1
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Liu Y, Zhang M, Jang H, Nussinov R. The allosteric mechanism of mTOR activation can inform bitopic inhibitor optimization. Chem Sci 2024; 15:1003-1017. [PMID: 38239681 PMCID: PMC10793652 DOI: 10.1039/d3sc04690g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/06/2023] [Indexed: 01/22/2024] Open
Abstract
mTOR serine/threonine kinase is a cornerstone in the PI3K/AKT/mTOR pathway. Yet, the detailed mechanism of activation of its catalytic core is still unresolved, likely due to mTOR complexes' complexity. Its dysregulation was implicated in cancer and neurodevelopmental disorders. Using extensive molecular dynamics (MD) simulations and compiled published experimental data, we determine exactly how mTOR's inherent motifs can control the conformational changes in the kinase domain, thus kinase activity. We also chronicle the critical regulation by the unstructured negative regulator domain (NRD). When positioned inside the catalytic cleft (NRD IN state), mTOR tends to adopt a deep and closed catalytic cleft. This is primarily due to the direct interaction with the FKBP-rapamycin binding (FRB) domain which restricts it, preventing substrate access. Conversely, when outside the catalytic cleft (NRD OUT state), mTOR favors an open conformation, exposing the substrate-binding site on the FRB domain. We further show how an oncogenic mutation (L2427R) promotes shifting the mTOR ensemble toward the catalysis-favored state. Collectively, we extend mTOR's "active-site restriction" mechanism and clarify mutation action. In particular, our mechanism suggests that RMC-5552 (RMC-6272) bitopic inhibitors may benefit from adjustment of the (PEG8) linker length when targeting certain mTOR variants. In the cryo-EM mTOR/RMC-5552 structure, the distance between the allosteric and orthosteric inhibitors is ∼22.7 Å. With a closed catalytic cleft, this linker bridges the sites. However, in our activation mechanism, in the open cleft it expands to ∼24.7 Å, offering what we believe to be the first direct example of how discovering an activation mechanism can potentially increase the affinity of inhibitors targeting mutants.
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Affiliation(s)
- Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute Frederick MD 21702 USA
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research Frederick MD 21702 USA +1-301-846-5579
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research Frederick MD 21702 USA +1-301-846-5579
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research Frederick MD 21702 USA +1-301-846-5579
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University Tel Aviv 69978 Israel
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2
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Carm KT, Johannessen B, Bogaard M, Bakken AC, Maltau AV, Hoff AM, Axcrona U, Axcrona K, Lothe RA, Skotheim RI. Somatic mutations reveal complex metastatic seeding from multifocal primary prostate cancer. Int J Cancer 2023; 152:945-951. [PMID: 35880692 PMCID: PMC10087486 DOI: 10.1002/ijc.34226] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/27/2022] [Accepted: 07/05/2022] [Indexed: 01/06/2023]
Abstract
Primary prostate cancer shows a striking intraorgan molecular heterogeneity, with multiple spatially separated malignant foci in the majority of patients. Metastatic prostate cancer, however, typically reveals more homogenous molecular profiles, suggesting a monoclonal origin of the metastatic lesions. Longitudinal mutational spectra, comparing multiple primary lesions with metastases from the same patients remain poorly defined. We have here analyzed somatic mutations in multisampled, spatio-temporal biobanked lesions (38 samples from primary foci and 1 sample from each of 8 metastases from seven prostate cancer patients) applying a custom-designed panel targeting 68 prostate cancer relevant genes. The metastatic samples were taken at time of primary surgery and up to 7 years later, and sampling included circulating tumor DNA in plasma or solid metastatic tissue samples. A total of 282 somatic mutations were detected, with a range of 0 to 25 mutations per sample. Although seven samples had solely private mutations, the remaining 39 samples had both private and shared mutations. Seventy-four percent of mutations in metastases were not found in any primary samples, and vice versa, 96% of mutations in primary cancers were not found in any metastatic samples. However, for three patients, shared mutations were found suggesting the focus of origin, including mutations in AKT1, FOXA1, HOXB13, RB1 and TP53. In conclusion, the spatio-temporal heterogeneous nature of multifocal disease is emphasized in our study, and underlines the importance of testing a recent sample in genomics-based precision medicine for metastatic prostate cancer.
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Affiliation(s)
- Kristina T Carm
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Bjarne Johannessen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | - Mari Bogaard
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Pathology, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | - Anne Cathrine Bakken
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | - Aase V Maltau
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | - Andreas M Hoff
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | - Ulrika Axcrona
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway.,Department of Pathology, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | - Karol Axcrona
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway.,Department of Urology, Akershus University Hospital, Lørenskog, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Rolf I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway.,Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
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3
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Abd Elghani F, Safory H, Hamza H, Savyon M, Farhoud M, Toren‐Hershoviz M, Vitic Z, Ebanks K, Shani V, Bisharat S, Shaulov L, Brodski C, Song Z, Bandopadhyay R, Engelender S. SIAH proteins regulate the degradation and intra-mitochondrial aggregation of PINK1: Implications for mitochondrial pathology in Parkinson's disease. Aging Cell 2022; 21:e13731. [PMID: 36307912 PMCID: PMC9741505 DOI: 10.1111/acel.13731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/17/2022] [Accepted: 10/04/2022] [Indexed: 01/25/2023] Open
Abstract
Parkinson's disease (PD) is characterized by degeneration of neurons, particularly dopaminergic neurons in the substantia nigra. PD brains show accumulation of α-synuclein in Lewy bodies and accumulation of dysfunctional mitochondria. However, the mechanisms leading to mitochondrial pathology in sporadic PD are poorly understood. PINK1 is a key for mitophagy activation and recycling of unfit mitochondria. The activation of mitophagy depends on the accumulation of uncleaved PINK1 at the outer mitochondrial membrane and activation of a cascade of protein ubiquitination at the surface of the organelle. We have now found that SIAH3, a member of the SIAH proteins but lacking ubiquitin-ligase activity, is increased in PD brains and cerebrospinal fluid and in neurons treated with α-synuclein preformed fibrils (α-SynPFF). We also observed that SIAH3 is aggregated together with PINK1 in the mitochondria of PD brains. SIAH3 directly interacts with PINK1, leading to their intra-mitochondrial aggregation in cells and neurons and triggering a cascade of toxicity with PINK1 inactivation along with mitochondrial depolarization and neuronal death. We also found that SIAH1 interacts with PINK1 and promotes ubiquitination and proteasomal degradation of PINK1. Similar to the dimerization of SIAH1/SIAH2, SIAH3 interacts with SIAH1, promoting its translocation to mitochondria and preventing its ubiquitin-ligase activity toward PINK1. Our results support the notion that the increase in SIAH3 and intra-mitochondrial aggregation of SIAH3-PINK1 may mediate α-synuclein pathology by promoting proteotoxicity and preventing the elimination of dysfunctional mitochondria. We consider it possible that PINK1 activity is decreased in sporadic PD, which impedes proper mitochondrial renewal in the disease.
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Affiliation(s)
- Fatimah Abd Elghani
- Department of Biochemistry, Rappaport Faculty of MedicineTechnion‐Israel Institute of TechnologyHaifaIsrael
| | - Hazem Safory
- Department of Biochemistry, Rappaport Faculty of MedicineTechnion‐Israel Institute of TechnologyHaifaIsrael
| | - Haya Hamza
- Department of Biochemistry, Rappaport Faculty of MedicineTechnion‐Israel Institute of TechnologyHaifaIsrael
| | - Mor Savyon
- Department of Biochemistry, Rappaport Faculty of MedicineTechnion‐Israel Institute of TechnologyHaifaIsrael
| | - Malik Farhoud
- Department of Biochemistry, Rappaport Faculty of MedicineTechnion‐Israel Institute of TechnologyHaifaIsrael
| | - Michal Toren‐Hershoviz
- Department of Biochemistry, Rappaport Faculty of MedicineTechnion‐Israel Institute of TechnologyHaifaIsrael
| | - Zagorka Vitic
- Department of Physiology and Cell Biology, Zlotowski Center for Neuroscience, Faculty of Health SciencesBen‐Gurion University of the NegevBe'er ShevaIsrael
| | - Kirsten Ebanks
- Reta Lila Weston Institute of Neurological StudiesUCL Queen Square Institute of NeurologyLondonUK
| | - Vered Shani
- Department of Biochemistry, Rappaport Faculty of MedicineTechnion‐Israel Institute of TechnologyHaifaIsrael
| | - Sleman Bisharat
- Department of Biochemistry, Rappaport Faculty of MedicineTechnion‐Israel Institute of TechnologyHaifaIsrael
| | - Lihi Shaulov
- Department of Biochemistry, Rappaport Faculty of MedicineTechnion‐Israel Institute of TechnologyHaifaIsrael
| | - Claude Brodski
- Department of Physiology and Cell Biology, Zlotowski Center for Neuroscience, Faculty of Health SciencesBen‐Gurion University of the NegevBe'er ShevaIsrael
| | - Zhiyin Song
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and MetabolismWuhan UniversityWuhanChina
| | - Rina Bandopadhyay
- Reta Lila Weston Institute of Neurological StudiesUCL Queen Square Institute of NeurologyLondonUK
| | - Simone Engelender
- Department of Biochemistry, Rappaport Faculty of MedicineTechnion‐Israel Institute of TechnologyHaifaIsrael
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4
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Kuick CH, Tan JY, Jasmine D, Sumanty T, Ng AYJ, Venkatesh B, Chen H, Loh E, Jain S, Seow WY, Ng EHQ, Lian DWQ, Soh SY, Chang KTE, Chen ZX, Loh AHP. Mutations of 1p genes do not consistently abrogate tumor suppressor functions in 1p-intact neuroblastoma. BMC Cancer 2022; 22:717. [PMID: 35768791 PMCID: PMC9245282 DOI: 10.1186/s12885-022-09800-0] [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: 11/25/2021] [Accepted: 06/21/2022] [Indexed: 11/26/2022] Open
Abstract
Background Deletion of 1p is associated with poor prognosis in neuroblastoma, however selected 1p-intact patients still experience poor outcomes. Since mutations of 1p genes may mimic the deleterious effects of chromosomal loss, we studied the incidence, spectrum and effects of mutational variants in 1p-intact neuroblastoma. Methods We characterized the 1p status of 325 neuroblastoma patients, and correlated the mutational status of 1p tumor suppressors and neuroblastoma candidate genes with survival outcomes among 100 1p-intact cases, then performed functional validation of selected novel variants of 1p36 genes identified from our patient cohort. Results Among patients with adverse disease characteristics, those who additionally had 1p deletion had significantly worse overall survival. Among 100 tumor-normal pairs sequenced, somatic mutations of 1p tumor suppressors KIF1Bβ and CHD5 were most frequent (2%) after ALK and ATRX (8%), and BARD1 (3%). Mutations of neuroblastoma candidate genes were associated with other synchronous mutations and concurrent 11q deletion (P = 0.045). In total, 24 of 38 variants identified were novel and predicted to be deleterious or pathogenic. Functional validation identified novel KIF1Bβ I1355M variant as a gain-of-function mutation with increased expression and tumor suppressive activity, correlating with indolent clinical behavior; another novel variant CHD5 E43Q was a loss-of-function mutation with decreased expression and increased long-term cell viability, corresponding with aggressive disease characteristics. Conclusions Our study showed that chromosome 1 gene mutations occurred frequently in 1p-intact neuroblastoma, but may not consistently abrogate the function of bonafide 1p tumor suppressors. These findings may augment the evolving model of compounding contributions of 1p gene aberrations toward tumor suppressor inactivation in neuroblastoma. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09800-0.
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Affiliation(s)
- Chik Hong Kuick
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Jia Ying Tan
- Neurodevelopment and Cancer Laboratory, NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Deborah Jasmine
- Neurodevelopment and Cancer Laboratory, NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Tohari Sumanty
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore, 138673, Singapore
| | - Alvin Y J Ng
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore, 138673, Singapore
| | - Byrrappa Venkatesh
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore, 138673, Singapore
| | - Huiyi Chen
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Eva Loh
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Sudhanshi Jain
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Wan Yi Seow
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Eileen H Q Ng
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Derrick W Q Lian
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Shui Yen Soh
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, 229899, Singapore.,Department of Paediatric Subspecialties Haematology Oncology Service, KK Women's and Children's Hospital, Singapore, 229899, Singapore.,Duke NUS Medical School, Singapore, 169857, Singapore
| | - Kenneth T E Chang
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore.,VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, 229899, Singapore.,Duke NUS Medical School, Singapore, 169857, Singapore
| | - Zhi Xiong Chen
- Neurodevelopment and Cancer Laboratory, NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore. .,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore. .,VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, 229899, Singapore. .,National University Cancer Institute, Singapore, 119074, Singapore.
| | - Amos H P Loh
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, 229899, Singapore. .,Duke NUS Medical School, Singapore, 169857, Singapore. .,Department of Paediatric Surgery, KK Women's and Children's Hospital, Singapore, 229899, Singapore.
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5
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Tonmoy MIQ, Fariha A, Hami I, Kar K, Reza HA, Bahadur NM, Hossain MS. Computational epigenetic landscape analysis reveals association of CACNA1G-AS1, F11-AS1, NNT-AS1, and MSC-AS1 lncRNAs in prostate cancer progression through aberrant methylation. Sci Rep 2022; 12:10260. [PMID: 35715447 PMCID: PMC9205881 DOI: 10.1038/s41598-022-13381-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 05/24/2022] [Indexed: 12/24/2022] Open
Abstract
Aberrant expression of long non-coding RNAs (lncRNAs), caused by alterations in DNA methylation, is a driving factor in several cancers. Interplay between lncRNAs’ aberrant methylation and expression in prostate cancer (PC) progression still remains largely elusive. Therefore, this study characterized the genome-wide epigenetic landscape and expression profiles of lncRNAs and their clinical impact by integrating multi-omics data implementing bioinformatics approaches. We identified 62 differentially methylated CpG-sites (DMCs) and 199 differentially expressed lncRNAs (DElncRNAs), where 32 DElncRNAs contain 32 corresponding DMCs within promoter regions. Significant negative correlation was observed between 8 DElncRNAs-DMCs pairs. 3 (cg23614229, cg23957912, and cg11052780) DMCs and 4 (CACNA1G-AS1, F11-AS1, NNT-AS1, and MSC-AS1) DElncRNAs were identified as high-risk factors for poor prognosis of PC patients. Overexpression of hypo-methylated CACNA1G-AS1, F11-AS1, and NNT-AS1 and down-regulation of hyper-methylated MSC-AS1 significantly lower the survival of PC patients and could be a potential prognostic and therapeutic biomarker. These DElncRNAs were found to be associated with several molecular functions whose deregulation can lead to cancer. Involvement of these epigenetically deregulated DElncRNAs in cancer-related biological processes was also noticed. These findings provide new insights into the understanding of lncRNA regulation by aberrant DNA methylation which will help to clarify the epigenetic mechanisms underlying PC.
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Affiliation(s)
- Mahafujul Islam Quadery Tonmoy
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh.,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Atqiya Fariha
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh.,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Ithmam Hami
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Kumkum Kar
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Hasan Al Reza
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh.,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Shahadat Hossain
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh. .,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh.
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6
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Stover EH, Oh C, Keskula P, Choudhury AD, Tseng YY, Adalsteinsson VA, Lohr JG, Thorner AR, Ducar M, Kryukov GV, Ha G, Rosenberg M, Freeman SS, Zhang Z, Wu X, Van Allen EM, Takeda DY, Loda M, Wu CL, Taplin ME, Garraway LA, Boehm JS, Huang FW. Implementation of a prostate cancer-specific targeted sequencing panel for credentialing of patient-derived cell lines and genomic characterization of patient samples. Prostate 2022; 82:584-597. [PMID: 35084050 PMCID: PMC8887817 DOI: 10.1002/pros.24305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Primary and metastatic prostate cancers have low mutation rates and recurrent alterations in a small set of genes, enabling targeted sequencing of prostate cancer-associated genes as an efficient approach to characterizing patient samples (compared to whole-exome and whole-genome sequencing). For example, targeted sequencing provides a flexible, rapid, and cost-effective method for genomic assessment of patient-derived cell lines to evaluate fidelity to initial patient tumor samples. METHODS We developed a prostate cancer-specific targeted next-generation sequencing (NGS) panel to detect alterations in 62 prostate cancer-associated genes as well as recurring gene fusions with ETS family members, representing the majority of common alterations in prostate cancer. We tested this panel on primary prostate cancer tissues and blood biopsies from patients with metastatic prostate cancer. We generated patient-derived cell lines from primary prostate cancers using conditional reprogramming methods and applied targeted sequencing to evaluate the fidelity of these cell lines to the original patient tumors. RESULTS The prostate cancer-specific panel identified biologically and clinically relevant alterations, including point mutations in driver oncogenes and ETS family fusion genes, in tumor tissues from 29 radical prostatectomy samples. The targeted panel also identified genomic alterations in cell-free DNA and circulating tumor cells (CTCs) from patients with metastatic prostate cancer, and in standard prostate cancer cell lines. We used the targeted panel to sequence our set of patient-derived cell lines; however, no prostate cancer-specific mutations were identified in the tumor-derived cell lines, suggesting preferential outgrowth of normal prostate epithelial cells. CONCLUSIONS We evaluated a prostate cancer-specific targeted NGS panel to detect common and clinically relevant alterations (including ETS family gene fusions) in prostate cancer. The panel detected driver mutations in a diverse set of clinical samples of prostate cancer, including fresh-frozen tumors, cell-free DNA, CTCs, and cell lines. Targeted sequencing of patient-derived cell lines highlights the challenge of deriving cell lines from primary prostate cancers and the importance of genomic characterization to credential candidate cell lines. Our study supports that a prostate cancer-specific targeted sequencing panel provides an efficient, clinically feasible approach to identify genetic alterations across a spectrum of prostate cancer samples and cell lines.
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Affiliation(s)
- Elizabeth H. Stover
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | - Coyin Oh
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | - Atish D. Choudhury
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | | | - Jens G. Lohr
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | | | - Gregory V. Kryukov
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | - Gavin Ha
- Fred Hutchinson Cancer Research Center, Seattle WA
| | | | | | - Zhenwei Zhang
- Dana-Farber Cancer Institute, Boston MA
- University of Massachusetts Memorial Medical Center, Worcester MA
| | | | - Eliezer M. Van Allen
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | - Massimo Loda
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- New York-Presbyterian/Weill Cornell Medical Center, New York, NY
| | - Chin-Lee Wu
- Harvard Medical School, Boston MA
- Massachusetts General Hospital, Boston MA
| | - Mary-Ellen Taplin
- Dana-Farber Cancer Institute, Boston MA
- Harvard Medical School, Boston MA
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7
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Jacob A, Raj R, Allison DB, Myint ZW. Androgen Receptor Signaling in Prostate Cancer and Therapeutic Strategies. Cancers (Basel) 2021; 13:5417. [PMID: 34771580 PMCID: PMC8582395 DOI: 10.3390/cancers13215417] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/21/2021] [Accepted: 10/27/2021] [Indexed: 11/17/2022] Open
Abstract
Understanding of the molecular mechanisms of prostate cancer has led to development of therapeutic strategies targeting androgen receptor (AR). These androgen-receptor signaling inhibitors (ARSI) include androgen synthesis inhibitor-abiraterone and androgen receptor antagonists-enzalutamide, apalutamide, and darolutamide. Although these medications provide significant improvement in survival among men with prostate cancer, drug resistance develops in nearly all patients with time. This could be through androgen-dependent or androgen-independent mechanisms. Even weaker signals and non-canonical steroid ligands can activate AR in the presence of truncated AR-splice variants, AR overexpression, or activating mutations in AR. AR splice variant, AR-V7 is the most studied among these and is not targeted by available ARSIs. Non-androgen receptor dependent resistance mechanisms are mediated by activation of an alternative signaling pathway when AR is inhibited. DNA repair pathway, PI3K/AKT/mTOR pathway, BRAF-MAPK and Wnt signaling pathway and activation by glucocorticoid receptors can restore downstream signaling in prostate cancer by alternative proteins. Multiple clinical trials are underway exploring therapeutic strategies to overcome these resistance mechanisms.
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Affiliation(s)
- Aasems Jacob
- Department of Medicine, Division of Hematology & Oncology, Pikeville Medical Center, Pikeville, KY 41501, USA;
| | - Rishi Raj
- Department of Medicine, Division of Endocrinology, Diabetes & Metabolism, Pikeville Medical Center, Pikeville, KY 41501, USA;
| | - Derek B. Allison
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA;
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY 40536, USA
- Department of Urology, University of Kentucky, Lexington, KY 40536, USA
| | - Zin W. Myint
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA;
- Department of Medicine, Division of Medical Oncology, University of Kentucky, Lexington, KY 40536, USA
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8
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Abstract
Interpreting the effects of genetic variants is key to understanding individual susceptibility to disease and designing personalized therapeutic approaches. Modern experimental technologies are enabling the generation of massive compendia of human genome sequence data and associated molecular and phenotypic traits, together with genome-scale expression, epigenomics and other functional genomic data. Integrative computational models can leverage these data to understand variant impact, elucidate the effect of dysregulated genes on biological pathways in specific disease and tissue contexts, and interpret disease risk beyond what is feasible with experiments alone. In this Review, we discuss recent developments in machine learning algorithms for genome interpretation and for integrative molecular-level modelling of cells, tissues and organs relevant to disease. More specifically, we highlight existing methods and key challenges and opportunities in identifying specific disease-causing genetic variants and linking them to molecular pathways and, ultimately, to disease phenotypes.
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9
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Erickson A, Hayes A, Rajakumar T, Verrill C, Bryant RJ, Hamdy FC, Wedge DC, Woodcock DJ, Mills IG, Lamb AD. A Systematic Review of Prostate Cancer Heterogeneity: Understanding the Clonal Ancestry of Multifocal Disease. Eur Urol Oncol 2021; 4:358-369. [PMID: 33888445 DOI: 10.1016/j.euo.2021.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/31/2021] [Accepted: 02/26/2021] [Indexed: 11/24/2022]
Abstract
CONTEXT Studies characterising genomic changes in prostate cancer (PCa) during natural progression have greatly increased our understanding of the disease. A better understanding of the evolutionary history of PCa would allow advances in diagnostics, prognostication, and novel therapies that together will improve patient outcomes. OBJECTIVE To review the molecular heterogeneity of PCa and assess recent efforts to profile intratumoural heterogeneity and clonal evolution. EVIDENCE ACQUISITION We screened a total of 1313 abstracts from PubMed published between 2009 and 2020, of which we reviewed 84 full-text articles. We excluded 49, resulting in 35 studies for qualitative analysis. EVIDENCE SYNTHESIS In studies of primary disease (16 studies, 4793 specimens), there is a lack of consensus regarding the monoclonal or polyclonal origin of primary PCa. There is no consistent mutation giving rise to primary PCa. Detailed clonal analysis of primary PCa has been limited by current techniques. By contrast, clonal relationships between PCa metastases and a potentiating clone have been consistently identified (19 studies, 732 specimens). Metastatic specimens demonstrate consistent truncal genomic aberrations that suggest monoclonal metastatic progenitors. CONCLUSIONS The relationship between the clonal dynamics of PCa and clinical outcomes needs further investigation. It is likely that this will provide a biological rationale for whether radical treatment of the primary tumour benefits patients with oligometastatic PCa. Future studies on the mutational burden in primary disease at single-cell resolution should permit the identification of clonal patterns underpinning the origin of lethal PCa. PATIENT SUMMARY Prostate cancers arise in different parts of the prostate because of DNA mutations that occur by chance at different times. These cancer cells and their origin can be tracked by DNA mapping. In this review we summarise the state of the art and outline what further science is needed to provide the missing answers.
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Affiliation(s)
- Andrew Erickson
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Alicia Hayes
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Oxford NIHR Biomedical Research Centre, University of Oxford, UK
| | - Timothy Rajakumar
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Oxford National Institute for Health Research Biomedical Research Centre, Oxford, UK; Oxford NIHR Biomedical Research Centre, University of Oxford, UK
| | - Richard J Bryant
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Oxford NIHR Biomedical Research Centre, University of Oxford, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Oxford NIHR Biomedical Research Centre, University of Oxford, UK
| | - David C Wedge
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK
| | - Dan J Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Oxford Big Data Institute, University of Oxford, Oxford, UK
| | - Ian G Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Oxford NIHR Biomedical Research Centre, University of Oxford, UK
| | - Alastair D Lamb
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Oxford NIHR Biomedical Research Centre, University of Oxford, UK.
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10
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Piedade WP, Famulski JK. E3 ubiquitin ligase-mediated regulation of vertebrate ocular development; new insights into the function of SIAH enzymes. Biochem Soc Trans 2021; 49:327-340. [PMID: 33616626 PMCID: PMC7924998 DOI: 10.1042/bst20200613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 01/18/2023]
Abstract
Developmental regulation of the vertebrate visual system has been a focus of investigation for generations as understanding this critical time period has direct implications on our understanding of congenital blinding disease. The majority of studies to date have focused on transcriptional regulation mediated by morphogen gradients and signaling pathways. However, recent studies of post translational regulation during ocular development have shed light on the role of the ubiquitin proteasome system (UPS). This rather ubiquitous yet highly diverse system is well known for regulating protein function and localization as well as stability via targeting for degradation by the 26S proteasome. Work from many model organisms has recently identified UPS activity during various milestones of ocular development including retinal morphogenesis, retinal ganglion cell function as well as photoreceptor homeostasis. In particular work from flies and zebrafish has highlighted the role of the E3 ligase enzyme family, Seven in Absentia Homologue (Siah) during these events. In this review, we summarize the current understanding of UPS activity during Drosophila and vertebrate ocular development, with a major focus on recent findings correlating Siah E3 ligase activity with two major developmental stages of vertebrate ocular development, retinal morphogenesis and photoreceptor specification and survival.
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11
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Common targets for a deadly duo of diabetes mellitus and colon cancer: Catching two fish with one worm. Eur J Pharmacol 2021; 893:173805. [PMID: 33359221 DOI: 10.1016/j.ejphar.2020.173805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/05/2020] [Accepted: 12/08/2020] [Indexed: 12/21/2022]
Abstract
Colon cancer is a major health issue and number of cases are increasing every year. Diabetes mellitus is also a significant health issue that is growing day by day worldwide having negative influences on the survival of individuals. Research has shown a strong relationship between the two malignant diseases. The risk of colon cancer with patients who have type 2 diabetes mellitus has spiked by 30%. The scientific research suggests insulin has a major role in the spread of cancer and the condition unifying between the two diseases is hyperinsulinemia. Several anti-diabetic agents are used for the treatment of type 2 diabetesmellitus. However, their mechanism of action against cancer activity is a question and only a few agents have shown positive signs of action in colon cancer associated with type 2 diabetesmellitus. Hence, the identification of targets, which is common for both colon cancer, associated with type 2 diabetesmellitus has become an urgent requirement. Novel targets such as Liver X receptors, Histone deacetylase inhibitors (HDACi), Glucose Transporters (GLUTs), Peroxisome proliferator activator receptors (PPARs), Dipeptidyl peptidase-IV inhibitors (DPP4i), Cyclin-dependent kinase 4 inhibitors (CDK4i), Estrogen receptors,Mechanistic target of rapamycin (mTOR), Insulin-like growth factor receptors (IGF) are some of the targets which are common for both, type 2 diabetesmellitus and colon cancer. This current review gives an overview of the targets (using one worm) which are common for both viz. diabetes mellitus and colon cancer (two fish).
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12
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Prostate cancer evolution from multilineage primary to single lineage metastases with implications for liquid biopsy. Nat Commun 2020; 11:5070. [PMID: 33033260 PMCID: PMC7545111 DOI: 10.1038/s41467-020-18843-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/01/2020] [Indexed: 02/08/2023] Open
Abstract
The evolutionary progression from primary to metastatic prostate cancer is largely uncharted, and the implications for liquid biopsy are unexplored. We infer detailed reconstructions of tumor phylogenies in ten prostate cancer patients with fatal disease, and investigate them in conjunction with histopathology and tumor DNA extracted from blood and cerebrospinal fluid. Substantial evolution occurs within the prostate, resulting in branching into multiple spatially intermixed lineages. One dominant lineage emerges that initiates and drives systemic metastasis, where polyclonal seeding between sites is common. Routes to metastasis differ between patients, and likely genetic drivers of metastasis distinguish the metastatic lineage from the lineage that remains confined to the prostate within each patient. Body fluids capture features of the dominant lineage, and subclonal expansions that occur in the metastatic phase are non-uniformly represented. Cerebrospinal fluid analysis reveals lineages not detected in blood-borne DNA, suggesting possible clinical utility.
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13
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Yang S, Jiang Y, Ren X, Feng D, Zhang L, He D, Hong S, Jin L, Zhang F, Lu S. FOXA1-induced circOSBPL10 potentiates cervical cancer cell proliferation and migration through miR-1179/UBE2Q1 axis. Cancer Cell Int 2020; 20:389. [PMID: 32831649 PMCID: PMC7422615 DOI: 10.1186/s12935-020-01360-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 06/17/2020] [Indexed: 01/30/2023] Open
Abstract
Background Recently, extensive evidence has clarified the crucial role of circular RNAs (circRNAs) as a pro-tumor or anti-cancer participant in human malignancies. A new circRNA derived from oxysterol binding protein like 10 (OSBPL10) (circOSBPL10) has not been researched in cervical cancer (CC) yet. Methods The expression of molecules was analyzed by RT-qPCR or western blot. Several functional assays were applied to explore the biological influence of circOSBPL10 on CC. The interaction between RNAs was estimated via luciferase reporter, RNA immunoprecipitation and RNA pull-down assays. Results CircOSBPL10 characterized with cyclic structure was revealed to possess elevated expression in CC cells. CircOSBPL10 downregulation elicited suppressive impacts on CC cell proliferation and migration. Interestingly, circOSBPL10 regulated CC progression by interacting with microRNA-1179 (miR-1179). Moreover, ubiquitin conjugating enzyme E2 Q1 (UBE2Q1) targeted by miR-1179 was positively regulated by circOSBPL10 in CC. Furthermore, enhanced UBE2Q1 expression or suppressed miR-1179 level countervailed the repressive effect of circOSBPL10 depletion on the malignant phenotypes of CC cells. Moreover, forkhead box A1 (FOXA1) was confirmed to induce circOSBPL10 expression in CC cells. Conclusions FOXA1-induced circOSBPL10 facilitates CC progression through miR-1179/UBE2Q1 axis, highlighting a strong potential for circOSBPL10 to serve as a promising therapeutic target in CC.
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Affiliation(s)
- Shanshan Yang
- Department of Gynecological Radiotherapy, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Nangang District, Harbin, 150081 Heilongjiang China
| | - Yiwen Jiang
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
| | - Xiaoli Ren
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
| | - Dan Feng
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
| | - Liaoyun Zhang
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China.,Pharmacy Department, Sichuan Jinxin Women and Children's Hospital, No. 66 Jingxiu Road, Jinjiang District, Chengdu, 610061 Sichuan China
| | - Deying He
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
| | - Shiyao Hong
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
| | - Li Jin
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
| | - Fang Zhang
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
| | - Shun Lu
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
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14
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Miller ET, You S, Cadaneanu RM, Kim M, Yoon J, Liu ST, Li X, Kwan L, Hodge J, Quist MJ, Grasso CS, Lewis MS, Knudsen BS, Freeman MR, Garraway IP. Chromosomal instability in untreated primary prostate cancer as an indicator of metastatic potential. BMC Cancer 2020; 20:398. [PMID: 32380981 PMCID: PMC7204307 DOI: 10.1186/s12885-020-06817-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022] Open
Abstract
Background Metastatic prostate cancer (PC) is highly lethal. The ability to identify primary tumors capable of dissemination is an unmet need in the quest to understand lethal biology and improve patient outcomes. Previous studies have linked chromosomal instability (CIN), which generates aneuploidy following chromosomal missegregation during mitosis, to PC progression. Evidence of CIN includes broad copy number alterations (CNAs) spanning > 300 base pairs of DNA, which may also be measured via RNA expression signatures associated with CNA frequency. Signatures of CIN in metastatic PC, however, have not been interrogated or well defined. We examined a published 70-gene CIN signature (CIN70) in untreated and castration-resistant prostate cancer (CRPC) cohorts from The Cancer Genome Atlas (TCGA) and previously published reports. We also performed transcriptome and CNA analysis in a unique cohort of untreated primary tumors collected from diagnostic prostate needle biopsies (PNBX) of localized (M0) and metastatic (M1) cases to determine if CIN was linked to clinical stage and outcome. Methods PNBX were collected from 99 patients treated in the VA Greater Los Angeles (GLA-VA) Healthcare System between 2000 and 2016. Total RNA was extracted from high-grade cancer areas in PNBX cores, followed by RNA sequencing and/or copy number analysis using OncoScan. Multivariate logistic regression analyses permitted calculation of odds ratios for CIN status (high versus low) in an expanded GLA-VA PNBX cohort (n = 121). Results The CIN70 signature was significantly enriched in primary tumors and CRPC metastases from M1 PC cases. An intersection of gene signatures comprised of differentially expressed genes (DEGs) generated through comparison of M1 versus M0 PNBX and primary CRPC tumors versus metastases revealed a 157-gene “metastasis” signature that was further distilled to 7-genes (PC-CIN) regulating centrosomes, chromosomal segregation, and mitotic spindle assembly. High PC-CIN scores correlated with CRPC, PC-death and all-cause mortality in the expanded GLA-VA PNBX cohort. Interestingly, approximately 1/3 of M1 PNBX cases exhibited low CIN, illuminating differential pathways of lethal PC progression. Conclusions Measuring CIN in PNBX by transcriptome profiling is feasible, and the PC-CIN signature may identify patients with a high risk of lethal progression at the time of diagnosis.
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Affiliation(s)
- Eric T Miller
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA
| | - Sungyong You
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Radu M Cadaneanu
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA
| | - Minhyung Kim
- Department of Surgery, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Junhee Yoon
- Department of Surgery, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Sandy T Liu
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA.,Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine at UCLA, California, Los Angeles, USA
| | - Xinmin Li
- Department of Pathology, David Geffen School of Medicine at UCLA, California, Los Angeles, USA.,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA
| | - Lorna Kwan
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA
| | - Jennelle Hodge
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Michael J Quist
- Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine at UCLA, California, Los Angeles, USA
| | - Catherine S Grasso
- Department of Surgery, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Michael S Lewis
- Department of Pathology, Greater Los Angeles Veterans Affairs Health System, California, Los Angeles, USA
| | - Beatrice S Knudsen
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Michael R Freeman
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Isla P Garraway
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA. .,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA. .,Division of Urology, Greater Los Angeles Veterans Affairs Healthcare Center, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA.
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15
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Li X, Chu SG, Shen XN, Hou XH, Xu W, Ou YN, Dong Q, Tan L, Yu JT. Genome-wide association study identifies SIAH3 locus influencing the rate of ventricular enlargement in non-demented elders. Aging (Albany NY) 2019; 11:9862-9874. [PMID: 31711042 PMCID: PMC6874439 DOI: 10.18632/aging.102435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/29/2019] [Indexed: 12/16/2022]
Abstract
Ventricular enlargement occurs in several neurodegenerative and psychiatric diseases. A large genome-wide association study (GWAS) has identified seven loci associated with ventricular volume. The rate of ventricular enlargement increased in the progression of disease from normal cognition to dementia. Here, we aimed to use the rate of ventricular enlargement as an endophenotype for the development and progression of neurodegenerative diseases to discover more common genetic variants. We performed a GWAS of the rate of ventricular enlargement using 507 nondemented non-Hispanic white participants from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort. Linear regression model was used to identify the association of the rate of ventricular enlargement with single nucleotide polymorphisms (SNPs) in PLINK software. The associations of genome-wide significant SNPs with other four phenotypes were further discussed. Two SNPs (rs11620312, P = 4.04×10−8; rs79174114, P = 4.28×10−8) within SIAH3 gene in linkage disequilibrium (LD) reached genome-wide significance for association with increased rate of ventricular enlargement. Some intergenic SNPs and SNPs within NKAIN2, TBC1D2, GALNT18, ABCC1 and SRCIN1 genes were identified as potential candidates. SIAH3 rs11620312-C carriers were associated with poor cognition and brain hypometabolism longitudinally. Our findings indicated that SIAH3 gene may have potential influence on the pathogenesis of neurodegenerative diseases.
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Affiliation(s)
- Xian Li
- Department of Neurology, Qingdao Municipal Hospital, Dalian Medical University, Dalian, China
| | - Shu-Guang Chu
- Department of Radiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xue-Ning Shen
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao-He Hou
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Wei Xu
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Ya-Nan Ou
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Qiang Dong
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, Dalian Medical University, Dalian, China
| | - Jin-Tai Yu
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
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16
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Lang SH, Swift SL, White H, Misso K, Kleijnen J, Quek RG. A systematic review of the prevalence of DNA damage response gene mutations in prostate cancer. Int J Oncol 2019; 55:597-616. [PMID: 31322208 PMCID: PMC6685596 DOI: 10.3892/ijo.2019.4842] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/28/2019] [Indexed: 02/06/2023] Open
Abstract
Several ongoing international prostate cancer (PC) clinical trials are exploring therapies that target the DNA damage response (DDR) pathway. This systematic review summarizes the prevalence of DDR mutation carriers in the unselected (general) PC and familial PC populations. A total of 11 electronic databases, 10 conference proceedings, and grey literature sources were searched from their inception to December 2017. Studies reporting the prevalence of somatic and/or germline DDR mutations were summarized. Metastatic PC (mPC), castration‑resistant PC (CRPC) and metastatic CRPC (mCRPC) subgroups were included. A total of 11,648 records were retrieved, and 80 studies (103 records) across all PC populations were included; 59 records were of unselected PC and 13 records of familial PC. Most data were available for DDR panels (n=12 studies), ataxia telangiectasia mutated (ATM; n=13), breast cancer susceptibility gene (BRCA)1 (n=14) and BRCA2 (n=20). ATM, BRCA2 and partner and localizer of BRCA2 (PALB2) had the highest mutation rates (≥4%). Median prevalence rates for DDR germline mutations were 18.6% in PC (range, 17.2‑19%; three studies, n=1,712), 11.6% in mPC (range, 11.4‑11.8%; two studies, n=1,261) and 8.3% in mCRPC (range, 7.5‑9.1%; two studies, n=738). Median prevalence rates for DDR somatic mutations were 10.7% in PC (range, 4.9‑22%; three studies, n=680), 13.2% in mPC (range, 10‑16.4%; two studies, n=105) and not reported (NR) in mCRPC. The prevalence of DDR germline and/or somatic mutations was 27% in PC (one study, n=221), 22.67% in mCRPC (one study, n=150) and NR in mPC. In familial PC, median mutation prevalence was 12.1% (range, 7.3‑16.9%) for germline DDR (two studies, n=315) and 3.7% (range, 1.3‑7.9%) for BRCA2 (six studies, n=945). In total, 88% of studies were at a high risk of bias. The prevalence of DDR gene mutations in PC varied widely within somatic subgroups depending on study size, genetic screening techniques, DDR mutation definition and PC diagnosis; somatic and/or germline DDR mutation prevalence was in the range of 23‑27% in PC. These findings support DDR mutation testing for all patients with PC (including those with mCRPC). With the advent of the latest clinical practice PC guidelines highlighting the importance of DDR mutation screening, and ongoing mCRPC clinical trials evaluating DDR mutation‑targeted drugs, future larger epidemiological studies are warranted to further quantify the international burden of DDR mutations in PC.
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Affiliation(s)
| | | | | | - Kate Misso
- Information Department, Kleijnen Systematic Reviews Ltd., Escrick, York YO19 6FD, UK
| | - Jos Kleijnen
- Reviews Department
- School for Public Health and Primary Care, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Ruben G.W. Quek
- Health Economics and Outcomes Research, Pfizer Inc., San Francisco, CA 94105, USA
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17
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Murugan AK. mTOR: Role in cancer, metastasis and drug resistance. Semin Cancer Biol 2019; 59:92-111. [PMID: 31408724 DOI: 10.1016/j.semcancer.2019.07.003] [Citation(s) in RCA: 253] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 06/14/2019] [Accepted: 07/03/2019] [Indexed: 02/09/2023]
Abstract
Mammalian target of rapamycin (mTOR) is a serine/threonine kinase that gets inputs from the amino acids, nutrients, growth factor, and environmental cues to regulate varieties of fundamental cellular processes which include protein synthesis, growth, metabolism, aging, regeneration, autophagy, etc. The mTOR is frequently deregulated in human cancer and activating somatic mutations of mTOR were recently identified in several types of human cancer and hence mTOR is therapeutically targeted. mTOR inhibitors were commonly used as immunosuppressors and currently, it is approved for the treatment of human malignancies. This review briefly focuses on the structure and biological functions of mTOR. It extensively discusses the genetic deregulation of mTOR including amplifications and somatic mutations, mTOR-mediated cell growth promoting signaling, therapeutic targeting of mTOR and the mechanisms of resistance, the role of mTOR in precision medicine and other recent advances in further understanding the role of mTOR in cancer.
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Affiliation(s)
- Avaniyapuram Kannan Murugan
- Department of Molecular Oncology, King Faisal Specialist Hospital & Research Centre, PO Box 3354, Research Center (MBC 03), Riyadh, 11211, Saudi Arabia.
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18
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De Lara S, Nyqvist J, Werner Rönnerman E, Helou K, Kenne Sarenmalm E, Einbeigi Z, Karlsson P, Parris TZ, Kovács A. The prognostic relevance of FOXA1 and Nestin expression in breast cancer metastases: a retrospective study of 164 cases during a 10-year period (2004-2014). BMC Cancer 2019; 19:187. [PMID: 30819139 PMCID: PMC6394077 DOI: 10.1186/s12885-019-5373-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/17/2019] [Indexed: 12/30/2022] Open
Abstract
Background Current prognostic markers cannot adequately predict the clinical outcome of breast cancer patients. Therefore, additional biomarkers need to be included in routine immune panels. FOXA1 was a significant predictor of favorable outcome in primary breast cancer, while Nestin expression is preferentially found in triple-negative tumors with increased rate of nodal metastases, and reduced survival. No studies have investigated the prognostic value of FOXA1 and Nestin expression in breast cancer metastases. Methods Breast cancer metastases (n = 164) from various anatomical sites were retrospectively analyzed by immunohistochemistry for FOXA1, Nestin and GATA3 expression. Cox regression analysis assessed the prognostic value of FOXA1 and Nestin expression. Results In breast cancer metastases, FOXA1 expression was associated with Nestin-negativity, GATA3-positivity, ER-positivity, HER2-positivity and non-triple-negative status (P < 0.05). In contrast, Nestin expression was associated with FOXA1-negative, GATA3-negative, ER-negative, and triple-negative metastases (P < 0.05). Univariate Cox regression analysis showed FOXA1 expression was predictive of overall survival (OS, P = 0.00048) and metastasis-free survival (DMFS, P = 0.0011), as well as, distant metastasis-free survival in ER-positive patients (P = 0.036) and overall survival in ER-negative patients (P = 0.024). Multivariate analysis confirmed the significance of FOXA1 for both survival endpoints in metastatic breast cancer patients (OS, P = 0.0033; DMFS, P = 0.015). Conclusions In our study, FOXA1 was expressed mostly in ER-positive breast cancer metastases. Expression of Nestin was related to triple-negative metastases, where brain was the most frequent metastatic site. These findings highlight the clinical utility of FOXA1 and Nestin expression and warrant their inclusion in routine immunohistochemical panels for breast carcinoma.
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Affiliation(s)
- Shahin De Lara
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gula stråket 8, SE-41345, Gothenburg, Sweden
| | - Jenny Nyqvist
- Department of Surgery, Skaraborgs Hospital, Lidköping and Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Elisabeth Werner Rönnerman
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gula stråket 8, SE-41345, Gothenburg, Sweden.,Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Khalil Helou
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | | | - Zakaria Einbeigi
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Per Karlsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Toshima Z Parris
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Anikó Kovács
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gula stråket 8, SE-41345, Gothenburg, Sweden.
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19
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Chen B, Yu J, Lu L, Dong F, Zhou F, Tao X, Sun E. Upregulated forkhead-box A3 elevates the expression of forkhead-box A1 and forkhead-box A2 to promote metastasis in esophageal cancer. Oncol Lett 2019; 17:4351-4360. [PMID: 30944629 DOI: 10.3892/ol.2019.10078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/04/2019] [Indexed: 11/06/2022] Open
Abstract
Esophageal cancer (EC) is one of the most lethal cancers currently known. Members of the forkhead-box A (FOXA) family, including FOXA1 and FOXA2, have been reported to regulate EC progression. However, the role of FOXA3, which is another FOXA member, has not yet been investigated. In the present study, public dataset analyses and immunohistochemistry of 96 samples from patients with EC were performed to determine the potential roles of FOXA3 in EC. The results revealed that FOXA3 was significantly upregulated in EC tumor tissues and Barrett's esophagus tissues. In addition, FOXA3 upregulation was positively associated with tumor invasion, distant metastasis, tumor-node-metastasis stage and shorter overall survival in patients with EC, and multivariate analysis identified FOXA3 as an independent prognostic marker. In vitro experiments demonstrated that the migratory and invasive abilities of EC109 and EC9706 cell lines were inhibited following FOXA3 knockdown. Notably, FOXA3 expression levels were positively correlated with FOXA1 and FOXA2 expression levels according to The Cancer Genome Atlas dataset analysis. Furthermore, FOXA3 knockdown decreased the expression levels of FOXA1 and FOXA2 in EC109 and EC9706 cell lines. Conversely, FOXA1 or FOXA2 overexpression compensated for the effects of FOXA3 knockdown on the migratory and invasive capacities of EC cells. In conclusion, the present study demonstrated that FOXA3 upregulation in EC cells promoted metastasis through regulation of other FOXA members.
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Affiliation(s)
- Bing Chen
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Jiegen Yu
- Department of Management Science, School of Humanities and Management, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Linming Lu
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Fangyuan Dong
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Fangfang Zhou
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Xiangxiang Tao
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Entao Sun
- Department of Health Inspection and Quarantine, School of Laboratory Medicine, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
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20
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Köcher S, Beyer B, Lange T, Nordquist L, Volquardsen J, Burdak‐Rothkamm S, Schlomm T, Petersen C, Rothkamm K, Mansour WY. A functional
ex vivo
assay to detect PARP1‐EJ repair and radiosensitization by PARP‐inhibitor in prostate cancer. Int J Cancer 2019; 144:1685-1696. [DOI: 10.1002/ijc.32018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/13/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Sabrina Köcher
- Laboratory of Radiobiology and Experimental RadiooncologyUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Burkhard Beyer
- Martini‐Klinik, Prostate Cancer CenterUniversity Medical Hamburg Eppendorf Hamburg Germany
| | - Tobias Lange
- Institute of AnatomyUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Lena Nordquist
- Laboratory of Radiobiology and Experimental RadiooncologyUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Jennifer Volquardsen
- Laboratory of Radiobiology and Experimental RadiooncologyUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Susanne Burdak‐Rothkamm
- Department of Radiotherapy and RadiooncologyUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Thorsten Schlomm
- Martini‐Klinik, Prostate Cancer CenterUniversity Medical Hamburg Eppendorf Hamburg Germany
| | - Cordula Petersen
- Department of Radiotherapy and RadiooncologyUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Kai Rothkamm
- Laboratory of Radiobiology and Experimental RadiooncologyUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Wael Yassin Mansour
- Laboratory of Radiobiology and Experimental RadiooncologyUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
- Department of Tumor BiologyNational Cancer Institute, Cairo University Cairo Egypt
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21
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Sondhi A, Shojaie A. The Reduced PC-Algorithm: Improved Causal Structure Learning in Large Random Networks. JOURNAL OF MACHINE LEARNING RESEARCH : JMLR 2019; 20:https://jmlr.org/papers/v20/17-601.html. [PMID: 37799538 PMCID: PMC10552884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
We consider the task of estimating a high-dimensional directed acyclic graph, given observations from a linear structural equation model with arbitrary noise distribution. By exploiting properties of common random graphs, we develop a new algorithm that requires conditioning only on small sets of variables. The proposed algorithm, which is essentially a modified version of the PC-Algorithm, offers significant gains in both computational complexity and estimation accuracy. In particular, it results in more efficient and accurate estimation in large networks containing hub nodes, which are common in biological systems. We prove the consistency of the proposed algorithm, and show that it also requires a less stringent faithfulness assumption than the PC-Algorithm. Simulations in low and high-dimensional settings are used to illustrate these findings. An application to gene expression data suggests that the proposed algorithm can identify a greater number of clinically relevant genes than current methods.
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Affiliation(s)
- Arjun Sondhi
- Department of Biostatistics, University of Washington
| | - Ali Shojaie
- Department of Biostatistics, University of Washington
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22
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Schmidt L, Møller M, Haldrup C, Strand SH, Vang S, Hedegaard J, Høyer S, Borre M, Ørntoft T, Sørensen KD. Exploring the transcriptome of hormone-naive multifocal prostate cancer and matched lymph node metastases. Br J Cancer 2018; 119:1527-1537. [PMID: 30449885 PMCID: PMC6288156 DOI: 10.1038/s41416-018-0321-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/09/2018] [Accepted: 10/09/2018] [Indexed: 11/09/2022] Open
Abstract
Background The current inability to predict whether a primary prostate cancer (PC) will progress to metastatic disease leads to overtreatment of indolent PCs as well as undertreatment of aggressive PCs. Here, we explored the transcriptional changes associated with metastatic progression of multifocal hormone-naive PC. Methods Using total RNA-sequencing, we analysed laser micro-dissected primary PC foci (n = 23), adjacent normal prostate tissue samples (n = 23) and lymph node metastases (n = 9) from ten hormone-naive PC patients. Genes important for PC progression were identified using differential gene expression and clustering analysis. From these, two multi-gene-based expression signatures (models) were developed, and their prognostic potential was evaluated using Cox-regression and Kaplan–Meier analyses in three independent radical prostatectomy (RP) cohorts (>650 patients). Results We identified several novel PC-associated transcripts deregulated during PC progression, and these transcripts were used to develop two novel gene-expression-based prognostic models. The models showed independent prognostic potential in three RP cohorts (n = 405, n = 107 and n = 91), using biochemical recurrence after RP as the primary clinical endpoint. Conclusions We identified several transcripts deregulated during PC progression and developed two new prognostic models for PC risk stratification, each of which showed independent prognostic value beyond routine clinicopathological factors in three independent RP cohorts.
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Affiliation(s)
- Linnéa Schmidt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mia Møller
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Christa Haldrup
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Siri H Strand
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jakob Hedegaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Høyer
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Borre
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Torben Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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23
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Siswanto FM, Jawi IM, Kartiko BH. The role of E3 ubiquitin ligase seven in absentia homolog in the innate immune system: An overview. Vet World 2018; 11:1551-1557. [PMID: 30587887 PMCID: PMC6303497 DOI: 10.14202/vetworld.2018.1551-1557] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/03/2018] [Indexed: 12/27/2022] Open
Abstract
The innate immune system has been considered as an ancient system and less important than the adaptive immune system. However, the interest in innate immunity has grown significantly in the past few years marked by the identification of Toll-like receptors, a member of pattern recognition receptors (PRRs). The PRRs are crucial for the identification of self- and non-self-antigen and play a role in the initiation of signaling events that activate the effective immune response. These sensor signals through interweaving signaling cascades which result in the production of interferons and cytokines as the effector of immune system. Ubiquitin and ubiquitin-like modifiers (UBLs) actively mediate the rapid and versatile regulatory processes that initiate the activation of the innate immune system cascade. The seven in absentia homolog (SIAH) is a potent RING finger E3 ubiquitin ligase that is known to involve in several stress responses, including hypoxia, oxidative stress, DNA damage stress, and inflammation. In this review, the role of SIAH will be discussed as an E3 ubiquitin ligase on the regulation of innate immune.
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Affiliation(s)
- Ferbian Milas Siswanto
- Department of Biochemistry, Faculty of Health Science and Technology, Dhyana Pura University, Badung, Indonesia
| | - I Made Jawi
- Department of Pharmacology, Faculty of Medicine, Udayana University, Denpasar, Indonesia
| | - Bambang Hadi Kartiko
- Department of Biochemistry, Faculty of Health Science and Technology, Dhyana Pura University, Badung, Indonesia
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24
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ERG alterations and mTOR pathway activation in primary prostate carcinomas developing castration-resistance. Pathol Res Pract 2018; 214:1675-1680. [PMID: 30190183 DOI: 10.1016/j.prp.2018.08.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/20/2018] [Accepted: 08/28/2018] [Indexed: 01/03/2023]
Abstract
INTRODUCTION One of the most common sites of distant metastasization of prostate cancer is bone, but to date reliable biomarkers able to predict the risk and timing of bone metastasization are still lacking. PATIENTS AND METHODS Surgically resected paraffin embedded samples from 12 primary prostate cancers that developed metachronous bone metastasis at different time points were studied (six cases within 2 years, six cases after 5 years from surgery). A targeted next-generation DNA and RNA sequencing able to assess simultaneously mutations, copy number alterations and fusion events of multiple genes was used. Immunohistochemistry was used to assess mTOR pathway activation. RESULTS Rearrangements of ETS family genes, molecular alterations in PTEN and TP53 genes were detected in 10, 6 and 5 cancers, respectively. Nine samples showed TMPRSS2-ERG fusions, which were associated with increased ERG expression at immunohistochemistry. mTOR pathway activation was documented in 6 patients, with a clear trend of prevalence in late-metastatic patients (p = 0.08). CONCLUSIONS A simultaneous next-generation targeted DNA and RNA sequencing is applicable on routine formalin-fixed paraffin-embedded tissues to assess the multigene molecular asset of individual prostate cancers. This approach, coupled with immunohistochemistry for ERG and mTOR pathway proteins, may help to better characterize prostate cancer molecular features with a potential impact on clinical decisions.
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25
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Bustelo XR. RHO GTPases in cancer: known facts, open questions, and therapeutic challenges. Biochem Soc Trans 2018; 46:741-760. [PMID: 29871878 PMCID: PMC7615761 DOI: 10.1042/bst20170531] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/17/2018] [Accepted: 05/03/2018] [Indexed: 02/06/2023]
Abstract
RHO GTPases have been traditionally associated with protumorigenic functions. While this paradigm is still valid in many cases, recent data have unexpectedly revealed that RHO proteins can also play tumor suppressor roles. RHO signaling elements can also promote both pro- and antitumorigenic effects using GTPase-independent mechanisms, thus giving an extra layer of complexity to the role of these proteins in cancer. Consistent with these variegated roles, both gain- and loss-of-function mutations in RHO pathway genes have been found in cancer patients. Collectively, these observations challenge long-held functional archetypes for RHO proteins in both normal and cancer cells. In this review, I will summarize these data and discuss new questions arising from them such as the functional and clinical relevance of the mutations found in patients, the mechanistic orchestration of those antagonistic functions in tumors, and the pros and cons that these results represent for the development of RHO-based anticancer drugs.
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Affiliation(s)
- Xosé R Bustelo
- Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer, and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain
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26
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Yadav SS, Stockert JA, Hackert V, Yadav KK, Tewari AK. Intratumor heterogeneity in prostate cancer. Urol Oncol 2018; 36:349-360. [PMID: 29887240 DOI: 10.1016/j.urolonc.2018.05.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/20/2018] [Accepted: 05/08/2018] [Indexed: 12/25/2022]
Abstract
Prostate cancer (PCa) has long been thought of as a disease with a heterogeneous phenotype. It can manifest in men as benign growths that can be safely watched or as more aggressive malignancies that can prove fatal. Recent investigations at the genomic, histopathological and molecular levels have identified tumor heterogeneity, the phenomenon of individual tumor cells presenting distinct genomic and phenotypic characteristics, as one of the most confounding and complex factors underlying PCa diagnosis, prognosis, and treatment. Despite tremendous progress made over the course of the last decade we still have an incomplete understanding of the extent and effect of intra- and inter-tumoral heterogeneity in the course of PCa progression. For example, a primary tumor can be classified into one of several molecular subgroups depending on whether the cancer has a particular gene fusion or a mutation which in turn might yield some patient-specific therapeutic regimen, but this same type of heterogeneous growth can be spatially or temporally restricted proving it difficult to detect during biopsy. We therefore present here a comprehensive review of the various studies addressing intra-tumor heterogeneity in PCa and in the context of that seen in other solid tumors. We discuss the impact of heterogeneity on clinical decision-making in treating both primary and metastatic lesions and how our understanding of this heterogeneity might help in developing better diagnostic tools and biomarkers and in guiding the selection of better therapeutic strategies.
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Affiliation(s)
- Shalini S Yadav
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jennifer A Stockert
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Victoria Hackert
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kamlesh K Yadav
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY.
| | - Ashutosh K Tewari
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY
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27
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Prostate Cancer Genomics: Recent Advances and the Prevailing Underrepresentation from Racial and Ethnic Minorities. Int J Mol Sci 2018; 19:ijms19041255. [PMID: 29690565 PMCID: PMC5979433 DOI: 10.3390/ijms19041255] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 04/15/2018] [Accepted: 04/15/2018] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer (CaP) is the most commonly diagnosed non-cutaneous cancer and the second leading cause of male cancer deaths in the United States. Among African American (AA) men, CaP is the most prevalent malignancy, with disproportionately higher incidence and mortality rates. Even after discounting the influence of socioeconomic factors, the effect of molecular and genetic factors on racial disparity of CaP is evident. Earlier studies on the molecular basis for CaP disparity have focused on the influence of heritable mutations and single-nucleotide polymorphisms (SNPs). Most CaP susceptibility alleles identified based on genome-wide association studies (GWAS) were common, low-penetrance variants. Germline CaP-associated mutations that are highly penetrant, such as those found in HOXB13 and BRCA2, are usually rare. More recently, genomic studies enabled by Next-Gen Sequencing (NGS) technologies have focused on the identification of somatic mutations that contribute to CaP tumorigenesis. These studies confirmed the high prevalence of ERG gene fusions and PTEN deletions among Caucasian Americans and identified novel somatic alterations in SPOP and FOXA1 genes in early stages of CaP. Individuals with African ancestry and other minorities are often underrepresented in these large-scale genomic studies, which are performed primarily using tumors from men of European ancestry. The insufficient number of specimens from AA men and other minority populations, together with the heterogeneity in the molecular etiology of CaP across populations, challenge the generalizability of findings from these projects. Efforts to close this gap by sequencing larger numbers of tumor specimens from more diverse populations, although still at an early stage, have discovered distinct genomic alterations. These research findings can have a direct impact on the diagnosis of CaP, the stratification of patients for treatment, and can help to address the disparity in incidence and mortality of CaP. This review examines the progress of understanding in CaP genetics and genomics and highlight the need to increase the representation from minority populations.
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28
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PLOD2 regulated by transcription factor FOXA1 promotes metastasis in NSCLC. Cell Death Dis 2017; 8:e3143. [PMID: 29072684 PMCID: PMC5680920 DOI: 10.1038/cddis.2017.553] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/06/2017] [Accepted: 09/19/2017] [Indexed: 12/31/2022]
Abstract
In multiple types of tumors, fibrotic collagen is regarded as the 'highway' for cancer cell migration, which is mainly modified by lysyl hydroxylase 2 (PLOD2). The previous findings have demonstrated that the expression of PLOD2 was regulated by multiple factors, including HIF-1α, TGF-β and microRNA-26a/b. Although PLOD2 was confirmed to be related to poor prognosis in lung adenocarcinoma, the regulatory mechanism and function of PLOD2 in human lung adenocarcinoma is poorly understood. On the other hand, upregulation or hyperactivation of epidermal growth factor receptor is considered as a prognostic marker in many cancers, especially in non-small-cell lung cancer (NSCLC). In this study, we found that PLOD2 was elevated in NSCLC specimens and positively links to NSCLC poor prognosis. Gain- and loss-of-function studies and orthotopic implantation metastasis model pinpointed that PLOD2 promotes NSCLC metastasis directly by enhancing migration and indirectly by inducing collagen reorganization. In addition, we revealed that PLOD2 was regulated by PI3K/AKT-FOXA1 axis. The transcription factor FOXA1 directly bound to the PLOD2 promoter, and turned on PLOD2 transcription. In summary, our findings revealed a regulatory mechanism of NSCLC metastasis through EGFR-PI3K/AKT-FOXA1-PLOD2 pathway, and provided PLOD2 as a therapeutic target for NSCLC treatment.
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29
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Bramhecha YM, Guérard KP, Rouzbeh S, Scarlata E, Brimo F, Chevalier S, Hamel L, Dragomir A, Aprikian AG, Lapointe J. Genomic Gain of 16p13.3 in Prostate Cancer Predicts Poor Clinical Outcome after Surgical Intervention. Mol Cancer Res 2017; 16:115-123. [PMID: 28993510 DOI: 10.1158/1541-7786.mcr-17-0270] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/27/2017] [Accepted: 10/04/2017] [Indexed: 11/16/2022]
Abstract
Identifying tumors with high metastatic potential is key to improving the clinical management of prostate cancer. Recently, we characterized a chromosome 16p13.3 gain frequently observed in prostate cancer metastases and now demonstrate the prognostic value of this genomic alteration in surgically treated prostate cancer. Dual-color FISH was used to detect 16p13.3 gain on a human tissue microarray representing 304 primary radical prostatectomy (RP) cases with clinical follow-up data. The results were validated in an external dataset. The 16p13.3 gain was detected in 42% (113/267) of the specimens scorable by FISH and was significantly associated with clinicopathologic features of aggressive prostate cancer, including high preoperative PSA (P = 0.03) levels, high Gleason score (GS, P < 0.0001), advanced pathologic tumor stage (P < 0.0001), and positive surgical margins (P = 0.009). The 16p13.3 gain predicted biochemical recurrence (BCR) in the overall cohort (log-rank P = 0.0005), and in subsets of patients with PSA ≤10 or GS ≤7 (log-rank P = 0.02 and P = 0.006, respectively). Moreover, combining the 16p13.3 gain status with standard prognostic markers improved BCR risk stratification and identified a subgroup of patients with high probability of recurrence. The 16p13.3 gain status was also associated with an increased risk of developing distant metastases (log-rank P = 0.03) further substantiating its role in prostate cancer progression.Implications: This study demonstrates the prognostic significance of the 16p13.3 genomic gain in primary prostate tumors, suggesting potential utility in the clinical management of the disease by identifying patients at high risk of recurrence who may benefit from adjuvant therapies. Mol Cancer Res; 16(1); 115-23. ©2017 AACR.
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Affiliation(s)
- Yogesh M Bramhecha
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada.,Division of Experimental Medicine, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Karl-Philippe Guérard
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Shaghayegh Rouzbeh
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Eleonora Scarlata
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Fadi Brimo
- Department of Pathology, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Simone Chevalier
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada.,Division of Experimental Medicine, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Lucie Hamel
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Alice Dragomir
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Armen G Aprikian
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Jacques Lapointe
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada. .,Division of Experimental Medicine, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
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30
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Hughesman CB, Lu XJD, Liu KYP, Zhu Y, Towle RM, Haynes C, Poh CF. Detection of clinically relevant copy number alterations in oral cancer progression using multiplexed droplet digital PCR. Sci Rep 2017; 7:11855. [PMID: 28928368 PMCID: PMC5605662 DOI: 10.1038/s41598-017-11201-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023] Open
Abstract
Copy number alterations (CNAs), a common genomic event during carcinogenesis, are known to affect a large fraction of the genome. Common recurrent gains or losses of specific chromosomal regions occur at frequencies that they may be considered distinctive features of tumoral cells. Here we introduce a novel multiplexed droplet digital PCR (ddPCR) assay capable of detecting recurrent CNAs that drive tumorigenesis of oral squamous cell carcinoma. Applied to DNA extracted from oral cell lines and clinical samples of various disease stages, we found good agreement between CNAs detected by our ddPCR assay with those previously reported using comparative genomic hybridization or single nucleotide polymorphism arrays. Furthermore, we demonstrate that the ability to target specific locations of the genome permits detection of clinically relevant oncogenic events such as small, submicroscopic homozygous deletions. Additional capabilities of the multiplexed ddPCR assay include the ability to infer ploidy level, quantify the change in copy number of target loci with high-level gains, and simultaneously assess the status and viral load for high-risk human papillomavirus types 16 and 18. This novel multiplexed ddPCR assay therefore may have clinical value in differentiating between benign oral lesions from those that are at risk of progressing to oral cancer.
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Affiliation(s)
- Curtis B Hughesman
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - X J David Lu
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Kelly Y P Liu
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Yuqi Zhu
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Rebecca M Towle
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Charles Haynes
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
| | - Catherine F Poh
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 2B5, Canada.
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31
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Ren S, Wei GH, Liu D, Wang L, Hou Y, Zhu S, Peng L, Zhang Q, Cheng Y, Su H, Zhou X, Zhang J, Li F, Zheng H, Zhao Z, Yin C, He Z, Gao X, Zhau HE, Chu CY, Wu JB, Collins C, Volik SV, Bell R, Huang J, Wu K, Xu D, Ye D, Yu Y, Zhu L, Qiao M, Lee HM, Yang Y, Zhu Y, Shi X, Chen R, Wang Y, Xu W, Cheng Y, Xu C, Gao X, Zhou T, Yang B, Hou J, Liu L, Zhang Z, Zhu Y, Qin C, Shao P, Pang J, Chung LWK, Xu J, Wu CL, Zhong W, Xu X, Li Y, Zhang X, Wang J, Yang H, Wang J, Huang H, Sun Y. Whole-genome and Transcriptome Sequencing of Prostate Cancer Identify New Genetic Alterations Driving Disease Progression. Eur Urol 2017; 73:322-339. [PMID: 28927585 DOI: 10.1016/j.eururo.2017.08.027] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/24/2017] [Indexed: 01/25/2023]
Abstract
BACKGROUND Global disparities in prostate cancer (PCa) incidence highlight the urgent need to identify genomic abnormalities in prostate tumors in different ethnic populations including Asian men. OBJECTIVE To systematically explore the genomic complexity and define disease-driven genetic alterations in PCa. DESIGN, SETTING, AND PARTICIPANTS The study sequenced whole-genome and transcriptome of tumor-benign paired tissues from 65 treatment-naive Chinese PCa patients. Subsequent targeted deep sequencing of 293 PCa-relevant genes was performed in another cohort of 145 prostate tumors. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The genomic alteration landscape in PCa was analyzed using an integrated computational pipeline. Relationships with PCa progression and survival were analyzed using nonparametric test, log-rank, and multivariable Cox regression analyses. RESULTS AND LIMITATIONS We demonstrated an association of high frequency of CHD1 deletion with a low rate of TMPRSS2-ERG fusion and relatively high percentage of mutations in androgen receptor upstream activator genes in Chinese patients. We identified five putative clustered deleted tumor suppressor genes and provided experimental and clinical evidence that PCDH9, deleted/loss in approximately 23% of tumors, functions as a novel tumor suppressor gene with prognostic potential in PCa. Furthermore, axon guidance pathway genes were frequently deregulated, including gain/amplification of PLXNA1 gene in approximately 17% of tumors. Functional and clinical data analyses showed that increased expression of PLXNA1 promoted prostate tumor growth and independently predicted prostate tumor biochemical recurrence, metastasis, and poor survival in multi-institutional cohorts of patients with PCa. A limitation of this study is that other genetic alterations were not experimentally investigated. CONCLUSIONS There are shared and salient genetic characteristics of PCa in Chinese and Caucasian men. Novel genetic alterations in PCDH9 and PLXNA1 were associated with disease progression. PATIENT SUMMARY We reported the first large-scale and comprehensive genomic data of prostate cancer from Asian population. Identification of these genetic alterations may help advance prostate cancer diagnosis, prognosis, and treatment.
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Affiliation(s)
- Shancheng Ren
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Gong-Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Dongbing Liu
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Yong Hou
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Shida Zhu
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China; Division of Genomics and Bioinformatics, CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Hong Kong, China
| | - Lihua Peng
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Qin Zhang
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Yanbing Cheng
- BGI-Shenzhen, Shenzhen, China; Division of Genomics and Bioinformatics, CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Hong Kong, China
| | - Hong Su
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Xiuqing Zhou
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | | | - Fuqiang Li
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | | | - Zhikun Zhao
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China; School of Biological Science and Medical Engineering, Southeast University, Nanjing, China; State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
| | - Changjun Yin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | | | - Xin Gao
- Department of Urology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Haiyen E Zhau
- Uro-Oncology Research Program, Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Chia-Yi Chu
- Uro-Oncology Research Program, Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jason Boyang Wu
- Uro-Oncology Research Program, Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Colin Collins
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Stanislav V Volik
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Robert Bell
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jiaoti Huang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Kui Wu
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Danfeng Xu
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yongwei Yu
- Department of Pathology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Lianhui Zhu
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Meng Qiao
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Hang-Mao Lee
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Yuehong Yang
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Yasheng Zhu
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xiaolei Shi
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Rui Chen
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yang Wang
- Department of Pathology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Weidong Xu
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yanqiong Cheng
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Chuanliang Xu
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xu Gao
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Tie Zhou
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Bo Yang
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jianguo Hou
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Li Liu
- BGI-Shenzhen, Shenzhen, China
| | - Zhensheng Zhang
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yao Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Chao Qin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pengfei Shao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Pang
- Department of Urology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Leland W K Chung
- Uro-Oncology Research Program, Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jianfeng Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Weide Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | | | | | - Jian Wang
- BGI-Shenzhen, Shenzhen, China; James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China; James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China; Department of Biology, University of Copenhagen, Copenhagen, Denmark; The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; King Abdulaziz University, Jeddah, Saudi Arabia
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Yinghao Sun
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China.
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Separation of low and high grade colon and rectum carcinoma by eukaryotic translation initiation factors 1, 5 and 6. Oncotarget 2017; 8:101224-101243. [PMID: 29254159 PMCID: PMC5731869 DOI: 10.18632/oncotarget.20642] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 07/31/2017] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cause of cancer related death worldwide. Furthermore, with more than 1.2 million cases registered per year, it constitutes the third most frequent diagnosed cancer entity worldwide. Deregulation of protein synthesis has received considerable attention as a major step in cancer development and progression. Eukaryotic translation initiation factors (eIFs) are involved in the regulation of protein synthesis and are functionally linked to the phosphatidylinositol-3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) signaling pathway. The identification of factors accounting for colorectal carcinoma (CRC) development is a major gap in the field. Besides the importance of eIF3 subunits and the eIF4 complex, eIF1, eIF5 and eIF6 were found to be altered in primary and metastatic CRC. We observed significant difference in the expression profile between low and high grade CRC. eIF1, eIF5 and eIF6 are involved in translational control in CRC. Our findings also indicate a probable clinical impact when separating them into low and high grade colon and rectum carcinoma. eIF and mTOR expression were analysed on protein and mRNA level in primary low and high grade colon carcinoma (CC) and rectum carcinoma (RC) samples in comparison to non-neoplastic tissue without any disease-related pathology. To assess the therapeutic potential of targeting eIF1, eIF5 and eIF6 siRNA knockdown in HCT116 and HT29 cells was performed. We evaluated the eIF knockdown efficacy on protein and mRNA level and investigated proliferation, apoptosis, invasion, as well as colony forming and polysome associated fractions. These results indicate that eIFs, in particular eIF1, eIF5 and eIF6 play a major role in translational control in colon and rectum cancer.
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Camacho N, Van Loo P, Edwards S, Kay JD, Matthews L, Haase K, Clark J, Dennis N, Thomas S, Kremeyer B, Zamora J, Butler AP, Gundem G, Merson S, Luxton H, Hawkins S, Ghori M, Marsden L, Lambert A, Karaszi K, Pelvender G, Massie CE, Kote-Jarai Z, Raine K, Jones D, Howat WJ, Hazell S, Livni N, Fisher C, Ogden C, Kumar P, Thompson A, Nicol D, Mayer E, Dudderidge T, Yu Y, Zhang H, Shah NC, Gnanapragasam VJ, Isaacs W, Visakorpi T, Hamdy F, Berney D, Verrill C, Warren AY, Wedge DC, Lynch AG, Foster CS, Lu YJ, Bova GS, Whitaker HC, McDermott U, Neal DE, Eeles R, Cooper CS, Brewer DS. Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data. PLoS Genet 2017; 13:e1007001. [PMID: 28945760 PMCID: PMC5628936 DOI: 10.1371/journal.pgen.1007001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 10/05/2017] [Accepted: 08/28/2017] [Indexed: 12/13/2022] Open
Abstract
A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer. 64 recurrent regions of loss and gain were detected, of which 28 were novel, including regions of loss with more than 15% frequency at Chr4p15.2-p15.1 (15.53%), Chr6q27 (16.50%) and Chr18q12.3 (17.48%). Comprehensive mutation screens of genes, lincRNA encoding sequences, control regions and conserved domains within SCNAs demonstrated that a two-hit genetic model was supported in only a minor proportion of recurrent SCNA losses examined (15/40). We found that recurrent breakpoints and regions of inversion often occur within Knudson model SCNAs, leading to the identification of ZNF292 as a target gene for the deletion at 6q14.3-q15 and NKX3.1 as a two-hit target at 8p21.3-p21.2. The importance of alterations of lincRNA sequences was illustrated by the identification of a novel mutational hotspot at the KCCAT42, FENDRR, CAT1886 and STCAT2 loci at the 16q23.1-q24.3 loss. Our data confirm that the burden of SCNAs is predictive of biochemical recurrence, define nine individual regions that are associated with relapse, and highlight the possible importance of ion channel and G-protein coupled-receptor (GPCR) pathways in cancer development. We concluded that a two-hit genetic model accounts for about one third of SCNA indicating that mechanisms, such haploinsufficiency and epigenetic inactivation, account for the remaining SCNA losses.
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Affiliation(s)
- Niedzica Camacho
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Sandra Edwards
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Jonathan D. Kay
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Molecular Diagnostics and Therapeutics Group, University College London, London, United Kingdom
| | - Lucy Matthews
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Kerstin Haase
- Cancer Genomics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Jeremy Clark
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom
| | - Nening Dennis
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Sarah Thomas
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Barbara Kremeyer
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Jorge Zamora
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Adam P. Butler
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Gunes Gundem
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Epidemiology & Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Sue Merson
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Hayley Luxton
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Molecular Diagnostics and Therapeutics Group, University College London, London, United Kingdom
| | - Steve Hawkins
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Mohammed Ghori
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Luke Marsden
- Department of Physiology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Adam Lambert
- Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, Oxford, Oxfordshire, United Kingdom
| | - Katalin Karaszi
- Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, Oxford, Oxfordshire, United Kingdom
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Gill Pelvender
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Charlie E. Massie
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- CRUK Cambridge Centre, Early Detection Programme, Urological Malignancies Programme, Hutchison-MRC Research Centre, Cambridge, Cambridgeshire, United Kingdom
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Keiran Raine
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - David Jones
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - William J. Howat
- Histopathology and in situ hybridization Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Steven Hazell
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Naomi Livni
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Cyril Fisher
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Christopher Ogden
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Pardeep Kumar
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Alan Thompson
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - David Nicol
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Erik Mayer
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Tim Dudderidge
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Yongwei Yu
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Hongwei Zhang
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Nimish C. Shah
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, United Kingdom
| | - Vincent J. Gnanapragasam
- Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | | | - William Isaacs
- School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tapio Visakorpi
- Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Freddie Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Dan Berney
- Centre for Molecular Oncology, Barts Cancer Institute, The Barts and London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Clare Verrill
- Department of Cellular Pathology and Oxford Biomedical Research Centre, Oxford University Hospitals NHS Trust, Oxford, Oxfordshire, United Kingdom
| | - Anne Y. Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, United Kingdom
| | - David C. Wedge
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Oxford Big Data Institute & Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, Oxford, Oxfordshire, United Kingdom
| | - Andrew G. Lynch
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- School of Mathematics and Statistics/School of Medicine, University of St Andrews, St Andrews, Fife, Scotland
| | | | - Yong Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, The Barts and London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - G. Steven Bova
- Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Hayley C. Whitaker
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Molecular Diagnostics and Therapeutics Group, University College London, London, United Kingdom
| | - Ultan McDermott
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - David E. Neal
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Colin S. Cooper
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom
| | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom
- Organisms and Ecosystems, The Earlham Institute, Norwich, Norfolk, United Kingdom
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Grellety T, Lucchesi C, Hostein I, Auzanneau C, Khalifa E, Soubeyran I, Italiano A. High-depth sequencing of paired primary and metastatic tumours: Implications for personalised medicine. Eur J Cancer 2017; 84:250-256. [PMID: 28841542 DOI: 10.1016/j.ejca.2017.07.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 07/18/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Next-generation sequencing of large panel of genes had been associated with clinical benefit in a significant proportion of patients with advanced cancer. However, the molecular profile of the primary tumour from the initial surgical specimen might significantly differ from the molecular profile in a tumour sample obtained from a biopsy of a metastatic site. PATIENTS AND METHODS We compare the genetic profile of primary tumours and paired metastases by using a large panel of cancer genes. Training and validation set including a total of 152 primary and metastatic tumour pairs were sequenced (up to 429 genes) focussing on variants described in the Catalogue of Somatic Mutations in Cancer (COSMIC). RESULTS Training and validation set including a total of 152 primary and metastatic tumour pairs were sequenced focussing on variants described in COSMIC. Agreement rate between the couples of primary and metastasis on COSMIC variants was 65% (24/37) and 43% (49/115) in the training and validation cohort, respectively. That rose to 74% (20/27) and 58% (42/73) when focussing on targetable mutations. In five cases, the discordance was related to appearance of secondary resistance mutation, giving a targetable refined agreement rate of 67% (67/100). CONCLUSION Up to 40% of paired primary tumour/metastases have discordant molecular profile. Liquid biopsies may overcome, in the near future, the limits of tumour tissue genotyping.
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Affiliation(s)
- T Grellety
- Department of Medical Oncology, Institut Bergonié, 229 Cours de L'Argonne, 33076 Bordeaux, France; National Institute of Health and Medical Research, INSERM U1218, Institut Bergonié, Bordeaux, France
| | - C Lucchesi
- National Institute of Health and Medical Research, INSERM U1218, Institut Bergonié, Bordeaux, France
| | - I Hostein
- Department of Pathology, Institut Bergonié, 229 Cours de L'Argonne, 33076 Bordeaux, France
| | - C Auzanneau
- Department of Pathology, Institut Bergonié, 229 Cours de L'Argonne, 33076 Bordeaux, France
| | - E Khalifa
- Department of Pathology, Institut Bergonié, 229 Cours de L'Argonne, 33076 Bordeaux, France
| | - I Soubeyran
- Department of Pathology, Institut Bergonié, 229 Cours de L'Argonne, 33076 Bordeaux, France
| | - A Italiano
- Department of Medical Oncology, Institut Bergonié, 229 Cours de L'Argonne, 33076 Bordeaux, France.
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35
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Pepper IJ, Van Sciver RE, Tang AH. Phylogenetic analysis of the SINA/SIAH ubiquitin E3 ligase family in Metazoa. BMC Evol Biol 2017; 17:182. [PMID: 28784114 PMCID: PMC5547486 DOI: 10.1186/s12862-017-1024-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/26/2017] [Indexed: 12/21/2022] Open
Abstract
Background The RAS signaling pathway is a pivotal developmental pathway that controls many fundamental biological processes including cell proliferation, differentiation, movement and apoptosis. Drosophila Seven-IN-Absentia (SINA) is a ubiquitin E3 ligase that is the most downstream signaling “gatekeeper” whose biological activity is essential for proper RAS signal transduction. Vertebrate SINA homologs (SIAHs) share a high degree of amino acid identity with that of Drosophila SINA. SINA/SIAH is the most conserved signaling component in the canonical EGFR/RAS/RAF/MAPK signal transduction pathway. Results Vertebrate SIAH1, 2, and 3 are the three orthologs to invertebrate SINA protein. SINA and SIAH1 orthologs are found in all major taxa of metazoans. These proteins have four conserved functional domains, known as RING (Really Interesting New Gene), SZF (SIAH-type zinc finger), SBS (substrate binding site) and DIMER (Dimerization). In addition to the siah1 gene, most vertebrates encode two additional siah genes (siah2 and siah3) in their genomes. Vertebrate SIAH2 has a highly divergent and extended N-terminal sequence, while its RING, SZF, SBS and DIMER domains maintain high amino acid identity/similarity to that of SIAH1. But unlike vertebrate SIAH1 and SIAH2, SIAH3 lacks a functional RING domain, suggesting that SIAH3 may be an inactive E3 ligase. The SIAH3 subtree exhibits a high degree of amino acid divergence when compared to the SIAH1 and SIAH2 subtrees. We find that SIAH1 and SIAH2 are expressed in all human epithelial cell lines examined thus far, while SIAH3 is only expressed in a limited subset of cancer cell lines. Conclusion Through phylogenetic analyses of metazoan SINA and SIAH E3 ligases, we identified many invariant and divergent amino acid residues, as well as the evolutionarily conserved functional motifs in this medically relevant gene family. Our phylomedicinal study of this unique metazoan SINA/SIAH protein family has provided invaluable evolution-based support towards future effort to design logical, potent, and durable anti-SIAH-based anticancer strategies against oncogenic K-RAS-driven metastatic human cancers. Thus, this method of evolutionary study should be of interest in cancer biology. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1024-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ian J Pepper
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Leroy T. Canoles Jr. Cancer Research Center, Harry T. Lester Hall, Room 454-457, 651 Colley Avenue, Norfolk, VA, 23501, USA
| | - Robert E Van Sciver
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Leroy T. Canoles Jr. Cancer Research Center, Harry T. Lester Hall, Room 454-457, 651 Colley Avenue, Norfolk, VA, 23501, USA
| | - Amy H Tang
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Leroy T. Canoles Jr. Cancer Research Center, Harry T. Lester Hall, Room 454-457, 651 Colley Avenue, Norfolk, VA, 23501, USA.
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36
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Stankiewicz E, Mao X, Mangham DC, Xu L, Yeste-Velasco M, Fisher G, North B, Chaplin T, Young B, Wang Y, Kaur Bansal J, Kudahetti S, Spencer L, Foster CS, Møller H, Scardino P, Oliver RT, Shamash J, Cuzick J, Cooper CS, Berney DM, Lu YJ. Identification of FBXL4 as a Metastasis Associated Gene in Prostate Cancer. Sci Rep 2017; 7:5124. [PMID: 28698647 PMCID: PMC5505985 DOI: 10.1038/s41598-017-05209-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/24/2017] [Indexed: 01/26/2023] Open
Abstract
Prostate cancer is the most common cancer among western men, with a significant mortality and morbidity reported for advanced metastatic disease. Current understanding of metastatic disease is limited due to difficulty of sampling as prostate cancer mainly metastasizes to bone. By analysing prostate cancer bone metastases using high density microarrays, we found a common genomic copy number loss at 6q16.1-16.2, containing the FBXL4 gene, which was confirmed in larger series of bone metastases by fluorescence in situ hybridisation (FISH). Loss of FBXL4 was also detected in primary tumours and it was highly associated with prognostic factors including high Gleason score, clinical stage, prostate-specific antigen (PSA) and extent of disease, as well as poor patient survival, suggesting that FBXL4 loss contributes to prostate cancer progression. We also demonstrated that FBXL4 deletion is detectable in circulating tumour cells (CTCs), making it a potential prognostic biomarker by 'liquid biopsy'. In vitro analysis showed that FBXL4 plays a role in regulating the migration and invasion of prostate cancer cells. FBXL4 potentially controls cancer metastasis through regulation of ERLEC1 levels. Therefore, FBXL4 could be a potential novel prostate cancer suppressor gene, which may prevent cancer progression and metastasis through controlling cell invasion.
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Affiliation(s)
- Elzbieta Stankiewicz
- Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Xueying Mao
- Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - D Chas Mangham
- The Robert Jones and Agnes Hunt Orthopaedic Hospital, Department of Pathology, Oswestry, Shropshire, SY10 7AG, UK
| | - Lei Xu
- Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Marc Yeste-Velasco
- Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Gabrielle Fisher
- Cancer Research UK Centre for Epidemiology, Mathematics and Statistics, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, EC1 6BQ, UK
| | - Bernard North
- Cancer Research UK Centre for Epidemiology, Mathematics and Statistics, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, EC1 6BQ, UK
| | - Tracy Chaplin
- Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Bryan Young
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Yuqin Wang
- Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Jasmin Kaur Bansal
- Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Sakunthala Kudahetti
- Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Lucy Spencer
- Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Christopher S Foster
- Division of Cellular and Molecular Pathology, University of Liverpool, Liverpool, L69 3BX, UK
- HCA Pathology Laboratories, Shropshire House, Capper Street, London, WC1E6JA, UK
| | - Henrik Møller
- King's College London, Cancer Epidemiology and Population Health, London, SE1 9RT, UK
| | - Peter Scardino
- Department of Urology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - R Tim Oliver
- Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Jonathan Shamash
- Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Jack Cuzick
- Cancer Research UK Centre for Epidemiology, Mathematics and Statistics, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, EC1 6BQ, UK
| | - Colin S Cooper
- School of Medicine, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Daniel M Berney
- Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Yong-Jie Lu
- Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
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37
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Simple quantitative PCR analysis for allelic Pten loss in tumor progression. Anal Biochem 2017; 526:50-57. [DOI: 10.1016/j.ab.2017.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 12/30/2022]
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38
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Poniah P, Mohd Zain S, Abdul Razack AH, Kuppusamy S, Karuppayah S, Sian Eng H, Mohamed Z. Genome-wide copy number analysis reveals candidate gene loci that confer susceptibility to high-grade prostate cancer. Urol Oncol 2017; 35:545.e1-545.e11. [PMID: 28527622 DOI: 10.1016/j.urolonc.2017.04.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 04/08/2017] [Accepted: 04/23/2017] [Indexed: 01/20/2023]
Abstract
BACKGROUND Two key issues in prostate cancer (PCa) that demand attention currently are the need for a more precise and minimally invasive screening test owing to the inaccuracy of prostate-specific antigen and differential diagnosis to distinguish advanced vs. indolent cancers. This continues to pose a tremendous challenge in diagnosis and prognosis of PCa and could potentially lead to overdiagnosis and overtreatment complications. Copy number variations (CNVs) in the human genome have been linked to various carcinomas including PCa. Detection of these variants may improve clinical treatment as well as an understanding of the pathobiology underlying this complex disease. METHODS To this end, we undertook a pilot genome-wide CNV analysis approach in 36 subjects (18 patients with high-grade PCa and 18 controls that were matched by age and ethnicity) in search of more accurate biomarkers that could potentially explain susceptibility toward high-grade PCa. We conducted this study using the array comparative genomic hybridization technique. Array results were validated in 92 independent samples (46 high-grade PCa, 23 benign prostatic hyperplasia, and 23 healthy controls) using polymerase chain reaction-based copy number counting method. RESULTS A total of 314 CNV regions were found to be unique to PCa subjects in this cohort (P<0.05). A log2 ratio-based copy number analysis revealed 5 putative rare or novel CNV loci or both associated with susceptibility to PCa. The CNV gain regions were 1q21.3, 15q15, 7p12.1, and a novel CNV in PCa 12q23.1, harboring ARNT, THBS1, SLC5A8, and DDC genes that are crucial in the p53 and cancer pathways. A CNV loss and deletion event was observed at 8p11.21, which contains the SFRP1 gene from the Wnt signaling pathway. Cross-comparison analysis with genes associated to PCa revealed significant CNVs involved in biological processes that elicit cancer pathogenesis via cytokine production and endothelial cell proliferation. CONCLUSION In conclusion, we postulated that the CNVs identified in this study could provide an insight into the development of advanced PCa.
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Affiliation(s)
- Prevathe Poniah
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Shamsul Mohd Zain
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Shanggar Kuppusamy
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Shankar Karuppayah
- National Advanced IPv6 Centre, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Hooi Sian Eng
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Zahurin Mohamed
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
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39
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Mills AA. The Chromodomain Helicase DNA-Binding Chromatin Remodelers: Family Traits that Protect from and Promote Cancer. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026450. [PMID: 28096241 DOI: 10.1101/cshperspect.a026450] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A plethora of mutations in chromatin regulators in diverse human cancers is emerging, attesting to the pivotal role of chromatin dynamics in tumorigenesis. A recurrent theme is inactivation of the chromodomain helicase DNA-binding (CHD) family of proteins-ATP-dependent chromatin remodelers that govern the cellular machinery's access to DNA, thereby controlling fundamental processes, including transcription, proliferation, and DNA damage repair. This review highlights what is currently known about how genetic and epigenetic perturbation of CHD proteins and the pathways that they regulate set the stage for cancer, providing new insight for designing more effective anti-cancer therapies.
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Affiliation(s)
- Alea A Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724
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40
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Sharma S, Zapatero-Rodríguez J, O'Kennedy R. Prostate cancer diagnostics: Clinical challenges and the ongoing need for disruptive and effective diagnostic tools. Biotechnol Adv 2017; 35:135-149. [DOI: 10.1016/j.biotechadv.2016.11.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 11/20/2016] [Accepted: 11/28/2016] [Indexed: 02/06/2023]
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41
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Perkins G, Lu H, Garlan F, Taly V. Droplet-Based Digital PCR: Application in Cancer Research. Adv Clin Chem 2016; 79:43-91. [PMID: 28212714 DOI: 10.1016/bs.acc.2016.10.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The efficient characterization of genetic and epigenetic alterations in oncology, virology, or prenatal diagnostics requires highly sensitive and specific high-throughput approaches. Nevertheless, with the use of conventional methods, sensitivity and specificity were largely limited. By partitioning individual target molecules within distinct compartments, digital PCR (dPCR) could overcome these limitations and detect very rare sequences with unprecedented precision and sensitivity. In dPCR, the sample is diluted such that each individual partition will contain no more than one target sequence. Following the assay reaction, the dPCR process provides an absolute value and analyzable quantitative data. The recent coupling of dPCR with microfluidic systems in commercial platforms should lead to an essential tool for the management of patients with cancer, especially adapted to the analysis of precious samples. Applications in cancer research range from the analysis of tumor heterogeneity to that of a range of body fluids. Droplet-based dPCR is indeed particularly appropriate for the emerging field of liquid biopsy analysis. In this review, following an overview of the development in dPCR technology and different strategies based on the use of microcompartments, we will focus particularly on the applications and latest development of microfluidic droplet-based dPCR in oncology.
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Affiliation(s)
- G Perkins
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France; European Georges Pompidou Hospital, AP-HP - Paris Descartes University, Paris, France
| | - H Lu
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France
| | - F Garlan
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France
| | - V Taly
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France.
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42
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43
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Clinical Applications of Next-Generation Sequencing in Cancer Diagnosis. Pathol Oncol Res 2016; 23:225-234. [PMID: 27722982 DOI: 10.1007/s12253-016-0124-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 10/04/2016] [Indexed: 12/22/2022]
Abstract
With the advancement and improvement of new sequencing technology, next-generation sequencing (NGS) has been applied increasingly in cancer genomics research fields. More recently, NGS has been adopted in clinical oncology to advance personalized treatment of cancer. NGS is utilized to novel diagnostic and rare cancer mutations, detection of translocations, inversions, insertions and deletions, detection of copy number variants, detect familial cancer mutation carriers, provide the molecular rationale for appropriate targeted, therapeutic and prognostic. NGS holds many advantages, such as the ability to fully sequence all types of mutations for a large number of genes (hundreds to thousands) and the sensitivity, speed in a single test at a relatively low cost compared to be other sequencing modalities. Here we described the technology, methods and applications that can be immediately considered and some of the challenges that lie ahead.
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44
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Flavokawain A induces deNEDDylation and Skp2 degradation leading to inhibition of tumorigenesis and cancer progression in the TRAMP transgenic mouse model. Oncotarget 2016; 6:41809-24. [PMID: 26497688 PMCID: PMC4747190 DOI: 10.18632/oncotarget.6166] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/04/2015] [Indexed: 01/11/2023] Open
Abstract
S phase kinase-associated protein 2 (Skp2) has been shown to be required for spontaneous tumor development that occurs in the retinoblastoma protein (pRb) deficient mice. Here we have demonstrated that flavokawain A (FKA), a novel chalcone from the kava plant, selectively inhibited the growth of pRb deficient cell lines and resulted in a proteasome-dependent and ubiquitination-mediated Skp2 degradation. Degradation of Skp2 by FKA was found to be involved in a functional Cullin1, but independent of Cdh1 expression. Further studies have demonstrated that FKA docked into the ATP binding pocket of the precursor cell-expressed developmentally down-regulated 8 (NEDD8)-activating enzyme (NAE) complex, inhibited NEDD8 conjugations to both Cullin1 and Ubc12 in PC3 cells and Ubc12 NEDDylation in an in vitro assay. Finally, dietary feeding of the autochthonous transgenic adenocarcinoma of the mouse prostate (TRAMP) mice with FKA inhibited the formation of high-grade prostatic intra-epithelial neoplasia lesions (HG-PIN) and prostate adenocarcinomas, reduced the tumor burden and completely abolished distant organ metastasis. Immunohistochemistry studies revealed that dietary FKA feeding resulted in marked anti-proliferative and apoptotic effects via down-regulation of Skp2 and NEDD8 and up-regulation of p27/Kip1 in the prostate of TRAMP mice. Our findings therefore provide evidence that FKA is a promising NEDDylation inhibitor for targeting Skp2 degradation in prostate cancer prevention and treatment.
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45
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Yao J, Zhang L, Hu L, Guo B, Hu X, Borjigin U, Wei Z, Chen Y, Lv M, Lau JTY, Wang X, Li G, Hu YP. Tumorigenic potential is restored during differentiation in fusion-reprogrammed cancer cells. Cell Death Dis 2016; 7:e2314. [PMID: 27468690 PMCID: PMC4973342 DOI: 10.1038/cddis.2016.189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 05/27/2016] [Accepted: 06/01/2016] [Indexed: 12/27/2022]
Abstract
Detailed understanding of the mechanistic steps underlying tumor initiation and malignant progression is critical for insights of potentially novel therapeutic modalities. Cellular reprogramming is an approach of particular interest because it can provide a means to reset the differentiation state of the cancer cells and to revert these cells to a state of non-malignancy. Here, we investigated the relationship between cellular differentiation and malignant progression by the fusion of four independent mouse cancer cell lines from different tissues, each with differing developmental potentials, to pluripotent mouse embryonic stem (ES) cells. Fusion was accompanied by loss of differentiated properties of the four parental cancer cell lines and concomitant emergence of pluripotency, demonstrating the feasibility to reprogram the malignant and differentiative properties of cancer cells. However, the original malignant and differentiative phenotypes re-emerge upon withdrawal of the fused cells from the embryonic environment in which they were maintained. cDNA array analysis of the malignant hepatoma progression implicated a role for Foxa1, and silencing Foxa1 prevented the re-emergence of malignant and differentiation-associated gene expression. Our findings support the hypothesis that tumor progression results from deregulation of stem cells, and our approach provides a strategy to analyze possible mechanisms in the cancer initiation.
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Affiliation(s)
- J Yao
- Department of Cell Biology, Center for Stem Cells and Medicine, Second Military Medical University, Shanghai 200433, People's Republic of China.,Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xian 710061, People's Republic of China
| | - L Zhang
- Key Laboratory of Molecular and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - L Hu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xian 710061, People's Republic of China.,Basic Medical College, Shanxi University of Traditional Chinese Medicine, Shanxi 030024, People's Republic of China
| | - B Guo
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xian 710061, People's Republic of China
| | - X Hu
- Key Laboratory of Molecular and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - U Borjigin
- Key Laboratory of National Education Ministry for Mammalian Reproductive Biology and Biotechnology, Inner Mongolia University, Huhhot 010021, People's Republic of China
| | - Z Wei
- Key Laboratory of National Education Ministry for Mammalian Reproductive Biology and Biotechnology, Inner Mongolia University, Huhhot 010021, People's Republic of China
| | - Y Chen
- Pearl Laboratory Animal Science and Technology Co. Ltd, Guangzhou, People's Republic of China
| | - M Lv
- Pearl Laboratory Animal Science and Technology Co. Ltd, Guangzhou, People's Republic of China
| | - J T Y Lau
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - X Wang
- Key Laboratory of Molecular and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China.,Key Laboratory of National Education Ministry for Mammalian Reproductive Biology and Biotechnology, Inner Mongolia University, Huhhot 010021, People's Republic of China.,Hepatoscience Inc., Sunnyvale, CA, USA
| | - G Li
- Key Laboratory of National Education Ministry for Mammalian Reproductive Biology and Biotechnology, Inner Mongolia University, Huhhot 010021, People's Republic of China
| | - Y-P Hu
- Department of Cell Biology, Center for Stem Cells and Medicine, Second Military Medical University, Shanghai 200433, People's Republic of China
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46
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Yap TA, Smith AD, Ferraldeschi R, Al-Lazikani B, Workman P, de Bono JS. Drug discovery in advanced prostate cancer: translating biology into therapy. Nat Rev Drug Discov 2016; 15:699-718. [DOI: 10.1038/nrd.2016.120] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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47
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Ulz P, Belic J, Graf R, Auer M, Lafer I, Fischereder K, Webersinke G, Pummer K, Augustin H, Pichler M, Hoefler G, Bauernhofer T, Geigl JB, Heitzer E, Speicher MR. Whole-genome plasma sequencing reveals focal amplifications as a driving force in metastatic prostate cancer. Nat Commun 2016; 7:12008. [PMID: 27328849 PMCID: PMC4917969 DOI: 10.1038/ncomms12008] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 05/20/2016] [Indexed: 02/08/2023] Open
Abstract
Genomic alterations in metastatic prostate cancer remain incompletely characterized. Here we analyse 493 prostate cancer cases from the TCGA database and perform whole-genome plasma sequencing on 95 plasma samples derived from 43 patients with metastatic prostate cancer. From these samples, we identify established driver aberrations in a cancer-related gene in nearly all cases (97.7%), including driver gene fusions (TMPRSS2:ERG), driver focal deletions (PTEN, RYBP and SHQ1) and driver amplifications (AR and MYC). In serial plasma analyses, we observe changes in focal amplifications in 40% of cases. The mean time interval between new amplifications was 26.4 weeks (range: 5-52 weeks), suggesting that they represent rapid adaptations to selection pressure. An increase in neuron-specific enolase is accompanied by clonal pattern changes in the tumour genome, most consistent with subclonal diversification of the tumour. Our findings suggest a high plasticity of prostate cancer genomes with newly occurring focal amplifications as a driving force in progression.
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Affiliation(s)
- Peter Ulz
- Institute of Human Genetics, Medical University of Graz, A-8010 Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Medical University of Graz, A-8010 Graz, Austria
| | - Ricarda Graf
- Institute of Human Genetics, Medical University of Graz, A-8010 Graz, Austria
| | - Martina Auer
- Institute of Human Genetics, Medical University of Graz, A-8010 Graz, Austria
| | - Ingrid Lafer
- Institute of Human Genetics, Medical University of Graz, A-8010 Graz, Austria
| | - Katja Fischereder
- Department of Urology, Medical University of Graz, A-8036 Graz, Austria
| | - Gerald Webersinke
- Department of Internal Medicine I, Hospital Barmherzige Schwestern Linz, A-4020 Linz, Austria
| | - Karl Pummer
- Department of Urology, Medical University of Graz, A-8036 Graz, Austria
| | - Herbert Augustin
- Department of Urology, Medical University of Graz, A-8036 Graz, Austria
| | - Martin Pichler
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, A-8036 Graz, Austria
| | - Gerald Hoefler
- Institute of Pathology, Medical University of Graz, A-8036 Graz, Austria
| | - Thomas Bauernhofer
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, A-8036 Graz, Austria
| | - Jochen B. Geigl
- Institute of Human Genetics, Medical University of Graz, A-8010 Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, A-8010 Graz, Austria
| | - Michael R. Speicher
- Institute of Human Genetics, Medical University of Graz, A-8010 Graz, Austria
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48
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Premasekharan G, Gilbert E, Okimoto RA, Hamirani A, Lindquist KJ, Ngo VT, Roy R, Hough J, Edwards M, Paz R, Foye A, Sood R, Copren KA, Gubens M, Small EJ, Bivona TG, Collisson EA, Friedlander TW, Paris PL. An improved CTC isolation scheme for pairing with downstream genomics: Demonstrating clinical utility in metastatic prostate, lung and pancreatic cancer. Cancer Lett 2016; 380:144-52. [PMID: 27343980 DOI: 10.1016/j.canlet.2016.06.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 12/29/2022]
Abstract
Improvements in technologies to yield purer circulating tumor cells (CTCs) will enable a broader range of clinical applications. We have previously demonstrated the use of a commercially available cell-adhesion matrix (CAM) assay to capture invasive CTCs (iCTCs). To improve the purity of the isolated iCTCs, here we used fluorescence-activated cell sorting (FACS) in combination with the CAM assay (CAM + FACS). Our results showed an increase of median purity from the CAM assay to CAM + FACS for the spiked-in cell lines and patient samples analyzed from three different metastatic cancer types: castration resistant prostate cancer (mCRPC), non-small cell lung cancer (mNSCLC) and pancreatic ductal adenocarcinoma cancer (mPDAC). Copy number profiles for spiked-in mCRPC cell line and mCRPC patient iCTCs were similar to expected mCRPC profiles and a matched biopsy. A somatic epidermal growth factor receptor (EGFR) mutation specific to mNSCLC was observed in the iCTCs recovered from EGFR(+) mNSCLC cell lines and patient samples. Next-generation sequencing (NGS) of spiked-in pancreatic cancer cell line and mPDAC patient iCTCs showed mPDAC common mutations. CAM + FACS iCTC enrichment enables multiple downstream genomic characterizations across different tumor types.
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Affiliation(s)
- Gayatri Premasekharan
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Elizabeth Gilbert
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Ross A Okimoto
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Ashiya Hamirani
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Karla J Lindquist
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Vy T Ngo
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Ritu Roy
- Computational Biology Core, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Jeffrey Hough
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Matthew Edwards
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Rosa Paz
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Adam Foye
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Riddhi Sood
- Genome Analysis Core, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Kirsten A Copren
- Genome Analysis Core, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Matthew Gubens
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Eric J Small
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Trever G Bivona
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Eric A Collisson
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Terence W Friedlander
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Pamela L Paris
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA; Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
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49
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Li M, Zhang W, Liu C, Shi Y, Tang W, Chen S, Gu H, Yin J, Zhang Z, Jiang P. Forkhead box A1 (FOXA1) tagging polymorphisms and esophageal cancer risk in a Chinese population: a fine-mapping study. Biomarkers 2016; 21:523-9. [DOI: 10.3109/1354750x.2016.1160425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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50
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Van Etten JL, Dehm SM. Clonal origin and spread of metastatic prostate cancer. Endocr Relat Cancer 2016; 23:R207-17. [PMID: 27000662 PMCID: PMC4895916 DOI: 10.1530/erc-16-0049] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 03/17/2016] [Indexed: 12/24/2022]
Abstract
Metastatic disease is responsible for the majority of prostate cancer deaths. The standard treatment for metastatic disease is surgical or chemical castration in the form of androgen deprivation therapy. Despite initial success and disease regression, resistance to therapy ultimately develops and the disease transitions to castration-resistant prostate cancer, which is uniformly fatal. Thus, developing an understanding of genetic evolution in metastasis and in response to therapy has been a focus of recent studies. Large-scale sequencing studies have provided an expansive catalog of the mutation events that occur in the prostate cancer genome at various stages of disease progression. Small-scale studies have interrogated the genomic composition of multiple metastatic sites within individual patients or have tracked clonal evolution longitudinally in tissues, circulating tumor cells, or circulating tumor DNA. Collectively, these efforts have provided a new conceptual framework for understanding the origin of prostate cancer, as well as the origin and evolution of metastatic disease. In this review, we highlight these recent insights into the spatiotemporal landscape of genetic evolution of prostate cancer.
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Affiliation(s)
| | - Scott M Dehm
- Masonic Cancer CenterUniversity of Minnesota, Minneapolis, MN, USA Department of Laboratory Medicine and PathologyUniversity of Minnesota, Minneapolis, MN, USA Department of UrologyUniversity of Minnesota, Minneapolis, MN, USA
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