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For: Ye Y, Huang A, Huang C, Liu J, Wang B, Lin K, Chen Q, Zeng Y, Chen H, Tao X, Wei G, Wu Y. Comparative mitochondrial proteomic analysis of hepatocellular carcinoma from patients. Proteomics Clin Appl 2013;7:403-415. [PMID: 23589362 DOI: 10.1002/prca.201100103] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 10/22/2012] [Accepted: 11/06/2012] [Indexed: 01/22/2023]

For:	Ye Y, Huang A, Huang C, Liu J, Wang B, Lin K, Chen Q, Zeng Y, Chen H, Tao X, Wei G, Wu Y. Comparative mitochondrial proteomic analysis of hepatocellular carcinoma from patients. Proteomics Clin Appl 2013;7:403-415. [PMID: 23589362 DOI: 10.1002/prca.201100103] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 10/22/2012] [Accepted: 11/06/2012] [Indexed: 01/22/2023]

Number

Cited by Other Article(s)

Lin G, Gao Z, Wu S, Zheng J, Guo X, Zheng X, Chen R. scRNA-seq revealed high stemness epithelial malignant cell clusters and prognostic models of lung adenocarcinoma. Sci Rep 2024;14:3709. [PMID: 38355636 PMCID: PMC10867035 DOI: 10.1038/s41598-024-54135-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/08/2024] [Indexed: 02/16/2024] Open

Abstract

Lung adenocarcinoma (LUAD) is one of the sole causes of death in lung cancer patients. This study combined with single-cell RNA-seq analysis to identify tumor stem-related prognostic models to predict the prognosis of lung adenocarcinoma, chemotherapy agents, and immunotherapy efficacy. mRNA expression-based stemness index (mRNAsi) was determined by One Class Linear Regression (OCLR). Differentially expressed genes (DEGs) were detected by limma package. Single-cell RNA-seq analysis in GSE123902 dataset was performed using Seurat package. Weighted Co-Expression Network Analysis (WGCNA) was built by rms package. Cell differentiation ability was determined by CytoTRACE. Cell communication analysis was performed by CellCall and CellChat package. Prognosis model was constructed by 10 machine learning and 101 combinations. Drug predictive analysis was conducted by pRRophetic package. Immune microenvironment landscape was determined by ESTIMATE, MCP-Counter, ssGSEA analysis. Tumor samples have higher mRNAsi, and the high mRNAsi group presents a worse prognosis. Turquoise module was highly correlated with mRNAsi in TCGA-LUAD dataset. scRNA analysis showed that 22 epithelial cell clusters were obtained, and higher CSCs malignant epithelial cells have more complex cellular communication with other cells and presented dedifferentiation phenomenon. Cellular senescence and Hippo signaling pathway are the major difference pathways between high- and low CSCs malignant epithelial cells. The pseudo-temporal analysis shows that cluster1, 2, high CSC epithelial cells, are concentrated at the end of the differentiation trajectory. Finally, 13 genes were obtained by intersecting genes in turquoise module, Top200 genes in hdWGCNA, DEGs in high- and low- mRNAsi group as well as DEGs in tumor samples vs. normal group. Among 101 prognostic models, average c-index (0.71) was highest in CoxBoost + RSF model. The high-risk group samples had immunosuppressive status, higher tumor malignancy and low benefit from immunotherapy. This work found that malignant tumors and malignant epithelial cells have high CSC characteristics, and identified a model that could predict the prognosis, immune microenvironment, and immunotherapy of LUAD, based on CSC-related genes. These results provided reference value for the clinical diagnosis and treatment of LUAD.

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Proteomic Analysis of Prostate Cancer FFPE Samples Reveals Markers of Disease Progression and Aggressiveness. Cancers (Basel) 2022;14:cancers14153765. [PMID: 35954429 PMCID: PMC9367334 DOI: 10.3390/cancers14153765] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 01/27/2023] Open

Abstract

Simple Summary

Prostate cancer (PCa) is the second most frequently diagnosed type of cancer in men. The lack of tools for accurate risk assessment is causing over-treatment of men with indolent PCa but also delayed detection of metastatic disease and thus high mortality. The aim of our study was to identify proteins related to the progression and aggressiveness of PCa that could serve as potential biomarkers for better risk stratification. To this end, we performed proteomic analysis of Formalin Fixed Paraffin Embedded (FFPE) prostate tissue specimens (n = 86) and compared them based on grade groups and biochemical recurrence status. Based on the valuable data generated by these comparisons, we have selected seven proteins (NMP1, UQCRH, HSPA9, MRPL3, VCAN, SERBP1, HSPE1) as common denominators of PCa aggressiveness and persistence that could potentially be used for the development of risk assessment tools. Notably, our observations are largely validated by transcriptomics data and literature.

Abstract

Prostate cancer (PCa) is the second most common cancer in men. Diagnosis and risk assessment are widely based on serum Prostate Specific Antigen (PSA) and biopsy, which might not represent the exact degree of PCa risk. Towards the discovery of biomarkers for better patient stratification, we performed proteomic analysis of Formalin Fixed Paraffin Embedded (FFPE) prostate tissue specimens using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Comparative analysis of 86 PCa samples among grade groups 1–5 identified 301 significantly altered proteins. Additional analysis based on biochemical recurrence (BCR; BCR+ n = 14, BCR- n = 51) revealed 197 significantly altered proteins that indicate disease persistence. Filtering the overlapping proteins of these analyses, seven proteins (NPM1, UQCRH, HSPA9, MRPL3, VCAN, SERBP1, HSPE1) had increased expression in advanced grades and in BCR+/BCR- and may play a critical role in PCa aggressiveness. Notably, all seven proteins were significantly associated with progression in Prostate Cancer Transcriptome Atles (PCTA) and NPM1NPM1, UQCRH, and VCAN were further validated in The Cancer Genome Atlas (TCGA), where they were upregulated in BCR+/BCR-. UQCRH levels were also associated with poorer 5-year survival. Our study provides valuable insights into the key regulators of PCa progression and aggressiveness. The seven selected proteins could be used for the development of risk assessment tools.

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Huang J, Xie ZF. Identification of SSBP1 as a prognostic marker in human lung adenocarcinoma using bioinformatics approaches. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022;19:3022-3035. [PMID: 35240818 DOI: 10.3934/mbe.2022139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]

Lennartz M, Gehrig E, Weidemann S, Gorbokon N, Menz A, Büscheck F, Hube-Magg C, Hinsch A, Reiswich V, Höflmayer D, Fraune C, Jacobsen F, Bernreuther C, Lebok P, Sauter G, Wilczak W, Steurer S, Burandt E, Marx AH, Simon R, Krech T, Clauditz TS, Minner S, Dum D, Uhlig R. Large-Scale Tissue Microarray Evaluation Corroborates High Specificity of High-Level Arginase-1 Immunostaining for Hepatocellular Carcinoma. Diagnostics (Basel) 2021;11:diagnostics11122351. [PMID: 34943588 PMCID: PMC8699869 DOI: 10.3390/diagnostics11122351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/01/2021] [Accepted: 12/09/2021] [Indexed: 12/19/2022] Open

Affiliation(s)

Maximilian Lennartz Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Eva Gehrig Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Sören Weidemann Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Natalia Gorbokon Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Anne Menz Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Franziska Büscheck Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Claudia Hube-Magg Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Andrea Hinsch Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Viktor Reiswich Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Doris Höflmayer Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Christoph Fraune Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Frank Jacobsen Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Christian Bernreuther Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Patrick Lebok Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Guido Sauter Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Waldemar Wilczak Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Stefan Steurer Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Eike Burandt Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Andreas H. Marx Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.) Department of Pathology, Academic Hospital Fuerth, 90766 Fuerth, Germany
Ronald Simon Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.) Correspondence: ; Tel.: +49-40-74105-7214
Till Krech Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.) Institute of Pathology, Clinical Center Osnabrueck, 49076 Osnabrueck, Germany
Till S. Clauditz Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Sarah Minner Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
David Dum Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
Ria Uhlig Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)

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Antitumoral and Anti-inflammatory Roles of Somatostatin and Its Analogs in Hepatocellular Carcinoma. Anal Cell Pathol (Amst) 2021;2021:1840069. [PMID: 34873567 PMCID: PMC8643256 DOI: 10.1155/2021/1840069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/12/2021] [Indexed: 11/22/2022] Open

Zheng H, Liu J, Yu J, McAlinden A. Expression profiling of mitochondria-associated microRNAs during osteogenic differentiation of human MSCs. Bone 2021;151:116058. [PMID: 34144232 PMCID: PMC8944210 DOI: 10.1016/j.bone.2021.116058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/28/2021] [Accepted: 06/08/2021] [Indexed: 12/31/2022]

Abstract

Small non-coding microRNAs (miRNAs) have the ability to target and bind to many mRNAs within the cytosol resulting in reduced protein expression and modulation of a number of cellular pathways and networks. In addition to the cytosol, miRNAs have been identified in other cellular compartments and organelles, including the mitochondria. While a few mitochondria-associated miRNAs (mitomiRs) are predicted to be derived from the mitochondrial genome, the majority appear to be transcribed from nuclear DNA and somehow transported into the mitochondria. These findings raise interesting questions about why miRNAs are located in the mitochondria and if they play a role in regulating processes within these organelles. Previously published work from our laboratory showed that miR-181a/b can regulate osteogenesis, in part, by enhancing mitochondrial metabolism. In other published studies, miR-181 paralogs and many other miRNAs have been identified in mitochondrial extracts derived from common cell lines and specific primary cells and tissues. Taken together, we were motivated to identify mitomiR expression profiles during in vitro osteogenesis. Specifically, we obtained RNA from purified mitochondrial extracts of human bone marrow-derived mesenchymal stem/stromal cells (MSCs) and from whole cell extracts of MSCs at day 0 or following osteogenic induction for 3, 7 and 14 days. Utilizing Affymetrix GeneChip™ miRNA 4.0 arrays, mitomiR expression signatures were determined at each time point. Based on the Affymetrix detection above background algorithm, the total number of miRNAs detected in MSC mitochondria extracts was 527 (non-induced MSCs), 627 (day 3 induced), 372 (day 7 induced) and 498 (day 14 induced). In addition, we identified significantly differentially-expressed mitomiRs at day 7 and day 14 of osteogenic induction when compared to day 0 (fold change ≥1.5; adjusted p value <0.05). In general, the most pronounced and highly significant changes in mitomiR expression during osteogenesis were observed at the day 7 time point. Interestingly, most miRNAs found to be differentially-expressed in mitochondria extracts did not show significantly altered expression in whole cell extracts at the same time points during osteoblast differentiation. This array study provides novel information on miRNAs associated with the mitochondria in MSCs during differentiation toward the osteoblast phenotype. These findings will guide future research to identify new miRNA candidates that may function in regulating mitochondrial function and/or bone formation, homeostasis or repair.

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Santos EC, Gomes RB, Fernandes PV, Ferreira MA, Abdelhay ESFW. The protein-protein interaction network of intestinal gastric cancer patients reveals hub proteins with potential prognostic value. Cancer Biomark 2021;33:83-96. [PMID: 34366321 DOI: 10.3233/cbm-203225] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]

Abstract

BACKGROUND

Gastric cancer (GC) is the third leading cause of cancer worldwide. According to the Lauren classification, gastric adenocarcinoma is divided into two subtypes: diffuse and intestinal. The development of intestinal gastric cancer (IGC) can take years and involves multiple factors.

OBJECTIVE

To investigate the protein profile of tumor samples from patients with IGC in comparison with adjacent nontumor tissue samples.

METHODS

We used label-free nano-LC-MS/MS to identify proteins from the tissues samples. The results were analyzed using MetaCore™ software to access functional enrichment information. Protein-protein interactions (PPI) were predicted using STRING analysis. Hub proteins were determined using the Cytoscape plugin, CytoHubba. Survival analysis was performed using KM plotter. We identified 429 differentially expressed proteins whose pathways and processes were related to protein folding, apoptosis, and immune response.

RESULTS

The PPI network of these proteins showed enrichment modules related to the regulation of cell death, immune system, neutrophil degranulation, metabolism of RNA and chromatin DNA binding. From the PPI network, we identified 20 differentially expressed hub proteins, and assessed the prognostic value of the expression of genes that encode them. Among them, the expression of four hub genes was significantly associated with the overall survival of IGC patients.

CONCLUSIONS

This study reveals important findings that affect IGC development based on specific biological alterations in IGC patients. Bioinformatics analysis showed that the pathogenesis of IGC patients is complex and involves different interconnected biological processes. These findings may be useful in research on new targets to develop novel therapies to improve the overall survival of patients with IGC.

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Tang Y, Yang Y, Luo J, Liu S, Zhan Y, Zang H, Zheng H, Zhang Y, Feng J, Fan S, Wen Q. Overexpression of HSP10 correlates with HSP60 and Mcl-1 levels and predicts poor prognosis in non-small cell lung cancer patients. Cancer Biomark 2021;30:85-94. [PMID: 32986659 PMCID: PMC7990427 DOI: 10.3233/cbm-200410] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]

Gao H, Shi X, Chen Q, Che B, Yin H, Li Y. Deep proteome profiling of SW837 cells treated by photodynamic therapy (PDT) reveals the underlying mechanisms of metronomic and acute PDTs. Photodiagnosis Photodyn Ther 2020;31:101809. [PMID: 32437970 DOI: 10.1016/j.pdpdt.2020.101809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 11/17/2022]

Shin H, Cha HJ, Lee MJ, Na K, Park D, Kim CY, Han DH, Kim H, Paik YK. Identification of ALDH6A1 as a Potential Molecular Signature in Hepatocellular Carcinoma via Quantitative Profiling of the Mitochondrial Proteome. J Proteome Res 2020;19:1684-1695. [PMID: 31985234 DOI: 10.1021/acs.jproteome.9b00846] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]

Abstract

Various liver diseases, including hepatocellular carcinoma (HCC), have been linked to mitochondrial dysfunction, reduction of reactive oxygen species (ROS), and elevation of nitric oxide (NO). In this study, we subjected the human liver mitochondrial proteome to extensive quantitative proteomic profiling analysis and molecular characterization to identify potential signatures indicative of cancer cell growth and progression. Sequential proteomic analysis identified 2452 mitochondrial proteins, of which 1464 and 2010 were classified as nontumor and tumor (HCC) mitochondrial proteins, respectively, with 1022 overlaps. Further metabolic mapping of the HCC mitochondrial proteins narrowed our biological characterization to four proteins, namely, ALDH4A1, LRPPRC, ATP5C1, and ALDH6A1. The latter protein, a mitochondrial methylmalonate semialdehyde dehydrogenase (ALDH6A1), was most strongly suppressed in HCC tumor regions (∼10-fold decrease) in contrast to LRPPRC (∼6-fold increase) and was predicted to be present in plasma. Accordingly, we selected ALDH6A1 for functional analysis and engineered Hep3B cells to overexpress this protein, called ALDH6A1-O/E cells. Since ALDH6A1 is predicted to be involved in mitochondrial respiration, we assessed changes in the levels of NO and ROS in the overexpressed cell lines. Surprisingly, in ALDH6A1-O/E cells, NO was decreased nearly 50% but ROS was increased at a similar level, while the former was restored by treatment with S-nitroso-N-acetyl-penicillamine. The lactate levels were also decreased relative to control cells. Propidium iodide and Rhodamine-123 staining suggested that the decrease in NO and increase in ROS in ALDH6A1-O/E cells could be caused by depolarization of the mitochondrial membrane potential (ΔΨ). Taken together, our results suggest that hepatic neoplastic transformation appears to suppress the expression of ALDH6A1, which is accompanied by a respective increase and decrease in NO and ROS in cancer cells. Given the close link between ALDH6A1 suppression and abnormal cancer cell growth, this protein may serve as a potential molecular signature or biomarker of hepatocarcinogenesis and treatment responses.

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Yang Y, Pan C, Yu L, Ruan H, Chang L, Yang J, Zheng Z, Zheng F, Liu T. SSBP1 Upregulation In Colorectal Cancer Regulates Mitochondrial Mass. Cancer Manag Res 2019;11:10093-10106. [PMID: 31819642 PMCID: PMC6896925 DOI: 10.2147/cmar.s211292] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 09/28/2019] [Indexed: 12/27/2022] Open

Wang S, Li M, Xing L, Yu J. High expression level of peptidylprolyl isomerase A is correlated with poor prognosis of liver hepatocellular carcinoma. Oncol Lett 2019;18:4691-4702. [PMID: 31611978 PMCID: PMC6781733 DOI: 10.3892/ol.2019.10846] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/20/2019] [Indexed: 12/19/2022] Open

Liu Z, Xu S, Li L, Zhong X, Chen C, Fan Y, Shen W, Zu L, Xue F, Wang M, Zhou Q. Comparative mitochondrial proteomic analysis of human large cell lung cancer cell lines with different metastasis potential. Thorac Cancer 2019;10:1111-1128. [PMID: 30950202 PMCID: PMC6501018 DOI: 10.1111/1759-7714.13052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/03/2019] [Indexed: 02/05/2023] Open

Wang G, Wang Q, Huang Q, Chen Y, Sun X, He L, Zhan L, Guo X, Yin C, Fang Y, He X, Xing J. Upregulation of mtSSB by interleukin-6 promotes cell growth through mitochondrial biogenesis-mediated telomerase activation in colorectal cancer. Int J Cancer 2018;144:2516-2528. [PMID: 30415472 DOI: 10.1002/ijc.31978] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/08/2018] [Accepted: 10/30/2018] [Indexed: 12/17/2022]

Abstract

It is now widely accepted that mitochondrial biogenesis is inhibited in most cancer cells. Interestingly, one of the possible exceptions is colorectal cancer (CRC), in which the content of mitochondria has been found to be higher than in normal colon mucosa. However, to date, the causes and effects of this phenomenon are still unclear. In the present study, we systematically investigated the functional role of mitochondrial single-strand DNA binding protein (mtSSB), a key molecule in the regulation of mitochondrial DNA (mtDNA) replication, in the mitochondrial biogenesis and CRC cell growth. Our results demonstrated that mtSSB was frequently upregulated in CRC tissues and that upregulated mtSSB was associated with poor prognosis in CRC patients. Furthermore, overexpression of mtSSB promoted CRC cell growth in vitro by regulating cell proliferation. The in vivo assay confirmed these results, indicating that the forced expression of mtSSB significantly increases the growth capacity of xenograft tumors. Mechanistically, the survival advantage conferred by mtSSB was primarily caused by increased mitochondrial biogenesis and subsequent ROS production, which induced telomerase reverse transcriptase (TERT) expression and telomere elongation via Akt/mTOR pathway in CRC cells. In addition, FOXP1, a member of the forkhead box family, was identified as a new transcription factor for mtSSB. Moreover, our results also demonstrate that proinflammatory IL-6/STAT3 signaling facilitates mtSSB expression and CRC cell proliferation via inducing FOXP1 expression. Collectively, our findings demonstrate that mtSSB induced by inflammation plays a critical role in the regulation of mitochondrial biogenesis, telomerase activation, and subsequent CRC proliferation, providing a strong evidence for mtSSB as drug target in CRC treatment.

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Affiliation(s)

Gang Wang State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an, China.,Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
Qian Wang State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an, China.,Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
Qichao Huang State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an, China
Yibing Chen State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an, China.,Center of Genetic & Prenatal Diagnosis, First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
Xiacheng Sun State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an, China
Linjie He State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an, China
Lei Zhan Department of Gastroenterology, Second Affiliated Hospital, Harbin Medical University, Harbin, China
Xu Guo State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an, China
Chun Yin State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an, China
Yujiang Fang Department of Microbiology, Immunology & Pathology, Des Moines University, Des Moines, IA
Xianli He Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
Jinliang Xing State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an, China

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Ahmad F, Alamoudi W, Haque S, Salahuddin M, Alsamman K. Simple, reliable, and time-efficient colorimetric method for the assessment of mitochondrial function and toxicity. Bosn J Basic Med Sci 2018;18:367-374. [PMID: 29984676 DOI: 10.17305/bjbms.2018.3323] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 01/10/2023] Open

Eremina L, Pashintseva N, Kovalev L, Kovaleva M, Shishkin S. Proteomics of mammalian mitochondria in health and malignancy: From protein identification to function. Anal Biochem 2018;552:4-18. [DOI: 10.1016/j.ab.2017.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 03/07/2017] [Accepted: 03/23/2017] [Indexed: 12/28/2022]

Li D, Gao D, Qi J, Chai R, Zhan Y, Xing C. Conjugated Polymer/Graphene Oxide Complexes for Photothermal Activation of DNA Unzipping and Binding to Protein. ACS APPLIED BIO MATERIALS 2018. [DOI: 10.1021/acsabm.8b00047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]

Fan W, Fan SS, Feng J, Xiao D, Fan S, Luo J. Elevated expression of HSP10 protein inhibits apoptosis and associates with poor prognosis of astrocytoma. PLoS One 2017;12:e0185563. [PMID: 29028811 PMCID: PMC5640213 DOI: 10.1371/journal.pone.0185563] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/14/2017] [Indexed: 11/18/2022] Open

Abstract

Astrocytoma is the most common type of primary malignant brain tumor, with pretty lowly 5-year survival rate in patients. Although extended surgical removal of the tumor and postoperative chemotherapy/radiotherapy executed, still there is large recurrence rate, mainly because diffuse glioma tumor cells ubiquitously infiltrate into normal parenchyma. So it becomes a priority to hunt novel molecular and signaling pathway targets to suppress astrocyma progression. HSP10, an important member of Heat shock proteins (Hsps) family, classically works as molecular chaperone folding or degradating of target proteins. Evolutionarily, HSP10 is also reported to be involved in immunomodulation and tumor progression. Poly (ADP-ribose) polymerase (PARP), important in DNA repair, is one of the main cleavage targets of caspase. And cleaved PARP (c-PARP) can serve as a marker of cells undergoing apoptosis. So far, whether the expression of HSP10 or c-PARP is associated with clinicopathologic implication for astrocytoma has not been reported. Meanwhile, it is unclear about the relationship between HSP10 and cell apoptosis. The purpose of this research is to elucidate the association between the expression of HSP10 and c-PARP and clinicopathological characteristics of astrocytoma by immunohistochemistry. The results showed that positive percentage of high HSP10 expression in astrocytoma 42/103, 40.8%) was significantly higher than that in the non-tumor control brain tissues (8/43, 18.6%) (P = 0.01). While no apparent difference of high c-PARP expression existed between astrocytoma and non-tumor control brain tissues. Furthermore, elevated expression of HSP10 was negative related to low expression of c-PARP (r = -0.224, P = 0.023), indicating high expression of HSP10 in astrocytoma inhibited apoptosis process effectively. And overexpression of HSP10 was proved to be the independent poor prognostic factor for astrocytoma by multivariate analysis. Taken together, our results suggest that elevated expression of HSP10 protein inhibits apoptosis and associates with poor prognosis of astrocytoma.

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Zhao X, He R, Liu Y, Wu Y, Kang L. UPregulated single-stranded DNA-binding protein 1 induces cell chemoresistance to cisplatin in lung cancer cell lines. Mol Cell Biochem 2017;431:21-27. [PMID: 28210897 DOI: 10.1007/s11010-017-2970-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/02/2017] [Indexed: 12/17/2022]

An innovative strategy to clone positive modifier genes of defects caused by mtDNA mutations: MRPS18C as suppressor gene of m.3946G>A mutation in MT-ND1 gene. Hum Genet 2017;136:885-896. [PMID: 28526948 DOI: 10.1007/s00439-017-1812-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/13/2017] [Indexed: 12/31/2022]

Di Venere M, Viglio S, Sassera D, Fumagalli M, Bardoni A, Salvini R, Cagnone M, Iadarola P. Do the complementarities of electrokinetic and chromatographic procedures represent the "Swiss knife" in proteomic investigation? An overview of the literature in the past decade. Electrophoresis 2017;38:1538-1550. [PMID: 28130906 DOI: 10.1002/elps.201600504] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/11/2017] [Accepted: 01/11/2017] [Indexed: 12/21/2022]

Chu S, Wen Q, Qing Z, Luo J, Wang W, Chen L, Feng J, Xu L, Zang H, Fan S. High expression of heat shock protein 10 correlates negatively with estrogen/progesterone receptor status and predicts poor prognosis in invasive ductal breast carcinoma. Hum Pathol 2016;61:173-180. [PMID: 27993580 DOI: 10.1016/j.humpath.2016.09.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/17/2016] [Accepted: 09/22/2016] [Indexed: 11/25/2022]

Cheng S, Luo M, Ding C, Peng C, Lv Z, Tong R, Xiao H, Xie H, Zhou L, Wu J, Zheng S. Downregulation of Peptidylprolyl isomerase A promotes cell death and enhances doxorubicin-induced apoptosis in hepatocellular carcinoma. Gene 2016;591:236-244. [PMID: 27397650 DOI: 10.1016/j.gene.2016.07.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 07/04/2016] [Accepted: 07/06/2016] [Indexed: 02/05/2023]

Affiliation(s)

Shaobing Cheng Department of Hepatobiliary Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
Mengchao Luo Department of Hepatobiliary Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
Chaofeng Ding Department of Hepatobiliary Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
Chuanhui Peng Department of Hepatobiliary Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
Zhen Lv Department of Hepatobiliary Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
Rongliang Tong Department of Hepatobiliary Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
Heng Xiao Department of Hepatobiliary Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
Haiyang Xie Department of Hepatobiliary Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
Lin Zhou Department of Hepatobiliary Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
Jian Wu Department of Hepatobiliary Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
Shusen Zheng Department of Hepatobiliary Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China.

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Panis C. Unraveling Oxidation-Induced Modifications in Proteins by Proteomics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014;94:19-38. [DOI: 10.1016/b978-0-12-800168-4.00002-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]