Chromosome-8-coded proteome of Chinese Chromosome Proteome Data Set (CCPD) 2.0 with partial immunohistochemical verifications

Yang Liu; Wantao Ying; Zhe Ren; Wei Gu; Yang Zhang; Guoquan Yan; Pengyuan Yang; Yinkun Liu; Xuefei Yin; Cheng Chang; Jing Jiang; Fengxu Fan; Chengpu Zhang; Ping Xu; Quanhui Wang; Bo Wen; Liang Lin; Tingyou Wang; Chaoqin Du; Jiayong Zhong; Tong Wang; Qing Yu He; Xiaohong Qian; Xiaomin Lou; Gong Zhang; Fan Zhong

doi:10.1021/pr400902u

Chromosome-8-coded proteome of Chinese Chromosome Proteome Data Set (CCPD) 2.0 with partial immunohistochemical verifications

Yang Liu, Wantao Ying, Zhe Ren, Wei Gu, Yang Zhang, Guoquan Yan, Pengyuan Yang, Yinkun Liu, Xuefei Yin, Cheng Chang, Jing Jiang, Fengxu Fan, Chengpu Zhang, Ping Xu, Quanhui Wang, Bo Wen, Liang Lin, Tingyou Wang, Chaoqin Du, Jiayong ZhongTong Wang, Qing Yu He, Xiaohong Qian, Xiaomin Lou, Gong Zhang, Fan Zhong

Research output: Contribution to journal › Article › peer-review

11 Scopus citations

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.

Original language	English (US)
Pages (from-to)	126-136
Number of pages	11
Journal	Journal of Proteome Research
Volume	13
Issue number	1
DOIs	https://doi.org/10.1021/pr400902u
State	Published - Jan 3 2014
Externally published	Yes

Keywords

chromosome 8
hepatocellular carcinoma
immunohistochemistry
metastasis
missing protein
neXtProt
proteome

Publisher link

10.1021/pr400902u

Find It

Find It at U of M Libraries

Cite this

Liu, Y., Ying, W., Ren, Z., Gu, W., Zhang, Y., Yan, G., Yang, P., Liu, Y., Yin, X., Chang, C., Jiang, J., Fan, F., Zhang, C., Xu, P., Wang, Q., Wen, B., Lin, L., Wang, T., Du, C., ... Zhong, F. (2014). Chromosome-8-coded proteome of Chinese Chromosome Proteome Data Set (CCPD) 2.0 with partial immunohistochemical verifications. Journal of Proteome Research, 13(1), 126-136. https://doi.org/10.1021/pr400902u

Liu, Y, Ying, W, Ren, Z, Gu, W, Zhang, Y, Yan, G, Yang, P, Liu, Y, Yin, X, Chang, C, Jiang, J, Fan, F, Zhang, C, Xu, P, Wang, Q, Wen, B, Lin, L, Wang, T, Du, C, Zhong, J, Wang, T, He, QY, Qian, X, Lou, X, Zhang, G & Zhong, F 2014, 'Chromosome-8-coded proteome of Chinese Chromosome Proteome Data Set (CCPD) 2.0 with partial immunohistochemical verifications', Journal of Proteome Research, vol. 13, no. 1, pp. 126-136. https://doi.org/10.1021/pr400902u

@article{5d0d8bc06aa540b0b786b91548c84b8c,

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.",

keywords = "chromosome 8, hepatocellular carcinoma, immunohistochemistry, metastasis, missing protein, neXtProt, proteome",

author = "Yang Liu and Wantao Ying and Zhe Ren and Wei Gu and Yang Zhang and Guoquan Yan and Pengyuan Yang and Yinkun Liu and Xuefei Yin and Cheng Chang and Jing Jiang and Fengxu Fan and Chengpu Zhang and Ping Xu and Quanhui Wang and Bo Wen and Liang Lin and Tingyou Wang and Chaoqin Du and Jiayong Zhong and Tong Wang and He, {Qing Yu} and Xiaohong Qian and Xiaomin Lou and Gong Zhang and Fan Zhong",

year = "2014",

month = jan,

day = "3",

doi = "10.1021/pr400902u",

language = "English (US)",

volume = "13",

pages = "126--136",

journal = "Journal of Proteome Research",

issn = "1535-3893",

publisher = "American Chemical Society",

number = "1",

}

TY - JOUR

T1 - Chromosome-8-coded proteome of Chinese Chromosome Proteome Data Set (CCPD) 2.0 with partial immunohistochemical verifications

AU - Liu, Yang

AU - Ying, Wantao

AU - Ren, Zhe

AU - Gu, Wei

AU - Zhang, Yang

AU - Yan, Guoquan

AU - Yang, Pengyuan

AU - Liu, Yinkun

AU - Yin, Xuefei

AU - Chang, Cheng

AU - Jiang, Jing

AU - Fan, Fengxu

AU - Zhang, Chengpu

AU - Xu, Ping

AU - Wang, Quanhui

AU - Wen, Bo

AU - Lin, Liang

AU - Wang, Tingyou

AU - Du, Chaoqin

AU - Zhong, Jiayong

AU - Wang, Tong

AU - He, Qing Yu

AU - Qian, Xiaohong

AU - Lou, Xiaomin

AU - Zhang, Gong

AU - Zhong, Fan

PY - 2014/1/3

Y1 - 2014/1/3

N2 - 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.

AB - 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.

KW - chromosome 8

KW - hepatocellular carcinoma

KW - immunohistochemistry

KW - metastasis

KW - missing protein

KW - neXtProt

KW - proteome

UR - http://www.scopus.com/inward/record.url?scp=84891801560&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84891801560&partnerID=8YFLogxK

U2 - 10.1021/pr400902u

DO - 10.1021/pr400902u

M3 - Article

C2 - 24328083

AN - SCOPUS:84891801560

SN - 1535-3893

VL - 13

SP - 126

EP - 136

JO - Journal of Proteome Research

JF - Journal of Proteome Research

IS - 1

ER -

Chromosome-8-coded proteome of Chinese Chromosome Proteome Data Set (CCPD) 2.0 with partial immunohistochemical verifications

Abstract

Keywords

Publisher link

Find It

Other files and links

Fingerprint

Cite this