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Oh KS, Mahalingam M. Melanoma and Glioblastoma-Not a Serendipitous Association. Adv Anat Pathol 2023; 30:00125480-990000000-00051. [PMID: 36624550 DOI: 10.1097/pap.0000000000000393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Recently, we came across a patient with malignant melanoma and primary glioblastoma. Given this, we parsed the literature to ascertain the relationship, if any, between these 2 malignancies. We begin with a brief overview of melanoma and glioma in isolation followed by a chronologic overview of case reports and epidemiologic studies documenting both neoplasms. This is followed by studies detailing genetic abnormalities common to both malignancies with a view to identifying unifying genetic targets for therapeutic strategies as well as to explore the possibility of a putative association and an inherited cancer susceptibility trait. From a scientific perspective, we believe we have provided evidence favoring an association between melanoma and glioma. Future studies that include documentation of additional cases, as well as a detailed molecular analyses, will lend credence to our hypothesis that the co-occurrence of these 2 conditions is likely not serendipitous.
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Affiliation(s)
- Kei Shing Oh
- Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL
| | - Meera Mahalingam
- Dermatopathology Section, Department of Pathology and Laboratory Medicine, VA-Integrated-Service-Network-1 (VISN1), West Roxbury, MA
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2
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Nawrocka PM, Galka-Marciniak P, Urbanek-Trzeciak MO, M-Thirusenthilarasan I, Szostak N, Philips A, Susok L, Sand M, Kozlowski P. Profile of Basal Cell Carcinoma Mutations and Copy Number Alterations - Focus on Gene-Associated Noncoding Variants. Front Oncol 2021; 11:752579. [PMID: 34900699 PMCID: PMC8656283 DOI: 10.3389/fonc.2021.752579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Basal cell carcinoma (BCC) of the skin is the most common cancer in humans, characterized by the highest mutation rate among cancers, and is mostly driven by mutations in genes involved in the hedgehog pathway. To date, almost all BCC genetic studies have focused exclusively on protein-coding sequences; therefore, the impact of noncoding variants on the BCC genome is unrecognized. In this study, with the use of whole-exome sequencing of 27 tumor/normal pairs of BCC samples, we performed an analysis of somatic mutations in both protein-coding sequences and gene-associated noncoding regions, including 5'UTRs, 3'UTRs, and exon-adjacent intron sequences. Separately, in each region, we performed hotspot identification, mutation enrichment analysis, and cancer driver identification with OncodriveFML. Additionally, we performed a whole-genome copy number alteration analysis with GISTIC2. Of the >80,000 identified mutations, ~50% were localized in noncoding regions. The results of the analysis generally corroborated the previous findings regarding genes mutated in coding sequences, including PTCH1, TP53, and MYCN, but more importantly showed that mutations were also clustered in specific noncoding regions, including hotspots. Some of the genes specifically mutated in noncoding regions were identified as highly potent cancer drivers, of which BAD had a mutation hotspot in the 3'UTR, DHODH had a mutation hotspot in the Kozak sequence in the 5'UTR, and CHCHD2 frequently showed mutations in the 5'UTR. All of these genes are functionally implicated in cancer-related processes (e.g., apoptosis, mitochondrial metabolism, and de novo pyrimidine synthesis) or the pathogenesis of UV radiation-induced cancers. We also found that the identified BAD and CHCHD2 mutations frequently occur in melanoma but not in other cancers via The Cancer Genome Atlas analysis. Finally, we identified a frequent deletion of chr9q, encompassing PTCH1, and unreported frequent copy number gain of chr9p, encompassing the genes encoding the immune checkpoint ligands PD-L1 and PD-L2. In conclusion, this study is the first systematic analysis of coding and noncoding mutations in BCC and provides a strong basis for further analyses of the variants in BCC and cancer in general.
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Affiliation(s)
- Paulina Maria Nawrocka
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Paulina Galka-Marciniak
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | | | | | - Natalia Szostak
- Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Philips
- Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Laura Susok
- Department of Dermatology, Venereology and Allergology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Michael Sand
- Department of Dermatology, Venereology and Allergology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany.,Department of Plastic Surgery, St. Josef Hospital, Catholic Clinics of the Ruhr Peninsula, Essen, Germany Department of Plastic, Reconstructive and Aesthetic Surgery, St. Josef Hospital, Essen, Germany
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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3
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Bae WJ, Ahn JM, Byeon HE, Kim S, Lee D. PTPRD-inactivation-induced CXCL8 promotes angiogenesis and metastasis in gastric cancer and is inhibited by metformin. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:484. [PMID: 31805999 PMCID: PMC6896474 DOI: 10.1186/s13046-019-1469-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/28/2019] [Indexed: 01/21/2023]
Abstract
Background Protein tyrosine phosphatase receptor delta (PTPRD) is frequently inactivated in various types of cancers. Here, we explored the underlying mechanism of PTPRD-loss-induced cancer metastasis and investigated an efficient treatment option for PTPRD-inactivated gastric cancers (GCs). Methods PTPRD expression was evaluated by immunohistochemistry. Microarray analysis was used to identify differentially expressed genes in PTPRD-inactivated cancer cells. Quantitative reverse transcription (qRT-PCR), western blotting, and/or enzyme-linked immunosorbent assays were used to investigate the PTPRD-CXCL8 axis and the expression of other related genes. An in vitro tube formation assay was performed using HUVECs. The efficacy of metformin was assessed by MTS assay. Results PTPRD was frequently downregulated in GCs and the loss of PTPRD expression was associated with advanced stage, worse overall survival, and a higher risk of distant metastasis. Microarray analysis revealed a significant increase in CXCL8 expression upon loss of PTPRD. This was validated in various GC cell lines using transient and stable PTPRD knockdown. PTPRD-loss-induced angiogenesis was mediated by CXCL8, and the increase in CXCL8 expression was mediated by both ERK and STAT3 signaling. Thus, specific inhibitors targeting ERK or STAT3 abrogated the corresponding signaling nodes and inhibited PTPRD-loss-induced angiogenesis. Additionally, metformin was found to efficiently inhibit PTPRD-loss-induced angiogenesis, decrease cell viability in PTPRD-inactivated cancers, and reverse the decrease in PTPRD expression. Conclusions Thus, the PTPRD-CXCL8 axis may serve as a potential therapeutic target, particularly for the suppression of metastasis in PTPRD-inactivated GCs. Hence, we propose that the therapeutic efficacy of metformin in PTPRD-inactivated cancers should be further investigated.
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Affiliation(s)
- Won Jung Bae
- Department of Pathology, Ajou University School of Medicine, 164, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Ji Mi Ahn
- Department of Pathology, Ajou University School of Medicine, 164, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Hye Eun Byeon
- Institute of Medical Science, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Seokwhi Kim
- Department of Pathology, Ajou University School of Medicine, 164, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Dakeun Lee
- Department of Pathology, Ajou University School of Medicine, 164, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea.
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4
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Tuna M, Liu W, Amos CI, Mills GB. Genome-Wide Profiling of Acquired Uniparental Disomy Reveals Prognostic Factors in Head and Neck Squamous Cell Carcinoma. Neoplasia 2019; 21:1102-1109. [PMID: 31734631 PMCID: PMC6889229 DOI: 10.1016/j.neo.2019.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 01/04/2023] Open
Abstract
Acquired uniparental disomy (aUPD) leads to homozygosity facilitating identification of monoallelically expressed genes. We analyzed single-nucleotide polymorphism array-based genotyping data of 448 head and neck squamous cell carcinoma (HNSCC) samples from The Cancer Genome Atlas to determine the frequency and distribution of aUPD regions and their association with survival, as well as to gain a better understanding of their influence on the tumor genome. We used expression data from the same dataset to identify differentially expressed genes between groups with and without aUPD. Univariate and multivariable Cox proportional hazards models were performed for survival analysis. We found that 82.14% of HNSCC samples carried aUPD; the most common regions were in chromosome 17p (31.25%), 9p (30.13%), and 9q (27.46%). In univariate analysis, five independent aUPD regions at chromosome 9p, two regions at chromosome 9q, and the CDKN2A region were associated with poor overall survival in all groups, including training and test sets and human papillomavirus (HPV)-negative samples. Forty-three genes in areas of aUPD including PD-L1 and CDKN2A were differentially expressed in samples with aUPD compared to samples without aUPD. In multivariable analysis, aUPD at the CDKN2A region was a significant predictor of overall survival in the whole cohort and in patients with HPV-negative HNSCC. aUPD at specific regions in the genome influences clinical outcomes of HNSCC and may be beneficial for selection of personalized therapy to prolong survival in patients with this disease.
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Affiliation(s)
- Musaffe Tuna
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Medicine, Baylor College of Medicine, Houston, TX.
| | - Wenbin Liu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Cell, Developmental & Cancer Biology, School of Medicine, Oregon Health Science University, Portland, OR; Precision Oncology, Knight Cancer Institute, Portland, OR
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5
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Wu A, Yang X, Zhang B, Wang S, Li G. miR-516a-3p promotes proliferation, migration, and invasion and inhibits apoptosis in lung adenocarcinoma by targeting PTPRD. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:4222-4231. [PMID: 31933822 PMCID: PMC6949792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
Background: Multiple previous studies have indicated miR-516a-3p was associated with carcinogenesis in lung cancer. However, its biologic functions in lung adenocarcinoma remain unknown. The aim of this study was to investigate the expression of miR-516a-3p in lung adenocarcinoma, its molecular mechanisms of miR-516a-3p, and its effects on cell proliferation, migration, invasion, and apoptosis. Methods: The expression of miR-516a-3p and PTPRD was tested by reverse transcription-quantitative polymerase chain reaction. Cell migration and invasion assays were used to evaluate the migration and invasion ability of cells. Flow cytometry was performed to observe the effects of miR-516a-3p on the cell apoptosis. Western blot analysis was used to assess the protein levels of PTPRD. Luciferase reporter assay was utilized to identify whether PTPRD was a direct target of miR-516a-3p. Results: There was upregulated expression of miR-516a-3p in lung adenocarcinoma tissues as well as cell lines. In addition, miR-516a-3p expression knock-down could inhibit cell proliferation, invasion, and migration, but promote apoptosis in lung adenocarcinoma. By contrast, overexpression of miR-516a-3p resulted in the opposite effect. Dual luciferase assay, RT-PCR and western blot analysis results confirmed that PTPRD was a direct target for miR-516a-3p. Further studies also found PTPRD was down-regulated in lung adenocarcinoma and there was a negative correlation between miR-516a-3p and PTPRD expression in lung adenocarcinoma. Moreover, miR-516a-3p and PTPRD were significantly correlated with the clinical stage of lung adenocarcinoma. Conclusions: Our current findings showed that miR-516a-3p was up-regulated in lung adenocarcinoma, functioning as a tumor-promoting gene by targeting PTPRD.
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Affiliation(s)
- Anhao Wu
- Department of Thoracic Surgery Ward II, Third Affiliated Hospital, Kunming Medical University, Tumor Hospital of Yunnan Kunming ProvinceKunming, Yunnan, P. R. China
| | - Xin Yang
- Department of Blood Transfusion, The First People’s Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and TechnologyKunming, Yunnan, P. R. China
| | - Bing Zhang
- Department of Thoracic Surgery Ward II, Third Affiliated Hospital, Kunming Medical University, Tumor Hospital of Yunnan Kunming ProvinceKunming, Yunnan, P. R. China
| | - Shuting Wang
- Department of Thoracic Surgery Ward II, Third Affiliated Hospital, Kunming Medical University, Tumor Hospital of Yunnan Kunming ProvinceKunming, Yunnan, P. R. China
| | - Gaofeng Li
- Department of Thoracic Surgery Ward II, Third Affiliated Hospital, Kunming Medical University, Tumor Hospital of Yunnan Kunming ProvinceKunming, Yunnan, P. R. China
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6
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Ilska-Warner JJ, Psifidi A, Seeker LA, Wilbourn RV, Underwood SL, Fairlie J, Whitelaw B, Nussey DH, Coffey MP, Banos G. The Genetic Architecture of Bovine Telomere Length in Early Life and Association With Animal Fitness. Front Genet 2019; 10:1048. [PMID: 31749836 PMCID: PMC6843005 DOI: 10.3389/fgene.2019.01048] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/30/2019] [Indexed: 12/19/2022] Open
Abstract
Health and survival are key goals for selective breeding in farm animals. Progress, however, is often limited by the low heritability of these animal fitness traits in addition to measurement difficulties. In this respect, relevant early-life biomarkers may be useful for breeding purposes. Telomere length (TL), measured in leukocytes, is a good candidate biomarker since TL has been associated with health, ageing, and stress in humans and other species. However, telomere studies are very limited in farm animals. Here, we examined the genetic background, genomic architecture, and factors affecting bovine TL measurements in early life, and the association of the latter with animal fitness traits expressed later in life associated with survival, longevity, health, and reproduction. We studied two TL measurements, one at birth (TLB) and another during the first lactation (TLFL) of a cow. We performed a genome-wide association study of dairy cattle TL, the first in a non-human species, and found that TLB and TLFL are complex, polygenic, moderately heritable, and highly correlated traits. However, genomic associations with distinct chromosomal regions were identified for the two traits suggesting that their genomic architecture is not identical. This is reflected in changes in TL throughout an individual’s life. TLB had a significant association with survival, length of productive life and future health status of the animal, and could be potentially used as an early-life biomarker for disease predisposition and longevity in dairy cattle.
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Affiliation(s)
- Joanna J Ilska-Warner
- Animal and Veterinary Sciences, Scotland's Rural College, Edinburgh, United Kingdom.,The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Androniki Psifidi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.,Royal Veterinary College, University of London, London, United Kingdom
| | - Luise A Seeker
- Animal and Veterinary Sciences, Scotland's Rural College, Edinburgh, United Kingdom.,MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Rachael V Wilbourn
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah L Underwood
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jennifer Fairlie
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Bruce Whitelaw
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel H Nussey
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Mike P Coffey
- Animal and Veterinary Sciences, Scotland's Rural College, Edinburgh, United Kingdom
| | - Georgios Banos
- Animal and Veterinary Sciences, Scotland's Rural College, Edinburgh, United Kingdom.,The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
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7
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Wu M, Song D, Li H, Yang Y, Ma X, Deng S, Ren C, Shu X. Negative regulators of STAT3 signaling pathway in cancers. Cancer Manag Res 2019; 11:4957-4969. [PMID: 31213912 PMCID: PMC6549392 DOI: 10.2147/cmar.s206175] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/17/2019] [Indexed: 12/19/2022] Open
Abstract
STAT3 is the most ubiquitous member of the STAT family and involved in many biological processes, such as cell proliferation, differentiation, and apoptosis. Mounting evidence has revealed that STAT3 is aberrantly activated in many malignant tumors and plays a critical role in cancer progression. STAT3 is usually regarded as an effective molecular target for cancer treatment, and abolishing the STAT3 activity may diminish tumor growth and metastasis. Recent studies have shown that negative regulators of STAT3 signaling such as PIAS, SOCS, and PTP, can effectively retard tumor progression. However, PIAS, SOCS, and PTP have also been reported to correlate with tumor malignancy, and their biological function in tumorigenesis and antitumor therapy are somewhat controversial. In this review, we summarize actual knowledge on the negative regulators of STAT3 in tumors, and focus on the potential role of PIAS, SOCS, and PTP in cancer treatment. Furthermore, we also outline the STAT3 inhibitors that have entered clinical trials. Targeting STAT3 seems to be a promising strategy in cancer therapy.
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Affiliation(s)
- Moli Wu
- College of Pharmacy, Dalian Medical University, Dalian 116044, People's Republic of China.,College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, People's Republic of China
| | - Danyang Song
- College of Pharmacy, Dalian Medical University, Dalian 116044, People's Republic of China
| | - Hui Li
- College of Pharmacy, Dalian Medical University, Dalian 116044, People's Republic of China
| | - Yang Yang
- College of Pharmacy, Dalian Medical University, Dalian 116044, People's Republic of China
| | - Xiaodong Ma
- College of Pharmacy, Dalian Medical University, Dalian 116044, People's Republic of China
| | - Sa Deng
- College of Pharmacy, Dalian Medical University, Dalian 116044, People's Republic of China
| | - Changle Ren
- Surgery Department of Dalian Municipal Central Hospital, Dalian Medical University, Dalian 116033, People's Republic of China
| | - Xiaohong Shu
- College of Pharmacy, Dalian Medical University, Dalian 116044, People's Republic of China
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8
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García-Díez I, Hernández-Muñoz I, Hernández-Ruiz E, Nonell L, Puigdecanet E, Bódalo-Torruella M, Andrades E, Pujol RM, Toll A. Transcriptome and cytogenetic profiling analysis of matched in situ/invasive cutaneous squamous cell carcinomas from immunocompetent patients. Genes Chromosomes Cancer 2019; 58:164-174. [DOI: 10.1002/gcc.22712] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 11/01/2018] [Accepted: 11/22/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Irene García-Díez
- Department of Dermatology; Hospital del Mar, Universitat Autònoma de Barcelona (UAB); Barcelona Spain
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Inmaculada Hernández-Muñoz
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Eugenia Hernández-Ruiz
- Department of Dermatology; Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB); Barcelona Spain
| | - Lara Nonell
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Eulàlia Puigdecanet
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Marta Bódalo-Torruella
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Evelyn Andrades
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Ramon M. Pujol
- Department of Dermatology; Hospital del Mar, Universitat Autònoma de Barcelona (UAB); Barcelona Spain
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Agustí Toll
- Department of Dermatology; Hospital del Mar, Universitat Autònoma de Barcelona (UAB); Barcelona Spain
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
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Abstract
Culturing keratinocytes to form coherent epithelial tissue sheets has improved the treatment of extensively burned patients. Keratinocyte culture is also used to investigate various cellular and molecular mechanisms involved in different skin pathologies. To preserve stem cells during epithelial cell culture, reliable methods and conditions are of the utmost importance. Properly cultured keratinocytes will exhibit a consistent cuboid morphology and can proliferate for many passages. This chapter details materials needed and methods for all aspects of efficient keratinocyte culture for clinical applications, namely tissue sampling and transportation, isolation, routine culture, subculture, and cryopreservation.
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10
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Protein Tyrosine Phosphatases as Potential Regulators of STAT3 Signaling. Int J Mol Sci 2018; 19:ijms19092708. [PMID: 30208623 PMCID: PMC6164089 DOI: 10.3390/ijms19092708] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 08/29/2018] [Accepted: 09/06/2018] [Indexed: 02/07/2023] Open
Abstract
The signal transducer and activator of transcription 3 (STAT3) protein is a major transcription factor involved in many cellular processes, such as cell growth and proliferation, differentiation, migration, and cell death or cell apoptosis. It is activated in response to a variety of extracellular stimuli including cytokines and growth factors. The aberrant activation of STAT3 contributes to several human diseases, particularly cancer. Consequently, STAT3-mediated signaling continues to be extensively studied in order to identify potential targets for the development of new and more effective clinical therapeutics. STAT3 activation can be regulated, either positively or negatively, by different posttranslational mechanisms including serine or tyrosine phosphorylation/dephosphorylation, acetylation, or demethylation. One of the major mechanisms that negatively regulates STAT3 activation is dephosphorylation of the tyrosine residue essential for its activation by protein tyrosine phosphatases (PTPs). There are seven PTPs that have been shown to dephosphorylate STAT3 and, thereby, regulate STAT3 signaling: PTP receptor-type D (PTPRD), PTP receptor-type T (PTPRT), PTP receptor-type K (PTPRK), Src homology region 2 (SH-2) domain-containing phosphatase 1(SHP1), SH-2 domain-containing phosphatase 2 (SHP2), MEG2/PTP non-receptor type 9 (PTPN9), and T-cell PTP (TC-PTP)/PTP non-receptor type 2 (PTPN2). These regulators have great potential as targets for the development of more effective therapies against human disease, including cancer.
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Cortez Ghio S, Cantin-Warren L, Guignard R, Larouche D, Germain L. Are the Effects of the Cholera Toxin and Isoproterenol on Human Keratinocytes' Proliferative Potential Dependent on Whether They Are Co-Cultured with Human or Murine Fibroblast Feeder Layers? Int J Mol Sci 2018; 19:E2174. [PMID: 30044428 PMCID: PMC6121595 DOI: 10.3390/ijms19082174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 07/18/2018] [Indexed: 12/12/2022] Open
Abstract
Human keratinocyte culture has provided the means to treat burns, wounds and skin pathologies. To date, to efficiently culture keratinocytes, cells are cultured on an irradiated feeder layer (iFL), either comprising human (iHFL) or murine (i3T3FL) fibroblasts, and the culture medium is supplemented with a cyclic adenosine monophosphate (cAMP) accumulation inducing agent such as isoproterenol (ISO) or cholera toxin (CT). Previous studies have characterized how the feeder layer type and the cAMP inducer type influence epithelial cells' phenotype independently from one another, but it is still unknown if an optimal combination of feeder layer and cAMP inducer types exists. We used sophisticated statistical models to search for a synergetic effect of feeder layer and cAMP inducer types on human keratinocytes' proliferative potential. Our data suggests that, when culturing human keratinocytes, using iHFL over i3T3FL increases population doublings and colony-forming efficiency through signaling pathways involving Ak mouse strain thymoma (Akt, also known as protein kinase B) isoforms 1 to 3, signal transducer and activator of transcription 5 (STAT5), p53, and adenosine monophosphate activated protein kinase α1 (AMPKα1). Both tested cAMP inducers ISO and CT yielded comparable outcomes. However, no significant synergy between feeder layer and cAMP inducer types was detected. We conclude that, to promote human keratinocyte growth in the early passages of culture, co-culturing them with a human feeder layer is preferable to a murine feeder layer.
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Affiliation(s)
- Sergio Cortez Ghio
- Université Laval Research Center on Experimental Organogenesis/LOEX, Québec, QC G1J 1Z4, Canada.
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Québec, QC G1J 1Z4, Canada.
- Department of Surgery, Faculty of Medicine, Université Laval, Québec, QC G1V 0A6, Canada.
| | - Laurence Cantin-Warren
- Université Laval Research Center on Experimental Organogenesis/LOEX, Québec, QC G1J 1Z4, Canada.
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Québec, QC G1J 1Z4, Canada.
- Department of Surgery, Faculty of Medicine, Université Laval, Québec, QC G1V 0A6, Canada.
| | - Rina Guignard
- Université Laval Research Center on Experimental Organogenesis/LOEX, Québec, QC G1J 1Z4, Canada.
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Québec, QC G1J 1Z4, Canada.
- Department of Surgery, Faculty of Medicine, Université Laval, Québec, QC G1V 0A6, Canada.
| | - Danielle Larouche
- Université Laval Research Center on Experimental Organogenesis/LOEX, Québec, QC G1J 1Z4, Canada.
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Québec, QC G1J 1Z4, Canada.
- Department of Surgery, Faculty of Medicine, Université Laval, Québec, QC G1V 0A6, Canada.
| | - Lucie Germain
- Université Laval Research Center on Experimental Organogenesis/LOEX, Québec, QC G1J 1Z4, Canada.
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Québec, QC G1J 1Z4, Canada.
- Department of Surgery, Faculty of Medicine, Université Laval, Québec, QC G1V 0A6, Canada.
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12
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Van Renne N, Roca Suarez AA, Duong FHT, Gondeau C, Calabrese D, Fontaine N, Ababsa A, Bandiera S, Croonenborghs T, Pochet N, De Blasi V, Pessaux P, Piardi T, Sommacale D, Ono A, Chayama K, Fujita M, Nakagawa H, Hoshida Y, Zeisel MB, Heim MH, Baumert TF, Lupberger J. miR-135a-5p-mediated downregulation of protein tyrosine phosphatase receptor delta is a candidate driver of HCV-associated hepatocarcinogenesis. Gut 2018; 67:953-962. [PMID: 28159835 PMCID: PMC5540823 DOI: 10.1136/gutjnl-2016-312270] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 01/12/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS HCV infection is a leading risk factor of hepatocellular carcinoma (HCC). However, even after viral clearance, HCC risk remains elevated. HCV perturbs host cell signalling to maintain infection, and derailed signalling circuitry is a key driver of carcinogenesis. Since protein phosphatases are regulators of signalling events, we aimed to identify phosphatases that respond to HCV infection with relevance for hepatocarcinogenesis. METHODS We assessed mRNA and microRNA (miRNA) expression profiles in primary human hepatocytes, liver biopsies and resections of patients with HCC, and analysed microarray and RNA-seq data from paired liver biopsies of patients with HCC. We revealed changes in transcriptional networks through gene set enrichment analysis and correlated phosphatase expression levels to patient survival and tumour recurrence. RESULTS We demonstrate that tumour suppressor protein tyrosine phosphatase receptor delta (PTPRD) is impaired by HCV infection in vivo and in HCC lesions of paired liver biopsies independent from tissue inflammation or fibrosis. In liver tissue adjacent to tumour, high PTPRD levels are associated with a dampened transcriptional activity of STAT3, an increase of patient survival from HCC and reduced tumour recurrence after surgical resection. We identified miR-135a-5p as a mechanistic regulator of hepatic PTPRD expression in patients with HCV. CONCLUSIONS We previously demonstrated that STAT3 is required for HCV infection. We conclude that HCV promotes a STAT3 transcriptional programme in the liver of patients by suppressing its regulator PTPRD via upregulation of miR-135a-5p. Our results show the existence of a perturbed PTPRD-STAT3 axis potentially driving malignant progression of HCV-associated liver disease.
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Affiliation(s)
- Nicolaas Van Renne
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France,Université de Strasbourg, Strasbourg, France
| | - Armando Andres Roca Suarez
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France,Université de Strasbourg, Strasbourg, France
| | - Francois H T Duong
- Department of Biomedicine, Hepatology Laboratory, University of Basel, Basel, Switzerland
| | - Claire Gondeau
- Inserm, U1183, Institut de Médecine Régénératrice et Biothérapie, Université de Montpellier, Montpellier, France,Département d'Hépato-gastro-entérologie A, Hôpital Saint Eloi, CHU Montpellier, Montpellier, France
| | - Diego Calabrese
- Department of Biomedicine, Hepatology Laboratory, University of Basel, Basel, Switzerland
| | - Nelly Fontaine
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France,Université de Strasbourg, Strasbourg, France
| | - Amina Ababsa
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France,Université de Strasbourg, Strasbourg, France
| | - Simonetta Bandiera
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France,Université de Strasbourg, Strasbourg, France
| | - Tom Croonenborghs
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA,Program in Translational NeuroPsychiatric Genomics, Brigham and Women's Hospital, Harvard Medical School, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Nathalie Pochet
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA,Program in Translational NeuroPsychiatric Genomics, Brigham and Women's Hospital, Harvard Medical School, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Vito De Blasi
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France,Université de Strasbourg, Strasbourg, France,Pôle Hépato-digestif, Institut Hospitalo-universitaire, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Patrick Pessaux
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France,Université de Strasbourg, Strasbourg, France,Pôle Hépato-digestif, Institut Hospitalo-universitaire, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Tullio Piardi
- Department of General, Digestive and Endocrine Surgery, Hôpital Robert Debré, Centre Hospitalier Universitaire de Reims, Université de Reims Champagne-Ardenne, Reims, France
| | - Daniele Sommacale
- Department of General, Digestive and Endocrine Surgery, Hôpital Robert Debré, Centre Hospitalier Universitaire de Reims, Université de Reims Champagne-Ardenne, Reims, France
| | - Atsushi Ono
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA,Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan,Laboratory for Digestive Diseases, RIKEN Center for Integrative Medical Sciences, The Institute of Physical and Chemical Research (RIKEN), Hiroshima, Japan,Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Masashi Fujita
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Hidewaki Nakagawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Yujin Hoshida
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mirjam B Zeisel
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France,Université de Strasbourg, Strasbourg, France
| | - Markus H Heim
- Department of Biomedicine, Hepatology Laboratory, University of Basel, Basel, Switzerland
| | - Thomas F Baumert
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France,Université de Strasbourg, Strasbourg, France,Pôle Hépato-digestif, Institut Hospitalo-universitaire, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Joachim Lupberger
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France,Université de Strasbourg, Strasbourg, France
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Meeusen B, Janssens V. Tumor suppressive protein phosphatases in human cancer: Emerging targets for therapeutic intervention and tumor stratification. Int J Biochem Cell Biol 2017; 96:98-134. [PMID: 29031806 DOI: 10.1016/j.biocel.2017.10.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 02/06/2023]
Abstract
Aberrant protein phosphorylation is one of the hallmarks of cancer cells, and in many cases a prerequisite to sustain tumor development and progression. Like protein kinases, protein phosphatases are key regulators of cell signaling. However, their contribution to aberrant signaling in cancer cells is overall less well appreciated, and therefore, their clinical potential remains largely unexploited. In this review, we provide an overview of tumor suppressive protein phosphatases in human cancer. Along their mechanisms of inactivation in defined cancer contexts, we give an overview of their functional roles in diverse signaling pathways that contribute to their tumor suppressive abilities. Finally, we discuss their emerging roles as predictive or prognostic markers, their potential as synthetic lethality targets, and the current feasibility of their reactivation with pharmacologic compounds as promising new cancer therapies. We conclude that their inclusion in clinical practice has obvious potential to significantly improve therapeutic outcome in various ways, and should now definitely be pushed forward.
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Affiliation(s)
- Bob Meeusen
- Laboratory of Protein Phosphorylation & Proteomics, Dept. of Cellular & Molecular Medicine, Faculty of Medicine, KU Leuven & Leuven Cancer Institute (LKI), KU Leuven, Belgium
| | - Veerle Janssens
- Laboratory of Protein Phosphorylation & Proteomics, Dept. of Cellular & Molecular Medicine, Faculty of Medicine, KU Leuven & Leuven Cancer Institute (LKI), KU Leuven, Belgium.
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Phosphoinositide 3-Kinase-Dependent Signalling Pathways in Cutaneous Squamous Cell Carcinomas. Cancers (Basel) 2017; 9:cancers9070086. [PMID: 28696382 PMCID: PMC5532622 DOI: 10.3390/cancers9070086] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/26/2017] [Accepted: 07/03/2017] [Indexed: 01/11/2023] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) derives from keratinocytes in the epidermis and accounts for 15–20% of all cutaneous malignancies. Although it is usually curable by surgery, 5% of these tumours metastasise leading to poor prognosis mostly because of a lack of therapies and validated biomarkers. As the incidence rate is rising worldwide it has become increasingly important to better understand the mechanisms involved in cSCC development and progression in order to develop therapeutic strategies. Here we discuss some of the evidence indicating that activation of phosphoinositide 3-kinases (PI3Ks)-dependent signalling pathways (in particular the PI3Ks targets Akt and mTOR) has a key role in cSCC. We further discuss available data suggesting that inhibition of these pathways can be beneficial to counteract the disease. With the growing number of different inhibitors currently available, it would be important to further investigate the specific contribution of distinct components of the PI3Ks/Akt/mTOR pathways in order to identify the most promising molecular targets and the best strategy to inhibit cSCC.
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Acun T, Demir K, Oztas E, Arango D, Yakicier MC. PTPRD is homozygously deleted and epigenetically downregulated in human hepatocellular carcinomas. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:220-9. [PMID: 25831062 DOI: 10.1089/omi.2015.0010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PTPRD (protein tyrosine phosphatase, receptor type, D) is a tumor suppressor gene, frequently inactivated through deletions or epigenetic mechanisms in several cancers with importance for global health. In this study, we provide new and functionally integrated evidence on genetic and epigenetic alterations of PTPRD gene in hepatocellular carcinomas (HCCs). Importantly, HCC is the sixth most common malignancy and the third most common cause of cancer-related mortality worldwide. We used a high throughput single nucleotide polymorphism (SNP) microarray assay (Affymetrix, 10K2.0 Assay) covering the whole genome to screen an extensive panel of HCC cell lines (N=14 in total) to detect DNA copy number changes. PTPRD expression was determined in human HCCs by Q-RT-PCR and immunohistochemistry. Promoter hypermethylation was assessed by combined bisulfite restriction analysis (COBRA). DNA methyl transferase inhibitor 5-azacytidine (5-AzaC) and/or histone deacetylase inhibitor Trichostain A (TSA) were used to restore the expression. We identified homozygous deletions in Mahlavu and SNU475 cells, in the 5'UTR and coding regions, respectively. PTPRD mRNA expression was downregulated in 78.5% of cell lines and 82.6% of primary HCCs. PTPRD protein expression was also found to be lost or reduced in HCC tumor tissues. We found promoter hypermethylation in 22.2% of the paired HCC samples and restored PTPRD expression by 5-AzaC and/or TSA treatments. In conclusion, PTPRD is homozygously deleted and epigenetically downregulated in HCCs. We hypothesize PTPRD as a tumor suppressor candidate and potential cancer biomarker in human HCCs. This hypothesis is consistent with compelling evidences in other organ systems, as discussed in this article. Further functional assays in larger samples may ascertain the contribution of PTPRD to hepatocarcinogenesis in greater detail, not to forget its broader importance for diagnostic medicine and the emerging field of personalized medicine in oncology.
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Affiliation(s)
- Tolga Acun
- 1 Department of Molecular Biology and Genetics, Bülent Ecevit University , Zonguldak, Turkey
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Cutcutache I, Wu AY, Suzuki Y, McPherson JR, Lei Z, Deng N, Zhang S, Wong WK, Soo KC, Chan WH, Ooi LL, Welsch R, Tan P, Rozen SG. Abundant copy-number loss of CYCLOPS and STOP genes in gastric adenocarcinoma. Gastric Cancer 2016; 19. [PMID: 26205786 PMCID: PMC4824836 DOI: 10.1007/s10120-015-0514-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Gastric cancer, a leading cause of cancer death worldwide, has been little studied compared with other cancers that impose similar health burdens. Our goal is to assess genomic copy-number loss and the possible functional consequences and therapeutic implications thereof across a large series of gastric adenocarcinomas. METHODS We used high-density single-nucleotide polymorphism microarrays to determine patterns of copy-number loss and allelic imbalance in 74 gastric adenocarcinomas. We investigated whether suppressor of tumorigenesis and/or proliferation (STOP) genes are associated with genomic copy-number loss. We also analyzed the extent to which copy-number loss affects Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS (CYCLOPS) genes-genes that may be attractive targets for therapeutic inhibition when partially deleted. RESULTS The proportion of the genome subject to copy-number loss varies considerably from tumor to tumor, with a median of 5.5 %, and a mean of 12 % (range 0-58.5 %). On average, 91 STOP genes were subject to copy-number loss per tumor (median 35, range 0-452), and STOP genes tended to have lower copy-number compared with the rest of the genes. Furthermore, on average, 1.6 CYCLOPS genes per tumor were both subject to copy-number loss and downregulated, and 51.4 % of the tumors had at least one such gene. CONCLUSIONS The enrichment of STOP genes in regions of copy-number loss indicates that their deletion may contribute to gastric carcinogenesis. Furthermore, the presence of several deleted and downregulated CYCLOPS genes in some tumors suggests potential therapeutic targets in these tumors.
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Affiliation(s)
- Ioana Cutcutache
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Alice Yingting Wu
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
| | - Yuka Suzuki
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - John Richard McPherson
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Zhengdeng Lei
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Niantao Deng
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
| | - Shenli Zhang
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Wai Keong Wong
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
| | - Khee Chee Soo
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
- />Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Weng Hoong Chan
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
| | - London Lucien Ooi
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
- />Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Roy Welsch
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
- />Engineering Systems Division and Sloan School of Management, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Patrick Tan
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
- />Duke-NUS Genome Biology Facility, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Genome Institute of Singapore, A* STAR, Singapore, Singapore
| | - Steven G. Rozen
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
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Peyser ND, Du Y, Li H, Lui V, Xiao X, Chan TA, Grandis JR. Loss-of-Function PTPRD Mutations Lead to Increased STAT3 Activation and Sensitivity to STAT3 Inhibition in Head and Neck Cancer. PLoS One 2015; 10:e0135750. [PMID: 26267899 PMCID: PMC4534317 DOI: 10.1371/journal.pone.0135750] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/25/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Protein tyrosine phosphatase receptor type D (PTPRD) is a putative tumor suppressor in several cancers including head and neck squamous cell carcinoma (HNSCC). STAT3 is a frequently hyperactivated oncogene in HNSCC. As STAT3 is a direct substrate of PTPRD, we sought to determine the genetic or epigenetic alterations of PTPRD that contribute to overactive STAT3 in HNSCC. METHODS We analyzed data from The Cancer Genome Atlas (TCGA) and our previous whole-exome sequencing study and summarized the mutation, methylation, and copy number status of PTPRD in HNSCC and other cancers. In vitro studies involved standard transfection and MTT protocols, as well as methylation-specific PCR. RESULTS Our findings indicate that PTPRD mutation, rather than methylation or copy number alteration, is the primary mechanism by which PTPRD function is lost in HNSCC. We demonstrate that overexpression of wild-type PTPRD in HNSCC cells significantly inhibits growth and STAT3 activation while PTPRD mutants do not, suggesting that mutation may lead to loss of function and subsequent hyper-phosphorylation of PTPRD substrates, especially STAT3. Importantly, we determined that HNSCC cells harboring an endogenous PTPRD mutation are more sensitive to STAT3 blockade than PTPRD wild-type cells. We additionally found that PTPRD mRNA expression does not correlate with pSTAT3 expression, suggesting that alterations that manifest through altered mRNA expression, including hypermethylation and gene copy number alterations, do not significantly contribute to STAT3 overactivation in HNSCC. CONCLUSION PTPRD mutation, but not methylation or copy number loss, may serve as a predictive biomarker of sensitivity to STAT3 inhibitors in HNSCC.
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Affiliation(s)
- Noah D. Peyser
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America, 15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America, 15213
| | - Yu Du
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America, 15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America, 15213
- School of Medicine, Tsinghua University, Beijing, China, 100084
| | - Hua Li
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America, 15213
| | - Vivian Lui
- Pharmacogenomics and Precision Therapeutics Laboratory, Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong SAR, China
- Department of Biochemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Xiao Xiao
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America, 15213
| | - Timothy A. Chan
- Human Oncology and Pathogenesis Program and Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, United States of America, 10065
| | - Jennifer R. Grandis
- Department of Otolaryngology, University of California San Francisco, San Francisco, CA, United States of America, 94143
- * E-mail:
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Wang D, Wang L, Zhou J, Pan J, Qian W, Fu J, Zhang G, Zhu Y, Liu C, Wang C, Jin Z, He Z, Wu J, Shi B. Reduced expression of PTPRD correlates with poor prognosis in gastric adenocarcinoma. PLoS One 2014; 9:e113754. [PMID: 25412184 PMCID: PMC4239117 DOI: 10.1371/journal.pone.0113754] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 10/28/2014] [Indexed: 11/18/2022] Open
Abstract
Background PTPRD, encoding protein tyrosine phosphatases receptor type D, is located at chromosome 9p23–24.1, a loci frequently lost in many types of tumors. Recently, PTPRD has been proposed to function as a tumor suppressor gene. The current study aimed to investigate PTPRD expression and its prognostic significance in primary gastric adenocarcinoma. Methods and Results Quantitative real time reverse transcription PCR (qRT-PCR) and western blotting were used to examine PTPRD expression in paired gastric tumourous and paracancerous tissues. Compared with the matched normal gastric mucosa tissues, both the mRNA (P = 0.0138) and protein (P = 0.0093) expression of PTPRD in fresh surgical specimens were significantly reduced. Clinicopathological and prognostic roles of PTPRD in gastric adenocarcinoma were investigated using immunohistochemistry with 513 paraffin-embedded gastric adenocarcinoma tissue blocks. Statistical analysis revealed that reduced PTPRD expression was significantly associated with T stage (P = 0.004), TNM stage (P<0.001) and tumor size (P = 0.003). Furthermore, Kaplan-Meier survival analysis revealed that low expression of PTPRD significantly correlated with poor survival of gastric cancer patients (P<0.001). Cox regression analysis confirmed PTPRD expression as independent predictor of the overall survival of gastric cancer patients. The MTT assay determined the effects of PTPRD on cell proliferation of MGC803 and GES1 cell lines. Restoring PTPRD expression in MGC803 cells significantly inhibited their growth rate. Silencing PTPRD expression by siRNA treatment in GES1 significantly enhanced cell proliferation compared with mock siRNA treatment. Methylation analysis of PTPRD promoter CpG island in 3 primary GC samples showed one case with partial methylation. Conclusions These results indicated that PTPRD is a candidate tumour suppressor in gastric cancer. Thus, PTPRD may play an important role in gastric tumorigenesis and serve as a valuable prognostic marker of gastric adenocarcinoma.
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Affiliation(s)
- Dandan Wang
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Leilei Wang
- Biology Institute of Shandong Academy of Sciences, Jinan, People's Republic of China
| | - Jun Zhou
- Departments of Oncology, Provincial Hospital Affiliated to Shandong University, Jinan, People's Republic of China
| | - Jihong Pan
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Wei Qian
- The General Hospital of Jinan Military Command, Jinan, People's Republic of China
| | - Jiafang Fu
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Genglin Zhang
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Youming Zhu
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Chunshan Liu
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Chunliang Wang
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Zongkun Jin
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Ziqing He
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Jianmei Wu
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
- * E-mail: (BS); (JW)
| | - Bin Shi
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
- * E-mail: (BS); (JW)
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Du Y, Grandis JR. Receptor-type protein tyrosine phosphatases in cancer. CHINESE JOURNAL OF CANCER 2014; 34:61-9. [PMID: 25322863 PMCID: PMC4360074 DOI: 10.5732/cjc.014.10146] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein tyrosine phosphatases (PTPs) play an important role in regulating cell signaling events in coordination with tyrosine kinases to control cell proliferation, apoptosis, survival, migration, and invasion. Receptor-type protein tyrosine phosphatases (PTPRs) are a subgroup of PTPs that share a transmembrane domain with resulting similarities in function and target specificity. In this review, we summarize genetic and epigenetic alterations including mutation, deletion, amplification, and promoter methylation of PTPRs in cancer and consider the consequences of PTPR alterations in different types of cancers. We also summarize recent developments using PTPRs as prognostic or predictive biomarkers and/or direct targets. Increased understanding of the role of PTPRs in cancer may provide opportunities to improve therapeutic approaches.
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Affiliation(s)
- Yu Du
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
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Zhao S, Sedwick D, Wang Z. Genetic alterations of protein tyrosine phosphatases in human cancers. Oncogene 2014; 34:3885-94. [PMID: 25263441 PMCID: PMC4377308 DOI: 10.1038/onc.2014.326] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 12/12/2022]
Abstract
Protein tyrosine phosphatases (PTPs) are enzymes that remove phosphate from tyrosine residues in proteins. Recent whole-exome sequencing of human cancer genomes reveals that many PTPs are frequently mutated in a variety of cancers. Among these mutated PTPs, protein tyrosine phosphatase T (PTPRT) appears to be the most frequently mutated PTP in human cancers. Beside PTPN11 which functions as an oncogene in leukemia, genetic and functional studies indicate that most of mutant PTPs are tumor suppressor genes. Identification of the substrates and corresponding kinases of the mutant PTPs may provide novel therapeutic targets for cancers harboring these mutant PTPs.
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Affiliation(s)
- S Zhao
- 1] Division of Gastroenterology and Hepatology and Shanghai Institution of Digestive Disease, Shanghai Jiao-Tong University School of Medicine Renji Hospital, Shanghai, China [2] Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA [3] Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - D Sedwick
- 1] Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA [2] Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Z Wang
- 1] Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA [2] Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
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21
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Lambert SR, Mladkova N, Gulati A, Hamoudi R, Purdie K, Cerio R, Leigh I, Proby C, Harwood CA. Key differences identified between actinic keratosis and cutaneous squamous cell carcinoma by transcriptome profiling. Br J Cancer 2013; 110:520-9. [PMID: 24335922 PMCID: PMC3899778 DOI: 10.1038/bjc.2013.760] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 10/25/2013] [Accepted: 11/07/2013] [Indexed: 12/19/2022] Open
Abstract
Background: Cutaneous squamous cell carcinoma (cSCC) is one of the most common malignancies in fair-skinned populations worldwide and its incidence is increasing. Despite previous observations of multiple genetic abnormalities in cSCC, the oncogenic process remains elusive. The purpose of this study was to elucidate key molecular events associated with progression from premalignant actinic keratoses (AKs) to invasive cSCC by transcriptome profiling. Methods: We combined laser capture microdissection with the Affymetrix HGU133 Plus 2.0 microarrays to profile 30 cSCC and 10 AKs. Results: We identified a core set of 196 genes that are differentially expressed between AK and cSCC, and are enriched for processes including epidermal differentiation, cell migration, cell-cycle regulation and metabolism. Gene set enrichment analysis highlighted a key role for the mitogen activated protein kinase (MAPK) pathway in cSCC compared with AK. Furthermore, the histological subtype of the tumour was shown to influence the expression profile. Conclusion: These data indicate that the MAPK pathway may be pivotal to the transition from AK to cSCC, thus representing a potential target for cSCC prevention. In addition, transcriptome differences identified between cSCC subtypes have important implications for future development of targeted therapies for this malignancy.
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Affiliation(s)
- S R Lambert
- 1] Centre for Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK [2] Cancer Research UK Skin Tumour Laboratory, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - N Mladkova
- Centre for Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - A Gulati
- Centre for Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - R Hamoudi
- Research Department of Pathology, Cancer Institute, Faculty of Medical Sciences, University College London, London WC1E 6BT, UK
| | - K Purdie
- 1] Centre for Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK [2] Cancer Research UK Skin Tumour Laboratory, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - R Cerio
- Centre for Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - I Leigh
- 1] Cancer Research UK Skin Tumour Laboratory, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK [2] Skin Tumour Laboratory, Division of Cancer Research, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - C Proby
- 1] Cancer Research UK Skin Tumour Laboratory, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK [2] Skin Tumour Laboratory, Division of Cancer Research, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - C A Harwood
- 1] Centre for Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK [2] Cancer Research UK Skin Tumour Laboratory, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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22
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Leufke C, Leykauf J, Krunic D, Jauch A, Holtgreve-Grez H, Böhm-Steuer B, Bröcker EB, Mauch C, Utikal J, Hartschuh W, Purdie KJ, Boukamp P. The telomere profile distinguishes two classes of genetically distinct cutaneous squamous cell carcinomas. Oncogene 2013; 33:3506-18. [DOI: 10.1038/onc.2013.323] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 05/14/2013] [Accepted: 06/17/2013] [Indexed: 12/12/2022]
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23
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Fleming JL, Dworkin AM, Allain DC, Fernandez S, Wei L, Peters SB, Iwenofu OH, Ridd K, Bastian BC, Toland AE. Allele-specific imbalance mapping identifies HDAC9 as a candidate gene for cutaneous squamous cell carcinoma. Int J Cancer 2013; 134:244-8. [PMID: 23784969 DOI: 10.1002/ijc.28339] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/07/2013] [Accepted: 05/31/2013] [Indexed: 12/21/2022]
Abstract
More than 3.5 million nonmelanoma skin cancers were treated in 2006; of these 700,000 were cutaneous squamous cell carcinomas (cSCCs). Despite clear environmental causes for cSCC, studies also suggest genetic risk factors. A cSCC susceptibility locus, Skts5, was identified on mouse chromosome 12 by linkage analysis. The orthologous locus to Skts5 in humans maps to 7p21 and 7q31. These loci show copy number increases in ∼10% of cSCC tumors. Here, we show that an additional 15-22% of tumors exhibit copy-neutral loss of heterozygosity. Furthermore, our previous data identified microsatellite markers on 7p21 and 7q31 that demonstrate preferential allelic imbalance (PAI) in cSCC tumors. On the basis of these results, we hypothesized that the human orthologous locus to Skts5 would house a gene important in human cSCC development and that tumors would demonstrate allele-specific somatic alterations. To test this hypothesis, we performed quantitative genotyping of 108 single nucleotide polymorphisms (SNPs) mapping to candidate genes at human SKTS5 in paired normal and tumor DNAs. Nine SNPs in HDAC9 (rs801540, rs1178108, rs1178112, rs1726610, rs10243618, rs11764116, rs1178355, rs10269422 and rs12540872) showed PAI in tumors. These data suggest that HDAC9 variants may be selected for during cSCC tumorigenesis.
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Affiliation(s)
- Jessica L Fleming
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH; The Ohio State University Comprehensive Cancer Center, Columbus, OH
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24
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Amyere M, Aerts V, Brouillard P, McIntyre BAS, Duhoux FP, Wassef M, Enjolras O, Mulliken JB, Devuyst O, Antoine-Poirel H, Boon LM, Vikkula M. Somatic uniparental isodisomy explains multifocality of glomuvenous malformations. Am J Hum Genet 2013; 92:188-96. [PMID: 23375657 DOI: 10.1016/j.ajhg.2012.12.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 10/26/2012] [Accepted: 12/20/2012] [Indexed: 11/28/2022] Open
Abstract
Inherited vascular malformations are commonly autosomal dominantly inherited with high, but incomplete, penetrance; they often present as multiple lesions. We hypothesized that Knudson's two-hit model could explain this multifocality and partial penetrance. We performed a systematic analysis of inherited glomuvenous malformations (GVMs) by using multiple approaches, including a sensitive allele-specific pairwise SNP-chip method. Overall, we identified 16 somatic mutations, most of which were not intragenic but were cases of acquired uniparental isodisomy (aUPID) involving chromosome 1p. The breakpoint of each aUPID is located in an A- and T-rich, high-DNA-flexibility region (1p13.1-1p12). This region corresponds to a possible new fragile site. Occurrences of these mutations render the inherited glomulin variant in 1p22.1 homozygous in the affected tissues without loss of genetic material. This finding demonstrates that a double hit is needed to trigger formation of a GVM. It also suggests that somatic UPID, only detectable by sensitive pairwise analysis in heterogeneous tissues, might be a common phenomenon in human cells. Thus, aUPID might play a role in the pathogenesis of various nonmalignant disorders and might explain local impaired function and/or clinical variability. Furthermore, these data suggest that pairwise analysis of blood and tissue, even on heterogeneous tissue, can be used for localizing double-hit mutations in disease-causing genes.
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Affiliation(s)
- Mustapha Amyere
- Laboratory of Human Molecular Genetics, de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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25
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Hameetman L, Commandeur S, Bavinck JNB, Wisgerhof HC, de Gruijl FR, Willemze R, Mullenders L, Tensen CP, Vrieling H. Molecular profiling of cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients. BMC Cancer 2013; 13:58. [PMID: 23379751 PMCID: PMC3570297 DOI: 10.1186/1471-2407-13-58] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 01/30/2013] [Indexed: 01/06/2023] Open
Abstract
Background The risk of developing cutaneous squamous cell carcinoma (SCC) is markedly increased in organ transplant recipients (OTRs) compared to the normal population. Next to sun exposure, the immunosuppressive regimen is an important risk factor for the development of SCC in OTRs. Various gene mutations (e.g. TP53) and genetic alterations (e.g. loss of CDKN2A, amplification of RAS) have been found in SCCs. The aim of this genome-wide study was to identify pathways and genomic alterations that are consistently involved in the formation of SCCs and their precursor lesions, actinic keratoses (AKs). Methods To perform the analysis in an isogenic background, RNA and DNA were isolated from SCC, AK and normal (unexposed) epidermis (NS) from each of 13 OTRs. Samples were subjected to genome-wide expression analysis and genome SNP analysis using Illumina’s HumanWG-6 BeadChips and Infinium II HumanHap550 Genotyping BeadChips, respectively. mRNA expression results were verified by quantitative PCR. Results Hierarchical cluster analysis of mRNA expression profiles showed SCC, AK and NS samples to separate into three distinct groups. Several thousand genes were differentially expressed between epidermis, AK and SCC; most upregulated in SCCs were hyperproliferation related genes and stress markers, such as keratin 6 (KRT6), KRT16 and KRT17. Matching to oncogenic pathways revealed activation of downstream targets of RAS and cMYC in SCCs and of NFκB and TNF already in AKs. In contrast to what has been reported previously, genome-wide SNP analysis showed very few copy number variations in AKs and SCCs, and these variations had no apparent relationship with observed changes in mRNA expression profiles. Conclusion Vast differences in gene expression profiles exist between SCC, AK and NS from immunosuppressed OTRs. Moreover, several pathways activated in SCCs were already activated in AKs, confirming the assumption that AKs are the precursor lesions of SCCs. Since the drastic changes in gene expression appeared unlinked to specific genomic gains or losses, the causal events driving SCC development require further investigation. Other molecular mechanisms, such as DNA methylation or miRNA alterations, may affect gene expression in SCCs of OTRs. Further study is required to identify the mechanisms of early activation of NFκB and TNF, and to establish whether these pathways offer a feasible target for preventive intervention among OTRs.
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Affiliation(s)
- Liesbeth Hameetman
- Department of Toxicogenetics, Leiden University Medical Center, PO Box 9600, 2300, RC Leiden, the Netherlands
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26
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Du Y, Su T, Tan X, Li X, Xie J, Wang G, Shen J, Hou J, Cao G. Polymorphism in protein tyrosine phosphatase receptor delta is associated with the risk of clear cell renal cell carcinoma. Gene 2013; 512:64-9. [DOI: 10.1016/j.gene.2012.09.094] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 08/28/2012] [Accepted: 09/27/2012] [Indexed: 10/27/2022]
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27
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Hao JJ, Gong T, Zhang Y, Shi ZZ, Xu X, Dong JT, Zhan QM, Fu SB, Wang MR. Characterization of gene rearrangements resulted from genomic structural aberrations in human esophageal squamous cell carcinoma KYSE150 cells. Gene 2012; 513:196-201. [PMID: 23026210 DOI: 10.1016/j.gene.2012.09.091] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 07/10/2012] [Accepted: 09/12/2012] [Indexed: 01/14/2023]
Abstract
Chromosomal rearrangements and involved genes have been reported to play important roles in the development and progression of human malignancies. But the gene rearrangements in esophageal squamous cell carcinoma (ESCC) remain to be identified. In the present study, array-based comparative genomic hybridization (array-CGH) was performed on the ESCC cell line KYSE150. Eight disrupted genes were detected according to the obviously distinct unbalanced breakpoints. The splitting of these genes was validated by dual-color fluorescence in-situ hybridization (FISH). By using rapid amplification of cDNA ends (RACE), genome walking and sequencing analysis, we further identified gene disruptions and rearrangements. A fusion transcript DTL-1q42.2 was derived from an intrachromosomal rearrangement of chromosome 1. Highly amplified segments of DTL and PTPRD were self-rearranged. The sequences on either side of the junctions possess micro-homology with each other. FISH results indicated that the split DTL and PTPRD were also involved in comprising parts of the derivative chromosomes resulted from t(1q;9p;12p) and t(9;1;9). Further, we found that regions harboring DTL (1q32.3) and PTPRD (9p23) were also splitting in ESCC tumors. The data supplement significant information on the existing genetic background of KYSE150, which may be used as a model for studying these gene rearrangements.
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Affiliation(s)
- Jia-Jie Hao
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100021, China
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28
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Kaushal M, Mishra AK, Sharma J, Zomawia E, Kataki A, Kapur S, Saxena S. Genomic alterations in breast cancer patients in betel quid and non betel quid chewers. PLoS One 2012; 7:e43789. [PMID: 22937096 PMCID: PMC3427153 DOI: 10.1371/journal.pone.0043789] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/24/2012] [Indexed: 01/12/2023] Open
Abstract
Betel Quid (BQ) chewing independently contributes to oral, hepatic and esophageal carcinomas. Strong association of breast cancer risk with BQ chewing in Northeast Indian population has been reported where this habit is prodigal. We investigated genomic alterations in breast cancer patients with and without BQ chewing exposure. Twenty six BQ chewers (BQC) and 17 non BQ chewer (NBQC) breast cancer patients from Northeast India were analyzed for genomic alterations and pathway networks using SNP array and IPA. BQC tumors showed significantly (P<0.01) higher total number of alterations, as compared with NBQC tumors, 48±17% versus 32±25 respectively. Incidence of gain in fragile sites in BQC tumors were significantly (P<0.001) higher as compared with NBQC tumors, 34 versus 23% respectively. Two chromosomal regions (7q33 and 21q22.13) were significantly (p<0.05) associated with BQC tumors while two regions (19p13.3–19p12 and 20q11.22) were significantly associated with NBQC tumors. GO terms oxidoreductase and aldo-keto reductase activity in BQC tumors in contrast to G-protein coupled receptor protein signaling pathway and cell surface receptor linked signal transduction in NBQC tumors were enriched in DAVID. One network “Drug Metabolism, Molecular Transport, Nucleic Acid Metabolism” including genes AKR1B1, AKR1B10, ETS2 etc in BQC and two networks “Molecular Transport, Nucleic Acid Metabolism, Small Molecule Biochemistry” and “Cellular Development, Embryonic Development, Organismal Development” including genes RPN2, EMR3, VAV1, NNAT and MUC16 etc were seen in NBQC. Common alterations (>30%) were seen in 27 regions. Three networks were significant in common regions with key roles of PTK2, RPN2, EMR3, VAV1, NNAT, MUC16, MYC and YWHAZ genes. These data show that breast cancer arising by environmental carcinogens exemplifies genetic alterations differing from those observed in the non exposed ones. A number of genetic changes are shared in both tumor groups considered as crucial in breast cancer progression.
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Affiliation(s)
- Mishi Kaushal
- National Institute of Pathology, ICMR, Safdarjung Hospital Campus, New Delhi, India
| | - Ashwani K. Mishra
- National Institute of Pathology, ICMR, Safdarjung Hospital Campus, New Delhi, India
| | | | | | - Amal Kataki
- Dr. B. Borrooah Cancer Institute, Guwahati, India
| | - Sujala Kapur
- National Institute of Pathology, ICMR, Safdarjung Hospital Campus, New Delhi, India
| | - Sunita Saxena
- National Institute of Pathology, ICMR, Safdarjung Hospital Campus, New Delhi, India
- * E-mail:
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29
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Whitmore TE, Peterson A, Holzman T, Eastham A, Amon L, McIntosh M, Ozinsky A, Nelson PS, Martin DB. Integrative Analysis of N-Linked Human Glycoproteomic Data Sets Reveals PTPRF Ectodomain as a Novel Plasma Biomarker Candidate for Prostate Cancer. J Proteome Res 2012; 11:2653-65. [DOI: 10.1021/pr201200n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Theodore E. Whitmore
- Institute for Systems Biology, 1441 N. 34th St., Seattle, Washington 98103,
United States
| | - Amelia Peterson
- Department
of Chemistry, University of Wisconsin,
Madison, Wisconsin, United States
| | | | - Ashley Eastham
- Analytical & Formulation Sciences, Amgen Inc., Seattle, Washington 98119, United States
| | | | | | - Adrian Ozinsky
- Institute for Systems Biology, 1441 N. 34th St., Seattle, Washington 98103,
United States
| | | | - Daniel B. Martin
- Seattle Cancer Care Alliance,
825 Eastlake Avenue East, P.O. Box 19023, Seattle, Washington 98109,
United States
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30
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Shao Y, Zhang J, Zhang R, Wan J, Zhang W, Yu B. Examination of Smad2 and Smad4 copy-number variations in skin cancers. Clin Transl Oncol 2012; 14:138-42. [DOI: 10.1007/s12094-012-0773-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Meehan M, Parthasarathi L, Moran N, Jefferies CA, Foley N, Lazzari E, Murphy D, Ryan J, Ortiz B, Fabius AWM, Chan TA, Stallings RL. Protein tyrosine phosphatase receptor delta acts as a neuroblastoma tumor suppressor by destabilizing the aurora kinase A oncogene. Mol Cancer 2012; 11:6. [PMID: 22305495 PMCID: PMC3395855 DOI: 10.1186/1476-4598-11-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 02/05/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Protein tyrosine phosphatase receptor delta (PTPRD) is a member of a large family of protein tyrosine phosphatases which negatively regulate tyrosine phosphorylation. Neuroblastoma is a major childhood cancer arising from precursor cells of the sympathetic nervous system which is known to acquire deletions and alterations in the expression patterns of PTPRD, indicating a potential tumor suppressor function for this gene. The molecular mechanism, however, by which PTPRD renders a tumor suppressor effect in neuroblastoma is unknown. RESULTS As a molecular mechanism, we demonstrate that PTPRD interacts with aurora kinase A (AURKA), an oncogenic protein that is over-expressed in multiple forms of cancer, including neuroblastoma. Ectopic up-regulation of PTPRD in neuroblastoma dephosphorylates tyrosine residues in AURKA resulting in a destabilization of this protein culminating in interfering with one of AURKA's primary functions in neuroblastoma, the stabilization of MYCN protein, the gene of which is amplified in approximately 25 to 30% of high risk neuroblastoma. CONCLUSIONS PTPRD has a tumor suppressor function in neuroblastoma through AURKA dephosphorylation and destabilization and a downstream destabilization of MYCN protein, representing a novel mechanism for the function of PTPRD in neuroblastoma.
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Affiliation(s)
- Maria Meehan
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Dublin, Ireland
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32
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Ratushny V, Gober MD, Hick R, Ridky TW, Seykora JT. From keratinocyte to cancer: the pathogenesis and modeling of cutaneous squamous cell carcinoma. J Clin Invest 2012; 122:464-72. [PMID: 22293185 DOI: 10.1172/jci57415] [Citation(s) in RCA: 379] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) is the second most common human cancer with over 250,000 new cases annually in the US and is second in incidence only to basal cell carcinoma. cSCC typically manifests as a spectrum of progressively advanced malignancies, ranging from a precursor actinic keratosis (AK) to squamous cell carcinoma (SCC) in situ (SCCIS), invasive cSCC, and finally metastatic SCC. In this Review we discuss clinical and molecular parameters used to define this range of cutaneous neoplasia and integrate these with the multiple experimental approaches used to study this disease. Insights gained from modeling cSCCs have suggested innovative therapeutic targets for treating these lesions.
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Affiliation(s)
- Vladimir Ratushny
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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33
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Lambert SR, Harwood CA, Purdie KJ, Gulati A, Matin RN, Romanowska M, Cerio R, Kelsell DP, Leigh IM, Proby CM. Metastatic cutaneous squamous cell carcinoma shows frequent deletion in the protein tyrosine phosphatase receptor Type D gene. Int J Cancer 2011; 131:E216-26. [DOI: 10.1002/ijc.27333] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 10/06/2011] [Indexed: 11/08/2022]
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34
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Mao X, Chaplin T, Young BD. Integrated genomic analysis of sézary syndrome. GENETICS RESEARCH INTERNATIONAL 2011; 2011:980150. [PMID: 22567373 PMCID: PMC3335609 DOI: 10.4061/2011/980150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 08/07/2011] [Accepted: 08/29/2011] [Indexed: 02/05/2023]
Abstract
Sézary syndrome (SS) is a rare variant of primary cutaneous T-cell lymphoma. Little is known about the underlying pathogenesis of S. To address this issue, we used Affymetrix 10K SNP microarray to analyse 13 DNA samples isolated from 8 SS patients and qPCR with ABI TaqMan SNP genotyping assays for the validation of the SNP microarray results. In addition, we tested the impact of SNP loss of heterozygosity (LOH) identified in SS cases on the gene expression profiles of SS cases detected with Affymetrix GeneChip U133A. The results showed: (1) frequent SNP copy number change and LOH involving 1, 2p, 3, 4q, 5q, 6, 7p, 8, 9, 10, 11, 12q, 13, 14, 16q, 17, and 20, (2) reduced SNP copy number at FAT gene (4q35) in 75% of SS cases, and (3) the separation of all SS cases from normal control samples by SNP LOH gene clusters at chromosome regions of 9q31q34, 10p11q26, and 13q11q12. These findings provide some intriguing information for our current understanding of the molecular pathogenesis of this tumour and suggest the possibility of presence of functional SNP LOH in SS tumour cells.
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Affiliation(s)
- Xin Mao
- Centre for Cutaneous Research, Institute of Cell and Molecular Sciences, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
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35
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Watt SA, Pourreyron C, Purdie K, Hogan C, Cole CL, Foster N, Pratt N, Bourdon JC, Appleyard V, Murray K, Thompson AM, Mao X, Mein C, Bruckner-Tuderman L, Evans A, McGrath JA, Proby CM, Foerster J, Leigh IM, South AP. Integrative mRNA profiling comparing cultured primary cells with clinical samples reveals PLK1 and C20orf20 as therapeutic targets in cutaneous squamous cell carcinoma. Oncogene 2011; 30:4666-77. [PMID: 21602893 PMCID: PMC3219832 DOI: 10.1038/onc.2011.180] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 03/30/2011] [Accepted: 04/01/2011] [Indexed: 01/03/2023]
Abstract
Identifying therapeutic targets for cancer treatment relies on consistent changes within particular types or sub-types of malignancy. The ability to define either consistent changes or sub-types of malignancy is often masked by tumor heterogeneity. To elucidate therapeutic targets in cutaneous squamous cell carcinoma (cSCC), the most frequent skin neoplasm with malignant potential, we have developed an integrated approach to gene expression profiling beginning with primary keratinocytes in culture. Candidate drivers of cSCC development were derived by first defining a set of in vitro cancer genes and then comparing their expression in a range of clinical data sets containing normal skin, cSCC and the benign hyper-proliferative condition psoriasis. A small interfering RNA (siRNA) screen of the resulting 21 upregulated genes has yielded targets capable of reducing xenograft tumor volume in vivo. Small-molecule inhibitors for one target, Polo-like kinase-1 (PLK1), are already in clinical trials for other malignancies, and our data show efficacy in cSCC. Another target, C20orf20, is identified as being overexpressed in cSCC, and siRNA-mediated knockdown induces apoptosis in vitro and reduces tumor growth in vivo. Thus, our approach has shown established and uncharacterized drivers of tumorigenesis with potent efficacy as therapeutic targets for the treatment of cSCC.
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Affiliation(s)
- S A Watt
- Centre for Oncology and Molecular Medicine, Division of Medical Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - C Pourreyron
- Centre for Oncology and Molecular Medicine, Division of Medical Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - K Purdie
- Centre for Cutaneous Research, Institute of Cell and Molecular Science, Whitechapel, London, UK
| | - C Hogan
- Centre for Oncology and Molecular Medicine, Division of Medical Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - C L Cole
- Centre for Oncology and Molecular Medicine, Division of Medical Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - N Foster
- Department of Human Genetics, Ninewells Hospital Dundee, Dundee, UK
| | - N Pratt
- Department of Human Genetics, Ninewells Hospital Dundee, Dundee, UK
| | - J-C Bourdon
- Centre for Oncology and Molecular Medicine, Division of Medical Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - V Appleyard
- Centre for Oncology and Molecular Medicine, Division of Medical Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - K Murray
- Centre for Oncology and Molecular Medicine, Division of Medical Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - A M Thompson
- Centre for Oncology and Molecular Medicine, Division of Medical Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - X Mao
- Centre for Cutaneous Research, Institute of Cell and Molecular Science, Whitechapel, London, UK
| | - C Mein
- Genome Centre, Barts and The London, Queen Mary University of London, Whitechapel, London, UK
| | - L Bruckner-Tuderman
- Department of Dermatology, University Medical Center Freiburg and Freiburg Institute for Advanced Studies, School of Life Sciences LifeNet, Freiburg, Germany
| | - A Evans
- Department of Pathology, Ninewells Hospital Dundee, Dundee, UK
| | - J A McGrath
- Genetic Skin Disease Group, Division of Genetics and Molecular Medicine, St John's Institute of Dermatology, King's College School of Medicine, St Thomas' Hospital, London, UK
| | - C M Proby
- Centre for Oncology and Molecular Medicine, Division of Medical Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - J Foerster
- Centre for Oncology and Molecular Medicine, Division of Medical Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - I M Leigh
- Centre for Oncology and Molecular Medicine, Division of Medical Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - A P South
- Centre for Oncology and Molecular Medicine, Division of Medical Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
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Molecular markers in cutaneous squamous cell carcinoma. Int J Surg Oncol 2011; 2011:231475. [PMID: 22312497 PMCID: PMC3265276 DOI: 10.1155/2011/231475] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 06/04/2011] [Indexed: 02/08/2023] Open
Abstract
Nonmelanoma skin carcinoma (NMSC) is the most frequent cancer in the USA with over 1.3 million new diagnoses a year; however due to an underappreciation of its associated mortality and growing incidence and its ability to be highly aggressive, the molecular mechanism is not well delineated. Whereas the molecular profiles of melanoma have been well characterized, those for cutaneous squamous cell carcinoma (cSCC) have trailed behind. This importance of the new staging paradigm is linked to the ability currently to better clinically cluster similar biologic behavior in order to risk-stratify lesions and patients. In this paper we discuss the trends in NMSC and the etiologies for the subset of NMSC with the most mortality, cutaneous SCC, as well as where the field stands in the discovery of a molecular profile. The molecular markers are highlighted to demonstrate the recent advances in cSCC.
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Forche A, Abbey D, Pisithkul T, Weinzierl MA, Ringstrom T, Bruck D, Petersen K, Berman J. Stress alters rates and types of loss of heterozygosity in Candida albicans. mBio 2011; 2:e00129-11. [PMID: 21791579 PMCID: PMC3143845 DOI: 10.1128/mbio.00129-11] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 06/30/2011] [Indexed: 01/27/2023] Open
Abstract
UNLABELLED Genetic diversity is often generated during adaptation to stress, and in eukaryotes some of this diversity is thought to arise via recombination and reassortment of alleles during meiosis. Candida albicans, the most prevalent pathogen of humans, has no known meiotic cycle, and yet it is a heterozygous diploid that undergoes mitotic recombination during somatic growth. It has been shown that clinical isolates as well as strains passaged once through a mammalian host undergo increased levels of recombination. Here, we tested the hypothesis that stress conditions increase rates of mitotic recombination in C. albicans, which is measured as loss of heterozygosity (LOH) at specific loci. We show that LOH rates are elevated during in vitro exposure to oxidative stress, heat stress, and antifungal drugs. In addition, an increase in stress severity correlated well with increased LOH rates. LOH events can arise through local recombination, through homozygosis of longer tracts of chromosome arms, or by whole-chromosome homozygosis. Chromosome arm homozygosis was most prevalent in cultures grown under conventional lab conditions. Importantly, exposure to different stress conditions affected the levels of different types of LOH events, with oxidative stress causing increased recombination, while fluconazole and high temperature caused increases in events involving whole chromosomes. Thus, C. albicans generates increased amounts and different types of genetic diversity in response to a range of stress conditions, a process that we term "stress-induced LOH" that arises either by elevating rates of recombination and/or by increasing rates of chromosome missegregation. IMPORTANCE Stress-induced mutagenesis fuels the evolution of bacterial pathogens and is mainly driven by genetic changes via mitotic recombination. Little is known about this process in other organisms. Candida albicans, an opportunistic fungal pathogen, causes infections that require adaptation to different host environmental niches. We measured the rates of LOH and the types of LOH events that appeared in the absence and in the presence of physiologically relevant stresses and found that stress causes a significant increase in the rates of LOH and that this increase is proportional to the degree of stress. Furthermore, the types of LOH events that arose differed in a stress-dependent manner, indicating that eukaryotic cells generate increased genetic diversity in response to a range of stress conditions. We propose that this "stress-induced LOH" facilitates the rapid adaptation of C. albicans, which does not undergo meiosis, to changing environments within the host.
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Affiliation(s)
- A. Forche
- Department of Biology, Bowdoin College, Brunswick, Maine, USA, and
| | - D. Abbey
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - T. Pisithkul
- Department of Biology, Bowdoin College, Brunswick, Maine, USA, and
| | - M. A. Weinzierl
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - T. Ringstrom
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - D. Bruck
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - K. Petersen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - J. Berman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
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Li X, Tan X, Yu Y, Chen H, Chang W, Hou J, Xu D, Ma L, Cao G. D9S168 microsatellite alteration predicts a poor prognosis in patients with clear cell renal cell carcinoma and correlates with the down-regulation of protein tyrosine phosphatase receptor delta. Cancer 2011; 117:4201-11. [DOI: 10.1002/cncr.26028] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 01/12/2011] [Accepted: 01/18/2011] [Indexed: 11/09/2022]
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Purdie KJ, Pourreyron C, South AP. Isolation and culture of squamous cell carcinoma lines. Methods Mol Biol 2011; 731:151-9. [PMID: 21516406 DOI: 10.1007/978-1-61779-080-5_14] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cutaneous squamous cell carcinoma (SCC) keratinocytes readily grow, expand in culture, and continuously passage, suggesting either spontaneous immortalisation at the early stage of culture or inherent proliferative capacity. One feature of SCC keratinocytes is genomic DNA rearrangement and single-nucleotide polymorphism studies of fresh frozen primary tumour, early and late passage SCC keratinocytes suggest that these rearrangements are stable in culture and retain the parental tumour lesions. SCC keratinocytes are isolated using standard primary culture techniques and become feeder cell independent with little or no observed "crisis" period. SCC keratinocytes readily form tumours in vivo, which retain histological features of the parental tumour, making them an excellent model for the study and development of cancer therapies.
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Affiliation(s)
- Karin J Purdie
- Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital & Medical School, Dundee, UK
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40
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Giefing M, Zemke N, Brauze D, Kostrzewska-Poczekaj M, Luczak M, Szaumkessel M, Pelinska K, Kiwerska K, Tönnies H, Grenman R, Figlerowicz M, Siebert R, Szyfter K, Jarmuz M. High resolution ArrayCGH and expression profiling identifies PTPRD and PCDH17/PCH68 as tumor suppressor gene candidates in laryngeal squamous cell carcinoma. Genes Chromosomes Cancer 2010; 50:154-66. [PMID: 21213369 DOI: 10.1002/gcc.20840] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 10/22/2010] [Indexed: 12/21/2022] Open
Abstract
Many classical tumor suppressor genes (TSG) were identified by delineation of bi-allelic losses called homozygous deletions. To identify systematically homozygous deletions in laryngeal squamous cell carcinoma (LSCC) and to unravel novel putative tumor suppressor genes, we screened 10 LSCC cell lines using high resolution array comparative genomic hybridization (arrayCGH) and array based expression analysis. ArrayCGH identified altogether 113 regions harboring protein coding genes that showed strong reduction in copy number indicating a potential homozygous deletion. Out of the 113 candidate regions, 22 novel homozygous deletions that affected the coding sequences of 15 genes were confirmed by multiplexPCR. Three genes were homozygously lost in two cell lines: PCDH17/PCH68, PRR20, and PTPRD. For the 15 homozygously deleted genes, four showed statistically significant downregulation of expression in LSCC cell lines as compared with normal human laryngeal controls. These were ATG7 (1/10 cell line), ZMYND11 (BS69) (1/10 cell line), PCDH17/PCH68 (9/10 cell lines), and PTPRD (7/10 cell lines). Quantitative real-time PCR was used to confirm the downregulation of the candidate genes in 10 expression array-studied cell lines and an additional cohort of cell lines; statistical significant downregulation of PCDH17/PCH68 and PTPRD was observed. In line with this also Western blot analyses demonstrated a complete absence of the PCDH17 and PTPRD proteins. Thus, expression profiling confirmed recurrent alterations of two genes identified primarily by delineation of homozygous deletions. These were PCDH17/PCH68, the protocadherin gene, and the STAT3 inhibiting receptor protein tyrosine phosphatase gene PTPRD. These genes are good candidates for novel TSG in LSCC.
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Affiliation(s)
- Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.
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Hu N, Clifford RJ, Yang HH, Wang C, Goldstein AM, Ding T, Taylor PR, Lee MP. Genome wide analysis of DNA copy number neutral loss of heterozygosity (CNNLOH) and its relation to gene expression in esophageal squamous cell carcinoma. BMC Genomics 2010; 11:576. [PMID: 20955586 PMCID: PMC3091724 DOI: 10.1186/1471-2164-11-576] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Accepted: 10/18/2010] [Indexed: 12/14/2022] Open
Abstract
Background Genomic instability plays an important role in human cancers. We previously characterized genomic instability in esophageal squamous cell carcinomas (ESCC) in terms of loss of heterozygosity (LOH) and copy number (CN) changes in tumors using the Affymetrix GeneChip Human Mapping 500K array in 30 cases from a high-risk region of China. In the current study we focused on copy number neutral (CN = 2) LOH (CNNLOH) and its relation to gene expression in ESCC. Results Overall we found that 70% of all LOH observed was CNNLOH. Ninety percent of ESCCs showed CNNLOH (median frequency in cases = 60%) and this was the most common type of LOH in two-thirds of cases. CNNLOH occurred on all 39 autosomal chromosome arms, with highest frequencies on 19p (100%), 5p (96%), 2p (95%), and 20q (95%). In contrast, LOH with CN loss represented 19% of all LOH, occurred in just half of ESCCs (median frequency in cases = 0%), and was most frequent on 3p (56%), 5q (47%), and 21q (41%). LOH with CN gain was 11% of all LOH, occurred in 93% of ESCCs (median frequency in cases = 13%), and was most common on 20p (82%), 8q (74%), and 3q (42%). To examine the effect of genomic instability on gene expression, we evaluated RNA profiles from 17 pairs of matched normal and tumor samples (a subset of the 30 ESCCs) using Affymetrix U133A 2.0 arrays. In CN neutral regions, expression of 168 genes (containing 1976 SNPs) differed significantly in tumors with LOH versus tumors without LOH, including 101 genes that were up-regulated and 67 that were down-regulated. Conclusion Our results indicate that CNNLOH has a profound impact on gene expression in ESCC, which in turn may affect tumor development.
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Affiliation(s)
- Nan Hu
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
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Sekulic A, Kim SY, Hostetter G, Savage S, Einspahr JG, Prasad A, Sagerman P, Curiel-Lewandrowski C, Krouse R, Bowden GT, Warneke J, Alberts DS, Pittelkow MR, DiCaudo D, Nickoloff BJ, Trent JM, Bittner M. Loss of inositol polyphosphate 5-phosphatase is an early event in development of cutaneous squamous cell carcinoma. Cancer Prev Res (Phila) 2010; 3:1277-83. [PMID: 20876729 DOI: 10.1158/1940-6207.capr-10-0058] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cutaneous squamous cell carcinoma (SCC) occurs commonly and can metastasize. Identification of specific molecular aberrations and mechanisms underlying the development and progression of cutaneous SCC may lead to better prognostic and therapeutic approaches and more effective chemoprevention strategies. To identify genetic changes associated with early stages of cutaneous SCC development, we analyzed a series of 40 archived skin tissues ranging from normal skin to invasive SCC. Using high-resolution array-based comparative genomic hybridization, we identified deletions of a region on chromosome 10q harboring the INPP5A gene in 24% of examined SCC tumors. Subsequent validation by immunohistochemistry on an independent sample set of 71 SCC tissues showed reduced INPP5A protein levels in 72% of primary SCC tumors. Decrease in INPP5A protein levels seems to be an early event in SCC development, as it also is observed in 9 of 26 (35%) examined actinic keratoses, the earliest stage in SCC development. Importantly, further reduction of INPP5A levels is seen in a subset of SCC patients as the tumor progresses from primary to metastatic stage. The observed frequency and pattern of loss indicate that INPP5A, a negative regulator of inositol signaling, may play a role in development and progression of cutaneous SCC tumors.
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Cheung KJJ, Delaney A, Ben-Neriah S, Schein J, Lee T, Shah SP, Cheung D, Johnson NA, Mungall AJ, Telenius A, Lai B, Boyle M, Connors JM, Gascoyne RD, Marra MA, Horsman DE. High resolution analysis of follicular lymphoma genomes reveals somatic recurrent sites of copy-neutral loss of heterozygosity and copy number alterations that target single genes. Genes Chromosomes Cancer 2010; 49:669-81. [PMID: 20544841 DOI: 10.1002/gcc.20780] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A multiplatform approach, including conventional cytogenetic techniques, BAC array comparative genomic hybridization, and Affymetrix 500K SNP arrays, was applied to the study of the tumor genomes of 25 follicular lymphoma biopsy samples with paired normal DNA samples to characterize balanced translocations, copy number imbalances, and copy-neutral loss of heterozygosity (cnLOH). In addition to the t(14;18), eight unique balanced translocations were found. Commonly reported FL-associated copy number regions were revealed including losses of 1p32-36, 6q, and 10q, and gains of 1q, 6p, 7, 12, 18, and X. The most frequent regions affected by copy-neutral loss of heterozygosity were 1p36.33 (28%), 6p21.3 (20%), 12q21.2-q24.33 (16%), and 16p13.3 (24%). We also identified by SNP analysis, 45 aberrant regions that each affected one gene, including CDKN2A, CDKN2B, FHIT, KIT, PEX14, and PTPRD, which were associated with canonical pathways involved in tumor development. This study illustrates the power of using complementary high-resolution platforms on paired tumor/normal specimens and computational analysis to provide potential insights into the significance of single-gene somatic aberrations in FL tumorigenesis.
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Affiliation(s)
- K-John J Cheung
- Center for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, BC, Canada.
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Salgado R, Toll A, Alameda F, Baró T, Martín-Ezquerra G, Sanmartín O, Martorell-Calatayud A, Salido M, Almenar S, Solé F, Pujol RM, Espinet B. CKS1B amplification is a frequent event in cutaneous squamous cell carcinoma with aggressive clinical behaviour. Genes Chromosomes Cancer 2010; 49:1054-61. [DOI: 10.1002/gcc.20814] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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45
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Okamoto R, Ogawa S, Nowak D, Kawamata N, Akagi T, Kato M, Sanada M, Weiss T, Haferlach C, Dugas M, Ruckert C, Haferlach T, Koeffler HP. Genomic profiling of adult acute lymphoblastic leukemia by single nucleotide polymorphism oligonucleotide microarray and comparison to pediatric acute lymphoblastic leukemia. Haematologica 2010; 95:1481-8. [PMID: 20435627 DOI: 10.3324/haematol.2009.011114] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Differences in survival have been reported between pediatric and adult acute lymphoblastic leukemia. The inferior prognosis in adult acute lymphoblastic leukemia is not fully understood but could be attributed, in part, to differences in genomic alterations found in adult as compared to in pediatric acute lymphoblastic leukemia. DESIGN AND METHODS We compared two different sets of high-density single nucleotide polymorphism array genotyping data from 75 new diagnostic adult and 399 previously published diagnostic pediatric acute lymphoblastic leukemia samples. The patients' samples were randomly acquired from among Caucasian and Asian populations and hybridized to either Affymetrix 50K or 250K single nucleotide polymorphism arrays. The array data were investigated with Copy Number Analysis for GeneChips (CNAG) software for allele-specific copy number analysis. RESULTS The high density single nucleotide polymorphism array analysis of 75 samples of adult acute lymphoblastic leukemia led to the identification of numerous cryptic and submicroscopic genomic lesions with a mean of 7.6 genomic alterations per sample. The patterns and frequencies of lesions detected in the adult samples largely reproduced known genomic hallmarks detected in previous single nucleotide polymorphism-array studies of pediatric acute lymphoblastic leukemia, such as common deletions of 3p14.2 (FHIT), 5q33.3 (EBF), 6q, 9p21.3 (CDKN2A/B), 9p13.2 (PAX5), 13q14.2 (RB1) and 17q11.2 (NF1). Some differences between adult and pediatric acute lymphoblastic leukemia were identified when the pediatric data set was partitioned into hyperdiploid and non-hyperdiploid cases and then compared to the nearly exclusively non-hyperdiploid adult samples. In this analysis, adult samples had a higher rate of deletions of chromosome 17p (TP53) and duplication of 17q. CONCLUSIONS Our analysis of adult acute lymphoblastic leukemia cases led to the identification of new potential target lesions relevant for the pathogenesis of acute lymphoblastic leukemia. However, no unequivocal pattern of submicroscopic genomic alterations was found to separate adult acute lymphoblastic leukemia from pediatric acute lymphoblastic leukemia. Therefore, apart from different therapy regimen, differences of prognosis between adult and pediatric acute lymphoblastic leukemia are probably based on genetic subgroups according to cytogenetically detectable lesions but not focal genomic copy number microlesions.
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Affiliation(s)
- Ryoko Okamoto
- Division of Hematology and Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, 8700, Beverly Blvd, Los Angeles, CA90048, USA.
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Chari R, Thu KL, Wilson IM, Lockwood WW, Lonergan KM, Coe BP, Malloff CA, Gazdar AF, Lam S, Garnis C, MacAulay CE, Alvarez CE, Lam WL. Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer. Cancer Metastasis Rev 2010; 29:73-93. [PMID: 20108112 DOI: 10.1007/s10555-010-9199-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Advances in high-throughput, genome-wide profiling technologies have allowed for an unprecedented view of the cancer genome landscape. Specifically, high-density microarrays and sequencing-based strategies have been widely utilized to identify genetic (such as gene dosage, allelic status, and mutations in gene sequence) and epigenetic (such as DNA methylation, histone modification, and microRNA) aberrations in cancer. Although the application of these profiling technologies in unidimensional analyses has been instrumental in cancer gene discovery, genes affected by low-frequency events are often overlooked. The integrative approach of analyzing parallel dimensions has enabled the identification of (a) genes that are often disrupted by multiple mechanisms but at low frequencies by any one mechanism and (b) pathways that are often disrupted at multiple components but at low frequencies at individual components. These benefits of using an integrative approach illustrate the concept that the whole is greater than the sum of its parts. As efforts have now turned toward parallel and integrative multidimensional approaches for studying the cancer genome landscape in hopes of obtaining a more insightful understanding of the key genes and pathways driving cancer cells, this review describes key findings disseminating from such high-throughput, integrative analyses, including contributions to our understanding of causative genetic events in cancer cell biology.
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Affiliation(s)
- Raj Chari
- Genetics Unit - Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
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Purdie KJ, Harwood CA, Gibbon K, Chaplin T, Young BD, Cazier JB, Singh N, Leigh IM, Proby CM. High-resolution genomic profiling of human papillomavirus-associated vulval neoplasia. Br J Cancer 2010; 102:1044-51. [PMID: 20234371 PMCID: PMC2844038 DOI: 10.1038/sj.bjc.6605589] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background: The incidence of human papillomavirus-associated vulval neoplasia is increasing worldwide; yet the associated genetic changes remain poorly understood. Methods: We have used single-nucleotide polymorphism microarray analysis to perform the first high-resolution investigation of genome-wide allelic imbalance in vulval neoplasia. Our sample series comprised 21 high-grade vulval intraepithelial neoplasia and 6 vulval squamous cell carcinomas, with paired non-lesional samples used to adjust for normal copy number variation. Results: Overall the most common recurrent aberrations were gains at 1p and 20, with the most frequent deletions observed at 2q, 3p and 10. Copy-neutral loss of heterozygosity at 6p was a recurrent event in vulval intraepithelial neoplasia. The pattern of genetic alterations differed from the characteristic changes we previously identified in cutaneous squamous cell carcinomas. Vulval neoplasia samples did not exhibit gain at 5p, a frequent recurrent aberration in a series of cervical tumours analysed elsewhere using an identical protocol. Conclusion: This series of 27 vulval samples comprises the largest systematic genome-wide analysis of vulval neoplasia performed to date. Despite shared papillomavirus status and regional proximity, our data suggest that the frequency of certain genetic alterations may differ in vulval and cervical tumours.
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Affiliation(s)
- K J Purdie
- Centre for Cutaneous Research, Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, UK.
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Huang HY, Li SH, Yu SC, Chou FF, Tzeng CC, Hu TH, Uen YH, Tian YF, Wang YH, Fang FM, Huang WW, Wei YC, Wu JM, Li CF. Homozygous deletion of MTAP gene as a poor prognosticator in gastrointestinal stromal tumors. Clin Cancer Res 2009; 15:6963-72. [PMID: 19887491 DOI: 10.1158/1078-0432.ccr-09-1511] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Chromosome 9 is frequently deleted in high-risk gastrointestinal stromal tumors (GISTs), whereas its specific tumor suppressor genes (TSGs) are less understood. We did an integrative study of MTAP gene at 9p21 to analyze its implication in GISTs. EXPERIMENTAL DESIGN To search TSGs on chromosome 9, we used ultrahigh-resolution array comparative genomic hybridization to profile DNA copy number alterations of 22 GISTs, with special attention to MTAP gene. MTAP immunoexpression was assessable for 306 independent GISTs on tissue microarrays, with 146 cases analyzed for MTAP homozygous deletion, 181 for mutations of KIT and PDGFRA receptor tyrosine kinase genes, and 7 for MTAP hypermethylation. RESULTS Array comparative genomic hybridization identified 11 candidate TSGs on 9p and six on 9q. MTAP and/or CDKN2A/CDKN2B at 9p21.3 were deleted in one intermediate-risk (11%) and seven high-risk (70%) GISTs with two cases homozygously codeleted at both loci. MTAP homozygous deletion, present in 25 of 146 cases, was highly associated with larger size and higher mitotic rate, Ki-67 index, and risk level (all P < 0.01) but not with receptor tyrosine kinase genotypes. Whereas MTAP homozygous deletion correlated with MTAP protein loss (P < 0.001), 7 of 30 GISTs without MTAP expression did not show homozygous deletion, including three MTAP-hypermethylated cases. MTAP homozygous deletion was univariately predictive of decreased disease-free survival (P < 0.0001) and remained multivariately independent (P = 0.0369, hazard ratio = 2.166), together with high-risk category (P < 0.0001), Ki-67 index >5% (P = 0.0106), and nongastric location (P = 0.0416). CONCLUSIONS MTAP homozygous deletion, the predominant mechanism to deplete protein expression, is present in 17% of GISTs. It correlates with important prognosticators and independently predicts worse outcomes, highlighting the role in disease progression.
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Affiliation(s)
- Hsuan-Ying Huang
- Departments of Pathology, Surgery, and Radiation Oncology, and Divisions of Oncology and Gastroenterology, Department of Internal Medicine, Chang Gung Memorial Hospital-Kaohsiung Medical Center, Chang Gung University College of Medicine, Kaohsiung, Taiwan
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Kresse SH, Ohnstad HO, Paulsen EB, Bjerkehagen B, Szuhai K, Serra M, Schaefer KL, Myklebost O, Meza-Zepeda LA. LSAMP, a novel candidate tumor suppressor gene in human osteosarcomas, identified by array comparative genomic hybridization. Genes Chromosomes Cancer 2009; 48:679-93. [PMID: 19441093 DOI: 10.1002/gcc.20675] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Osteosarcomas are the most common primary malignant tumor of bone, and almost all conventional osteosarcomas are high-grade tumors with complex karyotypes. We have examined DNA copy number changes in 36 osteosarcoma tumors and 20 cell lines using microarray-based comparative genomic hybridization. The most frequent minimal recurrent regions of gain identified in the tumor samples were in 1q21.2-q21.3 (78% of the samples), 1q21.3-q22 (78%), and 8q22.1 (72%). Minimal recurrent regions in 10q22.1-q22.2 (81%), 6q16.1 (67%), 13q14.2 (67%), and 13q21.1 (67%) were most frequently lost. A small region in 3q13.31 (2.1 Mb) containing the gene limbic system-associated membrane protein (LSAMP) was frequently deleted (56%). LSAMP has previously been reported to be a candidate tumor suppressor gene in other cancer types. The deletion was validated using fluorescence in situ hybridization, and the expression level and promoter methylation status of LSAMP were investigated using quantitative real-time reverse transcription PCR and methylation-specific PCR, respectively. LSAMP showed low expression compared to two normal bone samples in 6/15 tumors and 5/9 cell lines with deletion of 3q13.31, and also in 5/14 tumors and 3/11 cell lines with normal copy number or gain. Partial or full methylation of the investigated CpG island was identified in 3/30 tumors and 7/20 cell lines. Statistical analyses revealed that loss of 11p15.4-p15.3 and low expression of LSAMP (both P = 0.011) were significantly associated with poor survival. Our results show that LSAMP is a novel candidate tumor suppressor gene in osteosarcomas.
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Affiliation(s)
- Stine H Kresse
- Department of Tumor Biology, The Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
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Solomon DA, Kim JS, Yang XR, Tucker MA, Goldstein AM, Samuels Y, Waldman T. Lack of inherited mutations of PTPRD in familial melanoma and melanoma-astrocytoma syndrome. Pigment Cell Melanoma Res 2009; 22:489-91. [PMID: 19500277 PMCID: PMC2758084 DOI: 10.1111/j.1755-148x.2009.00587.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- David A. Solomon
- Department of Oncology, Lombardi Cancer Center, Georgetown University School of Medicine, Washington, DC, USA
| | - Jung-Sik Kim
- Department of Oncology, Lombardi Cancer Center, Georgetown University School of Medicine, Washington, DC, USA
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Margaret A. Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alisa M. Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yardena Samuels
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Todd Waldman
- Department of Oncology, Lombardi Cancer Center, Georgetown University School of Medicine, Washington, DC, USA
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