PXD017610

PXD017610 is an original dataset announced via ProteomeXchange.

Title	A multi-omics approach to liver diseases: integration of Single Nuclei Transcriptomics with Proteomics and Hi-Cap Bulk Data in human liver
Description	Abstract 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 sub-populations. In this study, we performed snRNA-seq of a liver sample to identify sub-populations of cells based on nuclear transcriptomics. In 4,282 single nuclei we detected on average 1,377 active genes and we identified seven major cell types. We integrated data from 94,286 distal interactions (p<0.05) for 7,682 promoters from a targeted chromosome conformation capture technique (HiCap) and mass spectrometry (MS) 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 fluoropyrimidines 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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:17:01.031.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	atul shahaji deshmukh
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-02-19 01:42:10	ID requested
1	2020-12-21 03:27:55	announced
⏵ 2	2024-10-22 05:17:01	announced	2024-10-22: Updated project metadata.

10.1089/omi.2019.0215;

Cavalli M, Diamanti K, Pan G, Spalinskas R, Kumar C, Deshmukh AS, Mann M, Sahl, é, n P, Komorowski J, Wadelius C, A Multi-Omics Approach to Liver Diseases: Integration of Single Nuclei Transcriptomics with Proteomics and HiCap Bulk Data in Human Liver. OMICS, 24(4):180-194(2020) [pubmed]

submitter keyword: Human Liver Single nuclei LCMS

Claes Wadelius
contact affiliation	Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 751 23 Uppsala, Sweden
contact email	claes.wadelius@igp.uu.se
lab head
atul shahaji deshmukh
contact affiliation	Copenhagen University
contact email	atul.deshmukh@cpr.ku.dk
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/12/PXD017610

PRIDE project URI

• PRIDE
  1. PXD017610
     1. Label: PRIDE project
     2. Name: A multi-omics approach to liver diseases: integration of Single Nuclei Transcriptomics with Proteomics and Hi-Cap Bulk Data in human liver