Biology subjects

Xia, C.

Publications and source records attributed to Xia, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

An Integrated Single-Cell Atlas Reveals Hepatic Stellate Cell Heterogeneity and Spatiotemporal Dynamics after Liver Injury

BackgroundHepatic stellate cells (HSCs) orchestrate fibrosis-free repair after acute liver injury (ALI) and sustain fibrogenesis in chronic liver injury (CLI). However, the heterogeneity and spatiotemporal dynamics of HSCs across these different injury models remain elusive. This study sought to construct a cross-etiological HSC atlas to delineate HSC states and transitions during liver injury. MethodsWe integrated 86,072 single-cell transcriptomes from 84 mouse samples across four etiologies and validated findings using multi-omics data from 277 mouse and 798 human samples. Cellular dynamics were characterized through clustering, trajectory inference, spatial analysis, and multicellular coordination network analysis. Experimental validation included liver injury models and gain-of-functional assays in primary mouse HSCs and LX-2 cells. ResultsWe established a cross-etiological, spatiotemporally resolved HSC atlas comprising 11 subpopulations. Trajectory analysis delineated a continuous quiescence-activation-attenuation (QAA) trajectory, recapitulating the in vivo full spectrum of state transitions and being supported by sequential pathway activation validated in vitro. In ALI, HSCs spatiotemporally completed the QAA trajectory around injury zones, whereas collagen-producing S100a6 HSCs pathologically accumulated in mouse and human CLI due to trajectory dysregulation. Notably, the atlas identified a previously unrecognized apoptosis-prone Mrc2 HSC subtype strongly co-localized with p53 in both mice and humans. Overexpression of transcription factors confirmed that Hbp1, Tbx20, Atoh8, and Plagl1 enriched in Mrc2+ HSCs promoted HSC apoptosis. Finally, we revealed the microenvironment of distinct cellular modules which coordinated HSC progression along the QAA trajectory. A 531-gene signature derived from the inflammatory-fibrotic cellular module significantly correlated with fibrosis stage and hepatocellular carcinoma risk in human cohorts. ConclusionsWe established a comprehensive HSC atlas and delineates HSC heterogeneity and spatiotemporal dynamic across etiologies. Dysregulation of the QAA trajectory underlies fibrotic progression, providing a resource for identifying antifibrotic targets.

cell biology↗

bioRxiv2025

The host range paradox of Meloidogyne incognita: a physiological and transcriptomic analysis of nine susceptible interactions across six plant orders

The plant-parasitic nematode Meloidogyne incognita is the pathogen with the broadest host range among all known biotrophic interactions. This species is also the single most damaging of a group of agriculturally important plant-parasites, which together are estimated to contribute to losses in excess of $170 billion/year to world agriculture. Understanding how M. incognita is able to infect representatives from most orders of flowering plants, covering more than 3000 species, addresses a fundamentally important question of how pathogens adapt to their host-environment, and may inform control of a pathogen which threatens global food security. Here, we analyse the plant-nematode infection phenotype, and cross-kingdom transcriptome, of nine interactions across six orders of flowering plants at 25 days post infection. At this stage, majority of nematodes found within roots were immature and mature females (49.2% - 91.8%). Our data show that the phylogenetic distribution of hosts does not explain the phenotypic distribution of parasitism. Interestingly, though, M. incognita do have distinct transcriptional responses to different groups of hosts, but in a pattern which is independent of host phylogenetic. Three distinct nematode "transcriptional programmes" - Group 1, 2, and 3 - are evident, and we find that effectors are neither uniformly deployed across hosts, nor across groups of hosts. Importantly, we show that this differential deployment of effectors can have profound consequences for host specificity. Finally, we show that there is essentially no widespread core gall transcriptome at 25 days post infection, prompting the proposal of a model best described as "all roads lead to Rome".

plant biology↗

bioRxiv2025

A benchmark of the somatic mutation landscape using single-cell and single-molecule whole-genome sequencing

Accurate detection of somatic mutations in noncancerous cells is critical for studying somatic mosaicism, a process implicated in aging and multiple chronic diseases. However, single-cell and single-molecule DNA sequencing platforms differ in their error profiles, coverage biases, and sensitivity to specific mutation types, complicating cross-platform comparisons. Here, we present in vitro and in silico benchmarks to quantify true-positive and false-positive rates in single-cell whole-genome sequencing using Single-Cell Multiple Displacement Amplification, and in single-molecule sequencing using Nanorate Sequencing (NS) and whole-genome NS (WGNS). Using standard cell lines, we show that all three methods detect single-nucleotide variants (sSNVs) and small insertions and deletions (sINDELs) with high accuracy, but differ in genomic coverage and susceptibility to artifacts. Method-specific biases influence mutational signatures and hotspot detection. Applying results of the benchmark to IMR-90 fibroblasts, we estimate higher in vitro mutation rates using NS than expected from in vivo data, consistent with potential replication stress and culture-associated DNA damage. Overall, our study highlights the substantial impact of sequencing platform-specific biases on somatic mutation detection and interpretation, and lays the foundation for standardized, cross-platform-comparable analyses of somatic mosaicism in normal human tissues.

genomics↗

bioRxiv2025

Plant-Compatible Xenium In Situ Sequencing: Optimised Protocol for Spatial Transcriptomics in Medicago truncatula Roots and Nodules

Elucidating the spatial and temporal regulation of gene expression during plant organogenesis is crucial for enabling precise crop improvement strategies that incorporate beneficial traits into crops while avoiding adverse effects. Root nodules, specialised organs formed in symbiosis with nitrogen-fixing bacteria, provide a valuable system to study cell-type-specific gene networks in a symbiosis-induced developmental context. However, capturing these dynamics at cellular resolution in intact plant tissues remains technically challenging. Spatial transcriptomics technologies developed for animal systems are often not directly transferable to plant tissues due to fundamental differences in tissue composition between plants and animals, including rigid and heterogeneous plant cell walls, high cell wall autofluorescence, and large vacuoles in plant cells that complicate probe access and signal detection. To address these challenges, we present an optimised protocol for applying the Xenium in situ sequencing platform to formalin-fixed paraffin-embedded (FFPE) sections of plant tissues, including Medicago truncatula roots and nodules. Key technical adaptations include customised tissue preparation, optimised section thickness, hybridisation conditions, post-Xenium staining, imaging, and downstream image analysis, all tailored specifically for plant samples. To mitigate autofluorescence and enhance detection sensitivity, we employed a strategic approach to codeword selection during probe design. Furthermore, we developed a modular probe design approach combining a custom 380-gene standalone panel with a 100-gene add-on panel. This design allows flexibility for addressing diverse research questions and includes orthologous gene sequences from two Medicago ecotypes, ensuring compatibility for downstream functional validation using mutant lines available in both genetic backgrounds. We validated the protocol across nodules at multiple developmental stages using both the 50-gene panel targeting mature nodule cell identity and the extended 480-gene panel, which includes markers across different cell types and developmental stages, as well as genes of interest identified from prior single-cell and bulk RNA-seq analyses. This optimised workflow provides a reproducible and scalable method for high-resolution spatial transcriptomics in plant tissues, establishing a robust foundation for adaptation to other plant species and developmental systems.

plant biology↗

bioRxiv2025

Pluripotent stem cell-derived siTNK cells attack tumors via a synthetic CD8-CD28 TCR complex

Tumor-associated antigen-specific T cell receptor (TCR)-engineered T cells offer a promising strategy for cancer therapy. Natural killer (NK) cells exhibit broad anti-tumor activity with low side effects but lack the capacity to recognize intracellular antigens. Here, we found that the human pluripotent stem cell (hPSC)-derived iNK cells, unlike tissue-isolated NK cells, expressed all four CD3 subunits at the transcriptome level. We introduced a synthetic gene-expressing complex (SCOTR), encoding a tumor antigen- specific TCR, CD8 coreceptor, and CD28 costimulatory molecule, into hPSCs to generate SCOTR-hPSCs. The SCOTR-hPSCs gave rise to abundant synthetic TCR complex-expressing iNK (siTNK) cells via an organoid induction method. These siTNK cells showed HLA-dependent, antigen-specific cytotoxicity against tumor cells and significantly suppressed tumor growth in tumor xenograft animal models, while also preserving universal non-specific tumor-killing activity. Collectively, siTNK cells, as hPSC-derived hybrid cells with dual features of adaptive T and inherent NK cells, offer an artificial cell source for human immunotherapies.

immunology↗

bioRxiv2025

RNA-seq reveals transcriptomic differences in circadian-related genes of the choroid plexus in a preclinical chronic migraine model.

BackgroundMigraine patients show choroid plexus (CP) changes, impairing the blood-CSF barrier. The CP regulates circadian rhythms, but links between CP circadian genes and migraine are unexplored. ObjectiveThis study examined CP circadian gene transcriptome changes in a chronic migraine rat model versus controls to identify migraine-related pathways. DesignChronic migraine model: Sprague Dawley rats (3 females, 3 males) received nitroglycerine (NTG) every other day for 9 days; controls (3 females, 3 males) got saline. CP from the 4th ventricle was collected 2 hours post-final injection for RNAseq. MethodsMigraine Behavior: Von Frey hair tests on days 1, 5, and 9, pre- and 2 hours post-NTG/saline injection, assessed basal and NTG-induced pain thresholds. RNAseq & Analysis: Differentially expressed genes (p < 0.05, fold change > 1) were identified. GO, KEGG, and Reactome enrichment analyses evaluated circadian gene expression changes. ResultsO_LINTG group showed reduced basal and NTG-induced pain thresholds on days 1, 5, and 9. C_LIO_LIFemales had more upregulated genes (MT2A, SLC7A11), males upregulated ZBTB16, S100A8. SLC7A11, SCG2, GRIA1 showed inverse regulation (up in females, down in males). C_LIO_LICircadian gene expression altered: 10 genes upregulated (e.g., SERPINE1, MAPK9, ATF4), 13 downregulated (e.g., PER2, DBP, EZH2). Sex-specific differences: females (FBXL12, GPR157), males (NKX2-1, ATF4, CLOCK). C_LIO_LIGO/KEGG analyses revealed significant enrichment of circadian rhythm-related pathways, insulin resistance, and inflammatory response processes, with sex-specific differences: females showed HIF-1 signaling and hemoglobin-related pathways, while males exhibited arachidonic acid and leukotriene production. C_LI ConclusionCP transcriptomics in the rat migraine model revealed sex-specific gene regulation, with females upregulating antioxidant genes (MT2A, SLC7A11) and males upregulating inflammatory factors (ZBTB16, S100A8), alongside circadian disruption (e.g., SERPINE1 upregulated, PER2 downregulated). Pathway analyses indicate enriched circadian rhythms, HIF-1 signaling (females), inflammatory processes (males), lipid metabolism (PPAR), and heme signaling, highlighting sex-specific and circadian targets for migraine therapy.

neuroscience↗

bioRxiv2025

AI-Guided Precision in Antibody Humanization: Structural Modeling to Minimize Immunogenicity and Preserve Efficacy

Antibody humanization is an essential part of converting animal-derived antibodies into clinical candidates however conventional CDR grafting techniques often faces challenges, especially when essential antigen-binding sites extend beyond CDR regions. Additionally, the CDR grafting process tends to retain undesired non-human elements within the CDR regions. In this study, we overcame these challenges by using our proprietary AI-predicted antigen-antibody complex algorithm to effectively humanize a murine antibody. During our AI-powered humanization process, in contrast to traditional CDR grafting techniques, only the crucial paratopes identified through our AI-predicted complex structure were precision grafted onto a select human germline. This paratope grafting technique significantly reduced the antibodies immunogenicity risk while maintaining bioactivity. Moreover, all AI-guided deep humanized antibody variants demonstrated favorable developability, including thermal stability, poly-reactivity, and hydrophobicity. These results not only advance antibody humanization techniques but also demonstrate the power of AI in expediting antibody engineering and derisking clinical research.

bioengineering↗

bioRxiv2025

Avoidance of fratricide and improved efficacy of CD33-MSLN CAR-iNK cells in treating acute myeloid leukemia

Acute myeloid leukemia (AML) patients are often older, which brings challenges of endurance and persistent efficacy of autologous CAR-T cell therapies. Allogenic CAR-NK cell therapies may offer reduced toxicities and enhanced anti-leukemic potential against AML. In this study, we designed a novel CD33-mesothelin loop CAR (Loop CAR) and evaluated its anti-tumor efficacy in human umbilical cord blood-derived NK (UCB-NK) cells and human pluripotent stem cell-derived NK (hPSC-iNK) cells. The Loop CAR exhibited superior cytotoxicity against dual-antigen-positive tumor cell lines and primary AML cells. To further avoid fratricide caused by endogenous CD33 expression in NK cells, we established a hPSC-derived cell line via knockout of CD33 gene (CD33KO) and engineered Loop CAR. Rather than enforced expression of exogenous CD16, we generated abundant mature CD33KO-Loop CAR-iNK cells highly expressing endogenous CD16 via an organoid induction approach. This innovative strategy effectively mitigated NK cell fratricide and significantly enhanced CD33 and mesothelin-mediated specific cytotoxicity. Moreover, the CD33KO-Loop CAR-iNK cells demonstrated superior tumor-killing activity in AML xenograft mice and significantly prolonged survival. hPSC-derived CD33KO-Loop CAR-iNK cells possess unique advantages and translational potential for treating AML.

cancer biology↗

bioRxiv2025

Engineered CRO-CD7 CAR-NK cells derived from pluripotent stem cells avoid fratricide and efficiently suppress human T-cell malignancies

BackgroundT cell malignancies are highly aggressive hematological tumors with limited effective treatment options. CAR-NK cell therapy targeting CD7 has emerged as a promising approach for treating T-cell malignancies. However, conventional CAR-NK cell therapy faces the challenges of cell fratricide due to CD7 expression on both malignant cells and normal NK cells. Additionally, engineering CARs into human tissue-derived NK cells demonstrates heterogeneity, low transduction efficiency, and high manufacturing costs. MethodsThe human pluripotent stem cells (hPSCs) were genetically modified by knocking out the CD7 gene and introducing the CD7 CAR expression cassette to generate CD7 KO-CD7 CAR-hPSCs. These modified hPSCs were subsequently differentiated into CD7 KO-CD7 CAR-iNK cells using an efficient organoid induction method. The cytotoxicity of CD7 KO-CD7 CAR-iNK cells against CD7+ tumor cells was evaluated. Furthermore, we overexpressed the CXCR4 gene in CD7 KO-CD7 CAR-hPSCs and derived CXCR4-expressing CD7 KO-CD7 CAR-iNK (CRO-CD7 CAR-iNK) cells. The dynamics of CRO-CD7 CAR-iNK cells in vivo were tracked, and their therapeutic efficacy was assessed using human T-cell acute lymphoblastic leukemia (T-ALL) xenograft models. ResultsThe CD7 KO-CD7 CAR-iNK cells derived from CD7 KO-CD7 CAR-hPSCs effectively avoided fratricide, demonstrated normal expansion, and exhibited potent and specific anti-tumor activity against CD7+ T-cell tumor cell lines and primary T-ALL cells. CXCR4 overexpression in CRO-CD7 CAR-iNK cells improved their homing capacity and extended their persistence in vivo. The CRO-CD7 CAR iNK cells significantly suppressed tumor growth and prolonged the survival of T-ALL tumor-bearing mice. ConclusionsOur study provides a reliable strategy for the large-scale generation of fratricide-resistant CD7 CAR-iNK cells with robust anti-tumor effects from hPSCs, offering a promising cell product to treat T-cell malignancy.

cancer biology↗

bioRxiv2025

Pluripotent stem cell-derived NK progenitor cell therapy prevents tumour occurrence and eradicates minimal residual disease

The lack of persistence and short-term efficacy presents a major challenge for CAR-NK cell therapy. Here, we addressed this issue by developing pluripotent stem cell-derived NK lineage-committed progenitor (iNKP) cell therapy. For the first time, we generated abundant iNKP cells via an organoid culture system. The iNKP cells, engineered to express CXCR4 and chimeric antigen receptors (CAR), efficiently migrated to the bone marrow and generated CAR-iNK cells persisting in peripheral blood (PB) for over 80 days. Notably, CAR-iNKP cell therapy durably protected animals from tumour occurrence. Furthermore, a single low-dose infusion of CAR-iNKP cells following conventional chemotherapy eradicated minimal residual disease (MRD), leading to long-term complete remission. Our findings present a novel strategy to overcome the limitations of traditional CAR-NK cell therapy and offer dural breakthroughs for the prevention of tumour occurrence and relapse.

cancer biology↗

bioRxiv2025

Cycling Molecular Assemblies for Selective Cancer Cell Golgi Disruption

The Golgi apparatus is a critical organelle responsible for intracellular trafficking and signaling, orchestrating essential processes such as protein and lipid sorting1-5. Dysregulation of its function has been implicated in various pathologies, including obesity, diabetes, and cancer, highlighting its importance as a potential therapeutic target. Despite this, the development of tools to selectively target the Golgi in specific cell types remain a significant unmet challenge in imaging and drug discovery. Golgi-specific enzyme activities, such as those mediated by protein acyltransferases and thioesterases6, offer an untapped opportunity to develop subcellularly localized therapeutics. Current approaches predominantly rely on direct protein binding but lack the necessary cell selectivity7, underscoring the unmet need for innovative strategies to selectively disrupt Golgi function in cancer cells. Here, we report the development of cycling molecular assemblies (CyMA), a novel class of small peptide derivatives (e.g., dipeptides), which exploit the unique enzymatic environment of the Golgi to establish futile cycles of reversible S-acylation. These assemblies selectively accumulate in cancer cell Golgi, interfering with protein S-acylation cycles and disrupting organelle homeostasis. CyMA impair key Golgi functions, including protein trafficking, glycosylation, and secretion, while demonstrating selective sparing hepatocytes and immune cells such as M1 macrophages. This selective activity represents a paradigm shift, utilizing an enzyme switch and leveraging intracellular environment rather than direct protein binding. Unlike conventional approaches, CyMA reduce tumor growth, drug resistance, and metastasis by pleiotropically disrupting Golgi related functions. By demonstrating the potential of futile cycles as a therapeutic strategy8, this study introduces a generalizable method for targeting organelle-specific enzyme activities. These findings not only underscore the therapeutic potential of CyMA in cancer but also pave the way for future applications in other Golgi-associated diseases.

biochemistry↗

bioRxiv2024

Astrocyte-specific secretome profiling reveals its correlation with neurological disorders

Secreted proteins mediate intercellular communication throughout the lives of multicellular organisms. However, due to the lack of new technology for secreted protein capturing, the progress of "secretomics lags behind. Here, we report a two-step secretome enrichment method (tsSEM) combining unnatural amino acid labeling and click chemistry-based biorthogonal reaction, which enables in vitro secretome profiling in the presence of serum. Using this novel method, we systematically investigated the secretome of human iPSCs-derived astrocytes (iAst) in different disease models and identified a panel of astrocyte-secreted proteins that are responsible for its non-cell autonomous toxicity under disease conditions. Furthermore, we validated two astrocytes-derived novel neurotrophic proteins, FAM3C and KITLG, which we identified from disease models, and found that they could boost neurite outgrowth, protect neurons, and promote neural progenitor proliferation. Our study highlights the utility of secretome profiling of iAst and demonstrates its applications in disease study and target identification and validation in drug development.

neuroscience↗

bioRxiv2024

Lifetime brain atrophy estimated from a single MRI: measurement characteristics and genome-wide correlates

A measure of lifetime brain atrophy (LBA) obtained from a single magnetic resonance imaging (MRI) scan could be an attractive candidate to boost statistical power in uncovering novel genetic signals and mechanisms of neurodegeneration. We analysed data from five young and old adult cohorts (MRi-Share, Human Connectome Project, UK Biobank, Generation Scotland Subsample, and Lothian Birth Cohort 1936 [LBC1936]) to test the validity and utility of LBA inferred from cross-sectional MRI data, i.e., a single MRI scan per participant. LBA was simply calculated based on the relationship between total brain volume (TBV) and intracranial volume (ICV), using three computationally distinct approaches: the difference (ICV-TBV), ratio (TBV/ICV), and regression-residual method (TBV[~]ICV). LBA derived with all three methods were substantially correlated with well-validated neuroradiological atrophy rating scales (r = 0.37-0.44). Compared with the difference or ratio method, LBA computed with the residual method most strongly captured phenotypic variance associated with cognitive decline (r = 0.36), frailty (r = 0.24), age-moderated brain shrinkage (r = 0.45), and longitudinally-measured atrophic changes (r = 0.36). LBA computed using a difference score was strongly correlated with baseline (i.e., ICV; r = 0.81) and yielded GWAS signal similar to ICV (rg = 0.75). We performed the largest genetic study of LBA to date (N = 43,110), which was highly heritable (h2 SNP GCTA = 41% [95% CI = 38-43%]) and had strong polygenic signal (LDSC h2 = 26%; mean{chi} 2 = 1.23). The strongest association in our genome-wide association study (GWAS) implicated WNT16, a gene previously linked with neurodegenerative diseases such as Alzheimer, and Parkinson disease, and amyotrophic lateral sclerosis. This study is the first side-by-side evaluation of different computational approaches to estimate lifetime brain changes and their measurement characteristics. Careful assessment of methods for LBA computation had important implications for the interpretation of existing phenotypic and genetic results, and showed that relying on the residual method to estimate LBA from a single MRI scan captured brain shrinkage rather than current brain size. This makes this computationally-simple definition of LBA a strong candidate for more powerful analyses, promising accelerated genetic discoveries by maximising the use of available cross-sectional data.

genetics↗

bioRxiv2024

Integrated temporal profiling of iPSCs-derived motor neurons from ALS patients carrying C9orf72, FUS, TARDBP, and SOD1 mutations

Amyotrophic Lateral Sclerosis (ALS) is a lethal neurodegenerative disease that damages motor neurons in the central nervous system, causing progressive muscle weakness that ultimately leads to death. However, its underlying mechanisms still need to be fully understood, particularly the heterogeneity and similarity between various gene mutants during disease progression. In this study, we conducted temporal RNA-seq profiling in human induced pluripotent stem cells (hiPSCs) and iPSC-derived motor neurons (iMNs) carrying the C9orf72, FUS, TARDBP, and SOD1 mutations from both ALS patients and healthy individuals. We discovered dysregulated gene expression and alternative splicing (AS) throughout iMN development and maturation, and ALS iMNs display enrichment of cytoskeletal defects and synaptic alterations from premature stage to mature iMNs. Our findings indicate that synaptic gene dysfunction is the common molecular hallmark of fALS, which might result in neuronal susceptibility and progressive motor neuron degeneration. Analysis of upstream splicing factors revealed that differentially expressed RNA-binding proteins (RBPs) in ALS iMNs may cause abnormal AS events, suggesting the importance of studying RBP defects in ALS research. Overall, our research provides a comprehensive and valuable resource for gaining insights into the shared mechanisms of ALS pathogenesis during motor neuron development and maturation in iMN models.

neuroscience↗

bioRxiv2024

Efficient generation of CAR NK cells from human umbilical cord blood CD34+ stem and progenitors for democratizing affordable immunotherapy

Chimeric antigen receptor (CAR) natural killer cells (CAR NK) cells, leveraging safety and not requiring HLA match in adoptive infusion, have emerged as promising alternative cells to CAR-T cells for immunotherapies. High and multiple doses of CAR NK cell infusions are essential to maintain therapeutic efficacy in clinical trials. This requires efficient methods for generating large-scale CAR NK cells and significantly reducing CAR engineering costs. In this study, we develop a three-step strategy to generate highly high yields of induced NK (iNK) and CAR iNK cells from human umbilical cord blood CD34+ hematopoietic stem and progenitor cells (CD34+ HSPCs). Starting from a single umbilical cord blood CD34+ HSPC, our reliable method efficiently produces 14-83 million mature iNK cells or 7-32 million CAR iNK cells with high expression levels of CD16 and zero T cell contaminations. Introducing CAR expression elements at the HSPC level reduces the quantities of CAR pseudoviruses to 1 / 140.000 - 1 / 600,000 compared to engineering CARs in mature NK cells. The iNK and CAR iNK cells, including fresh cells and thawed cells from cryopreserved conditions, demonstrate remarkable tumoricidal activities against various human cancer cells and significantly prolong the survival of human tumor-bearing animals. The high yields of CAR NK cells and negligible costs of CAR engineering of our method support the broad applications of CAR NK cells for treating cancer patients.

cell biology↗

bioRxiv2024

Single-molecule live-cell RNA imaging with CRISPR-Csm

High-resolution, real-time imaging of RNA is essential for understanding the diverse, dynamic behaviors of individual RNA molecules in single cells. However, single-molecule live-cell imaging of unmodified endogenous RNA has not yet been achieved. Here, we present single-molecule live-cell fluorescence in situ hybridization (smLiveFISH), a robust approach that combines the programmable RNA-guided, RNA-targeting CRISPR-Csm complex with multiplexed guide RNAs for efficient, direct visualization of single RNA molecules in a range of cell types, including primary cells. Using smLiveFISH, we tracked individual endogenous NOTCH2 and MAP1B mRNA transcripts in living cells and identified two distinct localization mechanisms: co-translational translocation of NOTCH2 mRNA at the endoplasmic reticulum, and directional transport of MAP1B mRNA toward the cell periphery. This method has the potential to unlock principles governing the spatiotemporal organization of native transcripts in health and disease.

biophysics↗

bioRxiv2024

Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits

Unraveling the regulatory mechanisms that govern complex traits is pivotal for advancing crop improvement. Here we present a comprehensive regulome atlas for rice (Oryza sativa), charting the chromatin accessibility across 23 distinct tissues from three representative varieties. Our study uncovers 117,176 unique open chromatin regions (OCRs), accounting for [~]15% of the rice genome, a notably higher proportion compared to previous reports in plants. Integrating RNA-seq data from matched tissues, we confidently predict 59,075 OCR-to-gene links, with enhancers constituting 69.54% of these associations, including many known enhancer-to-gene links. Leveraging this resource, we re-evaluate genome-wide association study results and discover a previously unknown function of OsbZIP06 in seed germination, which we subsequently confirm through experimental validation. We optimize deep learning models to decode regulatory grammar, achieving robust modeling of tissue-specific chromatin accessibility. This approach allows to predict cross-variety regulatory dynamics from genomic sequences, shedding light on the genetic underpinnings of cis-regulatory divergence and morphological disparities between varieties. Overall, our study establishes a foundational resource for rice functional genomics and precision molecular breeding, providing valuable insights into regulatory mechanisms governing complex traits.

genomics↗

bioRxiv2024

Deciphering the Influence of Socioeconomic Status on Brain Structure: Insights from Mendelian Randomization

Socioeconomic status (SES) influences physical and mental health, however its relation with brain structure is less well documented. Here, we examine the role of SES on brain structure using Mendelian randomisation. First, we conduct a multivariate genome-wide association study of SES using individual, household, and area-based measures of SES, with an effective sample size of n=893,604. We identify 469 loci associated with SES and distil these loci into those that are common across measures of SES and those specific to each indicator. Second, using an independent sample of [~]35,000 we provide evidence to suggest that total brain volume is a causal factor in higher SES, and that SES is protective against white matter hyperintensities as a proportion of intracranial volume (WMHicv). Third, we find evidence that whilst differences in cognitive ability explain some of the causal effect of SES on WMHicv, differences in SES still afford a protective effect against WMHicv, independent of that made by cognitive ability.

genetics↗