Dataset Information

Single-cell and Spatial Architecture of Primary Liver Cancer

ABSTRACT: Using single-cell RNA sequencing, spatial transcriptomic and bulk multi-omics, we elaborated a molecular architecture of 3 PLC types, namely hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC) and combined hepatocellular-cholangiocarcinoma (CHC) from a high-resolution perspective.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Liver

SUBMITTER: peiyun zhou

LAB HEAD: Peiyun Zhou

PROVIDER: PXD044778 | Pride | 2024-01-26

REPOSITORIES: Pride

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Single-cell and spatial architecture of primary liver cancer.

Zhou Pei-Yun PY Zhou Cheng C Gan Wei W Tang Zheng Z Sun Bao-Ye BY Huang Jin-Long JL Liu Gao G Liu Wei-Ren WR Tian Meng-Xin MX Jiang Xi-Fei XF Wang Han H Tao Chen-Yang CY Fang Yuan Y Qu Wei-Feng WF Huang Run R Zhu Gui-Qi GQ Huang Cheng C Fu Xiu-Tao XT Ding Zhen-Bin ZB Gao Qiang Q Zhou Jian J Shi Ying-Hong YH Yi Yong Y Fan Jia J Qiu Shuang-Jian SJ

Communications biology 20231120 1

Primary liver cancer (PLC) poses a leading threat to human health, and its treatment options are limited. Meanwhile, the investigation of homogeneity and heterogeneity among PLCs remains challenging. Here, using single-cell RNA sequencing, spatial transcriptomic and bulk multi-omics, we elaborated a molecular architecture of 3 PLC types, namely hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC) and combined hepatocellular-cholangiocarcinoma (CHC). Taking a high-resolution pers ...[more]

PMID: 37985711

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Project description:Hepatocellular carcinoma is one of the most frequently diagnosed cancers in the world. Post-translational modifications (PTMs) play an essential role during cancer development. Phosphorylation is an important PTMs. To identify the modifications of phosphorylation in HCC, a multiplexed tandem mass tag (TMT) approach combined with LC−MS/MS was used. A total of 4,780 phosphorylated sites distributed on 2,209 proteins were identified and quantified, including 74 and 459 phosphorylated up-regulated and down-regulated proteins, respectively. Bio-informatic analysis revealed the differences and commonalities between HCC and normal tissues. Gene ontology enrichment analysis provided the information on biological processes, molecular functions, cellular components, and sub-cellular localizations. Protein domains enrichment of differentially expressed proteins were analyzed by InterPro database. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed the pathways that could potentially be involved in HCC. Integrative analysis of the functions, pathways, motifs of phosphorylated peptides, protein domains and protein interactions could establish a profile of phosphoproteome of HCC, which may contribute to identify new biomarkers for diagnosis and prognosis for HCC and novel therapeutic targets for HCC treatment.Hepatocellular carcinoma is one of the most frequently diagnosed cancers in the world. Post-translational modifications (PTMs) play an essential role during cancer development. Phosphorylation is an important PTMs. To identify the modifications of phosphorylation in HCC, a multiplexed tandem mass tag (TMT) approach combined with LC−MS/MS was used. A total of 4,780 phosphorylated sites distributed on 2,209 proteins were identified and quantified, including 74 and 459 phosphorylated up-regulated and down-regulated proteins, respectively. Bio-informatic analysis revealed the differences and commonalities between HCC and normal tissues. Gene ontology enrichment analysis provided the information on biological processes, molecular functions, cellular components, and sub-cellular localizations. Protein domains enrichment of differentially expressed proteins were analyzed by InterPro database. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed the pathways that could potentially be involved in HCC. Integrative analysis of the functions, pathways, motifs of phosphorylated peptides, protein domains and protein interactions could establish a profile of phosphoproteome of HCC, which may contribute to identify new biomarkers for diagnosis and prognosis for HCC and novel therapeutic targets for HCC treatment.

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	C9093TQB101.zip	Other
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