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Wei X, Wang L, Yang B, Ma Y, Yuan W, Ma J. Orosomucoid 2 upregulation mediates liver injury-induced colorectal cancer liver metastasis by promoting EMT and cell migration. Cancer Sci 2024. [PMID: 38475962 DOI: 10.1111/cas.16131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/06/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
The relationship between drug-induced liver injury and liver metastasis of colorectal cancer and the underlying mechanisms are not well understood. In this study, we used carbon tetrachloride to construct a classic mouse liver injury model and injected CT26 colorectal cancer cells into the mouse spleen to simulate the natural route of colorectal cancer liver metastasis. Liver injury significantly increased the number of colorectal cancer liver metastases. Transcriptome sequencing and data-independent acquisition protein quantification identified proteins that were significantly differentially expressed in injured livers, and orosomucoid (ORM) 2 was identified as a target protein for tumor liver metastasis. In vitro experiments showed that exogenous ORM2 protein increased the expression of EMT markers such as Twist, Zeb1, Vim, Snail1 and Snail2 and chemokine ligands to promote CT26 cell migration. In addition, liver-specific overexpression of the ORM2 protein in the mouse model significantly promoted tumor cell liver metastasis without inducing liver injury. Our results indicate that drug-induced liver injury can promote colorectal cancer liver metastasis and that ORM2 can promote cell migration by inducing EMT in tumor cells.
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Affiliation(s)
- Xundong Wei
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Lei Wang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Medical Laboratory Center, Chifeng Municipal Hospital/Chifeng Clinical College, Inner Mongolia Medical University, Chifeng, China
| | - Bing Yang
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuanyuan Ma
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Yuan
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Ma
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
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2
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Li X, Wang C, Yang H, Pei D, Liu Y, Yan S, Li Y. Screening and verification of genes related to polycystic ovary syndrome. J Int Med Res 2023; 51:3000605221147444. [PMID: 36628439 PMCID: PMC9837284 DOI: 10.1177/03000605221147444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVE To identify key genes involved in occurrence and development of polycystic ovary syndrome (PCOS). METHODS By downloading the GSE85932 dataset from the GEO database, we used bioinformatical analysis to analyse differentially expressed genes (DEGs) from blood samples of eight women with PCOS and eight matched controls. Following bioinformatic analysis, we performed a cross-sectional study of serum samples taken from 79 women with PCOS and 36 healthy controls. RESULTS From the 178 DEGs identified by bioinformatical analysis, 15 genes were identified as significant, and of these, ORM1 and ORM2 were selected for further verification as potential biomarkers for PCOS. Serum ORM1 and ORM2 levels were significantly increased in women with PCOS, and had a high diagnostic value. ORM1 and ORM2 were positively correlated with testosterone, cholesterol, and triglycerides. ORM1 levels were negatively correlated with high density lipoprotein (HDL) while ORM2 levels showed no significant correlation. CONCLUSIONS ORM may be an effective biomarker for the diagnosis of PCOS and its monitoring may be a useful therapeutic strategy.
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Affiliation(s)
| | - Chunxia Wang
- Chunxia Wang, Department of Medical Laboratory, Henan Provincial Hospital of Traditional Chinese Medicine (The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), 6 Dongfeng Road, Jinshui, Zhengzhou, Henan 450002, China.
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3
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Ge Y, Xu B, Cai H, Jing W, Ouyang Q, Yuan Q, Li X, Fan Y, Shen Y, Shi Q, Wang Q, Cui L, Yin X, Ma G. Diagnostic role of plasma ORM2 in differentiating prostate cancer from benign prostatic hyperplasia. J Cancer Res Clin Oncol 2022; 149:2301-2310. [PMID: 36198834 DOI: 10.1007/s00432-022-04380-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/23/2022] [Indexed: 11/26/2022]
Abstract
PURPOSE Markers are needed to increase the diagnostic accuracy of prostate-specific antigen (PSA) in prostate cancer (PCa) screening. Mounting evidence has shown that plasma proteins can be hopeful biomarkers for cancer diagnosis. METHODS Tandem mass tag (TMT)-based proteomics and parallel reaction monitoring (PRM) analysis were used to screen the differential proteins and further validated in other independent studies (n = 539). Receiver-operating characteristic (ROC), decision curves and nomograms were applied to assess the diagnostic accuracy of biomarkers. RESULTS Three candidate proteins (DBP, LCAT and ORM2) were preliminarily screened. Subsequent validation studies revealed significant upregulation of ORM2 in PCa patients across other independent cohorts. ORM2 yielded excellent discriminative power for PCa from benign prostatic hyperplasia (BPH) patients (AUC = 0.861 and 0.814 in validation phases 2a and 2b, respectively). Importantly, the combination of ORM2 and PSA gave better predictive accuracy than PSA alone. We incorporated age, PSA and ORM2 into a nomogram, which yielded C-index of 0.883 in validation phase 2a. A similar C-index of 0.879 was obtained in external validation phase 2b. CONCLUSIONS In summary, our study suggests that ORM2 could be treated as a complementary biomarker for PSA in distinguishing PCa from BPH.
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Affiliation(s)
- Yuqiu Ge
- Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, 211198, China
- Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, 214122, China
| | - Bin Xu
- Department of Urology, The Affiliated Zhongda Hospital of Southeast University, Nanjing, 210003, China
| | - Hongzhou Cai
- Department of Urologic Surgery, The Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, 210009, China
| | - Wentao Jing
- Department of Urology, Yixing People's Hospital, Wuxi, 214200, China
| | - Qiong Ouyang
- Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, 211198, China
| | - Qinbo Yuan
- Department of Urology, Wuxi Fifth People's Hospital, Wuxi, 214011, China
| | - Xu Li
- Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, 211198, China
| | - Yuanming Fan
- Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, 211198, China
| | - Yang Shen
- Department of Urology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210000, China
| | - Qianqian Shi
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, 213000, China
| | - Qiangdong Wang
- Department of Urology, Huaiyin Hospital of Huai'an City, Huai'an, China.
- Department of Urology, Huaiyin People's Hospital of Huai'an City, Huai'an, China.
| | - Li Cui
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, 213000, China.
| | - Xiaojian Yin
- State Key Laboratory of Natural Medicines, Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Gaoxiang Ma
- Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, 211198, China.
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
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4
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Tyrrell DJ, Chen J, Li BY, Wood SC, Rosebury-Smith W, Remmer HA, Jiang L, Zhang M, Salmon M, Ailawadi G, Yang B, Goldstein DR. Aging Alters the Aortic Proteome in Health and Thoracic Aortic Aneurysm. Arterioscler Thromb Vasc Biol 2022; 42:1060-1076. [PMID: 35510553 PMCID: PMC9339483 DOI: 10.1161/atvbaha.122.317643] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Aging enhances most chronic diseases but its impact on human aortic tissue in health and in thoracic aortic aneurysms (TAA) remains unclear. METHODS We employed a human aortic biorepository of healthy specimens (n=17) and those that underwent surgical repair for TAA (n=20). First, we performed proteomics comparing aortas of healthy donors to aneurysmal specimens, in young (ie, <60 years of age) and old (ie, ≥60 years of age) subjects. Second, we measured proteins, via immunoblotting, involved in mitophagy (ie, Parkin) and also mitochondrial-induced inflammatory pathways, specifically TLR (toll-like receptor) 9, STING (stimulator of interferon genes), and IFN (interferon)-β. RESULTS Proteomics revealed that aging transformed the aorta both quantitatively and qualitatively from health to TAA. Whereas young aortas exhibited an enrichment of immunologic processes, older aortas exhibited an enrichment of metabolic processes. Immunoblotting revealed that the expression of Parkin directly correlated to subject age in health but inversely to subject age in TAA. In TAA, but not in health, phosphorylation of STING and the expression of IFN-β was impacted by aging regardless of whether subjects had bicuspid or tricuspid valves. In subjects with bicuspid valves and TAAs, TLR9 expression positively correlated with subject age. Interestingly, whereas phosphorylation of STING was inversely correlated with subject age, IFN-β positively correlated with subject age. CONCLUSIONS Aging transforms the human aortic proteome from health to TAA, leading to a differential regulation of biological processes. Our results suggest that the development of therapies to mitigate vascular diseases including TAA may need to be modified depending on subject age.
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Affiliation(s)
| | - Judy Chen
- Department of Internal Medicine, University of Michigan, USA,Program on Immunology, University of Michigan, USA
| | - Benjamin Y. Li
- Department of Internal Medicine, University of Michigan, USA
| | - Sherri C. Wood
- Department of Internal Medicine, University of Michigan, USA
| | | | | | - Longtan Jiang
- Department of Cardiac Surgery, University of Michigan, USA
| | - Min Zhang
- Department of Biostatistics, University of Michigan, USA
| | - Morgan Salmon
- Department of Cardiac Surgery, University of Michigan, USA
| | - Gorav Ailawadi
- Department of Cardiac Surgery, University of Michigan, USA
| | - Bo Yang
- Department of Cardiac Surgery, University of Michigan, USA
| | - Daniel R. Goldstein
- Department of Internal Medicine, University of Michigan, USA,Program on Immunology, University of Michigan, USA,Department of Microbiology and Immunology, University of Michigan, USA
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5
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Tognetti M, Sklodowski K, Müller S, Kamber D, Muntel J, Bruderer R, Reiter L. Biomarker Candidates for Tumors Identified from Deep-Profiled Plasma Stem Predominantly from the Low Abundant Area. J Proteome Res 2022; 21:1718-1735. [PMID: 35605973 PMCID: PMC9251764 DOI: 10.1021/acs.jproteome.2c00122] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The plasma proteome
has the potential to enable a holistic analysis
of the health state of an individual. However, plasma biomarker discovery
is difficult due to its high dynamic range and variability. Here,
we present a novel automated analytical approach for deep plasma profiling
and applied it to a 180-sample cohort of human plasma from lung, breast,
colorectal, pancreatic, and prostate cancers. Using a controlled quantitative
experiment, we demonstrate a 257% increase in protein identification
and a 263% increase in significantly differentially abundant proteins
over neat plasma. In the cohort, we identified 2732 proteins. Using
machine learning, we discovered biomarker candidates such as STAT3
in colorectal cancer and developed models that classify the diseased
state. For pancreatic cancer, a separation by stage was achieved.
Importantly, biomarker candidates came predominantly from the low
abundance region, demonstrating the necessity to deeply profile because
they would have been missed by shallow profiling.
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Affiliation(s)
| | | | | | | | - Jan Muntel
- Biognosys, Schlieren, Zurich 8952, Switzerland
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Rajczewski AT, Han Q, Mehta S, Kumar P, Jagtap PD, Knutson CG, Fox JG, Tretyakova NY, Griffin TJ. Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow. Proteomes 2022; 10:proteomes10020011. [PMID: 35466239 PMCID: PMC9036229 DOI: 10.3390/proteomes10020011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/27/2022] [Accepted: 04/07/2022] [Indexed: 11/24/2022] Open
Abstract
Chronic inflammation of the colon causes genomic and/or transcriptomic events, which can lead to expression of non-canonical protein sequences contributing to oncogenesis. To better understand these mechanisms, Rag2−/−Il10−/− mice were infected with Helicobacter hepaticus to induce chronic inflammation of the cecum and the colon. Transcriptomic data from harvested proximal colon samples were used to generate a customized FASTA database containing non-canonical protein sequences. Using a proteogenomic approach, mass spectrometry data for proximal colon proteins were searched against this custom FASTA database using the Galaxy for Proteomics (Galaxy-P) platform. In addition to the increased abundance in inflammatory response proteins, we also discovered several non-canonical peptide sequences derived from unique proteoforms. We confirmed the veracity of these novel sequences using an automated bioinformatics verification workflow with targeted MS-based assays for peptide validation. Our bioinformatics discovery workflow identified 235 putative non-canonical peptide sequences, of which 58 were verified with high confidence and 39 were validated in targeted proteomics assays. This study provides insights into challenges faced when identifying non-canonical peptides using a proteogenomics approach and demonstrates an integrated workflow addressing these challenges. Our bioinformatic discovery and verification workflow is publicly available and accessible via the Galaxy platform and should be valuable in non-canonical peptide identification using proteogenomics.
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Affiliation(s)
- Andrew T. Rajczewski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.T.R.); (Q.H.); (S.M.); (P.K.); (P.D.J.)
| | - Qiyuan Han
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.T.R.); (Q.H.); (S.M.); (P.K.); (P.D.J.)
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.T.R.); (Q.H.); (S.M.); (P.K.); (P.D.J.)
| | - Praveen Kumar
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.T.R.); (Q.H.); (S.M.); (P.K.); (P.D.J.)
| | - Pratik D. Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.T.R.); (Q.H.); (S.M.); (P.K.); (P.D.J.)
| | - Charles G. Knutson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.)
| | - James G. Fox
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.)
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry, the Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.T.R.); (Q.H.); (S.M.); (P.K.); (P.D.J.)
- Correspondence:
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Kopylov AT, Papysheva O, Gribova I, Kaysheva AL, Kotaysch G, Kharitonova L, Mayatskaya T, Nurbekov MK, Schipkova E, Terekhina O, Morozov SG. Severe types of fetopathy are associated with changes in the serological proteome of diabetic mothers. Medicine (Baltimore) 2021; 100:e27829. [PMID: 34766598 PMCID: PMC8589259 DOI: 10.1097/md.0000000000027829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/27/2022] Open
Abstract
ABSTRACT Pregestational or gestational diabetes are the main risk factors for diabetic fetopathy. There are no generalized signs of fetopathy before the late gestational age due to insufficient sensitivity of currently employed instrumental methods. In this cross-sectional observational study, we investigated several types of severe diabetic fetopathy (cardiomyopathy, central nervous system defects, and hepatomegaly) established in type 2 diabetic mothers during 30 to 35 gestational weeks and confirmed upon delivery. We examined peripheral blood plasma and determined a small proportion of proteins strongly associated with a specific type of fetopathy or anatomical malfunction. Most of the examined markers participate in critical processes at different stages of embryogenesis and regulate various phases of morphogenesis. Alterations in CDCL5 had a significant impact on mRNA splicing and DNA repair. Patients with central nervous system defects were characterized by the greatest depletion (ca. 7% of the basal level) of DFP3, a neurotrophic factor needed for the proper specialization of oligodendrocytes. Dysregulation of noncanonical wingless-related integration site signaling pathway (Wnt) signaling guided by pigment epithelium-derived factor (PEDF) and disheveled-associated activator of morphogenesis 2 (DAAM2) was also profound. In addition, deficiency in retinoic acid and thyroxine transport was exhibited by the dramatic increase of transthyretin (TTHY). The molecular interplay between the identified serological markers leads to pathologies in fetal development on the background of a diabetic condition. These warning serological markers can be quantitatively examined, and their profile may reflect different severe types of diabetic fetopathy, producing a beneficial effect on the current standard care for pregnant women and infants.
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Affiliation(s)
- Arthur T. Kopylov
- Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, Russia
| | - Olga Papysheva
- S.S. Yudin 7th State Clinical Hospital, 4 Kolomenskaya str., Moscow, Russia
| | - Iveta Gribova
- N.E. Bauman 29th State Clinical Hospital, 2 Hospitalnaya sq., Moscow, Russia
| | - Anna L. Kaysheva
- Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, Russia
| | - Galina Kotaysch
- N.E. Bauman 29th State Clinical Hospital, 2 Hospitalnaya sq., Moscow, Russia
| | - Lubov Kharitonova
- N.I. Pirogov Medical University, 1 Ostrovityanova st., Moscow, Russia
| | | | - Malik K. Nurbekov
- Institute of General Pathology and Pathophysiology, 8 Baltyiskaya str., Moscow, Russia
| | - Ekaterina Schipkova
- Institute of General Pathology and Pathophysiology, 8 Baltyiskaya str., Moscow, Russia
| | - Olga Terekhina
- Institute of General Pathology and Pathophysiology, 8 Baltyiskaya str., Moscow, Russia
| | - Sergey G. Morozov
- N.E. Bauman 29th State Clinical Hospital, 2 Hospitalnaya sq., Moscow, Russia
- Institute of General Pathology and Pathophysiology, 8 Baltyiskaya str., Moscow, Russia
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Lei M, Zhang D, Sun Y, Zou C, Wang Y, Hong Y, Jiao Y, Cai C. Web-based transcriptome analysis determines a sixteen-gene signature and associated drugs on hearing loss patients: A bioinformatics approach. J Clin Lab Anal 2021; 35:e24065. [PMID: 34758154 PMCID: PMC8649328 DOI: 10.1002/jcla.24065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022] Open
Abstract
Background Hearing loss is becoming more and more general. It may occur at all age and affect the language learning ability of children and trigger serious social problems. Methods The hearing loss differentially expressed genes (HL‐DEGs) were recognized through a comparison with healthy subjects. The Gene Ontology (GO) analysis was executed by DAVID. The reactome analysis of HL‐DEGs was performed by Clue‐GO. Next, we used STRING, an online website, to identify crucial protein‐protein interactions among HL‐DEGs. Cytoscape software was employed to construct a protein‐protein interaction network. MCODE, a plug‐in of the Cytoscape software, was used for module analysis. Finally, we used DGIdb database to ascertain the targeted drugs for MCODE genes. Results Four hundred four HL‐DEGs were identified, among which the most up‐regulated 10 genes were AL008707.1, SDR42E1P5, BX005040.1, AL671883.2, MT1XP1, AC016957.1, U2AF1L5, XIST, DAAM2, and ADAMTS2, and the most down‐regulated 10 genes were ALOX15, PRSS33, IL5RA, SMPD3, IGHV1‐2, IGLV3‐9, RHOXF1P1, CACNG6, MYOM2, and RSAD2. Through STRING database and MCODE analysis, we finally got 16 MCODE genes. These genes can be regarded as hearing loss related genes. Through biological analysis, it is found that these genes are enriched in pathways related to apoptosis such as tumor necrosis factor. Among them, MMP8, LTF, ORM2, FOLR3, and TCN1 have corresponding targeted drugs. Foremost, MCODE genes should be investigated for its usefulness as a new biomarker for diagnosis and treatment. Conclusion In summary, our study produced a sixteen‐gene signature and associated drugs that could be diagnosis and treatment of hearing loss patients.
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Affiliation(s)
- Min Lei
- Department of Otorhinolaryngology - Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Dongdong Zhang
- Department of Otorhinolaryngology - Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Yixin Sun
- School of Medicine, Xiamen University, Xiamen, China
| | - Cong Zou
- Department of Otorhinolaryngology - Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Yue Wang
- Department of Otorhinolaryngology - Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Yongjun Hong
- Department of Otorhinolaryngology - Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Yanchao Jiao
- Department of Otorhinolaryngology - Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Chengfu Cai
- Department of Otorhinolaryngology - Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China.,Department of Otorhinolaryngology Head and Neck Surgery, Teaching Hospital of Fujian Medical University, Xiamen, China.,Department of Otorhinolaryngology - Head and Neck Surgery, Xiamen University, Xiamen, China
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9
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Feltes BC, Poloni JDF, Dorn M. Benchmarking and Testing Machine Learning Approaches with BARRA:CuRDa, a Curated RNA-Seq Database for Cancer Research. J Comput Biol 2021; 28:931-944. [PMID: 34264745 DOI: 10.1089/cmb.2020.0463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
RNA-seq is gradually becoming the dominating technique employed to access the global gene expression in biological samples, allowing more flexible protocols and robust analysis. However, the nature of RNA-seq results imposes new data-handling challenges when it comes to computational analysis. With the increasing employment of machine learning (ML) techniques in biomedical sciences, databases that could provide curated data sets treated with state-of-the-art approaches already adapted to ML protocols, become essential for testing new algorithms. In this study, we present the Benchmarking of ARtificial intelligence Research: Curated RNA-seq Database (BARRA:CuRDa). BARRA:CuRDa was built exclusively for cancer research and is composed of 17 handpicked RNA-seq data sets for Homo sapiens that were gathered from the Gene Expression Omnibus, using rigorous filtering criteria. All data sets were individually submitted to sample quality analysis, removal of low-quality bases and artifacts from the experimental process, removal of ribosomal RNA, and estimation of transcript-level abundance. Moreover, all data sets were tested using standard approaches in the field, which allows them to be used as benchmark to new ML approaches. A feature selection analysis was also performed on each data set to investigate the biological accuracy of basic techniques. Results include genes already related to their specific tumoral tissue a large amount of long noncoding RNA and pseudogenes. BARRA:CuRDa is available at http://sbcb.inf.ufrgs.br/barracurda.
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Affiliation(s)
- Bruno César Feltes
- Institute of Informatics, Department of Theoretical Computer Science, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Institute of Biosciences, Department of Biophysics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Joice De Faria Poloni
- Institute of Informatics, Department of Theoretical Computer Science, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,EMBRAPA Agroenergy, Distrito Federal, Brasília, Brazil
| | - Márcio Dorn
- Institute of Informatics, Department of Theoretical Computer Science, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Center of Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,National Institute of Science and Technology, Forensic Science, Porto Alegre, Brazil
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10
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Chen X, Sun J, Wang X, Yuan Y, Cai L, Xie Y, Fan Z, Liu K, Jiao X. A Meta-Analysis of Proteomic Blood Markers of Colorectal Cancer. Curr Med Chem 2021; 28:1176-1196. [PMID: 32338203 DOI: 10.2174/0929867327666200427094054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/23/2020] [Accepted: 03/24/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Early diagnosis will significantly improve the survival rate of colorectal cancer (CRC); however, the existing methods for CRC screening were either invasive or inefficient. There is an emergency need for novel markers in CRC's early diagnosis. Serum proteomics has gained great potential in discovering novel markers, providing markers that reflect the early stage of cancer and prognosis prediction of CRC. In this paper, the results of proteomics of CRC studies were summarized through a meta-analysis in order to obtain the diagnostic efficiency of novel markers. METHODS A systematic search on bibliographic databases was performed to collect the studies that explore blood-based markers for CRC applying proteomics. The detection and validation methods, as well as the specificity and sensitivity of the biomarkers in these studies, were evaluated. Newcastle- Ottawa Scale (NOS) case-control studies version was used for quality assessment of included studies. RESULTS Thirty-four studies were selected from 751 studies, in which markers detected by proteomics were summarized. In total, fifty-nine proteins were classified according to their biological function. The sensitivity, specificity, or AUC varied among these markers. Among them, Mammalian STE20-like protein kinase 1/ Serine threonine kinase 4 (MST1/STK4), S100 calcium-binding protein A9 (S100A9), and Tissue inhibitor of metalloproteinases 1 (TIMP1) were suitable for effect sizes merging, and their diagnostic efficiencies were recalculated after merging. MST1/STK4 obtained a sensitivity of 68% and a specificity of 78%. S100A9 achieved a sensitivity of 72%, a specificity of 83%, and an AUC of 0.88. TIMP1 obtained a sensitivity of 42%, a specificity of 88%, and an AUC of 0.71. CONCLUSION MST1/STK4, S100A9, and TIMP1 showed excellent performance for CRC detection. Several other markers also presented optimized diagnostic efficacy for CRC early detection, but further verification is still needed before they are suitable for clinical use. The discovering of more efficient markers will benefit CRC treatment.
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Affiliation(s)
- Xiang Chen
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Jiayu Sun
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Xue Wang
- Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yumeng Yuan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Leshan Cai
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yanxuan Xie
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Zhiqiang Fan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Kaixi Liu
- Shantou Central Hospital, Shantou, Guangdong 515041, China
| | - Xiaoyang Jiao
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
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11
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Mohanty V, Subbannayya Y, Patil S, Abdulla R, Ganesh MS, Pal A, Ray JG, Sidransky D, Gowda H, Prasad TSK, Chatterjee A. Molecular alterations in oral cancer between tobacco chewers and smokers using serum proteomics. Cancer Biomark 2021; 31:361-373. [PMID: 34024816 DOI: 10.3233/cbm-203077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Tobacco exposure (through smoking or chewing) is one of the predominant risk factors associated with the development of oral squamous cell carcinoma (OSCC). Despite the growing number of patients diagnosed with OSCC, there are few circulating biomarkers for identifying individuals at a higher risk of developing the disease. Successful identification of candidate molecular markers for risk assessment could aid in the early detection of oral lesions and potentially be used for community screening of high-risk populations. OBJECTIVE Identification of differentially expressed proteins in the serum of oral cancer patients which can serve as biomarkers for the diagnosis of the onset of oral cancer among tobacco users. METHODS We employed a tandem mass tag (TMT)-based quantitative proteomics approach to study alterations in the serum proteomes of OSCC patients based on their tobacco exposure habits (chewing and smoking) compared to healthy individuals with no history of using any form of tobacco or any symptoms of the disease. RESULTS Mass spectrometry-based analysis resulted in the identification of distinct signatures in the serum of OSCC patients who either chewed or smoked tobacco. Pathway analysis revealed opposing effects of dysregulated proteins enriched in the complement-coagulation signaling cascades with a high expression of the Serpin family of proteins observed in OSCC patients who chewed tobacco compared to healthy individuals whereas these proteins showed decreased levels in OSCC patients who smoked. ELISA-based validation further confirmed our findings revealing higher expression of SERPINA6 and SERPINF1 across serum of OSCC patients who chewed tobacco compared to healthy individuals. CONCLUSIONS This study serves as a benchmark for the identification of serum-based protein markers that may aid in the identification of high-risk patients who either chew tobacco or smoke tobacco.
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Affiliation(s)
- Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Shankargouda Patil
- Division of Oral Pathology, College of Dentistry, Department of Maxillofacial Surgery and Diagnostic Sciences, Jazan University, Jazan, Saudi Arabia
| | - Riaz Abdulla
- Department of Oral Pathology, Yenepoya Dental College, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Mandakulutur S Ganesh
- Department of Surgical Oncology, Vydehi Institute of Oncology, Bangalore, Karnataka, India
| | - Arnab Pal
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Jay Gopal Ray
- Department of Oral Pathology, Dr. R Ahmed Dental College and Hospital, Kolkata, West Bengal, India
- Department of Pathology, Burdwan Dental College and Hospital, Burdwan, West Bengal, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Harsha Gowda
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
- Institute of Bioinformatics, International Tech Park, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Aditi Chatterjee
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
- Institute of Bioinformatics, International Tech Park, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
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12
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de Waal GM, de Villiers WJS, Forgan T, Roberts T, Pretorius E. Colorectal cancer is associated with increased circulating lipopolysaccharide, inflammation and hypercoagulability. Sci Rep 2020; 10:8777. [PMID: 32472080 PMCID: PMC7260372 DOI: 10.1038/s41598-020-65324-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
Gut dysbiosis contributes to the development of a dysfunctional gut barrier, facilitating the translocation of bacteria and inflammagens, and is implicated in colorectal cancer (CRC) pathogenesis. Such 'leaky gut' conditions result in systemic inflammation, of which a hallmark is increased hypercoagulability. Fluorescence antibody confocal microscopy was used to determine circulating levels of lipopolysaccharide (LPS) in control and CRC populations. Here we showed that circulating levels of LPS are significantly elevated in the CRC population. We also showed that markers of inflammation and hypercoagulability are increased in this population. Furthermore, anomalous blood clotting and structural changes in blood components are presented. Importantly, the association between LPS levels, inflammation, and hematological dysfunction was analysed. Statistical regression models were applied to identify markers with strong association with CRC, and to investigate the correlation between markers. A core aim is enhanced biomarker discovery for CRC. We conclude that circulating LPS can promote systemic inflammation and contribute to the development of a pathological coagulation system, with resulting chronic inflammation and an activated coagulation system implicated in tumorigenesis. Blood-based screening tools are an emerging research area of interest for CRC screening. We propose the use of additional (novel) biomarkers to effectively screen for CRC.
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Affiliation(s)
- Greta M de Waal
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
| | - Willem J S de Villiers
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
- Department of Internal Medicine, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
| | - Timothy Forgan
- Consultant Colorectal Surgeon, Division of Surgery, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Academic Hospital, Western Cape, South Africa
| | - Timothy Roberts
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
- Department of Biochemistry, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St, Liverpool, L69 7ZB, UK
- University College London Hospital NHS Foundation Trust, 250 Euston Road, London, NW1 2PB, UK
| | - Etheresia Pretorius
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa.
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13
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Zhu HZ, Zhou WJ, Wan YF, Ge K, Lu J, Jia CK. Downregulation of orosomucoid 2 acts as a prognostic factor associated with cancer-promoting pathways in liver cancer. World J Gastroenterol 2020; 26:804-817. [PMID: 32148378 PMCID: PMC7052533 DOI: 10.3748/wjg.v26.i8.804] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/04/2020] [Accepted: 01/11/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Liver cancer has a high mortality and morbidity rate throughout the world. In clinical practice, the prognosis of liver cancer patients is poor, and the complex reasons contribute to treatment failures, including fibrosis, hepatitis viral infection, drug resistance and metastasis. Thus, screening novel prognostic biomarkers is of great importance for guiding liver cancer therapy. Orosomucoid genes (ORMs) encode acute phase plasma proteins, including orosomucoid 1 (ORM1) and ORM2. Previous studies showed their upregulation upon inflammation, but the specific function of ORMs has not yet been determined, especially in the development of liver cancer. AIM To determine the expression of ORMs and their potential function in liver cancer. METHODS Analysis of the expression of ORMs in different human tissues was performed on data from the HPA RNA-seq normal tissues project. The expression ratio of ORMs was determined using the HCCDB database, including the ratio between liver cancer and other cancers, normal liver and other normal tissues, liver cancer and adjacent normal liver tissues. Analysis of ORM expression in different cancer types was performed using The Cancer Genome Atlas and TIMER database. The expression of ORMs in liver tumor tissues and adjacent normal tissues were further confirmed using Gene Expression Omnibus data, including GSE36376 and GSE14520. The 10-year overall survival (OS), progression-free survival (PFS) and relapse-free survival (RFS) rates between high and low ORM expression groups in liver cancer patients were determined using the Kaplan-Meier plotter tool. Gene Set Enrichment Analysis (GSEA) was employed to explore the ORM2-associated signaling network. Correlations between ORM2 expression and tumor purity or the infiltration level of macrophages in liver tumor tissues were determined using the TIMER database. The correlation between ORM2 gene levels, tumor-associated macrophage (TAM) markers (including CD68 and TGFβ1) and T cell immunosuppression (including CTLA4 and PD-1) in liver tumor tissues and liver GTEx was determined using the GEPIA database. RESULTS ORM1 and ORM2 were highly expressed in normal liver and liver tumor tissues. ORM1 and ORM2 expression was significantly decreased in liver tumor tissues compared with adjacent normal tissues, and similar results were also noted in cholangiocarcinoma, esophageal carcinoma, and lung squamous cell carcinoma. Further analysis of the Gene Expression Omnibus Database also confirmed the downregulation of ORM1 and ORM2 in liver tumors. Survival analysis showed that the high ORM2 group had better survival rates in OS, PFS and RFS. ORM1 only represented better performance in PFS, but not in OS or RFS. GSEA analysis of ORM2 from The Cancer Genome Atlas liver cancer data identified that ORM2 positively associated with the G2/M checkpoint, E2F target signaling, as well as Wnt/β-catenin and Hedgehog signaling. Moreover, apoptosis, IFN-α responses, IFN-γ responses and humoral immune responses were upregulated in the ORM2 high group. ORM2 expression was negatively correlated with the macrophage infiltration level, CD68, TGFβ1, CTLA4 and PD-1 levels. CONCLUSION The results showed that ORM1 and ORM2 were highly expressed specifically in liver tissues, whereas ORM1 and ORM2 were downregulated in liver tumor tissues. ORM2 is a better prognostic factor for liver cancer. Furthermore, ORM2 is closely associated with cancer-promoting pathways.
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Affiliation(s)
- Han-Zhang Zhu
- Department of Hepatopancreatobiliary Surgery, Hangzhou First People’s Hospital, The Affiliated Hospital of Medical School of Zhejiang University. Hangzhou 310006, Zhejiang Province, China
| | - Wei-Jiang Zhou
- Department of Hepatopancreatobiliary Surgery, Hangzhou First People’s Hospital, The Affiliated Hospital of Medical School of Zhejiang University. Hangzhou 310006, Zhejiang Province, China
| | - Ya-Feng Wan
- Department of Hepatopancreatobiliary Surgery, Hangzhou First People’s Hospital, The Affiliated Hospital of Medical School of Zhejiang University. Hangzhou 310006, Zhejiang Province, China
| | - Ke Ge
- Department of Hepatopancreatobiliary Surgery, Hangzhou First People’s Hospital, The Affiliated Hospital of Medical School of Zhejiang University. Hangzhou 310006, Zhejiang Province, China
| | - Jun Lu
- Department of Hepatopancreatobiliary Surgery, Hangzhou First People’s Hospital, The Affiliated Hospital of Medical School of Zhejiang University. Hangzhou 310006, Zhejiang Province, China
| | - Chang-Ku Jia
- Department of Hepatopancreatobiliary Surgery, Hangzhou First People’s Hospital, The Affiliated Hospital of Medical School of Zhejiang University. Hangzhou 310006, Zhejiang Province, China
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14
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Revelation of Proteomic Indicators for Colorectal Cancer in Initial Stages of Development. Molecules 2020; 25:molecules25030619. [PMID: 32023884 PMCID: PMC7036866 DOI: 10.3390/molecules25030619] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023] Open
Abstract
Background: Colorectal cancer (CRC) at a current clinical level is still hardly diagnosed, especially with regard to nascent tumors, which are typically asymptotic. Searching for reliable biomarkers of early diagnosis is an extremely essential task. Identification of specific post-translational modifications (PTM) may also significantly improve net benefits and tailor the process of CRC recognition. We examined depleted plasma samples obtained from 41 healthy volunteers and 28 patients with CRC at different stages to conduct comparative proteome-scaled analysis. The main goal of the study was to establish a constellation of protein markers in combination with their PTMs and semi-quantitative ratios that may support and realize the distinction of CRC until the disease has a poor clinical manifestation. Results: Proteomic analysis revealed 119 and 166 proteins for patients in stages I–II and III–IV, correspondingly. Plenty of proteins (44 proteins) reflected conditions of the immune response, lipid metabolism, and response to stress, but only a small portion of them were significant (p < 0.01) for distinguishing stages I–II of CRC. Among them, some cytokines (Clusterin (CLU), C4b-binding protein (C4BP), and CD59 glycoprotein (CD59), etc.) were the most prominent and the lectin pathway was specifically enhanced in patients with CRC. Significant alterations in Inter-alpha-trypsin inhibitor heavy chains (ITIH1, ITIH2, ITIH3, and ITIH4) levels were also observed due to their implication in tumor growth and the malignancy process. Other markers (Alpha-1-acid glycoprotein 2 (ORM2), Alpha-1B-glycoprotein (A1BG), Haptoglobin (HP), and Leucine-rich alpha-2-glycoprotein (LRG1), etc.) were found to create an ambiguous core involved in cancer development but also to exactly promote tumor progression in the early stages. Additionally, we identified post-translational modifications, which according to the literature are associated with the development of colorectal cancer, including kininogen 1 protein (T327-p), alpha-2-HS-glycoprotein (S138-p) and newly identified PTMs, i.e., vitamin D-binding protein (K75-ac and K370-ac) and plasma protease C1 inhibitor (Y294-p), which may also contribute and negatively impact on CRC progression. Conclusions: The contribution of cytokines and proteins of the extracellular matrix is the most significant factor in CRC development in the early stages. This can be concluded since tumor growth is tightly associated with chronic aseptic inflammation and concatenated malignancy related to loss of extracellular matrix stability. Due attention should be paid to Apolipoprotein E (APOE), Apolipoprotein C1 (APOC1), and Apolipoprotein B-100 (APOB) because of their impact on the malfunction of DNA repair and their capability to regulate mTOR and PI3K pathways. The contribution of the observed PTMs is still equivocal, but a significant decrease in the likelihood between modified and native proteins was not detected confidently.
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15
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Huang J, Wang Q, Hu Y, Qi Z, Lin Z, Ying W, Zhou M. Proteomic Profiling for Serum Biomarkers in Mice Exposed to Ionizing Radiation. Dose Response 2019; 17:1559325819894794. [PMID: 31853238 PMCID: PMC6909274 DOI: 10.1177/1559325819894794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/30/2019] [Accepted: 11/06/2019] [Indexed: 12/11/2022] Open
Abstract
In response to large-scale radiological incidents, rapid, accurate, and early triage biodosimeters are urgently required. In this study, we investigated candidate radiation-responsive biomarkers using proteomics approaches in mouse models. A total of 452 dysregulated proteins were identified in the serum samples of mice exposed to 0, 2, 5.5, 7, and 8 Gy at 6, 24, and 72 hours postirradiation. Ninety-eight proteins, including 46 at 6 hours, 36 at 24 hours, and 36 at 72 hours, were identified as radiation-responsive proteins (RRPs). Gene Ontology analysis showed the RRPs were involved in proteolysis, extracellular space, hydrolase activity, and carbohydrate binding. Kyoto Encyclopedia of Genes and Genome enrichment showed the RRPs were regulated in "the pentose phosphate pathway," "the proteasome," and "AGE-RAGE signaling in diabetic complications." There were 3 proteins changed and overlapped at all the 3 time points, 8 proteins changed at 6 and 24 hours, 4 proteins changed at 24 and 72hours, and 2 proteins changed at both 6 and 72 hours. Of these proteins, ORM2, HP, SAA1, SAA2, MBL2, COL1A1, and APCS were identified as candidate biomarkers for biodosimeter-based diagnosis through Pearson correlation analysis.
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Affiliation(s)
- Jinfeng Huang
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, People’s Republic of China
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, People’s Republic of China
| | - Qi Wang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, People’s Republic of China
| | - Yingchun Hu
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, People’s Republic of China
| | - Zhenhua Qi
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, People’s Republic of China
| | - Zhongwu Lin
- Science Research Management Department of the Academy of Military Sciences, Beijing, People’s Republic of China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, People’s Republic of China
| | - Meijuan Zhou
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, People’s Republic of China
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16
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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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17
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Moulder R, Bhosale SD, Goodlett DR, Lahesmaa R. Analysis of the plasma proteome using iTRAQ and TMT-based Isobaric labeling. MASS SPECTROMETRY REVIEWS 2018; 37:583-606. [PMID: 29120501 DOI: 10.1002/mas.21550] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/26/2017] [Indexed: 05/23/2023]
Abstract
Over the past decade, chemical labeling with isobaric tandem mass tags, such as isobaric tags for relative and absolute quantification reagents (iTRAQ) and tandem mass tag (TMT) reagents, has been employed in a wide range of different clinically orientated serum and plasma proteomics studies. In this review the scope of these works is presented with attention to the areas of research, methods employed and performance limitations. These applications have covered a wide range of diseases, disorders and infections, and have implemented a variety of different preparative and mass spectrometric approaches. In contrast to earlier works, which struggled to quantify more than a few hundred proteins, increasingly these studies have provided deeper insight into the plasma proteome extending the numbers of quantified proteins to over a thousand.
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Affiliation(s)
- Robert Moulder
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Santosh D Bhosale
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | | | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
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18
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Cheng Y, Meng Q, Huang L, Shi X, Hou J, Li X, Liang J. iTRAQ-based quantitative proteomic analysis and bioinformatics study of proteins in retinoblastoma. Oncol Lett 2018; 14:8084-8091. [PMID: 29344252 DOI: 10.3892/ol.2017.7221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/16/2017] [Indexed: 01/08/2023] Open
Abstract
The aim of the present study was to analyze proteins in the aqueous humor (AH) of patients' retinoblastoma (RB), and investigate their potential role in RB using the comparative proteomic technique of isobaric tags for relative and absolute quantitation (iTRAQ) coupled with offline two-dimensional liquid chromatography-tandem mass spectrometry. A total of 0.1 ml AH was collected from 10 children with RB (mean age, 3.8 years; range, 2-5 years) and patients with senile cataracts (mean age, 70.4 years; range, 65-79 years), which was used as the control. iTRAQ was used to analyze proteins in the AH of patients and controls. Proteins with a fold change of >1.20 or <0.83 were considered to be significantly differentially expressed (with corrected P<0.05). The identified proteins were subjected to subsequent gene ontology (GO) analysis using the DAVID database. A total of 83 proteins that were expressed differently between the controls and patients' AH samples were identified using iTRAQ analysis. Of these proteins, 44 were upregulated and 39 were downregulated. On the basis of biological processes in GO, the identified proteins were primarily involved in glycoprotein, amyloid acute-inflammatory and defensive responses. Among these proteins, pigment epithelium-derived factor serves a potential role in the treatment of RB, and stimulated by retinoic acid 6 may serve as a potential protein involved in RB development. To the best of our knowledge, the present study is the first to identify 83 proteins associated with RB using iTRAQ technology. The results of the present study will aid in furthering the understanding of RB and developing novel therapy targets in the future.
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Affiliation(s)
- Yong Cheng
- Ophthalmology Department, Peking University People's Hospital, Beijing 100044, P.R. China.,Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing 100044, P.R. China.,Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Qingyu Meng
- Ophthalmology Department, Peking University People's Hospital, Beijing 100044, P.R. China.,Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing 100044, P.R. China.,Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Lvzhen Huang
- Ophthalmology Department, Peking University People's Hospital, Beijing 100044, P.R. China.,Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing 100044, P.R. China.,Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Xuan Shi
- Ophthalmology Department, Peking University People's Hospital, Beijing 100044, P.R. China.,Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing 100044, P.R. China.,Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Jing Hou
- Ophthalmology Department, Peking University People's Hospital, Beijing 100044, P.R. China.,Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing 100044, P.R. China.,Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Xiaoxin Li
- Ophthalmology Department, Peking University People's Hospital, Beijing 100044, P.R. China.,Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing 100044, P.R. China.,Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Jianhong Liang
- Ophthalmology Department, Peking University People's Hospital, Beijing 100044, P.R. China.,Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing 100044, P.R. China.,Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, Peking University People's Hospital, Beijing 100044, P.R. China
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19
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Geyer PE, Holdt LM, Teupser D, Mann M. Revisiting biomarker discovery by plasma proteomics. Mol Syst Biol 2017; 13:942. [PMID: 28951502 PMCID: PMC5615924 DOI: 10.15252/msb.20156297] [Citation(s) in RCA: 504] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/04/2017] [Accepted: 08/15/2017] [Indexed: 01/13/2023] Open
Abstract
Clinical analysis of blood is the most widespread diagnostic procedure in medicine, and blood biomarkers are used to categorize patients and to support treatment decisions. However, existing biomarkers are far from comprehensive and often lack specificity and new ones are being developed at a very slow rate. As described in this review, mass spectrometry (MS)-based proteomics has become a powerful technology in biological research and it is now poised to allow the characterization of the plasma proteome in great depth. Previous "triangular strategies" aimed at discovering single biomarker candidates in small cohorts, followed by classical immunoassays in much larger validation cohorts. We propose a "rectangular" plasma proteome profiling strategy, in which the proteome patterns of large cohorts are correlated with their phenotypes in health and disease. Translating such concepts into clinical practice will require restructuring several aspects of diagnostic decision-making, and we discuss some first steps in this direction.
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Affiliation(s)
- Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Lesca M Holdt
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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Safety, pharmacokinetics and pharmacogenetics of a single ascending dose of pradefovir, a novel liver-targeting, anti-hepatitis B virus drug, in healthy Chinese subjects. Hepatol Int 2017; 11:390-400. [PMID: 28560658 DOI: 10.1007/s12072-017-9797-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/28/2017] [Indexed: 01/13/2023]
Abstract
BACKGROUND Pradefovir is efficiently converted to adefovir [9-(2-phosphonylmethoxyethyl) adenine (PMEA)], producing high hepatic PMEA concentration but low levels in the systemic circulation and kidney. The aim of this study is to evaluate the tolerability, adverse effect (AEs), pharmacokinetics and pharmacogenetics of a single ascending dose of pradefovir. METHODS Fifty healthy subjects were divided into five groups and randomized within each group at a ratio of 3:1:1 to receive a single ascending dose of pradefovir (10, 30, 60, 90, or 120 mg), and 10 mg adefovir dipivoxil (ADP) or placebo. Blood and urine samples were collected and analyzed. A total of 1930 polymorphic loci were analyzed in 6 blood samples collected from the 90 mg pradefovir group. RESULTS The single oral dose of pradefovir up to 120 mg was well tolerated. A total of 29 dose-limited mild AEs were reported in 17 subjects. The peak plasma concentration (C max) and area under the curve (AUC)0-48 of serum pradefovir ranged from (21.41 ± 12.98) to (447.33 ± 79.34) ng/mL and (46.10 ± 29.45) to (748.18 ± 134.15) ng h/mL across the dose range, respectively. The C max and AUC0-48 of serum PMEA ranged from 18.10 ± 4.96 to 312.33 ± 114.19 ng/mL and 72.65 ± 28.25 to 1095.48 ± 248.47 ng h/mL. Generally, no kidney impairment was observed. Pharmacogenetic analysis identified three metabolism-related single nucleotide polymorphism (SNP) locis, P450 (cytochrome) oxidoreductase [POR (rs6965343)], arylamine N-acetyltransferases [NAT1 (rs4986993)] and CYP2F1 (rs305968)], and one distribution-related loci, orosomucoid 2 [ORM2 (rs12685968)]. CONCLUSIONS The single oral dose of pradefovir 10-120 mg was well tolerated. SNPs may be associated with variable rates of adverse events. TRIAL REGISTRATION NUMBER CTR20140341.
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21
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Rucksaken R, Charoensuk L, Pinlaor P, Pairojkul C, Khuntikeo N, Pinlaor S. Plasma orosomucoid 2 as a potential risk marker of cholangiocarcinoma. Cancer Biomark 2017; 18:27-34. [PMID: 27814272 DOI: 10.3233/cbm-160670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Cholangiocarcinoma (CCA), a malignant tumor of the biliary epithelium, is a tumor with an ineffective diagnosis and poor prognosis. We have previously identified an overexpression of orosomucoid 2 (ORM2) along with CCA development in hamsters using a proteomics technique. OBJECTIVE To evaluate plasma ORM2 as a candidate risk biomarker for CCA in humans. METHODS Overexpression of ORM2 in CCA patients was assessed by western blotting and immunohistochemistry. The diagnostic efficacy of ORM2 was investigated in the plasma of patients with hepatobiliary diseases - including 46 cholangitis patients and 70 CCA patients - compared with 20 healthy individuals, using enzyme-linked immunosorbent assay (ELISA). RESULTS Overexpression of ORM2 was observed in the cytoplasm of bile duct tumor cells and in the adjacent normal hepatocytes at a much higher intensity than in normal bile duct cells. Western blot analysis revealed that its expression was significantly higher in the plasma of CCA patients compared with that of healthy individuals (P < 0.01). ELISA showed that plasma ORM2 levels were significantly elevated in CCA and cholangitis groups compared with healthy individuals (P < 0.0001). The sensitivity and specificity of ORM2 in distinguishing CCA patients from healthy patients were 92.86% and 73.68%, respectively. CONCLUSIONS Plasma ORM2 could serve as a new risk marker for CCA.
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Affiliation(s)
- Rucksak Rucksaken
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Lakhanawan Charoensuk
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Department of Clinical Pathology, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok 10300, Thailand
| | - Porntip Pinlaor
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Chawalit Pairojkul
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Narong Khuntikeo
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Somchai Pinlaor
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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22
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Quantitative proteomic analysis exploring progression of colorectal cancer: Modulation of the serpin family. J Proteomics 2016; 148:139-48. [PMID: 27492143 DOI: 10.1016/j.jprot.2016.07.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/04/2016] [Accepted: 07/28/2016] [Indexed: 12/12/2022]
Abstract
UNLABELLED Colorectal cancer (CRC) remains a major cause of cancer related-death in developed countries. The mortality risk is correlated with the stage of CRC determined at the primary diagnosis and early diagnosis is associated with enhanced survival rate. Currently, only faecal occult blood tests are used to screen for CRC. Consequently, there is an incentive to identify specific markers of CRC. We used quantitative proteomic analysis of serum samples to characterize protein profiles in adenoma, CRC and healthy control samples. We identified 89 distinct proteins modulated between normal, colorectal adenoma and carcinoma patients. This list emphasizes proteins involved in enzyme regulator activities and in particular the serpin family. In serum samples, protein profiles of three members of the serpin family (SERPINA1, SERPINA3 and SERPINC1) were confirmed by ELISA assays. We obtained sensitivity/specificity values of 95%/95% for both SERPINA1 and SERPINC1, and 95%/55% for SERPINA3. This study supports the idea that serum proteins can discriminate adenoma and CRC patients from unaffected patients and reveals a panel of regulated proteins that might be useful for selecting patients for colonoscopy. By evaluating SERPINA1, SERPINA3 and SERPINC1, we highlight the potential role of the serpin family during the development and progression of CRC. SIGNIFICANCE Colorectal cancer (CRC) remains a major cause of cancer mortality throughout the world. However, very few CRC biomarkers have satisfactory sensitivity and specificity in clinical practice. To the best of our knowledge our study is the first to profile sera proteomes between adenoma, CRC and healthy patients. We report a comprehensive list of proteins that may be used as early diagnostic biomarkers of CRC. It is noteworthy that 17% of these modulated proteins have been previously described as candidate biomarkers in CRC. Enzyme regulator activity was found to be the main molecular function among these proteins and, in particular, there was an enrichment of members of the serpin family. The subsequent verification on a new cohort by ELISA demonstrates that these serpins could be useful to discriminate healthy from colorectal carcinoma patients with a high sensitivity and specificity. The combination of these biomarkers should increase predictive powers of CRC diagnosis. The remaining candidates form a reserve for further evaluation of additional biomarkers for CRC diagnosis.
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Likhitrattanapisal S, Tipanee J, Janvilisri T. Meta-analysis of gene expression profiles identifies differential biomarkers for hepatocellular carcinoma and cholangiocarcinoma. Tumour Biol 2016; 37:12755-12766. [PMID: 27448818 DOI: 10.1007/s13277-016-5186-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/13/2016] [Indexed: 02/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA) are the members of hepatobiliary diseases. Both types of cancer often exert high levels of similarity in terms of phenotypic characteristics, thus leading to difficulties in HCC and CCA differential diagnoses. In this study, a transcriptome meta-analysis was performed on HCC and CCA microarray data to identify differential transcriptome networks and potential biomarkers for HCC and CCA. Raw data from nine gene expression profiling datasets, consisting of 1,185 samples in total, were methodologically compiled and analyzed. To evaluate differentially expressed (DE) genes in HCC and CCA, the levels of gene expression were compared between cancer and its normal counterparts (i.e., HCC versus normal liver and CCA versus normal bile duct) using t test (P < 0.05) and k-fold validation. A total of 226 DE genes were specific to HCC, 249 DE genes specific to CCA, and 41 DE genes in both HCC and CCA. Gene ontology and pathway enrichment analyses revealed different patterns between functional transcriptome networks of HCC and CCA. Cell cycle and glycolysis/gluconeogenesis pathways were exclusively dysregulated in HCC whereas complement and coagulation cascades as well as glycine, serine, and threonine metabolism were prodominantly differentially expressed in CCA. Our meta-analysis revealed distinct dysregulation in transcriptome networks between HCC and CCA. Certain genes in these networks were discussed in the context of HCC and CCA transition, unique characteristics of HCC and CCA, and their potentials as HCC and CCA differential biomarkers.
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Affiliation(s)
| | - Jaitip Tipanee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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24
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Fang T, Cui M, Sun J, Ge C, Zhao F, Zhang L, Tian H, Zhang L, Chen T, Jiang G, Xie H, Cui Y, Yao M, Li H, Li J. Orosomucoid 2 inhibits tumor metastasis and is upregulated by CCAAT/enhancer binding protein β in hepatocellular carcinomas. Oncotarget 2016; 6:16106-19. [PMID: 25965830 PMCID: PMC4599259 DOI: 10.18632/oncotarget.3867] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/31/2015] [Indexed: 12/19/2022] Open
Abstract
Cancer metastasis is a complex process, and the incidence of metastasis is influenced by many biological factors. Orosomucoid 2 (ORM2) is an important glycoprotein that is mainly biosynthesized and secreted by hepatocytes. As an acute-phase protein, ORM2 likely plays important roles in anti-inflammation, immunomodulation and drug delivery. However, little is known regarding the function of ORM2 in hepatocellular carcinoma (HCC). In this study, we determined that ORM2 expression in HCC tissues was negatively associated with intrahepatic metastasis and histological grade. Moreover, the ectopic overexpression of ORM2 decreased HCC cell migration and invasion in vitro and intrahepatic metastasis in vivo, whereas silencing ORM2 expression resulted in increased tumor cell migration and invasion in vitro. The CCAAT/enhancer binding protein β (C/EBPβ) upregulated ORM2 expression, while only the LAP1/2 (C/EBPβ isoforms) possessed transcription-promoting activity on the ORM2 promoter. Subsequently, we found that LAP1 repressed HCC cell migration and invasion via the induction of ORM2 expression. Consistently, the protein expression of C/EBPβ was negatively associated with histological grade and positively correlated with ORM2 protein expression in HCC tissues. Collectively, our findings indicate that ORM2 is a functional downstream target of C/EBPβ and functions as a tumor suppressor in HCC.
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Affiliation(s)
- Tao Fang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Meiling Cui
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ji Sun
- Shanghai Medical Colloge, Fudan University, Shanghai, China
| | - Chao Ge
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Fangyu Zhao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lin Zhang
- Shanghai Medical Colloge, Fudan University, Shanghai, China
| | - Hua Tian
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lixing Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Taoyang Chen
- Qi Dong Liver Cancer Institute, Qi Dong, Jiangsu Province, China
| | - Guoping Jiang
- Department of General Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Haiyang Xie
- Department of General Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ying Cui
- Cancer Institute of Guangxi, Nanning, China
| | - Ming Yao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hong Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jinjun Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Gemoll T, Meyer R, Habermann JK. Applying Genomics and Proteomics in Translational Surgical Oncology Research. Eur Surg Res 2015; 55:184-97. [PMID: 26339997 DOI: 10.1159/000438860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/20/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND Translational surgical research can range from investigating clinically oriented basic pathophysiological research via the correlation of molecular findings with a patient's clinical outcome to conducting treatment response studies. Herein, the specialist's opinion as a 'surgeon scientist' plays a pivotal role, e.g. in planning experimental setups focusing on the clinically most relevant needs. SUMMARY AND KEY MESSAGES: This review provides a survey of genomic and proteomic technologies and gives an up-to-date overview of those studies applying these technologies exemplarily in colorectal cancer-based biomarker research. Although current results are promising, future validation studies within multicenter networks are required to promote the translation of 'omics' from bench to bedside. In this endeavor, departments of surgery and institutes of experimental surgery together should play a fundamental role. The program for 'clinician scientists' recently launched by the German Research Society (DFG) could be one tool to promote interdisciplinary networks and surgeons' impact on translational research.
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Affiliation(s)
- Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lx00FC;beck and University Medical Center Schleswig-Holstein (UKSH), Lx00FC;beck, Germany
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26
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Zeng X, Tao H. Diagnostic and prognostic serum marker of cholangiocarcinoma (Review). Oncol Lett 2014; 9:3-8. [PMID: 25435926 PMCID: PMC4247112 DOI: 10.3892/ol.2014.2696] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 10/24/2014] [Indexed: 12/12/2022] Open
Abstract
Cholangiocarcinoma (CCA) is a fatal disease that is typically diagnosed late and treated ineffectively. As the morbidity and mortality rates for CCA rise markedly, patietns with CCA currently have a poor prognosis. However, if it were possible to diagnose CCA early while effective treat methods are available, CCA patients would achieve a better quality of life. Therefore, preventing the process of CCA in the early stages is an urgent problem to solve. An accurate, quick and safe method to diagnose early-stage CCA is required. The present review discusses the risk factors, status of research and certain serum markers of CCA. The sensitivity and specificity of these markers differ from each other. To explore the more accurate serum markers may be a novel direction and method for the diagnosis of CCA in laboratory medicine in the future.
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Affiliation(s)
- Xiaojun Zeng
- Department of Laboratory Medicine, Luzhou Medical College, Luzhou, Sichuan 646000, P.R. China
| | - Hualin Tao
- Department of Laboratory Medicine, Affiliated Hospital of Luzhou Medical College, Luzhou, Sichuan 646000, P.R. China
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27
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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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28
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Lin Q, Tan HT, Lim TK, Khoo A, Lim KH, Chung MCM. iTRAQ analysis of colorectal cancer cell lines suggests Drebrin (DBN1) is overexpressed during liver metastasis. Proteomics 2014; 14:1434-43. [DOI: 10.1002/pmic.201300462] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 02/18/2014] [Accepted: 03/04/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Qifeng Lin
- Department of Biochemistry; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
| | - Hwee Tong Tan
- Department of Biochemistry; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
| | - Teck Kwang Lim
- Department of Biological Sciences; Faculty of Science; National University of Singapore; Singapore
| | - Avery Khoo
- Department of Pathology; Singapore General Hospital; Singapore
| | - Kiat Hon Lim
- Department of Pathology; Singapore General Hospital; Singapore
| | - Maxey C. M. Chung
- Department of Biochemistry; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- Department of Biological Sciences; Faculty of Science; National University of Singapore; Singapore
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29
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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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30
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Wang K, Huang C, Nice EC. Proteomics, genomics and transcriptomics: their emerging roles in the discovery and validation of colorectal cancer biomarkers. Expert Rev Proteomics 2014; 11:179-205. [PMID: 24611605 DOI: 10.1586/14789450.2014.894466] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Colorectal cancer (CRC) is the second most common cancer in females and the third in males. Since CRC is often diagnosed at an advanced stage when prognosis is poor, identification of biomarkers for early diagnosis is urgently required. Recent advances in proteomics, genomics and transcriptomics have facilitated high-throughput profiling of data generated from CRC-related genes and proteins, providing a window of information for biomarker discovery and validation. However, transfer of candidate biomarkers from bench to bedside remains a dilemma. In this review, we will discuss emerging proteomic technologies and highlight various sample types utilized for proteomics-based identification of CRC biomarkers. Moreover, recent breakthroughs in genomics and transcriptomics for the identification of CRC biomarkers, with particular emphasis on the merits of emerging methylomic and miRNAomic strategies, will be discussed. Integration of proteomics, genomics and transcriptomics will facilitate the discovery and validation of CRC biomarkers leading to the emergence of personalized medicine.
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Affiliation(s)
- Kui Wang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University , Chengdu, 610041 , P.R. China
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31
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Luo Y, Wang L, Wang J. Developing proteomics-based biomarkers for colorectal neoplasms for clinical practice: opportunities and challenges. Proteomics Clin Appl 2014; 7:30-41. [PMID: 23255431 DOI: 10.1002/prca.201200071] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/30/2012] [Accepted: 11/20/2012] [Indexed: 12/17/2022]
Abstract
Colorectal cancer (CRC) arises from the normal colon epithelium through the accumulation of genetic mutations and epigenetic alterations that are associated with progression along the histological adenoma-adenocarcinoma sequence. Elucidating the molecular alterations underlying disease progression will not only provide insight into the behavior of the tumors, but also could lead to the discovery of useful biomarkers for diagnosis, monitoring treatment responsiveness, or predicting disease outcomes. In the past a few years, there have been several evaluating differentially expressed protein biomarkers by employing proteomics technologies coupled with mass spectrometry. In the current review, we will briefly summarize the results from selected recent studies using tissue or serum samples from CRC patients in the past 5 years and discuss the opportunities and challenges in translating these findings from the research setting to clinical practice.
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Affiliation(s)
- Yanxin Luo
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
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Martínez-Aguilar J, Chik J, Nicholson J, Semaan C, McKay MJ, Molloy MP. Quantitative mass spectrometry for colorectal cancer proteomics. Proteomics Clin Appl 2014; 7:42-54. [PMID: 23027722 DOI: 10.1002/prca.201200080] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 09/05/2012] [Accepted: 09/12/2012] [Indexed: 12/15/2022]
Abstract
This review documents the uses of quantitative MS applied to colorectal cancer (CRC) proteomics for biomarker discovery and molecular pathway profiling. Investigators are adopting various labeling and label-free MS approaches to quantitate differential protein levels in cells, tumors, and plasma/serum. We comprehensively review recent uses of this technology to examine mouse models of CRC, CRC cell lines, their secretomes and subcellular fractions, CRC tumors, CRC patient plasma/serum, and stool samples. For biomarker discovery these approaches are uncovering proteins with potential diagnostic and prognostic utility, while in vitro cell culture experiments are characterizing proteomic and phosphoproteomic responses to disrupted signaling pathways due to mutations or to inhibition of drugable enzymes.
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Affiliation(s)
- Juan Martínez-Aguilar
- Australian Proteome Analysis Facility (APAF), Department of Chemistry & Biomolecular Sciences, Macquarie University, Sydney, Australia
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Huang H, Han Y, Gao J, Feng J, Zhu L, Qu L, Shen L, Shou C. High level of serum AMBP is associated with poor response to paclitaxel-capecitabine chemotherapy in advanced gastric cancer patients. Med Oncol 2013; 30:748. [PMID: 24135868 DOI: 10.1007/s12032-013-0748-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 10/02/2013] [Indexed: 12/13/2022]
Abstract
Gastric cancer is one of the most common human cancers and ranks the second in the global cancer-related mortality. The clinical outcome of patients with advanced gastric cancer (AGC) is markedly dependent on their response to the chemotherapy. Paclitaxel plus capecitabine, as a first-line regimen, is widely administrated in AGC patients, but more than a half of the patients have a poor response, possibly due to their resistance to the treatment. Therefore, it is important to identify potential responders to improve the efficacy of the chemotherapy. In the present study, we used an isobaric tag approach for relative and absolute quantification combined with ESI-QUAD-TOF/MS to identify potential predictive biomarkers for the chemotherapy. We found 211 serum proteins, and confirmed 17 candidates that were differentially present in the progression of disease (PD) group and the partial response (PR) group to the treatment of paclitaxel plus capecitabine. In further validation of the 17 candidates in the set of 12 PD and 12 PR AGC patients, we identified a higher level of AMBP (Alpha-1-Microglobulin/Bikunin Precursor) in the sera of PD patients than of the PR patients assayed by ELISA (9.13 ± 0.45 vs. 8.11 ± 0.26 μg/mL, p = 0.06) and by the Western blotting (relative gray value 396.4 ± 39.1 vs. 275.0 ± 34.76, p = 0.03), respectively. The receiver operating characteristics curve showed 75% sensitivity and 75% specificity of AMBP in AGC patients treated with the chemotherapy. Our data indicated that the high level of serum AMBP could predict the poor response of the AGC patients treated with the paclitaxel-capecitabine chemotherapy, which could be used as a potential biomarker to identify patients who would benefit from this chemotherapeutic regimen.
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Affiliation(s)
- Hao Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, Peking University Cancer Hospital and Institute, 52 Fucheng Road, Haidian District, Beijing, 100142, China
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Chemical and cytokine features of innate immunity characterize serum and tissue profiles in inflammatory bowel disease. Proc Natl Acad Sci U S A 2013; 110:E2332-41. [PMID: 23754421 DOI: 10.1073/pnas.1222669110] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel disease (IBD) arises from inappropriate activation of the mucosal immune system resulting in a state of chronic inflammation with causal links to colon cancer. Helicobacter hepaticus-infected Rag2(-/-) mice emulate many aspects of human IBD, and our recent work using this experimental model highlights the importance of neutrophils in the pathology of colitis. To define molecular mechanisms linking colitis to the identity of disease biomarkers, we performed a translational comparison of protein expression and protein damage products in tissues of mice and human IBD patients. Analysis in inflamed mouse colons identified the neutrophil- and macrophage-derived damage products 3-chlorotyrosine (Cl-Tyr) and 3-nitrotyrosine, both of which increased with disease duration. Analysis also revealed higher Cl-Tyr levels in colon relative to serum in patients with ulcerative colitis and Crohn disease. The DNA chlorination damage product, 5-chloro-2'-deoxycytidine, was quantified in diseased human colon samples and found to be present at levels similar to those in inflamed mouse colons. Multivariate analysis of these markers, together with serum proteins and cytokines, revealed a general signature of activated innate immunity in human IBD. Signatures in ulcerative colitis sera were strongly suggestive of neutrophil activity, and those in Crohn disease and mouse sera were suggestive of both macrophage and neutrophil activity. These data point to innate immunity as a major determinant of serum and tissue profiles and provide insight into IBD disease processes.
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de Wit M, Fijneman RJ, Verheul HM, Meijer GA, Jimenez CR. Proteomics in colorectal cancer translational research: Biomarker discovery for clinical applications. Clin Biochem 2013; 46:466-79. [DOI: 10.1016/j.clinbiochem.2012.10.039] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/30/2012] [Accepted: 10/31/2012] [Indexed: 12/22/2022]
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Detection of differential levels of proteins in the urine of patients with endometrial cancer: analysis using two-dimensional gel electrophoresis and o-glycan binding lectin. Int J Mol Sci 2012; 13:9489-9501. [PMID: 22949810 PMCID: PMC3431808 DOI: 10.3390/ijms13089489] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/26/2012] [Accepted: 07/02/2012] [Indexed: 02/08/2023] Open
Abstract
Cancers can cause some proteins to be aberrantly excreted or released in the urine, which can be used as biomarkers. To screen for potential biomarkers for endometrial cancer (ECa), the urinary proteins from patients who were newly diagnosed with early stage ECa and untreated controls were separated using two-dimensional gel electrophoresis (2-DE) and followed by image analysis. The altered levels of zinc alpha-2 glycoprotein, alpha 1-acid glycoprotein, and CD59 were detected in the patients compared to the controls. In addition, the urine of the ECa patients was also found to contain relatively lower levels of a fragment of nebulin when the 2-DE separated urinary proteins were probed using champedak galactose binding (CGB) lectin. The different levels of the nebulin fragment were further validated by subjecting the urinary protein samples to CGB lectin affinity chromatography and analysis of the bound fractions by LC-MS/MS. Our data is suggestive of the potential use of the differentially expressed urinary proteins as biomarkers for ECa although this requires further extensive validation on clinically representative populations.
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