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Wang W, Wang R, Han X, Zhang W, Zhu L, Gu Y. Epidemiological and clinicopathological features of KRAS, NRAS, BRAF mutations and MSI in Chinese patients with stage I-III colorectal cancer. Medicine (Baltimore) 2024; 103:e37693. [PMID: 38579072 PMCID: PMC10994587 DOI: 10.1097/md.0000000000037693] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/01/2024] [Indexed: 04/07/2024] Open
Abstract
The selection of appropriate treatment modalities based on the presence or absence of mutations in KRAS, NRAS, BRAF, and the microsatellite instability (MSI) status has become a crucial consensus in colorectal cancer (CRC) therapy. However, the distribution pattern of these genetic mutations and the prevalence of MSI status in Chinese stage I-III CRCs remain unclear. We retrospectively analyzed clinicopathological features, mutations in the KRAS, NRAS, and BRAF genes, as well as MSI status of 411 patients with stage I-III CRC who underwent surgery from June 2020 to December 2022 in the First Affiliated Hospital of Nanjing Medical University. The mutation rates of KRAS, NRAS, and BRAF were 48.9%, 2.2%, and 3.2%, respectively, and the microsatellite instability-high rate was 9.5%. KRAS mutation was independently associated with mucinous adenocarcinoma. Multivariate analysis suggested that tumor location and mucinous adenocarcinoma were independently associated with BRAF mutation. Only T stage was associated with NRAS mutations in the univariate analysis. Multivariate analysis revealed that factors such as larger tumor size, tumor location, younger age, and poor differentiation were independently associated with microsatellite instability-high status. The results illustrate the mutation frequencies of KRAS, NRAS, BRAF genes and MSI status in stage I-III CRC from the eastern region of China. These findings further validate the associations between these genes status and various clinicopathological characteristics.
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Affiliation(s)
- Weicheng Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Rui Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiao Han
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wei Zhang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lijun Zhu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yanhong Gu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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Joignant AN, Knizner KT, Xi Y, Muddiman DC. Evaluating the optimal tissue thickness for mass spectrometry imaging using infrared matrix-assisted laser desorption electrospray ionization. Rapid Commun Mass Spectrom 2023; 37:e9638. [PMID: 37817341 PMCID: PMC10881192 DOI: 10.1002/rcm.9638] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/26/2023] [Accepted: 08/26/2023] [Indexed: 10/12/2023]
Abstract
RATIONALE Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) utilizes a 2970 nm mid-IR laser to desorb samples with depth resolutions (Z) on the order of micrometers. Conventionally, 5-20 μm thick tissue sections are used to characterize different applications of the IR-MALDESI source, but an optimal thickness has not been systematically investigated. METHODS Mouse liver was sectioned to various thicknesses and analyzed using IR-MALDESI mass spectrometry imaging (MSI). Height profiles of tissue sections of various cryosectioned thicknesses were acquired to affirm tissue thickness. Tissue sections of each thickness were measured using a Keyence microscope. Paraffin wax was cryosectioned, mounted on microscope slides, and measured using a chromatic confocal sensor system to determine the cryostat sectioning accuracy. RESULTS Analyzing sectioned tissues at higher thickness (>10 μm) leads to lower ion abundance, a decrease in signal over long analysis times, and more frequent instrument cleaning. Additionally, increasing tissue thickness above the optimum (7 μm) does not result in a significant increase in lipid annotations. CONCLUSIONS This work defines an optimal sample thickness for IR-MALDESI-MSI and demonstrates the utility of optimizing tissue thickness for MSI platforms of comparable Z resolution.
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Affiliation(s)
- Alena N. Joignant
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Kevan T. Knizner
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Ying Xi
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - David C. Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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Song YB, Bao WG, Liu DH, Wei LQ, Yang ST, Miao XJ, Lin CY, Li HJ, Lan D, He HM. Pan-cancer analysis of the prognostic significance and oncogenic role of GXYLT2. Medicine (Baltimore) 2023; 102:e35664. [PMID: 37986328 PMCID: PMC10659660 DOI: 10.1097/md.0000000000035664] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 11/22/2023] Open
Abstract
Growing evidence supports an oncogenic role for glucoside xylosyltransferase 2 (GXYLT2) in a number of malignancies. To evaluate the prognostic value and oncogenic function of GXYLT2 in diverse cancer types, we analyzed sequencing data from public databases on 33 tumor tissues and their corresponding normal tissues. We found that GXYLT2 was overexpressed in a number of tumors, and that its expression was positively correlated with disease progression and mortality in several major cancer types including stomach adenocarcinoma (STAD). GXYLT2 was also linked to tumor size, grade, and the immune and molecular subtypes of STAD. GO and KEGG pathway analyses of GXYLT2 co-expressed genes in STAD suggested that GXYLT2 possibly plays a role in epithelial-mesenchymal transition, extracellular matrix production and degradation, angiogenesis, apoptosis, as well as in tumor inflammation, such as cytokine production and T cell activation. Finally, prognostic nomograms were created and validated for predicting 1, 3, and 5-year survival of patients with STAD. Our findings indicate that GXYLT2 may play a role in tumorigenesis and tumor immunity, and it may serve as a prognostic marker and potential immunotherapeutic target for STAD and some other types of cancer.
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Affiliation(s)
- Yi-Bei Song
- Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning, China
| | - Wen-Guang Bao
- Department of Medical Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Deng-He Liu
- Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning, China
| | - Li-Qiang Wei
- Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning, China
| | - Shu-Ting Yang
- Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning, China
| | - Xue-Jing Miao
- Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning, China
| | - Chun-Yu Lin
- Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning, China
| | | | - Dong Lan
- Department of Medical Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hui-Min He
- Guangxi Medical University, Nanning, China
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Abstract
Mismatch repair deficiency (dMMR) results in microsatellite instability (MSI) and is strongly associated with responsiveness to programmed death-1 receptor (PD-1)-blocking antibodies. Probably the main driver for the observed high efficacy of immune checkpoint inhibitors in dMMR tumours is the remarkably high tumour mutational burden. MSI can be detected using immunohistochemistry and/or PCR. In addition, next-generation sequencing is becoming increasingly available to clinical laboratories as a cost-effective and scalable method to evaluate multiple genetic aberrations including MSI. Efficacy of PD-1-blockade in MSI tumours is similar for patients with colorectal cancer (CRC; objective response rate (ORR) 36%) or a different cancer type (ORR 46% across 14 other cancer types). Based on these results, PD-1-blocking antibody pembrolizumab was the first tumour-agnostic treatment to be granted Food and Drug Administration approval based on the presence of MSI as a biomarker. Currently, there is no approved PD-1-blocking antibody for MSI cancers in Europe. Here, we present our experience with the screening for MSI and the treatment of patients with advanced disease of MSI CRC and non-CRC with immunotherapy.
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Affiliation(s)
- Marleen Kok
- Medical Oncology, Nederlands Kanker Instituut - Antoni van Leeuwenhoek Ziekenhuis, Amsterdam, The Netherlands
| | - Myriam Chalabi
- Medical Oncology, Nederlands Kanker Instituut - Antoni van Leeuwenhoek Ziekenhuis, Amsterdam, The Netherlands
| | - John Haanen
- Medical Oncology, Nederlands Kanker Instituut - Antoni van Leeuwenhoek Ziekenhuis, Amsterdam, The Netherlands.
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Iqbal M, Raja NI, Mashwani ZUR, Wattoo FH, Hussain M, Ejaz M, Saira H. Assessment of AgNPs exposure on physiological and biochemical changes and antioxidative defence system in wheat ( Triticum aestivum L) under heat stress. IET Nanobiotechnol 2019; 13:230-236. [PMID: 31051456 PMCID: PMC8676053 DOI: 10.1049/iet-nbt.2018.5041] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 04/12/2018] [Revised: 09/01/2018] [Accepted: 09/27/2018] [Indexed: 07/25/2023] Open
Abstract
The present study was designed to check the role of silver nanoparticles (AgNPs) on physiological, biochemical parameters and antioxidants of wheat (Triticum aestivum L.) under heat stress. Plant extract of Moringa oleifera was used for AgNPs synthesis followed by characterization through UV-Vis spectroscopy, SEM, XRD and Zeta analyser. Heat stress was applied in range of 35-40°C for 3 hrs/ day for 3 days to wheat plants at trifoliate stage. Heat stress decreased the RWC (13.2%), MSI (16.3%), chl a (5.2%), chl b (4.1%) and TCCs (9.9%). Wheat plants treated with AgNPs showed significant increase in RWC (12.2%), MSI (26.5%), chl a (10%), chl b (16.4%), TCCs (19%), TPC (2.4%), TFC (2.5%), TASC (2.5%), SOD (1.3%), POX (1.5%), CAT (1.8%), APX (1.2%) and GPX (1.4%), under heat stress. Lower concentration of AgNPs (50 mg/l) decreased the sugar (5.8%) and proline contents (4%), while increase was observed in higher AgNPs concentrations. Overall, AgNPs treatment enhanced thermo-tolerance in wheat plants, but the mechanism of AgNPs action needs further investigation at genome and proteome level in wheat plants under heat stress.
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Affiliation(s)
- Muhammad Iqbal
- Department of Botany, PMAS Arid Agriculture University, Rawalpindi, Pakistan.
| | - Naveed Iqbal Raja
- Department of Botany, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | | | - Feroza Hamid Wattoo
- Department of Biochemistry, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | - Mubashir Hussain
- Department of Botany, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | - Muhammad Ejaz
- Department of Botany, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | - Hafiza Saira
- Department of Botany, PMAS Arid Agriculture University, Rawalpindi, Pakistan
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Pai RK, Dudley B, Karloski E, Brand RE, O’Callaghan N, Rosty C, Buchanan DD, Jenkins MA, Thibodeau SN, French AJ, Lindor NM, Pai RK. DNA mismatch repair protein deficient non-neoplastic colonic crypts: a novel indicator of Lynch syndrome. Mod Pathol 2018; 31:1608-1618. [PMID: 29884888 PMCID: PMC6396289 DOI: 10.1038/s41379-018-0079-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 03/02/2018] [Revised: 04/20/2018] [Accepted: 04/22/2018] [Indexed: 02/06/2023]
Abstract
Lynch syndrome is the most common form of hereditary colorectal carcinoma. However, establishing the diagnosis of Lynch syndrome is challenging, and ancillary studies that distinguish between sporadic DNA mismatch repair (MMR) protein deficiency and Lynch syndrome are needed, particularly when germline mutation studies are inconclusive. The aim of this study was to determine if MMR protein-deficient non-neoplastic intestinal crypts can help distinguish between patients with and without Lynch syndrome. We evaluated the expression of MMR proteins in non-neoplastic intestinal mucosa obtained from colorectal surgical resection specimens from patients with Lynch syndrome-associated colorectal carcinoma (n = 52) and patients with colorectal carcinoma without evidence of Lynch syndrome (n = 70), including sporadic MMR protein-deficient colorectal carcinoma (n = 30), MMR protein proficient colorectal carcinoma (n = 30), and "Lynch-like" syndrome (n = 10). MMR protein-deficient non-neoplastic colonic crypts were identified in 19 of 122 (16%) patients. MMR protein-deficient colonic crypts were identified in 18 of 52 (35%) patients with Lynch syndrome compared to only 1 of 70 (1%) patients without Lynch syndrome (p < 0.001). This one patient had "Lynch-like" syndrome and harbored two MSH2-deficient non-neoplastic colonic crypts. MMR protein-deficient non-neoplastic colonic crypts were not identified in patients with sporadic MMR protein-deficient or MMR protein proficient colorectal carcinoma. Our findings suggest that MMR protein-deficient colonic crypts are a novel indicator of Lynch syndrome, and evaluation for MMR protein-deficient crypts may be a helpful addition to Lynch syndrome diagnostics.
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Affiliation(s)
- Rish K. Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, Arizona
| | - Beth Dudley
- Department of Internal Medicine, Division of Gastroenterology, Hereditary Tumor Program, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Eve Karloski
- Department of Internal Medicine, Division of Gastroenterology, Hereditary Tumor Program, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Randall E. Brand
- Department of Internal Medicine, Division of Gastroenterology, Hereditary Tumor Program, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Neil O’Callaghan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia.,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia.,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia,Envoi Specialist Pathologists, Herston, QLD, Australia.,University of Queensland, School of Medicine, Herston, QLD, Australia
| | - Daniel D. Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia.,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia,Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Mark A. Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria 3010 Australia
| | | | - Amy J. French
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN
| | - Noralane M. Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, USA
| | - Reetesh K. Pai
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA
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Abstract
Kristen rat sarcoma viral oncogene homolog (KRAS) and microsatellite instability (MSI) are prognostic markers of colorectal cancer (CRC). However, the clinical value is still not fully understood, when giving the consideration to both the molecular makers. Five hundred fifty-one patients with CRC were retrospectively assessed by determining their clinicopathological features. KRAS mutations were detected by polymerase chain reaction. MSI, a defect in the mismatch repair (MMR) system, was detected by immunohistochemistry. The prognostic value of KRAS in combination with MSI was studied. Among 551 CRC patients, mutations in KRAS codon 12 and KRAS codon 13 were detected in 34.5% and 10.5% of patients, respectively. Four hundred one tumors were randomly selected to detect for MMR proteins expression. In this analysis, 30 (7.5%) tumors that had at least 1 MMR protein loss were defined as MMR protein-deficient (MMR-D), and the remaining tumors were classed as MMR protein-intact (MMR-I). According to KRAS mutation and MSI status, CRC was classified into 4 groups: Group 1, KRAS-mutated and MMR-I; Group 2, KRAS-mutated and MMR-D; Group 3, KRAS wild and MMR-I; and Group 4, KRAS wild and MMR-D. We found that patients in Group4 had the best prognosis. In conclusion, combination status of KRAS and MSI status may be used as a prognostic biomarker for CRC patient, if validated by larger studies.
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Affiliation(s)
- Jing Hu
- The Comprehensive Cancer Center, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University and Clinical Cancer Institute of Nanjing University
| | - Wen-Yue Yan
- The Comprehensive Cancer Center, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine
| | - Li Xie
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University and Clinical Cancer Institute of Nanjing University
| | - Lei Cheng
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University and Clinical Cancer Institute of Nanjing University
| | - Mi Yang
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University and Clinical Cancer Institute of Nanjing University
| | - Li Li
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University and Clinical Cancer Institute of Nanjing University
| | - Jiong Shi
- Department of Pathology, Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Bao-Rui Liu
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University and Clinical Cancer Institute of Nanjing University
| | - Xiao-Ping Qian
- The Comprehensive Cancer Center, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University and Clinical Cancer Institute of Nanjing University
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Slattery ML, Herrick JS, Mullany LE, Wolff E, Hoffman MD, Pellatt DF, Stevens JR, Wolff RK. Colorectal tumor molecular phenotype and miRNA: expression profiles and prognosis. Mod Pathol 2016; 29:915-27. [PMID: 27198570 PMCID: PMC4967007 DOI: 10.1038/modpathol.2016.73] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/29/2016] [Accepted: 03/06/2016] [Indexed: 02/08/2023]
Abstract
MiRNAs regulate gene expression by post-transcriptionally suppressing mRNA translation or by causing mRNA degradation. It has been proposed that unique miRNAs influence specific tumor molecular phenotype. In this paper, we test the hypotheses that miRNA expression differs by tumor molecular phenotype and that those differences may influence prognosis. Data come from population-based studies of colorectal cancer conducted in Utah and the Northern California Kaiser Permanente Medical Care Program. A total of 1893 carcinoma samples were run on the Agilent Human miRNA Microarray V19.0 containing 2006 miRNAs. We assessed differences in miRNA expression between TP53-mutated and non-mutated, KRAS-mutated and non-mutated, BRAF-mutated and non-mutated, CpG island methylator phenotype (CIMP) high and CIMP low, and microsatellite instability (MSI) and microsatellite stable (MSS) colon and rectal tumors. Using a Cox proportional hazard model we evaluated if those miRNAs differentially expressed by tumor phenotype influenced survival after adjusting for age, sex, and AJCC stage. There were 22 differentially expressed miRNAs for TP53-mutated colon tumors and 5 for TP53-mutated rectal tumors with a fold change of >1.49 (or <0.67). Additionally, 13 miRNAS were differentially expressed for KRAS-mutated rectal tumors, 8 differentially expressed miRNAs for colon CIMP high tumors, and 2 differentially expressed miRNAs for BRAF-mutated colon tumors. The majority of differentially expressed miRNAS were observed between MSI and MSS tumors (94 differentially expressed miRNAs for colon; 41 differentially expressed miRNAs for rectal tumors). Of these miRNAs differentially expressed between MSI and MSS tumors, the majority were downregulated. Ten of the differentially expressed miRNAs were associated with survival; after adjustment for MSI status, five miRNAS, miR-196b-5p, miR-31-5p, miR-99b-5p, miR-636, and miR-192-3p, were significantly associated with survival. In summary, it appears that the majority of miRNAs that are differentially expressed by tumor molecular phenotype are MSI tumors. However, these miRNAs appear to have minimal effect on prognosis.
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Affiliation(s)
- Martha L. Slattery
- Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah 84108
| | - Jennifer S. Herrick
- Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah 84108
| | - Lila E. Mullany
- Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah 84108
| | - Erica Wolff
- Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah 84108
| | - Michael D. Hoffman
- Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah 84108
| | - Daniel F. Pellatt
- Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah 84108
| | - John R. Stevens
- Department of Mathematics and Statistics, Utah State University, 3900 Old Main Hill, Logan UT 84322-3900
| | - Roger K. Wolff
- Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah 84108
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Sonay TB, Koletou M, Wagner A. A survey of tandem repeat instabilities and associated gene expression changes in 35 colorectal cancers. BMC Genomics 2015; 16:702. [PMID: 26376692 PMCID: PMC4574073 DOI: 10.1186/s12864-015-1902-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 09/09/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Colorectal cancer is a major contributor to cancer morbidity and mortality. Tandem repeat instability and its effect on cancer phenotypes remain so far poorly studied on a genome-wide scale. RESULTS Here we analyze the genomes of 35 colorectal tumors and their matched normal (healthy) tissues for two types of tandem repeat instability, de-novo repeat gain or loss and repeat copy number variation. Specifically, we study for the first time genome-wide repeat instability in the promoters and exons of 18,439 genes, and examine the association of repeat instability with genome-scale gene expression levels. We find that tumors with a microsatellite instable (MSI) phenotype are enriched in genes with repeat instability, and that tumor genomes have significantly more genes with repeat instability compared to healthy tissues. Genes in tumor genomes with repeat instability in their promoters are significantly less expressed and show slightly higher levels of methylation. Genes in well-studied cancer-associated signaling pathways also contain significantly more unstable repeats in tumor genomes. Genes with such unstable repeats in the tumor-suppressor p53 pathway have lower expression levels, whereas genes with repeat instability in the MAPK and Wnt signaling pathways are expressed at higher levels, consistent with the oncogenic role they play in cancer. CONCLUSIONS Our results suggest that repeat instability in gene promoters and associated differential gene expression may play an important role in colorectal tumors, which is a first step towards the development of more effective molecular diagnostic approaches centered on repeat instability.
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Affiliation(s)
- Tugce Bilgin Sonay
- Anthropological Institute and Museum, University of Zurich, Zurich, Switzerland.
- Institute of Evolutionary Biology and Environmental Sciences, University of Zurich, Zurich, Switzerland.
| | | | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Sciences, University of Zurich, Zurich, Switzerland.
- The Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- The Santa Fe Institute, Santa Fe, NM, United States of America.
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10
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Grady WM, Markowitz SD. The molecular pathogenesis of colorectal cancer and its potential application to colorectal cancer screening. Dig Dis Sci 2015; 60:762-72. [PMID: 25492499 DOI: 10.1007/s10620-014-3444-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [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: 09/12/2014] [Accepted: 11/15/2014] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Advances in our understanding of the molecular genetics and epigenetics of colorectal cancer have led to novel insights into the pathogenesis of this common cancer. These advances have revealed that there are molecular subtypes of colon polyps and colon cancer and that these molecular subclasses have unique and discrete clinical and pathological features. Although the molecular characterization of these subgroups of colorectal polyps and cancer is only partially understood at this time, it does appear likely that classifying colon polyps and cancers based on their genomic instability and/or epigenomic instability status will eventually be useful for informing approaches for the prevention and early detection of colon polyps and colorectal cancer. CONCLUSIONS In this review, we will discuss our current understanding of the molecular pathogenesis of the polyp to cancer sequence and the potential to use this information to direct screening and prevention programs.
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Weisenberger DJ, Levine AJ, Long TI, Buchanan DD, Walters R, Clendenning M, Rosty C, Joshi AD, Stern MC, LeMarchand L, Lindor NM, Daftary D, Gallinger S, Selander T, Bapat B, Newcomb PA, Campbell PT, Casey G, Ahnen DJ, Baron JA, Haile RW, Hopper JL, Young JP, Laird PW, Siegmund KD. Association of the colorectal CpG island methylator phenotype with molecular features, risk factors, and family history. Cancer Epidemiol Biomarkers Prev 2015; 24:512-519. [PMID: 25587051 PMCID: PMC4355081 DOI: 10.1158/1055-9965.epi-14-1161] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The CpG island methylator phenotype (CIMP) represents a subset of colorectal cancers characterized by widespread aberrant DNA hypermethylation at select CpG islands. The risk factors and environmental exposures contributing to etiologic heterogeneity between CIMP and non-CIMP tumors are not known. METHODS We measured the CIMP status of 3,119 primary population-based colorectal cancer tumors from the multinational Colon Cancer Family Registry. Etiologic heterogeneity was assessed by a case-case study comparing risk factor frequency of colorectal cancer cases with CIMP and non-CIMP tumors using logistic regression to estimate the case-case odds ratio (ccOR). RESULTS We found associations between tumor CIMP status and MSI-H (ccOR = 7.6), BRAF V600E mutation (ccOR = 59.8), proximal tumor site (ccOR = 9; all P < 0.0001), female sex [ccOR = 1.8; 95% confidence interval (CI), 1.5-2.1], older age (ccOR = 4.0 comparing over 70 years vs. under 50; 95% CI, 3.0-5.5), and family history of CRC (ccOR = 0.6; 95% CI, 0.5-0.7). While use of NSAIDs varied by tumor CIMP status for both males and females (P = 0.0001 and P = 0.02, respectively), use of multivitamin or calcium supplements did not. Only for female colorectal cancer was CIMP status associated with increased pack-years of smoking (Ptrend < 0.001) and body mass index (BMI; Ptrend = 0.03). CONCLUSIONS The frequency of several colorectal cancer risk factors varied by CIMP status, and the associations of smoking and obesity with tumor subtype were evident only for females. IMPACT Differences in the associations of a unique DNA methylation-based subgroup of colorectal cancer with important lifestyle and environmental exposures increase understanding of the molecular pathologic epidemiology of this heavily methylated subset of colorectal cancer. Cancer Epidemiol Biomarkers Prev; 24(3); 512-9. ©2015 AACR.
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Affiliation(s)
- Daniel J. Weisenberger
- USC Epigenome Center, University of Southern California, Los Angeles, CA
- Department of Biochemistry and Molecular Biology,University of Southern California, Los Angeles, CA, USA
| | - A. Joan Levine
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tiffany I. Long
- Department of Surgery, University of Southern California, Los Angeles, CA, USA
| | - Daniel D. Buchanan
- Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, VIC, Australia
| | - Rhiannon Walters
- Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology
| | - Mark Clendenning
- Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology
| | - Christophe Rosty
- Queensland Institute of Medical Research, Herston, QLD 4029, Australia
| | - Amit D. Joshi
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mariana C. Stern
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Loic LeMarchand
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, HI
| | | | - Darshana Daftary
- Department of Pathology and Laboratory Medicine, Samuel Lunenfield Research Institute, Mt. Sinai Hospital, Toronto, Ontario, Canada
| | - Steven Gallinger
- Department of Pathology and Laboratory Medicine, Samuel Lunenfield Research Institute, Mt. Sinai Hospital, Toronto, Ontario, Canada
| | - Teresa Selander
- Department of Pathology and Laboratory Medicine, Samuel Lunenfield Research Institute, Mt. Sinai Hospital, Toronto, Ontario, Canada
| | - Bharati Bapat
- Department of Pathology and Laboratory Medicine, Samuel Lunenfield Research Institute, Mt. Sinai Hospital, Toronto, Ontario, Canada
| | - Polly A. Newcomb
- Epidemiology Department, University of Washington and Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Graham Casey
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Dennis J. Ahnen
- Division of Gastroenterology, University of Colorado School of Medicine, Denver, Colorado
| | - John A. Baron
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Robert W. Haile
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, VIC, Australia
| | - Joanne P. Young
- Queensland Institute of Medical Research, Herston, QLD 4029, Australia
- The Queen Elizabeth Hospital, Woodville, SA 5011, Australia
| | - Peter W. Laird
- USC Epigenome Center, University of Southern California, Los Angeles, CA
- Department of Biochemistry and Molecular Biology,University of Southern California, Los Angeles, CA, USA
- Department of Surgery, University of Southern California, Los Angeles, CA, USA
| | - Kimberly D. Siegmund
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
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12
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Gould-Suarez M, El-Serag HB, Musher B, Franco LM, Chen GJ. Cost-effectiveness and diagnostic effectiveness analyses of multiple algorithms for the diagnosis of Lynch syndrome. Dig Dis Sci 2014; 59:2913-26. [PMID: 24957400 DOI: 10.1007/s10620-014-3248-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [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: 03/04/2014] [Accepted: 06/03/2014] [Indexed: 01/26/2023]
Abstract
BACKGROUND AND AIMS The optimal algorithm to identify Lynch syndrome (LS) among patients with colorectal cancer (CRC) is unclear. The definitive test for LS, germline testing, is too expensive to be applied in all cases. Initial screening with the revised Bethesda Guidelines (RBG) cannot be applied in a considerable number of cases due to missing information. METHODS We developed a model to evaluate the cost-effectiveness of 10 strategies for diagnosing LS. Three main issues are addressed: modeling estimates (20-40%) of RBG applicability; comparing sequential or parallel use of microsatellite instability (MSI) and immunohistochemistry (IHC); and a threshold analysis of the charge value below which universal germline testing becomes the most cost-effective strategy. RESULTS LS detection rates in RBG-based strategies decreased to 64.1-70.6% with 20% inapplicable RBG. The strategy that uses MSI alone had lower yield, but also lower cost than strategies that use MSI sequentially or in parallel with IHC. The use of MSI and IHC in parallel was less affected by variations in the sensitivity and specificity of these tests. Universal germline testing had the highest yield and the highest cost of all strategies. The model estimated that if charges for germline testing drop to $633-1,518, universal testing of all newly diagnosed CRC cases becomes the most cost-effective strategy. CONCLUSIONS The low applicability of RBG makes strategies employing initial laboratory-based testing more cost-effective. Of these strategies, parallel testing with MSI and IHC offers the most robust yield. With a considerable drop in cost, universal germline testing may become the most cost-effective strategy for the diagnosis of LS.
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13
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Velho S, Pinto A, Licastro D, Oliveira MJ, Sousa F, Stupka E, Seruca R. Dissecting the signaling pathways associated with the oncogenic activity of MLK3 P252H mutation. BMC Cancer 2014; 14:182. [PMID: 24628919 PMCID: PMC3995575 DOI: 10.1186/1471-2407-14-182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 02/25/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND MLK3 gene mutations were described to occur in about 20% of microsatellite unstable gastrointestinal cancers and to harbor oncogenic activity. In particular, mutation P252H, located in the kinase domain, was found to have a strong transforming potential, and to promote the growth of highly invasive tumors when subcutaneously injected in nude mice. Nevertheless, the molecular mechanism underlying the oncogenic activity of P252H mutant remained elusive. METHODS In this work, we performed Illumina Whole Genome arrays on three biological replicas of human HEK293 cells stably transfected with the wild-type MLK3, the P252H mutation and with the empty vector (Mock) in order to identify the putative signaling pathways associated with P252H mutation. RESULTS Our microarray results showed that mutant MLK3 deregulates several important colorectal cancer- associated signaling pathways such as WNT, MAPK, NOTCH, TGF-beta and p53, helping to narrow down the number of potential MLK3 targets responsible for its oncogenic effects. A more detailed analysis of the alterations affecting the WNT signaling pathway revealed a down-regulation of molecules involved in the canonical pathway, such as DVL2, LEF1, CCND1 and c-Myc, and an up-regulation of DKK, a well-known negative regulator of canonical WNT signaling, in MLK3 mutant cells. Additionally, FZD6 and FZD10 genes, known to act as negative regulators of the canonical WNT signaling cascade and as positive regulators of the planar cell polarity (PCP) pathway, a non-canonic WNT pathway, were found to be up-regulated in P252H cells. CONCLUSION The results provide an overall view of the expression profile associated with mutant MLK3, and they support the functional role of mutant MLK3 by showing a deregulation of several signaling pathways known to play important roles in the development and progression of colorectal cancer. The results also suggest that mutant MLK3 may be a novel modulator of WNT signaling, and pinpoint the activation of PCP pathway as a possible mechanism underlying the invasive potential of MLK3 mutant cells.
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Affiliation(s)
- Sérgia Velho
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto,Portugal
| | - Ana Pinto
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto,Portugal
- New Therapies Group, INEB-Institute for Biomedical Engineering, Porto, Portugal
| | | | - Maria José Oliveira
- New Therapies Group, INEB-Institute for Biomedical Engineering, Porto, Portugal
| | - Filipa Sousa
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto,Portugal
| | - Elia Stupka
- Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Raquel Seruca
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto,Portugal
- Medical Faculty of the University of Porto, Porto, Portugal
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14
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Zhu Y, Yang SR, Wang PP, Savas S, Wish T, Zhao J, Green R, Woods M, Sun Z, Roebothan B, Squires J, Buehler S, Dicks E, Zhao J, Mclaughlin JR, Parfrey PS, Campbell PT. Influence of pre-diagnostic cigarette smoking on colorectal cancer survival: overall and by tumour molecular phenotype. Br J Cancer 2014; 110:1359-66. [PMID: 24448365 PMCID: PMC3950884 DOI: 10.1038/bjc.2014.6] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 12/11/2013] [Accepted: 12/19/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Smoking is a risk factor for incident colorectal cancer (CRC); however, it is unclear about its influence on survival after CRC diagnosis. METHODS A cohort of 706 CRC patients diagnosed from 1999 to 2003 in Newfoundland and Labrador, Canada, was followed for mortality and recurrence until April 2010. Smoking and other relevant data were collected by questionnaire after cancer diagnosis, using a referent period of '2 years before diagnosis' to capture pre-diagnosis information. Molecular analyses of microsatellite instability (MSI) status and BRAF V600E mutation status were performed in tumour tissue using standard techniques. Multivariate hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated with Cox proportional hazards regression, controlling for major prognostic factors. RESULTS Compared with never smokers, all-cause mortality (overall survival, OS) was higher for current (HR: 1.78; 95% CI: 1.04-3.06), but not for former (HR: 1.06; 95% CI: 0.71-1.59) smokers. The associations of cigarette smoking with the study outcomes were higher among patients with ≥40 pack-years of smoking (OS: HR: 1.72; 95% CI: 1.03-2.85; disease-free survival (DFS: HR: 1.99; 95% CI: 1.25-3.19), those who smoked ≥30 cigarettes per day (DFS: HR: 1.80; 95% CI: 1.22-2.67), and those with microsatellite stable (MSS) or MSI-low tumours (OS: HR: 1.38; 95% CI: 1.04-1.82 and DFS: HR: 1.32; 95% CI: 1.01-1.72). Potential heterogeneity was noted for sex (DFS HR: 1.68 for men and 1.01 for women: P for heterogeneity=0.04), and age at diagnosis (OS: HR: 1.11 for patients aged <60 and 1.69 for patients aged ≥60: P for heterogeneity=0.03). CONCLUSIONS Pre-diagnosis cigarette smoking is associated with worsened prognosis among patients with CRC.
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Affiliation(s)
- Y Zhu
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
- Department of Epidemiology, School of Public Health, Tianjin Medical University, Tianjin, China
| | - S R Yang
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - P P Wang
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
- Department of Epidemiology, School of Public Health, Tianjin Medical University, Tianjin, China
| | - S Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - T Wish
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - J Zhao
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - R Green
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - M Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Z Sun
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - B Roebothan
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - J Squires
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - S Buehler
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - E Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - J Zhao
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - J R Mclaughlin
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - P S Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - P T Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
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15
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Abstract
With ever-increasing amounts of metabolomics data produced each year, there is an even greater need to disseminate data and knowledge produced in a standard and reproducible way. To assist with this a general purpose, open source metabolomics repository, MetaboLights, was launched in 2012. To promote a community standard, initially culminated as metabolomics standards initiative (MSI), COordination of Standards in MetabOlomicS (COSMOS) was introduced. COSMOS aims to link life science e-infrastructures within the worldwide metabolomics community as well as develop and maintain open source exchange formats for raw and processed data, ensuring better flow of metabolomics information.
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Affiliation(s)
- Reza M Salek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK
| | - Kenneth Haug
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Christoph Steinbeck
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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16
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Tran B, Kopetz S, Tie J, Gibbs P, Jiang ZQ, Lieu CH, Agarwal A, Maru DM, Sieber O, Desai J. Impact of BRAF mutation and microsatellite instability on the pattern of metastatic spread and prognosis in metastatic colorectal cancer. Cancer 2011; 117:4623-32. [PMID: 21456008 PMCID: PMC4257471 DOI: 10.1002/cncr.26086] [Citation(s) in RCA: 544] [Impact Index Per Article: 41.8] [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: 11/23/2010] [Revised: 12/30/2010] [Accepted: 12/30/2010] [Indexed: 02/03/2023]
Abstract
BACKGROUND It is hypothesized that BRAF mutant cancers represent a discrete subset of metastatic colorectal cancer (CRC) defined by poorer survival. This study investigates whether BRAF mutant CRC is further defined by a distinct pattern of metastatic spread and explores the impact of BRAF mutation and microsatellite instability (MSI) on prognosis in metastatic CRC. METHODS By using prospective clinical data and molecular analyses from 2 major centers (Royal Melbourne Hospital and The University of Texas MD Anderson Cancer Center), patients with known BRAF mutation status were analyzed for clinical characteristics, survival, and metastatic sites. RESULTS The authors identified 524 metastatic CRC patients where BRAF mutation status was known; 57 (11%) were BRAF mutant tumors. BRAF mutant tumors were significantly associated with right-sided primary tumor, MSI, and poorer survival (median, 10.4 months vs 34.7 months, P < .001). A distinct pattern of metastatic spread was observed in BRAF mutant tumors, namely higher rates of peritoneal metastases (46% vs 24%, P = .001), distant lymph node metastases (53% vs 38%, P = .008), and lower rates of lung metastases (35% vs 49%, P = .049). In additional survival analyses, MSI tumors had significantly poorer survival compared with microsatellite stable tumors (22.1 months vs 11.1 months, P = .017), but this difference was not evident in the BRAF mutant population. CONCLUSIONS The pattern of metastatic spread observed in this study further defines BRAF mutant CRC as a discrete disease subset. The authors demonstrated that, unlikely early stage disease, MSI is associated with poorer survival in metastatic CRC, although this is driven by its association with BRAF mutation.
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Affiliation(s)
- Ben Tran
- Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne, Australia
| | - Scott Kopetz
- The University of Texas M.D. Anderson Cancer Centre, Houston, Texas, USA
| | - Jeanne Tie
- Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne, Australia; Ludwig Colon Cancer Initiative Biomarker Laboratory, Ludwig Institute for Cancer Research, Melbourne, Australia
| | - Peter Gibbs
- Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne, Australia; Ludwig Colon Cancer Initiative Biomarker Laboratory, Ludwig Institute for Cancer Research, Melbourne, Australia; Biogrid Australia, Melbourne, Australia
| | - Zhi-Qin Jiang
- The University of Texas M.D. Anderson Cancer Centre, Houston, Texas, USA
| | - Christopher H Lieu
- The University of Texas M.D. Anderson Cancer Centre, Houston, Texas, USA
| | - Atin Agarwal
- The University of Texas M.D. Anderson Cancer Centre, Houston, Texas, USA
| | - Dipen M Maru
- The University of Texas M.D. Anderson Cancer Centre, Houston, Texas, USA
| | - Oliver Sieber
- Ludwig Colon Cancer Initiative Biomarker Laboratory, Ludwig Institute for Cancer Research, Melbourne, Australia; Biogrid Australia, Melbourne, Australia
| | - Jayesh Desai
- Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne, Australia; Ludwig Colon Cancer Initiative Biomarker Laboratory, Ludwig Institute for Cancer Research, Melbourne, Australia; Biogrid Australia, Melbourne, Australia
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17
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Grassl J, Taylor NL, Millar AH. Matrix-assisted laser desorption/ionisation mass spectrometry imaging and its development for plant protein imaging. Plant Methods 2011; 7:21. [PMID: 21726462 PMCID: PMC3141805 DOI: 10.1186/1746-4811-7-21] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 07/05/2011] [Indexed: 05/17/2023]
Abstract
Matrix-Assisted Laser Desorption/Ionisation (MALDI) mass spectrometry imaging (MSI) uses the power of high mass resolution time of flight (ToF) mass spectrometry coupled to the raster of lasers shots across the cut surface of tissues to provide new insights into the spatial distribution of biomolecules within biological tissues. The history of this technique in animals and plants is considered and the potential for analysis of proteins by this technique in plants is discussed. Protein biomarker identification from MALDI-MSI is a challenge and a number of different approaches to address this bottleneck are discussed. The technical considerations needed for MALDI-MSI are reviewed and these are presented alongside examples from our own work and a protocol for MALDI-MSI of proteins in plant samples.
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Affiliation(s)
- Julia Grassl
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, Crawley, WA 6009, Australia
| | - Nicolas L Taylor
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, Crawley, WA 6009, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, Crawley, WA 6009, Australia
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18
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Zimmerman TA, Rubakhin SS, Sweedler JV. MALDI mass spectrometry imaging of neuronal cell cultures. J Am Soc Mass Spectrom 2011; 22:828-36. [PMID: 21472517 PMCID: PMC3113696 DOI: 10.1007/s13361-011-0111-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 02/21/2011] [Accepted: 02/23/2011] [Indexed: 05/09/2023]
Abstract
Mass spectrometry imaging (MSI) provides the ability to detect and identify a broad range of analytes and their spatial distributions from a variety of sample types, including tissue sections. Here we describe an approach for probing neuropeptides from sparse cell cultures using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MSI--at single cell spatial resolution-in both MS and tandem MS modes. Cultures of Aplysia californica neurons are grown on an array of glass beads embedded in a stretchable layer of Parafilm M. As the membrane is stretched, the beads/neurons are separated physically and the separated beads/neurons analyzed via MALDI TOF MS. Compared with direct MS imaging of samples, the stretching procedure enhances analyte extraction and incorporation into the MALDI matrix, with negligible analyte spread between separated beads. MALDI tandem MSI using the stretched imaging approach yields localization maps of both parent and fragment ions from Aplysia pedal peptide, thereby confirming peptide identification. This methodology represents a flexible platform for MSI investigation of a variety of cell cultures, including functioning neuronal networks.
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Affiliation(s)
- Tyler A. Zimmerman
- Department of Chemistry, University of Illinois, 600 South Mathews Ave.; 63–5, Urbana, IL 61801, USA
- Beckman Institute, University of Illinois, Urbana, IL 61801, USA
| | - Stanislav S. Rubakhin
- Department of Chemistry, University of Illinois, 600 South Mathews Ave.; 63–5, Urbana, IL 61801, USA
- Beckman Institute, University of Illinois, Urbana, IL 61801, USA
| | - Jonathan V. Sweedler
- Department of Chemistry, University of Illinois, 600 South Mathews Ave.; 63–5, Urbana, IL 61801, USA
- Beckman Institute, University of Illinois, Urbana, IL 61801, USA
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Kulendran M, Stebbing JF, Marks CG, Rockall TA. Predictive and prognostic factors in colorectal cancer: a personalized approach. Cancers (Basel) 2011; 3:1622-38. [PMID: 24212777 PMCID: PMC3757382 DOI: 10.3390/cancers3021622] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2011] [Revised: 03/13/2011] [Accepted: 03/18/2011] [Indexed: 12/13/2022] Open
Abstract
It is an exciting time for all those engaged in the treatment of colorectal cancer. The advent of new therapies presents the opportunity for a personalized approach to the patient. This approach considers the complex genetic mechanisms involved in tumorigenesis in addition to classical clinicopathological staging. The potential predictive and prognostic biomarkers which have stemmed from the study of the genetic basis of colorectal cancer and therapeutics are discussed with a focus on mismatch repair status, KRAS, BRAF, 18qLOH, CIMP and TGF-β.
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Affiliation(s)
- Myutan Kulendran
- Department of Coloproctology, Royal Surrey County Hospital NHS Foundation Trust, Egerton Road, Guildford, UK.
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20
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Abstract
The promise of personalised medicine is now a clinical reality, with colorectal cancer genetics at the forefront of this next major advance in clinical medicine. This is no more evident than in the recent advances in testing of colorectal cancers for specific molecular alterations in order to guide treatment with the monoclonal antibody therapies cetuximab and panitumumab, which target the epidermal growth factor receptor. In this review, genetic mechanisms of colorectal cancer and how these alterations relate to emerging biomarkers for early detection and risk stratification (diagnostic markers), prognosis (prognostic markers) and the prediction of treatment responses (predictive markers) are examined.
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Affiliation(s)
- Colin C. Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - William M. Grady
- Clinical Research Division, Fred Hutchison Cancer Research Center, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
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21
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Steinbakk A, Malpica A, Slewa A, Gudlaugsson E, Janssen EAM, Arends M, Kruse AJ, Yinhua Y, Feng W, Baak JP. High frequency microsatellite instability has a prognostic value in endometrial endometrioid adenocarcinoma, but only in FIGO stage 1 cases. Anal Cell Pathol (Amst) 2010; 33:245-255. [PMID: 21079294 PMCID: PMC4605578 DOI: 10.3233/acp-clo-2010-0550] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
OBJECTIVES to analyze the prognostic value of microsatellite instability (MSI) in a population-based study of FIGO stage 1-4 endometrial endometrioid adenocarcinomas. STUDY DESIGN survival analysis in 273 patients of MSI status and clinico-pathologic features. Using a highly sensitive pentaplex polymerase chain reaction to establish MSI status, cases were divided into microsatellite stable (MSS), MSI-low (MSI-L, 1 marker positive) and MSI-high (MSI-H, 2-5 markers positive). RESULTS after 61 months median follow-up (1-209), 34 (12.5%) of the patients developed metastases but only 6.4% of the FIGO 1. MSI (especially as MSI-H vs. MSS/MSI-Lcombined) was prognostic in FIGO 1 but not in FIGO 2-4. The 5 and 10 year recurrence-free survival rates were 98% and 95% in the MSS/MSI-L vs. 85% and 73% in the MSI-H patients (p=0.005). CONCLUSIONS MSI-H status assessed by pentaplex polymerase chain reaction is an indicator of poor prognosis in FIGO 1, but not in FIGO 2-4 endometrial endometrioid adenocarcinomas.
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Affiliation(s)
- Anita Steinbakk
- Department of PathologyStavanger University HospitalStavangerNorway
- Department of GynaecologyStavanger University HospitalStavangerNorway
- The Gade InstituteUniversity of BergenBergenNorway
| | - Anais Malpica
- Departments of Pathology and Gynecologic OncologyThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Aida Slewa
- Department of PathologyStavanger University HospitalStavangerNorway
| | - Einar Gudlaugsson
- Department of PathologyStavanger University HospitalStavangerNorway
- The Gade InstituteUniversity of BergenBergenNorway
| | | | - Mark Arends
- Department of PathologyAddenbrooke’s HospitalUniversity of CambridgeCambridgeEngland
| | - Arnold Jan Kruse
- Department of GynecologyAcademic Medical CenterMaastrichtThe Netherlands
| | - Yu Yinhua
- Department of Experimental MedicineThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Weiwei Feng
- Department of GynecologyObstetrics and Gynecology Hospital of Fudan UniversityShanghaiChina
| | - Jan P. Baak
- Department of PathologyStavanger University HospitalStavangerNorway
- The Gade InstituteUniversity of BergenBergenNorway
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22
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Ogino S, Nosho K, Kirkner GJ, Kawasaki T, Meyerhardt JA, Loda M, Giovannucci EL, Fuchs CS. CpG island methylator phenotype, microsatellite instability, BRAF mutation and clinical outcome in colon cancer. Gut 2009; 58:90-6. [PMID: 18832519 PMCID: PMC2679586 DOI: 10.1136/gut.2008.155473] [Citation(s) in RCA: 611] [Impact Index Per Article: 40.7] [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] [Indexed: 12/12/2022]
Abstract
BACKGROUND The CpG island methylator phenotype (CIMP), characterised by widespread promoter methylation, is associated with microsatellite instability (MSI) and BRAF mutation in colorectal cancer. The independent effect of CIMP, MSI and BRAF mutation on prognosis remains uncertain. METHODS Utilising 649 colon cancers (stage I-IV) in two independent cohort studies, we quantified DNA methylation in eight CIMP-specific promoters (CACNA1G, CDKN2A (p16), CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1) as well as CHFR, HIC1, IGFBP3, MGMT, MINT1, MINT31, p14, and WRN by using MethyLight technology. We examined MSI, KRAS and BRAF status. Cox proportional hazard models computed hazard ratios (HRs) for colon cancer-specific and overall mortalities, adjusting for patient characteristics and tumoral molecular features. RESULTS After adjustment for other predictors of patient survival, patients with CIMP-high cancers (126 (19%) tumours with >or=6/8 methylated CIMP-specific promoters) experienced a significantly low colon cancer-specific mortality (multivariate HR 0.44, 95% confidence interval (CI) 0.22 to 0.88), whereas the BRAF mutation was significantly associated with a high cancer-specific mortality (multivariate HR 1.97, 95% CI 1.13 to 3.42). A trend toward a low cancer-specific mortality was observed for MSI-high tumours (multivariate HR 0.70, 95% CI 0.36 to 1.37). In stratified analyses, CIMP-high tumours were associated with a significant reduction in colon cancer-specific mortality, regardless of both MSI and BRAF status. The relation between CIMP-high and lower mortality appeared to be consistent across all stages. KRAS mutation was unrelated to prognostic significance. CONCLUSION CIMP-high appears to be an independent predictor of a low colon cancer-specific mortality, while BRAF mutation is associated with a high colon cancer-specific mortality.
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Affiliation(s)
- Shuji Ogino
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115 USA.
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Li JH, Shi XZ, Lv S, Liu M, Xu GW. Effect of Helicobacter pylori infection on p53 expression of gastric mucosa and adenocarcinoma with microsatellite instability. World J Gastroenterol 2005; 11:4363-6. [PMID: 16038035 PMCID: PMC4434663 DOI: 10.3748/wjg.v11.i28.4363] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2004] [Revised: 12/01/2004] [Accepted: 12/03/2004] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate the relationship between Helicobacter pylori (H pylori) infection, microsatellite instability and the expressions of the p53 in gastritis, intestinal metaplasia and gastric adenocarcinoma and to elucidate the mechanism of gastric carcinogenesis relating to H pylori infection. METHODS One hundred and eight endoscopic biopsies and gastric adenocarcinoma were available for the study including 33 cases of normal, 45 cases of gastritis, 30 cases of intestinal metaplasia, and 46 cases of gastric adenocarcinoma. Peripheral blood samples of these patients were also collected. H pylori infection and p53 expressions were detected by means of streptavidin-peroxidase (SP) immunohistochemical method. Microsatellite loci were studied by PCR-SSCP-CE using the markers BAT-26, D17S261, D3S1283, D2S123, and D3S1611. MSI was defined as the peak shift in the DNA of the gastric tissue compared with that of the peripheral blood samples. Based on the number of mutated MSI markers, specimens were characterized as high MSI (MSI-H) if they manifested instability at two or more markers, low MSI (MSI-L) if unstable at only one marker, and microsatellite stable (MSS) if they showed no instability at any marker. RESULTS H pylori infection was detected in the samples of gastritis, intestinal metaplasia, and gastric adenocarcinoma and the infection frequencies were 84.4%, 76.7%, and 65.2%, respectively, whereas no H pylori infection was detected in the samples of normal control. There was a significant difference in the infection rates between gastritis and carcinoma samples (P = 0.035). No MSI was detected in gastritis samples, one MSI-H and two MSI-L were detected among the 30 intestinal metaplasia samples, and 12 MSI-H and 3 MSI-L were detected in the 46 gastric carcinomas. In those gastric carcinomas, the MSI-H frequency in H pylori-positive group was significantly higher than that in H pylori-negative group. No p53 expression was detected in the normal and gastritis samples from dyspeptic patients. P53-positive immunohistochemical staining was detected in 13.3% of intestinal metaplasia samples and in 43.5% of gastric carcinoma samples. The levels of p53 in H pylori-positive samples were higher than those in the negative group when the carcinoma samples were subdivided into H pylori-positive and -negative groups (P = 0.013). Eight samples were detected with positive p53 expression out of the 11 MSI-H carcinomas with H pylori infection and no p53 expression could be seen in the H pylori-negative samples. CONCLUSION H pylori affect the p53 pattern in gastric mucosa when MMR system fails to work. Mutations of the p53 gene seem to be an early event in gastric carcinogenesis.
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Affiliation(s)
- Jian-Hua Li
- Laboratory Center of Molecular Biology, the Second Hospital of Dalian Medical University, Dalian 116027, Liaoning Province, China.
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Fernebro E, Halvarsson B, Baldetorp B, Nilbert M. Predominance of CIN versus MSI in the development of rectal cancer at young age. BMC Cancer 2002; 2:25. [PMID: 12379157 PMCID: PMC130963 DOI: 10.1186/1471-2407-2-25] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2002] [Accepted: 10/14/2002] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Development of proximal and distal colorectal cancers involve partly different mechanisms associated with the microsatellite instability (MSI) and the chromosomal instability (CIN) pathways. Colorectal cancers in patients under 50 years of age represent about 5% of the total number of tumors and have been associated with an increased frequency of MSI tumors. However, MSI and CIN may play different roles in the development of colon cancer and rectal cancer, and we have specifically investigated their contribution to the development of rectal cancer at young age. METHODS Thirty rectal cancers diagnosed before the age of 50 were characterized for DNA-ploidy, MSI, mutations of KRAS and CTNNB1 and immunohistochemical expression of p53, beta-catenin and of the mismatch repair (MMR) proteins MLH1 and MSH2. RESULTS DNA aneuploidy was detected in 21/30 tumors, KRAS mutations in 6 tumors, no mutations of CTNNB1 were detected but immunohistochemical staining for beta-catenin showed nuclear staining in 6 tumors, and immunohistochemical expression of p53 was detected in 18 tumors. MSI was detected in 3/30 tumors, all of which showed and immunohistochemical loss of staining for the MMR protein MSH2, which strongly indicates a phenotype associated with hereditary nonpolyposis colorectal cancer (HNPCC). CONCLUSIONS MSI occurs only in a small fraction of the tumors from young patients with rectal cancer, but when present it strongly indicates an underlying HNPCC-causing mutation, and other mechanisms than HNPCC thus cause rectal cancer in the majority of young patients.
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Affiliation(s)
- Eva Fernebro
- Department of Oncology, University Hospital, Lund, Sweden
| | | | - Bo Baldetorp
- Department of Oncology, University Hospital, Lund, Sweden
| | - Mef Nilbert
- Department of Oncology, University Hospital, Lund, Sweden
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Bras-Gonçalves RA, Rosty C, Laurent-Puig P, Soulié P, Dutrillaux B, Poupon MF. Sensitivity to CPT-11 of xenografted human colorectal cancers as a function of microsatellite instability and p53 status. Br J Cancer 2000; 82:913-23. [PMID: 10732766 PMCID: PMC2374412 DOI: 10.1054/bjoc.1999.1019] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Biological parameters influencing the response of human colorectal cancers (CRCs) to CPT-11, a topoisomerase 1 (top1) inhibitor, were investigated using a panel of nine CRCs xenografted into nude mice. CRC xenografts differed in their p53 status (wt or muf) and in their microsatellite instability phenotype (MSI+ when altered). Five CRC xenografts were established from clinical samples. All five had a functional p53, two were MSI+ and three were MSI-. Tumour-bearing nude mice were treated intraperitonealy (i.p.) with CPT-11. At 10 mg kg(-1) of CPT-11, four injections at 4-day intervals, four of the five xenografts responded to CPT-11 (growth delay of up to 10 days); the non-responder tumour was MSI-. At 40 mg kg(-1) of CPT-11, six injections at 4-day intervals, the five CRCs displayed variable but marked responses with complete regressions. In order to assess the role of p53 status in CPT-11 response, four CRC lines were used. HT29 cell line was MSI-/Ala273-mutp53, its subclone HT29A3 being transfected by wtp53. LoVo cell line was MSI+/wtp53, its subclone X17LoVo dominantly expressed Ala273-mutp53 after transfection. LoVo tumours (MSI+/mutp53) were more sensitive than X17LoVo (MSI+/mutp53. HT 29 tumours (MSI-Imutp53), were refractory to CPT-11 while HT29A3 tumours (MSI-/wtp53) were sensitive, showing that wtp53 improves the drug-response in these MSI- tumours. Levels of mRNA expression of top1, fasR, TP53 and mdr1 were semi-quantified by reverse transcription polymerase chain reaction. None of these parameters correlated with CPT-11 response. Taken together, these observations indicate that MSI and p53 alterations could be associated with different CPT-11 sensitivities; MSI phenotype moderately influences the CPT-11 sensitivity, MSI+ being more sensitive than MSI(-)CRC freshly obtained from patients, mutp53 status being associated with a poor response to CPT-11.
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Abstract
To pursue the pathogenesis of endometrial carcinogenesis, we investigated microsatellite instability, mutations in the PTEN, TGF beta RII, IGFIIR, and BAX genes, and LOHs on 10q in 18 putative endometrial premalignant lesions (11 endometrial atypical hyperplasias (ATHs), 2 complex hyperplasias, and 5 simple hyperplasias) as well as 8 endometrial cancers (ECs). In the ATH cases, MSIs as well as LOHs at 10q were observed at frequencies similar to those in ECs. Mutations in PTEN, BAX, and IGFIIR were observed only in ATHs and ECs. These results suggest that (1) PTEN, BAX, and IGFIIR are already mutated in ATHs, and (2) ATH is one of the precursor lesions which could lead to EC.
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Affiliation(s)
- K Yoshinaga
- Department of Molecular Pathology, Tohoku University School of Medicine, Sendai
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