CanCellVar: A database for single-cell variants map in human cancer.

Numerous variants, including both single-nucleotide variants (SNVs) in DNA and A>G RNA edits in mRNA as essential drivers of cellular proliferation and tumorigenesis, are commonly associated with cancer progression and growth. Thus, mining and summarizing single-cell variants will provide a refined and higher-resolution view of cancer and further contribute to precision medicine. Here, we established a database, CanCellVar, which aims to provide and visualize the comprehensive atlas of single-cell variants in tumor microenvironment. The current CanCellVar identified ∼3 million variants (∼1.4 million SNVs and ∼1.4 million A>G RNA edits) involved in 2,754,531 cells of 5 major cell types across 37 cancer types. CanCellVar provides the basic annotation information as well as cellular and molecular function properties of variants. In addition, the clinical relevance of variants can be obtained including tumor grade, treatment, metastasis, and others. Several flexible tools were also developed to aid retrieval and to analyze cell-cell interactions, gene expression, cell-development trajectories, regulation, and molecular structure affected by variants. Collectively, CanCellVar will serve as a valuable resource for investigating the functions and characteristics of single-cell variations and their roles in human tumor evolution and treatment.

Hidden hotspots of amphibian biodiversity in China.

Identifying and protecting hotspots of endemism and species richness is crucial for mitigating the global biodiversity crisis. However, our understanding of spatial diversity patterns is far from complete, which severely limits our ability to conserve biodiversity hotspots. Here, we report a comprehensive analysis of amphibian species diversity in China, one of the most species-rich countries on Earth. Our study combines 20 y of field surveys with new molecular analyses of 521 described species and also identifies 100 potential cryptic species. We identify 10 hotspots of amphibian diversity in China, each with exceptional species richness and endemism and with exceptional phylogenetic diversity and phylogenetic endemism (based on a new time-calibrated, species-level phylogeny for Chinese amphibians). These 10 hotspots encompass 59.6% of China's described amphibian species, 49.0% of cryptic species, and 55.6% of species endemic to China. Only four of these 10 hotspots correspond to previously recognized biodiversity hotspots. The six new hotspots include the Nanling Mountains and other mountain ranges in South China. Among the 186 species in the six new hotspots, only 9.7% are well covered by protected areas and most (88.2%) are exposed to high human impacts. Five of the six new hotspots are under very high human pressure and are in urgent need of protection. We also find that patterns of richness in cryptic species are significantly related to those in described species but are not identical.

SORC: an integrated spatial omics resource in cancer.

The interactions between tumor cells and the microenvironment play pivotal roles in the initiation, progression and metastasis of cancer. The advent of spatial transcriptomics data offers an opportunity to unravel the intricate dynamics of cellular states and cell-cell interactions in cancer. Herein, we have developed an integrated spatial omics resource in cancer (SORC, http://bio-bigdata.hrbmu.edu.cn/SORC), which interactively visualizes and analyzes the spatial transcriptomics data in cancer. We manually curated currently available spatial transcriptomics datasets for 17 types of cancer, comprising 722 899 spots across 269 slices. Furthermore, we matched reference single-cell RNA sequencing data in the majority of spatial transcriptomics datasets, involving 334 379 cells and 46 distinct cell types. SORC offers five major analytical modules that address the primary requirements of spatial transcriptomics analysis, including slice annotation, identification of spatially variable genes, co-occurrence of immune cells and tumor cells, functional analysis and cell-cell communications. All these spatial transcriptomics data and in-depth analyses have been integrated into easy-to-browse and explore pages, visualized through intuitive tables and various image formats. In summary, SORC serves as a valuable resource for providing an unprecedented spatially resolved cellular map of cancer and identifying specific genes and functional pathways to enhance our understanding of the tumor microenvironment.

FOXO3-Activated HOTTIP Sequesters miR-615-3p away from COL2A1 to Mitigate Intervertebral Disc Degeneration.

In this study, knockout of FOXO3 was found to impair intervertebral disc maturation and homeostasis in postnatal mice as well as facilitating extracellular matrix degradation. RNA sequencing can uncover disease-related gene expression and investigate disease pathophysiology. High-throughput transcriptome sequencing and experimental validations were used to identify the essential gene and mechanism involved in intervertebral disc degeneration (IDD). Nucleus pulposus (NP) tissue samples were collected from the mice with conditional knockout of FOXO3 (FOXO3 KO) for high-throughput sequencing, followed by screening of differentially expressed lncRNAs and mRNAs. The mRNAs were subjected to GO and KEGG enrichment analyses. Interactions among FOXO3, HOTTIP, miR-615-3p, and COL2A1 were analyzed. NP cells were subjected to a series of mimics, inhibitors, overexpression plasmids, and shRNAs to validate the mechanisms of FOXO3 in controlling HOTTIP/miR-615-3p/COL2A1 in IDD. Mechanistically, FOXO3 transcriptionally activated HOTTIP, facilitated the competitive HOTTIP binding to miR-615-3p, and increased the expression of the miR-615-3p target gene COL2A1. Thus, NP cell proliferation was induced, cell apoptosis was diminished, resulting in delayed development of IDD. Based on these data, the transcription factor FOXO3 may decrease miR-615-3p binding to COL2A1 and up-regulate COL2A1 expression by activating HOTTIP transcription, which in turn inhibits NP cell apoptosis and promotes its proliferation, to prevent the degradation of intervertebral disc matrix and maintain the normal physiological function of intervertebral disc, thereby preventing the occurrence and development of IDD.

ImmCluster: an ensemble resource for immunology cell type clustering and annotations in normal and cancerous tissues.

Single-cell transcriptome has enabled the transcriptional profiling of thousands of immune cells in complex tissues and cancers. However, subtle transcriptomic differences in immune cell subpopulations and the high dimensionality of transcriptomic data make the clustering and annotation of immune cells challenging. Herein, we introduce ImmCluster (http://bio-bigdata.hrbmu.edu.cn/ImmCluster) for immunology cell type clustering and annotation. We manually curated 346 well-known marker genes from 1163 studies. ImmCluster integrates over 420 000 immune cells from nine healthy tissues and over 648 000 cells from different tumour samples of 17 cancer types to generate stable marker-gene sets and develop context-specific immunology references. In addition, ImmCluster provides cell clustering using seven reference-based and four marker gene-based computational methods, and the ensemble method was developed to provide consistent cell clustering than individual methods. Five major analytic modules were provided for interactively exploring the annotations of immune cells, including clustering and annotating immune cell clusters, gene expression of markers, functional assignment in cancer hallmarks, cell states and immune pathways, cell-cell communications and the corresponding ligand-receptor interactions, as well as online tools. ImmCluster generates diverse plots and tables, enabling users to identify significant associations in immune cell clusters simultaneously. ImmCluster is a valuable resource for analysing cellular heterogeneity in cancer microenvironments.

Motion state-dependent motor learning based on explicit visual feedback has limited spatiotemporal properties compared with adaptation to physical perturbations.

We recently showed that subjects can learn motion state-dependent changes to motor output (temporal force patterns) based on explicit visual feedback of the equivalent force field (i.e., without the physical perturbation). Here, we examined the spatiotemporal properties of this learning compared with learning based on physical perturbations. There were two human subject groups and two experimental paradigms. One group (n = 40) experienced physical perturbations (i.e., a velocity-dependent force field, vFF), whereas the second (n = 40) was given explicit visual feedback (EVF) of the force-velocity relationship. In the latter, subjects moved in force channels and we provided visual feedback of the lateral force exerted during the movement, as well as the required force pattern based on movement velocity. In the first paradigm (spatial generalization), following vFF or EVF training, generalization of learning was tested by requiring subjects to move to 14 untrained target locations (0° to ±135° around the trained location). In the second paradigm (temporal stability), following training, we examined the decay of learning over eight delay periods (0 to 90 s). Results showed that learning based on EVF did not generalize to untrained directions, whereas the generalization for the vFF was significant for targets ≤ 45° away. In addition, the decay of learning for the EVF group was significantly faster than the FF group (a time constant of 2.72 ± 1.74 s vs. 12.53 ± 11.83 s). Collectively, our results suggest that recalibrating motor output based on explicit motion state information, in contrast to physical disturbances, uses learning mechanisms with limited spatiotemporal properties.NEW & NOTEWORTHY Adjustment of motor output based on limb motion state information can be achieved based on explicit information or from physical perturbations. Here, we investigated the spatiotemporal characteristics of short-term motor learning to determine the properties of the respective learning mechanisms. Our results suggest that adjustments based on physical perturbations are more temporally stable and applied over a greater spatial range than the learning based on explicit visual feedback, suggesting largely separate learning mechanisms.

Multiple Origins and Genomic Basis of Complex Traits in Sighthounds.

Sighthounds, a distinctive group of hounds comprising numerous breeds, have their origins rooted in ancient artificial selection of dogs. In this study, we performed genome sequencing for 123 sighthounds, including one breed from Africa, six breeds from Europe, two breeds from Russia, and four breeds and 12 village dogs from the Middle East. We gathered public genome data of five sighthounds and 98 other dogs as well as 31 gray wolves to pinpoint the origin and genes influencing the morphology of the sighthound genome. Population genomic analysis suggested that sighthounds originated from native dogs independently and were comprehensively admixed among breeds, supporting the multiple origins hypothesis of sighthounds. An additional 67 published ancient wolf genomes were added for gene flow detection. Results showed dramatic admixture of ancient wolves in African sighthounds, even more than with modern wolves. Whole-genome scan analysis identified 17 positively selected genes (PSGs) in the African population, 27 PSGs in the European population, and 54 PSGs in the Middle Eastern population. None of the PSGs overlapped in the three populations. Pooled PSGs of the three populations were significantly enriched in "regulation of release of sequestered calcium ion into cytosol" (gene ontology: 0051279), which is related to blood circulation and heart contraction. In addition, ESR1, JAK2, ADRB1, PRKCE, and CAMK2D were under positive selection in all three selected groups. This suggests that different PSGs in the same pathway contributed to the similar phenotype of sighthounds. We identified an ESR1 mutation (chr1: g.42,177,149 T > C) in the transcription factor (TF) binding site of Stat5a and a JAK2 mutation (chr1: g.93,277,007 T > A) in the TF binding site of Sox5. Functional experiments confirmed that the ESR1 and JAK2 mutation reduced their expression. Our results provide new insights into the domestication history and genomic basis of sighthounds.

Shedding light on the hidden human proteome expands immunopeptidome in cancer.

Unrestrained cellular growth and immune escape of a tumor are associated with the incidental errors of the genome and transcriptome. Advances in next-generation sequencing have identified thousands of genomic and transcriptomic aberrations that generate variant peptides that assemble the hidden proteome, further expanding the immunopeptidome. Emerging next-generation sequencing technologies and a number of computational methods estimated the abundance of immune infiltration from bulk transcriptome have advanced our understanding of tumor microenvironments. Here, we will characterize several major types of tumor-specific antigens arising from single-nucleotide variants, insertions and deletions, gene fusion, alternative splicing, RNA editing and non-coding RNAs. Finally, we summarize the current state-of-the-art computational and experimental approaches or resources and provide an integrative pipeline for the identification of candidate tumor antigens. Together, the systematic investigation of the hidden proteome in cancer will help facilitate the development of effective and durable immunotherapy targets for cancer.

PRES: a webserver for decoding the functional perturbations of RNA editing sites.

Rapid progresses in RNA-Seq and computational methods have assisted in quantifying A-to-I RNA editing and altered RNA editing sites have been widely observed in various diseases. Nevertheless, functional characterization of the altered RNA editing sites still remains a challenge. Here, we developed perturbations of RNA editing sites (PRES; http://bio-bigdata.hrbmu.edu.cn/PRES/) as the webserver for decoding functional perturbations of RNA editing sites based on editome profiling. After uploading an editome profile among samples of different groups, PRES will first annotate the editing sites to various genomic elements and detect differential editing sites under the user-selected method and thresholds. Next, the downstream functional perturbations of differential editing sites will be characterized from gain or loss miRNA/RNA binding protein regulation, RNA and protein structure changes, and the perturbed biological pathways. A prioritization module was developed to rank genes based on their functional consequences of RNA editing events. PRES provides user-friendly functionalities, ultra-efficient calculation, intuitive table and figure visualization interface to display the annotated RNA editing events, filtering options and elaborate application notebooks. We anticipate PRES will provide an opportunity for better understanding the regulatory mechanisms of RNA editing in human complex diseases.

Use of 3D echocardiography facilitates analysis of thrombolytic efficacy in patients with persistent atrial fibrillation.

ABSTRACT: This study seeks to identify the anticoagulant efficacy of rivaroxaban treatment on thrombi detected using echocardiography of the left atrial appendage in 275 patients with persistent atrial fibrillation (AF). During follow-up after 9 to 24 weeks of Rivaroxaban treatment, patients were divided into 'effective group' (n = 143) and 'ineffective group' (n = 132) according to the thrombolytic effect of the drug. Left atrial diameter (LAD), left atrial ejection fraction (LAEF), left ventricular ejection fraction (LVEF), mean diameter of left atrial appendage (LAADmean), angle between left atrial appendage and left atrial (LAA-A), velocity of blood flow in left atrial appendage (LAA-v) and thrombus size were compared before and after drug administration. Following treatment, LAEF, LVEF and LAA-v values were greater and LAD and LAADmean values were lower in the effective (P<0.05). Logistic regression analysis showed significant correlations of LAD, LAEF, LVEF, LAA-A and LAA-v with anticoagulant efficacy (P<0.05). The efficacy of Rivaroxaban in treatment of left atrial auricular thrombosis in patients with persistent AF was correlated with LAD, LAEF, LVEF, LAA-A and LAA-v. Multivariate logistic regression analysis further revealed LAEF (OR 1.7, 95% CI 0.45-16.9, P=0.008), 3D-EF (OR 6.4, 95% CI 1.06-16.9, P=0.039), and left ventricular global longitudinal strain (GLS) (OR 18.0, 95% CI 1.38-35.68, P=0.028) as factors related to left atrial appendage thrombus. Echocardiography with global longitudinal strain assessment could be effectively utilized to evaluate the functional parameters of LAA and thus aid in predicting the safety of Rivaroxaban as an anticoagulation agent.

PLAGL2 induces nucleus pulposus cell apoptosis via regulating RASSF5 expression and thus accelerates intervertebral disc degeneration.

Excessive apoptosis of nucleus pulposus (NP) cells is the main pathological change in intervertebral disc degeneration (IVDD) progression. Pleomorphic adenoma gene like-2 (PLAGL2) plays a key role in cell apoptosis, however, the effect of PLAGL2 on IVDD has not been clarified yet. In this study, we established mouse IVDD models via the annulus fibrosis needle puncture, TUNEL and safranin O staining were used to verify the successful establishment of IVDD models, and PLAGL2 expression was detected in disc tissues. Then, NP cells isolated from disc tissues were used to construct PLAGL2 knockdown cells. PLAGL2 expression in NP cells was analyzed with qRT-PCR and Western blot. The impact of PLAGL2 on the viability, apoptosis, and mitochondria function of NP cells was evaluated by MTT assay, TUNEL, JC1 staining, and flow cytometry assay. Additionally, the regulatory mechanism of PLAGL2 was further assessed. We found that PLAGL2 was upregulated in IVDD disc tissues and serum deprivation (SD)-stimulated NP cells. PLAGL2 knockdown inhibited apoptosis and mitochondria damage in NP cells. Moreover, knockdown of PLAGL2 downregulated the expression of downstream apoptosis-related factors RASSF5, Nip3, and p73. Mechanically, PLAGL2 transcriptionally activated RASSF5 via binding to its promoter. In general, our findings indicate that PLAGL2 induces apoptosis in NP cells and aggravates IVDD progression. This study provides a promising therapeutic target for IVDD treatment.

The association between non-alcoholic fatty liver disease and urinary incontinence among adult females in the United States.

BACKGROUND AND OBJECTIVES: Non-alcoholic fatty liver disease (NAFLD) and urinary incontinence (UI) are both highly prevalent and age-related diseases. Nevertheless, the link between NAFLD and UI is unclear. Hence, the study was designed to evaluate the association between the NAFLD and UI (including UI types) in a nationally representative sample of United States (US) female adults. METHODS: We conducted this study used data from U.S. female adults in the National Health and Nutrition Examination Survey (NHANES) 2017-March 2020 (pre-pandemic) cycles. The diagnosis of NAFLD is based on Vibration controlled transient elastography (VCTE) and absence of know liver diseases and significant alcohol consumption. The diagnosis and types of UI were assessment using a self-report questionnaire. Multivariable logistic regression models were used to analyze the association between NALFD and UI. Stratified analyses based on age, obesity, race, educational level, married status, PIR, and smoking status were conducted. RESULTS: Of the 2149 participants, the mean (95% CI) age was 53.9 (52.7-55.0), 686 (61.1%) were Non-Hispanic White. UI was significantly more common in participants with NAFLD [490 (64.7%)] than those without NAFLD [552 (44.9%)]. Adjusted for age, race/ethnicity, marital status, educational level, family poverty income ratio (PIR) status, alanine aminotransferase (ALT), aspartate aminotransferase (AST), smoking status, obesity, type 2 diabetes mellitus (T2DM), hypertension and insulin resistance (IR) in a multivariable logistic regression model, NALFD were associated with UI [OR: 1.93, 95%CI 1.23-3.02, P = 0.01] and urge UI [OR: 1.55, 95%CI 1.03-2.33, P = 0.03], while patients with NAFLD did not show an increased odds in stress UI and mixed UI when compared with those without NAFLD subject (P > 0.05). In the subgroup analyses, NAFLD remained significantly associated with UI, particularly among those participants without obesity (OR: 2.69, 95% CI 1.84-4.00) and aged ≥ 60 years (OR: 2.20, 95% CI 1.38-3.51). CONCLUSIONS: Among US female adults, NAFLD has a strong positive correlation with UI. Given that NAFLD is a modifiable disease, these results may help clinicians to target female patients with NAFLD for treatments and interventions that may help prevent the occurrence of UI and reduce the symptoms of UI.

Study on SR-Crossbar RF MEMS Switch Matrix Port Configuration Scheme with Optimized Consistency.

The performance consistency of an RF MEMS switch matrix is a crucial metric that directly impacts its operational lifespan. An improved crossbar-based RF MEMS switch matrix topology, SR-Crossbar, was investigated in this article. An optimized port configuration scheme was proposed for the RF MEMS switch matrix. Both the utilization probability of individual switch nodes and the path lengths in the switch matrix achieve their best consistency simultaneously under the proposed port configuration scheme. One significant advantage of this scheme lies in that it only adjusts the positions of the input and output ports, with the topology and individual switch nodes kept unchanged. This grants it a high level of generality and feasibility and also introduces an additional degree of freedom for optimizations. In this article, a universal utilization probability function of single nodes was constructed and an optimization objective function for the SR-Crossbar RF MEMS switch matrix was formulated, which provide a convenient approach to directly solving the optimized port configuration scheme for practical applications. Simulations to demonstrate the optimized dynamic and static consistencies were conducted. For an 8 × 8 SR-Crossbar switch matrix, the standard deviations of contact resistances of 128 units and losses of all 64 paths decreased from 1.00 and 0.42 to 0.51 and 0.23, respectively. These results aligned closely with theoretical calculations derived from the proposed model.

Species Persistence with Hybridization in Toad-Headed Lizards Driven by Divergent Selection and Low Recombination.

Speciation plays a central role in evolutionary studies, and particularly how reproductive isolation (RI) evolves. The origins and persistence of RI are distinct processes that require separate evaluations. Treating them separately clarifies the drivers of speciation and then it is possible to link the processes to understand large-scale patterns of diversity. Recent genomic studies have focused predominantly on how species or RI originate. However, we know little about how species persist in face of gene flow. Here, we evaluate a contact zone of two closely related toad-headed lizards (Phrynocephalus) using a chromosome-level genome assembly and population genomics. To some extent, recent asymmetric introgression from Phrynocephalus putjatai to P. vlangalii reduces their genomic differences. However, their highly divergent regions (HDRs) have heterogeneous distributions across the genomes. Functional gene annotation indicates that many genes within HDRs are involved in reproduction and RI. Compared with allopatric populations, contact areas exhibit recent divergent selection on the HDRs and a lower population recombination rate. Taken together, this implies that divergent selection and low genetic recombination help maintain RI. This study provides insights into the genomic mechanisms that drive RI and two species persistence in the face of gene flow during the late stage of speciation.

The role of consciously timed movements in shaping and improving auditory timing.

Our subjective sense of time is intertwined with a plethora of perceptual, cognitive and motor functions, and likewise, the brain is equipped to expertly filter, weight and combine these signals for seamless interactions with a dynamic world. Until relatively recently, the literature on time perception has excluded the influence of simultaneous motor activity, yet it has been found that motor circuits in the brain are at the core of most timing functions. Several studies have now identified that concurrent movements exert robust effects on perceptual timing estimates, but critically have not assessed how humans consciously judge the duration of their own movements. This creates a gap in our understanding of the mechanisms driving movement-related effects on sensory timing. We sought to address this gap by administering a sensorimotor timing task in which we explicitly compared the timing of isolated auditory tones and arm movements, or both simultaneously. We contextualized our findings within a Bayesian cue combination framework, in which separate sources of temporal information are weighted by their reliability and integrated into a unitary time estimate that is more precise than either unisensory estimate. Our results revealed differences in accuracy between auditory, movement and combined trials, and (crucially) that combined trials were the most accurately timed. Under the Bayesian framework, we found that participants' combined estimates were more precise than isolated estimates, yet were sub-optimal when compared with the model's prediction, on average. These findings elucidate previously unknown qualities of conscious motor timing and propose computational mechanisms that can describe how movements combine with perceptual signals to create unified, multimodal experiences of time.

SurvivalMeth: a web server to investigate the effect of DNA methylation-related functional elements on prognosis.

Aberrant DNA methylation is a fundamental characterization of epigenetics for carcinogenesis. Abnormality of DNA methylation-related functional elements (DMFEs) may lead to dysfunction of regulatory genes in the progression of cancers, contributing to prognosis of many cancers. There is an urgent need to construct a tool to comprehensively assess the impact of DMFEs on prognosis. Therefore, we developed SurvivalMeth (http://bio-bigdata.hrbmu.edu.cn/survivalmeth) to explore the prognosis-related DMFEs, which documented many kinds of DMFEs, including 309,465 CpG island-related elements, 104,748 transcript-related elements, 77,634 repeat elements, as well as cell-type specific 1,689,653 super enhancers (SE) and 1,304,902 CTCF binding regions for analysis. SurvivalMeth is a convenient tool which collected DNA methylation profiles of 36 cancers and allowed users to query their genes of interest in different datasets for prognosis. Furthermore, SurvivalMeth not only integrated different combinations, including single DMFE, multiple DMFEs, SEs and clinical data, to perform survival analysis on preupload data but also allowed for uploading customized DNA methylation profile of DMFEs from various diseases to analyze. SurvivalMeth provided a comprehensive resource and automated analysis for prognostic DMFEs, including DMFE methylation level, correlation analysis, clinical analysis, differential analysis, DMFE annotation, survival-related detailed result and visualization of survival analysis. In summary, we believe that SurvivalMeth will facilitate prognostic research of DMFEs in diverse cancers.

Diversification and introgression in four chromosomal taxa of the Pearson's horseshoe bat (Rhinolophus pearsoni) group.

Chromosomal variation among closely related taxa is common in both plants and animals, and can reduce rates of introgression as well as promote reproductive isolation and speciation. In mammals, studies relating introgression to chromosomal variation have tended to focus on a few model systems and typically characterized levels of introgression using small numbers of loci. Here we took a genome-wide approach to examine how introgression rates vary among four closely related horseshoe bats (Rhinolophus pearsoni group) that possess different diploid chromosome numbers (2n = 42, 44, 46, and 60) resulting from Robertsonian (Rb) changes (fissions/fusions). Using a sequence capture we obtained orthologous loci for thousands of nuclear loci, as well as mitogenomes, and performed phylogenetic and population genetic analyses. We found that the taxon with 2n = 60 was the first to diverge in this group, and that the relationships among the three other taxa (2n = 42, 44 and 46) showed discordance across our different analyses. Our results revealed signatures of multiple ancient introgression events between the four taxa, with evidence of mitonuclar discordance in phylogenetic trees and reticulation events in their evolutionary history. Despite this, we found no evidence of recent and/or ongoing introgression between taxa. Overall, our results indicate that the effects of Rb changes on the reduction of introgression are complicated and that these may contribute to reproductive isolation and speciation in concert with other factors (e.g. phenotypic and genic divergence).

Impacts of climate change on herpetofauna diversity in the Qinghai-Tibetan Plateau.

Although numerous studies on the impacts of climate change on biodiversity have been published, only a handful are focused on the intraspecific level or consider population-level models (separate models per population). We endeavored to fill this knowledge gap relative to the Qinghai-Tibetan plateau (QTP) by combining species distribution modeling (SDMs) with population genetics (i.e., population-level models) and phylogenetic methods (i.e., phylogenetic tree reconstruction and phylogenetic diversity analyses). We applied our models to 11 endemic and widely distributed herpetofauna species inhabiting high elevations in the QTP. We aimed to determine the influence of environmental heterogeneity on species' responses to climate change, the magnitude of climate-change impacts on intraspecific diversity, and the relationship between species range loss and intraspecific diversity losses under 2 shared socioeconomic pathways (SSP245 and SSP585) and 3 future periods (2050s, 2070s, and 2090s). The effects of global climatic change were more pronounced at the intraspecific level (22% of haplotypes lost and 36% of populations lost) than the morphospecies level in the SSP585 climate change scenario. Maintenance of genetic diversity was in general determined by a combination of factors including range changes, species genetic structure, and the part of the range predicted to be lost. This is owing to the fact that the loss and survival of populations were observed in species irrespective of the predicted range changes (contraction or expansion). In the southeast (mountainous regions), climate change had less of an effect on range size (>100% in 3 species) than in central and northern QTP plateau regions (range size <100% in all species). This may be attributed to environmental heterogeneity, which provided pockets of suitable climate in the southeast, whereas ecosystems in the north and central regions were homogeneous. Generally, our results imply that mountainous regions with high environmental heterogeneity and high genetic diversity may buffer the adverse impacts of climate change on species distribution and intraspecific diversity. Therefore, genetic structure and characteristics of the ecosystem may be crucial for conservation under climate change.

Impactos del cambio climático sobre la diversidad de herpetofauna en la meseta Qinghai-Tíbet Región Aunque se han publicado numerosos estudios sobre los impactos del cambio climática en la biodiversidad, son muy pocos los que se enfocan en el nivel intraespecífico o que consideran modelos a nivel poblacional (modelos separados por población). Intentamos cerrar este vacío de conocimiento en relación con la meseta Qinghai-Tíbet (MQT) con la combinación entre modelos de distribución de especies (MDE) y genética poblacional (modelos a nivel poblacional) y métodos filogenéticos (reconstrucción de árboles filogenéticos y análisis de diversidad filogenética). Aplicamos nuestros modelos a once especies endémicas de herpetofauna con distribución amplia en las elevaciones más altas de la MQT. Nos planteamos determinar la influencia de la heterogeneidad de las especies sobre la respuesta de las especies al cambio climático, la magnitud de los impactos del cambio climático sobre la diversidad intraespecífica y la relación entre la pérdida de distribución de la especie y las pérdidas de diversidad intraespecífica bajo dos vías socioeconómicas (SSP245 y SSP585) y tres periodos del futuro (2050s, 2070s y 2090s). Los efectos del cambio climático global fueron más pronunciados a nivel intraespecífico (22% de pérdida en los haplotipos y 36% en las poblaciones) que al nivel morfoespecie en el escenario de cambio climático SSP585. El mantenimiento de la diversidad genética casi siempre estuvo determinado por una combinación de factores que incluyen cambios en la distribución, estructura genética de las especies y la parte de la distribución que se pronosticó se perdería. Esto se debe a que observamos la pérdida y supervivencia de las poblaciones sin importar los cambios pronosticados en la distribución (contracción o expansión). En las regiones montañosas del sureste, el cambio climático tuvo un efecto menor sobre la distribución (>100% en tres especies) comparado con las regiones de la meseta central y del norte de la MQT (distribución <100% en todas las especies). Esto puede atribuirse a la heterogeneidad ambiental, la cual proporciona recovecos de clima adecuado en el sureste, mientras que los ecosistemas en las regiones central y norte fueron homogéneos. De manera general, nuestros resultados implican que las regiones montañosas con una elevada heterogeneidad ambiental y una gran diversidad genética podrían reducir los impactos adversos del cambio climático sobre la distribución de las especies y la diversidad intraespecífica. Por lo tanto, la estructura genética y las características del ecosistema pueden ser cruciales para conservar bajo el cambio climático.

ImmReg: the regulon atlas of immune-related pathways across cancer types.

Immune system gene regulation perturbation has been found to be a major cause of the development of various types of cancer. Numbers of mechanisms contribute to gene expression regulation, thus, systematically identification of potential regulons of immune-related pathways is critical to cancer immunotherapy. Here, we comprehensively chart the landscape of transcription factors, microRNAs, RNA binding proteins and long noncoding RNAs regulation in 17 immune-related pathways across 33 cancers. The potential immunology regulons are likely to exhibit higher expressions in immune cells, show expression perturbations in cancer, and are significantly correlated with immune cell infiltrations. We also identify a panel of clinically relevant immunology regulons across cancers. Moreover, the regulon atlas of immune-related pathways helps prioritizing cancer-related genes (i.e. ETV7, miR-146a-5p, ZFP36 and HCP5). We further identified two molecular subtypes of glioma (cold and hot tumour phenotypes), which were characterized by differences in immune cell infiltrations, expression of checkpoints, and prognosis. Finally, we developed a user-friendly resource, ImmReg (http://bio-bigdata.hrbmu.edu.cn/ImmReg/), with multiple modules to visualize, browse, and download immunology regulation. Our study provides a comprehensive landscape of immunology regulons, which will shed light on future development of RNA-based cancer immunotherapies.

Vitamin D metabolic pathway genes polymorphisms and vitamin D levels in association with neonatal hyperbilirubinemia in China: a single-center retrospective cohort study.

BACKGROUND: Neonatal hyperbilirubinemia (NH) is a major cause of hospitalization after birth. Previous studies indicated that vitamin D deficiency might play an important role in NH susceptibility, but the results were controversial. Meanwhile, there has been limited description of the association between vitamin D related genes single nucleotide polymorphisms (SNP) and NH susceptibility. We aimed to investigate the vitamin D metabolic pathway genes polymorphisms and vitamin D levels with NH susceptibility. METHODS: We retrospectively analyzed the clinical data, vitamin D levels and its metabolic pathway gene polymorphisms of 187 NH neonates and 149 controls at Tianjin Children's Hospital/Tianjin University Children's Hospital between April 2019 and August 2022. Vitamin D levels were measured by liquid chromatography-tandem mass spectrometry (LC-MS/MS) method, and the genetic polymorphism of NADSYN1/DHCR7, GC, CYP2R1, CYP24A1 and CYP27B1 was detected by high resolution melting (HRM) analysis. RESULTS: The frequency of vitamin D deficiency (25(OH)D < 15 ng/mL) was significantly increased in the NH group compared to controls. TT genotype of rs12785878 and GT genotype of rs10877012 were protective factors of vitamin D deficiency and NH, and GT genotype and dominant model carriers of rs12785878 had a higher risk of severe NH than the GG genotype carriers (GT genotype: OR: 2.43; 95% CI: 1.22-4.86; P = 0.012, dominant model: OR: 1.97; 95% CI: 1.04-3.73; P = 0.037). GC gene haplotype was associated with vitamin D deficiency. No significant SNP-SNP and SNP-vitamin D levels interaction combinations were found. CONCLUSIONS: There were associations among NH, vitamin D deficiency and NADSYN1/DHCR7 and CYP27B1 polymorphisms, TT genotype of rs12785878 and GT genotype of rs10877012 could reduce the risk of vitamin D deficiency and NH. Furthermore, rs12785878 was significantly associated with severe NH.