Proteomic Characterization of Colorectal Cancer Tissue from Patients Identifies Novel Putative Protein Biomarkers

Colorectal cancer (CRC) is one of the leading causes of cancer-related death over the world. There is a great need for biomarkers capable of early detection and as targets for treatment. Differential protein expression was investigated with two-dimensional gel electrophoresis (2D-PAGE) followed by identification with liquid chromatography–tandem mass spectrometry (LC-MS/MS) in CRC patient tissue from (i) the peripheral part of the tumor, (ii) the central part of the tumor as well as from (iii) a non-involved part of the colorectal tissue. The expression patterns of six identified proteins were further evaluated by one-dimensional Western blot (1D-WB) analysis of the CRC tissue. Proteins that were perturbed in expression level in the peripheral or in the central part of the tumor as compared with the non-involved part included S100A11, HNRNPF, HNRNPH1 or HNRNPH2, GSTP1, PKM and FABP1. These identified markers may have future diagnostic potential or may be novel treatment targets after further evaluation in larger patient cohorts.

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Abstract A76: Characterization of CXC‐chemokine expression in colorectal cancer tissue and its role in mediating chemoresistance of colorectal cancer cells to conventional and molecularly targeted therapies

10.1158/1535-7163.targ-09-a76 ◽

2009 ◽

Author(s):

Olabode Oladipo ◽

Colin Purcell ◽

Susie Conlon ◽

Catherine Wilson ◽

Kelly Redmond ◽

...

Keyword(s):

Colorectal Cancer ◽

Cancer Cells ◽

Targeted Therapies ◽

Cancer Tissue ◽

Colorectal Cancer Tissue ◽

Chemokine Expression ◽

Colorectal Cancer Cells ◽

Cxc Chemokine

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Proteomic Characterization of Colorectal Cancer Cells versus Normal-Derived Colon Mucosa Cells: Approaching Identification of Novel Diagnostic Protein Biomarkers in Colorectal Cancer

International Journal of Molecular Sciences ◽

10.3390/ijms21103466 ◽

2020 ◽

Vol 21 (10) ◽

pp. 3466 ◽

Cited By ~ 1

Author(s):

Maja Ludvigsen ◽

Louise Thorlacius-Ussing ◽

Henrik Vorum ◽

Mary Pat Moyer ◽

Mogens Tornby Stender ◽

...

Keyword(s):

Colorectal Cancer ◽

Cell Line ◽

Polyacrylamide Gel Electrophoresis ◽

Primary Adenocarcinoma ◽

Cellular Model ◽

Colon Mucosa ◽

Cellular Models ◽

Proteomic Approach ◽

Diagnostic Potential

In the western world, colorectal cancer (CRC) is the third most common cause of cancer-related deaths. Survival is closely related to the stage of cancer at diagnosis striking the clinical need for biomarkers capable of early detection. To search for possible biological parameters for early diagnosis of CRC we evaluated protein expression for three CREC (acronym: Cab45, reticulocalbin, ERC-55, calumenin) proteins: reticulocalbin, calumenin, and ERC-55 in a cellular model consisting of a normal derived colon mucosa cell line, NCM460, and a primary adenocarcinoma cell line of the colon, SW480. Furthermore, this cellular model was analyzed by a top-down proteomic approach, 2-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and liquid chromatography–tandem mass spectrometry (LC–MS/MS) for novel putative diagnostic markers by identification of differentially expressed proteins between the two cell lines. A different colorectal carcinoma cell line, HCT 116, was used in a bottom-up proteomic approach with label-free quantification (LFQ) LC–MS/MS. The two cellular models gave sets of putative diagnostic CRC biomarkers. Various of these novel putative markers were verified with increased expression in CRC patient neoplastic tissue compared to the expression in a non-involved part of the colon, including reticulocalbin, calumenin, S100A6 and protein SET. Characterization of these novel identified biological features for CRC patients may have diagnostic potential and therapeutic relevance in this malignancy characterized by a still unmet clinical need.

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Identification of proteins from colorectal cancer tissue by two-dimensional gel electrophoresis and SELDI mass spectrometry

International Journal of Molecular Medicine ◽

10.3892/ijmm.16.1.11 ◽

2005 ◽

Cited By ~ 2

Author(s):

Christian Melle ◽

Dirk Osterloh ◽

Günther Ernst ◽

Bettina Schimmel ◽

Annett Bleul ◽

...

Keyword(s):

Colorectal Cancer ◽

Mass Spectrometry ◽

Gel Electrophoresis ◽

Cancer Tissue ◽

Two Dimensional ◽

Two Dimensional Gel Electrophoresis ◽

Colorectal Cancer Tissue

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Differential Expression of Mimecan and Thioredoxin Domain–Containing Protein 5 in Colorectal Adenoma and Cancer: A Proteomic Study

Experimental Biology and Medicine ◽

10.3181/0701-rm-8 ◽

2007 ◽

Vol 232 (9) ◽

pp. 1152-1159 ◽

Cited By ~ 57

Author(s):

Yinghong Wang ◽

Yu Ma ◽

Bingjian Lü ◽

Enping Xu ◽

Qiong Huang ◽

...

Keyword(s):

Colorectal Cancer ◽

Colorectal Adenoma ◽

Normal Mucosa ◽

Colorectal Adenomas ◽

Differentially Expressed ◽

Cancer Tissue ◽

Differentially Expressed Proteins ◽

Two Dimensional Gel Electrophoresis ◽

Proteomic Study ◽

Cancer Tissues

Adenoma is the major precursor lesion of colorectal cancer, one of the most common cancers worldwide. The elucidation of the molecular mechanism underlying adenoma is essential for early detection, prevention, and intervention of colorectal cancer. Using a combination of two-dimensional gel electrophoresis and mass spectrometry, we identified 27 differentially expressed proteins in adenoma, compared with matched normal mucosa and cancer tissue. Seventeen proteins were upregulated and six downregulated in adenoma when compared with the same proteins in individual-matched normal mucosa. Four were downregulated, but none upregulated in adenoma when compared with the same proteins in matched cancer tissue. Two novel proteins, mimecan and thioredoxin domain–containing protein 5 (TXNDC5), were further validated by Western blot in 8 colorectal adenomas and 19 cancers that were matched with normal mucosa. All adenoma and cancer tissues did not express mimecan, but all normal mucosa did ( P < 0.01). In contrast, TXNDC5 was significantly upregulated in colorectal adenoma and cancer tissues as compared with that in normal mucosa ( P < 0.05). This study clearly demonstrated that absence of mimecan and upregulation of TXNDC5 are involved in the early development of colorectal cancer. Thus, the differentially expressed proteins might serve as potential biomarkers for colorectal cancer detection and intervention.

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Downregulation of Calreticulin and Annexin A2 in Cholesteatoma by 2-DE Analysis

10.21203/rs.2.20413/v1 ◽

2020 ◽

Author(s):

Kuen-Yao Ho ◽

Kuo-Feng Hung ◽

Chen-Yu Chien ◽

Chee-Yin Chai ◽

Wan-Tzu Chen ◽

...

Keyword(s):

Western Blotting ◽

Expression Patterns ◽

Immunohistochemical Analysis ◽

Annexin A2 ◽

Differentially Expressed ◽

Skin Tissue ◽

Epithelial Proliferation ◽

Two Dimensional Gel Electrophoresis ◽

Liquid Chromatography Tandem Mass ◽

Specific Proteins

Abstract Background: Many factors are thought to be associated with the development of cholesteatoma, while the mechanisms of its formation remain unclear. This study aimed to identify the potential mechanisms of the proliferation and growth of cholesteatoma by analysis of the differential expressions of proteins in cholesteatoma and retroauricular skin tissue collected from patients. Methods: Comparative proteomics analyses using two-dimensional gel electrophoresis (2-DE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), in addition to immunohistochemical analysis, were conducted to identify differentially-expressed proteins in cholesteatoma tissue as compared with retroauricular skin tissue. Western blotting was also employed to verify the expression patterns of the specific proteins identified by 2-DE and to measure the changes in potential modulators related to cholesteatoma proliferation and growth. Results: Calreticulin (CRT) and annexin A2 (AnxA2) were identified as being differentially-expressed in cholesteatoma by 2-DE and LC-MS/MS, the results of which were in agreement with the results of immunohistochemical analysis and western blotting. Downregulation of CRT and AnxA2 were observed in cholesteatoma. Conclusion: Our data suggested that CRT and AnxA2 were associated with cholesteatoma. We speculated that the reduced expression of CRT and the persistent inflammatory response play important roles in the epithelial proliferation of cholesteatoma.

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Comparison of Proteomic Technologies for Blood-Based Detection of Colorectal Cancer

International Journal of Molecular Sciences ◽

10.3390/ijms22031189 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1189

Author(s):

Megha Bhardwaj ◽

Tobias Terzer ◽

Petra Schrotz-King ◽

Hermann Brenner

Keyword(s):

Colorectal Cancer ◽

Multiple Reaction Monitoring ◽

Area Under The Curve ◽

Superior Performance ◽

Blood Protein ◽

Protein Biomarkers ◽

Serum Samples ◽

Functional Protein ◽

Novel Technologies ◽

Diagnostic Potential

Blood-based protein biomarkers are increasingly being explored as supplementary or efficient alternatives for population-based screening of colorectal cancer (CRC). The objective of the current study was to compare the diagnostic potential of proteins measured with different proteomic technologies. The concentrations of protein biomarkers were measured using proximity extension assays (PEAs), liquid chromatography/multiple reaction monitoring–mass spectrometry (LC/MRM-MS) and quantibody microarrays (QMAs) in plasma samples of 56 CRC patients and 99 participants free of neoplasms. In another approach, proteins were measured in serum samples of 30 CRC cases and 30 participants free of neoplasm using immunome full-length functional protein arrays (IpAs). From all the measurements, 9, 6, 35 and 14 protein biomarkers overlapped for comparative evaluation of (a) PEA and LC/MRM-MS, (b) PEA and QMA, (c) PEA and IpA, and (d) LC/MRM-MS and IpA measurements, respectively. Correlation analysis was performed, along with calculation of the area under the curve (AUC) for assessing the diagnostic potential of each biomarker. DeLong’s test was performed to assess the differences in AUC. Evaluation of the nine biomarkers measured with PEA and LC/MRM-MS displayed correlation coefficients >+0.6, similar AUCs and DeLong’s p-values indicating no differences in AUCs for biomarkers like insulin-like growth factor binding protein 2 (IGFBP2), matrix metalloproteinase 9 (MMP9) and serum paraoxonase lactonase 3 (PON3). Comparing six proteins measured with PEA and QMA showed good correlation and similar diagnostic performance for only one protein, growth differentiation factor 15 (GDF15). The comparison of 35 proteins measured with IpA and PEA and 14 proteins analyzed with IpA and LC/MRM-MS revealed poor concordance and comparatively better AUCs when measured with PEA and LC/MRM-MS. The comparison of different proteomic technologies suggests the superior performance of novel technologies like PEA and LC/MRM-MS over the assessed array-based technologies in blood-protein-based early detection of CRC.

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miRNA Clusters with Up-Regulated Expression in Colorectal Cancer

Cancers ◽

10.3390/cancers13122979 ◽

2021 ◽

Vol 13 (12) ◽

pp. 2979

Author(s):

Paulína Pidíková ◽

Iveta Herichová

Keyword(s):

Colorectal Cancer ◽

Target Genes ◽

Expression Patterns ◽

Clinicopathological Characteristics ◽

Cancer Tissue ◽

Poor Patient ◽

Regulated Expression ◽

Mirna Clusters ◽

Non Coding Rnas ◽

Poor Patient Survival

Colorectal cancer (CRC) is one of the most common malignancies in Europe and North America. Early diagnosis is a key feature of efficient CRC treatment. As miRNAs can be used as CRC biomarkers, the aim of the present study was to analyse experimentally validated data on frequently up-regulated miRNA clusters in CRC tissue and investigate their members with respect to clinicopathological characteristics of patients. Based on available data, 15 up-regulated clusters, miR-106a/363, miR-106b/93/25, miR-17/92a-1, miR-181a-1/181b-1, miR-181a-2/181b-2, miR-181c/181d, miR-183/96/182, miR-191/425, miR-200c/141, miR-203a/203b, miR-222/221, mir-23a/27a/24-2, mir-29b-1/29a, mir-301b/130b and mir-452/224, were selected. The positions of such clusters in the genome can be intronic or intergenic. Most clusters are regulated by several transcription factors, and miRNAs are also sponged by specific long non-coding RNAs. In some cases, co-expression of miRNA with other cluster members or host gene has been proven. miRNA expression patterns in cancer tissue, blood and faeces were compared. Based on experimental evidence, 181 target genes of selected clusters were identified. Panther analysis was used to reveal the functions of the target genes and their corresponding pathways. Clusters miR-17/92a-1, miR-106a/363, miR-106b/93/25 and miR-183/96/182 showed the strongest association with metastasis occurrence and poor patient survival, implicating them as the most promising targets of translational research.

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Rearrangements of Blood and Tissue Fatty Acid Profile in Colorectal Cancer - Molecular Mechanism and Diagnostic Potential

Frontiers in Oncology ◽

10.3389/fonc.2021.689701 ◽

2021 ◽

Vol 11 ◽

Author(s):

Adriana Mika ◽

Katarzyna Duzowska ◽

Lukasz P. Halinski ◽

Alicja Pakiet ◽

Aleksandra Czumaj ◽

...

Keyword(s):

Colorectal Cancer ◽

Fatty Acid ◽

Healthy Subjects ◽

Roc Analysis ◽

Normal Mucosa ◽

Cancer Tissue ◽

Normal Colon Mucosa ◽

Non Invasive ◽

Diagnostic Potential ◽

Ht 29

Colorectal cancer (CRC) is often diagnosed at an advanced stage due to the invasiveness of colonoscopy; thus, non-invasive CRC diagnostics are desirable. CRC is associated with lipid alterations. We aimed to verify whether fatty acid (FA) profiles in CRC patients may serve as a potential diagnostic tool for CRC diagnosis. FA profiles were assayed by GC-MS in cancer tissue, paired normal mucosa and serum from CRC patients and healthy controls. The levels of very long FAs – VLCFAs (26:0, 28:0 and 26:1) were the most highly increased FAs in cancer tissue compared to normal colon mucosa. Moreover, these FA were present in serum of CRC patients, they were absent in the serum of healthy subjects, or present in only trace amounts. To verify if cancer cells are the source of small amounts of these VLCFAs in the serum of patients we performed experiment in HT-29 CRC cells, which proved that CRC cells can produce and release VLCFAs into the blood. Most importantly, we defined a panel of FAs that may be assayed in a single analysis that definitely distinguishes CRC patients and healthy subjects, which was confirmed by PLS-DA and multivariate ROC analysis (AUC = 0.985). This study shows that selected FA panel may serve as a diagnostic marker for CRC.

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