1
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White B, Swietach P. What can we learn about acid-base transporters in cancer from studying somatic mutations in their genes? Pflugers Arch 2024; 476:673-688. [PMID: 37999800 PMCID: PMC11006749 DOI: 10.1007/s00424-023-02876-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/25/2023]
Abstract
Acidosis is a chemical signature of the tumour microenvironment that challenges intracellular pH homeostasis. The orchestrated activity of acid-base transporters of the solute-linked carrier (SLC) family is critical for removing the end-products of fermentative metabolism (lactate/H+) and maintaining a favourably alkaline cytoplasm. Given the critical role of pH homeostasis in enabling cellular activities, mutations in relevant SLC genes may impact the oncogenic process, emerging as negatively or positively selected, or as driver or passenger mutations. To address this, we performed a pan-cancer analysis of The Cancer Genome Atlas simple nucleotide variation data for acid/base-transporting SLCs (ABT-SLCs). Somatic mutation patterns of monocarboxylate transporters (MCTs) were consistent with their proposed essentiality in facilitating lactate/H+ efflux. Among all cancers, tumours of uterine corpus endometrial cancer carried more ABT-SLC somatic mutations than expected from median tumour mutation burden. Among these, somatic mutations in SLC4A3 had features consistent with meaningful consequences on cellular fitness. Definitive evidence for ABT-SLCs as 'cancer essential' or 'driver genes' will have to consider microenvironmental context in genomic sequencing because bulk approaches are insensitive to pH heterogeneity within tumours. Moreover, genomic analyses must be validated with phenotypic outcomes (i.e. SLC-carried flux) to appreciate the opportunities for targeting acid-base transport in cancers.
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Affiliation(s)
- Bobby White
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK.
| | - Pawel Swietach
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK
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2
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Demetriou AN, Chow F, Craig DW, Webb MG, Ormond DR, Battiste J, Chakravarti A, Colman H, Villano JL, Schneider BP, Liu JKC, Churchman ML, Zada G. Profiling the molecular and clinical landscape of glioblastoma utilizing the Oncology Research Information Exchange Network brain cancer database. Neurooncol Adv 2024; 6:vdae046. [PMID: 38665799 PMCID: PMC11044707 DOI: 10.1093/noajnl/vdae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024] Open
Abstract
Background Glioblastoma exhibits aggressive growth and poor outcomes despite treatment, and its marked variability renders therapeutic design and prognostication challenging. The Oncology Research Information Exchange Network (ORIEN) database contains complementary clinical, genomic, and transcriptomic profiling of 206 glioblastoma patients, providing opportunities to identify novel associations between molecular features and clinical outcomes. Methods Survival analyses were performed using the Logrank test, and clinical features were evaluated using Wilcoxon and chi-squared tests with q-values derived via Benjamini-Hochberg correction. Mutational analyses utilized sample-level enrichments from whole exome sequencing data, and statistical tests were performed using the one-sided Fisher Exact test with Benjamini-Hochberg correction. Transcriptomic analyses utilized a student's t-test with Benjamini-Hochberg correction. Expression fold changes were processed with Ingenuity Pathway Analysis to determine pathway-level alterations between groups. Results Key findings include an association of MUC17, SYNE1, and TENM1 mutations with prolonged overall survival (OS); decreased OS associated with higher epithelial growth factor receptor (EGFR) mRNA expression, but not with EGFR amplification or mutation; a 14-transcript signature associated with OS > 2 years; and 2 transcripts associated with OS < 1 year. Conclusions Herein, we report the first clinical, genomic, and transcriptomic analysis of ORIEN glioblastoma cases, incorporating sample reclassification under updated 2021 diagnostic criteria. These findings create multiple avenues for further investigation and reinforce the value of multi-institutional consortia such as ORIEN in deepening our knowledge of intractable diseases such as glioblastoma.
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Affiliation(s)
- Alexandra N Demetriou
- Keck School of Medicine, University of Southern California (USC), Los Angeles, California, USA
| | - Frances Chow
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - David W Craig
- Department of Integrative Translational Sciences, City of Hope, Duarte, California, USA
| | - Michelle G Webb
- Department of Integrative Translational Sciences, City of Hope, Duarte, California, USA
| | - D Ryan Ormond
- Department of Neurosurgery, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - James Battiste
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Arnab Chakravarti
- Department of Radiation Oncology, College of Medicine at The Ohio State University, Columbus, Ohio, USA
| | - Howard Colman
- Huntsman Cancer Institute and Department of Neurosurgery, University of Utah, Salt Lake City, Utah, USA
| | - John L Villano
- Department of Internal Medicine, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Bryan P Schneider
- Department of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - James K C Liu
- Department of Neuro-Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | | | - Gabriel Zada
- Department of Neurological Surgery, Keck School of Medicine of USC, Los Angeles, California, USA
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3
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Aska EM, Zagidullin B, Pitkänen E, Kauppi L. Single-Cell Mononucleotide Microsatellite Analysis Reveals Differential Insertion-Deletion Dynamics in Mouse T Cells. Front Genet 2022; 13:913163. [PMID: 35873465 PMCID: PMC9304711 DOI: 10.3389/fgene.2022.913163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Microsatellite sequences are particularly prone to slippage during DNA replication, forming insertion-deletion loops that, if left unrepaired, result in de novo mutations (expansions or contractions of the repeat array). Mismatch repair (MMR) is a critical DNA repair mechanism that corrects these insertion-deletion loops, thereby maintaining microsatellite stability. MMR deficiency gives rise to the molecular phenotype known as microsatellite instability (MSI). By sequencing MMR-proficient and -deficient (Mlh1+/+ and Mlh1−/−) single-cell exomes from mouse T cells, we reveal here several previously unrecognized features of in vivo MSI. Specifically, mutational dynamics of insertions and deletions were different on multiple levels. Factors that associated with propensity of mononucleotide microsatellites to insertions versus deletions were: microsatellite length, nucleotide composition of the mononucleotide tract, gene length and transcriptional status, as well replication timing. Here, we show on a single-cell level that deletions — the predominant MSI type in MMR-deficient cells — are preferentially associated with longer A/T tracts, long or transcribed genes and later-replicating genes.
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Affiliation(s)
- Elli-Mari Aska
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Bulat Zagidullin
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Esa Pitkänen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Liisa Kauppi
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- *Correspondence: Liisa Kauppi,
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4
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Bae JH, Zhang DY. Predicting stability of DNA bulge at mononucleotide microsatellite. Nucleic Acids Res 2021; 49:7901-7908. [PMID: 34308470 PMCID: PMC8373066 DOI: 10.1093/nar/gkab616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 11/14/2022] Open
Abstract
Mononucleotide microsatellites are clinically and forensically crucial DNA sequences due to their high mutability and abundance in the human genome. As a mutagenic intermediate of an indel in a microsatellite and a consequence of probe hybridization after such mutagenesis, a bulge with structural degeneracy sliding within a microsatellite is formed. Stability of such dynamic bulges, however, is still poorly understood despite their critical role in cancer genomics and neurological disease studies. In this paper, we have built a model that predicts the thermodynamics of a sliding bulge at a microsatellite. We first identified 40 common bulge states that can be assembled into any sliding bulges, and then characterized them with toehold exchange energy measurement and the partition function. Our model, which is the first to predict the free energy of sliding bulges with more than three repeats, can infer the stability penalty of a sliding bulge of any sequence and length with a median prediction error of 0.22 kcal/mol. Patterns from the prediction clearly explain landscapes of microsatellites observed in the literature, such as higher mutation rates of longer microsatellites and C/G microsatellites.
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Affiliation(s)
- Jin H Bae
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.,Systems, Synthetic, and Physical Biology, Rice University, Houston, TX 77005, USA
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5
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Zhou K, Amiri M, Salari A, Yu Y, Xu H, Seidler U, Nikolovska K. Functional characterization of the sodium/hydrogen exchanger 8 and its role in proliferation of colonic epithelial cells. Am J Physiol Cell Physiol 2021; 321:C471-C488. [PMID: 34288721 DOI: 10.1152/ajpcell.00582.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Intestinal NaCl, HCO3-, and fluid absorption are strongly dependent on apical Na+/H+ exchange. The intestine expresses three presumably apical sodium-hydrogen exchanger (NHE) isoforms: NHE2, NHE3, and NHE8. We addressed the role of NHE8 [solute carrier 9A8 (SLC9A8)] and its interplay with NHE2 (SLC9A2) in luminal proton extrusion during acute and chronic enterocyte acidosis and studied the differential effects of NHE8 and NHE2 on enterocyte proliferation. In contrast to NHE3, which was upregulated in differentiated versus undifferentiated colonoids, the expression of NHE2 and NHE8 remained constant during differentiation of colonoids and Caco2Bbe cells. Heterogeneously expressed Flag-tagged rat (r)Nhe8 and human (h)NHE8 translocated to the apical membrane of Caco2Bbe cells. rNhe8 and hNHE8, when expressed in NHE-deficient PS120 fibroblasts showed higher sensitivity to HOE642 compared to NHE2. Lentiviral shRNA knockdown of endogenous NHE2 in Caco2Bbe cells (C2Bbe/shNHE2) resulted in a decreased steady-state intracellular pH (pHi), an increased NHE8 mRNA expression, and augmented NHE8-mediated apical NHE activity. Lentiviral shRNA knockdown of endogenous NHE8 in Caco2Bbe cells (C2Bbe/shNHE8) resulted in a decreased steady-state pHi as well, accompanied by decreased NHE2 mRNA expression and activity, which together contributed to reduced apical NHE activity in the NHE8-knockdown cells. Chronic acidosis increased NHE8 but not NHE2 mRNA expression. Alterations in NHE2 and NHE8 expression/activity affected proliferation, with C2Bbe/shNHE2 cells having lower and C2Bbe/shNHE8 having higher proliferative capacity, accompanied by amplified ERK1/2 signaling pathway and increased EGFR expression in the latter cell line. Thus, both Na+/H+ exchangers have distinct functions during cellular homeostasis by triggering different signaling pathways to regulate cellular proliferation and pHi control.
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Affiliation(s)
- Kunyan Zhou
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Mahdi Amiri
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Azam Salari
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Yan Yu
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Hua Xu
- Department of Pediatrics, University of Arizona Health Science Center, Tucson, Arizona
| | - Ursula Seidler
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Katerina Nikolovska
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
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6
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Kondelin J, Martin S, Katainen R, Renkonen-Sinisalo L, Lepistö A, Koskensalo S, Böhm J, Mecklin JP, Cajuso T, Hänninen UA, Välimäki N, Ravantti J, Rajamäki K, Palin K, Aaltonen LA. No evidence of EMAST in whole genome sequencing data from 248 colorectal cancers. Genes Chromosomes Cancer 2021; 60:463-473. [PMID: 33527622 DOI: 10.1002/gcc.22941] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 12/20/2022] Open
Abstract
Microsatellite instability (MSI) is caused by defective DNA mismatch repair (MMR), and manifests as accumulation of small insertions and deletions (indels) in short tandem repeats of the genome. Another form of repeat instability, elevated microsatellite alterations at selected tetranucleotide repeats (EMAST), has been suggested to occur in 50% to 60% of colorectal cancer (CRC), of which approximately one quarter are accounted for by MSI. Unlike for MSI, the criteria for defining EMAST is not consensual. EMAST CRCs have been suggested to form a distinct subset of CRCs that has been linked to a higher tumor stage, chronic inflammation, and poor prognosis. EMAST CRCs not exhibiting MSI have been proposed to show instability of di- and trinucleotide repeats in addition to tetranucleotide repeats, but lack instability of mononucleotide repeats. However, previous studies on EMAST have been based on targeted analysis of small sets of marker repeats, often in relatively few samples. To gain insight into tetranucleotide instability on a genome-wide level, we utilized whole genome sequencing data from 227 microsatellite stable (MSS) CRCs, 18 MSI CRCs, 3 POLE-mutated CRCs, and their corresponding normal samples. As expected, we observed tetranucleotide instability in all MSI CRCs, accompanied by instability of mono-, di-, and trinucleotide repeats. Among MSS CRCs, some tumors displayed more microsatellite mutations than others as a continuum, and no distinct subset of tumors with the previously proposed molecular characters of EMAST could be observed. Our results suggest that tetranucleotide repeat mutations in non-MSI CRCs represent stochastic mutation events rather than define a distinct CRC subclass.
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Affiliation(s)
- Johanna Kondelin
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Samantha Martin
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Riku Katainen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Laura Renkonen-Sinisalo
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Anna Lepistö
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Selja Koskensalo
- The HUCH Gastrointestinal Clinic, Helsinki University Central Hospital, Helsinki, Finland
| | - Jan Böhm
- Department of Pathology, Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Jukka-Pekka Mecklin
- Department of Education and Research, Jyväskylä Central Hospital, Jyväskylä, Finland.,Department Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Tatiana Cajuso
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Ulrika A Hänninen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Niko Välimäki
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Janne Ravantti
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Kristiina Rajamäki
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Lauri A Aaltonen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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7
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Whole genome sequencing of metastatic colorectal cancer reveals prior treatment effects and specific metastasis features. Nat Commun 2021; 12:574. [PMID: 33495476 PMCID: PMC7835235 DOI: 10.1038/s41467-020-20887-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023] Open
Abstract
In contrast to primary colorectal cancer (CRC) little is known about the genomic landscape of metastasized CRC. Here we present whole genome sequencing data of metastases of 429 CRC patients participating in the pan-cancer CPCT-02 study (NCT01855477). Unsupervised clustering using mutational signature patterns highlights three major patient groups characterized by signatures known from primary CRC, signatures associated with received prior treatments, and metastasis-specific signatures. Compared to primary CRC, we identify additional putative (non-coding) driver genes and increased frequencies in driver gene mutations. In addition, we identify specific genes preferentially affected by microsatellite instability. CRC-specific 1kb-10Mb deletions, enriched for common fragile sites, and LINC00672 mutations are associated with response to treatment in general, whereas FBXW7 mutations predict poor response specifically to EGFR-targeted treatment. In conclusion, the genomic landscape of mCRC shows defined changes compared to primary CRC, is affected by prior treatments and contains features with potential clinical relevance.
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8
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Ballhausen A, Przybilla MJ, Jendrusch M, Haupt S, Pfaffendorf E, Seidler F, Witt J, Hernandez Sanchez A, Urban K, Draxlbauer M, Krausert S, Ahadova A, Kalteis MS, Pfuderer PL, Heid D, Stichel D, Gebert J, Bonsack M, Schott S, Bläker H, Seppälä T, Mecklin JP, Ten Broeke S, Nielsen M, Heuveline V, Krzykalla J, Benner A, Riemer AB, von Knebel Doeberitz M, Kloor M. The shared frameshift mutation landscape of microsatellite-unstable cancers suggests immunoediting during tumor evolution. Nat Commun 2020; 11:4740. [PMID: 32958755 PMCID: PMC7506541 DOI: 10.1038/s41467-020-18514-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 08/21/2020] [Indexed: 02/06/2023] Open
Abstract
The immune system can recognize and attack cancer cells, especially those with a high load of mutation-induced neoantigens. Such neoantigens are abundant in DNA mismatch repair (MMR)-deficient, microsatellite-unstable (MSI) cancers. MMR deficiency leads to insertion/deletion (indel) mutations at coding microsatellites (cMS) and to neoantigen-inducing translational frameshifts. Here, we develop a tool to quantify frameshift mutations in MSI colorectal and endometrial cancer. Our results show that frameshift mutation frequency is negatively correlated to the predicted immunogenicity of the resulting peptides, suggesting counterselection of cell clones with highly immunogenic frameshift peptides. This correlation is absent in tumors with Beta-2-microglobulin mutations, and HLA-A*02:01 status is related to cMS mutation patterns. Importantly, certain outlier mutations are common in MSI cancers despite being related to frameshift peptides with functionally confirmed immunogenicity, suggesting a possible driver role during MSI tumor evolution. Neoantigens resulting from shared mutations represent promising vaccine candidates for prevention of MSI cancers.
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Affiliation(s)
- Alexej Ballhausen
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Moritz Jakob Przybilla
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Michael Jendrusch
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Saskia Haupt
- Engineering Mathematics and Computing Lab (EMCL), Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Elisabeth Pfaffendorf
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Florian Seidler
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Johannes Witt
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Alejandro Hernandez Sanchez
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Katharina Urban
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Markus Draxlbauer
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Sonja Krausert
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Aysel Ahadova
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Martin Simon Kalteis
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Pauline L Pfuderer
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Daniel Heid
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Damian Stichel
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Maria Bonsack
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Vaccine Design, German Center for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sarah Schott
- Department of Obstetrics and Gynecology, University Hospital Heidelberg, Heidelberg, Germany
| | - Hendrik Bläker
- Institute of Pathology, University Hospital Leipzig, Leipzig, Germany
| | - Toni Seppälä
- Department of Gastrointestinal Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Jukka-Pekka Mecklin
- Department of Education and Research, Central Finland Central Hospital, Jyväskylä, Finland
- Department of Sports and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Sanne Ten Broeke
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Vincent Heuveline
- Engineering Mathematics and Computing Lab (EMCL), Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Julia Krzykalla
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika Beate Riemer
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Vaccine Design, German Center for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany.
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University Hospital and EMBL, Heidelberg, Germany.
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9
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Phung TN, Lenkiewicz E, Malasi S, Sharma A, Anderson KS, Wilson MA, Pockaj BA, Barrett MT. Unique genomic and neoepitope landscapes across tumors: a study across time, tissues, and space within a single lynch syndrome patient. Sci Rep 2020; 10:12190. [PMID: 32699259 PMCID: PMC7376229 DOI: 10.1038/s41598-020-68939-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
Lynch syndrome (LS) arises in patients with pathogenic germline variants in DNA mismatch repair genes. LS is the most common inherited cancer predisposition condition and confers an elevated lifetime risk of multiple cancers notably colorectal and endometrial carcinomas. A distinguishing feature of LS associated tumors is accumulation of variants targeting microsatellite repeats and the potential for high tumor specific neoepitope levels. Recurrent somatic variants targeting a small subset of genes have been identified in tumors with microsatellite instability. Notably these include frameshifts that can activate immune responses and provide vaccine targets to affect the lifetime cancer risk associated with LS. However the presence and persistence of targeted neoepitopes across multiple tumors in single LS patients has not been rigorously studied. Here we profiled the genomic landscapes of five distinct treatment naïve tumors, a papillary transitional cell renal cell carcinoma, a duodenal carcinoma, two metachronous colorectal carcinomas, and multi-regional sampling in a triple-negative breast tumor, arising in a LS patient over 10 years. Our analyses suggest each tumor evolves a unique complement of variants and that vaccines based on potential neoepitopes from one tissue may not be effective across all tumors that can arise during the lifetime of LS patients.
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Affiliation(s)
- Tanya N Phung
- School of Life Sciences, Arizona State University, Tempe, AZ, 85282, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85282, USA
| | - Elizabeth Lenkiewicz
- Division of Hematology-Oncology, Mayo Clinic in Arizona, Scottsdale, AZ, 85259, USA
| | - Smriti Malasi
- Division of Hematology-Oncology, Mayo Clinic in Arizona, Scottsdale, AZ, 85259, USA
| | - Amit Sharma
- The Biodesign Institute, Arizona State University, Tempe, AZ, 85282, USA
| | - Karen S Anderson
- School of Life Sciences, Arizona State University, Tempe, AZ, 85282, USA.,Division of Hematology-Oncology, Mayo Clinic in Arizona, Scottsdale, AZ, 85259, USA.,The Biodesign Institute, Arizona State University, Tempe, AZ, 85282, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, 85282, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85282, USA.,The Biodesign Institute, Arizona State University, Tempe, AZ, 85282, USA
| | - Barbara A Pockaj
- Division of General Surgery, Section of Surgical Oncology, Mayo Clinic in Arizona, Phoenix, AZ, 85054, USA
| | - Michael T Barrett
- Division of Hematology-Oncology, Mayo Clinic in Arizona, Scottsdale, AZ, 85259, USA.
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10
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Hasler D, Meister G, Fischer U. Stabilize and connect: the role of LARP7 in nuclear non-coding RNA metabolism. RNA Biol 2020; 18:290-303. [PMID: 32401147 DOI: 10.1080/15476286.2020.1767952] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
La and La-related proteins (LARPs) are characterized by a common RNA interaction platform termed the La module. This structural hallmark allows LARPs to pervade various aspects of RNA biology. The metazoan LARP7 protein binds to the 7SK RNA as part of a 7SK small nuclear ribonucleoprotein (7SK snRNP), which inhibits the transcriptional activity of RNA polymerase II (Pol II). Additionally, recent findings revealed unanticipated roles of LARP7 in the assembly of other RNPs, as well as in the modification, processing and cellular transport of RNA molecules. Reduced levels of functional LARP7 have been linked to cancer and Alazami syndrome, two seemingly unrelated human diseases characterized either by hyperproliferation or growth retardation. Here, we review the intricate regulatory networks centered on LARP7 and assess how malfunction of these networks may relate to the etiology of LARP7-linked diseases.
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Affiliation(s)
- Daniele Hasler
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
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11
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Fujimoto A, Fujita M, Hasegawa T, Wong JH, Maejima K, Oku-Sasaki A, Nakano K, Shiraishi Y, Miyano S, Yamamoto G, Akagi K, Imoto S, Nakagawa H. Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types. Genome Res 2020; 30:gr.255026.119. [PMID: 32209592 PMCID: PMC7111525 DOI: 10.1101/gr.255026.119] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/25/2020] [Indexed: 01/08/2023]
Abstract
Microsatellites are repeats of 1- to 6-bp units, and approximately 10 million microsatellites have been identified across the human genome. Microsatellites are vulnerable to DNA mismatch errors and have thus been used to detect cancers with mismatch repair deficiency. To reveal the mutational landscape of microsatellite repeat regions at the genome level, we analyzed approximately 20.1 billion microsatellites in 2717 whole genomes of pan-cancer samples across 21 tissue types. First, we developed a new insertion and deletion caller (MIMcall) that takes into consideration the error patterns of different types of microsatellites. Among the 2717 pan-cancer samples, our analysis identified 31 samples, including colorectal, uterus, and stomach cancers, with a higher proportion of mutated microsatellite (≥0.03), which we defined as microsatellite instability (MSI) cancers of genome-wide level. Next, we found 20 highly mutated microsatellites that can be used to detect MSI cancers with high sensitivity. Third, we found that replication timing and DNA shape were significantly associated with mutation rates of microsatellites. Last, analysis of mutations in mismatch repair genes showed that somatic SNVs and short indels had larger functional impacts than germline mutations and structural variations. Our analysis provides a comprehensive picture of mutations in the microsatellite regions and reveals possible causes of mutations, as well as provides a useful marker set for MSI detection.
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Affiliation(s)
- Akihiro Fujimoto
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 230-0045, Japan
- Department of Human Genetics, The University of Tokyo, Graduate School of Medicine, Tokyo 113-0033, Japan
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 230-0045, Japan
| | - Takanori Hasegawa
- Health Intelligence Center, Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Jing Hao Wong
- Department of Human Genetics, The University of Tokyo, Graduate School of Medicine, Tokyo 113-0033, Japan
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 230-0045, Japan
| | - Aya Oku-Sasaki
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 230-0045, Japan
| | - Kaoru Nakano
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 230-0045, Japan
| | - Yuichi Shiraishi
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Human Genome Center, Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Satoru Miyano
- Health Intelligence Center, Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan
- Human Genome Center, Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Go Yamamoto
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Seiya Imoto
- Health Intelligence Center, Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 230-0045, Japan
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12
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Kondelin J, Salokas K, Saarinen L, Ovaska K, Rauanheimo H, Plaketti RM, Hamberg J, Liu X, Yadav L, Gylfe AE, Cajuso T, Hänninen UA, Palin K, Ristolainen H, Katainen R, Kaasinen E, Tanskanen T, Aavikko M, Taipale M, Taipale J, Renkonen-Sinisalo L, Lepistö A, Koskensalo S, Böhm J, Mecklin JP, Ongen H, Dermitzakis ET, Kilpivaara O, Vahteristo P, Turunen M, Hautaniemi S, Tuupanen S, Karhu A, Välimäki N, Varjosalo M, Pitkänen E, Aaltonen LA. Comprehensive evaluation of coding region point mutations in microsatellite-unstable colorectal cancer. EMBO Mol Med 2019; 10:emmm.201708552. [PMID: 30108113 PMCID: PMC6402450 DOI: 10.15252/emmm.201708552] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Microsatellite instability (MSI) leads to accumulation of an excessive number of mutations in the genome, mostly small insertions and deletions. MSI colorectal cancers (CRCs), however, also contain more point mutations than microsatellite‐stable (MSS) tumors, yet they have not been as comprehensively studied. To identify candidate driver genes affected by point mutations in MSI CRC, we ranked genes based on mutation significance while correcting for replication timing and gene expression utilizing an algorithm, MutSigCV. Somatic point mutation data from the exome kit‐targeted area from 24 exome‐sequenced sporadic MSI CRCs and respective normals, and 12 whole‐genome‐sequenced sporadic MSI CRCs and respective normals were utilized. The top 73 genes were validated in 93 additional MSI CRCs. The MutSigCV ranking identified several well‐established MSI CRC driver genes and provided additional evidence for previously proposed CRC candidate genes as well as shortlisted genes that have to our knowledge not been linked to CRC before. Two genes, SMARCB1 and STK38L, were also functionally scrutinized, providing evidence of a tumorigenic role, for SMARCB1 mutations in particular.
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Affiliation(s)
- Johanna Kondelin
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Kari Salokas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Lilli Saarinen
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Kristian Ovaska
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Heli Rauanheimo
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Roosa-Maria Plaketti
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Jiri Hamberg
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Xiaonan Liu
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Leena Yadav
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Alexandra E Gylfe
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Tatiana Cajuso
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Ulrika A Hänninen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Heikki Ristolainen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Riku Katainen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Eevi Kaasinen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Tomas Tanskanen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Mervi Aavikko
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Minna Taipale
- Division of Functional Genomics, Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, Stockholm, Sweden
| | - Jussi Taipale
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Science for Life Center, Huddinge, Sweden
| | - Laura Renkonen-Sinisalo
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Anna Lepistö
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Selja Koskensalo
- The HUCH Gastrointestinal Clinic, Helsinki University Central Hospital, Helsinki, Finland
| | - Jan Böhm
- Department of Pathology, Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Jukka-Pekka Mecklin
- Department of Surgery, Jyväskylä Central Hospital, University of Eastern Finland, Jyväskylä, Finland.,Department Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Halit Ongen
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Outi Kilpivaara
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Pia Vahteristo
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Mikko Turunen
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Sampsa Hautaniemi
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Sari Tuupanen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Auli Karhu
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Niko Välimäki
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Esa Pitkänen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Lauri A Aaltonen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland .,Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
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13
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Hänninen UA, Wirta EV, Katainen R, Tanskanen T, Hamberg J, Taipale M, Böhm J, Renkonen-Sinisalo L, Lepistö A, Forsström LM, Pitkänen E, Palin K, Seppälä TT, Mäkinen N, Mecklin JP, Aaltonen LA. Exome and immune cell score analyses reveal great variation within synchronous primary colorectal cancers. Br J Cancer 2019; 120:922-930. [PMID: 30894686 PMCID: PMC6734647 DOI: 10.1038/s41416-019-0427-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/15/2022] Open
Abstract
Background Approximately 4% of colorectal cancer (CRC) patients have at least two simultaneous cancers in the colon. Due to the shared environment, these synchronous CRCs (SCRCs) provide a unique setting to study colorectal carcinogenesis. Understanding whether these tumours are genetically similar or distinct is essential when designing therapeutic approaches. Methods We performed exome sequencing of 47 primary cancers and corresponding normal samples from 23 patients. Additionally, we carried out a comprehensive mutational signature analysis to assess whether tumours had undergone similar mutational processes and the first immune cell score analysis (IS) of SCRC to analyse the interplay between immune cell invasion and mutation profile in both lesions of an individual. Results The tumour pairs shared only few mutations, favouring different mutations in known CRC genes and signalling pathways and displayed variation in their signature content. Two tumour pairs had discordant mismatch repair statuses. In majority of the pairs, IS varied between primaries. Differences were not explained by any clinicopathological variable or mutation burden. Conclusions The study shows major diversity within SCRCs. Rather than rely on data from one tumour, our study highlights the need to evaluate both tumours of a synchronous pair for optimised targeted therapy.
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Affiliation(s)
- Ulrika A Hänninen
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Erkki-Ville Wirta
- Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland
| | - Riku Katainen
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Tomas Tanskanen
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Jiri Hamberg
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Minna Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jan Böhm
- Department of Pathology, Central Finland Central Hospital, Jyväskylä, Finland
| | - Laura Renkonen-Sinisalo
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Anna Lepistö
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Linda M Forsström
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Esa Pitkänen
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland.,Genome Biology Unit, European Molecular Biology Unit (EMBL), Heidelberg, Germany
| | - Kimmo Palin
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Toni T Seppälä
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Netta Mäkinen
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Jukka-Pekka Mecklin
- Department of Surgery, Central Finland Central Hospital, Jyväskylä, Finland.,Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Lauri A Aaltonen
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. .,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland.
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14
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Mori T, Hamaya Y, Uotani T, Yamade M, Iwaizumi M, Furuta T, Miyajima H, Osawa S, Sugimoto K. Prevalence of elevated microsatellite alterations at selected tetranucleotide repeats in pancreatic ductal adenocarcinoma. PLoS One 2018; 13:e0208557. [PMID: 30532127 PMCID: PMC6285458 DOI: 10.1371/journal.pone.0208557] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/19/2018] [Indexed: 01/29/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) prognosis remains poor even after complete resection owing to no valuable biomarkers for recurrence and chemosensitivity. Tumors not expressing MSH3 show elevated microsatellite alterations at selected tetranucleotide repeats (EMAST). EMAST reportedly occurs in several tumors. In colorectal cancer (CRC), EMAST was reportedly correlated with 5-fluorouracil (5-FU) sensitivity. However, EMAST prevalence in PDAC and its significance as a prognostic biomarker are unknown. This study aimed to investigate EMAST prevalence in PDAC and the associations between EMAST and pathological factors, EMAST and prognosis, and EMAST and MSH3 expression via immunohistochemistry (IHC). We assessed 40 PDAC patients undergoing surgery. Genomic DNA was extracted from tumors and normal tissues. EMAST and microsatellite instability-high (MSI-H) were analyzed using five polymorphic tetranucleotide markers and five mononucleotide markers, respectively. Tumor sections were stained for MSH3, and staining intensity was evaluated via the Histoscore (H-score). Eighteen of 40 (45%) PDAC patients were EMAST-positive; however, none were MSI-H-positive. Clinicopathological characteristics including overall survival (OS) and recurrence-free survival (RFS) were not significantly different between EMAST-positive and EMAST-negative patients (P = 0.45, 0.98 respectively). IHC was performed to evaluate MSH3 protein expression levels for the PDAC tissue specimens. H-scores of EMAST-positive patients ranged from 0 to 300 (median, 40) and those of EMAST-negative patients ranged from 0 to 300 (median, 170). MSH3 protein was not significantly downregulated in EMAST-positive patients (P = 0.07). This study is a preliminary study and the number of cases investigated was small, and thus, study of a larger cohort will reveal the clinical implication of EMAST.
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Affiliation(s)
- Taiki Mori
- First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yasushi Hamaya
- First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
- * E-mail:
| | - Takahiro Uotani
- First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mihoko Yamade
- First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Moriya Iwaizumi
- Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takahisa Furuta
- Center for Clinical Research, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hiroaki Miyajima
- First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Satoshi Osawa
- Department of Endoscopic and Photodynamic Medicine, Hamamatsu, Japan
| | - Ken Sugimoto
- First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
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15
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Discovery of potential causative mutations in human coding and noncoding genome with the interactive software BasePlayer. Nat Protoc 2018; 13:2580-2600. [DOI: 10.1038/s41596-018-0052-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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16
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Xu H, Li J, Chen H, Ghishan FK. NHE8 Deficiency Promotes Colitis-Associated Cancer in Mice via Expansion of Lgr5-Expressing Cells. Cell Mol Gastroenterol Hepatol 2018; 7:19-31. [PMID: 30465020 PMCID: PMC6240644 DOI: 10.1016/j.jcmgh.2018.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/16/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Lgr5 overexpression has been detected in colorectal cancers (CRCs), including some cases of colitis-associated CRCs. In colitis-associated CRCs, chronic inflammation is a contributing factor in carcinogenesis. We recently reported that intestinal Na+/H+ exchanger isoform 8 (NHE8) plays an important role in intestinal mucosal protection and that loss of NHE8 expression results in an ulcerative colitis-like condition. Therefore, we hypothesized that NHE8 may be involved in the development of intestinal tumors. METHODS We assessed NHE8 expression in human CRCs by immunohistochemistry and studied tumor burden in NHE8 knockout (KO) mice using an azoxymethane/dextran sodium sulfate colon cancer model. We also evaluated cell proliferation in HT29NHE8KO cells and assessed tumor growth in NOD scid gamma (NSG) mice xenografted with HT29NHE8KO cells. To verify if a relationship exists between Lgr5 and NHE8 expression, we analyzed Lgr5 expression in NHE8KO mice by polymerase chain reaction and in situ hybridization. Lgr5 expression and cell proliferation in the absence of NHE8 were confirmed in colonic organoid cultures. The expression of β-catenin and c-Myc also were analyzed to evaluate Wnt/β-catenin activation. RESULTS NHE8 was undetectable in human CRC tissues. Although only 9% of NHE8 wild-type mice showed tumorigenesis in the azoxymethane/dextran sodium sulfate colon cancer model, almost 10 times more NHE8KO mice (89%) developed tumors. In the absence of NHE8, a higher colony formation unit was discovered in HT29NHE8KO cells. In NSG mice, larger tumors developed at the site where HT29NHE8KO cells were injected compared with HT29NHE8 wild type cells. Furthermore, NHE8 deficiency resulted in increased Lgr5 expression in the colon, in HT29-derived tumors, and in colonoids. The absence of NHE8 also increased Wnt/β-catenin activation. CONCLUSIONS NHE8 might be an intrinsic factor that regulates Wnt/β-catenin in the intestine.
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Key Words
- AOM, azoxymethane
- CRC, colorectal cancer
- CRISPR/Cas9, clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9
- Colorectal Tumor
- DMEM, Dulbecco's modified Eagle medium
- DSS, dextran sodium sulfate
- EGFP, enhanced green fluorescent protein
- EdU, 5-ethynyl-2’-deoxyuridine
- FACS, fluorescence-activated cell sorter
- KO, knockout
- Lgr5
- NHE, Na+/H+ exchanger
- NHE8
- NSG, NOD scid gamma
- PCR, polymerase chain reaction
- UC, ulcerative colitis
- WT, wild type
- mRNA, messenger RNA
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Affiliation(s)
- Hua Xu
- Department of Pediatrics, University of Arizona Health Sciences Center, Tucson, Arizona
| | - Jing Li
- Department of Pediatrics, University of Arizona Health Sciences Center, Tucson, Arizona
| | - Hao Chen
- Department of Pathology, University of Arizona Health Sciences Center, Tucson, Arizona
| | - Fayez K. Ghishan
- Department of Pediatrics, University of Arizona Health Sciences Center, Tucson, Arizona,Correspondence Address correspondence to: Fayez K. Ghishan, MD, Department of Pediatrics, Steele Children’s Research Center, 1501 North Campbell Avenue, Tucson, Arizona 85724. fax: (520) 626-4141.
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Jonchere V, Marisa L, Greene M, Virouleau A, Buhard O, Bertrand R, Svrcek M, Cervera P, Goloudina A, Guillerm E, Coulet F, Landman S, Ratovomanana T, Job S, Ayadi M, Elarouci N, Armenoult L, Merabtene F, Dumont S, Parc Y, Lefèvre JH, André T, Fléjou JF, Guilloux A, Collura A, de Reyniès A, Duval A. Identification of Positively and Negatively Selected Driver Gene Mutations Associated With Colorectal Cancer With Microsatellite Instability. Cell Mol Gastroenterol Hepatol 2018; 6:277-300. [PMID: 30116770 PMCID: PMC6089198 DOI: 10.1016/j.jcmgh.2018.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/05/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Recent studies have shown that cancers arise as a result of the positive selection of driver somatic events in tumor DNA, with negative selection playing only a minor role, if any. However, these investigations were concerned with alterations at nonrepetitive sequences and did not take into account mutations in repetitive sequences that have very high pathophysiological relevance in the tumors showing microsatellite instability (MSI) resulting from mismatch repair deficiency investigated in the present study. METHODS We performed whole-exome sequencing of 47 MSI colorectal cancers (CRCs) and confirmed results in an independent cohort of 53 MSI CRCs. We used a probabilistic model of mutational events within microsatellites, while adapting pre-existing models to analyze nonrepetitive DNA sequences. Negatively selected coding alterations in MSI CRCs were investigated for their functional and clinical impact in CRC cell lines and in a third cohort of 164 MSI CRC patients. RESULTS Both positive and negative selection of somatic mutations in DNA repeats was observed, leading us to identify the expected true driver genes associated with the MSI-driven tumorigenic process. Several coding negatively selected MSI-related mutational events (n = 5) were shown to have deleterious effects on tumor cells. In the tumors in which deleterious MSI mutations were observed despite the negative selection, they were associated with worse survival in MSI CRC patients (hazard ratio, 3; 95% CI, 1.1-7.9; P = .03), suggesting their anticancer impact should be offset by other as yet unknown oncogenic processes that contribute to a poor prognosis. CONCLUSIONS The present results identify the positive and negative driver somatic mutations acting in MSI-driven tumorigenesis, suggesting that genomic instability in MSI CRC plays a dual role in achieving tumor cell transformation. Exome sequencing data have been deposited in the European genome-phenome archive (accession: EGAS00001002477).
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Key Words
- CRC, colorectal cancer
- Colorectal Cancer
- Driver Gene Mutations
- HR, hazard ratio
- MLH1, MutL Homolog 1
- MMR, mismatch repair
- MSH, MutS Homolog
- MSI, microsatellite instability
- Microsatellite Instability
- NR, nonrepetitive
- PBS, phosphate-buffered saline
- PCR, polymerase chain reaction
- Positive and Negative Selection
- R, repetitive
- RFS, relapse-free survival
- RTCA, Real-Time Cell Analyzer
- Tumorigenic Process
- UTR, untranslated region
- WES, whole-exome sequencing
- WGA, whole-genome amplification
- bp, base pair
- indel, insertion/deletion
- mRNA, messenger RNA
- shRNA, short hairpin RNA
- siRNA, small interfering RNA
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Affiliation(s)
- Vincent Jonchere
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Laetitia Marisa
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Malorie Greene
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Alain Virouleau
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Laboratoire de Mathématiques et Modélisation d’Évry, University Évry, Évry, France,Centre National de la Recherche Scientifique, Université Paris-Saclay, Evry, France
| | - Olivier Buhard
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Romane Bertrand
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Magali Svrcek
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Service d’Anatomie et Cytologie Pathologiques, Assistance publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Pascale Cervera
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Service d’Anatomie et Cytologie Pathologiques, Assistance publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Anastasia Goloudina
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Inovarion, Collaborative research Department Paris, France
| | - Erell Guillerm
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Genetics Department, Assistance publique - Hôpitaux de Paris, Pitié Salpêtrière Hôpital, Paris, France
| | - Florence Coulet
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Genetics Department, Assistance publique - Hôpitaux de Paris, Pitié Salpêtrière Hôpital, Paris, France
| | - Samuel Landman
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Toky Ratovomanana
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Sylvie Job
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Mira Ayadi
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Nabila Elarouci
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Lucile Armenoult
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Fatiha Merabtene
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,University Pierre and Marie CURIE Paris 06, Unité Mixte de Service 30 L'Unité Mixte de service Imagerie Cytométrie, Plateforme d’Histomorphologie, Sorbonne Université Paris, France
| | - Sylvie Dumont
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,University Pierre and Marie CURIE Paris 06, Unité Mixte de Service 30 L'Unité Mixte de service Imagerie Cytométrie, Plateforme d’Histomorphologie, Sorbonne Université Paris, France
| | - Yann Parc
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Service de Chirurgie Générale et Digestive, Assistance publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Jérémie H. Lefèvre
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Service de Chirurgie Générale et Digestive, Assistance publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Thierry André
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Department of Oncology, Assistance publique - Hôpitaux de Paris, Hôpital Saint Antoine, Paris, France
| | - Jean-François Fléjou
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Service d’Anatomie et Cytologie Pathologiques, Assistance publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Agathe Guilloux
- Laboratoire de Mathématiques et Modélisation d’Évry, University Évry, Évry, France,Centre National de la Recherche Scientifique, Université Paris-Saclay, Evry, France
| | - Ada Collura
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Aurélien de Reyniès
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Alex Duval
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Correspondence Address correspondence to: Alex Duval, MD, PhD, Sorbonne Universite, UPMC Univ Paris 06, Inserm, UMR938, Equipe Instabilite Des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France. fax: (33) 149284603.
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