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The liver is the largest solid organ and a primary metabolic hub. In recent years, intact cell nuclei were used to perform single-nuclei RNA-seq (snRNA-seq) for tissues difficult to dissociate and for flash-frozen archived tissue samples to discover unknown and rare cell subpopulations. In this study, we performed snRNA-seq of a liver sample to identify subpopulations of cells based on nuclear transcriptomics. In 4282 single nuclei, we detected, on average, 1377 active genes and we identified seven major cell types. We integrated data from 94,286 distal interactions (p < 0.05) for 7682 promoters from a targeted chromosome conformation capture technique (HiCap) and mass spectrometry proteomics for the same liver sample. We observed a reasonable correlation between proteomics and in silico bulk snRNA-seq (r = 0.47) using tissue-independent gene-specific protein abundancy estimation factors. We specifically looked at genes of medical importance. The DPYD gene is involved in the pharmacogenetics of fluoropyrimidine toxicity and some of its variants are analyzed for clinical purposes. We identified a new putative polymorphic regulatory element, which may contribute to variation in toxicity. Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer and we investigated all known risk genes. We identified a complex regulatory landscape for the SLC2A2 gene with 16 candidate enhancers. Three of them harbor somatic motif breaking and other mutations in HCC in the Pan Cancer Analysis of Whole Genomes dataset and are candidates to contribute to malignancy. Our results highlight the potential of a multi-omics approach in the study of human diseases., QC 20200702

The limited biocompatibility of decellularized scaffolds is an ongoing challenge in tissue engineering. Here, we demonstrate the residual immunogenicity of an extensively decellularized equine carotid artery (dEAC intens) and identify the involved immunogenic components. EAC were submitted to an elaborated intensified decellularization protocol with SDS/sodium desoxycholate for 72 h using increased processing volumes (dEAC intens), and compared to dEACord prepared by an ordinary protocol (40 h, normal volumes). Matrix integrity was checked via correlative volumetric visualization which revealed only minor structural changes in the arterial wall. In dEACintens, a substantial depletion of cellular components was obvious for smooth muscle actin (100%), MHC I complexes (97.8%), alphaGal epitops (98.4% and 91.3%) and for DNA (final concentration of 0.34±0.16 ng/mg tissue). However, dEACintens still evoked antibody formation in mice after immunization with dEACintens extracts, although to a lower extent than dEACord. Mouse plasma antibodies recognized a 140 kDa band which was revealed to contain collagen VI alpha1 and alpha2 chains via mass spectrometry of both 2D electrophoretically separated and immunoprecipitated proteins. Thus, even the complete removal of cellular proteins did not yield non-immunogenic dEAC as the extracellular matrix still conferred immunogenicity by collagen VI. However, as lower antibody levels were achieved by the intensified decellularization protocol, this seems to be a promising basis for further development.