Biology subjects

Qian, G.

Publications and source records attributed to Qian, G..

At least 19 recordsLinked to original sources

bioRxiv2026

FAM83H couples keratin organization to Notch signaling during epidermal morphogenesis

Keratin intermediate filaments are essential for epidermal integrity, yet how keratin organization is coupled to the cell fate signaling that coordinates keratinocyte differentiation during epidermal morphogenesis remains poorly understood. Here, we identify FAM83H as a previously unrecognized regulator that links keratin cytoskeletal organization to epidermal cell fate decisions. Using mouse models and a human 3D microphysiological epidermis model, we show that loss of FAM83H disrupts epidermal architecture by impairing basal keratinocyte differentiation, organization, and cell-cell adhesion. Single-cell transcriptomic analysis of 3D epidermal tissues identified Notch signaling as prominently associated with cell populations lost upon FAM83H depletion. Mechanistically, FAM83H localizes to cell-cell junctions, where it organizes keratin filaments and desmosome integrity. Loss of FAM83H disrupts a desmoplakin-keratin-Notch1 complex at junctions, impairing Notch1 proteolytic activation and proper keratinocyte differentiation. Together, our work identifies FAM83H as a key regulator of epidermal morphogenesis that couples keratin cytoskeletal architecture to Notch1 signaling, and positions keratin-associated proteins as active participants in the epithelial fate decisions that govern epidermal homeostasis.

cell biology↗

bioRxiv2026

End-to-end evaluation of pipelines for metagenome-assembled genomes reveals hidden performance gaps

The generation of Metagenome Assembled Genomes (MAGs) has become a standard and basic step in the analysis of metagenomic data. This multi-step process, which includes assembly, binning, refinement, and quality control, has many alternative approaches, algorithms, and parameters. Determining the ideal approach for a given ecosystem and study, or highlighting algorithmic gaps in need of additional research and development, requires rigorous benchmarking. We present MAG-E (MAG pipeline Evaluator), a generalizable and expandable framework for end-to-end evaluation of entire MAG pipelines: from assembly, through binning, to quality control and filtering. MAG-E relies on simulations that are built to match an ecosystem of interest and provide a ground truth for accurate evaluation. To demonstrate the capabilities of MAG-E, we benchmark two assemblers, six binning algorithms, three binning modes, and three quality control and refinement methods in the context of the human gut microbiome. Our findings offer multiple insights into optimal MAG generation in this context. We find that metaSPAdes consistently outperforms MEGAHIT in terms of recall (completeness), and that COMEBin overall outperforms alternative binning algorithms, but has lower precision than SemiBin2. While multi-sample binning results in higher precision, as previously shown, single-sample binning has higher recall and leads to better overall performance with modern binners. Binning refinement, which combines bins from multiple different algorithms, leads to reduced performance. We further show that CheckM2 systematically overestimates completeness and underestimates contamination, and that this is partially ameliorated when using GUNC. Finally, we analyze performance at the contig level, and demonstrate that binning algorithms systematically underperform for prophages and fail to bin contigs that are shared between genomes. Overall, MAG-E offers deep insights into successes and gaps in this important analytic process.

bioinformatics↗

bioRxiv2026

Aggregation-mediated microcolony shields bacteria from contact-dependent competition and maintains phenotypic heterogeneity

Bacteria are adaptable microorganisms capable of surviving in a wide variety of environments. One common strategy for persistence and attachment to surfaces is the formation of microcolonies, often controlled by cell surfaces structures that mediate adhesion such as fimbriae. In this study, we show that type 1 fimbriae, and other adhesins structures such as autotransporter adhesins, trigger microcolony formation which confer resistance against a broad range of short-range contact-dependent weapons (e.g. T6SS, T4SS, CDI) but not against long-range diffusible weapons (e.g. diffusible toxins like colicins). Interestingly, we identify "sheltered" bacteria within microcolonies that benefit from collective protection without expressing the adhesive structure. Our findings demonstrate that adhesive structures not only improve survival in hostile environments by promoting microcolony formation but also maintain phenotypic heterogeneity within the microcolony, highlighting the importance of social behavior in bacterial adaptation to changing environments.

microbiology↗

bioRxiv2026

Engineering physically optimized T cells for increased sampling of complex tumor microenvironments

Pancreatic ductal adenocarcinoma (PDA) remains highly lethal, in part, because its dense fibroinflammatory stroma restricts therapy distribution, including adoptive T cell immunotherapies where direct interactions between T and carcinoma cells are essential for effective therapy. While T cell function must be maintained once effector-target engagement occurs, without inducing co-localization subsequent cytotoxic function steps cannot be undertaken. We therefore developed a strategy to "physically optimize" T cells to more effectively sample complex tumor volumes. Informed by pharmacologic perturbations and mathematical modeling we shifted T cell phenotype through expression of constitutively activated RhoA to increase cortical contractility, activation, migration, and sampling in PDA, while showing decreases in exhaustion markers. In CAR T cells this results in more efficient targeting through decreased sampling time and increased engagement with carcinoma cells, consistent with modeling predictions. This significantly increases T cell infiltration and distribution in PDA, resulting in improved tumor control in vivo, suggesting that this is an effective strategy to overcome stromal constraints, improve tumor engagement, and enhance the therapeutic performance of engineered T cell therapies in solid tumors.

bioengineering↗

bioRxiv2025

Selective impairment of spatial recognition memory and reduced frontal corticothalamic spine density following adolescent alcohol consumption

Heavy alcohol use is common during adolescence and is associated with increased risk of alcohol use disorder and prevalence of residual cognitive deficits, especially in behaviors associated with the latently developing prefrontal cortex (PFC). A major need for advancing our understanding of this relationship is replicable and accessible preclinical behavioral batteries that can be used to disassociate the effects of adolescent alcohol on select PFC circuits. Electrophysiological evidence implicates projections from the PFC to mediodorsal thalamus (PFC-MdT) as being uniquely impacted by adolescent intermittent alcohol consumption in mice. The present study aims to evaluate if voluntary consumption of alcohol during adolescence impacts anxiety or PFC-associated spatial and recognition memory and if they are associated with morphological changes to the PFC-MdT circuit. Our results indicate that compared to water-only controls, male and female mice that voluntarily consumed alcohol during adolescence demonstrate performance deficits in the object-in-place recognition task, without affecting the novel object recognition task, Y-maze alternation, anxiety or locomotion, an outcome consistent with PFC and MdT dysfunction. Morphological assessment of PFC neurons from male and female mice following behavioral tasks found a reduction in spine density in basal and apical, but not oblique dendrites of PFC-MdT neurons. Collectively, these results implicate the PFC to MdT circuit integrity as a potential locus of the effects of adolescent alcohol on spatial recognition memory.

neuroscience↗

bioRxiv2025

Associations Between Gut Microbiome and 24-Hour Blood Pressure Variability: A Cross-sectional Study Highlighting Sex Differences and Potential Therapeutic Targets

Blood pressure (BP) variability is an independent risk factor for cardiovascular disease (CVD). While gut microbiota (GM) and GM-derived short-chain fatty acids (SCFAs) are recognized to play a key role in BP regulation, their association with BP variability remains poorly understood. This cross-sectional study of 241 community-dwelling individuals from Hong Kong (113 men and 128 women, mean age 54{+/-}6 years) without symptomatic CVD examined the associations of GM, characterized by shotgun sequencing, and plasma SCFAs, with systolic and diastolic blood pressure (SBP/DBP) variability assessed by 24-hour BP monitoring. GM analyses, using covariate-adjusted statistical models, revealed that higher 24-hour SBP CoV associated negatively with GM -diversity (Shannon and Simpsons index, P<0.05) and positively with Firmicutes/Bacteroidetes ratio, driven by the female cohort. Parabacteroides merdae, Bacteroides dorei, Bifidobacterium pseudocatenulatum, Alistipes finegoldii and Bacteroides intestinalis were negatively associated with indices of SBP/DBP variability in a sex-specific manner. Further analysis indicated that B. dorei may mediate SBP CoV via plasma iso-butyric acid in women (bootstrapping 95% CI: -3.6 to -0.19; P<0.05). We demonstrated that higher SBP variability is associated with markers of gut dysbiosis and a reduction in beneficial gut bacteria, particularly in women. Notably, we identified several gut bacterial species with potential therapeutic implications for managing 24-hour SBP/DBP variability, warranting further investigation.

microbiology↗

bioRxiv2025

Abrogating TGFβ signaling in TCR-engineered T cells and enhancing antigen processing by tumor cells promotes sustained therapeutic activity in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDA) is a deadly malignancy with limited effective therapies. Adoptive cell therapy (ACT) is a promising treatment modality for patients with solid tumors but has been limited by the highly fibroinflammatory and immunosuppressive tumor microenvironment (TME). Transforming growth factor-{beta} (TGF{beta}) participates in the inordinately suppressive TME in PDA. Here, we test the impact of selective Tgfbr2 deletion using CRISPR/Cas9 or genetic approaches in mesothelin (Msln)-specific T cell receptor (TCR) engineered T cells during ACT of PDA. Abrogating TGF{beta} signaling augmented TCR-engineered T cell accumulation in autochthonous and orthotopic PDA models and promoted terminal effector T cells, although this largely required inclusion of a vaccine at the time of T cell transfer. While loss of Tgfbr2 impaired CD103 upregulation, it only modestly impaired donor T cell central, tissue resident, or Tcf1+Slamf6+ stem-like memory T cell formation. These attributes ultimately result in heightened functional capacity and delayed tumor growth. Unexpectedly, however, most tumor-infiltrating engineered T cells failed to differentiate into PD-1+Lag3+ exhausted T cells (TEX) regardless of TGF{beta}R2 expression and despite abundant Msln protein expression by PDA cells. Forcing Msln epitope processing in KPC tumor cells promoted donor T cell accumulation, acquisition of PD-1 and Lag3, increased IFN{gamma} production by TCR-engineered T cells refractory to TGF{beta} and bypassed the vaccine requirement for therapeutic efficacy. Thus, promoting increased antigen processing/presentation by tumor cells while abrogating Tgfbr2 in engineered T cells can sustain donor T cell function in the suppressive TME and enhance the therapeutic efficacy of ACT. Our study supports pursuit of strategies that modulate tumor intrinsic antigen processing while relieving T cell suppression to safely promote the antitumor activity of TCR-engineered T cells.

immunology↗

bioRxiv2024

Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines

This article describes the Cell Maps for Artificial Intelligence (CM4AI) project and its goals, methods, standards, current datasets, software tools, status, and future directions. CM4AI is the Functional Genomics Data Generation Project in the U.S. National Institute of Healths (NIH) Bridge2AI program. Its overarching mission is to produce ethical, AI-ready datasets of cell architecture, inferred from multimodal data collected for human cell lines, to enable transformative biomedical AI research.

systems biology↗

bioRxiv2024

Metagenomic coverage bias at transcription start sites is correlated with gene expression

Metagenomic sequencing is presumed to provide unbiased sampling of all the genetic material in a sample. Downstream analysis methods, such as binning, gene copy number analysis, structural variations, or single nucleotide polymorphism analysis, commonly assume an even distribution across the genome after accounting for known artefacts such as GC content. We discovered coverage bias across gut microbiome species, manifesting as a difference in coverage before and after bacterial transcription start sites. Using matched metatranscriptomic and metagenomic sequencing data, we demonstrate that this bias correlates with gene expression. Potential artefacts such as the sequencing technology, reference genome used for alignment, and mappability bias were investigated across multiple datasets and shown to not be factors for association. While GC bias was found correlated with coverage bias, the association of coverage bias with gene expression remains significant after adjusting for GC bias. Paired-end read mapping demonstrated an enrichment in 5 read ends immediately downstream of the TSS which was partly a byproduct of unmapped reads upstream of the TSS. Our observations suggest the existence of strain-level variation where sequence variation in the promoter site region is preventing proper read alignment to the reference genome. The correlation of this phenomenon with gene expression may also reflect evolutionary footprints for fine-tuning the regulation of gene expression. Understanding the source of this sequence variation and the biological implications of this artefact will be useful not only to better characterise microbial functions but also to improve interpretations of strain level dynamics. ImportanceSequencing coverage calculated from metagenomic sequencing data is extensively used in the microbiome field, providing valuable information about microbial abundances, gene (functional) abundances, growth rates, and genomic variations. Understanding factors that impact the distribution of coverage along genomes is therefore important for multiple applications. In this study, we report on uneven read coverage across the transcription start sites of bacterial genomes that is correlated with gene expression levels. We determine that this bias is independent of multiple factors including GC bias, and arises due to higher strain divergence from reference genomes upstream of the transcript start site. We propose that evolutionary finetuning of gene expression in competitive microbial ecosystems can drive genetic mutations at the promoter site. Our findings suggest the potential to glean gene regulatory information from metagenomic data, and better understand how ecological factors shape genomes in the microbiome and their sequencing coverage.

bioinformatics↗

bioRxiv2023

Nephron progenitors rhythmically alternate between renewal and differentiation in synchrony with kidney branching morphogenesis

The developing mammalian kidney exponentially duplicates nephron-forming stem cell niches at the tips of the urinary collecting duct tree to achieve massively parallel function. Nephron formation rate has a clinically meaningful effect on person-to-person variability in nephron endowment1-5, while exerting in vitro control could enable sustained waves of nephrogenesis in organoid-derived synthetic kidney tissues6,7. However, how the kidney arrives at an appropriate number and ratio of nephrons to collecting ducts is unclear. Here we show that nephron formation is rhythmic and synchronized with branching of the ureteric bud tree (the future urinary collecting ducts). We correlate human and mouse spatial transcriptomics data with the branching life-cycle to uncover rhythmically alternating signatures of nephron progenitor differentiation and renewal. The nephron progenitor rhythm parallels rhythmic nuclear elongation and other hallmarks of mechanical tension in surrounding stromal cells that we attribute to branching-induced deformation. Stroma-specific knockdown of actomyosin activity leads to a striking loss of synchronization between nephron formation and ureteric bud branching without blocking either. These results suggest that the stroma acts as a mechanically entrained pacemaker for nephron formation. Together, our findings uncover a feedback mechanism for clock-like coordination of organ composition during exponential growth.

developmental biology↗

bioRxiv2023

Bayesian inference for copy number intra-tumoral heterogeneity from single-cell RNA-sequencing data

High-resolution molecular characterization of intra-tumoral clonal structure defined by genomic and epigenomic alterations is crucial in understanding the natural history of tumors and advancing cancer treatment strategies. Copy number alterations (CNA) are of notable importance as both drivers and markers of clonal structure that can now be assayed at individual cell resolution. However, specific computational methods are needed for accurate inference of clonal profiles and cell states from sparse and noisy single-cell omics data. Here, we develop a new Bayesian model to utilize single-cell RNA sequencing (scRNA-seq) data for automatic analysis of intra-tumoral clonal structure with respect to CNAs, without reliance on prior knowledge. The model clusters cells into sub-tumoral clones while simultaneously identifying CNA events in each clone, jointly modelling input from gene expression and germline single-nucleotide polymorphisms. Unlike previous methods, our approach automatically infers the number of clones present in the tumor. In detailed simulation studies our model frequently achieves very high (>90%) cell clustering accuracy and high (>80%) CN state inference accuracy, even in settings of high variance and sparsity. Overall, our method compares strongly against existing software tools. Application to human metastatic melanoma tumor data demonstrates accurate clustering of tumor and non-tumor cells, and reveals clonal CNA profiles that highlight functional gene expression differences between clones from the same tumor. Our method is implemented in a publicly-available, open-source R package, Chloris.

bioinformatics↗

bioRxiv2023

MetaQuad: Shared Informative Variants Discovery in Metagenomic Samples

MotivationStrain-level analysis of metagenomic data has garnered significant interest in recent years. Microbial single nucleotide polymorphisms (SNPs) are genomic variants that can reflect strain-level differences within a microbial species. The diversity and emergence of SNPs in microbial genomes may reveal evolutionary history and environmental adaptation in microbial populations. However, efficient discovery of shared polymorphic variants in a large collection metagenomic samples remains a computational challenge. ResultsMetaQuad employs a density-based clustering technique to efficiently differentiate shared variants from non-polymorphic sites using shotgun metagenomic data. Empirical comparisons with other state-of-the-art methods show that MetaQuad significantly reduces the number of false-positive SNPs without greatly affecting the true-positive rate. We used MetaQuad to identify antibiotic-associated variants in patients who underwent Helicobacter pylori eradication therapy. MetaQuad detected 7,591 variants across 529 antibiotic resistance genes. The nucleotide diversity of some genes is increased six weeks after antibiotic treatment, potentially indicating the role of these genes in specific antibiotic treatments. AvailabilityMetaQuad is an open-source Python package available via https://github.com/holab-hku/MetaQuad. Contactjwkho@hku.hk Supplementary informationSupplementary data are available at XXXX online.

genomics↗

bioRxiv2023

Robust identification of perturbed cell types in single-cell RNA-seq data

Single-cell transcriptomics has emerged as a powerful tool for understanding how different cells contribute to disease progression by identifying cell types that change across diseases or conditions. However, detecting changing cell types is challenging due to individual-to-individual and cohort-to-cohort variability and naive approaches based on current computational tools lead to false positive findings. To address this, we propose a computational tool, scDist, based on a mixed-effects model that provides a statistically rigorous and computationally efficient approach for detecting transcriptomic differences. By accurately recapitulating known immune cell relationships and mitigating false positives induced by individual and cohort variation, we demonstrate that scDist outperforms current methods in both simulated and real datasets, even with limited sample sizes. Through the analysis of COVID-19 and immunotherapy datasets, scDist uncovers transcriptomic perturbations in dendritic cells, plasmacytoid dendritic cells, and FCER1G+NK cells, that provide new insights into disease mechanisms and treatment responses. As single-cell datasets continue to expand, our faster and statistically rigorous method offers a robust and versatile tool for a wide range of research and clinical applications, enabling the investigation of cellular perturbations with implications for human health and disease.

bioinformatics↗

bioRxiv2023

Syntaxin of plants 32 regulates pollen wall development and pollen tube cell wall integrity via controlling secretory pathway

Pollen tubes (PTs) elongate in a polar way to deliver sperm cells to the ovule. Pollen wall development and PT cell wall integrity (CWI) maintenance are critical for PT growth and double fertilization. Pollen wall development mainly relies on secretion of exine precursors in tapetum. RALF4/19-ANX/BUPS-MRI and RALF4/19-LRX-AUN are two distinct signaling pathways but converge to fine-tune CWI during PT growth. Here, we discovered that atsyp32+/-, AtSYP32 RNAi and AtSYP3132 RNAi lines were male sterile. The tapetum development in these lines were disturbed, and the pollen wall structure was impaired resulting in pollen grain and tube bursting and less PTs navigated to micropyles. Strikingly, there were numerous ectopic secretory vesicles retained in pollen cytoplasm, and the abundance or distribution of polysaccharides and AGPs altered significantly in PTs of the mutants and RNAi lines. AtSYP32 interacted with the vesicle transport regulators SEC31B, SEC22 and BET12, the PT CWI regulators RALF19 and LRX11, and the XyG xylosyltransferase XXT5, in the Golgi apparatus. Transcription of some genes related to pollen wall biosynthesis and PT CWI maintenance were seriously affected by AtSYP32 downregulation. Our findings illustrate that AtSYP32 plays essential roles in pollen wall development and PT CWI maintenance via controlling secretory pathway. IN A NUTSHELLO_ST_ABSBackgroundC_ST_ABSPollen wall is the most complex cell wall. Pollen wall development mainly relies on secretion of precursors of exine and pollen coat in tapetal cells. Pollen tubes (PTs) grow in a polar way to deliver sperm cells to the ovule. Maintenance of PT cell wall integrity (CWI) is critical for PT elongation and double fertilization. RALF4/19 ligands interact with BUPS-ANX receptors, signaling it in an autocrine manner to maintain CWI during PT elongation. RALF4/19-LRX-AUN pathway is distinct with RALF4/19-ANX/BUPS-MRI pathway but they converge to fine-tune CWI during PT growth. Biosynthesis of PT cell wall involves multiple subcellular compartments and vesicle transport pathways. Golgi apparatus acts as a hub in vesicle trafficking. Golgi-syntaxin AtSYP31 and AtSYP32 regulate pollen development by controlling intra-Golgi transport and Golgi morphology QuestionWhat is AtSYP32 role in pollen wall and tapetum development? Who are the AtSYP32 partners that regulate secretion of cell wall biosynthesis materials? FindingsWe found that no homozygote progeny was obtained from self-pollinated atsyp32+/- alleles due to pollen sterile. The tapetum development and degeneration in atsyp32+/- mutants was severely delayed, and the pollen wall and PT wall structure were impaired. Strikingly, there were numerous ectopic secretory vesicles retained in pollen cytoplasm in atsyp32+/- mutants, and the abundance or distribution of PT wall polysaccharides and AGPs altered obviously. AtSYP32 interacted with the vesicle transport regulators SEC31B, SEC22 and BET12, the PT CWI regulators RALF19 and LRX11, and XyG xylosyltransferase XXT5, in the Golgi. All these highlight that AtSYP32 regulates pollen wall development and maintenance of PT CWI via controlling secretory pathway. Next stepsThe biological significances and the molecular mechanisms of AtSYP32 interacting with XXT5, RALF19 and LRX11 are elusive but thought-provoking. We are going to clarify the mechanisms.

molecular biology↗

bioRxiv2022

High-throughput feedback-enabled optogenetic stimulation and spectroscopy in microwell plates

The ability to perform sophisticated, high-throughput optogenetic experiments has been greatly enhanced by recent open-source illumination devices that allow independent programming of light patterns in single wells of microwell plates. However, there is currently a lack of instrumentation to monitor such experiments in real time, necessitating repeated transfers of the samples to stand-alone analytical instruments, thus limiting the types of experiments that could be performed. Here we address this gap with the development of the optoPlateReader (oPR), an open-source, solid-state, compact device that allows automated optogenetic stimulation and spectroscopy in each well of a 96-well plate. The oPR integrates an optoPlate illumination module with a module called the optoReader, an array of 96 photodiodes and LEDs that allows 96 parallel light measurements. The oPR was optimized for stimulation with blue light and for measurements of optical density and fluorescence. After calibration of all device components, we used the oPR to measure growth and to induce and measure fluorescent protein expression in E. coli. We further demonstrated how the optical read/write capabilities of the oPR permit computer-in-the-loop feedback control, where the current state of the sample can be used to adjust the optical stimulation parameters of the sample according to pre-defined feedback algorithms. The oPR will thus help realize an untapped potential for optogenetic experiments by enabling automated reading, writing, and feedback in microwell plates through open-source hardware that is accessible, customizable, and inexpensive.

synthetic biology↗

bioRxiv2022

A transcriptional complex of FtMYB102 and FtbHLH4 coordinately regulates the accumulation of rutin in Fagopyrum tataricum

Tartary buckwheat is rich in flavonoids, which not only play an important role in plant-environment interaction, but are also beneficial to human health. Rutin is a therapeutic flavonol which is massively accumulated in Tartary buckwheat. It has been demonstrated that transcription factors control rutin biosynthesis. However, the transcriptional regulatory network of rutin is not fully clear. In this study, through transcriptome and target metabolomics, we validated the role of FtMYB102 and FtbHLH4 TFs at the different developmental stages of Tartary buckwheat. The elevated accumulation of rutin in the sprout appears to be closely associated with the expression of FtMYB102 and FtHLH4. Yeast two-hybrid, transient luciferase activity and co-immunoprecipitation demonstrated that FtMYB102 and FtbHLH4 can interact and form a transcriptional complex. Moreover, yeast one-hybrid showed that both FtMYB102 and FtbHLH4 directly bind to the promoter of chalcone isomerase (CHI), and they can coordinately induce CHI expression as shown by transient luciferase activity assay. Finally, we transferred the FtMYB102 and FtbHLH4 into the hairy roots of Tartary buckwheat and found that they both can promote the accumulation of rutin. Our results indicate that FtMYB102 and FtbHLH4 can form a transcriptional complex by inducing CHI expression to coordinately promote the accumulation of rutin.

plant biology↗

bioRxiv2021

Data-driven discovery of targets for bipotent anticancer drugs identifies Estrogen Related Receptor Alpha

Drugs that kill tumors through multiple mechanisms have potential for broad clinical benefits, with a reduced propensity to resistance. We developed BipotentR, a computational approach to find cancer-cell-specific regulators that simultaneously modulate tumor immunity and another oncogenic pathway. Using tumor metabolism as proof-of-principle, BipotentR identified 38 candidate immune-metabolic regulators by combining epigenomes with bulk and single-cell tumor transcriptomes from patients. Inhibition of top candidate ESRRA (Estrogen Related Receptor Alpha) killed tumors by direct effects on energy metabolism and two immune mechanisms: (i) cytokine induction, causing proinflammatory macrophage polarization (ii) antigen-presentation stimulation, recruiting CD8+T cells into tumors. ESRRA is activated in immune-suppressive and immunotherapy-resistant tumors of many types, suggesting broad clinical relevance. We also applied BipotentR to angiogenesis and growth-suppressor pathways, demonstrating a widely applicable approach to identify drug targets that act simultaneously through multiple mechanisms. BipotentR is publicly available at http://bipotentr.dfci.harvard.edu/. One-Sentence SummaryBipotentR identifies targets for bipotent anticancer drugs, as shown by the energy and immune effects of ESRRA inhibition.

cancer biology↗

bioRxiv2019

Müllerian-inhibiting substance (MIS) is both necessary and sufficient for testicular differentiation in Chinese soft-shelled turtle Pelodiscus sinensis

Mullerian-inhibiting substance (Mis, or anti-mullerian hormone, Amh), a member of TGF-{beta} superfamily, as initiator or key regulator in sexual development has been well documented in some vertebrates, especially in fish. However, its functional role has not been identified yet in reptiles. Here we characterized the Mis gene in Chinese soft-shelled turtle Pelodiscus sinensis (P. sinensis), a typical reptilian species exhibiting ZZ/ZW sex chromosomes. The mRNA of Mis was initially expressed in male embryonic gonads by stage 15, preceding gonadal sex differentiation, and exhibited male-specific expression pattern throughout embryogenesis. Moreover, Mis was rapidly up-regulated during female-to-male sex reversal induced by aromatase inhibitor letrozole. Most importantly, Mis loss of function by RNA interference led to complete feminization of genetic male (ZZ) gonads, suppression of the testicular marker Sox9, and upregulation of the ovarian regulator Cyp19a1. Conversely, overexpression of Mis in ZW embryos resulted in female-to-male sex reversal, characterized by the formation of testis structure, ectopic activation of Sox9, and a remarkable decline in Cyp19a1. Collectively, these findings provide the first solid evidence that Mis is both necessary and sufficient to drive testicular development in a reptilian species, P. sinensis, highlighting the significance of the TGF-{beta} pathway in reptilian sex determination.

developmental biology↗