Blood contains cfDNA fragments derived from dying cells 1 . cfDNA has a half-life of ~15 min 2 and, therefore, represents events that occurred close to sampling time. cfDNA analysis is used for assessment of fetus chromosomal aberrations, graft rejection, monitoring tumor dynamics and targeted treatment [3][4][5][6][7] . These applications rely on genetic differences between the host and the tissue of interest. Analysis of CpG methylation in cfDNA is emerging as an alternative independent of genetic alteration 5,[8][9][10][11] . CpG methylation profiles are determined during differentiation and are stable afterwards and, thus, are highly informative about cell identity (for example, liver or lung). However, genetic and methylation-based approaches do not report on recent transcriptional events, as mutations and methylation changes occur over developmental time scales.The basic repeating unit of chromatin is the nucleosome, which is a histone-DNA complex encompassing ~150 base pairs (bp) of DNA 12 . Histone proteins are subject to multiple covalent modifications, which are involved in nearly all aspects of messenger RNA (mRNA) biogenesis [13][14][15][16] . Histone modification patterns reflect recent events related to chromatin regulation and activity of RNA polymerase 13,15 , and different combinations of such modifications mark the location and activity of non-coding regions, enhancers, promoters and gene bodies [17][18][19][20][21][22] . Chromatin immunoprecipitation and sequencing (ChIP-seq) enables genome-wide mapping of histone modifications and provides detailed understanding of the regulatory activity within cells [17][18][19][23][24][25][26][27] .Upon cell death, the genome is fragmented, and chromatin, mostly in the form of nucleosomes, is released into the circulation as cell-free nucleosomes (cf-nucleosomes) 28-30 that retain some histone modifications [31][32][33] . We reasoned that capturing and DNA sequencing of modified nucleosomes from plasma might inform on DNA-related activities, including transcription, within the cells of origin (Fig. 1a). This currently inaccessible epigenetic information extends beyond cfDNA modalities examined to date [4][5][6][7][8][9][10][11][34][35][36][37][38][39][40][41][42][43] .In this study, we performed chromatin immunoprecipitation and sequencing of cell-free nucleosomes directly from human plasma (cfChIP-seq). We show that cfChIP-seq recapitulates the original genomic distribution of modifications associated with transcriptionally active promoters, enhancers and gene bodies, demonstrating that plasma nucleosomes retain the epigenetic information of their

Malignant cell growth is fueled by interactions between tumor cells and the stromal cells composing the tumor microenvironment. The human liver is a major site of tumors and metastases, but molecular identities and intercellular interactions of different cell types have not been resolved in these pathologies. Here, we apply single cell RNA‐sequencing and spatial analysis of malignant and adjacent non‐malignant liver tissues from five patients with cholangiocarcinoma or liver metastases. We find that stromal cells exhibit recurring, patient‐independent expression programs, and reconstruct a ligand–receptor map that highlights recurring tumor–stroma interactions. By combining transcriptomics of laser‐capture microdissected regions, we reconstruct a zonation atlas of hepatocytes in the non‐malignant sites and characterize the spatial distribution of each cell type across the tumor microenvironment. Our analysis provides a resource for understanding human liver malignancies and may expose potential points of interventions.

Bariatric surgery dramatically improves glycemic control, yet the underlying molecular mechanisms remain controversial because of confounding weight loss. We performed sleeve gastrectomy (SG) on obese and diabetic leptin receptor-deficient mice (/). One week postsurgery, mice weighed 5% less and displayed improved glycemia compared with sham-operated controls, and islets from SG mice displayed reduced expression of diabetes markers. One month postsurgery SG mice weighed more than preoperatively but remained near-euglycemic and displayed reduced hepatic lipid droplets. Pair feeding of SG and sham / mice showed that surgery rather than weight loss was responsible for reduced glycemia after SG. Although insulin secretion profiles from islets of sham and SG mice were indistinguishable, clamp studies revealed that SG causes a dramatic improvement in muscle and hepatic insulin sensitivity accompanied by hepatic regulation of hepatocyte nuclear factor-α and peroxisome proliferator-activated receptor-α targets. We conclude that long-term weight loss after SG requires leptin signaling. Nevertheless, SG elicits a remarkable improvement in glycemia through insulin sensitization independent of reduced feeding and weight loss.