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Miser-Salihoglu E, Demokan S, Karanlik H, Karahalil B, Önder S, Cömert S, Yardim-Akaydin S. Investigation of mRNA Expression Levels of Tip60 and Related DNA Repair Genes in Molecular Subtypes of Breast Cancer. Clin Breast Cancer 2023; 23:125-134. [PMID: 36463002 DOI: 10.1016/j.clbc.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/29/2022] [Accepted: 10/24/2022] [Indexed: 11/14/2022]
Abstract
INTRODUCTION Studies in breast cancer (BC) have been shown that many tumor cells carry mutations that disrupt the DNA damage response mechanism. In eukaryotic cells, the overexpression or deprivation of DSBs repair genes is linked closely to a higher risk of cancer. PATIENTS AND METHODS In this study, mRNA expression levels of some genes, such as Tip60, ATM, p53, CHK2, BRCA1, H2AX, which are associated with DNA damage repair, were measured using RT-PCR method in tumor and matched-normal tissues of 58 patients with BC. RESULTS According to the study results, 55% in Tip60, 59% in ATM, 57% in BRCA1, 48% in H2AX, 66% in CHK2, and 43% in p53 decreased in tumor tissue of patients compared to the matched normal tissue. When evaluated according to molecular subtypes, expression of all genes in the pathway was found significantly higher in normal tissues than in tumor tissues especially in Luminal B and Luminal B+HER2 groups. One of the most important results of the study is that CHK2 mRNA expressions in normal tissues were higher than tumor tissue in 90% of patients in Luminal B and Luminal B-HER2 + groups. This is the first study showing DNA repair genes' expressions in molecular subtypes of breast cancer. In general, the decrease in the expression of DNA damage repair genes in tumor tissue indicates that these genes may have a role in the development of BC. Our study results also suggest that CHK2 may be a candidate marker in the molecular classification of breast cancer.
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Affiliation(s)
- Ece Miser-Salihoglu
- Faculty of Pharmacy, Department of Biochemistry, Gazi University, Ankara, Turkey.
| | - Semra Demokan
- Department of Basic Oncology, Istanbul University, Oncology Institute, Istanbul, Turkey
| | - Hasan Karanlik
- Department of Surgery, Istanbul University, Institute of Oncology, Istanbul, Turkey
| | - Bensu Karahalil
- Faculty of Pharmacy, Department of Toxicology, Gazi University, Ankara, Turkey
| | - Semen Önder
- Istanbul University, Istanbul Medical Faculty, Department of Pathology, Istanbul, Turkey
| | - Sevde Cömert
- Department of Basic Oncology, Istanbul University, Oncology Institute, Istanbul, Turkey
| | - Sevgi Yardim-Akaydin
- Faculty of Pharmacy, Department of Biochemistry, Gazi University, Ankara, Turkey
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Abstract
Pancreatic ductal adenocarcinoma remains a major challenge in cancer medicine. Given the increase in incidence and mortality, interdisciplinary research is necessary to translate basic knowledge into therapeutic strategies improving the outcome of patients. On the 4th and 5th of February 2021, three German pancreatic cancer research centers, the Clinical Research Unit 5002 from Göttingen, the Collaborative Research Center 1321 from Munich, and Clinical Research Unit 325 from Marburg organized the 1st Virtual Göttingen-Munich-Marburg Pancreatic Cancer Meeting in order to foster scientific exchange. This report summarizes current research and proceedings presented during that meeting.
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Affiliation(s)
- Elisabeth Hessmann
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, Göttingen, Germany.
| | - Günter Schneider
- Medical Clinic and Policlinic II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.
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Krušlin B, Škara L, Vodopić T, Vrhovec B, Murgić J, Štimac G, Fröbe A, Lež C, Ulamec M, Gall-Trošelj K. Genetics of Prostate Carcinoma. Acta Med Acad 2021; 50:71-87. [PMID: 34075765 DOI: 10.5644/ama2006-124.327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 01/11/2021] [Indexed: 11/09/2022] Open
Abstract
The aim of this review is to provide a brief overview of some current approaches regarding diagnostics, pathologic features, treatment, and genetics of prostate carcinoma (PCa). Prostate carcinoma is the most common visceral tumor and the second most common cancer-related cause of death in males. Clinical outcomes for patients with localized prostate cancer are excellent, but despite advances in prostate cancer treatments, castrate-resistant prostate cancer and metastatic prostate cancer patients have a poor prognosis. Advanced large-scale genomic studies revealed a large number of genetic alterations in prostate cancer. The meaning of these alterations needs to be validated in the specific prostate cancer molecular subtype context. Along these lines, there is a critical need for establishing genetically engineered mouse models, which would include speckle type BTB/POZ protein and isocitrate Dehydrogenase (NADP (+)) 1 mutant, as well as androgen receptor neuroendocrine subtypes of prostate cancer. Another urgent need is developing highly metastatic prostate cancer models, as only up to 17% of available models display bone metastases and exhibit a less typical neuroendocrine prostate cancer or sarcomatoid carcinoma. Moreover, androgen deprivation and relapse should be mimicked in the genetically engineered mouse models, as androgen independence may yield a better model for metastatic castrate-resistant prostate cancer. The development of such refined animal models should be guided by comparative genomics of primary versus corresponding metastatic tumors. Such an approach will have the potential to illuminate the key genetic events associated with specific molecular prostate cancer subsets and indicate directions for effective therapy. CONCLUSION: Despite excellent results in the treatment of localized prostatic carcinoma, castrate-resistant prostate cancer and metastatic prostate cancer have a poor prognosis. Advanced large-scale genomic studies revealed a large number of genetic alterations in PCa. Experimental models of prostate carcinoma in genetically modified mice could provide new data about the genetic changes in such cancers and help in developing better animal models for treatment resistant prostate carcinomas.
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Affiliation(s)
- Božo Krušlin
- Ljudevit Jurak Department of Pathology and Cytology, Sestre Milosrdnice University Hospital Centre, Zagreb, Croatia; Department of Pathology, School of Medicine, University of Zagreb, Zagreb, Croatia.
| | - Lucija Škara
- University of Zagreb, School of Medicine, Scientific Group for Research on Epigenetic Biomarkers, Zagreb, Croatia
| | - Tonći Vodopić
- Department of Pathology, Cytology and Forensic Medicine, Varaždin General Hospital, Varaždin, Croatia
| | - Borna Vrhovec
- Department of Urology, Sestre Milosrdnice University Hospital Centre, Zagreb, Croatia
| | - Jure Murgić
- Department of Oncology, Sestre Milosrdnice University Hospital Centre, Zagreb, Croatia
| | - Goran Štimac
- Department of Urology, Sestre Milosrdnice University Hospital Centre, Zagreb, Croatia
| | - Ana Fröbe
- Department of Pathology, School of Medicine, University of Zagreb, Zagreb, Croatia; Department of Oncology, Sestre Milosrdnice University Hospital Centre, Zagreb, Croatia
| | - Cvjetko Lež
- Department of Pathology and Cytology, Zabok General Hospital, Bračak, Croatia and Josip Juraj Strossmayer University of Osijek, Faculty of Dental Medicine and Health Osijek, Croatia
| | - Monika Ulamec
- Ljudevit Jurak Department of Pathology and Cytology, Sestre Milosrdnice University Hospital Centre, Zagreb, Croatia; Department of Pathology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Koraljka Gall-Trošelj
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
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Abstract
Purpose of review Molecular pathways in colorectal carcinogenesis involve several complex genetic and epigenetic modulations that cause normal colonic mucosa to metamorphose into a benign polyp and subsequently into a malignant tumor. Our purpose is to recapitulate historical and recent genomic research in order to augment the understanding of colorectal cancer pathogenesis. Recent Findings In 2015, the molecular classification for colorectal cancers was unified into one system with four distinct groups, also called as consensus molecular subtypes. This led to an enhanced understanding of molecular and immune signatures which has implications on predicting the clinical behavior as well as response to different therapeutic agents. Summary In this review, we expound on the current literature as well as draw on our own experience to present the important molecular pathogenesis pathways, key genetic mutations, differences in pathogenesis of left versus right sided tumors as well as the molecular classification of colorectal cancers.
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Affiliation(s)
- Anup Kasi
- Department of Medicine, Division of Medical Oncology, Kansas University Medical Center, Kansas City, KS, U.S.A
| | - Shivani Handa
- Department of Internal Medicine, Icahn School of Medicine at Mount Sinai West & Morningside, NY, NY
| | - Sajjad Bhatti
- Department of Medicine, Division of Medical Oncology, Kansas University Medical Center, Kansas City, KS, U.S.A
| | - Shahid Umar
- Department of Medicine, Division of Surgery, Kansas University Medical Center, Kansas City, KS, U.S.A
| | - Ajay Bansal
- Department of Medicine, Division of Gastroenterology, Kansas University Medical Center, Kansas City, KS, U.S.A
| | - Weijing Sun
- Department of Medicine, Division of Medical Oncology, Kansas University Medical Center, Kansas City, KS, U.S.A
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Puleo F, Nicolle R, Blum Y, Cros J, Marisa L, Demetter P, Quertinmont E, Svrcek M, Elarouci N, Iovanna J, Franchimont D, Verset L, Galdon MG, Devière J, de Reyniès A, Laurent-Puig P, Van Laethem JL, Bachet JB, Maréchal R. Stratification of Pancreatic Ductal Adenocarcinomas Based on Tumor and Microenvironment Features. Gastroenterology 2018; 155:1999-2013.e3. [PMID: 30165049 DOI: 10.1053/j.gastro.2018.08.033] [Citation(s) in RCA: 295] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 07/31/2018] [Accepted: 08/22/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Genomic studies have revealed subtypes of pancreatic ductal adenocarcinoma (PDA) based on their molecular features, but different studies have reported different classification systems. It is a challenge to obtain high-quality, freshly frozen tissue for clinical analysis and determination of PDA subtypes. We aimed to redefine subtypes of PDA using a large number of formalin-fixed and paraffin-embedded PDA samples, which are more amenable to routine clinical evaluation. METHODS We collected PDA samples from 309 consecutive patients who underwent surgery from September 1996 through December 2010 at 4 academic hospitals in Europe; nontumor tissue samples were not included. Samples were formalin fixed and paraffin embedded. DNA and RNA were isolated; gene expression, targeted DNA sequencing, and immunohistochemical analyses were performed. We used independent component analysis to deconvolute normal, tumor, and microenvironment transcriptome patterns in samples. We devised classification systems from an unsupervised analysis using a consensus clustering approach of our data set after removing normal contamination components. We associated subtypes with overall survival and disease-free survival of patients using Cox proportional hazards regression with estimation of hazard ratios and 95% confidence interval. We used The Cancer Genome Consortium and International Cancer Genome Consortium PDA data sets as validation cohorts. RESULTS We validated the previously reported basal-like and classical tumor-specific subtypes of PDAs. We identified features of the PDA, including microenvironment gene expression patterns, that allowed tumors to be categorized into 5 subtypes, called pure basal like, stroma activated, desmoplastic, pure classical, and immune classical. These PDA subtypes have features of cancer cells and immune cells that could be targeted by pharmacologic agents. Tumor subtypes were associated with patient outcomes, based on analysis of our data set and the International Cancer Genome Consortium and The Cancer Genome Consortium PDA data sets. We also observed an exocrine signal associated with acinar cell contamination (from pancreatic tissue). CONCLUSIONS We identified a classification system based on gene expression analysis of formalin-fixed PDA samples. We identified 5 PDA subtypes, based on features of cancer cells and the tumor microenvironment. This system might be used to select therapies and predict patient outcomes. We found evidence that the previously reported exocrine-like (called ADEX) tumor subtype resulted from contamination with pancreatic acinar cells. ArrayExpress accession number: E-MTAB-6134.
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Affiliation(s)
- Francesco Puleo
- Medical Oncology Department, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium; Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium.
| | - Rémy Nicolle
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France
| | - Yuna Blum
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France
| | - Jérôme Cros
- Department of Pathology, Beaujon Hospital-Paris Diderot University, Clichy, France
| | - Laetitia Marisa
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France
| | | | - Eric Quertinmont
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium
| | - Magali Svrcek
- Department of Pathology, Saint-Antoine Hospital, Paris, France
| | - Nabila Elarouci
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Denis Franchimont
- Department of Gastroenterology and Digestive Oncology, Erasme Hospital, Brussels, Belgium
| | - Laurine Verset
- Department of Pathology, Erasme Hospital, Brussels, Belgium
| | - Maria Gomez Galdon
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Jacques Devière
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium; Department of Gastroenterology and Digestive Oncology, Erasme Hospital, Brussels, Belgium
| | - Aurélien de Reyniès
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France
| | - Pierre Laurent-Puig
- Université Paris Descartes UMRS-1147; Assistance Publique Hopitaux de Paris Hopital Européen Georges Pompidou, Paris, France
| | - Jean-Luc Van Laethem
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium; Department of Gastroenterology and Digestive Oncology, Erasme Hospital, Brussels, Belgium
| | - Jean-Baptiste Bachet
- Sorbonne Universités, UPMC Université, Department of Gastroenterology, Pitié-Salpetriére Hospital, Paris, France
| | - Raphaël Maréchal
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium; Department of Gastroenterology and Digestive Oncology, Erasme Hospital, Brussels, Belgium
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Sinicrope FA, Okamoto K, Kasi PM, Kawakami H. Molecular Biomarkers in the Personalized Treatment of Colorectal Cancer. Clin Gastroenterol Hepatol 2016; 14:651-8. [PMID: 26872400 DOI: 10.1016/j.cgh.2016.02.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 01/12/2016] [Accepted: 02/03/2016] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is a disease in which pathogenesis is influenced by genetic and epigenetic events that occur with tumor initiation and progression. Large variation exists in individual patient prognosis and response to chemotherapy, caused by molecular heterogeneity. Certain biomarkers have been identified that can predict clinical outcome beyond tumor staging, and inform treatment selection. Molecular testing is routinely performed in clinical practice for the selection of patients for targeted biological agents or immunotherapy, and is advocated for prognostic stratification. Estimating prognosis can avoid undertreatment or overtreatment and also guide the intensity of patient follow-up. Classifiers of CRC have been developed that integrate genetic and/or epigenetic features. The mutational status of KRAS and BRAF(V600E) oncogenes combined with analysis of the DNA mismatch repair system with/without the CpG island methylator phenotype (CIMP) has been shown to identify colon cancer subtypes with distinct clinical features and prognoses. Gene expression profiling has also been used to subtype CRCs and can overcome the limitations of single/limited gene testing. A recent effort identified 4 consensus molecular subtypes of biological relevance that were associated with different patient outcomes. Efforts to validate and refine these subtypes to include additional genomic features are ongoing. The focus of this article is to highlight molecular markers that can inform clinical decision-making in patients with CRC.
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