Project description:Background: The ability to form enduring social bonds is characteristic of human nature and as a result, impairments in social affiliation are central features of severe neuropsychiatric disorders including autism spectrum disorders and schizophrenia. Due to its ability to form long-term pair-bonds, the socially monogamous prairie vole (Microtus ochrogaster) has emerged as an excellent model to study the neurobiology of social attachment. Despite the enduring nature of the bond, however, surprisingly few genes have been implicated in the pair-bonding process in either sex. Results: Using RNA-sequencing, we aimed at identifying the transcriptomic regulations in the nucleus accumbens (NAc) underlying the formation and maintenance of a pair-bond in male and female prairie voles and found sex-specific response patterns despite similar behavioral indicators of pair-bond establishment. Indeed, 24 hrs of cohabitation with an opposite-sex partner induced widespread transcriptomic changes that remained sustained to some extent in females after 3 weeks, but returned to baseline before a second set of regulations in males. This led to a highly sexually-biased NAc transcriptome in the later phase of the bond related to processes such as neurotransmission, protein turnover, and DNA transcription. In particular, we found sex-specific alterations of mitochondrial dynamics following cohabitation, with a shift towards fission in males. Conclusions: In addition to identifying the genes, networks, and pathways involved in the pair-bonding process in the NAc, our work illustrates the vast extent of sex differences in the molecular mechanisms underlying pair-bonding in prairie voles, and paves the way to further our understanding of the complex social bonding process.
Project description:Ceramides contribute to the lipotoxicity that underlies diabetes, hepatic steatosis, and heart disease. By genetically engineering mice, we deleted the enzyme dihydroceramide desaturase-1 (DES1) which inserts a conserved double bond into the backbone of ceramides and other predominant sphingolipids. Ablation of DES1 from whole animals, or tissue-specific deletion in the liver, and/or adipose tissue resolved hepatic steatosis and insulin resistance in mice caused by leptin deficiency or obesogenic diets. Mechanistic studies revealed new ceramide actions that promoted lipid uptake and storage and impaired glucose utilization, none of which could be recapitulated by (dihydro)ceramides that lacked the critical double bond. These studies suggest that inhibition of DES1 may provide a means of treating hepatic steatosis and cardiometabolic disorders.
Project description:Genome graphs, including the recently released draft human pangenome graph, can represent the breadth of genetic diversity and thus transcend the limits of traditional linear reference genomes. However, there are no genome-graph-compatible tools for analyzing whole genome bisulfite sequencing (WGBS) data. To close this gap, we introduce methylGrapher, a tool tailored for accurate DNA methylation analysis by mapping WGBS data to a genome graph. Notably, methylGrapher can reconstruct methylation patterns along haplotype paths precisely and efficiently. To demonstrate the utility of methylGrapher, we analyzed the WGBS data derived from five individuals whose genomes were included in the first Human Pangenome draft as well as WGBS data from ENCODE (EN-TEx). Along with standard performance benchmarking, we show that methylGrapher fully recapitulates DNA methylation patterns defined by classic linear genome analysis approaches. Importantly, methylGrapher captures a substantial number of CpG sites that are missed by linear methods, and improves overall genome coverage while reducing alignment reference bias. Thus, methylGrapher is a first step towards unlocking the full potential of Human Pangenome graphs in genomic DNA methylation analysis.
Project description:T cells are often weakly responsive to tumor self-antigens because of central tolerance, which constrains their ability to eliminate tumors. Affinity-matured T cell receptors can exhibit enhanced tumor killing properties but in therapeutic settings have been accompanied by off-target cross-reactivity and toxicity, because high-affinity TCRs antigen specificity is altered compared to naturally selected TCRs. Here, we exploited the physiological biophysical mechanism of TCR activation through mechanical force, by engineering to a weakly reactive TCR specific for a non-mutated human prostate tumor associated antigen (TAA), Prostatic Acid Phosphatase (PAP). We isolated a catch bonding “hotspot” whose mutation enhanced T cell activity by increasing TCR-pMHC bond lifetime, whilst maintaining physiological affinities and antigen fine-specificities. T cells expressing these engineered TCRs showed vastly superior expansion and tumor killing properties in vitro and in vivo, as well as enhanced effector phenotypes and proliferation in the tumor, as measured by single-cell RNA-seq. High resolution structures and molecular dynamics simulations of the TCR-pMHC complexes reveal the structural hotspot in TCR CDR1 is primed for peptide interaction in the catch bond engineered TCR. These studies establish catch bond engineering as a viable biophysically-based strategy to convert tolerized anti-tumor T cells into potent TCR-T killers.
Project description:T cells are often weakly responsive to tumor self-antigens because of central tolerance, which constrains their ability to eliminate tumors. Affinity-matured T cell receptors can exhibit enhanced tumor killing properties but in therapeutic settings have been accompanied by off-target cross-reactivity and toxicity, because high-affinity TCRs antigen specificity is altered compared to naturally selected TCRs. Here, we exploited the physiological biophysical mechanism of TCR activation through mechanical force, by engineering to a weakly reactive TCR specific for a non-mutated human prostate tumor associated antigen (TAA), Prostatic Acid Phosphatase (PAP). We isolated a catch bonding “hotspot” whose mutation enhanced T cell activity by increasing TCR-pMHC bond lifetime, whilst maintaining physiological affinities and antigen fine-specificities. T cells expressing these engineered TCRs showed vastly superior expansion and tumor killing properties in vitro and in vivo, as well as enhanced effector phenotypes and proliferation in the tumor, as measured by single-cell RNA-seq. High resolution structures and molecular dynamics simulations of the TCR-pMHC complexes reveal the structural hotspot in TCR CDR1 is primed for peptide interaction in the catch bond engineered TCR. These studies establish catch bond engineering as a viable biophysically-based strategy to convert tolerized anti-tumor T cells into potent TCR-T killers.
Project description:Synthetic lethality (SL) has shown great promise for the discovery of novel targets in cancer. CRISPR double-knockout (CDKO) technologies can only screen several hundred genes and their combinations, but not genome-wide. Therefore, good SL prediction models are highly needed for genes and gene pairs selection in CDKO experiments. In this paper, we develop a novel multi-layer encoder for individual sample-specific SL prediction (MLEC-iSL). Unlike existing SL prediction models, MLEC-iSL is built to predict SL connectivity first. Because SL connectivity is scalable from existing genes in the training data to new genes in validation data, we hypothesize MLEC-iSL has better SL prediction performance. MLEC-iSL has three encoders, namely gene encoder, graph encoder, and transformer encoder. MLEC-iSL has high performance in K562 (AUPR, 0.73; AUC, 0.72) and Jurkat (AUPR, 0.73; AUC, 0.71) cells while no existing methods exceed 0.62 AUPR and AUC in either cell. MLEC-iSL guided CDKO experiment in 22Rv1 cells yielded a 46.8% SL ratio amongst its selected gene pairs. Six of top ten SL connectivity hub genes are validated in 22Rv1 cells. It reveals SL gene pairs and dependency between apoptosis and mitosis cell death pathways.