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Zhang T, Zhang SW, Xie MY, Li Y. Identifying cooperating cancer driver genes in individual patients through hypergraph random walk. J Biomed Inform 2024; 157:104710. [PMID: 39159864 DOI: 10.1016/j.jbi.2024.104710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 07/30/2024] [Accepted: 08/14/2024] [Indexed: 08/21/2024]
Abstract
OBJECTIVE Identifying cancer driver genes, especially rare or patient-specific cancer driver genes, is a primary goal in cancer therapy. Although researchers have proposed some methods to tackle this problem, these methods mostly identify cancer driver genes at single gene level, overlooking the cooperative relationship among cancer driver genes. Identifying cooperating cancer driver genes in individual patients is pivotal for understanding cancer etiology and advancing the development of personalized therapies. METHODS Here, we propose a novel Personalized Cooperating cancer Driver Genes (PCoDG) method by using hypergraph random walk to identify the cancer driver genes that cooperatively drive individual patient cancer progression. By leveraging the powerful ability of hypergraph in representing multi-way relationships, PCoDG first employs the personalized hypergraph to depict the complex interactions among mutated genes and differentially expressed genes of an individual patient. Then, a hypergraph random walk algorithm based on hyperedge similarity is utilized to calculate the importance scores of mutated genes, integrating these scores with signaling pathway data to identify the cooperating cancer driver genes in individual patients. RESULTS The experimental results on three TCGA cancer datasets (i.e., BRCA, LUAD, and COADREAD) demonstrate the effectiveness of PCoDG in identifying personalized cooperating cancer driver genes. These genes identified by PCoDG not only offer valuable insights into patient stratification correlating with clinical outcomes, but also provide an useful reference resource for tailoring personalized treatments. CONCLUSION We propose a novel method that can effectively identify cooperating cancer driver genes for individual patients, thereby deepening our understanding of the cooperative relationship among personalized cancer driver genes and advancing the development of precision oncology.
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Affiliation(s)
- Tong Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China; School of Electrical and Mechanical Engineering, Pingdingshan University, Pingdingshan 467000, China
| | - Shao-Wu Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China.
| | - Ming-Yu Xie
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yan Li
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
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Dubey AK, Kaur I, Madaan R, Raheja S, Bala R, Garg M, Kumar S, Lather V, Mittal V, Pandita D, Gundamaraju R, Singla RK, Sharma R. Unlocking the potential of oncology biomarkers: advancements in clinical theranostics. Drug Metab Pers Ther 2024; 39:5-20. [PMID: 38469723 DOI: 10.1515/dmpt-2023-0056] [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: 06/30/2023] [Accepted: 01/11/2024] [Indexed: 03/13/2024]
Abstract
INTRODUCTION Cancer biomarkers have revolutionized the field of oncology by providing valuable insights into tumor changes and aiding in screening, diagnosis, prognosis, treatment prediction, and risk assessment. The emergence of "omic" technologies has enabled biomarkers to become reliable and accurate predictors of outcomes during cancer treatment. CONTENT In this review, we highlight the clinical utility of biomarkers in cancer identification and motivate researchers to establish a personalized/precision approach in oncology. By extending a multidisciplinary technology-based approach, biomarkers offer an alternative to traditional techniques, fulfilling the goal of cancer therapeutics to find a needle in a haystack. SUMMARY AND OUTLOOK We target different forms of cancer to establish a dynamic role of biomarkers in understanding the spectrum of malignancies and their biochemical and molecular characterization, emphasizing their prospective contribution to cancer screening. Biomarkers offer a promising avenue for the early detection of human cancers and the exploration of novel technologies to predict disease severity, facilitating maximum survival and minimum mortality rates. This review provides a comprehensive overview of the potential of biomarkers in oncology and highlights their prospects in advancing cancer diagnosis and treatment.
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Affiliation(s)
- Ankit Kumar Dubey
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, 34753 Sichuan University , Chengdu, P.R. China
- iGlobal Research and Publishing Foundation, New Delhi, India
| | - Ishnoor Kaur
- Chitkara College of Pharmacy, 154025 Chitkara University Punjab , Rajpura, India
| | - Reecha Madaan
- Chitkara College of Pharmacy, 154025 Chitkara University Punjab , Rajpura, India
| | - Shikha Raheja
- Jan Nayak Ch. Devi Lal Memorial College of Pharmacy, Sirsa, Haryana, India
| | - Rajni Bala
- Chitkara College of Pharmacy, 154025 Chitkara University Punjab , Rajpura, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine & Stem Cell Research, 77282 Amity University, Sector-125 , Noida, India
| | - Suresh Kumar
- Department of Pharmaceutical Sciences and Drug Research, 429174 Punjabi University Patiala , Patiala, India
| | - Viney Lather
- Amity Institute of Pharmacy, 77282 Amity University , Noida, India
| | - Vineet Mittal
- Department of Pharmaceutical Sciences, 29062 Maharshi Dayanand University , Rohtak, Haryana, India
| | - Deepti Pandita
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University, PushpVihar, 633274 Govt. of NCT of Delhi , New Delhi, India
- Centre for Advanced Formulation and Technology (CAFT), Delhi Pharmaceutical Sciences and Research University, PushpVihar, Govt. of NCT of Delhi, New Delhi, India
| | - Rohit Gundamaraju
- ER Stress and Mucosal Immunology Lab, School of Health Sciences, 8785 University of Tasmania , Launceston, Tasmania, Australia
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rajeev K Singla
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, 34753 Sichuan University , Chengdu, P.R. China
- School of Pharmaceutical Sciences, 34753 Lovely Professional University , Phagwara, Punjab, India
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, 80095 Banaras Hindu University , Varanasi, Uttar Pradesh, India
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Orășeanu A, Brisc MC, Maghiar OA, Popa H, Brisc CM, Șolea SF, Maghiar TA, Brisc C. Landscape of Innovative Methods for Early Diagnosis of Gastric Cancer: A Systematic Review. Diagnostics (Basel) 2023; 13:3608. [PMID: 38132192 PMCID: PMC10742893 DOI: 10.3390/diagnostics13243608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
From a global perspective, gastric cancer (GC) persists as a significant healthcare issue. In the Western world, the majority of cases are discovered at late stages, when the treatment is generally unsuccessful. There are no organized screening programs outside of Asia (Japan and Republic of Korea). Traditional diagnosis techniques (such as upper endoscopy), conventional tumor markers (CEA, CA19-9, and CA72-4), radiographic imaging, and CT scanning all have drawbacks. The gold standard for the earliest detection of cancer and related premalignant lesions is still endoscopy with a proper biopsy follow-up. Since there are currently no clinically approved biomarkers for the early diagnosis of GC, the identification of non-invasive biomarkers is expected to help improve the prognosis and survival rate of these patients. The search for new screening biomarkers is currently underway. These include genetic biomarkers, such as circulating tumor cells, microRNAs, and exosomes, as well as metabolic biomarkers obtained from biofluids. Meanwhile, cutting-edge high-resolution endoscopic technologies are demonstrating promising outcomes in the visual diagnosis of mucosal lesions with the aid of linked color imaging and machine learning models. Following the PRISMA guidelines, this study examined the articles in databases such as PubMed, resulting in 167 included articles. This review discusses the currently available and emerging methods for diagnosing GC early on, as well as new developments in the endoscopic detection of early lesions of the stomach.
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Affiliation(s)
- Alexandra Orășeanu
- Clinic of Gastroenterology, Bihor Clinical County Emergency Hospital, 410169 Oradea, Romania; (A.O.); (S.F.Ș.)
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania; (O.A.M.); (T.A.M.); (C.B.)
| | | | - Octavian Adrian Maghiar
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania; (O.A.M.); (T.A.M.); (C.B.)
- Faculty of Medicine and Pharmacy, University of Oradea, 410068 Oradea, Romania;
| | - Horia Popa
- Clinical Emergency Hospital “Prof. Dr. Agrippa Ionescu”, 011356 Bucharest, Romania;
| | - Ciprian Mihai Brisc
- Faculty of Medicine and Pharmacy, University of Oradea, 410068 Oradea, Romania;
| | - Sabina Florina Șolea
- Clinic of Gastroenterology, Bihor Clinical County Emergency Hospital, 410169 Oradea, Romania; (A.O.); (S.F.Ș.)
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania; (O.A.M.); (T.A.M.); (C.B.)
| | - Teodor Andrei Maghiar
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania; (O.A.M.); (T.A.M.); (C.B.)
- Faculty of Medicine and Pharmacy, University of Oradea, 410068 Oradea, Romania;
| | - Ciprian Brisc
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania; (O.A.M.); (T.A.M.); (C.B.)
- Faculty of Medicine and Pharmacy, University of Oradea, 410068 Oradea, Romania;
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Niedermaier T, Gredner T, Hoffmeister M, Mons U, Brenner H. Impact of Reducing Intake of Red and Processed Meat on Colorectal Cancer Incidence in Germany 2020 to 2050-A Simulation Study. Nutrients 2023; 15:nu15041020. [PMID: 36839378 PMCID: PMC9966277 DOI: 10.3390/nu15041020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/10/2023] [Accepted: 02/12/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND According to the International Agency for Research on Cancer (IARC), there is sufficient evidence for the carcinogenicity of processed meat consumption in humans, specifically regarding colorectal cancer (CRC) risk. Evidence for the carcinogenicity of red meat consumption is more limited but points in the same direction. METHODS A macro-simulation approach was used to calculate age- and sex-specific potential impact fractions in a 30-year period (2020-2050). AIMS We estimated numbers and proportions of future CRC cases preventable under different scenarios of reducing the intake of processed and red meat in the German population. RESULTS Eliminating processed meat intake could reduce the burden of CRC by approximately 205,000 cases in Germany (9.6%) in 2020-2050, 2/3 among males (145,000) and 1/3 among females (60,000). Without red meat intake, approximately 63,000 CRC cases could be avoided (2.9%), 39,000 among males and 24,000 among females. Reductions in the mean consumption of both processed and red meat by one or two servings (each 11 or 22 g) per day would be expected to reduce CRC case numbers by 68,000 (3.1%) and 140,000 (6.5%), respectively. CONCLUSION A reduction in red and processed meat intake might substantially reduce the incidence of CRC in Germany. The means of achieving such a reduction might include price and taxation policies, food labeling, and clearer risk communication aiming to reduce individual intake.
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Affiliation(s)
- Tobias Niedermaier
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Correspondence:
| | - Thomas Gredner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ute Mons
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Cancer Prevention Unit, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Cardiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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Enomoto M, Igaki T. Cell-cell interactions that drive tumorigenesis in Drosophila. Fly (Austin) 2022; 16:367-381. [PMID: 36413374 PMCID: PMC9683056 DOI: 10.1080/19336934.2022.2148828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Cell-cell interactions within tumour microenvironment play crucial roles in tumorigenesis. Genetic mosaic techniques available in Drosophila have provided a powerful platform to study the basic principles of tumour growth and progression via cell-cell communications. This led to the identification of oncogenic cell-cell interactions triggered by endocytic dysregulation, mitochondrial dysfunction, cell polarity defects, or Src activation in Drosophila imaginal epithelia. Such oncogenic cooperations can be caused by interactions among epithelial cells, mesenchymal cells, and immune cells. Moreover, microenvironmental factors such as nutrients, local tissue structures, and endogenous growth signalling activities critically affect tumorigenesis. Dissecting various types of oncogenic cell-cell interactions at the single-cell level in Drosophila will greatly increase our understanding of how tumours progress in living animals.
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Affiliation(s)
- Masato Enomoto
- Laboratory of Genetics, Graduate School of Biostudies, Kyoto University, Yoshida-Konoecho, Kyoto, Japan
| | - Tatsushi Igaki
- Laboratory of Genetics, Graduate School of Biostudies, Kyoto University, Yoshida-Konoecho, Kyoto, Japan,CONTACT Tatsushi Igaki
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In Vitro Cytotoxicity Evaluation of Plastoquinone Analogues against Colorectal and Breast Cancers along with In Silico Insights. Pharmaceuticals (Basel) 2022; 15:ph15101266. [PMID: 36297378 PMCID: PMC9609592 DOI: 10.3390/ph15101266] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
Colorectal cancer (CRC) and breast cancer are leading causes of death globally, due to significant challenges in detection and management. The late-stage diagnosis and treatment failures require the discovery of potential anticancer agents to achieve a satisfactory therapeutic effect. We have previously reported a series of plastoquinone analogues to understand their cytotoxic profile. Among these derivatives, three of them (AQ-11, AQ-12, and AQ-15) were selected by the National Cancer Institute (NCI) to evaluate their in vitro antiproliferative activity against a panel of 60 human tumor cell lines. AQ-12 exhibited significant antiproliferative activity against HCT-116 CRC and MCF-7 breast cancer cells at a single dose and further five doses. MTT assay was also performed for AQ-12 at different concentrations against these two cells, implying that AQ-12 exerted notable cytotoxicity toward HCT-116 (IC50 = 5.11 ± 2.14 μM) and MCF-7 (IC50 = 6.06 ± 3.09 μM) cells in comparison with cisplatin (IC50 = 23.68 ± 6.81 μM and 19.67 ± 5.94 μM, respectively). This compound also augmented apoptosis in HCT-116 (62.30%) and MCF-7 (64.60%) cells comparable to cisplatin (67.30% and 78.80%, respectively). Molecular docking studies showed that AQ-12 bound to DNA, forming hydrogen bonding through the quinone scaffold. In silico pharmacokinetic determinants indicated that AQ-12 demonstrated drug-likeness with a remarkable pharmacokinetic profile for future mechanistic anti-CRC and anti-breast cancer activity studies.
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Li Z, Zhao B, Qin C, Wang Y, Li T, Wang W. Chromatin Dynamics in Digestive System Cancer: Commander and Regulator. Front Oncol 2022; 12:935877. [PMID: 35965507 PMCID: PMC9372441 DOI: 10.3389/fonc.2022.935877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Digestive system tumors have a poor prognosis due to complex anatomy, insidious onset, challenges in early diagnosis, and chemoresistance. Epidemiological statistics has verified that digestive system tumors rank first in tumor-related death. Although a great number of studies are devoted to the molecular biological mechanism, early diagnostic markers, and application of new targeted drugs in digestive system tumors, the therapeutic effect is still not satisfactory. Epigenomic alterations including histone modification and chromatin remodeling are present in human cancers and are now known to cooperate with genetic changes to drive the cancer phenotype. Chromatin is the carrier of genetic information and consists of DNA, histones, non-histone proteins, and a small amount of RNA. Chromatin and nucleosomes control the stability of the eukaryotic genome and regulate DNA processes such as transcription, replication, and repair. The dynamic structure of chromatin plays a key role in this regulatory function. Structural fluctuations expose internal DNA and thus provide access to the nuclear machinery. The dynamic changes are affected by various complexes and epigenetic modifications. Variation of chromatin dynamics produces early and superior regulation of the expression of related genes and downstream pathways, thereby controlling tumor development. Intervention at the chromatin level can change the process of cancer earlier and is a feasible option for future tumor diagnosis and treatment. In this review, we introduced chromatin dynamics including chromatin remodeling, histone modifications, and chromatin accessibility, and current research on chromatin regulation in digestive system tumors was also summarized.
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Yadav M, Abdalla M, Madhavi M, Chopra I, Bhrdwaj A, Soni L, Shaheen U, Prajapati L, Sharma M, Sikarwar MS, Albogami S, Hussain T, Nayarisseri A, Singh SK. Structure-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation and Pharmacokinetic modelling of Cyclooxygenase-2 (COX-2) inhibitor for the clinical treatment of Colorectal Cancer. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2068799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Manasi Yadav
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, PR People’s Republic of China
| | - Maddala Madhavi
- Department of Zoology, Osmania University, Hyderabad, Telangana State, India
| | - Ishita Chopra
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Indore, Madhya Pradesh, India
| | - Anushka Bhrdwaj
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Lovely Soni
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Uzma Shaheen
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Leena Prajapati
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Megha Sharma
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | | | - Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Tajamul Hussain
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Indore, Madhya Pradesh, India
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
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Aurora kinase A inhibition induces synthetic lethality in SMAD4-deficient colorectal cancer cells via spindle assembly checkpoint activation. Oncogene 2022; 41:2734-2748. [PMID: 35393542 DOI: 10.1038/s41388-022-02293-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/16/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023]
Abstract
SMAD4 loss-of-function mutations have been frequently observed in colorectal cancer (CRC) and are recognized as a drug target for therapeutic exploitation. In this study, we performed a synthetic lethal drug screening with SMAD4-isogenic CRC cells and found that aurora kinase A (AURKA) inhibition is synthetic lethal with SMAD4 loss. Inhibition of AURKA selectively inhibited the growth of SMAD4-/- CRC in vitro and in vivo. Mechanistically, SMAD4 negatively regulated AURKA level, resulting in the significant elevation of AURKA in SMAD4-/- CRC cells. Inhibition of AURKA induced G2/M cell cycle delay in SMAD4+/+ CRC cells, but induced apoptosis in SMAD4-/- CRC cells. We further observed that a high level of AURKA in SMAD4-/- CRC cells led to abnormal mitotic spindles, leading to cellular aneuploidy. Moreover, SMAD4-/- CRC cells expressed high levels of spindle assembly checkpoint (SAC) proteins, suggesting the hyperactivation of SAC. The silencing of key SAC proteins significantly rescued the AURKA inhibition-induced cell death in SMAD4-/- cells, suggesting that SMAD4-/- CRC cells are hyper-dependent on AURKA activity for mitotic exit and survival during SAC hyperactivation. This study presents a unique synthetic lethal interaction between SMAD4 and AURKA and suggests that AURKA could be a potential drug target in SMAD4-deficient CRC.
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Sadri S, Rejali L, Hadizadeh M, Aghdaei HA, Young C, Nazemalhosseini-Mojarad E, Zali MR, Bonab MA. ANRIL as a prognostic biomarker in colon pre-cancerous lesion detection via non-invasive sampling. Genes Genet Syst 2021; 96:285-292. [DOI: 10.1266/ggs.21-00102] [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] Open
Affiliation(s)
- Shadi Sadri
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Centre, Research Institute for Gastroenterology and Liver Diseases, Shaheed Beheshti University of Medical Sciences
| | - Leili Rejali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Centre, Research Institute for Gastroenterology and Liver Diseases, Shaheed Beheshti University of Medical Sciences
| | | | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Centre, Research Institute for Gastroenterology and Liver Diseases, Shaheed Beheshti University of Medical Sciences
| | - Chris Young
- Leicester School of Allied Health Sciences, Faculty of Health and Life Sciences, De Montfort University
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Centre, Research Institute for Gastroenterology and Liver Diseases, Shaheed Beheshti University of Medical Sciences
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Centre, Research Institute for Gastroenterology and Liver Diseases, Shaheed Beheshti University of Medical Sciences
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Atabilen B, Akbulut G, Bacanli M, Uncu D. Is the nuclear factor kappa-b (NF-κB) pathway and inflammatory status associated with colorectal cancer? Saudi J Gastroenterol 2021; 28:60-66. [PMID: 34380870 PMCID: PMC8919927 DOI: 10.4103/sjg.sjg_44_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Although genetic predisposition has a role in the etiology of colorectal cancer, there are many other factors that affect its development. In this study, it was aimed to evaluate the NF-κB pathway, inflammatory status and dietary antioxidant capacity in individuals with colorectal cancer. METHODS The study was carried out with 40 male subjects diagnosed with colorectal cancer aged between 39-65, years and a control group of the same number of healthy men. Subjects in the case and control groups were subdivided according to body mass index (BMI), as normal (BMI 20-24.9 kg/m2) or overweight/obese (BMI ≥25 kg/m2). RESULTS At the end of the study, NF-κB and interleukin-22 levels were higher in the case group, but no significant difference was found between the groups. Interleukin-23 and 8-Hydroxy-2-deoxyguanosine levels in the case group classified as overweight/obese according to BMI were significantly higher than in the control group (P = 0.001 and P < 0.001, respectively). Considering diet antioxidant capacity, it was higher in individuals in the control group than in the case group. However, there was no significant difference between the groups. CONCLUSION Inflammatory status and reduced dietary antioxidant capacity are risk factors in the development of colorectal cancer.
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Affiliation(s)
- Büşra Atabilen
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Gazi University, Ankara, Turkey,Address for correspondence: Prof. Büşra Atabilen, Emek Neighborhood Bişkek Street, 6th Street (Former 81st Street), Gazi University Faculty of Health Sciences, Department of Nutrition and Dietetics, Ankara, Turkey. E-mail:
| | - Gamze Akbulut
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Gazi University, Ankara, Turkey
| | - Merve Bacanli
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, University of Health Sciences Gülhane, Ankara, Turkey
| | - Doğan Uncu
- Department of Medical Oncology, University of Health Sciences, Ankara, Turkey
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İncetan K, Celik IO, Obeid A, Gokceler GI, Ozyoruk KB, Almalioglu Y, Chen RJ, Mahmood F, Gilbert H, Durr NJ, Turan M. VR-Caps: A Virtual Environment for Capsule Endoscopy. Med Image Anal 2021; 70:101990. [PMID: 33609920 DOI: 10.1016/j.media.2021.101990] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 02/06/2023]
Abstract
Current capsule endoscopes and next-generation robotic capsules for diagnosis and treatment of gastrointestinal diseases are complex cyber-physical platforms that must orchestrate complex software and hardware functions. The desired tasks for these systems include visual localization, depth estimation, 3D mapping, disease detection and segmentation, automated navigation, active control, path realization and optional therapeutic modules such as targeted drug delivery and biopsy sampling. Data-driven algorithms promise to enable many advanced functionalities for capsule endoscopes, but real-world data is challenging to obtain. Physically-realistic simulations providing synthetic data have emerged as a solution to the development of data-driven algorithms. In this work, we present a comprehensive simulation platform for capsule endoscopy operations and introduce VR-Caps, a virtual active capsule environment that simulates a range of normal and abnormal tissue conditions (e.g., inflated, dry, wet etc.) and varied organ types, capsule endoscope designs (e.g., mono, stereo, dual and 360∘ camera), and the type, number, strength, and placement of internal and external magnetic sources that enable active locomotion. VR-Caps makes it possible to both independently or jointly develop, optimize, and test medical imaging and analysis software for the current and next-generation endoscopic capsule systems. To validate this approach, we train state-of-the-art deep neural networks to accomplish various medical image analysis tasks using simulated data from VR-Caps and evaluate the performance of these models on real medical data. Results demonstrate the usefulness and effectiveness of the proposed virtual platform in developing algorithms that quantify fractional coverage, camera trajectory, 3D map reconstruction, and disease classification. All of the code, pre-trained weights and created 3D organ models of the virtual environment with detailed instructions how to setup and use the environment are made publicly available at https://github.com/CapsuleEndoscope/VirtualCapsuleEndoscopy and a video demonstration can be seen in the supplementary videos (Video-I).
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Affiliation(s)
- Kağan İncetan
- Institute of Biomedical Engineering, Bogazici University, Istanbul, Turkey
| | - Ibrahim Omer Celik
- Department of Computer Engineering, Bogazici University, Istanbul, Turkey
| | - Abdulhamid Obeid
- Institute of Biomedical Engineering, Bogazici University, Istanbul, Turkey
| | | | | | | | - Richard J Chen
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Faisal Mahmood
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Cancer Data Science, Dana Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hunter Gilbert
- Deparment of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA USA
| | - Nicholas J Durr
- Department of Biomedical Engineering, Johns Hopkins University (JHU), Baltimore, MD, USA
| | - Mehmet Turan
- Institute of Biomedical Engineering, Bogazici University, Istanbul, Turkey.
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13
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Kvetkina A, Malyarenko O, Pavlenko A, Dyshlovoy S, von Amsberg G, Ermakova S, Leychenko E. Sea Anemone Heteractis crispa Actinoporin Demonstrates In Vitro Anticancer Activities and Prevents HT-29 Colorectal Cancer Cell Migration. Molecules 2020; 25:molecules25245979. [PMID: 33348592 PMCID: PMC7766076 DOI: 10.3390/molecules25245979] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 02/07/2023] Open
Abstract
Actinoporins are the most abundant group of sea anemone cytolytic toxins. Their membranolytic activity is of high interest for the development of novel anticancer drugs. However, to date the activity of actinoporins in malignant cells has been poorly studied. Here, we report on recombinant analog of Hct-S3 (rHct-S3), belonging to the combinatory library of Heteractis crispa actinoporins. rHct-S3 exhibited cytotoxic activity against breast MDA-MB-231 (IC50 = 7.3 µM), colorectal HT-29 (IC50 = 6.8 µM), and melanoma SK-MEL-28 (IC50 = 8.3 µM) cancer cells. The actinoporin effectively prevented epidermal growth factor -induced neoplastic transformation of JB6 Cl41 cells by 34% ± 0.2 and decreased colony formation of HT-29 cells by 47% ± 0.9, MDA-MB-231 cells by 37% ± 1.2, and SK-MEL-28 cells by 34% ± 3.6. Moreover, rHct-S3 decreased proliferation and suppressed migration of colorectal carcinoma cells by 31% ± 5.0 and 99% ± 6.4, respectively. The potent anti-migratory activity was proposed to mediate by decreased matrix metalloproteinases-2 and -9 expression. In addition, rHct-S3 induced programmed cell death by cleavage of caspase-3 and poly (ADP-ribose) polymerase, as well as regulation of Bax and Bcl-2. Our results indicate rHct-S3 to be a promising anticancer drug with a high anti-migratory potential.
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Affiliation(s)
- Aleksandra Kvetkina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia; (O.M.); (A.P.); (S.E.); (E.L.)
- Correspondence: ; Tel.: +7-423-231-1168
| | - Olesya Malyarenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia; (O.M.); (A.P.); (S.E.); (E.L.)
| | - Aleksandra Pavlenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia; (O.M.); (A.P.); (S.E.); (E.L.)
| | - Sergey Dyshlovoy
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald-Tumorzentrum, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.D.); (G.v.A.)
- Martini-Klinik, Prostate Cancer Center, University Hospital Hamburg-Eppendorf, 20251 Hamburg, Germany
- School of Natural Sciences, Far Eastern Federal University, Vladivostok 690922, Russia
| | - Gunhild von Amsberg
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald-Tumorzentrum, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.D.); (G.v.A.)
- Martini-Klinik, Prostate Cancer Center, University Hospital Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Svetlana Ermakova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia; (O.M.); (A.P.); (S.E.); (E.L.)
| | - Elena Leychenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia; (O.M.); (A.P.); (S.E.); (E.L.)
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14
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Datorre JG, de Carvalho AC, Guimarães DP, Reis RM. The Role of Fusobacterium nucleatum in Colorectal Carcinogenesis. Pathobiology 2020; 88:127-140. [PMID: 33291114 DOI: 10.1159/000512175] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/06/2020] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most frequent and deadly neoplasms worldwide. Genetic factors, lifestyle habits, and inflammation are important risk factors associated with CRC development. In recent years, growing evidence has supporting the significant role of the intestinal microbiome in CRC carcinogenesis. Disturbances in the healthy microbial balance, known as dysbiosis, are frequently observed in these patients. Pathogenic microorganisms that induce intestinal dysbiosis have become an important target to determine the role of bacterial infection in tumorigenesis. Interestingly, the presence of different bacterial strains, such as Fusobacterium nucleatum, has been detected in tissue and stool from patients with CRC and associated with substantial clinical and molecular features, as well as with patient therapy response. Therefore, understanding how the presence and levels of F. nucleatumstrains in the gut affect the risk of CRC onset and progression may inform suitable candidates for interventions focused on modulation of this bacteria. Here we review new insights into the role of gut microbiota in CRC carcinogenesis and the clinical utility of using the detection of F. nucleatum in different settings such as screening, prognosis, and microbiota modulation as a means to prevent cancer, augment therapies, and reduce adverse effects of treatment.
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Affiliation(s)
| | | | - Denise Peixoto Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Prevention, Barretos Cancer Hospital, Barretos, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil, .,Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal, .,ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal,
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15
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Liu K, Wang C, Wang J, Zhan Y, Yue X, Kong D. Nomogram model characterized by mutant genes and clinical indexes to identify high-risk patients with stage III/IV colorectal cancer. J Gastrointest Oncol 2020; 11:1214-1223. [PMID: 33456994 DOI: 10.21037/jgo-20-548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Background The aim of the present study was to construct a nomogram model of high-risk stage III/IV colorectal cancer (CRC). Methods Gene mutation and clinical information of 251 CRC patients were downloaded from The Cancer Genome Atlas (TCGA). Targeted next-generation sequencing was performed on 44 patients to screen shared mutation genes with frequency >5% between TCGA and clinical cohorts. Univariable and multivariable logistic regression analyses were used to analyze the mutant genes and clinical indexes, and a high-risk stage III/IV nomogram model was constructed. The nomogram model was further validated in the clinical cohort. Results SMAD family member 4 (SMAD4), zinc finger homeobox 3 (ZFHX3), and phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 2 (PREX2) mutations; pathological location; and preoperative carcinoembryonic antigen (CEA) value were screened out to compose a high-risk III/IV nomogram model. The nomogram had good calibration and discriminative ability, with an area under the curve of 0.76 [95% confidence interval (CI): 0.69-0.84]. Hosmer-Leme show test indicated that the model had good goodness of fit (P=0.83). The decision curve revealed this a nomogram model was feasible in clinical practice. In our clinical cohort, the calibration curve did not show good calibration and discrimination. Conclusions We established a nomogram model, including the mutation status of SMAD4, ZFHX3, and PREX2; pathological location; and preoperative CEA value, which showed accuracy in the risk prediction of stage III/IV CRC patients.
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Affiliation(s)
- Kai Liu
- Department of Colorectal Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Cui Wang
- Department of Colorectal Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Jiefu Wang
- Department of Colorectal Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yang Zhan
- Department of Colorectal Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Xin Yue
- Department of Colorectal Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Dalu Kong
- Department of Colorectal Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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16
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Gorin SNS, Jimbo M, Heizelman R, Harmes KM, Harper DM. The future of cancer screening after COVID-19 may be at home. Cancer 2020; 127:498-503. [PMID: 33170520 DOI: 10.1002/cncr.33274] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 12/11/2022]
Abstract
LAY SUMMARY During the coronavirus disease 2019 (COVID-19) pandemic, cancer screening decreased precipitously; home screening for colorectal cancer diminished less than that for colonoscopy and breast and cervical cancer screening. The authors have highlighted approaches for home cancer screening in addition to telemedicine.
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Affiliation(s)
| | - Masahito Jimbo
- Department of Family Medicine, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Robert Heizelman
- Department of Family Medicine, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Kathryn M Harmes
- Department of Family Medicine, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Diane M Harper
- Department of Family Medicine, University of Michigan School of Medicine, Ann Arbor, Michigan.,Department of Obstetrics and Gynecology, University of Michigan School of Medicine, Ann Arbor, Michigan.,Department of Women's Studies, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, Michigan.,Hub Research Capacity Core, Michigan Institute for Clinical and Health Research, University of Michigan, Ann Arbor, Michigan
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17
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Zhang Y, Wu ZX, Yang Y, Wang JQ, Li J, Sun Z, Teng QX, Ashby CR, Yang DH. Poziotinib Inhibits the Efflux Activity of the ABCB1 and ABCG2 Transporters and the Expression of the ABCG2 Transporter Protein in Multidrug Resistant Colon Cancer Cells. Cancers (Basel) 2020; 12:cancers12113249. [PMID: 33158067 PMCID: PMC7694178 DOI: 10.3390/cancers12113249] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/28/2020] [Accepted: 11/02/2020] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Globally, colorectal cancer (CRC) is a leading cause of cancer deaths and chemotherapy, in combination with radiotherapy when appropriate, is used to treat the majority of CRC patients. However, the acquisition or development of drug resistance can decrease, or even abolish, the efficacy of chemotherapy. ATP-binding cassette (ABC) transporters, particularly, the ABCB1 and ABCG2 transporter, are mediators of multidrug resistance (MDR) in certain types of cancer cells. The aim of our in vitro study was to determine if poziotinib can overcome MDR to certain chemotherapeutic drugs in colon cancer cells. Our results indicated that in MDR CRC cell lines, poziotinib inhibits the transport function of the ABCB1 and ABCG2 transporters, increasing the intracellular accumulation of certain anticancer drugs, and thus, their efficacy. Furthermore, poziotinib decreased the expression of the ABCG2 protein. Therefore, if our results can be translated to humans, they suggest that using poziotinib in combination with certain anticancer drugs may be of therapeutic benefit in colorectal cancer patients. Abstract Colorectal cancer (CRC) is a leading cause of cancer deaths in the United States. Currently, chemotherapy is a first-line treatment for CRC. However, one major drawback of chemotherapy is the emergence of multidrug resistance (MDR). It has been well-established that the overexpression of the ABCB1 and/or ABCG2 transporters can produce MDR in cancer cells. In this study, we report that in vitro, poziotinib can antagonize both ABCB1- and ABCG2-mediated MDR at 0.1–0.6 μM in the human colon cancer cell lines, SW620/Ad300 and S1-M1-80. Mechanistic studies indicated that poziotinib increases the intracellular accumulation of the ABCB1 transporter substrates, paclitaxel and doxorubicin, and the ABCG2 transporter substrates, mitoxantrone and SN-38, by inhibiting their substrate efflux function. Accumulation assay results suggested that poziotinib binds reversibly to the ABCG2 and ABCB1 transporter. Furthermore, western blot experiments indicated that poziotinib, at 0.6 μM, significantly downregulates the expression of the ABCG2 but not the ABCB1 transporter protein, suggesting that the ABCG2 reversal effect produced by poziotinib is due to transporter downregulation and inhibition of substrate efflux. Poziotinib concentration-dependently stimulated the ATPase activity of both ABCB1 and ABCG2, with EC50 values of 0.02 μM and 0.21 μM, respectively, suggesting that it interacts with the drug-substrate binding site. Molecular docking analysis indicated that poziotinib binds to the ABCB1 (−6.6 kcal/mol) and ABCG2 (−10.1 kcal/mol) drug-substrate binding site. In summary, our novel results show that poziotinib interacts with the ABCB1 and ABCG2 transporter, suggesting that poziotinib may increase the efficacy of certain chemotherapeutic drugs used in treating MDR CRC.
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Affiliation(s)
- Yongchao Zhang
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University/Henan Cancer Hospital, Zhengzhou 450003, China
- Correspondence: (Y.Z.); (D.-H.Y.); Tel.: +86-1378-361-0295 (Y.Z.); Tel.: +1-718-990-6468 (D.-H.Y.)
| | - Zhuo-Xun Wu
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA; (Z.-X.W.); (Y.Y.); (J.-Q.W.); (Z.S.); (Q.-X.T.); (C.R.A.J.)
| | - Yuqi Yang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA; (Z.-X.W.); (Y.Y.); (J.-Q.W.); (Z.S.); (Q.-X.T.); (C.R.A.J.)
| | - Jing-Quan Wang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA; (Z.-X.W.); (Y.Y.); (J.-Q.W.); (Z.S.); (Q.-X.T.); (C.R.A.J.)
| | - Jun Li
- Department of Otolaryngology-Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China;
| | - Zoey Sun
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA; (Z.-X.W.); (Y.Y.); (J.-Q.W.); (Z.S.); (Q.-X.T.); (C.R.A.J.)
| | - Qiu-Xu Teng
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA; (Z.-X.W.); (Y.Y.); (J.-Q.W.); (Z.S.); (Q.-X.T.); (C.R.A.J.)
| | - Charles R. Ashby
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA; (Z.-X.W.); (Y.Y.); (J.-Q.W.); (Z.S.); (Q.-X.T.); (C.R.A.J.)
| | - Dong-Hua Yang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA; (Z.-X.W.); (Y.Y.); (J.-Q.W.); (Z.S.); (Q.-X.T.); (C.R.A.J.)
- Correspondence: (Y.Z.); (D.-H.Y.); Tel.: +86-1378-361-0295 (Y.Z.); Tel.: +1-718-990-6468 (D.-H.Y.)
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18
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Takita H, Darwich AS, Ahmad A, Rostami-Hodjegan A. Application of the Nested Enzyme-Within-Enterocyte (NEWE) Turnover Model for Predicting the Time Course of Pharmacodynamic Effects. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2020; 9:617-627. [PMID: 32989926 PMCID: PMC7679071 DOI: 10.1002/psp4.12557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/16/2020] [Indexed: 11/06/2022]
Abstract
The gut wall consists of many biological elements, including enterocytes. Rapid turnover, a prominent feature of the enterocytes, has generally been ignored in the development of enterocyte-targeting drugs, although it has a comparable rate to other kinetic rates. Here, we investigated the impact of enterocyte turnover on the pharmacodynamics of enterocyte-targeting drugs by applying a model accounting for turnover of enterocytes and target proteins. Simulations showed that the pharmacodynamics depend on enterocyte lifespan when drug-target affinity is strong and half-life of target protein is long. Interindividual variability of enterocyte lifespan, which can be amplified by disease conditions, has a substantial impact on the variability of response. However, our comprehensive literature search showed that the enterocyte turnover causes a marginal impact on currently approved enterocyte-targeting drugs due to their relatively weak target affinities. This study proposes a model-informed drug development approach for selecting enterocyte-targeting drugs and their optimal dosage regimens.
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Affiliation(s)
- Hiroyuki Takita
- Centre for Applied Pharmacokinetics Research, University of Manchester, Manchester, UK.,Laboratory for Safety Assessment and ADME, Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, Shizuoka, Japan
| | - Adam S Darwich
- Centre for Applied Pharmacokinetics Research, University of Manchester, Manchester, UK.,Logistics and Informatics in Health Care, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, Stockholm, Sweden
| | - Amais Ahmad
- Centre for Applied Pharmacokinetics Research, University of Manchester, Manchester, UK
| | - Amin Rostami-Hodjegan
- Centre for Applied Pharmacokinetics Research, University of Manchester, Manchester, UK.,Simcyp Division, Certara UK, Sheffield, UK
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19
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Bian X, Qian Y, Tan B, Li K, Hong X, Wong CC, Fu L, Zhang J, Li N, Wu JL. In-depth mapping carboxylic acid metabolome reveals the potential biomarkers in colorectal cancer through characteristic fragment ions and metabolic flux. Anal Chim Acta 2020; 1128:62-71. [PMID: 32825913 DOI: 10.1016/j.aca.2020.06.064] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 11/24/2022]
Abstract
Carboxylic acid metabolome plays vital roles in the study of pathological mechanisms about cancer. This study aimed to find potential biomarkers for colorectal cancer (CRC) using carboxylic acids profiling. However, the identification of much more carboxylic acids was limited due to poor ionization efficiency and lack of characteristic fragment ions. Derivatization-liquid chromatography-mass spectrometry, which contains characteristic MS/MS fragments ions, were performed for carboxylic acid metabolomics analysis in CRC serum samples. 1054 carboxylic acids were quickly and selectively identified after extraction using three characteristic fragment ions and elucidation using the most suitable CE at 30 eV. Among them, 605 carboxylic acids exhibit discriminating levels between healthy and CRC patients in training cohort. Furthermore, the differential metabolites were found to be mainly enriched in amino acid metabolism, fatty acid biosynthesis and TCA cycle by MetaboAnalyst and iPath analysis. Finally, serine, glycine, and methionine were determined as the potential biomarkers after further confirmation using validation cohort and in vitro metabolic flux analysis. The above results collectively demonstrated that a new set of carboxylic acids can be quickly and selectively discovered using characteristic fragment ions.
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Affiliation(s)
- Xiqing Bian
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, China
| | - Yun Qian
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, China
| | - Binbin Tan
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pharmacology and Carson International Cancer Research Centre, Shenzhen University School of Medicine, Shenzhen, 518060, China
| | - Kai Li
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, 510655, Guangzhou, China
| | - Xufen Hong
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chi Chun Wong
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong
| | - Li Fu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pharmacology and Carson International Cancer Research Centre, Shenzhen University School of Medicine, Shenzhen, 518060, China
| | - Jun Zhang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Na Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, China.
| | - Jian-Lin Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, China.
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20
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The role of histone methylation in the development of digestive cancers: a potential direction for cancer management. Signal Transduct Target Ther 2020; 5:143. [PMID: 32747629 PMCID: PMC7398912 DOI: 10.1038/s41392-020-00252-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/22/2020] [Accepted: 07/15/2020] [Indexed: 02/08/2023] Open
Abstract
Digestive cancers are the leading cause of cancer-related death worldwide and have high risks of morbidity and mortality. Histone methylation, which is mediated mainly by lysine methyltransferases, lysine demethylases, and protein arginine methyltransferases, has emerged as an essential mechanism regulating pathological processes in digestive cancers. Under certain conditions, aberrant expression of these modifiers leads to abnormal histone methylation or demethylation in the corresponding cancer-related genes, which contributes to different processes and phenotypes, such as carcinogenesis, proliferation, metabolic reprogramming, epithelial–mesenchymal transition, invasion, and migration, during digestive cancer development. In this review, we focus on the association between histone methylation regulation and the development of digestive cancers, including gastric cancer, liver cancer, pancreatic cancer, and colorectal cancer, as well as on its clinical application prospects, aiming to provide a new perspective on the management of digestive cancers.
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21
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Gonulcu SC, Unal B, Bassorgun IC, Ozcan M, Coskun HS, Elpek GO. Expression of Notch pathway components (Numb, Itch, and Siah-1) in colorectal tumors: A clinicopathological study. World J Gastroenterol 2020; 26:3814-3833. [PMID: 32774060 PMCID: PMC7383841 DOI: 10.3748/wjg.v26.i26.3814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/18/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The role of the Notch pathway in carcinogenesis and tumor progression has been demonstrated in many organs, including the colon. Accordingly, studies aimed at developing therapies targeting this pathway in various cancers require the identification of several factors that may play a role in regulating Notch-1 expression. Although Numb, Itch, and seven in absentia homolog-1 (Siah-1) have been shown to contribute to the regulation of Notch signaling, their role in colorectal carcinogenesis and tumor progression has not been fully elucidated to date.
AIM To evaluate Numb, Itch, and Siah-1 expression in colorectal tumors to clarify their relationship with Notch-1 expression and their role in carcinogenesis and tumor behavior.
METHODS Expression of Notch-1, Numb, Itch, and Siah-1 was investigated in 50 colorectal carcinomas, 30 adenomas, and 20 healthy colonic tissues by immunohistochemistry and quantitative real-time polymerase chain reaction (PCR) analyses.
RESULTS In contrast to Notch-1, which is expressed at higher levels in tumor tissues and adenomas, expression of Numb, Itch, and Siah-1 was stronger and more frequent in normal mucosa (P < 0.01). There was a positive correlation between Notch-1 expression and high histological grade, the presence of lymph node metastasis, and advanced-stage tumors, whereas expression of Numb, Itch, and Siah-1 was absent or reduced in tumors with these clinicopathological parameters (P < 0.05). In survival analysis, expression of Notch was related to poor prognosis but that of Numb, Itch, and Siah-1 correlated with improved survival (P < 0.05). Multivariate analysis revealed Notch-1 expression and loss of Numb expression to be independent prognostic parameters together with lymph node metastasis (P < 0.05).
CONCLUSION Our findings support the role of Notch-1 in colorectal carcinoma and indicate that loss of Numb, Itch, and Siah-1 expression is associated with carcinogenesis. Our data also suggest that these three proteins might be involved in the Notch-1 pathway during colorectal carcinoma (CRC) progression and might play an essential role in approaches targeting Notch as novel molecular therapies for CRC.
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Affiliation(s)
- Sinem Cil Gonulcu
- Department of Pathology, Akdeniz University, School of Medicine, Antalya 07070, Turkey
| | - Betul Unal
- Department of Pathology, Akdeniz University, School of Medicine, Antalya 07070, Turkey
| | | | - Mualla Ozcan
- Department of Pathology, Akdeniz University, School of Medicine, Antalya 07070, Turkey
| | - Hasan Senol Coskun
- Department of Oncology, Akdeniz University, School of Medicine, Antalya 07070, Turkey
| | - Gulsum Ozlem Elpek
- Department of Pathology, Akdeniz University, School of Medicine, Antalya 07070, Turkey
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González-González M, Gutiérrez ML, Sayagués JM, Muñoz-Bellvís L, Orfao A. Genomic profiling of sporadic liver metastatic colorectal cancer. Semin Cancer Biol 2020; 71:98-108. [PMID: 32485312 DOI: 10.1016/j.semcancer.2020.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
Sporadic colorectal cancer (sCRC) is the third leading cause of cancer death in the Western world. Approximately, a quarter of sCRC patients present metastatic dissemination at the moment of diagnosis, the liver being the most frequently affected organ. Additionally, this group of CRC patients is characterized by a worse prognosis. In the last decades, significant technological developments for genome analysis have fostered the identification and characterization of genetic alterations involved in the pathogenesis of sCRC. However, genetic alterations involved in the metastatic process through which tumor cells are able to colonize other tissues with a different microenvironment, still remain to be fully identified. Here, we review current knowledge about the most relevant genomic alterations involved in the liver metastatic process of sCRC, including detailed information about the genetic profile of primary colorectal tumors vs. their paired liver metastases.
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Affiliation(s)
- María González-González
- Department of Medicine and Cytometry Service (NUCLEUS), University of Salamanca, Salamanca, Spain; Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, Spain; Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain; Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, Spain
| | - María Laura Gutiérrez
- Department of Medicine and Cytometry Service (NUCLEUS), University of Salamanca, Salamanca, Spain; Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, Spain; Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain; Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, Spain
| | - José María Sayagués
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain; Department of Pathology, Universidad de Salamanca, Salamanca, Spain
| | - Luis Muñoz-Bellvís
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain; Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, Spain; Department of General and Gastrointestinal Surgery, University Hospital of Salamanca, Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and Cytometry Service (NUCLEUS), University of Salamanca, Salamanca, Spain; Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, Spain; Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain; Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, Spain.
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Girigoswami K, Girigoswami A. A Review on the Role of Nanosensors in Detecting Cellular miRNA Expression in Colorectal Cancer. Endocr Metab Immune Disord Drug Targets 2020; 21:12-26. [PMID: 32410567 DOI: 10.2174/1871530320666200515115723] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 03/10/2020] [Accepted: 03/20/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the leading causes of death across the globe. Early diagnosis with high sensitivity can prevent CRC progression, thereby reducing the condition of metastasis. OBJECTIVE The purpose of this review is (i) to discuss miRNA based biomarkers responsible for CRC, (ii) to brief on the different methods used for the detection of miRNA in CRC, (iii) to discuss different nanobiosensors so far found for the accurate detection of miRNAs in CRC using spectrophotometric detection, piezoelectric detection. METHODS The keywords for the review like micro RNA detection in inflammation, colorectal cancer, nanotechnology, were searched in PubMed and the relevant papers on the topics of miRNA related to CRC, nanotechnology-based biosensors for miRNA detection were then sorted and used appropriately for writing the review. RESULTS The review comprises a general introduction explaining the current scenario of CRC, the biomarkers used for the detection of different cancers, especially CRC and the importance of nanotechnology and a general scheme of a biosensor. The further subsections discuss the mechanism of CRC progression, the role of miRNA in CRC progression and different nanotechnology-based biosensors so far investigated for miRNA detection in other diseases, cancer and CRC. A scheme depicting miRNA detection using gold nanoparticles (AuNPs) is also illustrated. CONCLUSION This review may give insight into the different nanostructures, like AuNPs, quantum dots, silver nanoparticles, MoS2derived nanoparticles, etc., based approaches for miRNA detection using biosensors.
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Affiliation(s)
- Koyeli Girigoswami
- Medical Bionanotechnology Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Chettinad Health City, Kelambakkam, Chennai, 603103, India
| | - Agnishwar Girigoswami
- Medical Bionanotechnology Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Chettinad Health City, Kelambakkam, Chennai, 603103, India
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24
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A mountable toilet system for personalized health monitoring via the analysis of excreta. Nat Biomed Eng 2020; 4:624-635. [PMID: 32251391 DOI: 10.1038/s41551-020-0534-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/14/2020] [Indexed: 12/28/2022]
Abstract
Technologies for the longitudinal monitoring of a person's health are poorly integrated with clinical workflows, and have rarely produced actionable biometric data for healthcare providers. Here, we describe easily deployable hardware and software for the long-term analysis of a user's excreta through data collection and models of human health. The 'smart' toilet, which is self-contained and operates autonomously by leveraging pressure and motion sensors, analyses the user's urine using a standard-of-care colorimetric assay that traces red-green-blue values from images of urinalysis strips, calculates the flow rate and volume of urine using computer vision as a uroflowmeter, and classifies stool according to the Bristol stool form scale using deep learning, with performance that is comparable to the performance of trained medical personnel. Each user of the toilet is identified through their fingerprint and the distinctive features of their anoderm, and the data are securely stored and analysed in an encrypted cloud server. The toilet may find uses in the screening, diagnosis and longitudinal monitoring of specific patient populations.
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25
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Profiling of isomer-specific IgG N-glycosylation in cohort of Chinese colorectal cancer patients. Biochim Biophys Acta Gen Subj 2020; 1864:129510. [DOI: 10.1016/j.bbagen.2019.129510] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/19/2019] [Accepted: 12/24/2019] [Indexed: 12/24/2022]
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26
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IRE1α-targeting downregulates ABC transporters and overcomes drug resistance of colon cancer cells. Cancer Lett 2020; 476:67-74. [PMID: 32061752 DOI: 10.1016/j.canlet.2020.02.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 01/01/2023]
Abstract
Drug resistance is a big problem in cancer treatment and one of the most prominent mechanisms underlain is overexpression of ATP-binding cassette (ABC) transporters, particularly ABCB1, ABCC1 and ABCG2. Inhibition of ABC transporters is an important approach to overcome drug resistance. The inositol-requiring enzyme 1α (IRE1α), an arm of unfolded protein response (UPR), splices XBP1 mRNA to generate an active transcription factor XBP1s. UPR is implicated in drug resistance. However, the underlying mechanism is unclear. We found that the anticancer drugs such as 5-fluorouracil (5-FU) activated the IRE1α-XBP1 pathway to induce the expression of ABCB1, ABCC1 and ABCG2 in colon cancer cells. Inhibition of IRE1α RNase activity with small molecule 4μ8c suppressed the drug-induced expression of these ABC transporters and sensitized 5-FU-resistant colon cancer cells to drug treatment. In vivo xenograft assay indicates that administration of 4μ8C substantially enhanced the efficacy of 5-FU chemotherapy on 5-FU-resistant colon cancer cells. These results suggest that IRE1α-targeting might be a strategy to cope with drug resistance of colon cancer.
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27
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Oh IR, Raymundo B, Kim M, Kim CW. Mesenchymal stem cells co-cultured with colorectal cancer cells showed increased invasive and proliferative abilities due to its altered p53/TGF-β1 levels. Biosci Biotechnol Biochem 2019; 84:256-267. [PMID: 31601153 DOI: 10.1080/09168451.2019.1676692] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Signaling between cancer cells, their neighboring cells, and mesenchymal stem cells (MSCs) forms the tumor microenvironment. The complex heterogeneity of this microenvironment varies depending on the tumor type and its origins. However, most of the existing cancer-based studies have focused on cancer cells. In this study, we used a direct co-culture system (cross-talk signaling) to induce cross-interaction between cancer cells and mesenchymal stem cells. This induced deformation of MSCs. MSCs showed a diminished ability to maintain homeostasis. In particular, increase in the invasion ability of MSCs by TGF-β1 and decrease in p53, which plays a key role in cancer development, is an important discovery. It can thus be deduced that blocking these changes can effectively inhibit metastatic colorectal cancer. In conclusion, understanding the interactions and changes in MSCs associated with cancer will help develop novel therapeutic strategies for cancer.
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Affiliation(s)
- In-Rok Oh
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Bernardo Raymundo
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - MiJung Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea.,Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Chan-Wha Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea.,Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
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A Simple and Highly Specific MassARRAY-Based Stool DNA Assay to Prioritize Follow-up Decisions in Fecal Immunochemical Test-Positive Individuals. Cancers (Basel) 2019; 11:cancers11030423. [PMID: 30934598 PMCID: PMC6468462 DOI: 10.3390/cancers11030423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Seventy-five percent of fecal immunochemical test (FIT)-positive individuals are false positives and undergo unnecessary colonoscopies. Here, we established a stool DNA (sDNA) test that uses the Single Allele Base Extension Reaction (SABER) MassARRAY platform to improve the accuracy of FIT-based CRC detection. METHODS Twenty-one variants in five CRC-associated genes were selected for the sDNA panel. Cell line DNA and matched mutation-confirmed tissue and stool samples from 34 patients were used for accuracy assessment (cohort 1). The clinical performance of the sDNA assay was further evaluated in 101 independent FIT-positive stool samples (cohort 2). RESULTS In cohort 1, we obtained a 62% mutation concordance rate in paired tissue and stool samples of the CRC group, regardless of the FIT status. In cohort 2, 100% specificity in normal controls with positive FIT results was observed. By weighting the FIT value and the presence of a given variant type in stool and then summing the two scores, we found that a one-increment increase in the score was associated with a 4.538-fold risk (95% CI = 2.121⁻9.309) for malignancy in the FIT-positive setting. CONCLUSIONS Our highly specific sDNA assay can help prioritize the most at-risk FIT-positive persons to receive prompt colonoscopic confirmation of CRC.
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29
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Zhao S, He W, Ma Z, Liu P, Huang PH, Bachman H, Wang L, Yang S, Tian Z, Wang Z, Gu Y, Xie Z, Huang TJ. On-chip stool liquefaction via acoustofluidics. LAB ON A CHIP 2019; 19:941-947. [PMID: 30702741 PMCID: PMC6626638 DOI: 10.1039/c8lc01310a] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Microfluidic-based portable devices for stool analysis are important for detecting established biomarkers for gastrointestinal disorders and understanding the relationship between gut microbiota imbalances and various health conditions, ranging from digestive disorders to neurodegenerative diseases. However, the challenge of processing stool samples in microfluidic devices hinders the development of a standalone platform. Here, we present the first microfluidic chip that can liquefy stool samples via acoustic streaming. With an acoustic transducer actively generating strong micro-vortex streaming, stool samples and buffers in microchannel can be homogenized at a flow rate up to 30 μL min-1. After homogenization, an array of 100 μm wide micropillars can further purify stool samples by filtering out large debris. A favorable biocompatibility was also demonstrated for our acoustofluidic-based stool liquefaction chip by examining bacteria morphology and viability. Moreover, stool samples with different consistencies were liquefied. Our acoustofluidic chip offers a miniaturized, robust, and biocompatible solution for stool sample preparation in a microfluidic environment and can be potentially integrated with stool analysis units for designing portable stool diagnostics platforms.
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Affiliation(s)
- Shuaiguo Zhao
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA.
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30
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He Z, Gharaibeh RZ, Newsome RC, Pope JL, Dougherty MW, Tomkovich S, Pons B, Mirey G, Vignard J, Hendrixson DR, Jobin C. Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin. Gut 2019; 68:289-300. [PMID: 30377189 PMCID: PMC6352414 DOI: 10.1136/gutjnl-2018-317200] [Citation(s) in RCA: 232] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/12/2018] [Accepted: 10/04/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Campylobacter jejuni produces a genotoxin, cytolethal distending toxin (CDT), which has DNAse activity and causes DNA double-strand breaks. Although C. jejuni infection has been shown to promote intestinal inflammation, the impact of this bacterium on carcinogenesis has never been examined. DESIGN Germ-free (GF) ApcMin/+ mice, fed with 1% dextran sulfate sodium, were used to test tumorigenesis potential of CDT-producing C. jejuni. Cells and enteroids were exposed to bacterial lysates to determine DNA damage capacity via γH2AX immunofluorescence, comet assay and cell cycle assay. To examine the interplay of CDT-producing C. jejuni, gut microbiome and host in tumorigenesis, colonic RNA-sequencing and faecal 16S rDNA sequencing were performed. Rapamycin was administrated to investigate the prevention of CDT-producing C. jejuni-induced tumorigenesis. RESULTS GF ApcMin/+ mice colonised with human clinical isolate C. jejuni81-176 developed significantly more and larger tumours when compared with uninfected mice. C. jejuni with a mutated cdtB subunit, mutcdtB, attenuated C. jejuni-induced tumorigenesis in vivo and decreased DNA damage response in cells and enteroids. C. jejuni infection induced expression of hundreds of colonic genes, with 22 genes dependent on the presence of cdtB. The C. jejuni-infected group had a significantly different microbial gene expression profile compared with the mutcdtB group as shown by metatranscriptomic data, and different microbial communities as measured by 16S rDNA sequencing. Finally, rapamycin could diminish the tumorigenic capability of C. jejuni. CONCLUSION Human clinical isolate C. jejuni 81-176 promotes colorectal cancer and induces changes in microbial composition and transcriptomic responses, a process dependent on CDT production.
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Affiliation(s)
- Zhen He
- Department of Medicine, University of Florida, Gainesville, Florida, USA,Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Raad Z Gharaibeh
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Rachel C Newsome
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jllian L Pope
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | | | - Sarah Tomkovich
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Benoit Pons
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRA, ENVT, INP- Purpan, UPS, Toulouse, France
| | - Gladys Mirey
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRA, ENVT, INP- Purpan, UPS, Toulouse, France
| | - Julien Vignard
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRA, ENVT, INP- Purpan, UPS, Toulouse, France
| | - David R Hendrixson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida, USA,Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida, USA,Department of Infectious Diseases and Immunology, University of Florida, Gainesville, Florida, USA
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Wang L, Xu M, Lu P, Zhou F. microRNA-769 is downregulated in colorectal cancer and inhibits cancer progression by directly targeting cyclin-dependent kinase 1. Onco Targets Ther 2018; 11:9013-9025. [PMID: 30588014 PMCID: PMC6296200 DOI: 10.2147/ott.s183847] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND In recent years, microRNAs (miRNAs) have been reported to be aberrantly expressed in colorectal cancer (CRC). The deregulation of miRNAs is implicated in the formation and progression of CRC, and participates in the regulation of a wide range of biological behaviors. Considering the crucial role of miRNAs in CRC, miRNAs are thought to have significant promise in the diagnosis and therapy of patients with this malignancy. MATERIAL AND METHODS Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was performed to detect miR-769 expression in CRC tissues and cell lines. MTT assay and flow cytometry analysis were used to determine the effects of miR-769 upregulation in CRC cell proliferation and apoptosis, respectively. The influence of miR-769 overexpression in CRC cell migration and invasion was evaluated through migration and invasion assays. Notably, the possible mechanisms underlying the action of miR-769 in CRC cells were explored. RESULTS In the present study, miR-769 was frequently found to be poorly expressed in CRC tissues and cell lines. Functional assays showed that recovery of miR-769 expression suppressed CRC cell proliferation, migration, and invasion, increased cell apoptosis in vitro, and inhibited tumor growth in vivo. Cyclin-dependent kinase 1 (CDK1) was the direct target of miR-769 in CRC cells. CDK1 was overexpressed in CRC tissue samples and negatively correlated with miR-769 expression. In addition, CDK1 inhibition imitated the tumor suppressor activity of miR-769 in CRC cells, and restoration of CDK1 expression partially abolished the tumor-suppressing roles of miR-769 in malignant CRC cells. CONCLUSION The results of this study demonstrated that miR-769 was downregulated in CRC and directly targeted CDK1 to be implicated in the regulation of CRC cell proliferation, apoptosis, migration and invasion. Thus, the miR-769/CDK1 axis might be an effective therapeutic target for treating patients with CRC.
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Affiliation(s)
- Lei Wang
- Department of Clinical Laboratory, Shanghai Eighth People's Hospital, Xuhui Branch of Shanghai Sixth People's Hospital, Shanghai 200235, People's Republic of China,
| | - Minyi Xu
- Department of Clinical Laboratory, Shanghai Eighth People's Hospital, Xuhui Branch of Shanghai Sixth People's Hospital, Shanghai 200235, People's Republic of China,
| | - Pei Lu
- Department of Clinical Laboratory, Shanghai Eighth People's Hospital, Xuhui Branch of Shanghai Sixth People's Hospital, Shanghai 200235, People's Republic of China,
| | - Fangfang Zhou
- Department of Clinical Laboratory, Shanghai Eighth People's Hospital, Xuhui Branch of Shanghai Sixth People's Hospital, Shanghai 200235, People's Republic of China,
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32
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Miao S, Zhang RY, Wang W, Wang HB, Meng LL, Zu LD, Fu GH. Overexpression of dedicator of cytokinesis 2 correlates with good prognosis in colorectal cancer associated with more prominent CD8 + lymphocytes infiltration: a colorectal cancer analysis. J Cell Biochem 2018; 119:8962-8970. [PMID: 30076747 DOI: 10.1002/jcb.27151] [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: 12/13/2017] [Accepted: 05/18/2018] [Indexed: 12/24/2022]
Abstract
Recently, dedicator of cytokinesis 2 (DOCK2) has been reportedly exhibited high mutation prevalence in the Asian colorectal cancer (CRC) cohort. However, the expression pattern of DOCK2 and its clinical significance in CRC were still unknown. To characterize the role of DOCK2, a tissue microarray (TMA) containing 481 archived paraffin-embedded CRC specimens was performed by immunohistochemistry. Among which, 54 primary CRC tissues showed high expression of DOCK2 protein, while others were negative. Moreover, DOCK2 expression was positively associated with invasion depth (P < .001) and tumor size (P = .016). Significantly, Kaplan-Meier survival analysis revealed that patients with higher DOCK2 expression had a longer overall survival time (P = .017). Furthermore, univariate and multivariate Cox regression analysis confirmed that DOCK2 is an independent prognostic marker in CRC (P = .049,; HR, 0.519; 95% CI, 0.270 to 0.997). In addition, we observed a strong correlation between the infiltration of CD8+ T lymphocytes and DOCK2 expression (P = .0119). Our findings demonstrated that overexpressed DOCK2 might involve in recruiting CD8+ T lymphocytes and serve as a novel prognostic indicator and indicated a potential therapeutic strategy by restoring DOCK2 for CRC.
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Affiliation(s)
- Sen Miao
- Department of Pathology, Shanghai General Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Pathology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ren-Ya Zhang
- Department of Pathology, Affiliated Hospital of Ji-Ning Medical University, Shandong, China
| | - Wei Wang
- Department of Pathology, Affiliated Hospital of Ji-Ning Medical University, Shandong, China
| | - Hong-Bo Wang
- Department of Pathology, Affiliated Hospital of Ji-Ning Medical University, Shandong, China
| | - Li-Li Meng
- Department of Pathology, Shanghai General Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Pathology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li-Dong Zu
- Department of Pathology, Shanghai General Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Pathology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guo-Hui Fu
- Department of Pathology, Shanghai General Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Pathology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Pathology, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, Chin epartment of Pathology, Shanghai, China
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33
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Liu S, Cheng L, Fu Y, Liu BF, Liu X. Characterization of IgG N-glycome profile in colorectal cancer progression by MALDI-TOF-MS. J Proteomics 2018; 181:225-237. [DOI: 10.1016/j.jprot.2018.04.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/21/2018] [Accepted: 04/18/2018] [Indexed: 12/17/2022]
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35
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Shen J, Li M. MicroRNA-744 Inhibits Cellular Proliferation and Invasion of Colorectal Cancer by Directly Targeting Oncogene Notch1. Oncol Res 2018; 26:1401-1409. [PMID: 29471890 PMCID: PMC7844638 DOI: 10.3727/096504018x15188747585738] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Accumulated studies have strongly implicated aberrantly expressed microRNAs (miRNAs) in carcinogenesis and cancer progression of various cancers, including colorectal cancer (CRC). Hence, a comprehensive study of miRNAs and their association with CRC may be a promising therapeutic method for patients with this malignancy. MicroRNA-744 (miR-744) is abnormally expressed in several types of human cancer. Thus far, little is known about the expression, biological roles, and exact mechanisms of miR-744 in CRC. Thus, the present study measured the expression level of miR-744 and investigated its roles and associated molecular mechanisms in CRC. This study demonstrated that miR-744 expression was significantly underexpressed in CRC tissues and cell lines. Low miR-744 expression was positively associated with lymphatic metastasis and TNM stage. Functional experiments revealed that miR-744 overexpression obviously inhibited the proliferation and invasion of CRC cells. Furthermore, Notch1 was identified as a direct target of miR-744 in CRC. Moreover, the inhibition of Notch1 phenocopied the inhibitory effects of miR-744 overexpression on CRC cells. Restored Notch1 expression markedly rescued the tumor-suppressive effects of miR-744 overexpression on CRC cells. Overall, miR-744 exhibits an essential role in CRC progression, and the miR-744/Notch1 axis may provide novel insights into future treatments for patients with CRC.
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Affiliation(s)
- Jian Shen
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, P.R. China
| | - Minzhe Li
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, P.R. China
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36
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Peng L, Cantor DI, Huang C, Wang K, Baker MS, Nice EC. Tissue and plasma proteomics for early stage cancer detection. Mol Omics 2018; 14:405-423. [PMID: 30251724 DOI: 10.1039/c8mo00126j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The pursuit of novel and effective biomarkers is essential in the struggle against cancer, which is a leading cause of mortality worldwide. Here we discuss the relative advantages and disadvantages of the most frequently used proteomics techniques, concentrating on the latest advances and application of tissue and plasma proteomics for novel cancer biomarker discovery.
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Affiliation(s)
- Liyuan Peng
- Dept of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy
- Chengdu
- P. R. China
| | - David I. Cantor
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Macquarie University
- New South Wales
- Australia
| | - Canhua Huang
- Dept of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy
- Chengdu
- P. R. China
| | - Kui Wang
- Dept of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy
- Chengdu
- P. R. China
| | - Mark S. Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University
- Australia
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University
- Clayton
- Australia
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37
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Shin D, Lee J, Gong JR, Cho KH. Percolation transition of cooperative mutational effects in colorectal tumorigenesis. Nat Commun 2017; 8:1270. [PMID: 29097710 PMCID: PMC5668266 DOI: 10.1038/s41467-017-01171-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 08/24/2017] [Indexed: 11/13/2022] Open
Abstract
Cancer is caused by the accumulation of multiple genetic mutations, but their cooperative effects are poorly understood. Using a genome-wide analysis of all the somatic mutations in colorectal cancer patients in a large-scale molecular interaction network, here we find that a giant cluster of mutation-propagating modules in the network undergoes a percolation transition, a sudden critical transition from scattered small modules to a large connected cluster, during colorectal tumorigenesis. Such a large cluster ultimately results in a giant percolated cluster, which is accompanied by phenotypic changes corresponding to cancer hallmarks. Moreover, we find that the most commonly observed sequence of driver mutations in colorectal cancer has been optimized to maximize the giant percolated cluster. Our network-level percolation study shows that the cooperative effect rather than any single dominance of multiple somatic mutations is crucial in colorectal tumorigenesis. Cancer is caused by accumulating genetic mutations. Here, the authors investigate the cooperative effect of these mutations in colorectal cancer patients and identify a giant cluster of mutation-propagating modules that undergoes percolation transition during tumorigenesis.
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Affiliation(s)
- Dongkwan Shin
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jonghoon Lee
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jeong-Ryeol Gong
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Kwang-Hyun Cho
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
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38
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Yuan Z, Baker K, Redman MW, Wang L, Adams SV, Yu M, Dickinson B, Makar K, Ulrich N, Böhm J, Wurscher M, Westerhoff M, Medwell S, Moonka R, Sinanan M, Fichera A, Vickers K, Grady WM. Dynamic plasma microRNAs are biomarkers for prognosis and early detection of recurrence in colorectal cancer. Br J Cancer 2017; 117:1202-1210. [PMID: 28809863 PMCID: PMC5674097 DOI: 10.1038/bjc.2017.266] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/10/2017] [Accepted: 07/17/2017] [Indexed: 01/21/2023] Open
Abstract
Background: Plasma microRNAs (miRNAs) are promising non-invasive biomarkers for colorectal cancer (CRC) prognosis. However, the published studies to date have yielded conflicting and inconsistent results for specific plasma miRNAs. Methods: We have conducted a study using robust assays to assess a panel of nine miRNAs for CRC prognosis and early detection of recurrence. Plasma samples from 144 patients in a prospective CRC cohort study were collected at diagnosis, 6, 12, and 24 months after diagnosis. miRNAs were assayed by Taqman qRT–PCR to generate miRNA normalised copy numbers. Results: Preoperative high plasma miRNA levels were associated with increased recurrence risk for miR-200b (HR [95% CI]=2.04 [1.00, 4.16], P=0.05), miR-203 (HR=4.2 [1.48, 11.93], P=0.007), miR-29a (HR=2.61 [1.34,5.07], P=0.005), and miR-31 (HR=4.03 [1.76, 9.24], P=0.001). Both plasma miR-31 (AUC: 0.717) and miR-29a (AUC: 0.703) could discriminate recurrence from these patients without recurrence. In addition, high levels of miR-31 during surveillance was associated with a three-fold increased risk of recurrence across all time points. Dynamic postoperative plasma miR-141 and 16 levels correlated with recurrence in the surveillance samples. Conclusions: Pre-operative plasma miR-29a, 200b, 203, and 31 are potential CRC prognosis biomarkers. In addition, dynamic postoperative miR-31, 141 and 16 levels are potential biomarkers for the early detection of recurrence during CRC surveillance.
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Affiliation(s)
- Zixu Yuan
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510655, China.,Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, D4-100, Seattle, WA 98109, USA
| | - Kelsey Baker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, D4-100, Seattle, WA 98109, USA
| | - Mary W Redman
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, D4-100, Seattle, WA 98109, USA
| | - Lei Wang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510655, China
| | - Scott V Adams
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, D4-100, Seattle, WA 98109, USA
| | - Brandon Dickinson
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Karen Makar
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Neli Ulrich
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Jürgen Böhm
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Michelle Wurscher
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Maria Westerhoff
- Department of Pathology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Steve Medwell
- Colon and Rectal Surgery, The Polyclinic, Seattle, WA 98109, USA
| | - Ravi Moonka
- General surgery, Virginia Mason Hospital and Seattle Medical Center, Seattle, WA 98109, USA
| | - Mika Sinanan
- Department of Surgery, University of Washington School Medical Center, Seattle, WA 98109, USA
| | - Alessandro Fichera
- Department of Surgery, University of Washington School Medical Center, Seattle, WA 98109, USA
| | - Kathy Vickers
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, D4-100, Seattle, WA 98109, USA.,Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
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39
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Yoon H, Kim N, Park JH, Kim YS, Lee J, Kim HW, Choi YJ, Shin CM, Park YS, Lee DH, Jung HC. Comparisons of Gut Microbiota Among Healthy Control, Patients With Conventional Adenoma, Sessile Serrated Adenoma, and Colorectal Cancer. J Cancer Prev 2017; 22:108-114. [PMID: 28698865 PMCID: PMC5503223 DOI: 10.15430/jcp.2017.22.2.108] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 06/07/2017] [Indexed: 12/14/2022] Open
Abstract
Background Studies on gut microbiota regarding colorectal carcinogenesis, including sessile serrated adenoma (SSA), have been scarce. The aim of this study is to investigate the role of mucosa-associated gut microbiota in the colorectal carcinogenesis. Methods We collected biopsy samples of normal rectal mucosa during colonoscopy from healthy control and patients with conventional adenoma, SSA, and colorectal cancer (CRC), respectively (n = 6). Pyrosequencing for 16S rRNA gene of bacteria was performed to compare gut microbiota. Results The most abundant phylum in total samples was Proteobacteria (55.6%), followed by Firmicutes (27.4%) and Bacteroidetes (11.6%). There was no significant difference in relative abundance of the phylum level among the four groups. Fusobacterium nucleatum, known to be frequently detected during colorectal carcinogenesis, was found in only one sample of patient with SSA. The rarefaction curves showed that the diversity of mucosal communities of patients with CRC is the lowest among the four groups and the diversity of mucosal communities of patients with SSA is higher than that of healthy control. Among the four groups, Shannon’s and Simpson’s index for diversity was the lowest and the highest in the patients with CRC, respectively; it did not reach statistical significance. The proportion of genus Pseudomonas was very high in the samples of patients with stage II–IV CRC compared with those with stage I CRC (59.3% vs. 0.3%, P = 0.064). Conclusions Our study suggests no significant role of mucosa-associated gut microbiota in the colorectal carcinogenesis. Further study for many samples or using fecal material could be helpful.
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Affiliation(s)
- Hyuk Yoon
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Nayoung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.,Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Ji Hyun Park
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Yong Sung Kim
- Gastroenterology and Digestive Disease Research Institute, Wonkwang University Sanbon Hospital, Gunpo, Korea
| | - Jongchan Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Hyoung Woo Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Yoon Jin Choi
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Cheol Min Shin
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Young Soo Park
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Dong Ho Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.,Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun Chae Jung
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea
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40
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Weiswald LB, Hasan MR, Wong JCT, Pasiliao CC, Rahman M, Ren J, Yin Y, Gusscott S, Vacher S, Weng AP, Kennecke HF, Bièche I, Schaeffer DF, Yapp DT, Tai IT. Inactivation of the Kinase Domain of CDK10 Prevents Tumor Growth in a Preclinical Model of Colorectal Cancer, and Is Accompanied by Downregulation of Bcl-2. Mol Cancer Ther 2017; 16:2292-2303. [PMID: 28663269 DOI: 10.1158/1535-7163.mct-16-0666] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 03/15/2017] [Accepted: 06/23/2017] [Indexed: 11/16/2022]
Abstract
Cyclin-dependent kinase 10 (CDK10), a CDC2-related kinase, is highly expressed in colorectal cancer. Its role in the pathogenesis of colorectal cancer is unknown. This study examines the function of CDK10 in colorectal cancer, and demonstrates its role in suppressing apoptosis and in promoting tumor growth in vitro and in vivo Modulation of CDK10 expression in colorectal cancer cell lines demonstrates that CDK10 promotes cell growth, reduces chemosensitivity and inhibits apoptosis by upregulating the expression of Bcl-2. This effect appears to depend on its kinase activity, as kinase-defective mutant colorectal cancer cell lines have an exaggerated apoptotic response and reduced proliferative capacity. In vivo, inhibiting CDK10 in colorectal cancer following intratumoral injections of lentivirus-mediated CDK10 siRNA in a patient-derived xenograft mouse model demonstrated its efficacy in suppressing tumor growth. Furthermore, using a tissue microarray of human colorectal cancer tissues, the potential for CDK10 to be a prognostic biomarker in colorectal cancer was explored. In tumors of individuals with colorectal cancer, high expression of CDK10 correlates with earlier relapse and shorter overall survival. The findings of this study indicate that CDK10 plays a role in the pathogenesis in colorectal cancer and may be a potential therapeutic target for treatment. Mol Cancer Ther; 16(10); 2292-303. ©2017 AACR.
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Affiliation(s)
- Louis-Bastien Weiswald
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Mohammad R Hasan
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - John C T Wong
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Clarissa C Pasiliao
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Mahbuba Rahman
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Jianhua Ren
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Yaling Yin
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Cancer Surveillance & Outcomes, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Samuel Gusscott
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Sophie Vacher
- Department of Genetics, Institute Curie, Paris, France
| | - Andrew P Weng
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Hagen F Kennecke
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Ivan Bièche
- Department of Genetics, Institute Curie, Paris, France
| | - David F Schaeffer
- Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Donald T Yapp
- Experimental Therapeutics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Isabella T Tai
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada. .,Michael Smith Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
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41
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Zhang X, Ai F, Li X, Tian L, Wang X, Shen S, Liu F. MicroRNA-34a suppresses colorectal cancer metastasis by regulating Notch signaling. Oncol Lett 2017; 14:2325-2333. [PMID: 28781671 PMCID: PMC5530141 DOI: 10.3892/ol.2017.6444] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 04/04/2017] [Indexed: 12/19/2022] Open
Abstract
Dysregulation of microRNA (miRNA/miR) expression is causally associated with cancer initiation and progression. However, the precise mechanisms by which dysregulated miRNAs induce colorectal tumorigenesis remain unknown. In the present study, downregulation of miR-34a was identified in colorectal cancer cell lines and clinical specimens. Clinical studies revealed that miR-34a expression was negatively associated with distant metastasis, and positively associated with differentiation and survival of human colorectal cancer specimens. In vitro miRNA functional assays demonstrated that miR-34a bound to the putative 3'-untranslated regions of Notch1 and Jagged1 in SW480 cells, and thereby attenuated the migration and invasion of the colon cancer cells. It was additionally identified that miR-34a downregulated the expression of vimentin and fibronectin via Notch1 and Jagged1. Overall, these data indicate that miR-34a serves a key role in suppressing colorectal cancer metastasis by targeting and regulating Notch signaling.
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Affiliation(s)
- Xuemei Zhang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P.R. China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, Hunan 410008, P.R. China.,Cancer Research Institute, Central South University, Changsha, Hunan 410013, P.R. China
| | - Feiyan Ai
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P.R. China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, Hunan 410008, P.R. China
| | - Xiayu Li
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P.R. China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, Hunan 410008, P.R. China
| | - Li Tian
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P.R. China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, Hunan 410008, P.R. China
| | - Xiaoyan Wang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P.R. China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, Hunan 410008, P.R. China
| | - Shourong Shen
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P.R. China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, Hunan 410008, P.R. China
| | - Fen Liu
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P.R. China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, Hunan 410008, P.R. China
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42
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Singh MP, Rai S, Suyal S, Singh SK, Singh NK, Agarwal A, Srivastava S. Genetic and epigenetic markers in colorectal cancer screening: recent advances. Expert Rev Mol Diagn 2017; 17:665-685. [PMID: 28562109 DOI: 10.1080/14737159.2017.1337511] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Colorectal cancer (CRC) is a heterogenous disease which develops from benign intraepithelial lesions known as adenomas to malignant carcinomas. Acquired alterations in Wnt signaling, TGFβ, MAPK pathway genes and clonal propagation of altered cells are responsible for this transformation. Detection of adenomas or early stage cancer in asymptomatic patients and better prognostic and predictive markers is important for improving the clinical management of CRC. Area covered: In this review, the authors have evaluated the potential of genetic and epigenetic alterations as markers for early detection, prognosis and therapeutic predictive potential in the context of CRC. We have discussed molecular heterogeneity present in CRC and its correlation to prognosis and response to therapy. Expert commentary: Molecular marker based CRC screening methods still fail to gain trust of clinicians. Invasive screening methods, molecular heterogeneity, chemoresistance and low quality test samples are some key challenges which need to be addressed in the present context. New sequencing technologies and integrated omics data analysis of individual or population cohort results in GWAS. MPE studies following a GWAS could be future line of research to establish accurate correlations between CRC and its risk factors. This strategy would identify most reliable biomarkers for CRC screening and management.
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Affiliation(s)
- Manish Pratap Singh
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| | - Sandhya Rai
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| | - Shradha Suyal
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| | - Sunil Kumar Singh
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| | - Nand Kumar Singh
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| | - Akash Agarwal
- b Department of Surgical Oncology , Dr. Ram Manohar Lohia Institute of Medical Sciences (DRMLIMS) , Lucknow , India
| | - Sameer Srivastava
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
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Hao YX, Li YM, Ye M, Guo YY, Li QW, Peng XM, Wang Q, Zhang SF, Zhao HX, Zhang H, Li GH, Zhu JH, Xiao WH. KRAS and BRAF mutations in serum exosomes from patients with colorectal cancer in a Chinese population. Oncol Lett 2017; 13:3608-3616. [PMID: 28521461 PMCID: PMC5431267 DOI: 10.3892/ol.2017.5889] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 01/26/2017] [Indexed: 12/13/2022] Open
Abstract
The efficacy of epidermal growth factor receptor- targeted therapy is significantly associated with Kirsten rat sarcoma viral oncogene homolog (KRAS) and B-raf serine/threonine kinase proto-oncogene (BRAF) mutation in patients with colorectal cancer (CRC), for which the standard gene testing is currently performed using tumor tissue DNA. The aim of the present study was to compare the presence of KRAS and BRAF mutations in the serum exosome and primary tumor tissue from patients with CRC. Genomic DNA were extracted from the tumor tissues of 35 patients with histologically-confirmed CRC and exosomal mRNA were obtained from peripheral blood, which were collected from the corresponding patients prior to surgery. Three mutations in the KRAS gene (codons 12, 13 and 61) and a mutation in the BRAF gene (codon 600) were detected using a polymerase chain reaction-based sequencing method and their presence were compared between tumor tissues and the matched serum exosomes. The KRAS mutation rates in tumor tissues and the matched serum exosomes were 57.6 and 42.4%, respectively, which was not significantly different (P=0.063). The detection rate of the BRAF mutation was 24.2 and 18.2% in tumor tissues and the matched serum exosomes, respectively, and there was no significant difference (P=0.500). The patients with CRC that had a KRAS mutation of codon 12 in exon 2 in their tumor tissues and serum exosomes were significantly older compared with those without this mutation (tumor tissue, P=0.002; serum exosome, P=0.022). The sensitivity of KRAS and BRAF mutation detection using exosomal mRNA was 73.7 and 75%, respectively. The specificity of the detected mutations exhibited an efficiency of 100%, and the total consistency rate was 94.9 and 93.9% for KRAS and BRAF mutations, respectively. These results suggested that serum exosomal mRNA may be used as a novel source for the rapid and non-invasive genotyping of patients with CRC.
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Affiliation(s)
- Yi-Xin Hao
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Yong-Mei Li
- Department of Oncology, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Ming Ye
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Yan-Yan Guo
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Qiu-Wen Li
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Xiu-Mei Peng
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Qi Wang
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Shu-Fang Zhang
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Hui-Xia Zhao
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - He Zhang
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Guang-Hui Li
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Jian-Hua Zhu
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Wen-Hua Xiao
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
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44
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Ni Y, Wong VHY, Tai WCS, Li J, Wong WY, Lee MML, Fong FLY, El-Nezami H, Panagiotou G. A metagenomic study of the preventive effect of Lactobacillus rhamnosus GG on intestinal polyp formation in Apc Min/+ mice. J Appl Microbiol 2017; 122:770-784. [PMID: 28004480 DOI: 10.1111/jam.13386] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 12/12/2022]
Abstract
AIMS To investigate the in vivo effects of Lactobacillus rhamnosus GG (LGG) on intestinal polyp development and the interaction between this single-organism probiotic and the gut microbiota therein. METHODS AND RESULTS The ApcMin/+ mouse model was used to study the potential preventive effect of LGG on intestinal polyposis, while shotgun metagenomic sequencing was employed to characterize both taxonomic and functional changes within the gut microbial community. We found that the progression of intestinal polyps in the control group altered the community functional profile remarkably despite small variation in the taxonomic diversity. In comparison, the consumption of LGG helped maintain the overall functional potential and taxonomic profile in the resident microbes, thereby leading to a 25% decrease of total polyp counts. Furthermore, we found that LGG enriched those microbes or microbial activities related to short-chain fatty acid production (e.g. Roseburia and Coprococcus), as well as suppressed the ones that can lead to inflammation (e.g. Bilophila wadsworthia). CONCLUSIONS Our study using shotgun metagenomics highlights how single probiotic LGG may exert its beneficial effects and decrease polyp formation in mice by maintaining gut microbial functionality. SIGNIFICANCE AND IMPACT OF THE STUDY This probiotic intervention targeting microbiota may be used in conjugation with other dietary supplements or drugs as part of prevention strategies for early-stage colon cancer, after further clinical validations in human.
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Affiliation(s)
- Y Ni
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, The University of Hong Kong, Hong Kong, China
| | - V H Y Wong
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong, China
| | - W C S Tai
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
| | - J Li
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, The University of Hong Kong, Hong Kong, China
| | - W Y Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
| | - M M L Lee
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
| | - F L Y Fong
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong, China
| | - H El-Nezami
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong, China.,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - G Panagiotou
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, The University of Hong Kong, Hong Kong, China.,Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoll Institute, Jena, Germany
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45
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Uzozie AC, Selevsek N, Wahlander A, Nanni P, Grossmann J, Weber A, Buffoli F, Marra G. Targeted Proteomics for Multiplexed Verification of Markers of Colorectal Tumorigenesis. Mol Cell Proteomics 2017; 16:407-427. [PMID: 28062797 DOI: 10.1074/mcp.m116.062273] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 01/04/2017] [Indexed: 12/11/2022] Open
Abstract
Targeted proteomic methods can accelerate the verification of multiple tumor marker candidates in large series of patient samples. We utilized the targeted approach known as selected/multiple reaction monitoring (S/MRM) to verify potential protein markers of colorectal adenoma identified by our group in previous transcriptomic and quantitative shotgun proteomic studies of a large cohort of precancerous colorectal lesions. We developed SRM assays to reproducibly detect and quantify 25 (62.5%) of the 40 selected proteins in an independent series of precancerous and cancerous tissue samples (19 adenoma/normal mucosa pairs; 17 adenocarcinoma/normal mucosa pairs). Twenty-three proteins were significantly up-regulated (n = 17) or downregulated (n = 6) in adenomas and/or adenocarcinomas, as compared with normal mucosa (linear fold changes ≥ ±1.3, adjusted p value <0.05). Most changes were observed in both tumor types (up-regulation of ANP32A, ANXA3, SORD, LDHA, LCN2, NCL, S100A11, SERPINB5, CDV3, OLFM4, and REG4; downregulation of ARF6 and PGM5), and a five-protein biomarker signature distinguished neoplastic tissue from normal mucosa with a maximum area under the receiver operating curve greater than 0.83. Other changes were specific for adenomas (PPA1 and PPA2 up-regulation; KCTD12 downregulation) or adenocarcinoma (ANP32B, G6PD, RCN1, and SET up-regulation; downregulated AKR1B1, APEX1, and PPA1). Some changes significantly correlated with a few patient- or tumor-related phenotypes. Twenty-two (96%) of the 23 proteins have a potential to be released from the tumors into the bloodstream, and their detectability in plasma has been previously reported. The proteins identified in this study expand the pool of biomarker candidates that can be used to develop a standardized precolonoscopy blood test for the early detection of colorectal tumors.
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Affiliation(s)
| | - Nathalie Selevsek
- §Functional Genomics Center Zurich, University/ETH Zurich, Zurich, Switzerland
| | - Asa Wahlander
- §Functional Genomics Center Zurich, University/ETH Zurich, Zurich, Switzerland
| | - Paolo Nanni
- §Functional Genomics Center Zurich, University/ETH Zurich, Zurich, Switzerland
| | - Jonas Grossmann
- §Functional Genomics Center Zurich, University/ETH Zurich, Zurich, Switzerland
| | - Achim Weber
- ¶Institute of Surgical Pathology, University of Zurich, Switzerland
| | - Federico Buffoli
- ‖ Gastroenterology and Endoscopy Unit, Hospital of Cremona, Italy
| | - Giancarlo Marra
- From the ‡Institute of Molecular Cancer Research, University of Zurich, Switzerland;
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46
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Perkins G, Lu H, Garlan F, Taly V. Droplet-Based Digital PCR: Application in Cancer Research. Adv Clin Chem 2016; 79:43-91. [PMID: 28212714 DOI: 10.1016/bs.acc.2016.10.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The efficient characterization of genetic and epigenetic alterations in oncology, virology, or prenatal diagnostics requires highly sensitive and specific high-throughput approaches. Nevertheless, with the use of conventional methods, sensitivity and specificity were largely limited. By partitioning individual target molecules within distinct compartments, digital PCR (dPCR) could overcome these limitations and detect very rare sequences with unprecedented precision and sensitivity. In dPCR, the sample is diluted such that each individual partition will contain no more than one target sequence. Following the assay reaction, the dPCR process provides an absolute value and analyzable quantitative data. The recent coupling of dPCR with microfluidic systems in commercial platforms should lead to an essential tool for the management of patients with cancer, especially adapted to the analysis of precious samples. Applications in cancer research range from the analysis of tumor heterogeneity to that of a range of body fluids. Droplet-based dPCR is indeed particularly appropriate for the emerging field of liquid biopsy analysis. In this review, following an overview of the development in dPCR technology and different strategies based on the use of microcompartments, we will focus particularly on the applications and latest development of microfluidic droplet-based dPCR in oncology.
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Affiliation(s)
- G Perkins
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France; European Georges Pompidou Hospital, AP-HP - Paris Descartes University, Paris, France
| | - H Lu
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France
| | - F Garlan
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France
| | - V Taly
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France.
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47
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Sethi MK, Hancock WS, Fanayan S. Identifying N-Glycan Biomarkers in Colorectal Cancer by Mass Spectrometry. Acc Chem Res 2016; 49:2099-2106. [PMID: 27653471 DOI: 10.1021/acs.accounts.6b00193] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers worldwide. Delineating biological markers (biomarkers) for early detection, when treatment is most effective, is key to prevention and long-term survival of patients. Development of reliable biomarkers requires an increased understanding of the CRC biology and the underlying molecular and cellular mechanisms of the disease. With recent advances in new technologies and approaches, tremendous efforts have been put in proteomics and genomics fields to deliver detailed analysis of the two major biomolecules, genes and proteins, to gain a more complete understanding of cellular systems at both genomic and proteomic levels, allowing a mechanistic understanding of the human diseases, including cancer, and opening avenues for identification of novel gene and protein based prognostic and therapeutic markers. Although the importance of glycosylation in modulating protein function has long been appreciated, glycan analysis has been complicated by the diversity of the glycan structures and the large number of potential glycosylation combinations. Driven by recent technological advances, LC-MS/MS based glycomics is gaining momentum in cancer research and holds considerable potential to deliver new glycan-based markers. In our laboratory, we investigated alterations in N-glycosylation associated with CRC malignancy in a panel of CRC cell lines and CRC patient tissues. In an initial study, LC-MS/MS-based N-glycomics were utilized to map the N-glycome landscape associated with a panel of CRC cell lines (LIM1215, LIM1899, and LIM2405). These studies were subsequently extended to paired tumor and nontumorigenic CRC tissues to validate the findings in the cell line. Our studies in both CRC cell lines and tissues identified a strong representation of high mannose and α2,6-linked sialylated complex N-glycans, which corroborate findings from previous studies in CRC and other cancers. In addition, certain unique glycan determinants such as bisecting β1,4-GlcNAcylation and α2,3-sialylation, identified in the metastatic (LIM1215) and aggressive (LIM2405) CRC cell lines, respectively, were shown to be associated with epidermal growth factor receptor (EGFR) expression status. In this Account, we will describe the mass spectrometry based N-glycomics approach utilized in our laboratory to accurately profile the cell- and tissue-specific N-glycomes associated with CRC. We will highlight altered N-glycosylation observed by our studies, consistent with findings from other cancer studies, and discuss how the observed alterations can provide insights into CRC pathogenesis, opening new avenues to identify novel disease-associated glycan markers.
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Affiliation(s)
- Manveen K. Sethi
- Department
of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - William S. Hancock
- Barnett
Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Department
of Biomedical Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Susan Fanayan
- Department
of Biomedical Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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48
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Qian C, Ju S, Qi J, Zhao J, Shen X, Jing R, Yu J, Li L, Shi Y, Zhang L, Wang Z, Cong H. Alu-based cell-free DNA: a novel biomarker for screening of gastric cancer. Oncotarget 2016; 8:54037-54045. [PMID: 28903321 PMCID: PMC5589560 DOI: 10.18632/oncotarget.11079] [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: 01/18/2016] [Accepted: 07/18/2016] [Indexed: 12/12/2022] Open
Abstract
Gastric cancer (GC) is the fourth most common cancer and the second major cause of cancer-related deaths worldwide. In our previous study, a novel and sensitive method for quantifying cell-free DNA (CFD) in human blood was established and tested for its ability to predict patients with tumor. We want to investigate CFD expression in the sera of GC patients in an attempt to explore the clinical significance of CFD in improving the early screening of GC and monitoring GC progression by the branched DNA (bDNA)-based Alu assay. The concentration of CFD was quantitated by bDNA-based Alu assay. CEA, CA19-9, C72-4 and CA50 concentrations were determined by ABBOTT ARCHITECT I2000 SR. We found the CFD concentrations have significant differences between GC patients, benign gastric disease (BGD) patients and healthy controls (P < 0.05). CFD were weakly correlated with CEA (r = −0.197, P < 0.05) or CA50 (r = 0.206, P < 0.05), and no correlation with CA19-9 (r = −0.061, P > 0.05) or CA72-4 (r = 0.011, P > 0.05). In addition, CFD concentrations were significantly higher in stage I GC patients than BGD patients and healthy controls (P < 0.05), but there was no significant difference in CEA, CA19-9 and CA50 among the three traditional tumor markers (P > 0.05). Our analysis showed that CFD was more sensitive than CEA, CA19-9, CA72-4 or CA50 in early screening of GC. Compared with CEA, CA19-9, CA72-4 and CA50, CFD may prove to be a better biomarker for the screening of GC, thus providing a sensitive biomarker for screening and monitoring progression of GC.
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Affiliation(s)
- Chen Qian
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Shaoqing Ju
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China.,Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Jing Qi
- Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Jianmei Zhao
- Department of Pediatrics, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Xianjuan Shen
- Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Rongrong Jing
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Juan Yu
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Li Li
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Yingjuan Shi
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Lurong Zhang
- Department of Radiation Oncology, UF Shands Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Zhiwei Wang
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Hui Cong
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
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49
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Selinger CP. SEMS for Palliation of Malignant Colonic Obstruction: Why SEMi Available Is Not Good Enough. Dig Dis Sci 2016; 61:1781-2. [PMID: 26860512 DOI: 10.1007/s10620-016-4070-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Affiliation(s)
- Christian P Selinger
- Institute of Gastroenterology, Leeds Teaching Hospitals NHS Trust, St James University Hospital, Bexley Wing, Beckett Street, Leeds, LS20 8HL, UK.
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50
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Armengol G, Sarhadi VK, Ghanbari R, Doghaei-Moghaddam M, Ansari R, Sotoudeh M, Puolakkainen P, Kokkola A, Malekzadeh R, Knuutila S. Driver Gene Mutations in Stools of Colorectal Carcinoma Patients Detected by Targeted Next-Generation Sequencing. J Mol Diagn 2016; 18:471-9. [PMID: 27155048 DOI: 10.1016/j.jmoldx.2016.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 11/25/2015] [Accepted: 01/20/2016] [Indexed: 12/13/2022] Open
Abstract
Detection of driver gene mutations in stool DNA represents a promising noninvasive approach for screening colorectal cancer (CRC). Amplicon-based next-generation sequencing (NGS) is a good option to study mutations in many cancer genes simultaneously and from a low amount of DNA. Our aim was to assess the feasibility of identifying mutations in 22 cancer driver genes with Ion Torrent technology in stool DNA from a series of 65 CRC patients. The assay was successful in 80% of stool DNA samples. NGS results showed 83 mutations in cancer driver genes, 29 hotspot and 54 novel mutations. One to five genes were mutated in 75% of cases. TP53, KRAS, FBXW7, and SMAD4 were the top mutated genes, consistent with previous studies. Of samples with mutations, 54% presented concomitant mutations in different genes. Phosphatidylinositol 3-kinase/mitogen-activated protein kinase pathway genes were mutated in 70% of samples, with 58% having alterations in KRAS, NRAS, or BRAF. Because mutations in these genes can compromise the efficacy of epidermal growth factor receptor blockade in CRC patients, identifying mutations that confer resistance to some targeted treatments may be useful to guide therapeutic decisions. In conclusion, the data presented herein show that NGS procedures on stool DNA represent a promising tool to detect genetic mutations that could be used in the future for diagnosis, monitoring, or treating CRC.
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Affiliation(s)
- Gemma Armengol
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Unit of Biological Anthropology, Department of Animal Biology, Plant Biology and Ecology, Autonomous University of Barcelona, Barcelona, Spain
| | - Virinder K Sarhadi
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Reza Ghanbari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Reza Ansari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Sasan Alborz Biomedical Research Center, Masoud Clinic, Tehran, Iran
| | - Masoud Sotoudeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Sasan Alborz Biomedical Research Center, Masoud Clinic, Tehran, Iran
| | - Pauli Puolakkainen
- Gastrointestinal Clinic, The University Central Hospital of Helsinki, Helsinki, Finland
| | - Arto Kokkola
- Gastrointestinal Clinic, The University Central Hospital of Helsinki, Helsinki, Finland
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Sasan Alborz Biomedical Research Center, Masoud Clinic, Tehran, Iran
| | - Sakari Knuutila
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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