Collaborative projects such as The Cancer Genome Atlas (TCGA) have generated various -omics and clinical data on cancer. Many computational tools have been developed to facilitate the study of the molecular characterization of tumors using data from the TCGA. Alternative splicing of a gene produces splicing variants, and accumulating evidence has revealed its essential role in cancer-related processes, implying the urgent need to discover tumor-specific isoforms and uncover their potential functions in tumorigenesis. We developed TSVdb, a web-based tool, to explore alternative splicing based on TCGA samples with 30 clinical variables from 33 tumors. TSVdb has an integrated and well-proportioned interface for visualization of the clinical data, gene expression, usage of exons/junctions and splicing patterns. Researchers can interpret the isoform expression variations between or across clinical subgroups and estimate the relationships between isoforms and patient prognosis. TSVdb is available at http://www.tsvdb.com , and the source code is available at https://github.com/wenjie1991/TSVdb . TSVdb will inspire oncologists and accelerate isoform-level advances in cancer research.

Background: The etiology of mild traumatic brain injury (mTBI) remains elusive due to the tissue and cellular heterogeneity of the affected brain regions that underlie cognitive impairments and subsequent neurological disorders. This complexity is further exacerbated by disrupted circuits within and between cell populations across brain regions and the periphery, which occur at different timescales and in spatial domains.Methods: We profiled three tissues (hippocampus, frontal cortex, and blood leukocytes) at the acute (24-h) and subacute (7-day) phases of mTBI at single-cell resolution.Results: We demonstrated that the coordinated gene expression patterns across cell types were disrupted and re-organized by TBI at different timescales with distinct regional and cellular patterns. Gene expression-based network modeling implied astrocytes as a key regulator of the cell–cell coordination following mTBI in both hippocampus and frontal cortex across timepoints, andmt-Rnr2, which encodes the mitochondrial peptide humanin, as a potential target for intervention based on its broad regional and dynamic dysregulation following mTBI. Treatment of a murine mTBI model with humanin reversed cognitive impairment caused by mTBI through the restoration of metabolic pathways within astrocytes.Conclusions: Our results offer a systems-level understanding of the dynamic and spatial regulation of gene programs by mTBI and pinpoint key target genes, pathways, and cell circuits that are amenable to therapeutics.

High fructose intake is a major risk for metabolic syndrome; however, its effects seem to vary across individuals. To determine main factors involved in the inter-individual responses to fructose, we fed inbred mouse strains C57BL/6J (B6), DBA/2J (DBA) and FVB/NJ (FVB) with fructose. DBA mice showed the highest susceptibility to gain adiposity and glucose intolerance. Elevated insulin was found in DBA and FVB mice, and cholesterol levels were uniquely elevated in B6 mice. The transcriptional profiles of liver, hypothalamus, and adipose tissues showed strain- and tissue-specific pathways altered by fructose, such as fatty acid and cholesterol pathways for B6 and PPAR signaling for DBA in liver, and oxidative phosphorylation for B6 and protein processing for DBA in hypothalamus. Using network modeling, we predicted potential strain-specific key regulators of fructose response such as Fgf21 (DBA) and Lss (B6) in liver, and validated strain-biased responses as well as the regulatory actions of Fgf21 and Lss in primary hepatocytes. Our findings support that fructose perturbs individualized tissue networks and pathways and associates with distinct features of metabolic dysfunctions across genetically diverse mice. Our results elucidate the molecular pathways and gene regulatory mechanisms underlying inter-individual variability in response to high fructose diet.

Background: Obesity is a prevalent, systemic metabolic disease affecting not only various adipose depots but also the liver, where lipid accumulation results in metabolic dysfunction-associated fatty liver disease, dyslipidemia, and insulin resistance. While estradiol (E2) has been known to be hepatoprotective for glucose and lipid metabolism in females, whether E2’s effects on individual liver cell types are shared between sexes or are sex-specific with obesity remains poorly defined. Methods: We performed single-nucleus RNA sequencing on liver tissue of E2-treated obese, gonadectomized male (XY) and female (XX) mice with diet-induced obesity to evaluate the sex-concordant and discordant effects of chronic E2 treatment. Differential gene expression, pathway analysis, intracellular and intercellular regulatory network modeling, and human metabolic disease/trait association analysis were conducted. Results: E2-induced transcriptional effects among hepatocyte subtypes were largely sex-concordant in both males and females, along with sex-specific E2 changes. In pericentral hepatocytes, E2 concordantly reduced the expression of genes involved in insulin resistance, FOXO signaling, and lipid biosynthesis; in periportal hepatocytes, E2 treatment enhanced cholesterol efflux genes and suppressed oxidative stress response genes. XY-specific effects of E2 included additional suppression of lipid and energy metabolic pathways in pericentral hepatocytes and oxidative phosphorylation in periportal hepatocytes, while in XX mice E2 showed unique regulation of glucose and lipid utilization programs. Network analysis revealed that E2-responsive genes in hepatocyte subtypes in both sexes showed enriched transcription factors associated with estrogen receptor signaling and lipid sensing and metabolism, alongside sex-specific regulators. Intercellular signaling affected by E2 showed more changes in XY mice than in XX mice across hepatocyte subtypes. Lastly, while E2-responsive genes in hepatocyte subtypes of both sexes were enriched for human genetic signals associated with lipid profiles and coronary artery disease, we also identified sex-specific associations, such as the link of E2-downregulated genes in XY hepatocytes to body mass index in men. Conclusions: Our findings revealed that chronic E2 administration remodels gene regulatory programs in individual liver cell types through both shared and sex-specific mechanisms, highlighting the importance of considering sex chromosome-dependent E2 responses when developing therapeutic strategies for obesity and associated hepatic metabolic dysfunction.

Traumatic brain injury (TBI) and non-acquired brain damage represent a catastrophic global health burden, frequently resulting in persistent neurological impairment, long-term cognitive decline, and increased susceptibility to secondary psychiatric disorders

Background: It is unclear how high fructose consumption induces disparate metabolic responses in genetically diverse mouse strains. Objective: We aim to investigate whether the gut microbiota contributes to differential metabolic responses to fructose. Methods: Eight-week-old male C57BL/6J (B6), DBA/2J (DBA), and FVB/NJ (FVB) mice were given 8% fructose solution or regular water (control) for 12 weeks. The gut microbiota composition in cecum and feces was analyzed using 16S rDNA sequencing, and PERMANOVA was used to compare community across mouse strains, treatments, and time points. Microbiota abundance was correlated with metabolic phenotypes and host gene expression in hypothalamus, liver and adipose tissues using Biweight midcorrelation. To test the causal role of the gut microbiota in determining fructose response, we conducted fecal transplants from B6 to DBA mice and vice versa for 4 weeks, as well as gavaged antibiotic-treated DBA mice with Akkermansia for 9 weeks, accompanied with or without fructose treatment. Results: Compared to B6 and FVB, DBA mice had significantly higher Firmicutes/Bacteroidetes ratio and lower baseline levels of Akkermansia and S24-7 ( P < 0.05), accompanied by metabolic dysregulation after fructose consumption. Fructose altered specific microbial taxa in individual mouse strains, such as a 7.27-fold increase in Akkermansia in B6 and 0.374-fold change in Rikenellaceae in DBA (FDR < 5%), which demonstrated strain-specific correlations with host metabolic and transcriptomic phenotypes. Fecal transplant experiments indicated that B6 microbes conferred resistance to fructose-induced weight gain in DBA mice ( F = 43.1, P < 0.001), and Akkermansia colonization abrogated the fructose-induced weight gain ( F = 17.8, P <0.001) and glycemic dysfunctions ( F = 11.8, P = 0.004) in DBA mice. Conclusions: Our findings support that differential microbiota composition between mouse strains is partially responsible for host metabolic sensitivity to fructose, and that Akkermansia is a key bacterium that confers resistance to fructose-induced metabolic dysregulation.