1
|
Petrovic D, Bodinier B, Dagnino S, Whitaker M, Karimi M, Campanella G, Haugdahl Nøst T, Polidoro S, Palli D, Krogh V, Tumino R, Sacerdote C, Panico S, Lund E, Dugué PA, Giles GG, Severi G, Southey M, Vineis P, Stringhini S, Bochud M, Sandanger TM, Vermeulen RCH, Guida F, Chadeau-Hyam M. Epigenetic mechanisms of lung carcinogenesis involve differentially methylated CpG sites beyond those associated with smoking. Eur J Epidemiol 2022; 37:629-640. [PMID: 35595947 PMCID: PMC9288379 DOI: 10.1007/s10654-022-00877-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/25/2022] [Indexed: 12/24/2022]
Abstract
Smoking-related epigenetic changes have been linked to lung cancer, but the contribution of epigenetic alterations unrelated to smoking remains unclear. We sought for a sparse set of CpG sites predicting lung cancer and explored the role of smoking in these associations. We analysed CpGs in relation to lung cancer in participants from two nested case-control studies, using (LASSO)-penalised regression. We accounted for the effects of smoking using known smoking-related CpGs, and through conditional-independence network. We identified 29 CpGs (8 smoking-related, 21 smoking-unrelated) associated with lung cancer. Models additionally adjusted for Comprehensive Smoking Index-(CSI) selected 1 smoking-related and 49 smoking-unrelated CpGs. Selected CpGs yielded excellent discriminatory performances, outperforming information provided by CSI only. Of the 8 selected smoking-related CpGs, two captured lung cancer-relevant effects of smoking that were missed by CSI. Further, the 50 CpGs identified in the CSI-adjusted model complementarily explained lung cancer risk. These markers may provide further insight into lung cancer carcinogenesis and help improving early identification of high-risk patients.
Collapse
Affiliation(s)
- Dusan Petrovic
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Department of Epidemiology and Health Systems (DESS), University Centre for General Medicine and Public Health (UNISANTE), Lausanne, Switzerland
- Department and Division of Primary Care Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Barbara Bodinier
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Sonia Dagnino
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Matthew Whitaker
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Maryam Karimi
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Bureau de Biostatistique et d'Épidémiologie, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Oncostat U1018, Inserm, Équipe Labellisée Ligue Contre Le Cancer, Université Paris-Saclay, Villejuif, France
| | - Gianluca Campanella
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Therese Haugdahl Nøst
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Domenico Palli
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute-ISPO, Florence, Italy
| | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Rosario Tumino
- Hyblean Association for Epidemiological Research, AIRE- ONLUS, Ragusa, Italy
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology Città Della Salute e della Scienza University-Hospital, Via Santena 7, 10126, Turin, Italy
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Eiliv Lund
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- The Norwegian Cancer Registry, Oslo, Norway
| | - Pierre-Antoine Dugué
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Gianluca Severi
- Centre for Research in Epidemiology and Population Health, Inserm (Institut National de La Sante Et de a Recherche Medicale), Villejuif, France
| | - Melissa Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Australia
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Silvia Stringhini
- Department of Epidemiology and Health Systems (DESS), University Centre for General Medicine and Public Health (UNISANTE), Lausanne, Switzerland
- Department and Division of Primary Care Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Murielle Bochud
- Department of Epidemiology and Health Systems (DESS), University Centre for General Medicine and Public Health (UNISANTE), Lausanne, Switzerland
| | - Torkjel M Sandanger
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Roel C H Vermeulen
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
- Julius Centre for Health Sciences and Primary Care, University Medical Centre, Utrecht, Utrecht, The Netherlands
| | - Florence Guida
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Group of Genetic Epidemiology, International Agency for Research on Cancer (IARC) - World Health Organization (WHO), Lyon, France
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK.
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
2
|
Fan Y, Bai B, Liang Y, Ren Y, Liu Y, Zhou F, Lou X, Zi J, Hou G, Chen F, Zhao Q, Liu S. Proteomic Profiling of Gastric Signet Ring Cell Carcinoma Tissues Reveals Characteristic Changes of the Complement Cascade Pathway. Mol Cell Proteomics 2021; 20:100068. [PMID: 33676000 PMCID: PMC8121970 DOI: 10.1016/j.mcpro.2021.100068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/25/2020] [Accepted: 02/23/2021] [Indexed: 02/08/2023] Open
Abstract
Signet ring cell carcinoma (SRCC) is a histological subtype of gastric cancer with distinct features in multiple aspects compared with adenocarcinomas (ACs). The lack of a systematic molecular overview of this disease has led to slow progress in its clinical practice. In the present proteomics study, gastric tissues were collected from tumors and adjacent tissues, including 14 SRCCs and 34 ACs, and laser capture microdissection (LCM) was employed to eradicate the cellular heterogeneity of the tissues. The proteomes of tissues were profiled by data-independent acquisition (DIA) mass spectrometry (MS). Based on the over 6000 proteins quantified, univariate analysis and pathway enrichment revealed that some proteins and pathways demonstrated differences between SRCC and ACs. Importantly, the upregulation of a majority of complement-related proteins was notable for SRCC but not for ACs. A hypothesis, based on the proteomics evidence, was proposed that the complement cascade was evoked in the SRCC microenvironment upon infiltration, and the SRCC cells survived the complement cytotoxicity by secreting endogenous negative regulators. Moreover, an attempt was made to establish appropriate cell models for gastric SRCC through proteomic comparison of the 15 gastric cell lines and gastric tumors. The predictions of a supervised classifier suggested that none of these gastric cell lines qualified to mimic SRCC. This study discovered that the complement cascade is activated at a higher level in gastric SRCC than in ACs. LCM-DIA extracted unprecedented proteomic details of gastric in different subtypes. Complement cascade was found to be an SRCC-specific pathway for the first time. Gastric cell lines were evaluated based on proteomic features for the first time. Re-analyzable DIA data collected provide rich opportunity for future research.
Collapse
Affiliation(s)
- Yang Fan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China; Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Bin Bai
- State Key Laboratory of Cancer Biology & Department of Surgery, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Yuting Liang
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China; Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Yan Ren
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Yanxia Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Fenli Zhou
- State Key Laboratory of Cancer Biology & Department of Surgery, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Xiaomin Lou
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jin Zi
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Guixue Hou
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Qingchuan Zhao
- State Key Laboratory of Cancer Biology & Department of Surgery, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China.
| | - Siqi Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China; Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China.
| |
Collapse
|
3
|
Li W, Si X, Yang J, Zhang J, Yu K, Cao Y. Regulator of G-protein signalling 3 and its regulator microRNA-133a mediate cell proliferation in gastric cancer. Arab J Gastroenterol 2020; 21:237-245. [DOI: 10.1016/j.ajg.2020.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 05/31/2020] [Accepted: 07/29/2020] [Indexed: 12/18/2022]
|
4
|
Song WM, Lin X, Liao X, Hu D, Lin J, Sarpel U, Ye Y, Feferman Y, Labow DM, Walsh MJ, Zheng X, Zhang B. Multiscale network analysis reveals molecular mechanisms and key regulators of the tumor microenvironment in gastric cancer. Int J Cancer 2019; 146:1268-1280. [PMID: 31463974 PMCID: PMC7004118 DOI: 10.1002/ijc.32643] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/18/2019] [Accepted: 08/16/2019] [Indexed: 12/24/2022]
Abstract
Gastric cancer (GC) is the third leading cause of cancer deaths and the fourth most prevalent malignancy worldwide. The high incidence and mortality rates of gastric cancer result from multiple factors such as ineffective screening, diagnosis, and limited treatment options. In our study, we sought to systematically identify predictive molecular networks and key regulators to elucidate complex interacting signaling pathways in GC. We performed an integrative network analysis of the transcriptomic data in The Cancer Genome Atlas (TCGA) gastric cancer cohort and then comprehensively characterized the predictive subnetworks and key regulators by the matched genetic and epigenetic data. We identified 221 gene subnetworks (modules) in GC. The most prognostic subnetworks captured multiple aspects of the tumor microenvironment in GC involving interactions among stromal, epithelial and immune cells. We revealed the genetic and epigenetic underpinnings of those subnetworks and their key transcriptional regulators. We computationally predicted and experimentally validated specific mechanisms of anticancer effects of GKN2 in gastric cancer proliferation and invasion in vitro. The network models and the key regulators of the tumor microenvironment in GC identified here pave a way for developing novel therapeutic strategies for GC. What's new? Gene signatures have been identified for diagnosis and classification of gastric cancer (GC) as well as prediction of therapeutic response. However, key molecular mechanisms underlying prognosis remain to be revealed. Our study systematically identifies and characterizes predictive molecular networks and key regulators. The most prognostic subnetworks capture multiple aspects of the tumor microenvironment in GC involving interactions among stromal, epithelial, and immune cells. The authors computationally predicted and experimentally validated specific mechanisms of anti‐cancer effects of GKN2 in GC proliferation and invasion in vitro. These network models and key regulators pave the way for developing novel therapeutic strategies for GC.
Collapse
Affiliation(s)
- Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY.,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Xiandong Lin
- Laboratory of Radiation Oncology and Radiobiolog, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China.,Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, China
| | - Xuehong Liao
- Department of Pathology, Zhongshan Hospital of Xiamen University, Xiamen, Fujian, China
| | - Dan Hu
- Department of Pathology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
| | - Jieqiong Lin
- Department of Pathology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
| | - Umut Sarpel
- Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yunbin Ye
- Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, China.,Laboratory of Immuno-Oncology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
| | - Yael Feferman
- Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Daniel M Labow
- Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Martin J Walsh
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY.,The Mount Sinai Center for RNA Biology and Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Xiongwei Zheng
- Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, China.,Department of Pathology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY.,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY
| |
Collapse
|
5
|
Ercan A, Çelebier M, Varan G, Öncül S, Nenni M, Kaplan O, Bilensoy E. Global omics strategies to investigate the effect of cyclodextrin nanoparticles on MCF-7 breast cancer cells. Eur J Pharm Sci 2018; 123:377-386. [PMID: 30076952 DOI: 10.1016/j.ejps.2018.07.060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/25/2018] [Accepted: 07/31/2018] [Indexed: 12/20/2022]
Abstract
Cyclodextrins (CD) are natural macrocyclic oligosaccharides linked by α(1,4) glycosidic bonds. Hydrophobic cavity of CDs are able to incorporate small molecules, ions, macromolecules which makes them excellent delegates for forming nanoparticulate carriers upon chemical modification to render amphiphilicity to CDs. In this study, blank 6OCaproβCD nanoparticle was prepared and administered to MCF-7 breast cancer cells. The effects of these nanoparticles on the cells were investigated in depth through biochemical and proteomic tests following 48 h of incubation. Proteomics studies revealed that apoptosis-related protein levels of hnRNP and CBX1 were increased while HDGF was not affected supporting the idea that 6OCaproβCD nanoparticles prevent cell proliferation. Gene expression studies were generally in correlation with protein levels since gene expression was significantly stimulated while protein levels were lower compared to the control group suggesting that a post-transcriptional modification must have occurred. Furthermore, 6OCaproβCD was observed to not trigger multidrug resistance as proved with RT-PCR that effectuates another exquisite characteristic of 6OCaproβCD nanoparticle as carrier of chemotherapeutic drugs. Metabolomic pathways of CD effect on MCF7 cells were elucidated with HMDB as serine biosynthesis, transmembrane transport of small molecules, metabolism of steroid hormones, estrogen biosynthesis and phospholipid biosynthesis. In conclusion, 6OCaproβCD is a promising nanoparticulate carrier for chemotherapeutic drugs with intrinsic apoptotic effect to be employed in treatment of breast cancer and further studies should be conducted in order to comprehend the exact mechanism of action.
Collapse
Affiliation(s)
- Ayşe Ercan
- Department of Biochemistry, Faculty of Pharmacy, Hacettepe University, 06100 Ankara, Turkey
| | - Mustafa Çelebier
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, 06100 Ankara, Turkey
| | - Gamze Varan
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Hacettepe University, 06100 Ankara, Turkey
| | - Selin Öncül
- Department of Biochemistry, Faculty of Pharmacy, Hacettepe University, 06100 Ankara, Turkey
| | - Merve Nenni
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, 06100 Ankara, Turkey
| | - Ozan Kaplan
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, 06100 Ankara, Turkey
| | - Erem Bilensoy
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Hacettepe University, 06100 Ankara, Turkey.
| |
Collapse
|
6
|
Xiao H, Zhang Y, Kim Y, Kim S, Kim JJ, Kim KM, Yoshizawa J, Fan LY, Cao CX, Wong DTW. Differential Proteomic Analysis of Human Saliva using Tandem Mass Tags Quantification for Gastric Cancer Detection. Sci Rep 2016; 6:22165. [PMID: 26911362 PMCID: PMC4766442 DOI: 10.1038/srep22165] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/04/2016] [Indexed: 02/07/2023] Open
Abstract
Novel biomarkers and non-invasive diagnostic methods are urgently needed for the screening of gastric cancer to reduce its high mortality. We employed quantitative proteomics approach to develop discriminatory biomarker signatures from human saliva for the detection of gastric cancer. Salivary proteins were analyzed and compared between gastric cancer patients and matched control subjects by using tandem mass tags (TMT) technology. More than 500 proteins were identified with quantification, and 48 of them showed significant difference expression (p < 0.05) between normal controls and gastric cancer patients, including 7 up-regulated proteins and 41 down-regulated proteins. Five proteins were selected for initial verification by ELISA and three were successfully verified, namely cystatin B (CSTB), triosephosphate isomerase (TPI1), and deleted in malignant brain tumors 1 protein (DMBT1). All three proteins could differentiate gastric cancer patients from normal control subjects, dramatically (p < 0.05). The combination of these three biomarkers could reach 85% sensitivity and 80% specificity for the detection of gastric cancer with accuracy of 0.93. This study provides the proof of concept of salivary biomarkers for the non-invasive detection of gastric cancer. It is highly encouraging to turn these biomarkers into an applicable clinical test after large scale validation.
Collapse
Affiliation(s)
- Hua Xiao
- State Key Laboratory of Microbial Metabolism, Laboratory of Bioseparation and Analytical Biochemistry, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yong Kim
- Dental Research Institute, School of Dentistry, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Sung Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 030031, Korea
| | - Jae Joon Kim
- Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 030031, Korea
| | - Kyoung Mee Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 030031, Korea
| | - Janice Yoshizawa
- Dental Research Institute, School of Dentistry, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Liu-Yin Fan
- State Key Laboratory of Microbial Metabolism, Laboratory of Bioseparation and Analytical Biochemistry, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Cheng-Xi Cao
- State Key Laboratory of Microbial Metabolism, Laboratory of Bioseparation and Analytical Biochemistry, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - David T W Wong
- Dental Research Institute, School of Dentistry, University of California-Los Angeles, Los Angeles, California, 90095, USA
| |
Collapse
|
7
|
He CZ, Zhang KH. Serum protein and genetic tumor markers of gastric carcinoma. Asian Pac J Cancer Prev 2014; 14:3437-42. [PMID: 23886124 DOI: 10.7314/apjcp.2013.14.6.3437] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The high incidence of gastric cancer and consequent mortality pose severe threats to human health. Early screening, diagnosis and treatment are the key to improve the prognosis of the patients with gastric cancer. Gastroscopy with biopsy is an efficient method for the diagnosis of early gastric cancer, but the associated discomfort and high cost make it difficult to be a routine method for screening gastric cancer. Serum tumor marker assay is a simple and practical method for detection of gastric cancer, but it is limited by poor sensitivity and specificity. Therefore, people have been looking for novel serum markers of gastric cancer in recent years. Here we review the novel serum tumor markers of gastric cancer and their diagnostic significance, focusing on the discoveries from serum proteomics analyses and epigenetics researches.
Collapse
Affiliation(s)
- Chao-Zhu He
- Department of Gastroenterology, the First Affiliated Hospital of Nanchang University, Jiangxi Institute of Gastroenterology and Hepatology, Nanchang, China.
| | | |
Collapse
|
8
|
Identification of HSP90 as potential biomarker of biliary atresia using two-dimensional electrophoresis and mass spectrometry. PLoS One 2013; 8:e68602. [PMID: 23874684 PMCID: PMC3708914 DOI: 10.1371/journal.pone.0068602] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 05/31/2013] [Indexed: 12/26/2022] Open
Abstract
Biliary atresia (BA) is a devastating cholestatic liver disease targeting infants. Current diagnosis depends on surgical exploration of the biliary tree. The aim of the present study was to identify potential biomarkers for the diagnosis of biliary atresia (BA). Two-dimensional electrophoresis was utilized for the identification of proteins that were differentially expressed in liver biopsies of 20 BA patients and 12 infants with non-BA neonatal cholestasis (NC) as controls. Using mass spectrometry, we identified 15 proteins with expressions significantly altered. Out of the 15 proteins identified, heat shock protein (HSP) 90 was the most significantly altered and was down-regulated in BA samples compared to NC samples using immunoblotting analysis. Our findings suggest that HSP90 might be a potential biomarker for the diagnosis of BA and may be used for monitoring further development and therapy for BA. This study demonstrated that a comprehensive strategy of proteomic identification combined with further validation should be adopted in biomarker discovery.
Collapse
|
9
|
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.
Collapse
|
10
|
Kočevar N, Odreman F, Vindigni A, Grazio SF, Komel R. Proteomic analysis of gastric cancer and immunoblot validation of potential biomarkers. World J Gastroenterol 2012; 18:1216-28. [PMID: 22468085 PMCID: PMC3309911 DOI: 10.3748/wjg.v18.i11.1216] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 05/26/2011] [Accepted: 06/03/2011] [Indexed: 02/06/2023] Open
Abstract
AIM: To search for and validate differentially expressed proteins in patients with gastric adenocarcinoma.
METHODS: We used two-dimensional gel electrophoresis and mass spectrometry to search for differentially expressed proteins in patients with gastric adenocarcinoma. A set of proteins was validated with immunoblotting.
RESULTS: We identified 30 different proteins involved in various biological processes: metabolism, development, death, response to stress, cell cycle, cell communication, transport, and cell motility. Eight proteins were chosen for further validation by immunoblotting. Our results show that gastrokine-1, 39S ribosomal protein L12 (mitochondrial precursor), plasma cell-induced resident endoplasmic reticulum protein, and glutathione S-transferase mu 3 were significantly underexpressed in gastric adenocarcinoma relative to adjacent non-tumor tissue samples. On the other hand, septin-2, ubiquitin-conjugating enzyme E2 N, and transaldolase were significantly overexpressed. Translationally controlled tumor protein was shown to be differentially expressed only in patients with cancer of the gastric cardia/esophageal border.
CONCLUSION: This work presents a set of possible diagnostic biomarkers, validated for the first time. It might contribute to the efforts of understanding gastric cancer carcinogenesis.
Collapse
|
11
|
Yu LN, Pei J. [Application of differential proteomics in mechanism research of acupuncture]. ACTA ACUST UNITED AC 2012; 9:819-23. [PMID: 21849141 DOI: 10.3736/jcim20110802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Proteomics, a new branch of science, has been used to study protein expressions on the molecular level with a dynamic perspective. Organisms under varying states may express different proteins, which results in the set-up of differential proteomics. Research methods of differential proteomics include the separation and identification of proteins. Differential proteomics has a rapid development in recent years. In the study of acupuncture, researchers have reached certain achievements using differential proteomics to investigate the mechanisms of acupuncture treatment for some diseases, including acute spinal cord injury, ischemic cerebrovascular disease, Parkinson's disease and neuralgia.
Collapse
Affiliation(s)
- Lin-na Yu
- Department of Acupuncture and Moxibustion, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | | |
Collapse
|
12
|
Abstract
Two-dimensional electrophoresis (2-DE) is a high-resolution technique for analysis and comparison of complex protein mixtures. With the advent of recent technical developments, its application has become significant in a wide range of fields. This chapter describes a proteomic approach for the analysis of metastasis-associated proteins using pre-fractionation of glycosylated proteins via lectin (HPA) affinity chromatography prior to separation by 2-DE. Guidelines for the preparation and storage of buffers, experimental conditions and protocols of affinity chromatography, isoelectric focussing, and SDS-PAGE conditions are provided. Critical parameters associated with the different steps of 2-DE are discussed.
Collapse
Affiliation(s)
- Miriam Dwek
- Department of Molecular and Applied Biosciences, School of Life Sciences, University of Westminster, London, UK.
| | | |
Collapse
|
13
|
Identification of Cervical Cancer Proteins Associated With Treatment With Paclitaxel and Cisplatin in Patients. Int J Gynecol Cancer 2011; 21:1452-7. [DOI: 10.1097/igc.0b013e31822491d0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
|
14
|
Grigorieva ES, Bukurova YA, Krasnov GS, Afanas’ev SG, Cherdyntseva NV, Tuzikov SA, Choinzonov EL, Karpov VL, Lisitsyn NA, Beresten SF. Identification of proteins overexpressed in malignant gastric tumors: Comparison of results obtained by 2DE and bioinformatic search. Mol Biol 2011. [DOI: 10.1134/s0026893311030058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
15
|
Bones J, Byrne JC, O'Donoghue N, McManus C, Scaife C, Boissin H, Nastase A, Rudd PM. Glycomic and glycoproteomic analysis of serum from patients with stomach cancer reveals potential markers arising from host defense response mechanisms. J Proteome Res 2011; 10:1246-65. [PMID: 21142185 DOI: 10.1021/pr101036b] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite the reduced incidence of gastric cancer in the developed world, a diagnosis of stomach carcinoma still carries a poor prognosis due to the asymptomatic nature of the disease in the early stages, subsequent advanced stage diagnosis, and a low 5 year survival rate. Endoscopy remains the primary standard for diagnosis of stomach carcinoma and the current marker, carbohydrate antigen 19-9 (CA19-9) lacks the levels of sensitivity and specificity required in order to make it clinically useful for diagnostic monitoring. Therefore, there is a current need for additional markers to improve the diagnostic accuracy for the early stages of stomach cancer. Together, glycomic, proteomic, and glycoproteomic analyses of serum have the potential to identify such probable markers. A discovery study is reported here using preoperative serum from 80 stomach cancer patients, 10 patients bearing benign stomach disease, and 20 matched controls. Glycomic analysis of the total and immunoaffinity depleted serum revealed statistically significant increases in the levels of sialyl Lewis X epitopes (SLe(X)) present on triantennary glycans accompanied by increased levels of core fucosylated agalactosyl biantennary glycans present on IgG (referred to as the IgG G0 glycoform) which are associated with increasing disease pathogenesis. Protein expression analysis using 2D-DiGE returned a number of differentially expressed protein candidates in the depleted serum, many of which were shown to carry triantennary SLe(X) during subsequent glycomic investigations. Biological pathway analysis of the experimental data returned complement activation and acute phase response signaling as the most significantly altered pathways in the stomach cancer patient serum. Upon the basis of these findings, it is suggested that increased expression of IgG G0 and complement activation are a host response to the presence of the stomach tumor while the increased expression of SLe(X) and acute phase response proteins is a result of pro-inflammatory cytokine signaling, including IL-6, during carcinogenesis. The approach presented herein provides an insight into the underlying mechanisms of disease and the resulting changes in the glycome and glycoproteome offer promise as potential markers for diagnosis and prognostic monitoring in stomach cancer.
Collapse
Affiliation(s)
- Jonathan Bones
- NIBRT Dublin-Oxford Glycobiology Laboratory, The National Institute for Bioprocessing Research and Training, University College Dublin, Belfield, Dublin 4, Ireland
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Joshi S, Tiwari A, Mondal B, Sharma A. Oncoproteomics. Clin Chim Acta 2011; 412:217-26. [DOI: 10.1016/j.cca.2010.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 10/03/2010] [Accepted: 10/03/2010] [Indexed: 11/29/2022]
|
17
|
Kim HK, Reyzer ML, Choi IJ, Kim CG, Kim HS, Oshima A, Chertov O, Colantonio S, Fisher RJ, Allen JL, Caprioli RM, Green JE. Gastric cancer-specific protein profile identified using endoscopic biopsy samples via MALDI mass spectrometry. J Proteome Res 2010; 9:4123-30. [PMID: 20557134 PMCID: PMC3441055 DOI: 10.1021/pr100302b] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To date, proteomic analyses on gastrointestinal cancer tissue samples have been performed using surgical specimens only, which are obtained after a diagnosis is made. To determine if a proteomic signature obtained from endoscopic biopsy samples could be found to assist with diagnosis, frozen endoscopic biopsy samples collected from 63 gastric cancer patients and 43 healthy volunteers were analyzed using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. A statistical classification model was developed to distinguish tumor from normal tissues using half the samples and validated with the other half. A protein profile was discovered consisting of 73 signals that could classify 32 cancer and 22 normal samples in the validation set with high predictive values (positive and negative predictive values for cancer, 96.8% and 91.3%; sensitivity, 93.8%; specificity, 95.5%). Signals overexpressed in tumors were identified as alpha-defensin-1, alpha-defensin-2, calgranulin A, and calgranulin B. A protein profile was also found to distinguish pathologic stage Ia (pT1N0M0) samples (n = 10) from more advanced stage (Ib or higher) tumors (n = 48). Thus, protein profiles obtained from endoscopic biopsy samples may be useful in assisting with the diagnosis of gastric cancer and, possibly, in identifying early stage disease.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Jeffrey E. Green
- To whom correspondence should be addressed. Jeffrey E. Green, M.D., Laboratory of Cancer Biology and Genetics, National Cancer Institute, Building 37, Room 4054, 37 Convent Dr., Bethesda, MD 20892 (Phone 301-435-5193, Fax 301-496-8709, )
| |
Collapse
|
18
|
Lu HB, Zhou JH, Ma YY, Lu HL, Tang YL, Zhang QY, Zhao CH. Five serum proteins identified using SELDI-TOF-MS as potential biomarkers of gastric cancer. Jpn J Clin Oncol 2010; 40:336-42. [PMID: 20089528 DOI: 10.1093/jjco/hyp175] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE The aims of this study were to detect serum proteomic patterns in gastric cancer serum samples using Surface-enhanced Laser Desorption/ionization-Time-of-flight-Mass Spectrometry ProteinChip array technology, to screen biomarker candidates, to build diagnostic models and to evaluate their clinical significance. METHODS Serum samples from patients with gastric cancer and normal healthy control subjects (n = 125) were analysed using surface-enhanced laser desorption/ionization technology. The spectra were generated on weak cation exchange (WCX2) chips, and protein peak clustering and classification analyses were established using Ciphergen Biomarker Wizard and Biomarker Pattern software, respectively. The diagnostic models were developed and validated by discriminant analysis. In addition, the results of the surface-enhanced laser desorption/ionization model were compared with the biomarkers carcinoembryonic antigen and carbohydrate antigen 199 in a subset of samples using a microparticle enzyme immunoassay. RESULTS Five protein peaks at 2046, 3179, 1817, 1725 and 1929 m/z were automatically chosen as components of the best biomarker pattern for diagnosis of gastric cancer. In addition, we identified a single protein peak at 4665 m/z, which could distinguish between stage I/II and stage III/IV gastric cancer with a specificity and sensitivity of 91.6% (11/12) and 95.4% (21/22), respectively. When this biomarker was validated in the second set of samples, the specificity and sensitivity were 91.7% (11/12) and 86.3% (19/22), respectively. CONCLUSIONS The present results suggest that serum surface-enhanced laser desorption/ionization protein profiling can distinguish patients with gastric cancer, and in particular stage I/II patients, from normal subjects with a relatively high sensitivity and specificity. Surface-enhanced Laser Desorption/ionization-Time-of-flight-Mass Spectrometry is a potential new diagnostic tool for the screening of gastric cancer.
Collapse
Affiliation(s)
- Hai-bo Lu
- Department of Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, China.
| | | | | | | | | | | | | |
Collapse
|
19
|
Bornschein J, Weigt J, Selgrad M, Malfertheiner P. Molecular aspects in the diagnosis of gastric cancer. ACTA ACUST UNITED AC 2009; 3:585-96. [PMID: 23495987 DOI: 10.1517/17530050902862175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Gastric cancer (GC) represents the second most common cause of cancer-related death worldwide. The prognosis remains poor, with limited treatment options. A better understanding of the initiation and progression of GC would enable the development of general screening strategies and individualized treatment modalities. OBJECTIVE The assessment of tools and molecular markers for the early detection and diagnosis of GC. METHODS Human clinical studies published within the past 5 years are reviewed. Also, significant previous data on markers in clinical use or on relevant animal or cell culture experiments are considered. RESULTS/CONCLUSION Serum-based screening strategies are not ready for routine application but represent an opportunity for the identification of individuals at high risk with the need for primary gastroscopy and further surveillance, which would ultimately improve survival and prognosis of GC. Infection with Helicobacter pylori represents the principal risk factor for gastric carcinogenesis. Bacterial virulence and host genetic factors contribute to individual susceptibility. Key molecular alterations in gastric carcinogenesis are related to intra- and extracellular cascades that regulate cell proliferation, tumor invasion and metastastic spread. For the development of effective prevention and treatment modalities, it is essential to unravel the basic mechanisms of gastric carcinogenesis.
Collapse
Affiliation(s)
- Jan Bornschein
- Otto-von-Guericke-University of Magdeburg, Department of Gastroenterology, Hepatology and Infectious Diseases, Leipziger Str. 44, D-39120 Magdeburg, Germany +0049 391 6713100 ; +0049 391 6713105 ;
| | | | | | | |
Collapse
|