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Martinez-Val A, Van der Hoeven L, Bekker-Jensen DB, Jørgensen MM, Nors J, Franciosa G, Andersen CL, Bramsen JB, Olsen JV. Proteomics of colorectal tumors identifies the role of CAVIN1 in tumor relapse. Mol Syst Biol 2025:10.1038/s44320-025-00102-8. [PMID: 40269326 DOI: 10.1038/s44320-025-00102-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Revised: 03/28/2025] [Accepted: 04/02/2025] [Indexed: 04/25/2025] Open
Abstract
Colorectal cancer molecular signatures derived from omics data can be employed to stratify CRC patients and aid decisions about therapies or evaluate prognostic outcome. However, molecular biomarkers for identification of patients at increased risk of disease relapse are currently lacking. Here, we present a comprehensive multi-omics analysis of a Danish colorectal cancer tumor cohort composed of 412 biopsies from tumors of 371 patients diagnosed at TNM stage II or III. From mass spectrometry-based patient proteome profiles, we classified the tumors into four molecular subtypes, including a mesenchymal-like subtype. As the mesenchymal-rich tumors are known to represent the most invasive and metastatic phenotype, we focused on the protein signature defining this subtype to evaluate their potential as relapse risk markers. Among signature-specific proteins, we followed-up Caveolae-Associated Protein-1 (CAVIN1) and demonstrated its role in tumor progression in a 3D in vitro model of colorectal cancer. Compared to previous omics analyses of CRC, our multi-omics classification provided deeper insights into EMT in cancer cells with stronger correlations with risk of relapse.
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Affiliation(s)
- Ana Martinez-Val
- Novo Nordisk Foundation Center for Protein Research, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain.
| | - Leander Van der Hoeven
- Novo Nordisk Foundation Center for Protein Research, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dorte B Bekker-Jensen
- Novo Nordisk Foundation Center for Protein Research, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Evosep Biosystems, Odense, Denmark
| | - Margarita Melnikova Jørgensen
- Institute of Pathology, Randers Regional Hospital, Randers, Denmark
- Department of Pathology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Jesper Nors
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Giulia Franciosa
- Novo Nordisk Foundation Center for Protein Research, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Claus L Andersen
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark.
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
| | - Jesper B Bramsen
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark.
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Mehmetoğlu Gürbüz T, Oral EN, Dağoğlu Sakin RN, Karaman Ş, Durak Ş, Aksoyer Sezgin SB, Keskin M, Çelik F, Zeybek ŞÜ. Exon Sequence Analysis of the ATG5, ATG12, ATG9B Genes in Colorectal Cancer Patients During Radiotherapy. Indian J Clin Biochem 2025; 40:263-273. [PMID: 40123635 PMCID: PMC11928699 DOI: 10.1007/s12291-023-01177-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/15/2023] [Indexed: 03/25/2025]
Abstract
Radiotherapy (RT) which is a treatment regime for cancer patients may cause genetic instability and side effects. Etiological associations exist amongst autophagy-related gene (ATG) mutation and cancer. RT increases the rate of autophagy previously proven in vitro. The aforementioned background diverted us to conduct exon mutation analysis for ATG5, ATG12, and ATG9B genes of colorectal cancer patients who were receiving neoadjuvant RT. Peripheral blood DNA from different time points (before/middle/after RT) of the same patients was isolated and most tandem repeat-containing exons of ATG5, ATG12, and ATG9B were polymerase chain reaction-amplified and examined for mutations by Sanger sequencing. CA19-9/CEA (Tumor marker of colorectal cancer/Carcinoembryonic Antigen) serum levels were retrieved from the clinic. No exon variations detected for ATG5 and ATG12 genes. However, 4 patients (17.4%) showed frameshift mutation for ATG9B gene. Exon variation analysis of 2 (8.7%) patients resulted in GGG deletion at 8G mononucleotide tandem repeat region of ATG9B. Assigning patients as before RT and after RT, CA19-9 levels in ATG9B (Mutation) patients were higher compared to ATG9B (Wild Type) patients. ATG9B is highly likely to mutate during RT and ATG9B mutation correlates to higher CEA and CA19-9 levels and patients show poor prognosis. Supplementary Information The online version contains supplementary material available at 10.1007/s12291-023-01177-6.
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Affiliation(s)
- Tuğba Mehmetoğlu Gürbüz
- Aziz Sancar Institute of Experimental Medicine, Department of Molecular Medicine, Istanbul University, Topkapi, Gureba Hospital Street, Number: 69, 34093 Fatih/Istanbul, Turkey
| | - Ethem Nezih Oral
- Institute of Oncology, Department of Radiation Oncology, Istanbul University, Istanbul, Turkey
| | | | - Şule Karaman
- Institute of Oncology, Diagnostic Treatment and Care Services, Istanbul University, Istanbul, Turkey
| | - Şermin Durak
- Aziz Sancar Institute of Experimental Medicine, Department of Molecular Medicine, Istanbul University, Topkapi, Gureba Hospital Street, Number: 69, 34093 Fatih/Istanbul, Turkey
| | | | - Metin Keskin
- Istanbul Faculty of Medicine, Department of General Surgery, Istanbul, Turkey
| | - Faruk Çelik
- Aziz Sancar Institute of Experimental Medicine, Department of Molecular Medicine, Istanbul University, Topkapi, Gureba Hospital Street, Number: 69, 34093 Fatih/Istanbul, Turkey
| | - Ş. Ümit Zeybek
- Aziz Sancar Institute of Experimental Medicine, Department of Molecular Medicine, Istanbul University, Topkapi, Gureba Hospital Street, Number: 69, 34093 Fatih/Istanbul, Turkey
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Papin C, Ibrahim A, Sabir JSM, Le Gras S, Stoll I, Albiheyri RS, Zari AT, Bahieldin A, Bellacosa A, Bronner C, Hamiche A. MBD4 loss results in global reactivation of promoters and retroelements with low methylated CpG density. J Exp Clin Cancer Res 2023; 42:301. [PMID: 37957685 PMCID: PMC10644448 DOI: 10.1186/s13046-023-02882-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Inherited defects in the base-excision repair gene MBD4 predispose individuals to adenomatous polyposis and colorectal cancer, which is characterized by an accumulation of C > T transitions resulting from spontaneous deamination of 5'-methylcytosine. METHODS Here, we have investigated the potential role of MBD4 in regulating DNA methylation levels using genome-wide transcriptome and methylome analyses. Additionally, we have elucidated its function through a series of in vitro experiments. RESULTS Here we show that the protein MBD4 is required for DNA methylation maintenance and G/T mismatch repair. Transcriptome and methylome analyses reveal a genome-wide hypomethylation of promoters, gene bodies and repetitive elements in the absence of MBD4 in vivo. Methylation mark loss is accompanied by a broad transcriptional derepression phenotype affecting promoters and retroelements with low methylated CpG density. MBD4 in vivo forms a complex with the mismatch repair proteins (MMR), which exhibits high bi-functional glycosylase/AP-lyase endonuclease specific activity towards methylated DNA substrates containing a G/T mismatch. Experiments using recombinant proteins reveal that the association of MBD4 with the MMR protein MLH1 is required for this activity. CONCLUSIONS Our data identify MBD4 as an enzyme specifically designed to repair deaminated 5-methylcytosines and underscores its critical role in safeguarding against methylation damage. Furthermore, it illustrates how MBD4 functions in normal and pathological conditions.
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Affiliation(s)
- Christophe Papin
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
| | - Abdulkhaleg Ibrahim
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
- National Research Centre for Tropical and Transboundary Diseases (NRCTTD), Alzentan, 99316, Libya
| | - Jamal S M Sabir
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Stéphanie Le Gras
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
| | - Isabelle Stoll
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
| | - Raed S Albiheyri
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ali T Zari
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Bahieldin
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alfonso Bellacosa
- Cancer Biology Program, Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Christian Bronner
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France.
| | - Ali Hamiche
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France.
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4
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Kiweler N, Schwarz H, Nguyen A, Matschos S, Mullins C, Piée-Staffa A, Brachetti C, Roos WP, Schneider G, Linnebacher M, Brenner W, Krämer OH. The epigenetic modifier HDAC2 and the checkpoint kinase ATM determine the responses of microsatellite instable colorectal cancer cells to 5-fluorouracil. Cell Biol Toxicol 2023; 39:2401-2419. [PMID: 35608750 PMCID: PMC10547618 DOI: 10.1007/s10565-022-09731-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 05/10/2022] [Indexed: 11/02/2022]
Abstract
The epigenetic modifier histone deacetylase-2 (HDAC2) is frequently dysregulated in colon cancer cells. Microsatellite instability (MSI), an unfaithful replication of DNA at nucleotide repeats, occurs in about 15% of human colon tumors. MSI promotes a genetic frameshift and consequently a loss of HDAC2 in up to 43% of these tumors. We show that long-term and short-term cultures of colorectal cancers with MSI contain subpopulations of cells lacking HDAC2. These can be isolated as single cell-derived, proliferating populations. Xenografted patient-derived colon cancer tissues with MSI also show variable patterns of HDAC2 expression in mice. HDAC2-positive and HDAC2-negative RKO cells respond similarly to pharmacological inhibitors of the class I HDACs HDAC1/HDAC2/HDAC3. In contrast to this similarity, HDAC2-negative and HDAC2-positive RKO cells undergo differential cell cycle arrest and apoptosis induction in response to the frequently used chemotherapeutic 5-fluorouracil, which becomes incorporated into and damages RNA and DNA. 5-fluorouracil causes an enrichment of HDAC2-negative RKO cells in vitro and in a subset of primary colorectal tumors in mice. 5-fluorouracil induces the phosphorylation of KAP1, a target of the checkpoint kinase ataxia-telangiectasia mutated (ATM), stronger in HDAC2-negative cells than in their HDAC2-positive counterparts. Pharmacological inhibition of ATM sensitizes RKO cells to cytotoxic effects of 5-fluorouracil. These findings demonstrate that HDAC2 and ATM modulate the responses of colorectal cancer cells towards 5-FU.
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Affiliation(s)
- Nicole Kiweler
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
- Present Address: Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Helena Schwarz
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
| | - Alexandra Nguyen
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
| | - Stephanie Matschos
- Department of General Surgery, Molecular Oncology and Immunotherapy, Schillingallee 35, 18057 Rostock, Germany
| | - Christina Mullins
- Department of General Surgery, Molecular Oncology and Immunotherapy, Schillingallee 35, 18057 Rostock, Germany
| | - Andrea Piée-Staffa
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
| | - Christina Brachetti
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
| | - Wynand P. Roos
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
| | - Günter Schneider
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University Munich, 81675 Munich, Germany
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, Schillingallee 35, 18057 Rostock, Germany
| | - Walburgis Brenner
- Clinic for Obstetrics and Women’s Health, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Oliver H. Krämer
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
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5
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Ho V, Chung L, Wilkinson K, Lea V, Lim SH, Abubakar A, Ng W, Lee M, Roberts TL, Chua W, Lee CS. Prognostic Significance of MRE11 Overexpression in Colorectal Cancer Patients. Cancers (Basel) 2023; 15:cancers15092438. [PMID: 37173905 PMCID: PMC10177562 DOI: 10.3390/cancers15092438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Meiotic recombination 11 (MRE11) plays a critical role in the DNA damage response and maintenance of genome stability and is associated with the prognosis for numerous malignancies. Here, we explored the clinicopathological significance and prognostic value of MRE11 expression in colorectal cancer (CRC), a leading cause of cancer-related deaths worldwide. Samples from 408 patients who underwent surgery for colon and rectal cancer between 2006 and 2011, including a sub-cohort of 127 (31%) patients treated with adjuvant therapy, were analyzed. In Kaplan-Meier survival analyses, we found that high MRE11 expression in the tumor center (TC) was significantly associated with poor disease-free survival (DFS; p = 0.045) and overall survival (OS; p = 0.039). Intriguingly, high MRE11 expression in the TC was also significantly correlated with reduced DFS (p = 0.005) and OS (p = 0.010) in the subgroup with right-sided primary CRC. In multivariate analyses, high MRE11 expression (hazard ratio [HR] = 1.697, 95% confidence interval [CI]: 1.034-2.785; p = 0.036) and lymphovascular/perineural invasion (LVI/PNI; HR = 1.922, 95% CI 1.122-3.293; p = 0.017) showed significant association with worse OS in patients with right-sided tumors but not those with left-sided tumors. Moreover, in patients with right-sided tumors, high MRE11 was associated with worse OS for those with lymph node involvement (p = 0.006) and LVI/PNI (p = 0.049). Collectively, our results suggest that MRE11 may serve as an independent prognostic marker in those with right-sided severe CRC, with clinical value in the management of these patients.
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Affiliation(s)
- Vincent Ho
- School of Medicine, Western Sydney University, Sydney, NSW 2560, Australia
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
| | - Liping Chung
- School of Medicine, Western Sydney University, Sydney, NSW 2560, Australia
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
| | - Kate Wilkinson
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
- Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Vivienne Lea
- School of Medicine, Western Sydney University, Sydney, NSW 2560, Australia
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Stephanie H Lim
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
- Macarthur Cancer Therapy Centre, Campbelltown Hospital, Sydney, NSW 2560, Australia
| | - Askar Abubakar
- School of Medicine, Western Sydney University, Sydney, NSW 2560, Australia
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
| | - Weng Ng
- Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Mark Lee
- Department of Radiation Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Tara L Roberts
- School of Medicine, Western Sydney University, Sydney, NSW 2560, Australia
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
- South Western Sydney Clinical School, University of New South Wales, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Wei Chua
- School of Medicine, Western Sydney University, Sydney, NSW 2560, Australia
- Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia
- Discipline of Medical Oncology, School of Medicine, Western Sydney University, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Cheok Soon Lee
- School of Medicine, Western Sydney University, Sydney, NSW 2560, Australia
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia
- South Western Sydney Clinical School, University of New South Wales, Liverpool Hospital, Liverpool, NSW 2170, Australia
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, NSW 2560, Australia
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6
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Sun M, Moquet J, Ellender M, Bouffler S, Badie C, Baldwin-Cleland R, Monahan K, Latchford A, Lloyd D, Clark S, Anyamene NA, Ainsbury E, Burling D. Potential risks associated with the use of ionizing radiation for imaging and treatment of colorectal cancer in Lynch syndrome patients. Fam Cancer 2023; 22:61-70. [PMID: 35718836 PMCID: PMC9829596 DOI: 10.1007/s10689-022-00299-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/29/2022] [Indexed: 01/13/2023]
Abstract
The aim of this review is to investigate the literature pertaining to the potential risks of low-dose ionizing radiation to Lynch syndrome patients by use of computed tomography (CT), either diagnostic CT colonography (CTC), standard staging CT or CT surveillance. Furthermore, this review explores the potential risks of using radiotherapy for treatment of rectal cancer in these patients. No data or longitudinal observational studies of the impact of radiation exposure on humans with Lynch syndrome were identified. Limited experimental studies utilizing cell lines and primary cells exposed to both low and high radiation doses have been carried out to help determine radio-sensitivity associated with DNA mismatch repair gene deficiency, the defining feature of Lynch syndrome. On balance, these studies suggest that mismatch repair deficient cells may be relatively radio-resistant (particularly for low dose rate exposures) with higher mutation rates, albeit no firm conclusions can be drawn. Mouse model studies, though, showed an increased risk of developing colorectal tumors in mismatch repair deficient mice exposed to radiation doses around 2 Gy. With appropriate ethical approval, further studies investigating radiation risks associated with CT imaging and radiotherapy relevant doses using cells/tissues derived from confirmed Lynch patients or genetically modified animal models are urgently required for future clinical guidance.
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Affiliation(s)
- Mingzhu Sun
- UK Health Security Agency, Department of Radiation Effects, RCEHD, Chilton, Didcot, OX11 0RQ, UK.
| | - Jayne Moquet
- UK Health Security Agency, Department of Radiation Effects, RCEHD, Chilton, Didcot, OX11 0RQ UK
| | - Michele Ellender
- UK Health Security Agency, Department of Radiation Effects, RCEHD, Chilton, Didcot, OX11 0RQ UK
| | - Simon Bouffler
- UK Health Security Agency, Department of Radiation Effects, RCEHD, Chilton, Didcot, OX11 0RQ UK
| | - Christophe Badie
- UK Health Security Agency, Department of Radiation Effects, RCEHD, Chilton, Didcot, OX11 0RQ UK ,Environmental Research Group Within the School of Public Health, Faculty of Medicine at Imperial College of Science, Technology and Medicine, London, W12 0BZ UK
| | - Rachel Baldwin-Cleland
- Intestinal Imaging Centre, St Mark’s Hospital, London North West University Healthcare NHS Trust, Watford Road, Harrow, HA1 3UJ UK
| | - Kevin Monahan
- Lynch Syndrome Clinic, Centre for Familial Intestinal Cancer, St Mark’s Hospital, London North West University Healthcare NHS Trust, Watford Road, Harrow, HA1 3UJ UK
| | - Andrew Latchford
- Lynch Syndrome Clinic, Centre for Familial Intestinal Cancer, St Mark’s Hospital, London North West University Healthcare NHS Trust, Watford Road, Harrow, HA1 3UJ UK
| | - David Lloyd
- UK Health Security Agency, Department of Radiation Effects, RCEHD, Chilton, Didcot, OX11 0RQ UK
| | - Susan Clark
- Lynch Syndrome Clinic, Centre for Familial Intestinal Cancer, St Mark’s Hospital, London North West University Healthcare NHS Trust, Watford Road, Harrow, HA1 3UJ UK
| | - Nicola A. Anyamene
- East and North Hertfordshire NHS Trust, Mount Vernon Cancer Centre, Rickmansworth Road, Northwood, HA6 2RN Middlesex UK
| | - Elizabeth Ainsbury
- UK Health Security Agency, Department of Radiation Effects, RCEHD, Chilton, Didcot, OX11 0RQ UK ,Environmental Research Group Within the School of Public Health, Faculty of Medicine at Imperial College of Science, Technology and Medicine, London, W12 0BZ UK
| | - David Burling
- Intestinal Imaging Centre, St Mark’s Hospital, London North West University Healthcare NHS Trust, Watford Road, Harrow, HA1 3UJ UK
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7
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Mas-Ponte D, McCullough M, Supek F. Spectrum of DNA mismatch repair failures viewed through the lens of cancer genomics and implications for therapy. Clin Sci (Lond) 2022; 136:383-404. [PMID: 35274136 PMCID: PMC8919091 DOI: 10.1042/cs20210682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/02/2022] [Accepted: 02/28/2022] [Indexed: 12/15/2022]
Abstract
Genome sequencing can be used to detect DNA repair failures in tumors and learn about underlying mechanisms. Here, we synthesize findings from genomic studies that examined deficiencies of the DNA mismatch repair (MMR) pathway. The impairment of MMR results in genome-wide hypermutation and in the 'microsatellite instability' (MSI) phenotype-occurrence of indel mutations at short tandem repeat (microsatellite) loci. The MSI status of tumors was traditionally assessed by molecular testing of a selected set of MS loci or by measuring MMR protein expression levels. Today, genomic data can provide a more complete picture of the consequences on genomic instability. Multiple computational studies examined somatic mutation distributions that result from failed DNA repair pathways in tumors. These include analyzing the commonly studied trinucleotide mutational spectra of single-nucleotide variants (SNVs), as well as of other features such as indels, structural variants, mutation clusters and regional mutation rate redistribution. The identified mutation patterns can be used to rigorously measure prevalence of MMR failures across cancer types, and potentially to subcategorize the MMR deficiencies. Diverse data sources, genomic and pre-genomic, from human and from experimental models, suggest there are different ways in which MMR can fail, and/or that the cell-type or genetic background may result in different types of MMR mutational patterns. The spectrum of MMR failures may direct cancer evolution, generating particular sets of driver mutations. Moreover, MMR affects outcomes of therapy by DNA damaging drugs, antimetabolites, nonsense-mediated mRNA decay (NMD) inhibitors, and immunotherapy by promoting either resistance or sensitivity, depending on the type of therapy.
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Affiliation(s)
- David Mas-Ponte
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Marcel McCullough
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Fran Supek
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Pg Lluís Companys, 23, Barcelona 08010, Spain
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8
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Recine F, De Vita A, Fausti V, Pieri F, Bongiovanni A, Franchini E, Casadei R, Falasconi MC, Oboldi D, Matteucci F, Pallotti MC, Mercatali L, Riva N, Gurrieri L, Vanni S, Liverani C, Miserocchi G, Spadazzi C, Cocchi C, Ibrahim T. Case Report: Adult NTRK-Rearranged Spindle Cell Neoplasm: Early Tumor Shrinkage in a Case With Bone and Visceral Metastases Treated With Targeted Therapy. Front Oncol 2022; 11:740676. [PMID: 35070960 PMCID: PMC8776642 DOI: 10.3389/fonc.2021.740676] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Background NTRK (neurotrophic tyrosine receptor kinase)-rearranged spindle cell neoplasms are a new group of tumors included in the new 5th edition of the World Health Organization (WHO) classification of soft Tissue and Bone Sarcomas. These tumors are characterized by NTRK gene fusions and show a wide spectrum of histologies and clinical behavior. Several targeted therapies have recently been approved for tumors harboring NTRK fusions, including STS. Case Presentation A 26-year-old male with advanced, pretreated NTRK rearranged spindle cell neoplasm and liver, lung and bone metastases was treated with larotrectinib on a continuous 28-day schedule, at a dose of 100 mg twice daily. An 18FDG-PET/CT scan performed after 7 days of treatment showed tumor shrinkage in both visceral and bone lesions. There was no drug-related toxicity. Subsequent evaluations confirmed continued tumor regression in disease sites. The patient is well and continues treatment. Conclusion The clinical and radiological response of our patient with an uncommon TPM4 (exon 7)-NTRK1 (exon 12) gene fusion tumor treated with a first-generation TRK inhibitor could contribute to a better understanding of the biology of this new STS entity and help to improve patient management.
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Affiliation(s)
- Federica Recine
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Alessandro De Vita
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Valentina Fausti
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Federica Pieri
- Pathology Unit, Morgagni-Pierantoni Hospital, Forlì, Italy
| | - Alberto Bongiovanni
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Eugenia Franchini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | | | | | - Devil Oboldi
- Radiology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Federica Matteucci
- Nuclear Medicine Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Maria Caterina Pallotti
- Palliative Care Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Laura Mercatali
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Nada Riva
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Lorena Gurrieri
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Silvia Vanni
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Chiara Liverani
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giacomo Miserocchi
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Chiara Spadazzi
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Claudia Cocchi
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Toni Ibrahim
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
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9
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Pillozzi S, Bernini A, Palchetti I, Crociani O, Antonuzzo L, Campanacci D, Scoccianti G. Soft Tissue Sarcoma: An Insight on Biomarkers at Molecular, Metabolic and Cellular Level. Cancers (Basel) 2021; 13:cancers13123044. [PMID: 34207243 PMCID: PMC8233868 DOI: 10.3390/cancers13123044] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Soft tissue sarcoma is a rare mesenchymal malignancy. Despite the advancements in the fields of radiology, pathology and surgery, these tumors often recur locally and/or with metastatic disease. STS is considered to be a diagnostic challenge due to the large variety of histological subtypes with clinical and histopathological characteristics which are not always distinct. One of the important clinical problems is a lack of useful biomarkers. Therefore, the discovery of biomarkers that can be used to detect tumors or predict tumor response to chemotherapy or radiotherapy could help clinicians provide more effective clinical management. Abstract Soft tissue sarcomas (STSs) are a heterogeneous group of rare tumors. Although constituting only 1% of all human malignancies, STSs represent the second most common type of solid tumors in children and adolescents and comprise an important group of secondary malignancies. Over 100 histologic subtypes have been characterized to date (occurring predominantly in the trunk, extremity, and retroperitoneum), and many more are being discovered due to molecular profiling. STS mortality remains high, despite adjuvant chemotherapy. New prognostic stratification markers are needed to help identify patients at risk of recurrence and possibly apply more intensive or novel treatments. Recent scientific advancements have enabled a more precise molecular characterization of sarcoma subtypes and revealed novel therapeutic targets and prognostic/predictive biomarkers. This review aims at providing a comprehensive overview of the most relevant cellular, molecular and metabolic biomarkers for STS, and highlight advances in STS-related biomarker research.
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Affiliation(s)
- Serena Pillozzi
- Medical Oncology Unit, Careggi University Hospital, Largo Brambilla 3, 50134 Florence, Italy;
- Correspondence:
| | - Andrea Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy;
| | - Ilaria Palchetti
- Department of Chemistry Ugo Schiff, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy;
| | - Olivia Crociani
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy;
| | - Lorenzo Antonuzzo
- Medical Oncology Unit, Careggi University Hospital, Largo Brambilla 3, 50134 Florence, Italy;
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy;
| | - Domenico Campanacci
- Department of Health Science, University of Florence, Largo Brambilla 3, 50134 Florence, Italy;
| | - Guido Scoccianti
- Department of Orthopaedic Oncology and Reconstructive Surgery, University of Florence, Careggi University Hospital, Largo Brambilla 3, 50134 Florence, Italy;
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10
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Arai H, Elliott A, Xiu J, Wang J, Battaglin F, Kawanishi N, Soni S, Zhang W, Millstein J, Sohal D, Goldberg RM, Hall MJ, Scott AJ, Khushman M, Hwang JJ, Lou E, Weinberg BA, Marshall JL, Lockhart AC, Stafford P, Zhang J, Moretto R, Cremolini C, Korn WM, Lenz HJ. The Landscape of Alterations in DNA Damage Response Pathways in Colorectal Cancer. Clin Cancer Res 2021; 27:3234-3242. [PMID: 33766816 PMCID: PMC12047448 DOI: 10.1158/1078-0432.ccr-20-3635] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/13/2021] [Accepted: 03/22/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Defective DNA damage response (DDR) is a hallmark of cancer leading to genomic instability and is associated with chemosensitivity. Although the mismatch repair system has been extensively studied, the clinical implications of other mechanisms associated with DDR alterations in patients with colorectal cancer remain unclear. This study aimed to understand DDR pathways alterations and their association with common clinical features in patients with colorectal cancer. EXPERIMENTAL DESIGN Next-generation sequencing and whole-transcriptome sequencing were conducted using formalin-fixed paraffin-embedded samples submitted to a commercial Clinical Laboratory Improvement Amendments-certified laboratory. Samples with pathogenic or presumed pathogenic mutations in 29 specific DDR-related genes were considered as DDR-mutant (DDR-MT) and the remaining samples as DDR-wild type (DDR-WT). RESULTS Of 9,321 patients with colorectal cancer, 1,290 (13.8%) were DDR-MT. The frequency of DDR-MT was significantly higher in microsatellite instability-high (MSI-H) cases than in microsatellite stable cases (76.4% vs. 9.5%). The DDR-MT genotype was higher in the right-sided, RAS-wild, BRAF-mutant, and CMS1 subgroups. However, these associations were primarily confounded by the distribution of MSI status. Compared with the DDR-WT tumors, the DDR-MT tumors had a higher mutational burden and gene expression levels in the immune-related pathway, which were independent of MSI status. CONCLUSIONS We characterized a distinct subgroup of patients with colorectal cancer with tumors harboring mutations in the DDR-related genes. These patients more commonly had MSI-H tumors and exhibited an activated immune signature regardless of their tumor's MSI status. These findings warrant further investigations to develop personalized treatment strategies in this significant subgroup of patients with colorectal cancer.
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Affiliation(s)
- Hiroyuki Arai
- Division of Medical Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Andrew Elliott
- Clinical and Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, Arizona
| | - Joanne Xiu
- Clinical and Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, Arizona
| | - Jingyuan Wang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Francesca Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Natsuko Kawanishi
- Division of Medical Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Shivani Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Wu Zhang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Joshua Millstein
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Davendra Sohal
- Division of Hematology/Oncology, University of Cincinnati, Cincinnati, Ohio
| | | | - Michael J Hall
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Aaron J Scott
- Department of Medicine, University of Arizona Cancer Center, Tucson, Arizona
| | - Moh'd Khushman
- Medical Oncology, Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama
| | - Jimmy J Hwang
- Department of Solid Tumor Oncology, GI Medical Oncology, Levine Cancer Institute, Charlotte, North Carolina
| | - Emil Lou
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota
| | - Benjamin A Weinberg
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - John L Marshall
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Albert C Lockhart
- Department of Medicine, Division of Oncology, University of Miami, Miller School of Medicine, Miami, Florida
| | - Phillip Stafford
- Department of Bioinformatics, Caris Life Sciences, Phoenix, Arizona
| | - Jian Zhang
- Department of Bioinformatics, Caris Life Sciences, Phoenix, Arizona
| | - Roberto Moretto
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Chiara Cremolini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California.
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11
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Köberle B, Schoch S. Platinum Complexes in Colorectal Cancer and Other Solid Tumors. Cancers (Basel) 2021; 13:cancers13092073. [PMID: 33922989 PMCID: PMC8123298 DOI: 10.3390/cancers13092073] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Cisplatin is successfully used for the treatment of various solid cancers. Unfortunately, it shows no activity in colorectal cancer. The resistance phenotype of colorectal cancer cells is mainly caused by alterations in p53-controlled DNA damage signaling and/or defects in the cellular mismatch repair pathway. Improvement of platinum-based chemotherapy in cisplatin-unresponsive cancers, such as colorectal cancer, might be achieved by newly designed cisplatin analogues, which retain activity in unresponsive tumor cells. Moreover, a combination of cisplatin with biochemical modulators of DNA damage signaling might sensitize cisplatin-resistant tumor cells to the drug, thus providing another strategy to improve cancer therapy. Abstract Cisplatin is one of the most commonly used drugs for the treatment of various solid neoplasms, including testicular, lung, ovarian, head and neck, and bladder cancers. Unfortunately, the therapeutic efficacy of cisplatin against colorectal cancer is poor. Various mechanisms appear to contribute to cisplatin resistance in cancer cells, including reduced drug accumulation, enhanced drug detoxification, modulation of DNA repair mechanisms, and finally alterations in cisplatin DNA damage signaling preventing apoptosis in cancer cells. Regarding colorectal cancer, defects in mismatch repair and altered p53-mediated DNA damage signaling are the main factors controlling the resistance phenotype. In particular, p53 inactivation appears to be associated with chemoresistance and poor prognosis. To overcome resistance in cancers, several strategies can be envisaged. Improved cisplatin analogues, which retain activity in resistant cancer, might be applied. Targeting p53-mediated DNA damage signaling provides another therapeutic strategy to circumvent cisplatin resistance. This review provides an overview on the DNA repair pathways involved in the processing of cisplatin damage and will describe signal transduction from cisplatin DNA lesions, with special attention given to colorectal cancer cells. Furthermore, examples for improved platinum compounds and biochemical modulators of cisplatin DNA damage signaling will be presented in the context of colon cancer therapy.
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Affiliation(s)
- Beate Köberle
- Department of Food Chemistry and Toxicology, Karlsruhe Institute of Technology, Adenauerring 20a, 76131 Karlsruhe, Germany
| | - Sarah Schoch
- Department of Laboratory Medicine, Lund University, Scheelevägen 2, 223 81 Lund, Sweden
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12
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Ding G, Xu X, Li D, Chen Y, Wang W, Ping D, Jia S, Cao L. Fisetin inhibits proliferation of pancreatic adenocarcinoma by inducing DNA damage via RFXAP/KDM4A-dependent histone H3K36 demethylation. Cell Death Dis 2020; 11:893. [PMID: 33093461 PMCID: PMC7582166 DOI: 10.1038/s41419-020-03019-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/05/2020] [Accepted: 09/09/2020] [Indexed: 12/13/2022]
Abstract
Pancreatic adenocarcinoma (PDAC) is an extremely malignant tumor that is associated with low survival rates. Fisetin is a natural flavonoid that shows diverse antitumor effects, including DNA damage, in various cancers. Increasing studies have demonstrated that epigenetic modifications play critical roles in DNA-damage response. However, the epigenetic regulation mechanism of fisetin in cancers is hardly studied. RFXAP is a critical transcription factor for MHC II molecules, however, its transcriptional role in PDAC is poorly understood. The anti-PDAC effect of fisetin was measured by CCK-8, flow cytometry, xenograft tumor nude mice model. DNA-damage levels were examined by immunofluorescence. Bioinformatics analysis was used to examine the expression of RFXAP and other genes involved in DNA-damage response. ChIP sequencing was used to explore the transcriptional role of RFXAP. The expression of target gene KDM4A was measured by qRT-PCR and western blots. KDM4A promoter activity was analyzed using dual-luciferase reporter assay. RFXAP overexpressing or silencing of PDAC cells was used to explore the effect of RFXAP in DNA damage induced by fisetin. We found that fisetin inhibited cell proliferation and induced DNA damage and S-phase arrest in PDAC. Expression of RFXAP and other DNA-damage response genes were upregulated by fisetin. We revealed that RFXAP expression was relatively low in PDAC and correlated with tumor stage and poor prognosis. Then we explored the transcriptional role of RFXAP and found that RFXAP targeted KDM4A, a special demethylase specific for tri- and dimethylated histone H3K36. We found that overexpression of RFXAP upregulated KDM4A and attenuated methylation of H3K36, thereby impairing DNA repair and enhancing the DNA damage induced by fisetin, while RFXAP silencing showed the opposite effect. We also found the function of fisetin in enhancing the effect of chemotherapy on pancreatic cancer cells. Our findings revealed that fisetin induced DNA damage via RFXAP/KDM4A-dependent histone H3K36 demethylation, thus causing inhibition of proliferation in PDAC.
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Affiliation(s)
- Guoping Ding
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Xiaodong Xu
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Dan Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.,Department of General Surgery, School of Medicine, Affiliated Hospital of Hangzhou Normal University, Hangzhou, 310000, China
| | - Yuhao Chen
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.,Emergency Department, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Weimin Wang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.,Department of General Surgery, Huzhou Hospital, Zhejiang University School of Medicine, Huzhou, 313003, Zhejiang, China
| | - Dongnan Ping
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Shengnan Jia
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.
| | - Liping Cao
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China. .,Innovation Center for Minimally Invasive Technique and Device, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
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13
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Proteome activity landscapes of tumor cell lines determine drug responses. Nat Commun 2020; 11:3639. [PMID: 32686665 PMCID: PMC7371697 DOI: 10.1038/s41467-020-17336-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 06/22/2020] [Indexed: 01/02/2023] Open
Abstract
Integrated analysis of genomes, transcriptomes, proteomes and drug responses of cancer cell lines (CCLs) is an emerging approach to uncover molecular mechanisms of drug action. We extend this paradigm to measuring proteome activity landscapes by acquiring and integrating quantitative data for 10,000 proteins and 55,000 phosphorylation sites (p-sites) from 125 CCLs. These data are used to contextualize proteins and p-sites and predict drug sensitivity. For example, we find that Progesterone Receptor (PGR) phosphorylation is associated with sensitivity to drugs modulating estrogen signaling such as Raloxifene. We also demonstrate that Adenylate kinase isoenzyme 1 (AK1) inactivates antimetabolites like Cytarabine. Consequently, high AK1 levels correlate with poor survival of Cytarabine-treated acute myeloid leukemia patients, qualifying AK1 as a patient stratification marker and possibly as a drug target. We provide an interactive web application termed ATLANTiC (http://atlantic.proteomics.wzw.tum.de), which enables the community to explore the thousands of novel functional associations generated by this work.
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14
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Qu X, Zhao L, Zhang R, Wei Q, Wang M. Differential microRNA expression profiles associated with microsatellite status reveal possible epigenetic regulation of microsatellite instability in gastric adenocarcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:484. [PMID: 32395528 PMCID: PMC7210178 DOI: 10.21037/atm.2020.03.54] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Background Although microsatellite instability (MSI) is a powerful predictive biomarker for the efficacy of immunotherapy, the mechanism of MSI in sporadic gastrointestinal cancer is not fully understood. However, epigenetics, particularly microRNAs, has been suggested as one of the main regulators that contribute to the MSI formation. Methods We used microRNA expression data of 386 gastric adenocarcinoma samples from The Cancer Genome Atlas (TCGA) database to identify differential microRNA expression profiles by different MSI status. We also obtained putative common target genes of the top differential microRNAs with miRanda online tools, and we analyzed these data by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment (KEGG). Results We found that 56 and 67 gastric adenocarcinoma samples were positive for low and high MSI, respectively, and that a high MSI status was associated with age, sex and subregion (P=0.049, 0.014 and 0.007, respectively). In the 67 samples with a high MSI status, expression levels of 14 microRNAs were upregulated but five microRNAs were downregulated as assessed by the fold change (FC), compared with that of the 56 samples with a low MSI status (P<0.05, |FC| >2). Further analysis suggested that the expression of miR-210-3p, miR-582-3p, miR-30a-3p and miR-105-5p predicted a high MSI status (P=4.93×10−10, 5.63×10−10, 3.23×10−9 and 7.64×10−4, respectively). Regulation of the transcription pathways ranked the top of lists from both GO and KEGG analyses, and these microRNAs might regulate DNA damage-repair genes that were also associated with a high MSI status. Conclusions MiR-30a-3p and miR-105-5p are potential biomarkers for the MSI-H gastric adenocarcinoma, possibly by altering expression of DNA damage-repair genes.
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Affiliation(s)
- Xiaofei Qu
- Cancer institute, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Liqin Zhao
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Ruoxin Zhang
- Cancer institute, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Epidemiology and Biostatistics, Fudan University School of Public Health, Shanghai 200032, China
| | - Qingyi Wei
- Cancer institute, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Mengyun Wang
- Cancer institute, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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15
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Nano A, Bailis JM, Mariano NF, Pham ED, Threatt SD, Barton JK. Cell-Selective Cytotoxicity of a Fluorescent Rhodium Metalloinsertor Conjugate Results from Irreversible DNA Damage at Base Pair Mismatches. Biochemistry 2020; 59:717-726. [DOI: 10.1021/acs.biochem.9b01037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Adela Nano
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Julie M. Bailis
- Department of Oncology Research, Amgen Research, Amgen, Inc., South San Francisco, California 94080, United States
| | - Natalie F. Mariano
- Department of Oncology Research, Amgen Research, Amgen, Inc., South San Francisco, California 94080, United States
| | - Elizabeth D. Pham
- Department of Oncology Research, Amgen Research, Amgen, Inc., South San Francisco, California 94080, United States
| | - Stephanie D. Threatt
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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16
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Tsuboi M, Kondo K, Soejima S, Kajiura K, Kawakita N, Toba H, Kawakami Y, Yoshida M, Takizawa H, Tangoku A. Chromate exposure induces DNA hypermethylation of the mismatch repair gene MLH1 in lung cancer. Mol Carcinog 2019; 59:24-31. [PMID: 31579968 DOI: 10.1002/mc.23125] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 12/31/2022]
Abstract
Hexavalent chromium is recognized as a human carcinogen. Our previous studies revealed that lung cancer (LC) in chromate-exposed workers (chromate LC) had molecular features of frequent microsatellite instability (MSI), repression of MLH1 level, and aberrant DNA methylation of several tumor-suppressor genes, including MLH1. In the present study, we quantitatively investigated MLH1-promoter methylation status using bisulfite pyrosequencing of paired tumorous/nontumorous tissues from chromate and nonchromate LCs to determine the effect of chromate exposure on MLH1-promoter methylation. The methylation level of MLH1 promoter was significantly higher in chromate LC tumors (P < .001) than nonchromate LC tumors and, among chromate LC, significantly higher in tumorous tissue than nontumorous tissue (P = .004). Moreover, the methylation level of MLH1 promoter in normal lung tissue tended to be higher in chromate LC than nonchromate LC (P = .062). In addition, LC with reduced levels of MLH1 showed significantly higher methylation levels of MLH1 promoter than LC exhibiting normal MLH1 levels (P = .019). Moreover, immunohistochemical analyses determined that levels of SUV39H1, an H3K9me2-related methyltransferase, were higher in chromate LC than nonchromate LC (P = .076). Furthermore, we evaluated three DNA double-strand break-repair genes (MRE11, RAD50, and DNA-PKcs) as possible targets of MSI by fragment-length polymorphism analysis, revealing the mutation frequency of RAD50 as significantly higher in chromate LC than nonchromate LC (P = .047). These results suggest that chromate exposure might induce MLH1 hypermethylation in LC as a mechanism of chromate-induced carcinogenesis.
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Affiliation(s)
- Mitsuhiro Tsuboi
- Department of Thoracic, Endocrine Surgery and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Kazuya Kondo
- Department of Oncological Medical Services, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Shiho Soejima
- Department of Oncological Medical Services, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Koichiro Kajiura
- Department of Thoracic, Endocrine Surgery and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Naoya Kawakita
- Department of Thoracic, Endocrine Surgery and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Hiroaki Toba
- Department of Thoracic, Endocrine Surgery and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Yukikiyo Kawakami
- Department of Thoracic, Endocrine Surgery and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Mitsuteru Yoshida
- Department of Thoracic, Endocrine Surgery and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Hiromitsu Takizawa
- Department of Thoracic, Endocrine Surgery and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Akira Tangoku
- Department of Thoracic, Endocrine Surgery and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
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17
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Identification of gene expression levels in primary melanoma associated with clinically meaningful characteristics. Melanoma Res 2019; 28:380-389. [PMID: 29975213 DOI: 10.1097/cmr.0000000000000473] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Factors influencing melanoma survival include sex, age, clinical stage, lymph node involvement, as well as Breslow thickness, presence of tumor-infiltrating lymphocytes based on histological analysis of primary melanoma, mitotic rate, and ulceration. Identification of genes whose expression in primary tumors is associated with these key tumor/patient characteristics can shed light on molecular mechanisms of melanoma survival. Here, we show results from a gene expression analysis of formalin-fixed paraffin-embedded primary melanomas with extensive clinical annotation. The Cancer Genome Atlas data on primary melanomas were used for validation of nominally significant associations. We identified five genes that were significantly associated with the presence of tumor-infiltrating lymphocytes in the joint analysis after adjustment for multiple testing: IL1R2, PPL, PLA2G3, RASAL1, and SGK2. We also identified two genes significantly associated with melanoma metastasis to the regional lymph nodes (PIK3CG and IL2RA), and two genes significantly associated with sex (KDM5C and KDM6A). We found that LEF1 was significantly associated with Breslow thickness and CCNA2 and UBE2T with mitosis. RAD50 was the gene most significantly associated with survival, with a higher level of expression associated with worse survival.
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18
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Situ Y, Chung L, Lee CS, Ho V. MRN (MRE11-RAD50-NBS1) Complex in Human Cancer and Prognostic Implications in Colorectal Cancer. Int J Mol Sci 2019; 20:E816. [PMID: 30769804 PMCID: PMC6413120 DOI: 10.3390/ijms20040816] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/12/2019] [Accepted: 02/12/2019] [Indexed: 02/07/2023] Open
Abstract
The MRE11-RAD50-NBS1 (MRN) complex has been studied in multiple cancers. The identification of MRN complex mutations in mismatch repair (MMR)-defective cancers has sparked interest in its role in colorectal cancer (CRC). To date, there is evidence indicating a relationship of MRN expression with reduced progression-free survival, although the significance of the MRN complex in the clinical setting remains controversial. In this review, we present an overview of the function of the MRN complex, its role in cancer progression, and current evidence in colorectal cancer. The evidence indicates that the MRN complex has potential utilisation as a biomarker and as a putative treatment target to improve outcomes of colorectal cancer.
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Affiliation(s)
- Yiling Situ
- School of Medicine, Western Sydney University, Penrith, NSW 2751, Australia.
| | - Liping Chung
- School of Medicine, Western Sydney University, Penrith, NSW 2751, Australia.
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia.
| | - Cheok Soon Lee
- School of Medicine, Western Sydney University, Penrith, NSW 2751, Australia.
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia.
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia.
- Discipline of Pathology, School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia.
- Faculty of Medicine, South Western Sydney Clinical School, University of New South Wales, Liverpool, NSW 2170, Australia.
- Faculty of Medicine and Health, Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia.
| | - Vincent Ho
- School of Medicine, Western Sydney University, Penrith, NSW 2751, Australia.
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19
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The Tip of an Iceberg: Replication-Associated Functions of the Tumor Suppressor p53. Cancers (Basel) 2018; 10:cancers10080250. [PMID: 30060597 PMCID: PMC6115784 DOI: 10.3390/cancers10080250] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 12/13/2022] Open
Abstract
The tumor suppressor p53 is a transcriptional factor broadly mutated in cancer. Most inactivating and gain of function mutations disrupt the sequence-specific DNA binding domain, which activates target genes. This is perhaps the main reason why most research has focused on the relevance of such transcriptional activity for the prevention or elimination of cancer cells. Notwithstanding, transcriptional regulation may not be the only mechanism underlying its role in tumor suppression and therapeutic responses. In the past, a direct role of p53 in DNA repair transactions that include the regulation of homologous recombination has been suggested. More recently, the localization of p53 at replication forks has been demonstrated and the effect of p53 on nascent DNA elongation has been explored. While some data sets indicate that the regulation of ongoing replication forks by p53 may be mediated by p53 targets such as MDM2 (murine double minute 2) and polymerase (POL) eta other evidences demonstrate that p53 is capable of controlling DNA replication by directly interacting with the replisome and altering its composition. In addition to discussing such findings, this review will also analyze the impact that p53-mediated control of ongoing DNA replication has on treatment responses and tumor suppressor abilities of this important anti-oncogene.
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20
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Campanella NC, Lacerda CF, Berardinelli GN, Abrahão-Machado LF, Cruvinel-Carloni A, De Oliveira ATT, Scapulatempo-Neto C, Crema E, Adad SJ, Rodrigues MAM, Henry MACA, Guimarães DP, Reis RM. Presence of microsatellite instability in esophageal squamous cell carcinoma associated with chagasic megaesophagus. Biomark Med 2018; 12:573-582. [PMID: 29873509 DOI: 10.2217/bmm-2017-0329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
AIM The molecular pathogenesis of esophageal squamous cell carcinoma (ESCC) has been increasingly studied, but there is no report on the role of MSI in ESCC development associated with chagasic megaesophagus (CM).Results/methodology: In four ESCC/CM (4/19) we found microsatellite instability (MSI) alterations (21.1%), being three MSI-L (15.8%) and one MSI-H (5.3%). Four out of 35 ESCC cases showed MSI-L (11.4%) and only one out of 26 CM cases presented MSI-L (3.9%). The MSI-H was observed in an ESCC/CM patient that presents lack of MSH6 immunostaining corroborating deficiency in MMR pathway. Interestingly, the MSI-H ESCC/CM case also presented a deletion the HSP110 poly(T)17 gene. DISCUSSION/CONCLUSION Taking together, we concluded that MSI is a rare event in esophageal squamous cell carcinoma, but can be associated with CM.
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Affiliation(s)
- Nathália C Campanella
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Croider Franco Lacerda
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Department of Digestive Surgery, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | | | | | | | | | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Department of Pathology & Molecular Diagnostics, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Eduardo Crema
- Department of Digestive Surgery & Pathology, Medical School, UFTM -Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Sheila Jorge Adad
- Department of Digestive Surgery & Pathology, Medical School, UFTM -Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | | | | | - Denise Peixoto Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Department of Endoscopy, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Life & Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
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21
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Goumard C, Desbois-Mouthon C, Wendum D, Calmel C, Merabtene F, Scatton O, Praz F. Low Levels of Microsatellite Instability at Simple Repeated Sequences Commonly Occur in Human Hepatocellular Carcinoma. Cancer Genomics Proteomics 2018; 14:329-339. [PMID: 28871000 DOI: 10.21873/cgp.20043] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/07/2017] [Accepted: 07/12/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND/AIM The aim of this study was to assess the incidence of MSI in a large series of human hepatocellular carcinomas (HCC) with various etiologies. MATERIALS AND METHODS The MSI status was determined by polymerase chain reaction (PCR) using 5 mononucleotide and 13 CAn dinucleotide repeats. RESULTS None of the 122 HCC samples displayed an MSI-High phenotype, as defined by the presence of alterations at more than 30% of the microsatellite markers analyzed. Yet, limited microsatellite instability consisting in the insertion or deletion of a few repeat motifs was detected in 32 tumor samples (26.2%), regardless of the etiology of the underlying liver disease. MSI tended to be higher in patients with cirrhosis (p=0.051), possibly reflecting an impact of the inflammatory context in this process. CONCLUSION Based on a large series of HCC with various etiologies, our study allowed us to definitely conclude that MSI is not a hallmark of HCC.
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Affiliation(s)
- Claire Goumard
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | - Christele Desbois-Mouthon
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | - Dominique Wendum
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France.,APHP, Hôpital Saint-Antoine, Service d'Anatomie Pathologique, Paris, France
| | - Claire Calmel
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | - Fatiha Merabtene
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France.,Plateforme d'Histomorphologie Saint-Antoine, UMS 30, Paris, France
| | - Olivier Scatton
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France.,APHP, Hôpital Saint-Antoine, Service de Chirurgie Hépatobiliaire, Paris, France
| | - Françoise Praz
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France
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22
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Curigliano G. Targeting DNA Repair. Handb Exp Pharmacol 2018; 249:161-180. [PMID: 30341723 DOI: 10.1007/164_2017_31] [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] [Indexed: 06/08/2023]
Abstract
Genomic instability is a characteristic of most human cancers and plays critical roles in both cancer development and progression. There are various forms of genomic instability arising from many different pathways, such as DNA damage from endogenous and exogenous sources, centrosome amplification, telomere damage, and epigenetic modifications. DNA-repair pathways can enable tumor cells to survive DNA damage. The failure to respond to DNA damage is a characteristic associated with genomic instability. Understanding of genomic instability in cancer is still very limited, but the further understanding of the molecular mechanisms through which the DNA damage response (DDR) operates, in combination with the elucidation of the genetic interactions between DDR pathways and other cell pathways, will provide therapeutic opportunities for the personalized medicine of cancer.
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Affiliation(s)
- Giuseppe Curigliano
- Early Drug Development for Innovative Therapy Division, European Institute of Oncology, Via Ripamonti, 435 20141, Milan, Italy.
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23
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Arivazhagan R, Lee J, Bayarsaikhan D, Kwak P, Son M, Byun K, Salekdeh GH, Lee B. MicroRNA-340 inhibits the proliferation and promotes the apoptosis of colon cancer cells by modulating REV3L. Oncotarget 2017; 9:5155-5168. [PMID: 29435169 PMCID: PMC5797040 DOI: 10.18632/oncotarget.23703] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 12/05/2017] [Indexed: 11/25/2022] Open
Abstract
DNA Directed Polymerase Zeta Catalytic Subunit (REV3L) has recently emerged as an important oncogene. Although the expressions of REV3L are similar in normal and cancer cells, several mutations in REV3L have been shown to play important roles in cancer. These mutations cause proteins misfolding and mislocalization, which in turn alters their interactions and biological functions. miRNAs play important regulatory roles during the progression and metastasis of several human cancers. This study was undertaken to determine how changes in the location and interactions of REV3L regulate colon cancer progression. REV3L protein mislocalization confirmed from the immunostaining results and the known interactions of REV3L was found to be broken as seen from the PLA assay results. The mislocalized REV3L might interact with new proteins partners in the cytoplasm which in turn may play role in regulating colon cancer progression. hsa-miR-340 (miR-340), a microRNA down-regulated in colon cancer, was used to bind to and downregulate REV3L, and found to control the proliferation and induce the apoptosis of colon cancer cells (HCT-116 and DLD-1) via the MAPK pathway. Furthermore, this down-regulation of REV3L also diminished colon cancer cell migration, and down-regulated MMP-2 and MMP-9. Combined treatment of colon cancer cells with miR-340 and 5-FU enhanced the inhibitory effects of 5-FU. In addition, in vivo experiments conducted on nude mice revealed tumor sizes were smaller in a HCT-116-miR-340 injected group than in a HCT-116-pCMV injected group. Our findings suggest mutations in REV3L causes protein mislocalization to the cytoplasm, breaking its interaction and is believed to form new protein interactions in cytoplasm contributing to colon cancer progression. Accordingly, microRNA-340 appears to be a good candidate for colon cancer therapy.
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Affiliation(s)
- Roshini Arivazhagan
- Center for Genomics and Proteomics, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Republic of Korea
| | - Jaesuk Lee
- Center for Genomics and Proteomics, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Republic of Korea
| | - Delger Bayarsaikhan
- Center for Genomics and Proteomics, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Republic of Korea
| | - Peter Kwak
- Center for Genomics and Proteomics, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Republic of Korea
| | - Myeongjoo Son
- Center for Genomics and Proteomics, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Republic of Korea.,Department of Anatomy and Cell Biology, Gachon University Graduate School of Medicine, Incheon, Republic of Korea
| | - Kyunghee Byun
- Center for Genomics and Proteomics, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Republic of Korea.,Department of Anatomy and Cell Biology, Gachon University Graduate School of Medicine, Incheon, Republic of Korea
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Molecular Sciences, Macquarie University Sydney, New South Wales, Australia
| | - Bonghee Lee
- Center for Genomics and Proteomics, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Republic of Korea.,Department of Anatomy and Cell Biology, Gachon University Graduate School of Medicine, Incheon, Republic of Korea
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24
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Early Postoperative Low Expression of RAD50 in Rectal Cancer Patients Associates with Disease-Free Survival. Cancers (Basel) 2017; 9:cancers9120163. [PMID: 29189711 PMCID: PMC5742811 DOI: 10.3390/cancers9120163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Molecular biomarkers have the potential to predict response to the treatment of rectal cancer. In this study, we aimed to evaluate the prognostic and clinicopathological implication of RAD50 (DNA repair protein RAD50 homolog) expression in rectal cancer. METHODS A total of 266 rectal cancer patients who underwent surgery and received chemo- and radiotherapy between 2000 and 2011 were involved in the study. Postoperative RAD50 expression was determined by immunohistochemistry in surgical samples (n = 266). RESULTS Using Kaplan-Meier survival analysis, we found that low RAD50 expression in postoperative samples was associated with worse disease free survival (p = 0.001) and overall survival (p < 0.001) in early stage/low-grade tumors. In a comparison of patients with low vs. high RAD50 expression, we found that low levels of postoperative RAD50 expression in rectal cancer tissues were significantly associated with perineural invasion (p = 0.002). CONCLUSION Expression of RAD50 in rectal cancer may serve as a prognostic biomarker for long-term survival of patients with perineural invasion-positive tumors and for potential use in early stage and low-grade rectal cancer assessment.
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25
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MacKay HJ, Levine DA, Bae-Jump VL, Bell DW, McAlpine JN, Santin A, Fleming GF, Mutch DG, Nephew KP, Wentzensen N, Goodfellow PJ, Dorigo O, Nijman HW, Broaddus R, Kohn EC. Moving forward with actionable therapeutic targets and opportunities in endometrial cancer: NCI clinical trials planning meeting report on identifying key genes and molecular pathways for targeted endometrial cancer trials. Oncotarget 2017; 8:84579-84594. [PMID: 29137450 PMCID: PMC5663622 DOI: 10.18632/oncotarget.19961] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/15/2017] [Indexed: 12/21/2022] Open
Abstract
The incidence and mortality rates from endometrial cancer are increasing. There have been no new drugs approved for the treatment of endometrial cancer in decades. The National Cancer Institute, Gynecologic Cancer Steering Committee identified the integration of molecular and/or histologic stratification into endometrial cancer management as a top strategic priority. Based on this, they convened a group of experts to review the molecular data in this disease. Here we report on the actionable opportunities and therapeutic directions identified for incorporation into future clinical trials.
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Affiliation(s)
- Helen J. MacKay
- Division of Medical Oncology & Hematology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Douglas A. Levine
- Division of Gynecologic Cancer, Department of OB/GYN, NYU Langone Laura and Isaac Perlmutter Cancer Center, New York, NY, United States
| | - Victoria L. Bae-Jump
- Division of Gynecologic Oncology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, CA, United States
| | - Daphne W. Bell
- Reproductive Cancer Genetics Section, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute/NIH, MSC 8000, Bethesda, ML, United States
| | - Jessica N. McAlpine
- University of British Columbia & BC Cancer Agency, Division of Gynecologic Oncology, Vancouver, British Columbia, Canada
| | - Alessandro Santin
- Department of Gynecology, Obstetrics and Reproductive Sciences, Yale School of Medicine, New Haven, CT, United States
| | - Gini F. Fleming
- Section of Hematology-Oncology, Department of Medicine, The University of Chicago, Chicago, IL, United States
| | - David G. Mutch
- Department of Obstetrics & Gynecology, Washington University School of Medicine, St. Louis, MO, United States
| | - Kenneth P. Nephew
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN, United States
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, ML, United States
| | - Paul J. Goodfellow
- James Comprehensive Cancer Center and The Department of Obstetrics and Gynecology, Ohio State University, Columbus, OH, United States
| | - Oliver Dorigo
- Division Gynecologic Oncology, Department of Obstetrics and Gynecology, Stanford, CA, United States
| | - Hans W. Nijman
- Department of Gynecology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Russell Broaddus
- Department of Pathology, Unit 85, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Elise C. Kohn
- Clinical Investigations Branch of The Cancer Therapy Evaluation Program, National Cancer Institute, Rockville, ML, United States
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26
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Campanella NC, Scapulatempo-Neto C, Abrahão-Machado LF, Torres De Oliveira AT, Berardinelli GN, Guimarães DP, Reis RM. Lack of microsatellite instability in gastrointestinal stromal tumors. Oncol Lett 2017; 14:5221-5228. [PMID: 29113157 PMCID: PMC5662911 DOI: 10.3892/ol.2017.6884] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/09/2017] [Indexed: 12/18/2022] Open
Abstract
The microsatellite instability (MSI) phenotype may constitute an important biomarker for patient response to immunotherapy, particularly to anti-programmed death-1 inhibitors. MSI is a type of genomic instability caused by a defect in DNA mismatch repair (MMR) proteins, which is present mainly in colorectal cancer and its hereditary form, hereditary nonpolyposis colorectal cancer. Gastrointestinal stromal tumor (GIST) development is associated with activating mutations of KIT proto-oncogene receptor tyrosine kinase (KIT) or platelet-derived growth factor receptor α (PDGFRA), which are oncogenes that predict the response to imatinib mesylate. In addition to KIT/PDGFRA mutations, other molecular alterations are important in GIST development. In GISTs, the characterization of the MSI phenotype is scarce and the results are not consensual. The present study aimed to assess MSI in a series of 79 GISTs. The evaluation of MSI was performed by pentaplex polymerase chain reaction comprising five markers, followed by capillary electrophoresis. The expression of MMR proteins was evaluated by immunohistochemistry. Regarding the KIT/PDGFRA/B-Raf proto-oncogene, serine/threonine kinase molecular profile of the 79 GISTs, 83.6% of the tumors possessed KIT mutations, 10.1% had PDGFRA mutations and 6.3% were triple wild-type. The mutated-PDGFRA cases were associated with gastric location and a lower mitotic index compared with KIT-mutated and wild-types, and these patients were more likely to be alive and without cancer. MSI analysis identified 4 cases with instability in one marker, however, additional evaluation of normal tissue and immunohistochemical staining of MMR proteins confirmed their microsatellite-stable nature. The results of the present study indicated that MSI is not involved in GIST tumorigenesis and, therefore, cannot serve as a biomarker to immunotherapy response in GIST.
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Affiliation(s)
- Nathália C Campanella
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
| | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
| | | | | | - Gustavo N Berardinelli
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
| | - Denise Peixoto Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil.,Department of Endoscopy, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
| | - Rui M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil.,Life and Health Sciences Research Institute, Health Sciences School, University of Minho, Guimarães, Braga 4704-553, Portugal.,Life and Health Sciences Research Institute/3B's-PT Government Associate Laboratory, University of Minho, Guimarães, Braga 4704-553, Portugal
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27
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Meunier K, Ferron M, Calmel C, Fléjou JF, Pocard M, Praz F. Impact of MLH1 expression on tumor evolution after curative surgical tumor resection in a murine orthotopic xenograft model for human MSI colon cancer. Genes Chromosomes Cancer 2017; 56:681-690. [PMID: 28512763 DOI: 10.1002/gcc.22472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 04/27/2017] [Accepted: 04/27/2017] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancers (CRCs) displaying microsatellite instability (MSI) most often result from MLH1 deficiency. The aim of this study was to assess the impact of MLH1 expression per se on tumor evolution after curative surgical resection using a xenograft tumor model. Transplantable tumors established with the human MLH1-deficient HCT116 cell line and its MLH1-complemented isogenic clone, mlh1-3, were implanted onto the caecum of NOD/SCID mice. Curative surgical resection was performed at day 10 in half of the animals. The HCT116-derived tumors were more voluminous compared to the mlh1-3 ones (P = .001). Lymph node metastases and peritoneal carcinomatosis occurred significantly more often in the group of mice grafted with HCT116 (P = .007 and P = .035, respectively). Mlh1-3-grafted mice did not develop peritoneal carcinomatosis or liver metastasis. After surgical resection, lymph node metastases only arose in the group of mice implanted with HCT116 and the rate of cure was significantly lower than in the mlh1-3 group (P = .047). The murine orthotopic xenograft model based on isogenic human CRC cell lines allowed us to reveal the impact of MLH1 expression on tumor evolution in mice who underwent curative surgical resection and in mice whose tumor was left in situ. Our data indicate that the behavior of MLH1-deficient CRC is not only governed by mutations arising in genes harboring microsatellite repeated sequences but also from their defect in MLH1 as such.
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Affiliation(s)
- Katy Meunier
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | - Marianne Ferron
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | - Claire Calmel
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | - Jean-François Fléjou
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Service d'Anatomie Pathologique, Paris, France
| | - Marc Pocard
- Digestive and Oncology Surgery Department, Assistance Publique - Hôpitaux de Paris, Hôpital Lariboisière, Paris, France.,Paris Diderot University, USPC, Sorbonne Paris Cité, Paris, France.,INSERM UMR 965, Angiogenesis and Translational Research Department, Hôpital Lariboisière, Paris, France
| | - Françoise Praz
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France
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28
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Locatelli M, Curigliano G. Targeting Genome Instability and DNA Repair. Breast Cancer 2017. [DOI: 10.1007/978-3-319-48848-6_68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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29
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Involvement of MBD4 inactivation in mismatch repair-deficient tumorigenesis. Oncotarget 2016; 6:42892-904. [PMID: 26503472 PMCID: PMC4767479 DOI: 10.18632/oncotarget.5740] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/18/2015] [Indexed: 12/14/2022] Open
Abstract
The DNA glycosylase gene MBD4 safeguards genomic stability at CpG sites and is frequently mutated at coding poly-A tracks in mismatch repair (MMR)-defective colorectal tumors (CRC). Mbd4 biallelic inactivation in mice provided conflicting results as to its role in tumorigenesis. Thus, it is unclear whether MBD4 alterations are only secondary to MMR defects without functional consequences or can contribute to the mutator phenotype. We investigated MBD4 variants in a large series of hereditary/familial and sporadic CRC cases. Whereas MBD4 frameshifts were only detected in tumors, missense variants were found in both normal and tumor DNA. In CRC with double-MBD4/MMR and single-MBD4 variants, transition mutation frequency was increased, indicating that MBD4 defects may affect the mutational landscape independently of MMR defect. Mbd4-deficient mice showed reduced survival when combined with Mlh1−/− genotype. Taken together, these data suggest that MBD4 inactivation may contribute to tumorigenesis, acting as a modifier of MMR-deficient cancer phenotype.
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30
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Single-cell SNP analyses and interpretations based on RNA-Seq data for colon cancer research. Sci Rep 2016; 6:34420. [PMID: 27677461 PMCID: PMC5039670 DOI: 10.1038/srep34420] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/13/2016] [Indexed: 01/26/2023] Open
Abstract
Single-cell sequencing is useful for illustrating the cellular heterogeneities inherent in many intricate biological systems, particularly in human cancer. However, owing to the difficulties in acquiring, amplifying and analyzing single-cell genetic material, obstacles remain for single-cell diversity assessments such as single nucleotide polymorphism (SNP) analyses, rendering biological interpretations of single-cell omics data elusive. We used RNA-Seq data from single-cell and bulk colon cancer samples to analyze the SNP profiles for both structural and functional comparisons. Colon cancer-related pathways with single-cell level SNP enrichment, including the TGF-β and p53 signaling pathways, were also investigated based on both their SNP enrichment patterns and gene expression. We also detected a certain number of fusion transcripts, which may promote tumorigenesis, at the single-cell level. Based on these results, single-cell analyses not only recapitulated the SNP analysis results from the bulk samples but also detected cell-to-cell and cell-to-bulk variations, thereby aiding in early diagnosis and in identifying the precise mechanisms underlying cancers at the single-cell level.
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31
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Adam R, Spier I, Zhao B, Kloth M, Marquez J, Hinrichsen I, Kirfel J, Tafazzoli A, Horpaopan S, Uhlhaas S, Stienen D, Friedrichs N, Altmüller J, Laner A, Holzapfel S, Peters S, Kayser K, Thiele H, Holinski-Feder E, Marra G, Kristiansen G, Nöthen MM, Büttner R, Möslein G, Betz RC, Brieger A, Lifton RP, Aretz S. Exome Sequencing Identifies Biallelic MSH3 Germline Mutations as a Recessive Subtype of Colorectal Adenomatous Polyposis. Am J Hum Genet 2016; 99:337-51. [PMID: 27476653 DOI: 10.1016/j.ajhg.2016.06.015] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/14/2016] [Indexed: 12/20/2022] Open
Abstract
In ∼30% of families affected by colorectal adenomatous polyposis, no germline mutations have been identified in the previously implicated genes APC, MUTYH, POLE, POLD1, and NTHL1, although a hereditary etiology is likely. To uncover further genes with high-penetrance causative mutations, we performed exome sequencing of leukocyte DNA from 102 unrelated individuals with unexplained adenomatous polyposis. We identified two unrelated individuals with differing compound-heterozygous loss-of-function (LoF) germline mutations in the mismatch-repair gene MSH3. The impact of the MSH3 mutations (c.1148delA, c.2319-1G>A, c.2760delC, and c.3001-2A>C) was indicated at the RNA and protein levels. Analysis of the diseased individuals' tumor tissue demonstrated high microsatellite instability of di- and tetranucleotides (EMAST), and immunohistochemical staining illustrated a complete loss of nuclear MSH3 in normal and tumor tissue, confirming the LoF effect and causal relevance of the mutations. The pedigrees, genotypes, and frequency of MSH3 mutations in the general population are consistent with an autosomal-recessive mode of inheritance. Both index persons have an affected sibling carrying the same mutations. The tumor spectrum in these four persons comprised colorectal and duodenal adenomas, colorectal cancer, gastric cancer, and an early-onset astrocytoma. Additionally, we detected one unrelated individual with biallelic PMS2 germline mutations, representing constitutional mismatch-repair deficiency. Potentially causative variants in 14 more candidate genes identified in 26 other individuals require further workup. In the present study, we identified biallelic germline MSH3 mutations in individuals with a suspected hereditary tumor syndrome. Our data suggest that MSH3 mutations represent an additional recessive subtype of colorectal adenomatous polyposis.
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Affiliation(s)
- Ronja Adam
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Isabel Spier
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Bixiao Zhao
- Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Michael Kloth
- Institute of Pathology, University of Cologne, 50937 Cologne, Germany
| | - Jonathan Marquez
- Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Inga Hinrichsen
- Medical Clinic 1, Biomedical Research Laboratory, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Jutta Kirfel
- Institute of Pathology, University of Bonn, 53127 Bonn, Germany
| | - Aylar Tafazzoli
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany
| | - Sukanya Horpaopan
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Chiang Mai 50200, Thailand
| | - Siegfried Uhlhaas
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Dietlinde Stienen
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | | | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50937 Cologne, Germany; Institute of Human Genetics, University of Cologne, 50937 Cologne, Germany
| | - Andreas Laner
- Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, 80336 Munich, Germany; Medical Genetics Center, 80335 Munich, Germany
| | - Stefanie Holzapfel
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Katrin Kayser
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, 50937 Cologne, Germany
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, 80336 Munich, Germany; Medical Genetics Center, 80335 Munich, Germany
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany
| | - Reinhard Büttner
- Institute of Pathology, University of Cologne, 50937 Cologne, Germany
| | - Gabriela Möslein
- HELIOS Klinikum Wuppertal, University of Witten/Herdecke, 42283 Wuppertal, Germany
| | - Regina C Betz
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany
| | - Angela Brieger
- Medical Clinic 1, Biomedical Research Laboratory, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Richard P Lifton
- Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany.
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Chabanon RM, Pedrero M, Lefebvre C, Marabelle A, Soria JC, Postel-Vinay S. Mutational Landscape and Sensitivity to Immune Checkpoint Blockers. Clin Cancer Res 2016; 22:4309-21. [PMID: 27390348 DOI: 10.1158/1078-0432.ccr-16-0903] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 05/31/2016] [Indexed: 11/16/2022]
Abstract
Immunotherapy is currently transforming cancer treatment. Notably, immune checkpoint blockers (ICB) have shown unprecedented therapeutic successes in numerous tumor types, including cancers that were traditionally considered as nonimmunogenic. However, a significant proportion of patients do not respond to these therapies. Thus, early selection of the most sensitive patients is key, and the development of predictive companion biomarkers constitutes one of the biggest challenges of ICB development. Recent publications have suggested that the tumor genomic landscape, mutational load, and tumor-specific neoantigens are potential determinants of the response to ICB and can influence patients' outcomes upon immunotherapy. Furthermore, defects in the DNA repair machinery have consistently been associated with improved survival and durable clinical benefit from ICB. Thus, closely reflecting the DNA damage repair capacity of tumor cells and their intrinsic genomic instability, the mutational load and its associated tumor-specific neoantigens appear as key predictive paths to anticipate potential clinical benefits of ICB. In the era of next-generation sequencing, while more and more patients are getting the full molecular portrait of their tumor, it is crucial to optimally exploit sequencing data for the benefit of patients. Therefore, sequencing technologies, analytic tools, and relevant criteria for mutational load and neoantigens prediction should be homogenized and combined in more integrative pipelines to fully optimize the measurement of such parameters, so that these biomarkers can ultimately reach the analytic validity and reproducibility required for a clinical implementation. Clin Cancer Res; 22(17); 4309-21. ©2016 AACR.
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Affiliation(s)
- Roman M Chabanon
- Faculté de Médicine, Université Paris Saclay, Université Paris-Sud, Le Kremlin Bicêtre, France. Inserm Unit U981, Gustave Roussy, Villejuif, France
| | | | - Céline Lefebvre
- Faculté de Médicine, Université Paris Saclay, Université Paris-Sud, Le Kremlin Bicêtre, France. Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Aurélien Marabelle
- DITEP (Département d'Innovations Thérapeutiques et Essais Précoces), Gustave Roussy, Villejuif, France. Inserm Unit U1015, Gustave Roussy, Villejuif, France
| | - Jean-Charles Soria
- Faculté de Médicine, Université Paris Saclay, Université Paris-Sud, Le Kremlin Bicêtre, France. Inserm Unit U981, Gustave Roussy, Villejuif, France. DITEP (Département d'Innovations Thérapeutiques et Essais Précoces), Gustave Roussy, Villejuif, France
| | - Sophie Postel-Vinay
- Faculté de Médicine, Université Paris Saclay, Université Paris-Sud, Le Kremlin Bicêtre, France. Inserm Unit U981, Gustave Roussy, Villejuif, France. DITEP (Département d'Innovations Thérapeutiques et Essais Précoces), Gustave Roussy, Villejuif, France.
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Coveler AL, Richard P, Apisarnthanarax S, Chiorean EG. Is There a Best Radiosensitizing Agent in the Treatment of Locally Advanced Rectal Cancer? CURRENT COLORECTAL CANCER REPORTS 2016. [DOI: 10.1007/s11888-016-0324-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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34
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Jiang C, Starr S, Chen F, Wu J. Low-fidelity alternative DNA repair carcinogenesis theory may interpret many cancer features and anticancer strategies. Future Oncol 2016; 12:1897-910. [PMID: 27166654 DOI: 10.2217/fon-2016-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have proposed that the low-fidelity compensatory backup alternative DNA repair pathways drive multistep carcinogenesis. Here, we apply it to interpret the clinical features of cancer, such as mutator phenotype, tissue specificity, age specificity, diverse types of cancers originated from the same type of tissue, cancer susceptibility of patients with DNA repair-defective syndromes, development of cancer only for a selected number of individuals among those that share the same genetic defect, invasion and metastasis. Clinically, the theory predicts that to improve the efficacy of molecular targeted or synthetic lethal therapy, it may be crucial to inhibit the low-fidelity compensatory alternative DNA repair either directly or by blocking the signal transducers of the sustained microenvironmental stress.
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Affiliation(s)
- Chuo Jiang
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai 200444, China.,Central Laboratories, Xuhui Central Hospital, Shanghai Clinical Center, Chinese Academy of Sciences, 966 Middle Huaihai Road, Shanghai 200031, China
| | - Shane Starr
- Department of Pathology & Laboratory Medicine, Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, USA and currently Flint Medical Laboratory, 3490 Calkins Road, Flint, MI 48532, USA
| | - Fuxue Chen
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Jiaxi Wu
- Central Laboratories, Xuhui Central Hospital, Shanghai Clinical Center, Chinese Academy of Sciences, 966 Middle Huaihai Road, Shanghai 200031, China.,Department of Pathology & Laboratory Medicine, Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, USA and currently Flint Medical Laboratory, 3490 Calkins Road, Flint, MI 48532, USA
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Ferguson LR, Chen H, Collins AR, Connell M, Damia G, Dasgupta S, Malhotra M, Meeker AK, Amedei A, Amin A, Ashraf SS, Aquilano K, Azmi AS, Bhakta D, Bilsland A, Boosani CS, Chen S, Ciriolo MR, Fujii H, Guha G, Halicka D, Helferich WG, Keith WN, Mohammed SI, Niccolai E, Yang X, Honoki K, Parslow VR, Prakash S, Rezazadeh S, Shackelford RE, Sidransky D, Tran PT, Yang ES, Maxwell CA. Genomic instability in human cancer: Molecular insights and opportunities for therapeutic attack and prevention through diet and nutrition. Semin Cancer Biol 2015; 35 Suppl:S5-S24. [PMID: 25869442 PMCID: PMC4600419 DOI: 10.1016/j.semcancer.2015.03.005] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 03/08/2015] [Accepted: 03/13/2015] [Indexed: 02/06/2023]
Abstract
Genomic instability can initiate cancer, augment progression, and influence the overall prognosis of the affected patient. Genomic instability arises from many different pathways, such as telomere damage, centrosome amplification, epigenetic modifications, and DNA damage from endogenous and exogenous sources, and can be perpetuating, or limiting, through the induction of mutations or aneuploidy, both enabling and catastrophic. Many cancer treatments induce DNA damage to impair cell division on a global scale but it is accepted that personalized treatments, those that are tailored to the particular patient and type of cancer, must also be developed. In this review, we detail the mechanisms from which genomic instability arises and can lead to cancer, as well as treatments and measures that prevent genomic instability or take advantage of the cellular defects caused by genomic instability. In particular, we identify and discuss five priority targets against genomic instability: (1) prevention of DNA damage; (2) enhancement of DNA repair; (3) targeting deficient DNA repair; (4) impairing centrosome clustering; and, (5) inhibition of telomerase activity. Moreover, we highlight vitamin D and B, selenium, carotenoids, PARP inhibitors, resveratrol, and isothiocyanates as priority approaches against genomic instability. The prioritized target sites and approaches were cross validated to identify potential synergistic effects on a number of important areas of cancer biology.
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Affiliation(s)
| | - Helen Chen
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, Canada
| | - Andrew R Collins
- Department of Nutrition, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marisa Connell
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, Canada
| | - Giovanna Damia
- Department of Oncology, Instituti di Ricovero e Cura a Carattere Scientifico-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Santanu Dasgupta
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, United States
| | | | - Alan K Meeker
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Amr Amin
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates; Faculty of Science, Cairo University, Cairo, Egypt
| | - S Salman Ashraf
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Katia Aquilano
- Department of Biology, Università di Roma Tor Vergata, Rome, Italy
| | - Asfar S Azmi
- Department of Biology, University of Rochester, Rochester, United States
| | - Dipita Bhakta
- School of Chemical and BioTechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | - Alan Bilsland
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Chandra S Boosani
- Department of BioMedical Sciences, Creighton University, Omaha, NE, United States
| | - Sophie Chen
- Department of Research & Development, Ovarian and Prostate Cancer Research Trust Laboratory, Guildford, Surrey, United Kingdom
| | | | - Hiromasa Fujii
- Department of Orthopaedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Gunjan Guha
- School of Chemical and BioTechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | | | - William G Helferich
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - W Nicol Keith
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sulma I Mohammed
- Department of Comparative Pathobiology and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States
| | - Elena Niccolai
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Xujuan Yang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Kanya Honoki
- Department of Orthopaedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | | | - Satya Prakash
- School of Pharmacy, University College Cork, Cork, Ireland
| | - Sarallah Rezazadeh
- Department of Biology, University of Rochester, Rochester, United States
| | - Rodney E Shackelford
- Department of Pathology, Louisiana State University Health Shreveport, Shreveport, LA, United States
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Phuoc T Tran
- Departments of Radiation Oncology & Molecular Radiation Sciences, Oncology and Urology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Eddy S Yang
- Department of Radiation Oncology, University of Alabama at Birmingham School of Medicine, Birmingham, AL, United States
| | - Christopher A Maxwell
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, Canada.
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Du Q, Luu PL, Stirzaker C, Clark SJ. Methyl-CpG-binding domain proteins: readers of the epigenome. Epigenomics 2015; 7:1051-73. [DOI: 10.2217/epi.15.39] [Citation(s) in RCA: 265] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
How DNA methylation is interpreted and influences genome regulation remains largely unknown. Proteins of the methyl-CpG-binding domain (MBD) family are primary candidates for the readout of DNA methylation as they recruit chromatin remodelers, histone deacetylases and methylases to methylated DNA associated with gene repression. MBD protein binding requires both functional MBD domains and methyl-CpGs; however, some MBD proteins also bind unmethylated DNA and active regulatory regions via alternative regulatory domains or interaction with the nucleosome remodeling deacetylase (NuRD/Mi-2) complex members. Mutations within MBD domains occur in many diseases, including neurological disorders and cancers, leading to loss of MBD binding specificity to methylated sites and gene deregulation. Here, we summarize the current state of knowledge about MBD proteins and their role as readers of the epigenome.
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Affiliation(s)
- Qian Du
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Phuc-Loi Luu
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- St Vincent's Clinical School, University of NSW, Darlinghurst, NSW 2010, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- St Vincent's Clinical School, University of NSW, Darlinghurst, NSW 2010, Australia
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Wu J, Starr S. Low-fidelity compensatory backup alternative DNA repair pathways may unify current carcinogenesis theories. Future Oncol 2015; 10:1239-53. [PMID: 24947263 DOI: 10.2217/fon.13.272] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The somatic mutation carcinogenesis theory has dominated for decades. The alternative theory, tissue organization field theory, argues that the development of cancer is determined by the surrounding microenvironment. However, neither theory can explain all features of cancer. As cancers share the features of uncontrolled proliferation and genomic instability, they are likely to have the same pathogenesis. It has been found that various DNA repair pathways within a cell crosstalk with one another, forming a DNA repair network. When one DNA repair pathways is defective, the others may work as compensatory backups. The latter pathways are explored for synthetic lethal anticancer therapy. In this article, we extend the concept of compensatory alternative DNA repair to unify the theories. We propose that the microenvironmental stress can activate low-fidelity compensatory alternative DNA repair, causing mutations. If the mutation occurs to a DNA repair gene, this secondarily mutated gene can lead to even more mutated genes, including those related to other DNA repair pathways, eventually destabilizing the genome. Therefore, the low-fidelity compensatory alternative DNA repair may mediate microenvironment-dependent carcinogenesis. The proposal seems consistent with the view of evolution: the environmental stress causes mutations to adapt to the changing environment.
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Affiliation(s)
- Jiaxi Wu
- Central Laboratories, Xuhui Central Hospital, Shanghai Clinical Research Center, Chinese Academy of Sciences, 966 Middle Huaihai Road, Shanghai 200031, China
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38
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Campanella NC, Penna V, Ribeiro G, Abrah�o-Machado LF, Scapulatempo-Neto C, Reis RM. Absence of Microsatellite Instability In Soft Tissue Sarcomas. Pathobiology 2015; 82:36-42. [DOI: 10.1159/000369906] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 11/14/2014] [Indexed: 11/19/2022] Open
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Genther Williams SM, Kuznicki AM, Andrade P, Dolinski BM, Elbi C, O’Hagan RC, Toniatti C. Treatment with the PARP inhibitor, niraparib, sensitizes colorectal cancer cell lines to irinotecan regardless of MSI/MSS status. Cancer Cell Int 2015; 15:14. [PMID: 25685067 PMCID: PMC4326439 DOI: 10.1186/s12935-015-0162-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/14/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Cells with homologous recombination (HR) deficiency, most notably caused by mutations in the BRCA1 or BRCA2 genes, are sensitive to PARP inhibition. Microsatellite instability (MSI) accounts for 10-15% of colorectal cancer (CRC) and is hypothesized to lead to HR defects due to altered expression of Mre11, a protein required for double strand break (DSB) repair. Indeed, others have reported that PARP inhibition is efficacious in MSI CRC. METHODS Here we examine the response to niraparib, a potent PARP-1/PARP-2 inhibitor currently under clinical evaluation, in MSI versus microsatellite stable (MSS) CRC cell lines in vitro and in vivo. We compiled a large panel of MSI and MSS CRC cell lines and evaluated the anti-proliferative activity of niraparib. In addition to testing single agent cytotoxic activity of niraparib, we also tested irinotecan (or SN-38, the active metabolite of irinotecan) activity alone and in combination with niraparib in vitro and in vivo. RESULTS In contrast to earlier reports, MSI CRC cell lines were not more sensitive to niraparib than MSS CRC cell lines¸ suggesting that the MSI phenotype does not sensitize CRC cell lines to PARP inhibition. Moreover, even the most sensitive MSI cell lines had niraparib EC50s greater than 10 fold higher than BRCA-deficient cell lines. However, MSI lines were more sensitive to SN-38 than MSS lines, consistent with previous findings. We have also demonstrated that combination of niraparib and irinotecan was more efficacious than either agent alone in both MSI and MSS cell lines both in vitro and in vivo, and that niraparib potentiates the effect of irinotecan regardless of MSI status. CONCLUSIONS Our results support the clinical evaluation of this combination in all CRC patients, regardless of MSI status.
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Affiliation(s)
- Sybil M Genther Williams
- />Department of Oncology, Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115 USA
| | - Apryle M Kuznicki
- />Department of In Vivo Pharmacology, Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115 USA
| | - Paula Andrade
- />Department of In Vivo Pharmacology, Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115 USA
| | - Brian M Dolinski
- />Department of Oncology, Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115 USA
| | - Cem Elbi
- />Department of Oncology, Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115 USA
- />Current address: Bayer HealthCare, 100 Bayer Road, Whippany, NJ 07891 USA
| | - Ronan C O’Hagan
- />Department of Oncology, Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115 USA
| | - Carlo Toniatti
- />Department of Oncology, Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115 USA
- />Current address: Institute for Applied Cancer Science, 1901 East Road, Unit 1956, Room 4SCR6.1009, Houston, TX 77005 USA
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Pavelitz T, Renfro L, Foster NR, Caracol A, Welsch P, Lao VV, Grady WB, Niedzwiecki D, Saltz LB, Bertagnolli MM, Goldberg RM, Rabinovitch PS, Emond M, Monnat RJ, Maizels N. MRE11-deficiency associated with improved long-term disease free survival and overall survival in a subset of stage III colon cancer patients in randomized CALGB 89803 trial. PLoS One 2014; 9:e108483. [PMID: 25310185 PMCID: PMC4195600 DOI: 10.1371/journal.pone.0108483] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 08/19/2014] [Indexed: 11/19/2022] Open
Abstract
Purpose Colon cancers deficient in mismatch repair (MMR) may exhibit diminished expression of the DNA repair gene, MRE11, as a consequence of contraction of a T11 mononucleotide tract. This study investigated MRE11 status and its association with prognosis, survival and drug response in patients with stage III colon cancer. Patients and Methods Cancer and Leukemia Group B 89803 (Alliance) randomly assigned 1,264 patients with stage III colon cancer to postoperative weekly adjuvant bolus 5-fluorouracil/leucovorin (FU/LV) or irinotecan+FU/LV (IFL), with 8 year follow-up. Tumors from these patients were analyzed to determine stability of a T11 tract in the MRE11 gene. The primary endpoint was overall survival (OS), and a secondary endpoint was disease-free survival (DFS). Non-proportional hazards were addressed using time-dependent covariates in Cox analyses. Results Of 625 tumor cases examined, 70 (11.2%) exhibited contraction at the T11 tract in one or both MRE11 alleles and were thus predicted to be deficient in MRE11 (dMRE11). In pooled treatment analyses, dMRE11 patients showed initially reduced DFS and OS but improved long-term DFS and OS compared with patients with an intact MRE11 T11 tract. In the subgroup of dMRE11 patients treated with IFL, an unexplained early increase in mortality but better long-term DFS than IFL-treated pMRE11 patients was observed. Conclusions Analysis of this relatively small number of patients and events showed that the dMRE11 marker predicts better prognosis independent of treatment in the long-term. In subgroup analyses, dMRE11 patients treated with irinotecan exhibited unexplained short-term mortality. MRE11 status is readily assayed and may therefore prove to be a useful prognostic marker, provided that the results reported here for a relatively small number of patients can be generalized in independent analyses of larger numbers of samples. Trial Registration ClinicalTrials.gov NCT00003835
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Affiliation(s)
- Thomas Pavelitz
- Department of Immunology, University of Washington, Seattle, Washington, United States of America
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Lindsay Renfro
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Nathan R. Foster
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Amber Caracol
- Department of Immunology, University of Washington, Seattle, Washington, United States of America
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America
| | - Piri Welsch
- Department of Genome Sciences, University of Washington Medical School, Seattle, Washington, United States of America
| | - Victoria Valinluck Lao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Surgery, University of Washington Medical School, Seattle, Washington, United States of America
| | - William B. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Medicine, University of Washington Medical School, Seattle, Washington, United States of America
| | - Donna Niedzwiecki
- Cancer and Leukemia Group B Statistical Center, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Leonard B. Saltz
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Monica M. Bertagnolli
- Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | | | - Peter S. Rabinovitch
- Department of Pathology, University of Washington Medical School, Seattle, Washington, United States of America
| | - Mary Emond
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Raymond J. Monnat
- Department of Genome Sciences, University of Washington Medical School, Seattle, Washington, United States of America
- Department of Pathology, University of Washington Medical School, Seattle, Washington, United States of America
| | - Nancy Maizels
- Department of Immunology, University of Washington, Seattle, Washington, United States of America
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America
- Department of Pathology, University of Washington Medical School, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Zhang H, Lin Y, Mañas A, Zhao Y, Denning MF, Ma L, Xiang J. BaxΔ2 promotes apoptosis through caspase-8 activation in microsatellite-unstable colon cancer. Mol Cancer Res 2014; 12:1225-32. [PMID: 24842234 PMCID: PMC12019869 DOI: 10.1158/1541-7786.mcr-14-0162] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED Loss of apoptotic Bax due to microsatellite mutation contributes to tumor development and chemoresistance. Recently, a Bax microsatellite mutation was uncovered in combination with a specific alternative splicing event that could generate a unique Bax isoform (BaxΔ2) in otherwise Bax-negative cells. Like the prototype Baxα, BaxΔ2 is a potent proapoptotic molecule. However, the proapoptotic mechanism and therapeutic implication of BaxΔ2 remain elusive. Here, the isolation and analysis of isogenic subcell lines are described that represent different Bax microsatellite statuses from colorectal cancer. Colon cancer cells harboring Bax microsatellite G7/G7 alleles are capable of producing low levels of endogenous BaxΔ2 transcripts and proteins. Interestingly, BaxΔ2-positive cells are selectively sensitive to a subgroup of chemotherapeutics compared with BaxΔ2-negative cells. Unlike other Bax isoforms, BaxΔ2 recruits caspase-8 into the proximity for activation, and the latter, in turn, activates caspase-3 and apoptosis independent of the mitochondrial pathway. These data suggest that the expression of BaxΔ2 may provide alternative apoptotic and chemotherapeutic advantages for Bax-negative tumors. IMPLICATIONS "Bax-negative" colorectal tumors expressing a Bax isoform are sensitive to selective chemotherapeutics.
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Affiliation(s)
| | - Yuting Lin
- Department of Biological and Chemical Sciences
| | | | - Yu Zhao
- Department of Biological and Chemical Sciences
| | - Mitchell F Denning
- Department of Pathology, Loyola University Medical Center, Maywood, Illinois
| | - Li Ma
- Mumetel, LLC, University Technology Park, Illinois Institute of Technology, Chicago; and
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Shin JS, Tut TG, Ho V, Lee CS. Predictive markers of radiotherapy-induced rectal cancer regression. J Clin Pathol 2014; 67:859-64. [DOI: 10.1136/jclinpath-2014-202494] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Zhao H, Thienpont B, Yesilyurt BT, Moisse M, Reumers J, Coenegrachts L, Sagaert X, Schrauwen S, Smeets D, Matthijs G, Aerts S, Cools J, Metcalf A, Spurdle A, Amant F, Lambrechts D. Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks. eLife 2014; 3:e02725. [PMID: 25085081 PMCID: PMC4141275 DOI: 10.7554/elife.02725] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA replication errors that persist as mismatch mutations make up the molecular fingerprint of mismatch repair (MMR)-deficient tumors and convey them with resistance to standard therapy. Using whole-genome and whole-exome sequencing, we here confirm an MMR-deficient mutation signature that is distinct from other tumor genomes, but surprisingly similar to germ-line DNA, indicating that a substantial fraction of human genetic variation arises through mutations escaping MMR. Moreover, we identify a large set of recurrent indels that may serve to detect microsatellite instability (MSI). Indeed, using endometrial tumors with immunohistochemically proven MMR deficiency, we optimize a novel marker set capable of detecting MSI and show it to have greater specificity and selectivity than standard MSI tests. Additionally, we show that recurrent indels are enriched for the ‘DNA double-strand break repair by homologous recombination’ pathway. Consequently, DSB repair is reduced in MMR-deficient tumors, triggering a dose-dependent sensitivity of MMR-deficient tumor cultures to DSB inducers. DOI:http://dx.doi.org/10.7554/eLife.02725.001 Before a cell divides, it must first copy all of its genetic material. Any mistakes that are made during this process are called mutations. Mutations can give rise to new traits but are mostly harmful to the cells, or cause cancer; therefore, cells have evolved tools that can efficiently spot these mistakes and repair them. One of the main tools is called mismatch repair (MMR). Defects in the cell's mismatch repair tools can wreak havoc as this allows many mutations to accumulate. Zhao et al. looked at the genomes of tumors where mismatch repair was not working properly to see what makes these ‘MMR-deficient tumors’ different from other tumors. This revealed that MMR-deficient tumors have similar patterns of mutations to those seen in egg and sperm cells. This was unexpected and suggests that mutations that are not corrected by mismatch repair are an important source of the genetic differences found between different humans, and between humans and their ancestors. Identifying cancerous tumors that are MMR-deficient is vital, as these tumors tend not to respond to commonly used cancer treatments. However, current clinical methods to identify MMR-deficient tumors often fail or produce results that are difficult to interpret. MMR-deficient tumors commonly contain mutations called indels, where short fragments of DNA are inserted or deleted into longer DNA sequences. Zhao et al. have found 59 indels that can be used to detect MMR-deficient tumors, where each indel had been identified in several tumors taken from different tissues. This new approach allowed MMR-deficiency to be identified in several types of tumor, including colon and ovarian cancers, with greater sensitivity and accuracy than the existing methods. Zhao et al. also found that the indels in MMR-deficient tumors reduce the ability of the tumors to repair a type of DNA damage called double-strand breaks. In these, both strands of DNA that make up the double helix are broken and the DNA chain is severed. As this kind of damage is very harmful to a cell, making more double-strand breaks could therefore form part of a more effective treatment against MMR-deficient tumors; further research is needed to investigate this possibility. DOI:http://dx.doi.org/10.7554/eLife.02725.002
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Affiliation(s)
- Hui Zhao
- VIB Vesalius Research Center, KU Leuven, Leuven, Belgium Department of Oncology, KU Leuven, Leuven, Belgium
| | - Bernard Thienpont
- VIB Vesalius Research Center, KU Leuven, Leuven, Belgium Department of Oncology, KU Leuven, Leuven, Belgium
| | - Betül Tuba Yesilyurt
- VIB Vesalius Research Center, KU Leuven, Leuven, Belgium Department of Oncology, KU Leuven, Leuven, Belgium
| | - Matthieu Moisse
- VIB Vesalius Research Center, KU Leuven, Leuven, Belgium Department of Oncology, KU Leuven, Leuven, Belgium
| | - Joke Reumers
- VIB Vesalius Research Center, KU Leuven, Leuven, Belgium Department of Oncology, KU Leuven, Leuven, Belgium
| | - Lieve Coenegrachts
- Division of Gynaecologic Oncology, Department of Obstetrics and Gynaecology, University Hospital Gasthuisberg, Leuven, Belgium
| | - Xavier Sagaert
- Division of Pathology, University Hospital Gasthuisberg, Leuven, Belgium
| | - Stefanie Schrauwen
- Division of Gynaecologic Oncology, Department of Obstetrics and Gynaecology, University Hospital Gasthuisberg, Leuven, Belgium
| | - Dominiek Smeets
- VIB Vesalius Research Center, KU Leuven, Leuven, Belgium Department of Oncology, KU Leuven, Leuven, Belgium
| | - Gert Matthijs
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jan Cools
- Department of Human Genetics, KU Leuven, Leuven, Belgium VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium
| | - Alex Metcalf
- Division of Genetics and Computational Biology, Queensland Institute of Medical Research, Brisbane, Australia
| | - Amanda Spurdle
- Division of Genetics and Computational Biology, Queensland Institute of Medical Research, Brisbane, Australia
| | | | - Frederic Amant
- Division of Gynaecologic Oncology, Department of Obstetrics and Gynaecology, University Hospital Gasthuisberg, Leuven, Belgium
| | - Diether Lambrechts
- VIB Vesalius Research Center, KU Leuven, Leuven, Belgium Department of Oncology, KU Leuven, Leuven, Belgium
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Jekimovs C, Bolderson E, Suraweera A, Adams M, O’Byrne KJ, Richard DJ. Chemotherapeutic compounds targeting the DNA double-strand break repair pathways: the good, the bad, and the promising. Front Oncol 2014; 4:86. [PMID: 24795863 PMCID: PMC4001069 DOI: 10.3389/fonc.2014.00086] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 04/08/2014] [Indexed: 01/09/2023] Open
Abstract
The repair of DNA double-strand breaks (DSBs) is a critical cellular mechanism that exists to ensure genomic stability. DNA DSBs are the most deleterious type of insult to a cell's genetic material and can lead to genomic instability, apoptosis, or senescence. Incorrectly repaired DNA DSBs have the potential to produce chromosomal translocations and genomic instability, potentially leading to cancer. The prevalence of DNA DSBs in cancer due to unregulated growth and errors in repair opens up a potential therapeutic window in the treatment of cancers. The cellular response to DNA DSBs is comprised of two pathways to ensure DNA breaks are repaired: homologous recombination and non-homologous end joining. Identifying chemotherapeutic compounds targeting proteins involved in these DNA repair pathways has shown promise as a cancer therapy for patients, either as a monotherapy or in combination with genotoxic drugs. From the beginning, there have been a number of chemotherapeutic compounds that have yielded successful responses in the clinic, a number that have failed (CGK-733 and iniparib), and a number of promising targets for future studies identified. This review looks in detail at how the cell responds to these DNA DSBs and investigates the chemotherapeutic avenues that have been and are currently being explored to target this repair process.
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Affiliation(s)
- Christian Jekimovs
- Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Emma Bolderson
- Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Amila Suraweera
- Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Mark Adams
- Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Kenneth J. O’Byrne
- Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Derek J. Richard
- Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
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O’Sullivan CC, Moon DH, Kohn EC, Lee JM. Beyond Breast and Ovarian Cancers: PARP Inhibitors for BRCA Mutation-Associated and BRCA-Like Solid Tumors. Front Oncol 2014; 4:42. [PMID: 24616882 PMCID: PMC3937815 DOI: 10.3389/fonc.2014.00042] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 02/18/2014] [Indexed: 12/14/2022] Open
Abstract
Poly(ADP-ribose) polymerase inhibitors (PARPi) have shown clinical activity in patients with germline BRCA1/2 mutation (gBRCAm)-associated breast and ovarian cancers. Accumulating evidence suggests that PARPi may have a wider application in the treatment of cancers defective in DNA damage repair pathways, such as prostate, lung, endometrial, and pancreatic cancers. Several PARPi are currently in phase I/II clinical investigation, as single-agents and/or combination therapy in these solid tumors. Understanding more about the molecular abnormalities involved in BRCA-like phenotype in solid tumors beyond breast and ovarian cancers, exploring novel therapeutic trial strategies and drug combinations, and defining potential predictive biomarkers are critical to expanding the scope of PARPi therapy. This will improve clinical outcome in advanced solid tumors. Here, we briefly review the preclinical data and clinical development of PARPi, and discuss its future development in solid tumors beyond gBRCAm-associated breast and ovarian cancers.
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Affiliation(s)
- Ciara C. O’Sullivan
- Medical Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Dominic H. Moon
- Medical Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Medical Research Scholars Program, National Institutes of Health, Bethesda, MD, USA
| | - Elise C. Kohn
- Medical Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jung-Min Lee
- Medical Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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46
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Tahara M, Inoue T, Sato F, Miyakura Y, Horie H, Yasuda Y, Fujii H, Kotake K, Sugano K. The use of Olaparib (AZD2281) potentiates SN-38 cytotoxicity in colon cancer cells by indirect inhibition of Rad51-mediated repair of DNA double-strand breaks. Mol Cancer Ther 2014; 13:1170-80. [PMID: 24577941 DOI: 10.1158/1535-7163.mct-13-0683] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Potent application of topoisomerase I inhibitor plus PARP inhibitor has been suggested to be an effective strategy for cancer therapy. Reportedly, mismatch repair (MMR)-deficient colon cancer cells are sensitive to topoisomerase I inhibitor, presumably due to microsatellite instability (MSI) of the MRE11 locus. We examined the synergy of SN-38, an active metabolite of irinotecan, in combination with the PARP inhibitor olaparib in colon cancer cells showing different MMR status, such as MSI or microsatellite stable (MSS) phenotype. Treatment with SN-38 and olaparib in combination almost halved the IC50 of SN-38 for a broad spectrum of colon cancer cells independent of the MMR status. Furthermore, olaparib potentiated S-phase-specific double-strand DNA breaks (DSB) induced by SN-38, which is followed by Rad51 recruitment. siRNA-mediated knockdown of Rad51, but not Mre11 or Rad50, increased the sensitivity to olaparib and/or SN-38 treatment in colon cancer cells. In vivo study using mouse xenograft demonstrated that olaparib was effective to potentiate the antitumor effect of irinotecan. In conclusion, olaparib shows a synergistic effect in colon cancer cells in combination with SN-38 or irinotecan, potentiated by the Rad51-mediated HR pathway, irrespective of the Mre11-mediated failure of the MRN complex. These results may contribute to future clinical trials using PARP inhibitor plus topoisomerase I inhibitor in combination. Furthermore, the synergistic effect comprising topoisomerase I-mediated DNA breakage-reunion reaction, PARP and Rad51-mediated HR pathway suggests the triple synthetic lethal pathways contribute to this event and are applicable as a potential target for future chemotherapy.
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Affiliation(s)
- Makiko Tahara
- Authors' Affiliations: Oncogene Research Unit/Cancer Prevention Unit, Tochigi Cancer Center Research Institute, Department of Surgery, Tochigi Cancer Center, Utsunomiya; and Department of Gastrointestinal Surgery and Division of Clinical Oncology, Jichi Medical University, Shimotsuke, Tochigi, Japan
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47
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Haferkamp B, Zhang H, Kissinger S, Wang X, Lin Y, Schultz M, Xiang J. BaxΔ2 Family Alternative Splicing Salvages Bax Microsatellite-Frameshift Mutations. Genes Cancer 2014; 4:501-12. [PMID: 24386510 DOI: 10.1177/1947601913515906] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/14/2013] [Indexed: 12/15/2022] Open
Abstract
Mutation or aberrant splicing can interrupt gene expression. Tumor suppressor Bax is one of the susceptible genes prone to microsatellite frameshifting mutations in coding regions. As a result, tumors exhibiting microsatellite instability (MSI) often present a "Bax-negative" phenotype. We previously reported that some Bax-negative cells in fact contain a functional Bax isoform (BaxΔ2), generated when unique alternative splicing "salvages" the shifted reading frame introduced by a microsatellite mutation. Here we compared Bax alternative splicing profiles in a range of cell lines and primary tumors with and without Bax microsatellite mutations. We found that MSI tumors exhibit a high Bax alternative splicing frequency, especially in exon 2, and produce a family of alternatively spliced isoforms that retain many important Bax functional domains. Surprisingly, these BaxΔ2 family isoforms can rescue Bax from all common microsatellite frameshift mutations. Production of BaxΔ2 requires specific cis mutations, while trans components are not cell-type specific. Furthermore, all BaxΔ2 family isoforms are more potent cell death inducers than the parental Bax without directly targeting mitochondria. These results indicate that the BaxΔ2 family can potentially salvage Bax tumor suppressor expression otherwise lost to mutation.
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Affiliation(s)
- Bonnie Haferkamp
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Honghong Zhang
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Samuel Kissinger
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Xin Wang
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Yuting Lin
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Megan Schultz
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Jialing Xiang
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, IL, USA
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48
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Bailis JM, Gordon ML, Gurgel JL, Komor AC, Barton JK, Kirsch IR. An inducible, isogenic cancer cell line system for targeting the state of mismatch repair deficiency. PLoS One 2013; 8:e78726. [PMID: 24205301 PMCID: PMC3812133 DOI: 10.1371/journal.pone.0078726] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 09/17/2013] [Indexed: 11/18/2022] Open
Abstract
The DNA mismatch repair system (MMR) maintains genome stability through recognition and repair of single-base mismatches and small insertion-deletion loops. Inactivation of the MMR pathway causes microsatellite instability and the accumulation of genomic mutations that can cause or contribute to cancer. In fact, 10-20% of certain solid and hematologic cancers are MMR-deficient. MMR-deficient cancers do not respond to some standard of care chemotherapeutics because of presumed increased tolerance of DNA damage, highlighting the need for novel therapeutic drugs. Toward this goal, we generated isogenic cancer cell lines for direct comparison of MMR-proficient and MMR-deficient cells. We engineered NCI-H23 lung adenocarcinoma cells to contain a doxycycline-inducible shRNA designed to suppress the expression of the mismatch repair gene MLH1, and compared single cell subclones that were uninduced (MLH1-proficient) versus induced for the MLH1 shRNA (MLH1-deficient). Here we present the characterization of these MMR-inducible cell lines and validate a novel class of rhodium metalloinsertor compounds that differentially inhibit the proliferation of MMR-deficient cancer cells.
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Affiliation(s)
- Julie M. Bailis
- Oncology Research, Amgen Inc., South San Francisco, California, United States of America
- * E-mail:
| | - Marcia L. Gordon
- Oncology Research, Amgen Inc., Seattle, Washington, United States of America
| | - Jesse L. Gurgel
- Oncology Research, Amgen Inc., Seattle, Washington, United States of America
| | - Alexis C. Komor
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Ilan R. Kirsch
- Oncology Research, Amgen Inc., Seattle, Washington, United States of America
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Roepman P, Schlicker A, Tabernero J, Majewski I, Tian S, Moreno V, Snel MH, Chresta CM, Rosenberg R, Nitsche U, Macarulla T, Capella G, Salazar R, Orphanides G, Wessels LFA, Bernards R, Simon IM. Colorectal cancer intrinsic subtypes predict chemotherapy benefit, deficient mismatch repair and epithelial-to-mesenchymal transition. Int J Cancer 2013; 134:552-62. [PMID: 23852808 PMCID: PMC4234005 DOI: 10.1002/ijc.28387] [Citation(s) in RCA: 263] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 06/24/2013] [Indexed: 02/06/2023]
Abstract
In most colorectal cancer (CRC) patients, outcome cannot be predicted because tumors with similar clinicopathological features can have differences in disease progression and treatment response. Therefore, a better understanding of the CRC biology is required to identify those patients who will benefit from chemotherapy and to find a more tailored therapy plan for other patients. Based on unsupervised classification of whole genome data from 188 stages I–IV CRC patients, a molecular classification was developed that consist of at least three major intrinsic subtypes (A-, B- and C-type). The subtypes were validated in 543 stages II and III patients and were associated with prognosis and benefit from chemotherapy. The heterogeneity of the intrinsic subtypes is largely based on three biological hallmarks of the tumor: epithelial-to-mesenchymal transition, deficiency in mismatch repair genes that result in high mutation frequency associated with microsatellite instability and cellular proliferation. A-type tumors, observed in 22% of the patients, have the best prognosis, have frequent BRAF mutations and a deficient DNA mismatch repair system. C-type patients (16%) have the worst outcome, a mesenchymal gene expression phenotype and show no benefit from adjuvant chemotherapy treatment. Both A-type and B-type tumors have a more proliferative and epithelial phenotype and B-types benefit from adjuvant chemotherapy. B-type tumors (62%) show a low overall mutation frequency consistent with the absence of DNA mismatch repair deficiency. Classification based on molecular subtypes made it possible to expand and improve CRC classification beyond standard molecular and immunohistochemical assessment and might help in the future to guide treatment in CRC patients.
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Affiliation(s)
- Paul Roepman
- Department of Research and Development, Agendia NV, Amsterdam, The Netherlands
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Huang CJ, Yang SH, Lee CL, Cheng YC, Tai SY, Chien CC. Ribosomal protein S27-like in colorectal cancer: a candidate for predicting prognoses. PLoS One 2013; 8:e67043. [PMID: 23826192 PMCID: PMC3691124 DOI: 10.1371/journal.pone.0067043] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/13/2013] [Indexed: 01/25/2023] Open
Abstract
Background The development and progression of colorectal cancer (CRC) involve a complex process of multiple genetic changes. Tumor suppressor p53 is capable of determining the fate of CRC cells. However, the role of a p53-inducible modulator, ribosomal protein S27-like (RPS27L), in CRC is unknown. Methods Here, the differential expression of RPS27L was examined in the feces and colonic tissues of CRC patients, to explore its possible correlation with patient survival and to investigate the cellular mechanisms underlying their clinical outcomes. Eighty intermediate-stage CRC patients (42 at stage II and 38 at stage III) were divided into two groups according to their fecal RPS27L mRNA levels. The survival probabilities of the groups were estimated using the Kaplan–Meier method. The RPS27L protein in the colonic tissues of stage III patients with different prognoses was further examined immunohistochemically. RPS27L expression in LoVo cells was manipulated to examine the possible cellular responses in vitro. Results Elevated RPS27L expression, in either feces or tissues, was related to a better prognosis. In vitro, RPS27L-expressing LoVo cells ceased DNA synthesis and apoptotic activity while the expression of their DNA repair molecules was upregulated. Conclusions Elevated RPS27L may improve the prognoses of certain CRC patients by enhancing the DNA repair capacity of their colonic cells, and can be determined in feces. By integrating clinical, molecular, and cellular data, our study demonstrates that fecal RPS27L may be a useful index for predicting prognoses and guiding personalized therapeutic strategies, especially in patients with intermediate-stage CRC.
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Affiliation(s)
- Chi-Jung Huang
- Department of Medical Research, Cathay General Hospital, Taipei, Taiwan
- School of Medicine, Fu Jen Catholic University, New Taipei, Taiwan
- Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan
| | - Shung-Haur Yang
- Department of Surgery, Taipei-Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming University, Taipei, Taiwan
| | - Chia-Long Lee
- Department of Internal Medicine, Hsinchu Cathay General Hospital, Hsinchu, Taiwan
- Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Che Cheng
- Department of Medical Research, Cathay General Hospital, Taipei, Taiwan
| | - Szu-Yun Tai
- Department of Medical Research, Cathay General Hospital, Taipei, Taiwan
| | - Chih-Cheng Chien
- Department of Medical Research, Cathay General Hospital, Taipei, Taiwan
- School of Medicine, Fu Jen Catholic University, New Taipei, Taiwan
- Department of Anesthesiology, Sijhih Cathay General Hospital, New Taipei, Taiwan
- * E-mail:
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