Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multi-omics reveal the segmentation atlas of hepatocellular carcinoma

ABSTRACT: We used a comprehensive approach that combined proteome, lipidome, and metabolome data to investigate the segmentation atlas of hepatocellular carcinoma (HCC).

ORGANISM(S): Homo Sapiens

SUBMITTER: Yongsheng Li

PROVIDER: PXD050969 | iProX | Tue Mar 26 00:00:00 GMT 2024

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

Integrative multiomics analysis identifies molecular subtypes and potential targets of hepatocellular carcinoma.

Yang Shuai S Zheng Lu L Li Lingling L Zhang Jiangang J Wang Jingchun J Zhao Huakan H Chen Yu Y Liu Xudong X Gan Hui H Chen Junying J Yan Mei M He Chuanyin C Li Kai K Ding Chen C Li Yongsheng Y

Clinical and translational medicine 20240601 6

<h4>Background</h4>The liver is anatomically divided into eight segments based on the distribution of Glisson's triad. However, the molecular mechanisms underlying each segment and its association with hepatocellular carcinoma (HCC) heterogeneity are not well understood. In this study, our objective is to conduct a comprehensive multiomics profiling of the segmentation atlas in order to investigate potential subtypes and therapeutic approaches for HCC.<h4>Methods</h4>A high throughput liquid chr ...[more]

PMID: 38804617

Similar Datasets

Gene expression of hepatocellular carcinoma tissue in China Medical University Hospital (CMUH) cohort of Taiwanese patients

Project description:It’s unknown what, how, and why lipid metabolites involve in cancer prognosis. This work implementing multi-omics measurement in hepatocellular carcinoma (HCC) patient cohort to associate tumoral lipidome, transcriptome, and serological metabolome to disease prognosis. Data indicating that dietary related ether-lipids, e.g., PC O- and PE O-, promote cell mobility and poor prognosis through TRPV2-related cytoskeletal rearrangement. In addition, downregulation of Peroxisome Proliferator-Activated Receptorα (PPARα) and consequential lipophagic deficit increase ether-lipids in cancer cells. Unfortunately, pathological coupling of Very Low-Density Lipoprotein Receptor (VLDLR) overexpression in HCC patients, concordantly deteriorates ether-lipid accumulation and facilitate HCC prognosis via VLDL entrance, the diet direct responding lipoprotein. Knocking out hepatic VLDLR reduce HCC burden in human etiology-related spontaneous HCC mouse model, which demonstrated the pathological causality in HCC. At last, administration of VLDL-Mimicking Nanoparticle encapsulating Lenvatinib, or fenofibrate (PPAR αagonist) could effectively diminished tumor anarchy.

2025-08-29 | GSE242315 | GEO

Multiple Omics Analyses of Hispanic Hepatocellular Carcinoma

Project description:Multi-omics approaches were utilized to comprehensively analyze the molecular characteristics of hepatocellular carcinoma (HCC) in South Texas (STX) Hispanics. Exome sequencing revealed high mutation frequencies of AXIN2 and CTNNB1, suggesting a predominant activation of the Wnt/beta-catenin pathway. Cell cycles were positively-, and liver functions were negatively-enriched on gene set enrichment analysis of our transcriptomic and proteomic datasets. Enrichments of gene sets representing specific liver metabolic pathways were found to be associated with the dysregulation of corresponding metabolites. Significant reduction of the majority of lipids seen in serum samples of HCC patients and many fatty acids in HCC tumors corroborate negative adipogenesis and lipid metabolism enrichments. We identified two subtypes of HCC using enrichment scores from paired tumor-nontumor samples of STX-Hispanics or TCGA-LIHC. The subtype with better overall survival revealed pronounced positive enrichments of immune-, angiogenesis-, and negative enrichments of liver function-related hallmark gene sets than the other. The former had higher levels of immune checkpoint and immune exhaustion markers. Together, we report molecular features of HCC, specific and non-specific to Hispanics.

2023-07-11 | MSV000092403 | MassIVE

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

Project description:HLA class I ligandome dataset obtained from hepatocellular carcinoma (HCC) as well as corresponding adjacent benign liver tissue (n=16) characterizing respective HLA immunoprecipitates. Additionally, from a subset of the mentioned HCC/ adjacent benign liver samples datasets gained from shotgun protein identification, comprising HCC as well as adjacent benign liver tissue (n=7) are provided. Further, for one patient shotgun protein identification was also performed in serum (blood) samples obtained after HCC recurrence.

2019-05-06 | PXD013057 | Pride

A Single-Cell Atlas of the Multicellular Ecosystem of Primary and Metastatic Hepatocellular Carcinoma

Project description:Hepatocellular carcinoma (HCC) represents a paradigm of the relation between tumor microenvironment and tumor development. Here, we generated > 70,000 single-cell transcriptomes for 10 HCC patients from four relevant sites: primary tumor, portal vein tumor thrombus (PVTT), metastatic lymph node and non-tumor liver. We discovered a cluster of antitumor central memory T cells enriched in intratumoral tertiary lymphoid structures (TLSs) of HCC. We found chronic HBV/HCV infection increases the infiltration of CD8+ T cells in tumors but aggravates the exhaustion of tumor-infiltrating lymphocytes. We identified MMP9+ macrophages to be terminally differentiated tumor-associated macrophages (TAMs) and two distinct differentiation trajectories are related to their accumulation. We further demonstrated MMP9+ TAMs can promote HCC cells migration, invasion and angiogenesis. Our data also revealed the heterogeneous population of malignant hepatocytes and found they might play multifaceted roles in shaping the immune microenvironment of HCC. Finally, we identified seven TME subtypes of HCC that can predict patient prognosis. Collectively, this large-scale, single-cell atlas deepens our understanding of the ecosystem in primary and metastatic HCCs, might facilitating identification of new immune therapy strategies for this malignancy.

2020-04-30 | GSE149614 | GEO

Multi-omics Identifies Tumor-Intrinsic SREBP1 Driving Immune Exclusion in Hepatocellular Carcinoma

Project description:Immune checkpoint inhibitors (ICI) have improved patient outcomes in hepatocellular carcinoma (HCC); however most patients do not experience durable benefit. The non-T cell-inflamed tumor microenvironment (TME), characterized by limited CD8+ T cell infiltration, reduced dendritic cell function, and low IFNγ-associated gene expression, is associated with lower likelihood of response to ICI. To nominate new therapeutic targets for overcoming ICI resistance in HCC, we conduced single cell RNAseq using 10X Genomics on 6 primary HCC tumors.

2025-06-24 | GSE292298 | GEO

Identification of cholangiocarcinoma-like gene expression traits in hepatocellular carcinoma

Project description:We performed gene expression profiling of hepatocellular carcinoma (HCC), cholangiocarcinoma (CC), and mixed type of combined HCC and CC (CHC). In comparison of the profiles, a novel class of HCC expressing CC-like traits was identified. Gene expression profiling of 70 hepatocellular carcinoma (HCC), 13 cholangiocarcinoma (CC), and 7 mixed type of combined HCC and CC (CHC) were performed.

2010-06-09 | E-GEOD-15765 | biostudies-arrayexpress

Hepatocellular Carcinoma (HCC) biomarker discovery cohort for small RNA profiling

Project description:Patients with Hepatocellular Carcinoma (HCC) and without HCC used for small read cluster identification and small RNA profiling.

2022-06-01 | E-MTAB-8528 | biostudies-arrayexpress

Role of bcatenin in hepatocellular carcinoma

Project description:Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related deaths worldwide. β-catenin is widely thought to be a major oncogene in HCC based on the frequency of mutations associated with aberrant Wnt signaling in HCC patients. Challenging this model, our data reveal that β-catenin nuclear accumulation is restricted to the late stage of the disease. Until then, β-catenin is primarily located at the plasma membrane in complex with multiple cadherin family members where it drives tumor cell survival by enhancing the signaling of growth factor receptors such as EGFR. Therefore, our study reveals the evolving nature of β-catenin in HCC to establish it as a compound tumor promoter during the progression of the disease.

2019-03-29 | PXD013095 | Pride

Mesenchymal subtypes of hepatocellular carcinoma

Project description:Clinical heterogeneity of hepatocellular carcinoma (HCC) reflected in unequal outcome of treatment is poorly defined in molecular level, and molecular subtypes and their associated biomarkers have not been established to improve prognostification and treatment of HCC. Using microarray technologies, we analyzed gene expression profiling data from HCC patients, uncovered mesenchymal subtype, and identified gene expression signature associated with mesenchymal phenotype of HCC.

2020-07-01 | GSE134568 | GEO

Proteomic characterization of human hepatocellular carcinoma (HCC) tumor biopsies

Project description:We analyzed the proteome of tumor and matched non-tumor biopsies from 51 treatment-naive Hepatocellular carcinoma (HCC) patients by DIA (SWATH). Thereby we aim to find subgroups of patients characterized by specific pathway activation. Furthermore, we aim to find novel factors involved in HCC development and novel biomarkers.

2022-03-14 | PXD025705 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data