Region-resolved multi-omics of the mouse eye

Region and cell-type resolved multi-omic altas of the heart

The heart is a vital muscular organ in vertebrate animals, responsible for maintaining blood circulation through rhythmic contraction. Although previous studies have investigated the heart proteome, the full hierarchical molecular network at cell-type and region resolved level, illustrating the specialized roles and crosstalk among different cell types and regions, remains unclear. Here, we presented an atlas of cell-type resolved proteome for mouse heart and region resolved proteome for both mouse and human hearts. In-depth proteomic analysis identified 11,794 proteins across four cell types and 11,995 proteins across six regions of the mouse heart. To further illustrate protein expression patterns in both physiological and pathological conditions, we conducted proteomic analysis on human heart samples from four regions with dilated cardiomyopathy (DCM). We quantified 8,201 proteins in DCM tissue and 8,316 proteins in adjacent unaffected myocardium (AUM) tissue across the four human heart regions. Notably, we found that the retinoic acid synthesis pathway was significantly enriched in the DCM-affected left ventricle, and functional experiments demonstrated that all-trans retinoic acid (atRA) efficiently rescued Ang II-induced myocardial hypertrophy and transverse aorta constriction (TAC)- induced heart failure. In conclusion, our datasets uncovered the functional features of different cell types and their synergistic cooperation centered by cell-type specific transcription factors (ctsTF) in different regions, while these TF-TG (target gene) axes were significantly altered in DCM. Additionally, atRA was demonstrated to be an efficient treatment for heart failure. This work presented a panoramic heart proteome map, offering a valuable resource for future cardiovascular research.

Sub-5-min RP-UHPLC-TIMS for high-throughput untargeted lipidomics and its application to multiple matrices

Untargeted lipidomics, with its ability to take a snapshot of the lipidome landscape, is an important tool to highlight lipid changes in pathology or drug treatment models. One of the shortcomings of most untargeted lipidomics based on UHPLC-HRMS is the low throughput, which is not compatible with large-scale screening. In this contribution, we evaluate the application of a sub-5-min high-throughput four-dimensional trapped ion mobility mass spectrometry (HT-4D-TIMS) platform for the fast profiling of multiple complex biological matrices. Human AC-16 cells and mouse brain, liver, sclera, and feces were used as samples. By using a fast 4-min RP gradient, the implementation of TIMS allows us to differentiate coeluting isomeric and isobaric lipids, with correct precursor ion isolation, avoiding co-fragmentation and chimeric MS/MS spectra. Globally, the HT-4D-TIMS allowed us to annotate 1910 different lipid species, 1308 at the molecular level and 602 at the sum composition level, covering 58 lipid subclasses, together with quantitation capability covering more than three orders of magnitude. Notably, TIMS values were highly comparable with respect to longer LC gradients (CV% = 0.39%). These results highlight how HT-4D-TIMS-based untargeted lipidomics possess high coverage and accuracy, halving the analysis time with respect to conventional UHPLC methods, and can be used for fast and accurate untargeted analysis of complex matrices to rapidly evaluate changes of lipid metabolism in disease models or drug discovery campaigns.