Multi-tissue single cell profiling of genetically diverse mouse models reveals mechanisms of resilience to obesity and diabetes [scRNA_seq_adipose]

Despite the importance of genetic factors to metabolic health, the cellular and molecular mechanisms mediating interindividual variation in progression along the continuum from health to type 2 diabetes mellitus (T2D) remain incompletely characterized. We studied three genetically diverse mouse strains with variable baseline metabolic physiology and distinct responses to a high fat high sugar diet. To understand genetically encoded differences in cell type-specific responses to diet, we profiled two key metabolic tissues, white adipose and pancreatic islets, using single cell gene expression and chromatin accessibility. In both tissues, strain background most strongly influenced both cell composition and cell type-specific gene expression, with substantial but smaller contributions of biological sex and diet. Transcriptomics and chromatin profiling revealed considerable differences between strains in immune infiltration in both tissues. Mechanisms of adipose expansion and energy utilization differed between strains, highlighting the importance of metabolite transport (Acly, Slc25a1), catecholamine signaling (Adrb3, Gpr143), preadipocyte cell fate (Cd81), and adipocyte subsets with thermogenic capabilities (Ckb, Ucp1, PGC-1?). Gene expression patterns in pancreatic beta cells were unique in the most resilient mouse strain, pointing to the importance of beta cell maturation pathways (Mafa, Ucn3), glucose metabolism (Glp1r), the unfolded protein/endoplasmic reticulum stress response (Atf6, Wfs1), and oxidative stress (Atox1) in the face of increased demand for insulin and glucolipotoxicity. Transcription of the adipokine Adipsin (Cfd) demonstrated a cross-tissue link consistent with the preservation of beta cell health in CAST mice. Finally, linking obesity and T2D GWAS effector genes to chromatin and transcriptional signals in the mouse revealed plausible cell types and states where variants mediating human disease traits likely exert their effects. Overall, this single cell atlas of key metabolic tissues provides insights into inherited variability in metabolic susceptibility and resilience and serves as a framework for utilizing diverse mice to study the progression of complex disease in a controlled, reproducible system. Overall design: Cells from mice of (up to) three different strains were pooled in each sample, and genetic demultiplexing was used to split cells by genetic background after data generation.

尽管遗传因素对代谢健康至关重要，但介导从健康状态到2型糖尿病（type 2 diabetes mellitus, T2D）连续病程中个体间差异的细胞与分子机制，迄今仍未得到完全表征。
本研究选取3株遗传背景各异的小鼠品系，其基础代谢生理特征存在差异，且对高糖高脂饮食展现出截然不同的应答反应。
为解析遗传编码的细胞类型特异性饮食应答差异，我们对两种关键代谢组织——白色脂肪组织与胰岛——开展了单细胞基因表达谱及染色质开放谱分析。
在两种组织中，品系背景对细胞组成及细胞类型特异性基因表达的影响最为显著，而生物学性别与饮食的贡献虽可观但相对较弱。
转录组学与染色质谱分析显示，不同品系小鼠的两种组织内免疫浸润情况均存在显著差异。
不同品系小鼠的脂肪扩张与能量利用机制存在差异，凸显了代谢物转运（Acly、Slc25a1）、儿茶酚胺信号通路（Adrb3、Gpr143）、前脂肪细胞命运调控（Cd81）以及具有产热功能的脂肪细胞亚群（Ckb、Ucp1、PGC-1?）的重要作用。
在代谢韧性最强的小鼠品系中，胰岛β细胞的基因表达模式独具特色，这表明在胰岛素需求增加及糖脂毒性应激下，β细胞成熟通路（Mafa、Ucn3）、葡萄糖代谢（Glp1r）、未折叠蛋白/内质网应激应答（Atf6、Wfs1）以及氧化应激调控（Atox1）发挥着关键作用。
脂肪因子Adipsin（Cfd）的转录水平呈现跨组织关联，这与CAST小鼠的β细胞健康维持状态相符。
最后，将肥胖与2型糖尿病全基因组关联研究（Genome-Wide Association Study, GWAS）的效应基因与小鼠的染色质及转录信号进行关联分析，揭示了介导人类疾病性状的遗传变异可能发挥作用的潜在细胞类型与状态。
总体而言，这份关键代谢组织的单细胞图谱为理解代谢易感性与韧性的遗传变异提供了新视角，同时也为利用多样小鼠品系在可控、可重复的实验体系中研究复杂疾病进展提供了研究框架。
实验设计概述：每个样本均混合了最多3种不同品系小鼠的细胞，后续通过遗传解多重（genetic demultiplexing）技术，根据遗传背景对细胞进行分群。