Biology subjects

Bian, Z.

Publications and source records attributed to Bian, Z..

At least 19 recordsLinked to original sources

bioRxiv2026

Genomic hallmarks of parasexual reproduction in three hybrid groups of the human pathogen Cryptococcus neoformans

Hybridization is a major driver of fungal evolution, yet knowledge of the molecular mechanisms underpinning hybridization and its genomic impact remain limited. Here, we analyse 197 Cryptococcus neoformans genomic sequences, including 13 newly sequenced strains, identifying three genetically clustered and distinct hybrid groups (H1, H2 and H3) each with unique parental origins and ecological associations. Using phylogenomics, population structure analyses, and long-read genome assemblies, we identified hybrid genomes with chromosome-wide loss of heterozygosity (LOH), inheritance of large intact parental haplotype blocks and widespread aneuploidy within and across genomes. These patterns are also observed when progeny were generated with spo11{Delta} parents, indicating these features are a result of a meiotic-independent process such as parasex. This is further underscored by discovery of haploid and near-haploid recombinants in both spo11{Delta} mutant progeny and reanalysed wild-type hybrid progeny. We hypothesise these haploid and near-haploid recombinants are generated through ploidy reduction via independent chromosome assortment because of concerted chromosomal loss, which is a key feature of the parasexual cycle. Phenotypic assays demonstrated that several hybrid isolates have diverse growth and virulence patterns, underscoring functional consequences of genome plasticity. Together, our work suggests a non-meiotic reproductive process contributes to shape the genotypic and phenotypic diversity of Cryptococcus neoformans.

genomics↗

bioRxiv2025

Sourdough starter-inspired living materials grown from probiotic consortia with engineered division-of-labor

Genetic circuits enable precise control over cellular behavior. As circuits become more complex, implementing them within a single cell population becomes difficult. Tasks can instead be distributed in engineered consortia. However, selecting appropriate consortia and harnessing the natural traits of each species for such a division of labor remain unsolved challenges. Here, we report the creation of SINERGY, an engineered synthetic sourdough starter in which functional modules are distributed between the two constituent species. These modules, consisting of sensing, communication, and response, enable in vitro biosensing and in vivo drug delivery and modulate the gut ecosystem in an animal disease model. SINERGY not only preserves the safety and health-promoting properties of the natural components but also endows microbes with programmable functionalities, facilitating broad applications in biomedicine.

synthetic biology↗

bioRxiv2025

Meiosis-specific genes play roles in ploidy reduction in Cryptococcus neoformans titan cells

Cryptococcus neoformans is a fungal pathogen of humans that causes life-threatening meningoencephalitis. During infection, enlarged, polyploid titan cells are produced that promote persistence in the host, in part by resisting phagocytosis; under stress conditions, such as exposure to the antifungal drug fluconazole, titan cells can produce aneuploid or diploid, drug-resistant daughter cells. However, the mechanism underlying this ploidy reduction remains poorly understood. Interestingly, meiosis related genes have been shown to be activated during Cryptococcus infection, leading us to hypothesize that the depolyploidization of C. neoformans titan cells may occur through a process resembling the ploidy reduction during meiosis. In this study, we show that titan cells developed from diploid strains predominantly produce diploid daughter cells with haploid daughters observed infrequently. We further demonstrate that meiosis-specific genes, including DMC1 and SPO11, are critical for stable inheritance of a diploid genome in the daughter cells. Specifically, deletion of these genes in a heterozygous diploid background resulted in: 1) titan cells with a significantly reduced capacity to produce daughter cells; 2) increased phenotypic variation among daughter cells produced by the titan cells, including traits that could be relevant to cell growth and viability; and 3) daughter cells produced by the titan cells exhibiting high levels of loss of heterozygosity (LOH) and aneuploidy, suggesting elevated genome instability. Taken together, these findings demonstrate the importance of meiosis-specific genes in the ploidy reduction process of titan cells derived from a heterozygous diploid background in an important human fungal pathogen. SIGNIFICANCEPolyploid titan cells are central to Cryptococcus neoformans persistence during infection, yet how they reduce ploidy to generate daughter cells was unclear. In most eukaryotes, the meiosis-related proteins Spo11 and Dmc1 are best known for initiating (double-strand break formation) and executing (strand exchange) meiotic recombination, respectively. Here, we show that in C. neoformans, Dmc1 and Spo11 are critical for polyploid titan cells to produce viable daughter cells with reduced ploidy specifically in a heterozygous diploid context, ensuring genome stability without introducing detectable canonical meiotic recombination. Loss of either gene compromises daughter cell production and causes genome instability (LOH, aneuploidy) and phenotypic heterogeneity. These findings reveal a "para-meiosis" safeguard that preserves genomic configurations during titan cell depolyploidization in C. neoformans.

genetics↗

bioRxiv2025

Almost Free Enhancement of Multi-Population PRS: From Data-Fission to Pseudo-GWAS Subsampling

Many multi-population polygenic risk score (PRS) methods have been proposed to improve prediction accuracy in underrepresented populations; however, no single method outperforms other methods across all data scenarios. Although integrating PRS results across multiple methods and populations may lead to more accurate predictions, this approach may be limited by the availability of individual-level tuning data to calculate combination weights. In this manuscript, we introduce MIXPRS, a robust PRS integration framework based on data fission principles, to effectively combine multiple multi-population PRS methods using only genome-wide association study (GWAS) summary statistics from multiple populations. Specifically, MIXPRS employs SNP pruning to mitigate linkage disequilibrium (LD) mismatch between the training GWAS summary statistics and LD reference panels, and utilizes non-negative least squares regression to robustly estimate PRS combination weights. Extensive simulations and real-data analyses involving 22 continuous traits and four binary traits across five populations from the UK Biobank and All of Us datasets demonstrate that MIXPRS consistently outperforms the existing methods in prediction accuracy. Because MIXPRS relies solely on GWAS summary statistics, it enjoys broad accessibility, robustness, and generalizability for underrepresented populations.

genetics↗

bioRxiv2025

Unisexual reproduction in the global human fungal pathogen Cryptococcus neoformans

The human fungal pathogen Cryptococcus species complex (encompassing C. neoformans, C. deneoformans, and the C. gattii species complexes) exhibit diversity in sexual reproduction, including -a mating, pseudosexual reproduction, as well as unisexual reproduction initiated from a single isolate or between isolates of the same mating type. A central conundrum is that while most Cryptococcus natural populations exhibit significant mating-type bias, genetic and genomic analyses show recombination occurs in nature. The discovery of unisexual reproduction in C. deneoformans provided insight; however, thus far unisexual reproduction has never been directly observed in the predominant global pathogenic species C. neoformans. Here, we provide evidence that mutating the RIC8 gene, which encodes a conserved guanine nucleotide exchange factor (GEF) involved in both chaperoning and activating G proteins, enables unisexual reproduction in C. neoformans. Additionally, we show that genetic variation in the natural population promotes unisexual reproduction, and unisexual reproduction in C. neoformans involves canonical meiotic recombination. Finally, we found that deletion of both GPA2 and GPA3 in the MAT background leads to self-filamentation without sporulation, suggesting that differential modulation of the G proteins, likely involving Ric8, could underlie the switch between different modes of sexual reproduction in Cryptococcus. Our study further highlights that the highly conserved Ric8 GEF can act as an important regulator of cellular development in response to environmental stimuli and could modulate sexual reproduction in nature. We hypothesize that unisexual reproduction occurs much more frequently in nature than currently appreciated, and possibly in other fungi and microbial eukaryotes as well. Significance statementSexual reproduction is a central tenet of the eukaryotic life cycle, essential for the long-term survival of a species by promoting genetic diversity and facilitating natural selection. In eukaryotes such as unicellular basidiomycetous fungi, sexual reproduction leads to hyphal growth and spore production, enabling escape from harsh environments and long-distance dispersal. Here, we report that mutating the RIC8 gene, encoding a conserved guanine nucleotide exchange factor (GEF) involved in activation of G proteins, enables unisexual reproduction in the predominant human fungal pathogen Cryptococcus neoformans that involves canonical meiosis. Our findings suggest that conditions might exist in nature that could induce, and even promote, unisexual reproduction in Cryptococcus, highlighting the complexity and importance of sexual reproduction in this prominent fungal pathogen.

genetics↗

bioRxiv2025

Metabolic modulation of intratumoral cholesterol with gut microbiota for the treatment of colorectal cancer

Excess cholesterol is positively correlated with colorectal cancer (CRC). Current therapeutic strategies for modulating cholesterol levels in CRC are limited and often come with complications. Here, we demonstrated that microbiome shunting of intestinal cholesterol to anticancer metabolites is a safe and applicable therapeutic approach for CRC. By screening major microbial metabolic products of cholesterol, we found that 4-cholesten-3-one (4-C-3) was selectively depleted in fecal samples and tumor tissues of patients with CRC. 4-C-3 exhibits strong antitumor effects on human CRC cell lines, patient-derived organoids, and patient-derived xenograft (PDX) models. Mechanistically, 4-C-3 suppresses CRC tumorigenesis by dually targeting the epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma viral oncogene homologue (KRAS). 4-C-3 directly binds to EGFR, blocking its signal transduction by inhibiting the binding of EGFR ligands. Additionally, 4-C-3 inhibits oncogenic KRAS variants, such as KRASG12D, by suppressing nucleotide exchange activity and effector engagement. By targeting both EGFR and KRAS, 4-C-3 reduces primary resistance to anti-EGFR therapies caused by KRAS mutations in CRC. As a proof-of-concept study, we showed that delivery of 4-C-3 by Oscillibacter ruminantium, a 4-C-3- producing commensal bacterium that is reduced in CRC patients, or a nonpathogenic Escherichia coli strain engineered to specifically convert intestinal cholesterol into 4-C-3, removed intratumoral cholesterol and led to rapid tumor regression in multiple models of CRC. These results suggest that microbial therapies for restoring intestinal cholesterol homeostasis represent a new therapeutic avenue for CRC.

cancer biology↗

bioRxiv2025

Exploring Population Differences in the Human Gut Microbiome: from Microbial Abundance to Single Nucleotide Polymorphisms

The human gut microbiota exhibits significant diversity across populations, influenced by factors such as geography, diet, and lifestyle, particularly between the Han Chinese and non-Chinese populations. While previous studies have predominantly focused on the taxonomic abundance of the gut microbiome, the impact of single nucleotide polymorphisms (SNPs) in driving population-specific differences remains largely underexplored. In this study, we systematically investigated gut microbial differences between the Han Chinese and non-Chinese populations using the Human Gut Microbiome Reference Genome Catalog (HGMRGC). HGMRGC includes 271,480 non-redundant genomes from 5,785 prokaryotic species, which was generated by metagenomic sequencing data from 9,320 publicly available samples across 22 countries and 3,584 newly sequenced samples from Han Chinese individuals across 29 provinces and regions in China. We observed geography was the primary driver of microbial variation of abundance and SNPs. We identified 625 novel population-specific genome clusters from HGMRGC with functional differences in carbohydrate utilization and 126 species exhibiting distinct prevalence related to vitamin biosynthesis, antibiotic resistance, and carbohydrate metabolism. Beta diversity analysis highlighted significant inter-population differences in both microbial abundance and SNPs, while alpha diversity analysis revealed that non-Chinese populations exhibited higher diversity in microbial abundance, and Han Chinese populations displayed greater diversity in SNPs. These results provide valuable insights into population-specific microbial diversity, laying the groundwork for future research on its functional and health implications.

microbiology↗

bioRxiv2025

RAPID: Reliable and efficient Automatic generation of submission rePortIng checklists with large language moDels

ImportanceMedical reporting guidelines are significant in improving the transparency, quality, and integrity of medical research, particularly in randomized clinical trials; adherence to these guidelines supports research interpretability and has direct implications for downstream applications, such as patient treatment. However, with over 600 distinct reporting guidelines, manual assessments are often time-consuming and labor-intensive. ObjectiveTo evaluate an automated reporting checklist generation tool using large language models and retrieval augmentation generation technology, called RAPID. Design, Setting, and ParticipantsThis study used large language models to design a retrieval augmentation generation architecture and collected published journal articles as training and validation sets to optimize prompts within the framework and comprehensively evaluate the performance of the framework. Medical reporting experiments were collected from 50 randomized controlled trials without the intervention of AI tools and 41 randomized controlled trials with the intervention of AI tools. Main Outcomes and MeasuresFor effective evaluation of the performance of this tool, a classification accuracy metric (Reported/Not Reported) defined as the number of correct judgments divided by all judgments and a content consistent score metric defined as the number of contents retrieved by the tool that are the same as those retrieved by researchers divided by the total number of judgments were calculated. ResultsThe RAPID tool uses the widely used Word document and Portable Document Format as an input file. Fifty published journal articles without the intervention of AI tools and 41 published journal articles with the intervention of AI tools were collected as CONSORT and CONSORT-AI datasets. All of the CONSORT reporting items (37) were included in the tool. RAPID achieved a high average accuracy rate of 92.11% and a content consistency score of 81.14% on the CONSORT dataset. Of the CONSORT-AI reporting items, 11 items related to the intervention of AI tools were included in the tool. RAPID achieved an average accuracy of 83.81% with a content consistency score of 72.51% on the CONSORT-AI dataset. For these two reporting guidelines, a training set of 5 articles was selected from each dataset to refine the prompts used in the tools for CONSORT and CONSORT-AI reporting checklist. The validation set of the remaining articles was used to assess the performance of the RAPID. The RAPID tool used the Word document and Portable Document Format of the articles as input files. A RAPID graphical user interface was built using JavaScript and Vue. Conclusions and RelevanceThe RAPID tool is designed to assist in the reporting of various types of trials. RAPID has strong scalability, which can be easily adapted to different medical reporting guidelines without transfer learning on a large dataset. RAPID may effectively save time and improve working efficiency for different user groups, for example, 1) simplifying the submission process and improving report quality by verifying manuscript completeness for medical authors; 2) facilitating evaluation of report quality for medical researchers; 3) expediting manuscript distribution for medical editors; and 4) identifying reporting deficiencies and providing deeper insights for review comments for reviewers. Key PointsO_ST_ABSQuestionC_ST_ABSCan large language model tools automatically generate medical reporting checklists for manuscripts of different types of clinic trials? FindingsAn automated reporting checklist generation tool using large language models and retrieval augmentation generation technology, RAPID, was developed. RAPID was fully evaluated on all items across two separate datasets related to the Consolidated Standards of Reporting Trials (CONSORT) and CONSORT-AI reporting guidelines. In the first dataset corresponding to CONSORT, RAPID achieved an average accuracy of 92.11%, while in the second dataset associated with CONSORT - AI, it reached an average accuracy of 83.81%. Additionally, RAPID is highly scalable. It can be easily and smoothly adapted to different medical reporting guidelines without transfer learning on a large dataset. MeaningRAPID can effectively save time and improve working efficiency for different user groups such as medical authors, researchers, editors, and reviewers.

bioinformatics↗

bioRxiv2025

Butyrolactol A is a phospholipid flippase inhibitor that potentiates the bioactivity of caspofungin against resistant fungi

Fungal infections cause millions of deaths annually and are challenging to treat due to limited therapeutic options and rising resistance. Cryptococci are intrinsically resistant to the latest generation of antifungals, echinocandins, while Candida auris, a notorious global threat, is also increasingly resistant. We performed a natural product extract screen to rescue caspofungin fungicidal activity against Cryptococcus neoformans H99 and identified butyrolactol A, which restores echinocandin efficacy against resistant fungal pathogens, including multidrug-resistant C. auris. Mode of action studies revealed that butyrolactol A inhibits the phospholipid flippase Apt1-Cdc50, blocking phospholipid transport. Cryo-electron microscopy analysis of the Apt1*butyrolactol A complex revealed that the flippase is trapped in a dead-end state. Apt1 inhibition disrupts membrane asymmetry, vesicular trafficking, and cytoskeletal organization, thereby enhancing echinocandin uptake and potency. This study identifies lipid flippases as promising antifungal targets and demonstrates the potential of revisiting natural products to expand the antifungal arsenal and combat resistance.

biochemistry↗

bioRxiv2024

Essential genes encoded by the mating-type locus of the human fungal pathogen Cryptococcus neoformans

Fungal sexual reproduction is controlled by the mating-type (MAT) locus. In contrast to a majority of species in the phylum Basidiomycota that have tetrapolar mating-type systems, the opportunistic human pathogen Cryptococcus neoformans employs a bipolar mating-type system, with two mating types (a and ) determined by a single MAT locus that is unusually large ([~]120 kb) and contains more than 20 genes. While several MAT genes are associated with mating and sexual development, others control conserved cellular processes (e.g. cargo transport and protein synthesis), of which five (MYO2, PRT1, RPL22, RPL39, and RPO41) have been hypothesized to be essential. In this study, through genetic analysis involving sporulation of heterozygous diploid deletion mutants, as well as in some cases construction and analyses of conditional expression alleles of these genes, we confirmed that with the exception of MYO2, both alleles of the other four MAT genes are indeed essential for cell viability. We further showed that while MYO2 is not essential, its function is critical for infectious spore production, faithful cytokinesis, adaptation for growth at high temperature, and pathogenicity in vivo. Our results demonstrate the presence of essential genes in the MAT locus that are divergent between cells of opposite mating types. We discuss possible mechanisms to maintain functional alleles of these essential genes in a rapidly-evolving genomic region in the context of fungal sexual reproduction and mating-type evolution. IMPORTANCESexual reproduction is essential for long-term evolutionary success. Fungal cell type identity is governed by the MAT locus, which is typically rapidly evolving and highly divergent between different mating types. In this study, we show that the a and alleles of four genes encoded in the MAT locus of the opportunistic human fungal pathogen C. neoformans are essential. We demonstrate that a fifth gene, MYO2, which had been predicted to be essential, is in fact dispensable for cell viability. However, a functional MYO2 allele is important for cytokinesis and fungal pathogenicity. Our study highlights the need for careful genetic analyses in determining essential genes, which is complementary to high-throughput approaches. Additionally, the presence of essential genes in the MAT locus of C. neoformans provides insights into the function, maintenance, and evolution of these fast-evolving genomic regions.

genetics↗

bioRxiv2024

Bola-amphiphilic dendrimer empowers imatinib to target metastatic ovarian cancer stem cells via beta-catenin-HRP2 signaling axis

Ovarian cancer is the leading cause of death among all gynecological malignancies, and drug resistance renders the current chemotherapy agents ineffective for patients with advanced metastatic tumors. We report an effective treatment strategy for targeting metastatic ovarian cancer involving a nanoformulation (Bola/IM) - bola-amphiphilic dendrimer (Bola)-encapsulated imatinib (IM) - to target the critical mediator of ovarian cancer stem cells (CSCs) CD117 (c-Kit). Bola/IM offered significantly more effective targeting of CSCs compared to IM alone, through a novel and tumor-specific {beta}-catenin/HRP2 axis, allowing potent inhibition of cancer cell survival, stemness and metastasis in metastatic and drug-resistant ovarian cancer cells. Promising results were also obtained in clinically relevant patient-derived ascites and organoids, alongside high tumor-oriented accumulation and favorable pharmacokinetic properties in mouse models. Furthermore, Bola/IM displayed synergistic anticancer activity when combined with the first-line chemotherapeutic drug cisplatin in patient-derived xenograft mouse models, without any adverse effects. Our findings support the use of Bola/IM as a nanoformulation to empower IM, providing targeted and potent treatment of metastatic ovarian cancer. Our study thus represents a significant advancement towards addressing the unmet medical need for improved therapies targeting this challenging disease.

cancer biology↗

bioRxiv2023

Evolution is All You Need in Promoter Design and Optimization

Predicting the strength of promoters and guiding their directed evolution is a crucial task in synthetic biology. This approach significantly reduces the experimental costs in conventional promoter engineering. Previous studies employing machine learning or deep learning methods have shown some success in this task, but their outcomes were not satisfactory enough, primarily due to the neglect of evolutionary information. In this paper, we introduce the Chaos-Attention net for Promoter Evolution (CAPE) to address the limitations of existing methods. We comprehensively extract evolutionary information within promoters using chaos game representation and process the overall information with DenseNet and Transformer. Our model achieves state-of-the-art results on two kinds of distinct tasks. The incorporation of evolutionary information enhances the models accuracy, with transfer learning further extending its adaptability. Furthermore, experimental results confirm CAPEs efficacy in simulating in silico directed evolution of promoters, marking a significant advancement in predictive modeling for prokaryotic promoter strength. Our paper also presents a user-friendly website for the practical implementation of in silico directed evolution on promoters.

synthetic biology↗

bioRxiv2022

Notch-1 mediates epithelial-mucosal healing during murine colitis recovery phase

Inflammatory bowel disease (IBD) is marked by inflammation mediated epithelial-mucosal damage. The intestinal epithelial forms a tight barrier displaying two contrasting functions: restricting the entry of potentially harmful substances while, on the other hand allowing the selective passage of nutrients. The damaged epithelial-mucosal barrier causes the exposure of mucosa layers to luminal inflammatory contents. This eventually leads to the leaky epithelium, exposing the immune cells, release of various cytokines, and results in loss of epithelial homeostasis. Therefore, maintenance of healthy epithelial-mucosal lining is critical during IBD recovery. Notch signaling is an evolutionarily conserved molecular pathway crucial for the development and homeostasis of most tissues. Notably, the deregulation of Notch signaling is involved in IBD (Ulcerative colitis and Crohns disease). Notch signaling also plays a vital role in wound healing and tissue repair. Here, we investigated the role of Notch-1 signaling in wound healing and regeneration of colonic epithelium during colitis recovery phase by using conditional deletion of Notch-1 in colonic epithelium of mice. We used colonic carcinoma cell line HCT116 transiently transfected with Notch1 intracellular domain (NICD) to support in vivo data. We observed that deletion of Notch1 among mice was associated with compromised healing after colitis. Therefore, targeting the Notch-1 pathway might provide a novel therapeutic strategy for the patients recovering from colitis.

immunology↗

bioRxiv2021

SIRPα sequesters SHP-2 to promote IL-4/13 signaling and alternative activation of macrophages

The Th2 cytokines IL-4 and IL-13 through activation of their shared receptor IL-4R direct macrophage alternative activation to promote immunosuppression and wound healing. However, the mechanisms that control macrophage responses to IL-4/13 are not fully understood. Apart from driving JAK-STAT and PI3K-Akt pathways to polarize macrophages toward the alternative phenotype, the activated IL-4/13 receptors recruit negative regulators SHP-1 and SHP-2, which dephosphorylate IL-4R and decrease its signaling. Here we report that SIRP spatially restricts SHP-2 and, by such, promotes IL-4/13 signaling and macrophage alternative activation. SIRP executes this regulation via its cytoplasmic ITIMs/ITSMs that undergo phosphorylation by IL-4/13-induced, Src kinase-activated Brutons tyrosine kinase (Btk), resulting in recruitment of SHP-2 and preclusion of SHP-2 from binding to and inhibiting IL-4/13 receptors. Despite that this regulation occurs independent of CD47, extracellular CD47 ligation of SIRP facilitates its cytoplasmic phosphorylation and SHP-2 sequestration, leading to stronger IL-4/13 signaling and enhanced macrophage expression of IL-10, TGF{beta}, CD206, arginase-1, etc. Conversely, deficiency of SIRP allows SHP-2 to freely bind to {gamma}C or IL-13R1 and through which dephosphorylate IL-4R, dampening its signaling. Consistent with these findings, impaired wound healing in Sirp-/- mice under experimental colitis correlated with a deficit of immunosuppressive macrophages in the colon, a condition that was corrected by transfusion of ex vivo-produced SIRPhigh alternatively activated macrophages.

immunology↗

bioRxiv2021

High-throughput functional characterization of visceral afferents by optical recordings from thoracolumbar and lumbosacral dorsal root ganglions

Functional understanding of visceral afferents is important for developing new treatment to visceral hypersensitivity and pain. The sparse distribution of visceral afferents in dorsal root ganglions (DRGs) has challenged conventional electrophysiological recordings. Alternatively, Ca2+ indicators like GCaMP6f allow functional characterization by optical recordings. Here we report a turnkey microscopy system that enables simultaneous Ca2+ imaging at two parallel focal planes from intact DRG. By using consumer-grade optical components, the microscopy system is cost effective and can be made broadly available without loss of capacity. It records low-intensity fluorescent signals at a wide field of view (1.9 x 1.3 mm) to cover a whole mouse DRG, with a high pixel resolution of 0.7 micron/pixel, a fast frame rate of 50 frames/sec, and the capability of remote focusing without perturbing the sample. The wide scanning range (100 mm) of the motorized sample stage allows convenient recordings of multiple DRGs in thoracic, lumbar, and sacral vertebrae. As a demonstration, we characterized mechanical neural encoding of visceral afferents innervating distal colon and rectum (colorectum) in GCaMP6f mice driven by VGLUT2 promotor. A post-processing routine is developed for conducting unsupervised detection of visceral afferent responses from GCaMP6f recordings, which also compensates the motion artefacts caused by mechanical stimulation of the colorectum. The reported system offers a cost-effective solution for high-throughput recordings of visceral afferent activities from a large volume of DRG tissues. We anticipate a wide application of this microscopy system to expedite our functional understanding of visceral innervations in both health and diseases.

bioengineering↗

bioRxiv2020

Dissecting human skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses

Human skeletal stem cells (SSCs) have been discovered in fetal and adult bones. However, the spatiotemporal ontogeny of human SSCs during embryogenesis has been elusive. Here we map the transcriptional landscape of human embryonic skeletogenesis at single-cell resolution to address this fundamental question. We found remarkable heterogeneity within human limb bud mesenchyme and epithelium, as well as the earliest osteo-chondrogenic progenitors. Importantly, embryonic SSCs (eSSCs) were found in the perichondrium of human long bones, which self-renew and generate osteochondral lineage cells, but not adipocytes or hematopoietic stroma. eSSCs are marked by the adhesion molecule CADM1 and highly enrich FOXP1/2 transcriptional network. Interestingly, neural crest-derived cells with similar phenotypic markers and transcriptional network were also found in the sagittal suture of human embryonic calvaria. Taken together, this study revealed the cellular heterogeneity and lineage hierarchy during human embryonic skeletogenesis, and identified distinct skeletal stem/progenitor cells that orchestrate endochondral and intramembranous ossification.

developmental biology↗

bioRxiv2020

Immune Response Drives Outcomes in Prostate Cancer: Implications for Immunotherapy

BackgroundThe heterogeneity of the immune microenvironment leads to the different response results of immune checkpoint blockade therapy. We aimed to propose a robust molecular classification of prostate cancer microenvironment to identify ideal patients for delivering effective immunotherapy. MethodsA total of 1,557 prostate cancer patients were enrolled in the current study, including 69 real-world samples from the AHMU-PC cohort. Non-negative matrix factorization algorithm was employed to virtually microdissect the patients to immune and non-immune subclasses. The patients in the immune class were dichotomized to immune activated and suppressed subtypes by the nearest template prediction of activated stroma signature. The curative effects of different immune subclasses in response to immunotherapy were also predicted. ResultsWe termed the newly identified molecular class of tumors as "immune class", which was characterized by a high enrichment of T cell, B cell, NK cell, macrophage associated signatures, etc., compared with the non-immune class (all, P < 0.05). Subsequently, the immune class was subclassified into immune activated and suppressed subtypes determined by the activation status of WNT/TGF-{beta}, TGF-{beta}1, and C-ECM signatures. As a result, around 14.9% to 24.3% of overall patients belonged to the immune activated subgroup, and they were proved with the favorable recurrence-free survival outcomes than others and showed potential curative effects in response to the anti-PD-1/PD-L1 immunotherapy. ConclusionOur study identifies a novel immune class in prostate cancer, which is further described by active or exhausted immune responses. These findings provide novel insights into tailoring immunotherapeutic strategies for different prostate cancer subgroups. Highlights{blacksquare} Immunotherapy could trigger a durable response in advanced prostate cancer, but it only benefits a minority of patients; {blacksquare}Immune response drives recurrence-free survival outcomes in prostate cancer; {blacksquare}The robust molecular classification system helps identify more ideal patients for delivering anti-PD-1/PD-L1 immunotherapy.

immunology↗

bioRxiv2019

Identification of type 2 diabetes loci in 433,540 East Asian individuals

Meta-analyses of genome-wide association studies (GWAS) have identified >240 loci associated with type 2 diabetes (T2D), however most loci have been identified in analyses of European-ancestry individuals. To examine T2D risk in East Asian individuals, we meta-analyzed GWAS data in 77,418 cases and 356,122 controls. In the main analysis, we identified 298 distinct association signals at 178 loci, and across T2D association models with and without consideration of body mass index and sex, we identified 56 loci newly implicated in T2D predisposition. Common variants associated with T2D in both East Asian and European populations exhibited strongly correlated effect sizes. New associations include signals in/near GDAP1, PTF1A, SIX3, ALDH2, a microRNA cluster, and genes that affect muscle and adipose differentiation. At another locus, eQTLs at two overlapping T2D signals act through two genes, NKX6-3 and ANK1, in different tissues. Association studies in diverse populations identify additional loci and elucidate disease genes, biology, and pathways.\n\nType 2 diabetes (T2D) is a common metabolic disease primarily caused by insufficient insulin production and/or secretion by the pancreatic {beta} cells and insulin resistance in peripheral tissues1. Most genetic loci associated with T2D have been identified in populations of European (EUR) ancestry, including a recent meta-analysis of genome-wide association studies (GWAS) of nearly 900,000 individuals of European ancestry that identified >240 loci influencing the risk of T2D2. Differences in allele frequency between ancestries affect the power to detect associations within a population, particularly among variants rare or monomorphic in one population but more frequent in another3,4. Although smaller than studies in European populations, a recent T2D meta-analysis in almost 200,000 Japanese individuals identified 28 additional loci4. The relative contributions of different pathways to the pathophysiology of T2D may also differ between ancestry groups. For example, in East Asian (EAS) populations, T2D prevalence is greater than in European populations among people of similar body mass index (BMI) or waist circumference5. We performed the largest meta-analysis of East Asian individuals to identify new genetic associations and provide insight into T2D pathogenesis.

genetics↗