Protein expression profiling of nuclear membrane protein reveals potential biomarker of human hepatocellular carcinoma

Rizma Khan, Saadia Zahid, Yu-Jui Yvonne Wan, Jameson Forster, A. Bashar Abdul Karim, Atta M. Nawabi, Abid Azhar, M. Ataur Rahman, Nikhat Ahmed

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Background: Complex molecular events lead to development and progression of liver cirrhosis to HCC. Differentially expressed nuclear membrane associated proteins are responsible for the functional and structural alteration during the progression from cirrhosis to carcinoma. Although alterations/ post translational modifications in protein expression have been extensively quantified, complementary analysis of nuclear membrane proteome changes have been limited. Deciphering the molecular mechanism that differentiate between normal and disease state may lead to identification of biomarkers for carcinoma. Results: Many proteins displayed differential expression when nuclear membrane proteome of hepatocellular carcinoma (HCC), fibrotic liver, and HepG2 cell line were assessed using 2-DE and ESI-Q-TOF MS/MS. From the down regulated set in HCC, we have identified for the first time a 15 KDa cytochrome b5A (CYB5A), ATP synthase subunit delta (ATPD) and Hemoglobin subunit beta (HBB) with 11, 5 and 22 peptide matches respectively. Furthermore, nitrosylation studies with S-nitrosocysteine followed by immunoblotting with anti SNO-cysteine demonstrated a novel and biologically relevant post translational modification of thiols of CYB5A in HCC specimens only. Immunofluorescence images demonstrated increased protein S-nitrosylation signals in the tumor cells and fibrotic region of HCC tissues. The two other nuclear membrane proteins which were only found to be nitrosylated in case of HCC were up regulated ATP synthase subunit beta (ATPB) and down regulated HBB. The decrease in expression of CYB5A in HCC suggests their possible role in disease progression. Further insight of the functional association of the identified proteins was obtained through KEGG/ REACTOME pathway analysis databases. String 8.3 interaction network shows strong interactions with proteins at high confidence score, which is helpful in characterization of functional abnormalities that may be a causative factor of liver pathology. Conclusion: These findings may have broader implications for understanding the mechanism of development of carcinoma. However, large scale studies will be required for further verification of their critical role in development and progression of HCC.

Original languageEnglish (US)
Article number6
JournalClinical Proteomics
Volume10
Issue number1
DOIs
StatePublished - 2013
Externally publishedYes

Fingerprint

Nuclear Envelope
Biomarkers
Nuclear Proteins
Hepatocellular Carcinoma
Membrane Proteins
Hemoglobin Subunits
Cytochromes
Liver
Proteome
Proteins
Adenosine Triphosphate
Cells
Membranes
Protein S
Pathology
Post Translational Protein Processing
Carcinoma
Sulfhydryl Compounds
Cysteine
Tumors

Keywords

  • Cytochrome b5A
  • ESI-Q-TOF MS/MS mass spectrometry
  • Hepatocellular carcinoma
  • Proteomics
  • S-nitrosylation
  • Two dimensional gel electrophoresis

ASJC Scopus subject areas

  • Molecular Biology
  • Molecular Medicine
  • Clinical Biochemistry

Cite this

Protein expression profiling of nuclear membrane protein reveals potential biomarker of human hepatocellular carcinoma. / Khan, Rizma; Zahid, Saadia; Wan, Yu-Jui Yvonne; Forster, Jameson; Abdul Karim, A. Bashar; Nawabi, Atta M.; Azhar, Abid; Rahman, M. Ataur; Ahmed, Nikhat.

In: Clinical Proteomics, Vol. 10, No. 1, 6, 2013.

Research output: Contribution to journalArticle

Khan, Rizma ; Zahid, Saadia ; Wan, Yu-Jui Yvonne ; Forster, Jameson ; Abdul Karim, A. Bashar ; Nawabi, Atta M. ; Azhar, Abid ; Rahman, M. Ataur ; Ahmed, Nikhat. / Protein expression profiling of nuclear membrane protein reveals potential biomarker of human hepatocellular carcinoma. In: Clinical Proteomics. 2013 ; Vol. 10, No. 1.
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AU - Zahid, Saadia

AU - Wan, Yu-Jui Yvonne

AU - Forster, Jameson

AU - Abdul Karim, A. Bashar

AU - Nawabi, Atta M.

AU - Azhar, Abid

AU - Rahman, M. Ataur

AU - Ahmed, Nikhat

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N2 - Background: Complex molecular events lead to development and progression of liver cirrhosis to HCC. Differentially expressed nuclear membrane associated proteins are responsible for the functional and structural alteration during the progression from cirrhosis to carcinoma. Although alterations/ post translational modifications in protein expression have been extensively quantified, complementary analysis of nuclear membrane proteome changes have been limited. Deciphering the molecular mechanism that differentiate between normal and disease state may lead to identification of biomarkers for carcinoma. Results: Many proteins displayed differential expression when nuclear membrane proteome of hepatocellular carcinoma (HCC), fibrotic liver, and HepG2 cell line were assessed using 2-DE and ESI-Q-TOF MS/MS. From the down regulated set in HCC, we have identified for the first time a 15 KDa cytochrome b5A (CYB5A), ATP synthase subunit delta (ATPD) and Hemoglobin subunit beta (HBB) with 11, 5 and 22 peptide matches respectively. Furthermore, nitrosylation studies with S-nitrosocysteine followed by immunoblotting with anti SNO-cysteine demonstrated a novel and biologically relevant post translational modification of thiols of CYB5A in HCC specimens only. Immunofluorescence images demonstrated increased protein S-nitrosylation signals in the tumor cells and fibrotic region of HCC tissues. The two other nuclear membrane proteins which were only found to be nitrosylated in case of HCC were up regulated ATP synthase subunit beta (ATPB) and down regulated HBB. The decrease in expression of CYB5A in HCC suggests their possible role in disease progression. Further insight of the functional association of the identified proteins was obtained through KEGG/ REACTOME pathway analysis databases. String 8.3 interaction network shows strong interactions with proteins at high confidence score, which is helpful in characterization of functional abnormalities that may be a causative factor of liver pathology. Conclusion: These findings may have broader implications for understanding the mechanism of development of carcinoma. However, large scale studies will be required for further verification of their critical role in development and progression of HCC.

AB - Background: Complex molecular events lead to development and progression of liver cirrhosis to HCC. Differentially expressed nuclear membrane associated proteins are responsible for the functional and structural alteration during the progression from cirrhosis to carcinoma. Although alterations/ post translational modifications in protein expression have been extensively quantified, complementary analysis of nuclear membrane proteome changes have been limited. Deciphering the molecular mechanism that differentiate between normal and disease state may lead to identification of biomarkers for carcinoma. Results: Many proteins displayed differential expression when nuclear membrane proteome of hepatocellular carcinoma (HCC), fibrotic liver, and HepG2 cell line were assessed using 2-DE and ESI-Q-TOF MS/MS. From the down regulated set in HCC, we have identified for the first time a 15 KDa cytochrome b5A (CYB5A), ATP synthase subunit delta (ATPD) and Hemoglobin subunit beta (HBB) with 11, 5 and 22 peptide matches respectively. Furthermore, nitrosylation studies with S-nitrosocysteine followed by immunoblotting with anti SNO-cysteine demonstrated a novel and biologically relevant post translational modification of thiols of CYB5A in HCC specimens only. Immunofluorescence images demonstrated increased protein S-nitrosylation signals in the tumor cells and fibrotic region of HCC tissues. The two other nuclear membrane proteins which were only found to be nitrosylated in case of HCC were up regulated ATP synthase subunit beta (ATPB) and down regulated HBB. The decrease in expression of CYB5A in HCC suggests their possible role in disease progression. Further insight of the functional association of the identified proteins was obtained through KEGG/ REACTOME pathway analysis databases. String 8.3 interaction network shows strong interactions with proteins at high confidence score, which is helpful in characterization of functional abnormalities that may be a causative factor of liver pathology. Conclusion: These findings may have broader implications for understanding the mechanism of development of carcinoma. However, large scale studies will be required for further verification of their critical role in development and progression of HCC.

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KW - S-nitrosylation

KW - Two dimensional gel electrophoresis

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