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Quintanilha JCF, Sibley AB, Liu Y, Niedzwiecki D, Halabi S, Rogers L, O'Neil B, Kindler H, Kelly W, Venook A, McLeod HL, Ratain MJ, Nixon AB, Innocenti F, Owzar K. Common variation in a long non-coding RNA gene modulates variation of circulating TGF-β2 levels in metastatic colorectal cancer patients (Alliance). BMC Genomics 2024; 25:473. [PMID: 38745123 PMCID: PMC11092225 DOI: 10.1186/s12864-024-10354-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/25/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Herein, we report results from a genome-wide study conducted to identify protein quantitative trait loci (pQTL) for circulating angiogenic and inflammatory protein markers in patients with metastatic colorectal cancer (mCRC). The study was conducted using genotype, protein marker, and baseline clinical and demographic data from CALGB/SWOG 80405 (Alliance), a randomized phase III study designed to assess outcomes of adding VEGF or EGFR inhibitors to systemic chemotherapy in mCRC patients. Germline DNA derived from blood was genotyped on whole-genome array platforms. The abundance of protein markers was quantified using a multiplex enzyme-linked immunosorbent assay from plasma derived from peripheral venous blood collected at baseline. A robust rank-based method was used to assess the statistical significance of each variant and protein pair against a strict genome-wide level. A given pQTL was tested for validation in two external datasets of prostate (CALGB 90401) and pancreatic cancer (CALGB 80303) patients. Bioinformatics analyses were conducted to further establish biological bases for these findings. RESULTS The final analysis was carried out based on data from 540,021 common typed genetic variants and 23 protein markers from 869 genetically estimated European patients with mCRC. Correcting for multiple testing, the analysis discovered a novel cis-pQTL in LINC02869, a long non-coding RNA gene, for circulating TGF-β2 levels (rs11118119; AAF = 0.11; P-value < 1.4e-14). This finding was validated in a cohort of 538 prostate cancer patients from CALGB 90401 (AAF = 0.10, P-value < 3.3e-25). The analysis also validated a cis-pQTL we had previously reported for VEGF-A in advanced pancreatic cancer, and additionally identified trans-pQTLs for VEGF-R3, and cis-pQTLs for CD73. CONCLUSIONS This study has provided evidence of a novel cis germline genetic variant that regulates circulating TGF-β2 levels in plasma of patients with advanced mCRC and prostate cancer. Moreover, the validation of previously identified pQTLs for VEGF-A, CD73, and VEGF-R3, potentiates the validity of these associations.
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Affiliation(s)
- Julia C F Quintanilha
- UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Yingmiao Liu
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Donna Niedzwiecki
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
- Alliance Statistics and Data Management Center, Duke University, Durham, NC, USA
| | - Susan Halabi
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
- Alliance Statistics and Data Management Center, Duke University, Durham, NC, USA
| | - Layne Rogers
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Bert O'Neil
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
| | - Hedy Kindler
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - William Kelly
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Alan Venook
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Howard L McLeod
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Utah Tech University, St George, UT, USA
| | - Mark J Ratain
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Andrew B Nixon
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Federico Innocenti
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kouros Owzar
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA.
- Alliance Statistics and Data Management Center, Duke University, Durham, NC, USA.
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Quintanilha JC, Sibley AB, Liu Y, Niedzwiecki D, Halabi S, Rogers L, O’Neil B, Kindler H, Kelly W, Venook A, McLeod HL, Ratain MJ, Nixon AB, Innocenti F, Owzar K. Common variation in a long non-coding RNA gene modulates variation of circulating TGF- β2 levels in metastatic colorectal cancer patients (Alliance). MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.04.23298815. [PMID: 38106038 PMCID: PMC10723514 DOI: 10.1101/2023.12.04.23298815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Background Herein, we report results from a genome-wide study conducted to identify protein quantitative trait loci (pQTL) for circulating angiogenic and inflammatory protein markers in patients with metastatic colorectal cancer (mCRC).The study was conducted using genotype, protein marker, and baseline clinical and demographic data from CALGB/SWOG 80405 (Alliance), a randomized phase III study designed to assess outcomes of adding VEGF or EGFR inhibitors to systemic chemotherapy in mCRC patients. Germline DNA derived from blood was genotyped on whole-genome array platforms. The abundance of protein markers was quantified using a multiplex enzyme-linked immunosorbent assay from plasma derived from peripheral venous blood collected at baseline. A robust rank-based method was used to assess the statistical significance of each variant and protein pair against a strict genome-wide level. A given pQTL was tested for validation in two external datasets of prostate (CALGB 90401) and pancreatic cancer (CALGB 80303) patients. Bioinformatics analyses were conducted to further establish biological bases for these findings. Results The final analysis was carried out based on data from 540,021 common typed genetic variants and 23 protein markers from 869 genetically estimated European patients with mCRC. Correcting for multiple testing, the analysis discovered a novel cis-pQTL in LINC02869, a long non-coding RNA gene, for circulating TGF-β2 levels (rs11118119; AAF = 0.11; P-value < 1.4e-14). This finding was validated in a cohort of 538 prostate cancer patients from CALGB 90401 (AAF = 0.10, P-value < 3.3e-25). The analysis also validated a cis-pQTL we had previously reported for VEGF-A in advanced pancreatic cancer, and additionally identified trans-pQTLs for VEGF-R3, and cis-pQTLs for CD73. Conclusions This study has provided evidence of a novel cis germline genetic variant that regulates circulating TGF-β2 levels in plasma of patients with advanced mCRC and prostate cancer. Moreover, the validation of previously identified pQTLs for VEGF-A, CD73, and VEGF-R3, potentiates the validity of these associations.
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Affiliation(s)
- Julia C.F. Quintanilha
- UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alexander B. Sibley
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Yingmiao Liu
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Donna Niedzwiecki
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA
- Alliance Statistics and Data Management Center, Duke University, Durham, NC, USA
| | - Susan Halabi
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA
- Alliance Statistics and Data Management Center, Duke University, Durham, NC, USA
| | - Layne Rogers
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Bert O’Neil
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, USA
| | - Hedy Kindler
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - William Kelly
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Alan Venook
- Department of Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Howard L. McLeod
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; and Utah Tech University, St George, UT, USA (current); and Intermountain Healthcare, St George, UT, USA (current)
| | - Mark J. Ratain
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Andrew B. Nixon
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Federico Innocenti
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kouros Owzar
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA
- Alliance Statistics and Data Management Center, Duke University, Durham, NC, USA
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Vosough P, Khatami SH, Hashemloo A, Tajbakhsh A, Karimi-Fard F, Taghvimi S, Taheri-Anganeh M, Soltani Fard E, Savardashtaki A, Movahedpour A. Exosomal lncRNAs in gastrointestinal cancer. Clin Chim Acta 2023; 540:117216. [PMID: 36592922 DOI: 10.1016/j.cca.2022.117216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/24/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
Gastrointestinal cancer (GIC) remains a leading cause of morbidity and mortality worldwide. Unfortunately, these cancers are diagnosed in advanced metastatic stages due to lack of reliable biomarkers that are sufficiently specific and sensitive in early disease. There has been growing evidence that circulating exosomes can be used to diagnose cancer non-invasively with limited risks and side effects. Furthermore, exosomal long non-coding RNAs (lncRNAs) are emerging as a new class of promising biomarkers in cancer. This review provides an overview of the extraction and detection of exosomal lncRNAs with a focus on their potential role in GIC.
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Affiliation(s)
- Parisa Vosough
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Amir Tajbakhsh
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Sina Taghvimi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Elahe Soltani Fard
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran; Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Munro MJ, Wickremesekera SK, Tan ST, Peng L. Proteomic analysis of low- and high-grade human colon adenocarcinoma tissues and tissue-derived primary cell lines reveals unique biological functions of tumours and new protein biomarker candidates. Clin Proteomics 2022; 19:27. [PMID: 35842572 PMCID: PMC9287856 DOI: 10.1186/s12014-022-09364-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/22/2022] [Indexed: 11/10/2022] Open
Abstract
Background Colon cancer is the third most common cancer and second highest cause of cancer deaths worldwide. The aim of the study was to find new biomarkers for diagnosis, prognosis and therapeutic drug targets for this disease. Methods Four low-grade and four high-grade human colon adenocarcinoma tumours with patient-matched normal colon tissues were analysed. Additionally, tissue-derived primary cell lines were established from each tumour tissue. The cell lines were validated using DNA sequencing to confirm that they are a suitable in vitro model for colon adenocarcinoma based on conserved gene mutations. Label-free quantitation proteomics was performed to compare the proteomes of colon adenocarcinoma samples to normal colon samples, and of colon adenocarcinoma tissues to tissue-derived cell lines to find significantly differentially abundant proteins. The functions enriched within the differentially expressed proteins were assessed using STRING. Proteomics data was validated by Western blotting. Results A total of 4767 proteins were identified across all tissues, and 4711 across primary tissue-derived cell lines. Of these, 3302 proteins were detected in both the tissues and the cell lines. On average, primary cell lines shared about 70% of proteins with their parent tissue, and they retained mutations to key colon adenocarcinoma-related genes and did not diverge far genetically from their parent tissues. Colon adenocarcinoma tissues displayed upregulation of RNA processing, steroid biosynthesis and detoxification, and downregulation of cytoskeletal organisation and loss of normal muscle function. Tissue-derived cell lines exhibited increased interferon-gamma signalling and aberrant ferroptosis. Overall, 318 proteins were significantly up-regulated and 362 proteins significantly down-regulated by comparisons of high-grade with low-grade tumours and low-grade tumour with normal colon tissues from both sample types. Conclusions The differences exhibited between tissues and cell lines highlight the additional information that can be obtained from patient-derived primary cell lines. DNA sequencing and proteomics confirmed that these cell lines can be considered suitable in vitro models of the parent tumours. Various potential biomarkers for colon adenocarcinoma initiation and progression and drug targets were identified and discussed, including seven novel markers: ACSL4, ANK2, AMER3, EXOSC1, EXOSC6, GCLM, and TFRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-022-09364-y.
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Affiliation(s)
- Matthew J Munro
- School of Biological Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington, 6140, New Zealand.,Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand
| | - Susrutha K Wickremesekera
- Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand.,Upper Gastrointestinal, Hepatobiliary & Pancreatic Section, Department of General Surgery, Wellington Regional Hospital, Wellington, 6021, New Zealand
| | - Swee T Tan
- Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand. .,Wellington Regional Plastic, Maxillofacial & Burns Unit, Hutt Hospital, Lower Hutt, 5040, New Zealand. .,Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, 3050, Australia.
| | - Lifeng Peng
- School of Biological Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington, 6140, New Zealand.
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Chantada-Vázquez MDP, Conde-Amboage M, Graña-López L, Vázquez-Estévez S, Bravo SB, Núñez C. Circulating Proteins Associated with Response and Resistance to Neoadjuvant Chemotherapy in HER2-Positive Breast Cancer. Cancers (Basel) 2022; 14:cancers14041087. [PMID: 35205837 PMCID: PMC8870308 DOI: 10.3390/cancers14041087] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/24/2022] [Accepted: 02/16/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The goal of this study was to find circulating proteins that can be easily sampled and incorporated into a clinical setting to improve predictive treatment response in HER2-positive breast cancer patients receiving neoadjuvant chemotherapy. We looked for potential biomarkers in serum, which we identified using two proteomics techniques: qualitative LC-MS/MS and a quantitative assay that assessed protein expression between responders and non-responders HER2-positive breast cancer patients to neoadjuvant chemotherapy. Abstract Despite the increasing use of neoadjuvant chemotherapy (NAC) in HER2-positive breast cancer (BC) patients, the clinical problem of predicting individual treatment response remains unanswered. Furthermore, the use of ineffective chemotherapeutic regimens should be avoided. Serum biomarker levels are being studied more and more for their ability to predict therapy response and aid in the development of personalized treatment regimens. This study aims to identify effective protein networks and biomarkers to predict response to NAC in HER2-positive BC patients through an exhaustive large-scale LC-MS/MS-based qualitative and quantitative proteomic profiling of serum samples from responders and non-responders. Serum samples from HER2-positive BC patients were collected before NAC and were processed by three methods (with and without nanoparticles). The qualitative analysis revealed differences in the proteomic profiles between responders and non-responders, mainly in proteins implicated in the complement and coagulation cascades and apolipoproteins. Qualitative analysis confirmed that three proteins (AFM, SERPINA1, APOD) were correlated with NAC resistance. In this study, we show that serum biomarker profiles can predict treatment response and outcome in the neoadjuvant setting. If these findings are further developed, they will be of significant clinical utility in the design of treatment regimens for individual BC patients.
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Affiliation(s)
- María del Pilar Chantada-Vázquez
- Research Unit, Lucus Augusti University Hospital (HULA), Servizo Galego de Saúde (SERGAS), 27002 Lugo, Spain;
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
| | - Mercedes Conde-Amboage
- Models of Optimization Decision, Statistics and Applications Research Group (MODESTYA), Department of Statistics, Mathematical Analysis and Optimization, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
- CITMAga, 15782 Santiago de Compostela, Spain
| | - Lucía Graña-López
- Breast Pathology Group, Lucus Augusti University Hospital (HULA)-IDIS, Servizo Galego de Saúde (SERGAS), 27002 Lugo, Spain;
- Radiology Department, Lucus Augusti University Hospital (HULA), Servizo Galego de Saúde (SERGAS), 27002 Lugo, Spain
| | - Sergio Vázquez-Estévez
- Oncology Division, Lucus Augusti University Hospital (HULA), Servizo Galego de Saúde (SERGAS), 27002 Lugo, Spain;
| | - Susana B. Bravo
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
- Correspondence: (S.B.B.); (C.N.)
| | - Cristina Núñez
- Research Unit, Lucus Augusti University Hospital (HULA), Servizo Galego de Saúde (SERGAS), 27002 Lugo, Spain;
- Correspondence: (S.B.B.); (C.N.)
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Sebzda T, Gnus J, Dziadkowiec B, Latka M, Gburek J. Diagnostic usefulness of selected proteases and acute phase factors in patients with colorectal adenocarcinoma. World J Gastroenterol 2021; 27:6673-6688. [PMID: 34754160 PMCID: PMC8554409 DOI: 10.3748/wjg.v27.i39.6673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/07/2021] [Accepted: 09/02/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Uncontrolled growth and loss of control over basic metabolic functions, leading to invasive proliferation and metastases, are the salient traits of malignant tumors in general and colorectal cancer in particular. Invasion and metastases hinder effective tumor treatment. While surgical techniques and radiotherapy can be used to remove tumor focus, only chemotherapy can eliminate dispersed neoplastic cells. However, the efficacy of the latter method is limited in the advanced stages of the disease. Therefore, recognition of the mechanisms involved in neoplastic cell spreading is indispensable for developing effective therapies.
AIM To use a number of biomarkers involved in cancer progression and identify a panel that could be used for effective early diagnosis.
METHODS We recruited 185 patients with colorectal adenocarcinoma (98 men, 87 women with median age 63). Thirty-five healthy controls were sex and age-matched. Dukes’ staging was as follows: A = 22, B = 52, C = 72, D = 39. We analyzed patients' blood serum before surgery. We determined: (1) Cathepsin B (CB) with Barrett's method (fluorogenic substrate); (2) Leukocytic elastase (LE) in a complex with alpha 1 trypsin inhibitor (AAT) using the immunoenzymatic MERCK test; (3) Total sialic acid (TSA) with the colorimetric periodate-resorcinol method; (4) Lipid-bound sialic acid (LASA) with the colorimetric Taut's method; and (5) The antitrypsin activity (ATA) employing the colorimetric test.
RESULTS In patients, the values of the five biochemical parameters were as follows: CB = 16.1 ± 8.8 mU/L, LE = 875 ± 598 µg/L, TSA = 99 ± 31 mg%, LASA = 0.68 ± 0.33 mg%, and ATA = 3211 ± 1504 U/mL. Except for LASA, they were significantly greater than those of controls: CB = 11.4 ± 6.5 mU/L, LE = 379 ± 187 µg/L, TSA = 71.4 ± 15.1 mg%, LASA = 0.69 ± 0.28 mg%, and ATA = 2016 ± 690 U/mL. For CB and LASA, the differences between the four Dukes’ stages and controls were not statistically significant. The inter-stage differences for CB and LASA were also absent. The receiver operating characteristic (ROC) analysis revealed the potential diagnostic value of CB, TSA, and ATA. The area under ROC, sensitivity, and specificity for these three parameters were: 0.85, 72%, 90%; 0.75, 66%, 77%; and 0.77, 63%, 84%, respectively. The sensitivity and specificity for the three-parameter panel CB-TSA-ATA were equal to 88.2% and 100%, respectively.
CONCLUSION The increased value of CB, TSA, and ATA parameters are associated with tumor biology, invasion, and metastasis of colorectal cancer. The presented evidence suggests the potential value of the CB-TSA-ATA biochemical marker panel in early diagnostics.
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Affiliation(s)
- Tadeusz Sebzda
- Department of Pathophysiology, Wroclaw Medical University, Wroclaw 50-368, Poland
| | - Jan Gnus
- Department of Physiotherapy, Wroclaw Medical University, Wroclaw 50-355, Poland
| | - Barbara Dziadkowiec
- Department of Pathophysiology, Wroclaw Medical University, Wroclaw 50-368, Poland
| | - Miroslaw Latka
- Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland
| | - Jakub Gburek
- Department of Pharmaceutical Biochemistry, Wroclaw Medical University, Wroclaw 50-556, Poland
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Rao J, Wan X, Tou F, He Q, Xiong A, Chen X, Cui W, Zheng Z. Molecular Characterization of Advanced Colorectal Cancer Using Serum Proteomics and Metabolomics. Front Mol Biosci 2021; 8:687229. [PMID: 34386520 PMCID: PMC8353147 DOI: 10.3389/fmolb.2021.687229] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/16/2021] [Indexed: 01/20/2023] Open
Abstract
Colorectal cancer (CRC) is a growing public health concern due to its high mortality rate. Currently, there is a lack of valid diagnostic biomarkers and few therapeutic strategies are available for CRC treatment, especially for advanced CRC whose underlying pathogenic mechanisms remain poorly understood. In the present study, we investigated the serum samples from 20 patients with stage III or IV advanced CRC using data-independent acquisition (DIA)-based proteomics and ultra-performance liquid chromatography coupled to time-of-flight tandem mass spectrometry (UPLC-TOF-MS/MS) metabolomics techniques. Overall, 551 proteins and 719 metabolites were identified. Hierarchical clustering analysis revealed that the serum proteomes of advanced CRC are more diversified than the metabolomes. Ten biochemical pathways associated with cancer cell metabolism were enriched in the detected proteins and metabolites, including glycolysis/gluconeogenesis, biosynthesis of amino acids, glutathione metabolism, and arachidonic acid metabolism, etc. A protein-protein interaction network in advanced CRC serum was constructed with 80 proteins and 21 related metabolites. Correlation analysis revealed conserved roles of lipids and lipid-like molecules in a regulatory network of advanced CRC. Three metabolites (hydroquinone, leucenol and sphingomyelin) and two proteins (coagulation factor XIII A chain and plasma kallikrein) were selected to be potential biomarkers for advanced CRC, which are positively and significantly correlated with CEA and/or CA 19-9. Altogether, the results expanded our understanding of the physiopathology of advanced CRC and discovered novel potential biomarkers for further validation and application to improve the diagnosis and monitoring of advanced CRC.
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Affiliation(s)
- Jun Rao
- Jiangxi Cancer Hospital, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
| | - Xianghui Wan
- Jiangxi Cancer Hospital, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
| | - Fangfang Tou
- Jiangxi Cancer Hospital, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
| | - Qinsi He
- Jiangxi Cancer Hospital, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
| | - Aihua Xiong
- Jiangxi Cancer Hospital, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
| | - Xinyi Chen
- Department of Hematology and Oncology, Beijing University of Chinese Medicine, Beijing, China
| | - Wenhao Cui
- Department of Pharmacology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Zhi Zheng
- Jiangxi Cancer Hospital, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
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Li H, Vanarsa K, Zhang T, Soomro S, Cicalese PA, Duran V, Dasari S, Lee KH, Pedroza C, Kisiel JB, Qin H, Bresalier RS, Chia N, Mohan C. Comprehensive aptamer-based screen of 1317 proteins uncovers improved stool protein markers of colorectal cancer. J Gastroenterol 2021; 56:659-672. [PMID: 34117903 DOI: 10.1007/s00535-021-01795-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND To screen and validate novel stool protein biomarkers of colorectal cancer (CRC). METHODS A novel aptamer-based screen of 1317 proteins was used to uncover elevated proteins in the stool of patients with CRC, as compared to healthy controls (HCs) in a discovery cohort. Selected biomarker candidates from the discovery cohort were ELISA validated in three independent cross-sectional cohorts comprises 76 CRC patients, 15 adenoma patients, and 63 healthy controls, from two different ethnicities. The expression of the potential stool biomarkers within CRC tissue was evaluated using single-cell RNA-seq datasets. RESULTS A total of 92 proteins were significantly elevated in CRC samples as compared to HCs in the discovery cohort. Among Caucasians, the 5 most discriminatory proteins among the 16 selected proteins, ordered by their ability to distinguish CRC from adenoma and healthy controls, were MMP9, haptoglobin, myeloperoxidase, fibrinogen, and adiponectin. Except myeloperoxidase, the others were significantly associated with depth of tumor invasion. The 8 stool proteins with the highest AUC values were also discriminatory in a second cohort of Indian CRC patients. Several of the stool biomarkers elevated in CRC were also expressed within CRC tissue, based on the single-cell RNA-seq analysis. CONCLUSIONS Stool MMP9, fibrinogen, myeloperoxidase, and haptoglobin emerged as promising CRC stool biomarkers, outperforming stool Hemoglobin. Longitudinal studies are warranted to assess the clinical utility of these novel biomarkers in early diagnosis of CRC.
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Affiliation(s)
- Hao Li
- Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Biomedical Engineering, University of Houston, Houston, USA
| | - Kamala Vanarsa
- Department of Biomedical Engineering, University of Houston, Houston, USA
| | - Ting Zhang
- Department of Biomedical Engineering, University of Houston, Houston, USA
| | - Sanam Soomro
- Department of Biomedical Engineering, University of Houston, Houston, USA
| | | | - Valeria Duran
- Department of Biomedical Engineering, University of Houston, Houston, USA
| | - Shobha Dasari
- Department of Biomedical Engineering, University of Houston, Houston, USA
| | - Kyung Hyun Lee
- Center for Clinical Research and Evidence-Based Medicine, McGovern Medical School, UT Health Science Center At Houston, Houston, USA
| | - Claudia Pedroza
- Center for Clinical Research and Evidence-Based Medicine, McGovern Medical School, UT Health Science Center At Houston, Houston, USA
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, USA
| | - Huanlong Qin
- Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Robert S Bresalier
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Nicholas Chia
- Department of Surgical Research, Mayo Clinic, Rochester, USA
| | - Chandra Mohan
- Department of Biomedical Engineering, University of Houston, Houston, USA.
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Fayazfar S, Arefi Oskouie A, Safaei A, Zali H, Nazemalhosseini Mojarad E. Identification of key candidate genes and pathways associated with colorectal aberrant crypt foci-to-adenoma-to-carcinoma progression. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2021; 14:S41-S50. [PMID: 35154601 PMCID: PMC8817750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/12/2021] [Indexed: 06/14/2023]
Abstract
AIM The present study aimed to detect key candidate genes and pathways involved in colorectal aberrant crypt foci-to-adenoma-to-carcinoma progression. BACKGROUND Although colorectal cancer (CRC) is the third most common type of cancer, the involved signaling pathways and driver-genes remain largely unclear. CRC begins with the malignant transformation of precancerous lesions including aberrant crypt foci (ACF) and benign adenomatous polyp or adenoma. METHODS A list of formerly reported ACF, adenoma, and CRC-associated proteins was obtained from GeneCards, and then the data in online David Bioinformatics Resources was analyzed. The protein-protein interactions were surveyed utilizing String database and Cytoscape software. After hubs and bottlenecks were recognized, the key genes and pathways were identified through different bioinformatics analysis. RESULTS The most important pathways associated with colorectal aberrant crypt foci-to-adenoma progression were attributed to "pathways in cancer" and "chemokine signaling pathway" and those in adenoma-to-carcinoma progression were related to "pathways in cancer," "chemokine signaling pathway," and "Ras signaling pathway." The genes participating in these pathways are key ones. Furthermore, PRKACB, CUL2, and GSK3B were significant as the seed in the clusters related to adenoma and GNB1, RALBP1, ROCK1, and IKBKG in the clusters related to cancer. CONCLUSION The key candidate genes and pathways in progress CRC formed precursor lesions were identified by integrated bioinformatics analysis. The results could lead to a better understanding of the cause and underlying molecular events as well as detection of therapeutic targets for CRC.
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Affiliation(s)
- Setareh Fayazfar
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afsaneh Arefi Oskouie
- Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Akram Safaei
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hakimeh Zali
- School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical sciences, Tehran, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Mao WB, Lyu JY, Vaishnani DK, Lyu YM, Gong W, Xue XL, Shentu YP, Ma J. Application of artificial neural networks in detection and diagnosis of gastrointestinal and liver tumors. World J Clin Cases 2020; 8:3971-3977. [PMID: 33024753 PMCID: PMC7520792 DOI: 10.12998/wjcc.v8.i18.3971] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/10/2020] [Accepted: 06/28/2020] [Indexed: 02/05/2023] Open
Abstract
As a form of artificial intelligence, artificial neural networks (ANNs) have the advantages of adaptability, parallel processing capabilities, and non-linear processing. They have been widely used in the early detection and diagnosis of tumors. In this article, we introduce the development, working principle, and characteristics of ANNs and review the research progress on the application of ANNs in the detection and diagnosis of gastrointestinal and liver tumors.
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Affiliation(s)
- Wei-Bo Mao
- Department of Pathology, Lishui Hospital of Zhejiang University, Lishui Central Hospital, Lishui 323000, Zhejiang Province, China
| | - Jia-Yu Lyu
- Department of Psychiatry, The Affiliated Kangning Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China
| | - Deep K Vaishnani
- School of International Studies, Wenzhou Medical University, Wenzhou 325035, Zhejiang Province, China
| | - Yu-Man Lyu
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Wei Gong
- Department of Pathology, Lishui Hospital of Zhejiang University, Lishui Central Hospital, Lishui 323000, Zhejiang Province, China
| | - Xi-Ling Xue
- Department of Psychiatry, The Affiliated Kangning Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China
| | - Yang-Ping Shentu
- Department of Pathology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Jun Ma
- Department of Pathology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
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11
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Holm M, Joenväärä S, Saraswat M, Mustonen H, Tohmola T, Ristimäki A, Renkonen R, Haglund C. Identification of several plasma proteins whose levels in colorectal cancer patients differ depending on outcome. FASEB Bioadv 2019; 1:723-730. [PMID: 32123817 PMCID: PMC6996405 DOI: 10.1096/fba.2019-00062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 07/27/2019] [Accepted: 10/30/2019] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) stands for 10% of the worldwide cancer burden and has recently become the second most common cause of cancer death. The 5-year survival rate depends mainly on stage at diagnosis. Mass spectrometric proteomic analysis is widely used to study the plasma proteome, which is complex and contains multitudes of proteins. In this study, we have used Ultra Performance Liquid Chromatography-Ultra Definition Mass Spectrometry (UPLC-UDMSE)-based proteomics to analyze plasma samples from 76 CRC patients. We identified several plasma proteins, such as CP, TVP23C, FETUB, and IGFBP3, of which altered levels led to significant differences in survival, as seen by Cox regression and Kaplan-Meier analysis. Additionally, during Cox regression analysis, samples were adjusted for age and/or tumor stage, enabling stringent analysis. These proteins, although in need of further validation, could be of use during patient follow-up, as their levels can non-invasively be measured from blood samples, and could be of use in predicting patient outcome. Several of these proteins additionally have roles in metabolism and inflammation, two processes central to the development and progression of cancer, further indicating their importance in cancer.
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Affiliation(s)
- Matilda Holm
- Department of SurgeryFaculty of MedicineUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Department of PathologyFaculty of MedicineUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Translational Cancer Medicine Research ProgramFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Applied Tumor Genomics Research ProgramFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Sakari Joenväärä
- Transplantation LaboratoryHaartman InstituteUniversity of HelsinkiHelsinkiFinland
- HUSLABHelsinki University HospitalHelsinkiFinland
| | - Mayank Saraswat
- Transplantation LaboratoryHaartman InstituteUniversity of HelsinkiHelsinkiFinland
- HUSLABHelsinki University HospitalHelsinkiFinland
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Harri Mustonen
- Department of SurgeryFaculty of MedicineUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Tiialotta Tohmola
- Transplantation LaboratoryHaartman InstituteUniversity of HelsinkiHelsinkiFinland
- HUSLABHelsinki University HospitalHelsinkiFinland
- Department of BiosciencesFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Ari Ristimäki
- Department of PathologyFaculty of MedicineUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Applied Tumor Genomics Research ProgramFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
- HUSLABHelsinki University HospitalHelsinkiFinland
| | - Risto Renkonen
- Transplantation LaboratoryHaartman InstituteUniversity of HelsinkiHelsinkiFinland
- HUSLABHelsinki University HospitalHelsinkiFinland
| | - Caj Haglund
- Department of SurgeryFaculty of MedicineUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Translational Cancer Medicine Research ProgramFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
- HUSLABHelsinki University HospitalHelsinkiFinland
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12
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Hissong E, Pittman ME. Colorectal carcinoma screening: Established methods and emerging technology. Crit Rev Clin Lab Sci 2019; 57:22-36. [PMID: 31603697 DOI: 10.1080/10408363.2019.1670614] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Colorectal carcinoma screening programs have shown success in lowering both the incidence and mortality rate of colorectal carcinoma at a population level, in part because this carcinoma is relatively slow growing and has an identifiable premalignant lesion. Still, many patients do not undergo the recommended screening for colorectal carcinoma, and of those who do, a subset may be over- or under-diagnosed by the currently available testing methods. The primary purpose of this article is to review the data regarding currently available colorectal cancer screening modalities, which include fecal occult blood testing, direct colonic visualization, and noninvasive imaging techniques. In addition, readers will be introduced to a variety of biomarkers that may serve as stand-alone or adjunct tests in the future. Finally, there is a brief discussion of the current epidemiologic considerations that public health officials must address as they create population screening guidelines. The data we provide as laboratory physicians and scientists are critical to the construction of appropriate recommendations that ultimately decrease the burden of disease from colorectal carcinoma.
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Affiliation(s)
- Erika Hissong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Meredith E Pittman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
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13
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Jaberie H, Hosseini SV, Naghibalhossaini F. Evaluation of Alpha 1-Antitrypsin for the Early Diagnosis of Colorectal Cancer. Pathol Oncol Res 2019; 26:1165-1173. [PMID: 31183614 DOI: 10.1007/s12253-019-00679-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/29/2019] [Indexed: 01/19/2023]
Abstract
Previous proteomic studies have identified alpha 1-antitrypsin (A1AT) as a potential serum biomarker for colorectal cancer (CRC). In this case-control study, we evaluated plasma A1AT concentration and activity as a biomarker for the early diagnosis of colorectal cancer in a group of 113 sporadic CRC patients. We also analyzed A1AT gene promoter methylation, and genotypes in this group of CRC patients. The plasma A1AT and CEA concentrations were measured using the nephelometric and ELISA methods, respectively. A1AT activity was determined by Trypsin Inhibitor Capacity assay. The genomic DNA from blood samples were subjected to Z and S genotype analysis using PCR-RFLP method and the gene promoter methylation in tumors and their adjacent normal tissues was determined by methylation specific-PCR assay. The plasma levels of A1AT and CEA in patients (median, 2.3 g/L and 5.96 ng/ml, respectively) were significantly higher than those in healthy controls (medians, 1.43 g/L and 2.57 ng/ml, respectively) (p = 0.0001). The plasma A1AT activity and concentrations were positively correlated with the tumor stage and well-discriminated between early and advanced stages. The A1AT activity in plasma was the most useful marker for CRC diagnosis (median 4.8 mmol/min/ml in cases vs 1.91 mmol/min/ml in controls, p = 0.0001). No deficient Z or S alleles of A1AT was observed in patients' genotype and the gene promoter tends to be more methylated in normal mucosa than in tumor tissues. We conclude that plasma A1AT activity has better sensitivity and specificity than CEA measurement for the early detection of CRC. Promoter demethylation might play a role in increasing plasma A1AT levels in CRC patients.
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Affiliation(s)
- Hajar Jaberie
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Zand Street, Shiraz, 7134845794, Iran.,Department of Biochemistry, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | | | - Fakhraddin Naghibalhossaini
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Zand Street, Shiraz, 7134845794, Iran. .,Autoimmune Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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14
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Giudice G, Petsalaki E. Proteomics and phosphoproteomics in precision medicine: applications and challenges. Brief Bioinform 2019; 20:767-777. [PMID: 29077858 PMCID: PMC6585152 DOI: 10.1093/bib/bbx141] [Citation(s) in RCA: 25] [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] [Received: 07/01/2017] [Revised: 09/21/2017] [Indexed: 12/11/2022] Open
Abstract
Recent advances in proteomics allow the accurate measurement of abundances for thousands of proteins and phosphoproteins from multiple samples in parallel. Therefore, for the first time, we have the opportunity to measure the proteomic profiles of thousands of patient samples or disease model cell lines in a systematic way, to identify the precise underlying molecular mechanism and discover personalized biomarkers, networks and treatments. Here, we review examples of successful use of proteomics and phosphoproteomics data sets in as well as their integration other omics data sets with the aim of precision medicine. We will discuss the bioinformatics challenges posed by the generation, analysis and integration of such large data sets and present potential reasons why proteomics profiling and biomarkers are not currently widely used in the clinical setting. We will finally discuss ways to contribute to the better use of proteomics data in precision medicine and the clinical setting.
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Affiliation(s)
- Girolamo Giudice
- European Molecular Biology Laboratory European Bioinformatics Institute
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15
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Fayazfar S, Zali H, Arefi Oskouie A, Asadzadeh Aghdaei H, Rezaei Tavirani M, Nazemalhosseini Mojarad E. Early diagnosis of colorectal cancer via plasma proteomic analysis of CRC and advanced adenomatous polyp. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2019; 12:328-339. [PMID: 31749922 PMCID: PMC6820836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIM This paper aimed to identify new candidate biomarkers in blood for early diagnosis of CRC. BACKGROUND Colorectal cancer (CRC) is the third most widespread malignancies increasing globally. The high mortality rate associated with colorectal cancer is due to the delayed diagnosis in an advanced stage while the metastasis has occurred. For better clinical management and subsequently to reduce mortality of CRC, early detection biomarkers are in high demand. METHODS A 2D-PAGE separation of proteins was performed followed by tandem mass Spectrometry (MALDI-TOF-TOF) to discover potential plasma protein markers for CRC and AA (advanced adenomas). Furthermore, western blot method was used to confirm a part of the results in colorectal tissue samples. RESULTS The significantly altered proteins including HPR, HP, ALB, KRT1, APOA1, FGB, IGJ and C4A were down-regulated in polyp relative to normal, and CRC compare to polyp surprisingly, and inversely, ORM2 was up-regulated with the fold change ≥ 2 and p-value ≤ 0.05. We also surveyed APOA1, FGB, and C4A for further confirmation of their expression changes by western blotting. All three of them showed a decreasing trend from normal toward CRC tissue samples as it mentioned before, but just changes of FGB and C4A were significant. CONCLUSION The results demonstrated that plasma proteins can be less invasive markers for the detection of CRC. FGB and C4A can be considered as plasma potential biomarkers to early diagnosis of CRC patients and understanding the underlying procedures in tumorigenesis. Undoubtedly, the additional study must be conducted on large scale cohorts to verify the results.
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Affiliation(s)
- Setareh Fayazfar
- Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hakimeh Zali
- School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afsaneh Arefi Oskouie
- Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastroenterology Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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16
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Núñez C. Blood-based protein biomarkers in breast cancer. Clin Chim Acta 2018; 490:113-127. [PMID: 30597138 DOI: 10.1016/j.cca.2018.12.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/26/2018] [Accepted: 12/27/2018] [Indexed: 02/07/2023]
Abstract
Breast cancer (BCa) is a significant healthcare problem on women worldwide. Thus, early detection is very important to reduce mortality. Furthermore, better BCa prognosis could improve selection of patients eligible for adjuvant therapy. New markers for early diagnosis, accurate prognosis and prediction of response to treatment are necessary to improve BCa care. The present review summarizes important aspects of the potential usefulness of modern technologies, strategies, and scientific findings in proteomic research for discovery of breast cancer-associated blood-based protein biomarkers in the clinic.
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Affiliation(s)
- Cristina Núñez
- Research Unit, Hospital Universitario Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS), 27002 Lugo, Spain.
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17
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Colorectal cancer patients with different C-reactive protein levels and 5-year survival times can be differentiated with quantitative serum proteomics. PLoS One 2018; 13:e0195354. [PMID: 29630649 PMCID: PMC5891022 DOI: 10.1371/journal.pone.0195354] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 03/21/2018] [Indexed: 02/06/2023] Open
Abstract
Over 1.4 million people are diagnosed with colorectal cancer (CRC) each year, making it the third most common cancer in the world. Increased screening and therapeutic modalities including improved combination treatments have reduced CRC mortality, although incidence and mortality rates are still increasing in some areas. Serum-based biomarkers are mainly used for follow-up of cancer, and are ideal due to the ease and minimally invasive nature of sample collection. Unfortunately, CEA and other serum markers have too low sensitivity for screening and preoperative diagnostic purposes. Increasing interest is focused on the possible use of biomarkers for predicting treatment response and prognosis in cancer. In this study, we have performed mass spectrometry analysis (UPLC-UDMSE) of serum samples from 19 CRC patients. Increased levels of C-reactive protein (CRP), which occur during local inflammation and the presence of a systemic inflammatory response, have been linked to poor prognosis in CRC patients. We chose to analyze samples according to CRP values by dividing them into the categories CRP <30 and >30, and, separately, according to short and long 5-year survival. The aim was to discover differentially expressed proteins associated with poor prognosis and shorter survival. We quantified 256 proteins and performed detailed statistical analyses and pathway analysis. We discovered multiple proteins that are up- or downregulated in patients with CRP >30 as compared to CRP <30 and in patients with short as compared to long 5-year survival. Pathways that were enriched include LXR/RXR activation, FXR/RXR activation, complement and coagulation cascades and acute phase signaling response, with some of the proteins we identified having roles in these pathways. In this study, we have identified multiple proteins, of which a few have been previously identified as potential biomarkers, and others that have been identified as potential biomarkers for CRC for the first time, to the best of our knowledge. While these proteins still need to be validated in larger patient series, this pilot study will pave the way for future studies aiming to provide better biomarkers for patients with CRC.
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18
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Pang WW, Abdul-Rahman PS, Wan-Ibrahim WI, Hashim OH. Can the Acute-Phase Reactant Proteins be Used as Cancer Biomarkers? Int J Biol Markers 2018; 25:1-11. [DOI: 10.1177/172460081002500101] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The association between the acute-phase reactant proteins (APRPs) and cancer has long been established. There have been numerous reports correlating altered levels of various APRPs with different types of cancers. However, researchers are often quick to dismiss the use of these APRPs as potential biomarkers for the diagnosis and monitoring of cancer because alterations in APRP concentrations are observed in a wide range of diseases. Recent progress in proteomics studies which profiled the serum proteins of cancer patients and those of normal individuals indicated that the altered APRP expressions were different for distinct types, subtypes, and even stages of cancer. Interestingly, these data are in agreement with those observed earlier using immunochemical and biochemical assays. In view of this compelling association of different patterns of APRPs with various types of cancers and in an apparent shift of paradigm, we present in this review some indications that APRP fingerprinting may be used as complementary cancer biomarkers.
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Affiliation(s)
- Wei Wei Pang
- University of Malaya Centre for Proteomics Research, University of Malaya, Kuala Lumpur - Malaysia
| | - Puteri Shafinaz Abdul-Rahman
- University of Malaya Centre for Proteomics Research, University of Malaya, Kuala Lumpur - Malaysia
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur - Malaysia
| | - Wan Izlina Wan-Ibrahim
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur - Malaysia
| | - Onn Haji Hashim
- University of Malaya Centre for Proteomics Research, University of Malaya, Kuala Lumpur - Malaysia
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur - Malaysia
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19
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Lim LC, Lim YM. Proteome Heterogeneity in Colorectal Cancer. Proteomics 2018; 18. [PMID: 29316255 DOI: 10.1002/pmic.201700169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 12/17/2017] [Indexed: 01/26/2023]
Abstract
Tumor heterogeneity is an important feature of colorectal cancer (CRC) manifested by dynamic changes in gene expression, protein expression, and availability of different tumor subtypes. Recent publications in the past 10 years have revealed proteome heterogeneity between different colorectal tumors and within the same tumor site. This paper reviews recent research works on the proteome heterogeneity in CRC, which includes the heterogeneity within a single tumor (intratumor heterogeneity), between different anatomical sites at the same organ, and between primary and metastatic sites (intertumor heterogeneity). The potential use of proteome heterogeneity in precision medicine and its implications in biomarker discovery and therapeutic outcomes will be discussed. Identification of the unique proteome landscape between and within individual tumors is imperative for understanding cancer biology and the management of CRC patients.
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Affiliation(s)
- Lay Cheng Lim
- Centre for Cancer Research, Faculty of Medicine and Health Sciences, University of Tunku Abdul Rahman, Selangor, Malaysia
| | - Yang Mooi Lim
- Centre for Cancer Research, Faculty of Medicine and Health Sciences, University of Tunku Abdul Rahman, Selangor, Malaysia
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20
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Bhardwaj M, Gies A, Werner S, Schrotz-King P, Brenner H. Blood-Based Protein Signatures for Early Detection of Colorectal Cancer: A Systematic Review. Clin Transl Gastroenterol 2017; 8:e128. [PMID: 29189767 PMCID: PMC5717517 DOI: 10.1038/ctg.2017.53] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/10/2017] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES Blood-based proteins might be an attractive option for early detection of colorectal cancer (CRC), but individually they are unlikely to achieve the diagnostic performance required for population based screening. We aimed at summarizing current evidence of diagnostic performance of signatures based on multiple proteins for early detection of CRC. METHODS A systematic literature review adhering to the PRISMA (preferred reporting items for systematic reviews and meta-analysis) guidelines was performed. PubMed and Web of Science databases were searched for potentially relevant studies published until 28th August, 2017. Relevant studies were identified by predefined eligibility criteria. Estimates of indicators of diagnostic performance such as sensitivity, specificity, and the area under the curve (AUC), along with information on validation and other key methodological procedures were extracted. Study quality was assessed by a QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies 2) instrument tool. RESULTS Thirty six eligible studies with numbers of CRC cases ranging from 23 to 512 and the number of proteins included in signatures ranged from 3 to 13 were identified. Reported Youden's Index and AUC ranged from 0.19 to 0.95 and from 0.62 to 0.996, respectively. However most studies, especially those reporting better diagnostic performance, were conducted in clinical rather than screening setting and many studies lacked any internal or external validation of identified algorithm. CONCLUSIONS Blood-based tests using signatures of multiple proteins may be a promising approach for non-invasive CRC screening. However, promising signatures identified in clinical settings still require rigorous evaluation in large studies conducted in true screening setting.
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Affiliation(s)
- Megha Bhardwaj
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Anton Gies
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Simone Werner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Petra Schrotz-King
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Hermann Brenner
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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21
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Ajona D, Ortiz-Espinosa S, Pio R. Complement anaphylatoxins C3a and C5a: Emerging roles in cancer progression and treatment. Semin Cell Dev Biol 2017; 85:153-163. [PMID: 29155219 DOI: 10.1016/j.semcdb.2017.11.023] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/07/2017] [Accepted: 11/15/2017] [Indexed: 02/06/2023]
Abstract
Recent insights into the role of complement anaphylatoxins C3a and C5a in cancer provide new opportunities for the development of innovative biomarkers and therapeutic strategies. These two complement activation products can maintain chronic inflammation, promote an immunosuppressive microenvironment, induce angiogenesis, and increase the motility and metastatic potential of cancer cells. Still, the diverse heterogeneity of responses mediated by these peptides poses a challenge both to our understanding of the role played by these molecules in cancer progression and to the development of effective treatments. This review attempts to summarize the evidence surrounding the involvement of anaphylatoxins in the biological contexts associated with tumor progression. We also describe the recent developments that support the inhibition of anaphylatoxins, or their cognate receptors C3aR and C5aR1, as a treatment option for maximizing the clinical efficacy of current immunotherapies that target the PD-1/PD-L1 immune checkpoint.
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Affiliation(s)
- Daniel Ajona
- University of Navarra, Center for Applied Medical Research (CIMA), Program in Solid Tumors and Biomarkers, Pamplona, Spain; Navarra's Health Research Institute (IdiSNA), Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain; University of Navarra, School of Sciences, Department of Biochemistry and Genetics, Pamplona, Spain
| | - Sergio Ortiz-Espinosa
- University of Navarra, Center for Applied Medical Research (CIMA), Program in Solid Tumors and Biomarkers, Pamplona, Spain; University of Navarra, School of Sciences, Department of Biochemistry and Genetics, Pamplona, Spain
| | - Ruben Pio
- University of Navarra, Center for Applied Medical Research (CIMA), Program in Solid Tumors and Biomarkers, Pamplona, Spain; Navarra's Health Research Institute (IdiSNA), Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain; University of Navarra, School of Sciences, Department of Biochemistry and Genetics, Pamplona, Spain.
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22
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Piyathilake CJ, Oelschlager DK, Meleth S, Partridge EE, Grizzle WE. Plasma Protein Profiles Differ between Women Diagnosed with Cervical Intraepithelial Neoplasia (CIN) 1 and 3. Cancer Inform 2017. [DOI: 10.1177/117693510600200026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Early detection of precancerous cells in the cervix and their clinical management is the main purpose of cervical cancer prevention and treatment programs. Cytological findings or testing for high risk (HR)-human papillomavirus (HPV) are inadequately sensitive for use in triage of women at high risk for cervical cancer. The current study is an exploratory study to identify candidate surface-enhanced laser desorption/ionization (SELDI) time of flight (TOF) mass spectrometry (MS) protein profiles in plasma that may distinguish cervical intraepithelial neoplasia (CIN 3) from CIN 1 among women infected with HR-HPV. We evaluated the SELDI-TOF-MS plasma protein profiles of HR-HPV positive 32 women with CIN 3 (cases) and 28 women with CIN1 (controls). Case-control status was kept blinded and triplicates of each sample and quality control plasma samples were randomized and after robotic sample preparations were run on WCX2 chips. After alignment of mass/charge (m-z values), an iterative method was used to develop a classifier on a training data set that had 28 cases and 22 controls. The classifier developed was used to classify the subjects in a test data set that has six cases and six controls. The classifier separated the cases from controls in the test set with 100% sensitivity and 100% specificity suggesting the possibility of using plasma SELDI protein profiles to identify women who are likely to have CIN 3 lesions.
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Affiliation(s)
- Chandrika J. Piyathilake
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Denise K. Oelschlager
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Sreelatha Meleth
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Edward E. Partridge
- Department of Obstetrics & Gynecology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - William E. Grizzle
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35294
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23
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Kuppusamy P, Govindan N, Yusoff MM, Ichwan SJ. Proteins are potent biomarkers to detect colon cancer progression. Saudi J Biol Sci 2017; 24:1212-1221. [PMID: 28855814 PMCID: PMC5562385 DOI: 10.1016/j.sjbs.2014.09.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 09/21/2014] [Accepted: 09/24/2014] [Indexed: 01/11/2023] Open
Abstract
Colon cancer is the most common type of cancer and major cause of death worldwide. The detection of colon cancer is difficult in early stages. However, the secretory proteins have been used as ideal biomarker for the detection of colon cancer progress in cancer patients. Serum/tissue protein expression could help general practitioners to identify colon cancer at earlier stages. By this way, we use the biomarkers to evaluate the anticancer drugs and their response to therapy in cancer models. Recently, the biomarker discovery is important in cancer biology and disease management. Also, many measurable specific molecular components have been studied in colon cancer therapeutics. The biomolecules are mainly DNA, RNA, metabolites, enzymes, mRNA, aptamers and proteins. Thus, in this review we demonstrate the important protein biomarker in colon cancer development and molecular identification of protein biomarker discovery.
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Affiliation(s)
- Palaniselvam Kuppusamy
- Mammalian Cell Technology Laboratory, Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak 26300, Gambang, Kuantan, Pahang, Malaysia
| | - Natanamurugaraj Govindan
- Mammalian Cell Technology Laboratory, Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak 26300, Gambang, Kuantan, Pahang, Malaysia
| | - Mashitah M. Yusoff
- Mammalian Cell Technology Laboratory, Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak 26300, Gambang, Kuantan, Pahang, Malaysia
| | - Solachuddin J.A. Ichwan
- Kulliyyah of Dentistry, International Islamic University Malaysia, Bandar Indera Mahkota 125200, Kuantan, Pahang, Malaysia
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24
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Wang H, Luo C, Zhu S, Fang H, Gao Q, Ge S, Qu H, Ma Q, Ren H, Wang Y, Wang W. Serum peptidome profiling for the diagnosis of colorectal cancer: discovery and validation in two independent cohorts. Oncotarget 2017; 8:59376-59386. [PMID: 28938643 PMCID: PMC5601739 DOI: 10.18632/oncotarget.19587] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/29/2017] [Indexed: 01/05/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignant neoplasms worldwide. Except for the existing fecal occult blood test, colonoscopy and sigmoidoscopy, no widely accepted in vitro diagnostic methods have been available. To identify potential peptide biomarkers for CRC, serum samples from a discovery cohort (100 CRC patients and 100 healthy controls) and an independent validation cohort (91 CRC patients and 91 healthy controls) were collected. Peptides were fractionated by weak cation exchange magnetic beads (MB-WCX) and analysed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Five peptides (peaks at m/z 1895.3, 2020.9, 2080.7, 2656.8 and 3238.5) were identified as candidate biomarkers for CRC. A diagnostic panel based on the five peptides can discriminate CRC patients from healthy controls, with an accuracy of 91.8%, sensitivity of 95.6%, and specificity of 87.9% in the validation cohort. Peptide peaks at m/z 1895.3, 2020.9 and 3238.5 were identified as the partial sequences of complement component 4 (C4), complement component 3 (C3) and fibrinogen α chain (FGA), respectively. This study potentiated peptidomic analysis as a promising in vitro diagnostic tool for diagnosis of CRC. The identified peptides suggest the involvement of the C3, C4 and FGA in CRC pathogenesis.
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Affiliation(s)
- Hao Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Chenghua Luo
- Department of Retroperitoneal Tumors Surgery, Peking University International Hospital, Beijing 102206, China
| | - Shengtao Zhu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100069, China.,National Center for Clinical Medical Research of Digestive Diseases, Beijing 100069, China
| | - Honghong Fang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Qing Gao
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Siqi Ge
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.,School of Medical and Health Sciences, Edith Cowan University, Perth 6027, Australia
| | - Haixia Qu
- Bioyong (Beijing) Technology Co., Ltd., Beijing 100085, China
| | - Qingwei Ma
- Bioyong (Beijing) Technology Co., Ltd., Beijing 100085, China
| | - Hongwei Ren
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Wei Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.,School of Medical and Health Sciences, Edith Cowan University, Perth 6027, Australia
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25
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Shahbazy M, Vasighi M, Kompany-Zareh M, Ballabio D. Oblique rotation of factors: a novel pattern recognition strategy to classify fluorescence excitation-emission matrices of human blood plasma for early diagnosis of colorectal cancer. MOLECULAR BIOSYSTEMS 2017; 12:1963-75. [PMID: 27076033 DOI: 10.1039/c6mb00162a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Colorectal cancer (CRC) ranks high in both men and women, accounting for about 13% of all cancers. In this study, a novel pattern recognition strategy is proposed to improve early diagnosis of CRC through visualizing the relationship between different spectral patterns in a case-control research. Partial least squares-discriminant analysis (PLS-DA) and supervised Kohonen network (SKN) were used to classify the fluorescence excitation-emission matrices (EEMs) from 289 human blood plasma samples containing CRC patients, adenomas tumor, other non-malignant findings and healthy individuals. To obtain optimal factors, oblique rotation (OR) and genetic algorithm (GA) were used to rotate the factors by optimizing transformation matrix elements. Transformed factors were introduced to SKN to build a classification model and the model performance was examined via comparison with a common classifier; PLS-DA. Classification models were built for CRC-healthy and adenomas-healthy samples and the best results were obtained through applying GA-OR on PLS factors and introducing them to the classifiers. Non-error rates for SKN and PLS-DA models assisted with GA (for selecting more informative PLS factors) and OR were equal to 0.97 and 0.95 in cross validation and 0.93 and 0.90 for prediction of the external test set, respectively. Moreover, according to the acceptable results for adenomas-healthy cases using optimal factors, CRC can be diagnosed in early stages. Combining classifiers and optimal factors proved to be efficient for distinguishing healthy and malignant samples, and OR can significantly improve performance of the classification model.
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Affiliation(s)
- Mohammad Shahbazy
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), 45137-66731 Zanjan, Iran.
| | - Mahdi Vasighi
- Department of Computer Science and Information Technology, Institute for Advanced Studies in Basic Sciences (IASBS), 45137-66731 Zanjan, Iran.
| | - Mohsen Kompany-Zareh
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), 45137-66731 Zanjan, Iran.
| | - Davide Ballabio
- Milano Chemometrics and QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, P.za della Scienza 1, 20126 Milan, Italy
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26
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Corbo C, Cevenini A, Salvatore F. Biomarker discovery by proteomics-based approaches for early detection and personalized medicine in colorectal cancer. Proteomics Clin Appl 2017; 11. [PMID: 28019089 DOI: 10.1002/prca.201600072] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 11/29/2016] [Accepted: 12/22/2016] [Indexed: 12/14/2022]
Abstract
About one million people per year develop colorectal cancer (CRC) and approximately half of them die. The extent of the disease (i.e. local invasion at the time of diagnosis) is a key prognostic factor. The 5-year survival rate is almost 90% in the case of delimited CRC and 10% in the case of metastasized CRC. Hence, one of the great challenges in the battle against CRC is to improve early diagnosis strategies. Large-scale proteomic approaches are widely used in cancer research to search for novel biomarkers. Such biomarkers can help in improving the accuracy of the diagnosis and in the optimization of personalized therapy. Herein, we provide an overview of studies published in the last 5 years on CRC that led to the identification of protein biomarkers suitable for clinical application by using proteomic approaches. We discussed these findings according to biomarker application, including also the role of protein phosphorylation and cancer stem cells in biomarker discovery. Our review provides a cross section of scientific approaches and can furnish suggestions for future experimental strategies to be used as reference by scientists, clinicians and researchers interested in proteomics for biomarker discovery.
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Affiliation(s)
- Claudia Corbo
- CEINGE, Advanced Biotechnology s.c.a.r.l., Via G. Salvatore 486, Naples, Italy.,Center for Biomimetic Medicine, Houston Methodist Research Institute, Houston, TX, USA
| | - Armando Cevenini
- CEINGE, Advanced Biotechnology s.c.a.r.l., Via G. Salvatore 486, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Francesco Salvatore
- CEINGE, Advanced Biotechnology s.c.a.r.l., Via G. Salvatore 486, Naples, Italy
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27
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Ma Y, Xiao T, Xu Q, Shao X, Wang H. iTRAQ-based quantitative analysis of cancer-derived secretory proteome reveals TPM2 as a potential diagnostic biomarker of colorectal cancer. Front Med 2016; 10:278-85. [PMID: 27283175 DOI: 10.1007/s11684-016-0453-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 05/11/2016] [Indexed: 01/24/2023]
Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. We aimed to find novel molecules as potential biomarkers for the early diagnosis of CRC. A serum-free conditioned medium was successfully collected from three pairs of CRC tissue and adjacent normal tissue. iTRAQ-based quantitative proteomic analysis was applied to compare the differences in secretome between primary CRC mucosa and adjacent normal mucosa. A total of 145 kinds of proteins were identified. Of these proteins, 29 were significantly different between CRC and normal tissue. Tropomyosin 2 β (TPM2) exhibited the most significant differences; as such, this protein was selected for further validation. Quantitative real-time PCR indicated that the mRNA expression of TPM2 significantly decreased in the CRC tissue compared with the paired adjacent normal tissue. Immunohistochemical analysis also confirmed that TPM2 was barely detected at protein levels in the CRC tissue. In summary, this study revealed potential molecules for future biomarker applications and provided an efficient approach for the differential analysis of cancer-associated secretome. TPM2 may be valuable for the early diagnosis of CRC.
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Affiliation(s)
- Yiming Ma
- State Key Laboratory of Molecular Oncology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Quan Xu
- Department of Gastrointestinal Cancer Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xinxin Shao
- Department of Gastrointestinal Cancer Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Hongying Wang
- State Key Laboratory of Molecular Oncology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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28
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Ma H, Chen G, Guo M. Mass spectrometry based translational proteomics for biomarker discovery and application in colorectal cancer. Proteomics Clin Appl 2016; 10:503-15. [PMID: 26616366 DOI: 10.1002/prca.201500082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/17/2015] [Accepted: 11/25/2015] [Indexed: 12/29/2022]
Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related death in the world. Clinically, early detection of the disease is the most effective approach to tackle this tough challenge. Discovery and development of reliable and effective diagnostic tools for the assessment of prognosis and prediction of response to drug therapy are urgently needed for personalized therapies and better treatment outcomes. Among many ongoing efforts in search for potential CRC biomarkers, MS-based translational proteomics provides a unique opportunity for the discovery and application of protein biomarkers toward better CRC early detection and treatment. This review updates most recent studies that use preclinical models and clinical materials for the identification of CRC-related protein markers. Some new advances in the development of CRC protein markers such as CRC stem cell related protein markers, SRM/MRM-MS and MS cytometry approaches are also discussed in order to address future directions and challenges from bench translational research to bedside clinical application of CRC biomarkers.
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Affiliation(s)
- Hong Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-Africa Joint Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China.,Haematology and Oncology Division, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Guilin Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-Africa Joint Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-Africa Joint Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China
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29
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Kawahara R, Bollinger JG, Rivera C, Ribeiro ACP, Brandão TB, Paes Leme AF, MacCoss MJ. A targeted proteomic strategy for the measurement of oral cancer candidate biomarkers in human saliva. Proteomics 2015; 16:159-73. [PMID: 26552850 DOI: 10.1002/pmic.201500224] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 08/27/2015] [Accepted: 11/04/2015] [Indexed: 12/31/2022]
Abstract
Head and neck cancers, including oral squamous cell carcinoma (OSCC), are the sixth most common malignancy in the world and are characterized by poor prognosis and a low survival rate. Saliva is oral fluid with intimate contact with OSCC. Besides non-invasive, simple, and rapid to collect, saliva is a potential source of biomarkers. In this study, we build an SRM assay that targets fourteen OSCC candidate biomarker proteins, which were evaluated in a set of clinically-derived saliva samples. Using Skyline software package, we demonstrated a statistically significant higher abundance of the C1R, LCN2, SLPI, FAM49B, TAGLN2, CFB, C3, C4B, LRG1, SERPINA1 candidate biomarkers in the saliva of OSCC patients. Furthermore, our study also demonstrated that CFB, C3, C4B, SERPINA1 and LRG1 are associated with the risk of developing OSCC. Overall, this study successfully used targeted proteomics to measure in saliva a panel of biomarker candidates for OSCC.
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Affiliation(s)
- Rebeca Kawahara
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - James G Bollinger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - César Rivera
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Ana Carolina P Ribeiro
- Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo, Brazil
| | - Thaís Bianca Brandão
- Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo, Brazil
| | - Adriana F Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
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30
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Mehrabani D, Shamsdin SA, Dehghan A, Safarpour A. Clinical significance of serum vascular endothelial growth factor and complement 3a levels in patients with colorectal cancer in southern Iran. Asian Pac J Cancer Prev 2015; 15:9713-7. [PMID: 25520093 DOI: 10.7314/apjcp.2014.15.22.9713] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Colon cancer (CRC) is perhaps the second most common cause of cancer mortality. This study determined the clinical significance of serum vascular endothelial growth factor (VEGF) and serum complement 3a (C3a) levels in patients with CRC in Fars province, southern Iran. MATERIALS AND METHODS Between June 2010 and June 2012, 110 patients with CRC of both genders and different age groups were divided into 3 groups. Group A included patients who had just undergone surgery; Group B had undergone chemotherapy after surgery; and Group C had undergone chemotherapy and radiotherapy after surgery. Twenty one healthy subjects with normal colonoscopy were considered as a control group. ELISA was undertaken to determine VEGF and C3a levels before and after treatment measures. RESULTS The mean age of patients was 53.9±14.1 years. Considering VEGF level, a significant decrease was visible after treatment measures in groups A and B, but not Group C. For VEGF level, the difference was not statistically significant between two genders and various age groups before and after treatment. No significant difference was found for VEGF level between patients and normal group before any treatment. Regarding C3a levels in 101 subjects, they significantly decreased after treatment measures. Before and after treatment, the difference was statistically significant between two genders, but was not statistically significant among various age groups. CONCLUSIONS As VEGF and C3a levels were significantly lower in patients after treatment, these may be beneficial markers in assessment of CRC therapy especially in early stages.
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Affiliation(s)
- Davood Mehrabani
- Stem Cell and Transgenic Technology Research Center, Department of Pathology, Shiraz University of Medical Sciences, Shiraz, Iran E-mail :
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31
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Tan Y, Tang T, Xu H, Zhu C, Cunningham BT. High sensitivity automated multiplexed immunoassays using photonic crystal enhanced fluorescence microfluidic system. Biosens Bioelectron 2015; 73:32-40. [PMID: 26043313 DOI: 10.1016/j.bios.2015.05.041] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/14/2015] [Accepted: 05/17/2015] [Indexed: 12/26/2022]
Abstract
We demonstrate a platform that integrates photonic crystal enhanced fluorescence (PCEF) detection of a surface-based microspot fluorescent assay with a microfluidic cartridge to achieve simultaneous goals of high analytic sensitivity (single digit pg/mL), high selectivity, low sample volume, and assay automation. The PC surface, designed to provide optical resonances for the excitation wavelength and emission wavelength of Cyanines 5 (Cy5), was used to amplify the fluorescence signal intensity measured from a multiplexed biomarker microarray. The assay system is comprised of a plastic microfluidic cartridge for holding the PC and an assay automation system that provides a leak-free fluid interface during introduction of a sequence of fluids under computer control. Through the use of the assay automation system and the PC embedded within the microfluidic cartridge, we demonstrate pg/mL-level limits of detection by performing representative biomarker assays for interleukin 3 (IL3) and Tumor Necrosis Factor (TNF-α). The results are consistent with limits of detection achieved without the use of the microfluidic device with the exception that coefficients of variability from spot-to-spot are substantially lower than those obtained by performing assays with manual manipulation of assay liquids. The system's capabilities are compatible with the goal of diagnostic instruments for point-of-care settings.
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Affiliation(s)
- Yafang Tan
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801, USA
| | - Tiantian Tang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801, USA
| | - Haisheng Xu
- Department of Material Science, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801, USA
| | - Chenqi Zhu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801, USA
| | - Brian T Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801, USA.
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32
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Timms JF, Arslan-Low E, Kabir M, Worthington J, Camuzeaux S, Sinclair J, Szaub J, Afrough B, Podust VN, Fourkala EO, Cubizolles M, Kronenberg F, Fung ET, Gentry-Maharaj A, Menon U, Jacobs I. Discovery of serum biomarkers of ovarian cancer using complementary proteomic profiling strategies. Proteomics Clin Appl 2014; 8:982-93. [PMID: 25290619 PMCID: PMC4737403 DOI: 10.1002/prca.201400063] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/05/2014] [Accepted: 09/30/2014] [Indexed: 12/13/2022]
Abstract
Purpose Ovarian cancer is a devastating disease and biomarkers for its early diagnosis are urgently required. Serum may be a valuable source of biomarkers that may be revealed by proteomic profiling. Herein, complementary serum protein profiling strategies were employed for discovery of biomarkers that could discriminate cases of malignant and benign ovarian cancer. Experimental design Identically collected and processed serum samples from 22 cases of invasive epithelial ovarian cancer, 45 benign ovarian neoplasms, and 64 healthy volunteers were subjected to immunodepletion and protein equalization coupled to 2D‐DIGE/MS and multidimensional fractionation coupled to SELDI‐TOF profiling with MS/MS for protein identification. Selected candidates were verified by ELISA in samples from malignant (n = 70) and benign (n = 89) cases and combined marker panels tested against serum CA125. Results Both profiling platforms were complementary in identifying biomarker candidates, four of which (A1AT, SLPI, APOA4, VDBP) significantly discriminated malignant from benign cases. However, no combination of markers was as good as CA125 for diagnostic accuracy. SLPI was further tested as an early marker using prediagnosis serum samples. While it rose in cases toward diagnosis, it did not discriminate prediagnosis cases from controls. Conclusions and clinical relevance The candidate biomarkers warrant further validation in independent sample sets.
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Affiliation(s)
- John F Timms
- EGA Institute for Women's Health, University College London, London, UK
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33
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Aichler M, Luber B, Lordick F, Walch A. Proteomic and metabolic prediction of response to therapy in gastric cancer. World J Gastroenterol 2014; 20:13648-13657. [PMID: 25320503 PMCID: PMC4194549 DOI: 10.3748/wjg.v20.i38.13648] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 06/13/2014] [Indexed: 02/06/2023] Open
Abstract
Several new treatment options for gastric cancer have been introduced but the prognosis of patients diagnosed with gastric cancer is still poor. Disease prognosis could be improved for high-risk individuals by implementing earlier screenings. Because many patients are asymptomatic during the early stages of gastric cancer, the diagnosis is often delayed and patients present with unresectable locally advanced or metastatic disease. Cytotoxic treatment has been shown to prolong survival in general, but not all patients are responders. The application of targeted therapies and multimodal treatment has improved prognosis for those with advanced disease. However, these new therapeutic strategies do not uniformly benefit all patients. Predicting whether patients will respond to specific therapies would be of particular value and would allow for stratifying patients for personalized treatment strategies. Metabolic imaging by positron emission tomography was the first technique with the potential to predict the response of esophago-gastric cancer to neoadjuvant therapy. Exploring and validating tissue-based biomarkers are ongoing processes. In this review, we discuss the status of several targeted therapies for gastric cancer, as well as proteomic and metabolic methods for investigating biomarkers for therapy response prediction in gastric cancer.
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34
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Shevchenko VE, Arnotskaia NE, Ogorodnikova EV, Davydov MM, Ibraev MA, Turkin IN, Davydov MI. [Search for potential gastric cancer biomarkers using low molecular weight blood plasma proteome profiling by mass spectrometry]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2014; 60:503-14. [PMID: 25249535 DOI: 10.18097/pbmc20146004503] [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: 11/23/2022]
Abstract
Gastric cancer, one of the most widespread malignant tumors, still lacks reliable serum/plasma biomarkers of its early detection. In this study we have developed, unified, and tested a new methodology for search of gastric cancer biomarkers based on profiling of low molecular weight proteome (LMWP) (1-17 kDa). This approach included three main components: sample pre-fractionation, matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS), data analysis by a bioinformatics software package. Applicability and perspectives of the developed approach for detection of potential gastric cancer markers during LMWP analysis have been demonstrated using 69 plasma samples from patients with gastric cancer (stages I-IV) and 238 control samples. The study revealed peptides/polypeptides, which may be potentially used for detection of this pathology.
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35
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Reumer A, Maes E, Mertens I, Cho WCS, Landuyt B, Valkenborg D, Schoofs L, Baggerman G. Colorectal cancer biomarker discovery and validation using LC-MS/MS-based proteomics in blood: truth or dare? Expert Rev Proteomics 2014; 11:449-463. [PMID: 24702250 DOI: 10.1586/14789450.2014.905743] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Globally, colorectal cancer (CRC) is the third most common malignant neoplasm. However, highly sensitive, specific, noninvasive tests that allow CRC diagnosis at an early stage are still needed. As circulatory blood reflects the physiological status of an individual and/or the disease status for several disorders, efforts have been undertaken to identify candidate diagnostic CRC markers in plasma and serum. In this review, the challenges, bottlenecks and promising properties of mass spectrometry (MS)-based proteomics in blood are discussed. More specifically, important aspects in clinical design, sample retrieval, sample preparation, and MS analysis are presented. The recent developments in targeted MS approaches in plasma or serum are highlighted as well.
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Affiliation(s)
- Ank Reumer
- KU Leuven, Animal Physiology and Neurobiology Section, Naamsestraat 59, BE-3000 Leuven, Belgium
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Chung L, Moore K, Phillips L, Boyle FM, Marsh DJ, Baxter RC. Novel serum protein biomarker panel revealed by mass spectrometry and its prognostic value in breast cancer. Breast Cancer Res 2014; 16:R63. [PMID: 24935269 PMCID: PMC4095593 DOI: 10.1186/bcr3676] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 06/02/2014] [Indexed: 12/15/2022] Open
Abstract
Introduction Serum profiling using proteomic techniques has great potential to detect biomarkers that might improve diagnosis and predict outcome for breast cancer patients (BC). This study used surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS) to identify differentially expressed proteins in sera from BC and healthy volunteers (HV), with the goal of developing a new prognostic biomarker panel. Methods Training set serum samples from 99 BC and 51 HV subjects were applied to four adsorptive chip surfaces (anion-exchange, cation-exchange, hydrophobic, and metal affinity) and analyzed by time-of-flight MS. For validation, 100 independent BC serum samples and 70 HV samples were analyzed similarly. Cluster analysis of protein spectra was performed to identify protein patterns related to BC and HV groups. Univariate and multivariate statistical analyses were used to develop a protein panel to distinguish breast cancer sera from healthy sera, and its prognostic potential was evaluated. Results From 51 protein peaks that were significantly up- or downregulated in BC patients by univariate analysis, binary logistic regression yielded five protein peaks that together classified BC and HV with a receiver operating characteristic (ROC) area-under-the-curve value of 0.961. Validation on an independent patient cohort confirmed the five-protein parameter (ROC value 0.939). The five-protein parameter showed positive association with large tumor size (P = 0.018) and lymph node involvement (P = 0.016). By matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, immunoprecipitation and western blotting the proteins were identified as a fragment of apolipoprotein H (ApoH), ApoCI, complement C3a, transthyretin, and ApoAI. Kaplan-Meier analysis on 181 subjects after median follow-up of >5 years demonstrated that the panel significantly predicted disease-free survival (P = 0.005), its efficacy apparently greater in women with estrogen receptor (ER)-negative tumors (n = 50, P = 0.003) compared to ER-positive (n = 131, P = 0.161), although the influence of ER status needs to be confirmed after longer follow-up. Conclusions Protein mass profiling by MS has revealed five serum proteins which, in combination, can distinguish between serum from women with breast cancer and healthy control subjects with high sensitivity and specificity. The five-protein panel significantly predicts recurrence-free survival in women with ER-negative tumors and may have value in the management of these patients.
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Tsang AHF, Cheng KH, Wong ASP, Ng SSM, Ma BBY, Chan CML, Tsui NBY, Chan LWC, Yung BYM, Wong SCC. Current and future molecular diagnostics in colorectal cancer and colorectal adenoma. World J Gastroenterol 2014; 20:3847-3857. [PMID: 24744577 PMCID: PMC3983441 DOI: 10.3748/wjg.v20.i14.3847] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/10/2014] [Accepted: 02/27/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers in developed countries. On the other hand, CRC is also one of the most curable cancers if it is detected in early stages through regular colonoscopy or sigmoidoscopy. Since CRC develops slowly from precancerous lesions, early detection can reduce both the incidence and mortality of the disease. Fecal occult blood test is a widely used non-invasive screening tool for CRC. Although fecal occult blood test is simple and cost-effective in screening CRC, there is room for improvement in terms of the accuracy of the test. Genetic dysregulations have been found to play an important role in CRC development. With better understanding of the molecular basis of CRC, there is a growing expectation on the development of diagnostic tests based on more sensitive and specific molecular markers and those tests may provide a breakthrough to the limitations of current screening tests for CRC. In this review, the molecular basis of CRC development, the characteristics and applications of different non-invasive molecular biomarkers, as well as the technologies available for the detection were discussed. This review intended to provide a summary on the current and future molecular diagnostics in CRC and its pre-malignant state, colorectal adenoma.
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Álvarez-Chaver P, Otero-Estévez O, Páez de la Cadena M, Rodríguez-Berrocal FJ, Martínez-Zorzano VS. Proteomics for discovery of candidate colorectal cancer biomarkers. World J Gastroenterol 2014; 20:3804-3824. [PMID: 24744574 PMCID: PMC3983438 DOI: 10.3748/wjg.v20.i14.3804] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/24/2014] [Accepted: 03/10/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the second most common cause of cancer-related deaths in Europe and other Western countries, mainly due to the lack of well-validated clinically useful biomarkers with enough sensitivity and specificity to detect this disease at early stages. Although it is well known that the pathogenesis of CRC is a progressive accumulation of mutations in multiple genes, much less is known at the proteome level. Therefore, in the last years many proteomic studies have been conducted to find new candidate protein biomarkers for diagnosis, prognosis and as therapeutic targets for this malignancy, as well as to elucidate the molecular mechanisms of colorectal carcinogenesis. An important advantage of the proteomic approaches is the capacity to look for multiple differentially expressed proteins in a single study. This review provides an overview of the recent reports describing the different proteomic tools used for the discovery of new protein markers for CRC such as two-dimensional electrophoresis methods, quantitative mass spectrometry-based techniques or protein microarrays. Additionally, we will also focus on the diverse biological samples used for CRC biomarker discovery such as tissue, serum and faeces, besides cell lines and murine models, discussing their advantages and disadvantages, and summarize the most frequently identified candidate CRC markers.
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Fan NJ, Kang R, Ge XY, Li M, Liu Y, Chen HM, Gao CF. Identification alpha-2-HS-glycoprotein precursor and tubulin beta chain as serology diagnosis biomarker of colorectal cancer. Diagn Pathol 2014; 9:53. [PMID: 24618180 PMCID: PMC3975189 DOI: 10.1186/1746-1596-9-53] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 03/05/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) remains a major worldwide cause of cancer-related morbidity and mortality largely due to the insidious onset of the disease. The current clinical procedures utilized for disease diagnosis are invasive, unpleasant, and inconvenient. Hence, the need for simple blood tests that could be used for the early detection is crucial for its ultimate control and prevention. METHODS The present work is a case-control study focused on proteomic analysis of serum of healthy volunteers and CRC patients by the ClinProt profiling technology based on mass spectrometry. This approach allowed to identifying a pattern of proteins/peptides able to differentiate the studied populations. Moreover, some of peptides differentially expressed in the serum of patients as compared to healthy volunteers were identified by LTQ Orbitrap XL. RESULTS A Quick Classifier Algorithm was used to construct the peptidome patterns (m/z 1208, 1467, 1505, 1618, 1656 and 4215) for the identification of CRC from healthy volunteers with accuracy close to 100% (>CEA, P < 0.05). Peaks at m/z 1505 and 1618 were identified as alpha-2-HS-glycoprotein precursor and tubulin beta chain, respectively. CONCLUSIONS Alpha-2-HS-glycoprotein precursor and tubulin beta chain could be involved in the pathogenesis of CRC and perform as potential serology diagnosis biomarker. VIRTUAL SLIDES The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/4796578761089186.
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Affiliation(s)
| | | | | | | | | | | | - Chun-fang Gao
- Institute of Anal-colorectal Surgery, No,150 Central Hospital of PLA, Luoyang, RP China.
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Shafiee H, Lidstone EA, Jahangir M, Inci F, Hanhauser E, Henrich TJ, Kuritzkes DR, Cunningham BT, Demirci U. Nanostructured optical photonic crystal biosensor for HIV viral load measurement. Sci Rep 2014; 4:4116. [PMID: 24576941 PMCID: PMC3937800 DOI: 10.1038/srep04116] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/28/2014] [Indexed: 01/20/2023] Open
Abstract
Detecting and quantifying biomarkers and viruses in biological samples have broad applications in early disease diagnosis and treatment monitoring. We have demonstrated a label-free optical sensing mechanism using nanostructured photonic crystals (PC) to capture and quantify intact viruses (HIV-1) from biologically relevant samples. The nanostructured surface of the PC biosensor resonantly reflects a narrow wavelength band during illumination with a broadband light source. Surface-adsorbed biotarget induces a shift in the resonant Peak Wavelength Value (PWV) that is detectable with <10 pm wavelength resolution, enabling detection of both biomolecular layers and small number of viruses that sparsely populate the transducer surface. We have successfully captured and detected HIV-1 in serum and phosphate buffered saline (PBS) samples with viral loads ranging from 104 to 108 copies/mL. The surface density of immobilized biomolecular layers used in the sensor functionalization process, including 3-mercaptopropyltrimethoxysilane (3-MPS), N-gamma-Maleimidobutyryl-oxysuccinimide ester (GMBS), NeutrAvidin, anti-gp120, and bovine serum albumin (BSA) were also quantified by the PC biosensor.
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Affiliation(s)
- Hadi Shafiee
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Erich A Lidstone
- Department of Electrical & Computer Engineering, and Department of Bioengineering, University of Illinois at Urbana-Champaign, IL, USA
| | - Muntasir Jahangir
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Fatih Inci
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily Hanhauser
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, MA, USA
| | - Timothy J Henrich
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, MA, USA
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, MA, USA
| | - Brian T Cunningham
- Department of Electrical & Computer Engineering, and Department of Bioengineering, University of Illinois at Urbana-Champaign, IL, USA
| | - Utkan Demirci
- 1] Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA [2] Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, MA, USA [3] Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA
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Hudler P, Kocevar N, Komel R. Proteomic approaches in biomarker discovery: new perspectives in cancer diagnostics. ScientificWorldJournal 2014; 2014:260348. [PMID: 24550697 PMCID: PMC3914447 DOI: 10.1155/2014/260348] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 10/08/2013] [Indexed: 12/14/2022] Open
Abstract
Despite remarkable progress in proteomic methods, including improved detection limits and sensitivity, these methods have not yet been established in routine clinical practice. The main limitations, which prevent their integration into clinics, are high cost of equipment, the need for highly trained personnel, and last, but not least, the establishment of reliable and accurate protein biomarkers or panels of protein biomarkers for detection of neoplasms. Furthermore, the complexity and heterogeneity of most solid tumours present obstacles in the discovery of specific protein signatures, which could be used for early detection of cancers, for prediction of disease outcome, and for determining the response to specific therapies. However, cancer proteome, as the end-point of pathological processes that underlie cancer development and progression, could represent an important source for the discovery of new biomarkers and molecular targets for tailored therapies.
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Affiliation(s)
- Petra Hudler
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Nina Kocevar
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Radovan Komel
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
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Ebert M, Xing X, Burgermeister E, Schmid R, Röcken C. Perspectives of clinical proteomics in gastrointestinal cancer. Expert Rev Anticancer Ther 2014; 7:465-9. [PMID: 17428167 DOI: 10.1586/14737140.7.4.465] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Every year approximately 2 million Europeans develop a malignancy; the group of gastrointestinal cancers is the single largest group, with approximately 600,000 new cancers annually. Despite recent innovations and developments in the diagnosis and management of these cancers, prognosis remains poor and treatment options limited. In recent years, new technological advances in proteome analysis and its application to patient management have been made and are the subject of ongoing clinical studies. The identification of biomarkers and biomarker patterns has raised hope that noninvasive diagnosis of cancers in their early stages may soon be an option. However, before the results of proteome analysis can be implemented in the management of cancer patients, further validation of these markers and the issues of sensitivity, specificity, reproducibility and accuracy need to be addressed and solved.
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Affiliation(s)
- Matthias Ebert
- Technische Universität München, Department of Medicine II, Klinikum rechts der Isar, München, Germany.
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Zou X, Feng B, Dong T, Yan G, Tan B, Shen H, Huang A, Zhang X, Zhang M, Yang P, Zheng M, Zhang Y. Up-regulation of type I collagen during tumorigenesis of colorectal cancer revealed by quantitative proteomic analysis. J Proteomics 2013; 94:473-85. [DOI: 10.1016/j.jprot.2013.10.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 09/29/2013] [Accepted: 10/15/2013] [Indexed: 01/23/2023]
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Kim K, Lee KH, Lee J, Choi J. Overview of current standpoints in profiling of circulating tumor cells. Arch Pharm Res 2013; 37:88-95. [PMID: 24214218 DOI: 10.1007/s12272-013-0285-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 10/29/2013] [Indexed: 12/27/2022]
Abstract
The goal of this review is summarizing current technologies developed as the in vitro prognostic/diagnostic systems that can rapidly separate and detect circulating tumor cells (CTCs) from cancer patient's blood (1-10 CTCs of 1 billion red blood cells) by labeled and non-labeled method. The review is focused on three major areas of CTC research (1) Summary of previous research on capturing of CTCs, (2) New development of the in vitro prognostic diagnosis system of cancer that is capable of rapid separation of CTCs, (3) Future direction on development of new technologies for CTC profiling. Current CTC researches have helped on identifying patients who may benefit from chemotherapy before treatment, patients who may benefit from continued chemotherapy, and leading to clinical development of CTC-guided chemotherapy strategies. We analyze the feasibility of clinical application of these current CTC research for the ultimate goal of increasing the survivability of cancer patient. The biomolecular assays of viable CTCs from cancer patient may elucidate the mechanism of metastasis and tumor initiating cells and also may have high impact on the development of personalized medicine to overcome the incurable diseases.
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Affiliation(s)
- Kyobum Kim
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
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Zheng X, Xie G, Jia W. Metabolomic profiling in colorectal cancer: opportunities for personalized medicine. Per Med 2013; 10:741-755. [PMID: 29768755 DOI: 10.2217/pme.13.73] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is one of the most common types of cancer in the world, with high prevalence and mortality. Understanding the alterations of cancer metabolism and identifying reliable biomarkers would facilitate the development of novel technologies of CRC screening and early diagnosis, as well as new approaches to providing personalized medicine. Metabolomics, as an emerging molecular phenotyping approach, provides a clinical platform technology with an unprecedented amount of metabolic readout information, which is ideal for theranostic biomarker discovery. Metabolic signatures can link the unique pathophysiological states of patients to personalized health monitoring and intervention strategies. This article presents an overview of the metabolomic studies of CRC with a focus on recent advances in the biomarker discovery in serum, urine, fecal water and tissue samples for cancer diagnosis. The development and application of metabolomics towards personalized medicine, including early diagnosis, cancer staging, treatment and drug discovery are also discussed.
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Affiliation(s)
- Xiaojiao Zheng
- Center for Translational Medicine & Shanghai Key Laboratory of Diabetes Mellitus, Department of Endocrinology & Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Guoxiang Xie
- University of Hawaii Cancer Center, Honolulu, Hawaii 96813, USA
| | - Wei Jia
- E-institute of Shanghai Municipal Education Committee, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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Ivancic MM, Huttlin EL, Chen X, Pleiman JK, Irving AA, Hegeman AD, Dove WF, Sussman MR. Candidate serum biomarkers for early intestinal cancer using 15N metabolic labeling and quantitative proteomics in the ApcMin/+ mouse. J Proteome Res 2013; 12:4152-66. [PMID: 23924158 DOI: 10.1021/pr400467c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Current screening procedures for colorectal cancer are imperfect and highly invasive and result in increased mortality rates due to low compliance. The goal of the experiments reported herein is to identify potential blood-based biomarkers indicative of early stage intestinal cancers using the ApcMin/+ mouse model of intestinal cancer as an experimental system. Serum proteins from tumor-bearing ApcMin/+ mice were quantitatively compared to tumor-free Apc+/+ wild-type mice via in anima metabolic labeling with 14N/15N-labeled Spirulina algae and an LTQ Orbitrap mass spectrometer. Out of 1116 total serum proteins quantified, this study identified 40 that were differentially expressed and correlated with the increase in intestinal neoplasms. A subset of these differentially expressed proteins underwent a secondary quantitative screen using selected reaction monitoring-mass spectrometry with stable isotope-labeled peptides. Using both quantitative techniques, we identified MGAM and COL1A1 as downregulated and ITIH3 and F5 as upregulated in serum. All but COL1A1 were similarly differentially expressed in the mRNA of neoplastic colonic tissues of ApcMin/+ mice compared to normal wild-type tissue. These differentially expressed proteins identified in the ApcMin/+ mouse model have provided a set of candidate biomarkers for future validation screens in humans.
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Affiliation(s)
- Melanie M Ivancic
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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Choi JW, Liu H, Shin DH, Yu GI, Hwang JS, Kim ES, Yun JW. Proteomic and cytokine plasma biomarkers for predicting progression from colorectal adenoma to carcinoma in human patients. Proteomics 2013; 13:2361-74. [PMID: 23606366 DOI: 10.1002/pmic.201200550] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 03/28/2013] [Accepted: 03/30/2013] [Indexed: 12/12/2022]
Abstract
In the present study, we screened proteomic and cytokine biomarkers between patients with adenomatous polyps and colorectal cancer (CRC) in order to improve our understanding of the molecular mechanisms behind turmorigenesis and tumor progression in CRC. To this end, we performed comparative proteomic analysis of plasma proteins using a combination of 2DE and MS as well as profiled differentially regulated cytokines and chemokines by multiplex bead analysis. Proteomic analysis identified 11 upregulated and 13 downregulated plasma proteins showing significantly different regulation patterns with diagnostic potential for predicting progression from adenoma to carcinoma. Some of these proteins have not previously been implicated in CRC, including upregulated leucine-rich α-2-glycoprotein, hemoglobin subunit β, Ig α-2 chain C region, and complement factor B as well as downregulated afamin, zinc-α-2-glycoprotein, vitronectin, and α-1-antichymotrypsin. In addition, plasma levels of three cytokines/chemokines, including interleukin-8, interferon gamma-induced protein 10, and tumor necrosis factor α, were remarkably elevated in patients with CRC compared to those with adenomatous polyps. Although further clinical validation is required, these proteins and cytokines can be established as novel biomarkers for CRC and/or its progression from colon adenoma.
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Affiliation(s)
- Jung-Won Choi
- Department of Biotechnology, Daegu University, Kyungsan, Republic of Korea
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He K, Wen XY, Li AL, Li T, Wang J, Wang HX, Wang N. Serum peptidome variations in a healthy population: reference to identify cancer-specific peptides. PLoS One 2013; 8:e63724. [PMID: 23667664 PMCID: PMC3648468 DOI: 10.1371/journal.pone.0063724] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 04/11/2013] [Indexed: 11/18/2022] Open
Abstract
The emergence of mass spectrometry (MS)-based signatures as biomarkers has generated considerable enthusiasm among oncologists. However, variations in normal individuals also exist, and a better understanding of serum peptide patterns of healthy individuals will be important for further exploring disease-specific serum peptide patterns. Following development of a serum peptide pattern platform, we analyzed 500 serum samples obtained from healthy individuals. Samples from breast (n = 84), lung (n = 70), and rectal (n = 30) cancer patients were also examined. Extensive data analysis revealed negligible contributions of age to serum peptide patterns except in healthy individuals between 20–30 and 60+ years of age. Gender-related variations in the serum patterns of healthy individuals were only observed in 20–30 year-old individuals. Our results revealed substantial variation in individual peptide profiles, but 65 peptides were detected at a 20% higher frequency in the healthy population. A peptide profile was developed for each type of cancer, containing 10 discriminating peptides not prevalent in healthy individuals. Sequence identification of 111 signature peptides revealed that they fell into several tight clusters and most were exopeptidase products of serum resident proteins. We have obtained a MS-based serum peptide profile for healthy individuals, providing a reference for observing the occurrence of cancer-specific peptides.
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Affiliation(s)
- Kun He
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China
| | - Xin-Yu Wen
- The 301 General Hospital, Beijing, China
| | - Ai-Ling Li
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China
| | - Tao Li
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China
| | - Jie Wang
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China
| | - Hong-Xia Wang
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China
| | - Na Wang
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China
- * E-mail:
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