spark a widespread and toxic Pseudo-nitzschia bloom were absent, yet low-level DA was driven by similar mechanisms to those causing elevated DA. Three DA biosynthetic intermediate molecules were reported in the environment for the first time. Both shipboard and ESP sampling approaches identified DA biosynthetic gene expression at frontal zones. DA and expression of dabA, the gene encoding the first committed step of DA biosynthesis, were higher in association with recently upwelled water that supplied nutrients for growth and DA biosynthesis. Detection of subtle variations in dab gene expression in response to environmental variation provide a window into the ecological dynamics underpinning major toxic events. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/562961v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@1c1f554org.highwire.dtl.DTLVardef@d16b02org.highwire.dtl.DTLVardef@c856e1org.highwire.dtl.DTLVardef@bfd248_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Phosphorylation-dependent interactions of VAPB and ELYS contribute to the temporal progression of mitosis

ELYS is a nucleoporin that localizes to the nuclear side of the nuclear envelope in interphase cells. In mitosis, it serves as an assembly platform that interacts with chromatin and then with nucleoporin subcomplexes to initiate the formation of novel nuclear pore complexes. Here we describe the interaction of ELYS with the membrane protein VAPB. In mitosis, ELYS becomes phosphorylated at many sites, including a predicted FFAT (two phenylalanines in an acidic tract) motif, which is shown to mediate interaction with the MSP (major sperm protein)-domain of VAPB. Phosphorylation-dependent binding of VAPB to ELYS is demonstrated by peptide binding assays and co-immunoprecipitation experiments. In anaphase, the two proteins co-localize to the non-core region of the newly forming nuclear envelope. Depletion of VAPB resulted in prolonged mitosis and slow progression from meta-to anaphase and also to chromosome segregation defects. Together, our results suggest an active role of VAPB in recruiting membrane fragments to chromatin and in the biogenesis of a novel nuclear envelope during mitosis.

cell biology↗

bioRxiv2023

Investigating pedigree- and SNP-associated components of heritability in a wild population of Soay sheep

Estimates of narrow sense heritability derived from genomic data that contain related individuals may be biased due to the within-family effects such as dominance, epistasis and common environmental factors. However, for many wild populations, removal of related individuals from the data would result in small sample sizes. In 2013, Zaitlen et al. proposed a method to estimate heritability in populations that include close relatives by simultaneously fitting an identity-by-state genomic relatedness matrix (GRM) and an identity-by-descent GRM. The IBD GRM is identical to the IBS GRM, except relatedness estimates below a specified threshold are set to 0. We applied this method to a sample of 8557 wild Soay sheep from St. Kilda, with genotypic information for 419,281 single nucleotide polymorphisms to investigate polygenic and monogenic traits. We also implemented a variant of the model in which the IBD GRM was replaced by a GRM constructed from SNPs with low minor allele frequency to examine whether any additive genetic variance is captured by rare alleles. Each model was compared to an animal model with a single GRM based on all genotyped markers (the IBS GRM) using a log likelihood ratio test. Whilst the inclusion of the IBD GRM did not significantly improve the fit of the model for the monogenic traits, it improved the fit for some of the polygenic traits, suggesting that dominance, epistasis and/or common environment not already captured by the non-genetic random effects fitted in our models may influence these traits.

genetics↗

bioRxiv2022

The impact of SNP density on quantitative genetic analyses of body size traits in a wild population of Soay sheep

Understanding the genetic architecture underpinning quantitative traits in wild populations is pivotal to understanding the processes behind trait evolution. The animal model is a popular method for estimating quantitative genetic parameters such as heritability and genetic correlation and involves fitting an estimate of relatedness between individuals in the study population. Genotypes at genome-wide markers can be used to estimate relatedness; however, relatedness estimates vary with marker density, potentially affecting results. Increasing density of markers is also expected to increase the power to detect quantitative trait loci (QTL). In order to understand how the density of genetic markers affects the results of quantitative genetic analyses, we estimated heritability and performed genome-wide association studies (GWAS) on five body size traits in an unmanaged population of Soay sheep using two different SNP densities: a dataset of 37,037 genotyped SNPs, and an imputed dataset of 417,373 SNPs. Heritability estimates did not differ between the two SNP densities, but the high-density imputed SNP dataset revealed four new SNP-trait associations that were not found with the lower density dataset, as well as confirming all previously-found QTL. We also demonstrated that fitting fixed and random effects in the same step as performing GWAS is a more powerful approach than pre-correcting for covariates in a separate model.

genomics↗