title: Chromosome-8-coded proteome of Chinese Chromosome Proteome Data set (CCPD) 2.0 with partial immunohistochemical verifications.
abstract: We upgraded the preliminary CCPD 1.0 to CCPD 2.0 using the latest deep-profiling proteome (CCPD 2013) of three hepatocellular carcinoma (HCC) cell lines, namely, Hep3B, MHCC97H, and HCCLM3 (ProteomeXchange identifiers: PXD000529, PXD000533, and PXD000535). CCPD 2.0 totally covered 63.6% (438/689) of Chr. 8-coded proteins and 62.6% (439/701) of Chr. 8-coded protein-coding genes. Interestingly, we found that the missing proteins exhibited a tendency to form a cluster region in chromosomes, such as two β-defensins clusters in Chr. 8, caused perhaps by their inflammation-related features. For the 41 Chr. 8-coded proteins being weakly or barely identified previously, we have performed an immunohistochemical (IHC) verification in 30 pairs of carcinoma/para-carcinoma HCC and 20 noncancerous liver tissues and confirmed their expressional evidence and occurrence proportions in tissue samples. We also verified 13 Chr. 8-coded HCC tumorigenesis-associated depleting or deficient proteins reported in CCPD 1.0 using IHC and screened 16 positive and 24 negative HCC metastatic potential-correlated proteins from large-scale label-free proteome quantitation data of CCPD 2013. Our results suggest that the selection of proper samples and the methodology to look for targeted missing proteins should be carefully considered in further verifications for the remaining Chr. 8-coded proteins.
authors: Institutes of Biomedical Sciences, Fudan University , Mingdao Bldg. 815, 138 Yixueyuan Road, Shanghai 200032, China.
authors: Yang
authors: Y
authors: Liu
authors: Wantao
authors: W
authors: Ying
authors: Zhe
authors: Z
authors: Ren
authors: Wei
authors: W
authors: Gu
authors: Yang
authors: Y
authors: Zhang
authors: Guoquan
authors: G
authors: Yan
authors: Pengyuan
authors: P
authors: Yang
authors: Yinkun
authors: Y
authors: Liu
authors: Xuefei
authors: X
authors: Yin
authors: Cheng
authors: C
authors: Chang
authors: Jing
authors: J
authors: Jiang
authors: Fengxu
authors: F
authors: Fan
authors: Chengpu
authors: C
authors: Zhang
authors: Ping
authors: P
authors: Xu
authors: Quanhui
authors: Q
authors: Wang
authors: Bo
authors: B
authors: Wen
authors: Liang
authors: L
authors: Lin
authors: Tingyou
authors: T
authors: Wang
authors: Chaoqin
authors: C
authors: Du
authors: Jiayong
authors: J
authors: Zhong
authors: Tong
authors: T
authors: Wang
authors: Qing-Yu
authors: QY
authors: He
authors: Xiaohong
authors: X
authors: Qian
authors: Xiaomin
authors: X
authors: Lou
authors: Gong
authors: G
authors: Zhang
authors: Fan
authors: F
authors: Zhong
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000235:genetics / Q000473:pathology; D002681:China; D002898:Chromosomes, Human, Pair 8; D006801:Humans; D007150:Immunohistochemistry; D008113:Liver Neoplasms / Q000235:genetics / Q000473:pathology; D014176:Protein Biosynthesis; D020543:Proteome; D059467:Transcriptome
chemical_list: D020543:Proteome