1
|
Valente P, Galardi A, Di Giannatale A, Romanzo A, Novelli A, Orlando V, Colletti M, Russo I, De Vito R, Iarossi G, Petroni S, Sinibaldi L, Buzzonetti L. Case report: Clinical and genetic features of pediatric choroidal melanoma. Front Med (Lausanne) 2025; 11:1480111. [PMID: 40151649 PMCID: PMC11949099 DOI: 10.3389/fmed.2024.1480111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 12/09/2024] [Indexed: 03/29/2025] Open
Abstract
Uveal melanoma (UM) is the second most common type of primary melanoma in adults, but it is extremely rare in children. We report a 12-year-old boy with a rare juvenile case of UM characterized by specific clinical and genetic features, including eye imaging and cytogenetic analysis. The tumor was analyzed using immunohistochemistry in order to confirm the clinical diagnosis and using next-generation sequencing (NGS) in order to investigate the correlation between pathological features and prognosis. The NGS revealed a somatic mutation in the GNAQ gene. Furthermore, we established a primary cell line (Opbg-UM1) to better understand the biology of this tumor in the pediatric setting. However, our case identified several factors predictive of poor prognosis, such as tumor proximity to the fovea and optic disc, large size, lack of pigmentation with mushroom configuration in category T2, and a complex karyotype showing numerical abnormalities on chromosome 6 and a mosaic loss of the Y chromosome in blood and in the primary cell line. This mutation may represent a poor prognostic factor in older children with UM.
Collapse
Affiliation(s)
- Paola Valente
- Ophtalmology Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Angela Galardi
- Hematology/Oncology and Cell and Gene Therapy Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Angela Di Giannatale
- Hematology/Oncology and Cell and Gene Therapy Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Antonino Romanzo
- Ophtalmology Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Valeria Orlando
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Marta Colletti
- Hematology/Oncology and Cell and Gene Therapy Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Ida Russo
- Hematology/Oncology and Cell and Gene Therapy Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Rita De Vito
- Laboratories, Pathology Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Giancarlo Iarossi
- Ophtalmology Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Sergio Petroni
- Ophtalmology Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Lorenzo Sinibaldi
- Medical Genetics Unit, Bambino Gesù IRCCS Pediatric Hospital, Rome, Italy
| | - Luca Buzzonetti
- Ophtalmology Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| |
Collapse
|
2
|
Lei Q, Huang Y, Deng F, Zheng H, Hong X, Wang P, Lv J, Chen H, Ji Z. NOL-7 serves as a potential prognostic-related biomarker for hepatocellular carcinoma. Discov Oncol 2025; 16:69. [PMID: 39836310 PMCID: PMC11751243 DOI: 10.1007/s12672-024-01551-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 11/06/2024] [Indexed: 01/22/2025] Open
Abstract
BACKGROUND Nucleolar protein 7 (NOL7), a specific protein found in the nucleolus, is crucial for maintaining cell division and proliferation. While the involvement of NOL7 in influencing the unfavorable prognosis of metastatic melanoma has been reported, its significance in predicting the prognosis of patients with Hepatocellular Carcinoma (HCC) remains unclear. METHODS Aberrant expression of NOL7 in HCC and its prognostic value were evaluated using multiple databases, including TCGA, GTEx, Xiantao Academic, HCCDB, UALCAN, TISCH, and STRING. Immunohistochemistry (IHC) and quantitative real-time PCR were used to validate NOL7 expression levels in patients with HCC. RESULTS NOL7 expression was higher in the HCC samples than in the normal samples (P < 0.05). NOL7 was strongly associated with elevated AFP levels, vascular invasion, TNM stage, poorer tumor differentiation, and poorer survival (all P < 0.05). Elevated NOL7 expression correlated with decreased overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) (all P < 0.05). Multivariate analysis revealed that NOL7 was an independent prognostic factor that was significantly related to OS and DSS. The nomogram showed a good predictive performance based on the calibration plot. In addition, NOL7 expression was significantly correlated with cell cycle modulators, immune checkpoints, and various immune cell populations. In addition, we identified eight potential pathways associated with NOL7 as the most promising pathways for NOL7 in HCC. Low-risk specimens were more sensitive to oxaliplatin, cisplatin, irinotecan, sorafenib, and cytarabine than high-risk specimens. CONCLUSION NOL7 may serve as a potential biomarker for predicting clinical outcomes and may provide guidance for clinical therapy in patients with HCC.
Collapse
Affiliation(s)
- Qiucheng Lei
- School of Medicine, Southeast University, Nanjing, Jiangsu, China
- Organ Transplant Center, The First People's Hospital of Foshan, Foshan, Guangdong, China
| | - Yingchun Huang
- Department of Outpatient, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Feiwen Deng
- Organ Transplant Center, The First People's Hospital of Foshan, Foshan, Guangdong, China
| | - Huazhen Zheng
- Department of Clinical Laboratory, The First People's Hospital of Foshan, Foshan, Guangdong, China
| | - Xitao Hong
- Organ Transplant Center, The First People's Hospital of Foshan, Foshan, Guangdong, China
| | - Peng Wang
- Department of Gastrointestinal Surgery, The First People's Hospital of Foshan, Foshan, Guangdong, China
| | - Jin Lv
- Department of Pathology, The First People's Hospital of Foshan, Foshan, Guangdong, China
| | - Huanwei Chen
- Organ Transplant Center, The First People's Hospital of Foshan, Foshan, Guangdong, China
| | - Zhenling Ji
- School of Medicine, Southeast University, Nanjing, Jiangsu, China.
- Department of General Surgery, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China.
- Department of General Surgery, Nanjing Jiangbei Hospital, Nantong University Xinglin College, Nanjing, Jiangsu, China.
| |
Collapse
|
3
|
Zhao Y, Liu MJ, Zhang L, Yang Q, Sun QH, Guo JR, Lei XY, He KY, Li JQ, Yang JY, Jian YP, Xu ZX. High mobility group A1 (HMGA1) promotes the tumorigenesis of colorectal cancer by increasing lipid synthesis. Nat Commun 2024; 15:9909. [PMID: 39548107 PMCID: PMC11568219 DOI: 10.1038/s41467-024-54400-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 11/07/2024] [Indexed: 11/17/2024] Open
Abstract
Metabolic reprogramming is a hallmark of cancer, enabling tumor cells to meet the high energy and biosynthetic demands required for their proliferation. High mobility group A1 (HMGA1) is a structural transcription factor and frequently overexpressed in human colorectal cancer (CRC). Here, we show that HMGA1 promotes CRC progression by driving lipid synthesis in a AOM/DSS-induced CRC mouse model. Using conditional knockout (Hmga1△IEC) and knock-in (Hmga1IEC-OE/+) mouse models, we demonstrate that HMGA1 enhances CRC cell proliferation and accelerates tumor development by upregulating fatty acid synthase (FASN). Mechanistically, HMGA1 increases the transcriptional activity of sterol regulatory element-binding protein 1 (SREBP1) on the FASN promoter, leading to increased lipid accumulation in intestinal epithelial cells. Moreover, a high-fat diet exacerbates CRC progression in Hmga1△IEC mice, while pharmacological inhibition of FASN by orlistat reduces tumor growth in Hmga1IEC-OE/+ mice. Our findings suggest that targeting lipid metabolism could offer a promising therapeutic strategy for CRC.
Collapse
Affiliation(s)
- Yuan Zhao
- School of Life Sciences, Henan University, Kaifeng, Henan Province, China
| | - Meng-Jie Liu
- School of Life Sciences, Henan University, Kaifeng, Henan Province, China
| | - Lei Zhang
- School of Life Sciences, Henan University, Kaifeng, Henan Province, China
| | - Qi Yang
- School of Life Sciences, Henan University, Kaifeng, Henan Province, China
| | - Qian-Hui Sun
- School of Life Sciences, Henan University, Kaifeng, Henan Province, China
| | - Jin-Rong Guo
- School of Life Sciences, Henan University, Kaifeng, Henan Province, China
| | - Xin-Yuan Lei
- School of Life Sciences, Henan University, Kaifeng, Henan Province, China
| | - Kai-Yue He
- School of Life Sciences, Henan University, Kaifeng, Henan Province, China
| | - Jun-Qi Li
- School of Life Sciences, Henan University, Kaifeng, Henan Province, China
| | - Jing-Yu Yang
- School of Life Sciences, Henan University, Kaifeng, Henan Province, China
| | - Yong-Ping Jian
- School of Life Sciences, Henan University, Kaifeng, Henan Province, China.
| | - Zhi-Xiang Xu
- School of Life Sciences, Henan University, Kaifeng, Henan Province, China.
| |
Collapse
|
4
|
Giovannini S, Smirnov A, Concetti L, Scimeca M, Mauriello A, Bischof J, Rovella V, Melino G, Buonomo CO, Candi E, Bernassola F. A comprehensive molecular characterization of a claudin-low luminal B breast tumor. Biol Direct 2024; 19:66. [PMID: 39152485 PMCID: PMC11328405 DOI: 10.1186/s13062-024-00482-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 05/20/2024] [Indexed: 08/19/2024] Open
Abstract
Breast cancer is the most common cause of death from cancer in women. Here, we present the case of a 43-year-old woman, who received a diagnosis of claudin-low luminal B breast cancer. The lesion revealed to be a poorly differentiated high-grade infiltrating ductal carcinoma, which was strongly estrogen receptor (ER)/progesterone receptor (PR) positive and human epidermal growth factor receptor (HER2) negative. Her tumor underwent in-depth chromosomal, mutational and gene expression analyses. We found a pathogenic protein truncating mutation in the TP53 gene, which is predicted to disrupt its transcriptional activity. The patient also harbors germline mutations in some mismatch repair (MMR) genes, and her tumor displays the presence of immune infiltrates, high tumor mutational burden (TMB) status and the apolipoprotein B mRNA editing enzyme catalytic polypeptide 3 (APOBEC3) associated signatures, which, overall, are predictive for the use of immunotherapy. Here, we propose promising prognostic indicators as well as potential therapeutic strategies based on the molecular characterization of the tumor.
Collapse
Affiliation(s)
- Sara Giovannini
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Artem Smirnov
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
- Istituto Dermopatico Immacolata (IDI-IRCCS), 00100, Rome, Italy
| | - Livia Concetti
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Manuel Scimeca
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Alessandro Mauriello
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Julia Bischof
- Germany Biochemistry Laboratory, Indivumed GmbH, Falkenried, 88 Building D, 20251, Hamburg, Germany
| | - Valentina Rovella
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Claudio Oreste Buonomo
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
| | - Eleonora Candi
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
- Istituto Dermopatico Immacolata (IDI-IRCCS), 00100, Rome, Italy.
| | - Francesca Bernassola
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
| |
Collapse
|
5
|
Vriend J, Liu XQ. Survival-Related Genes on Chromosomes 6 and 17 in Medulloblastoma. Int J Mol Sci 2024; 25:7506. [PMID: 39062749 PMCID: PMC11277021 DOI: 10.3390/ijms25147506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Survival of Medulloblastoma (MB) depends on various factors, including the gene expression profiles of MB tumor tissues. In this study, we identified 967 MB survival-related genes (SRGs) using a gene expression dataset and the Cox proportional hazards regression model. Notably, the SRGs were over-represented on chromosomes 6 and 17, known for the abnormalities monosomy 6 and isochromosome 17 in MB. The most significant SRG was HMGA1 (high mobility group AT-hook 1) on chromosome 6, which is a known oncogene and a histone H1 competitor. High expression of HMGA1 was associated with worse survival, primarily in the Group 3γ subtype. The high expression of HMGA1 was unrelated to any known somatic copy number alteration. Most SRGs on chromosome 17p were associated with low expression in Group 4β, the MB subtype, with 93% deletion of 17p and 98% copy gain of 17q. GO enrichment analysis showed that both chromosomes 6 and 17 included SRGs related to telomere maintenance and provided a rationale for testing telomerase inhibitors in Group 3 MBs. We conclude that HMGA1, along with other SRGs on chromosomes 6 and 17, warrant further investigation as potential therapeutic targets in selected subgroups or subtypes of MB.
Collapse
Affiliation(s)
- Jerry Vriend
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Xiao-Qing Liu
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada;
- Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| |
Collapse
|
6
|
Berry JL, Pike S, Shah R, Reid MW, Peng CC, Wang Y, Yellapantula V, Biegel J, Kuhn P, Hicks J, Xu L. Aqueous Humor Liquid Biopsy as a Companion Diagnostic for Retinoblastoma: Implications for Diagnosis, Prognosis, and Therapeutic Options: Five Years of Progress. Am J Ophthalmol 2024; 263:188-205. [PMID: 38040321 PMCID: PMC11148850 DOI: 10.1016/j.ajo.2023.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
PURPOSE To define the prospective use of the aqueous humor (AH) as a molecular diagnostic and prognostic liquid biopsy for retinoblastoma (RB). METHODS This is a prospective, observational study wherein an AH liquid biopsy is performed at diagnosis and longitudinally through therapy for patients with RB. Tumor-derived cell-free DNA is isolated and sequenced for single nucleotide variant analysis of the RB1 gene and detection of somatic copy number alterations (SCNAs). The SCNAs are used to determine tumor fraction (TFx). Specific SCNAs, including 6p gain and focal MycN gain, along with TFx, are prospectively correlated with intraocular tumor relapse, response to therapy, and globe salvage. RESULTS A total of 26 eyes of 21 patients were included with AH taken at diagnosis. Successful ocular salvage was achieved in 19 of 26 (73.1%) eyes. Mutational analysis of 26 AH samples identified 23 pathogenic RB1 variants and 2 focal RB1 deletions; variant allele fraction ranged from 30.5% to 100% (median 93.2%). At diagnosis, SCNAs were detectable in 17 of 26 (65.4%) AH samples. Eyes with 6p gain and/or focal MycN gain had significantly greater odds of poor therapeutic outcomes (odds ratio = 6.75, 95% CI = 1.06-42.84, P = .04). Higher AH TFx was observed in eyes with vitreal progression (TFx = 46.0% ± 40.4) than regression (22.0 ± 29.1; difference: -24.0; P = .049). CONCLUSIONS Establishing an AH liquid biopsy for RB is aimed at addressing (1) our inability to biopsy tumor tissue and (2) the lack of molecular biomarkers for intraocular prognosis. Current management decisions for RB are made based solely on clinical features without objective molecular testing. This prognostic study shows great promise for using AH as a companion diagnostic. NOTE: Publication of this article is sponsored by the American Ophthalmological Society.
Collapse
Affiliation(s)
- Jesse L Berry
- From the Vision Center, Children's Hospital Los Angeles (J.L.B., S.P., M.W.R., C.-C.P., L.X.); USC Roski Eye Institute, Keck School of Medicine of the University of Southern California (J.L.B., S.P., M.W.R., C.-C.P., L.X.); the Saban Research Institute, Children's Hospital Los Angeles (J.L.B., V.Y., J.B., L.X.); Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California (J.L.B., P.K., J.H.).
| | - Sarah Pike
- From the Vision Center, Children's Hospital Los Angeles (J.L.B., S.P., M.W.R., C.-C.P., L.X.); USC Roski Eye Institute, Keck School of Medicine of the University of Southern California (J.L.B., S.P., M.W.R., C.-C.P., L.X.)
| | - Rachana Shah
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles (R.S.)
| | - Mark W Reid
- From the Vision Center, Children's Hospital Los Angeles (J.L.B., S.P., M.W.R., C.-C.P., L.X.); USC Roski Eye Institute, Keck School of Medicine of the University of Southern California (J.L.B., S.P., M.W.R., C.-C.P., L.X.)
| | - Chen-Ching Peng
- From the Vision Center, Children's Hospital Los Angeles (J.L.B., S.P., M.W.R., C.-C.P., L.X.); USC Roski Eye Institute, Keck School of Medicine of the University of Southern California (J.L.B., S.P., M.W.R., C.-C.P., L.X.)
| | - Yingfei Wang
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles (R.S.); Department of Quantitative and Computational Biology, University of Southern California (Y.W.)
| | - Venkata Yellapantula
- the Saban Research Institute, Children's Hospital Los Angeles (J.L.B., V.Y., J.B., L.X.); Center for Personalized Medicine, Children's Hospital Los Angeles (V.Y., J.B.)
| | - Jaclyn Biegel
- the Saban Research Institute, Children's Hospital Los Angeles (J.L.B., V.Y., J.B., L.X.)
| | - Peter Kuhn
- Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California (J.L.B., P.K., J.H.); USC Michelson Center for Convergent Biosciences and Department of Biological Sciences (P.K., J.H.), Los Angeles, California, USA
| | - James Hicks
- Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California (J.L.B., P.K., J.H.); USC Michelson Center for Convergent Biosciences and Department of Biological Sciences (P.K., J.H.), Los Angeles, California, USA
| | - Liya Xu
- From the Vision Center, Children's Hospital Los Angeles (J.L.B., S.P., M.W.R., C.-C.P., L.X.); USC Roski Eye Institute, Keck School of Medicine of the University of Southern California (J.L.B., S.P., M.W.R., C.-C.P., L.X.); the Saban Research Institute, Children's Hospital Los Angeles (J.L.B., V.Y., J.B., L.X.)
| |
Collapse
|
7
|
Schirizzi A, Arshadi A, Tolomeo D, Schirosi L, Valentini AM, De Leonardis G, Refolo MG, Donghia R, Storlazzi CT, Zito A, Ricci AD, Vallarelli S, Ostuni C, Bencivenga M, De Manzoni G, Messa C, Armentano R, Giannelli G, Lotesoriere C, D’Alessandro R. VEGFA Status as a Predictive Marker of Therapy Outcome in Metastatic Gastric Cancer Patients Following Ramucirumab-Based Treatment. Biomedicines 2023; 11:2721. [PMID: 37893095 PMCID: PMC10603940 DOI: 10.3390/biomedicines11102721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Metastatic gastric cancer (mGC) often has a poor prognosis and may benefit from a few targeted therapies. Ramucirumab-based anti-angiogenic therapy targeting the VEGFR2 represents a milestone in the second-line treatment of mGC. Several studies on different cancers are focusing on the major VEGFR2 ligand status, meaning VEGFA gene copy number and protein overexpression, as a prognostic marker and predictor of response to anti-angiogenic therapy. Following this insight, our study aims to examine the role of VEGFA status as a predictive biomarker for the outcome of second-line therapy with Ramucirumab and paclitaxel in mGC patients. To this purpose, the copy number of the VEGFA gene, by fluorescence in situ hybridization experiments, and its expression in tumor tissue as well as the density of micro-vessels, by immunohistochemistry experiments, were assessed in samples derived from mGC patients. This analysis found that amplification of VEGFA concomitantly with VEGFA overexpression and overexpression of VEGFA with micro-vessels density are more represented in patients showing disease control during treatment with Ramucirumab. In addition, in the analyzed series, it was found that amplification was not always associated with overexpression of VEGFA, but overexpression of VEGFA correlates with high micro-vessel density. In conclusion, overexpression of VEGFA could emerge as a potential biomarker to predict the response to anti-angiogenic therapy.
Collapse
Affiliation(s)
- Annalisa Schirizzi
- Laboratory of Experimental Oncology, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (A.S.); (G.D.L.); (C.M.)
| | - Aram Arshadi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (A.A.); (D.T.); (C.T.S.)
| | - Doron Tolomeo
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (A.A.); (D.T.); (C.T.S.)
| | - Laura Schirosi
- Pathology Department, IRCCS Istituto Tumori “Giovanni Paolo II”, 70124 Bari, Italy; (L.S.); (A.Z.)
| | - Anna Maria Valentini
- Histopathology Unit, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (A.M.V.); (R.A.)
| | - Giampiero De Leonardis
- Laboratory of Experimental Oncology, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (A.S.); (G.D.L.); (C.M.)
| | - Maria Grazia Refolo
- Clinical Pathology Unit, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy;
| | - Rossella Donghia
- Data Science Unit, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy;
| | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (A.A.); (D.T.); (C.T.S.)
| | - Alfredo Zito
- Pathology Department, IRCCS Istituto Tumori “Giovanni Paolo II”, 70124 Bari, Italy; (L.S.); (A.Z.)
| | - Angela Dalia Ricci
- Medical Oncology Unit, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (A.D.R.); (S.V.); (C.O.)
| | - Simona Vallarelli
- Medical Oncology Unit, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (A.D.R.); (S.V.); (C.O.)
| | - Carmela Ostuni
- Medical Oncology Unit, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (A.D.R.); (S.V.); (C.O.)
| | - Maria Bencivenga
- General and Upper GI Surgery Division, University of Verona, 37126 Verona, Italy; (M.B.); (G.D.M.)
| | - Giovanni De Manzoni
- General and Upper GI Surgery Division, University of Verona, 37126 Verona, Italy; (M.B.); (G.D.M.)
| | - Caterina Messa
- Laboratory of Experimental Oncology, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (A.S.); (G.D.L.); (C.M.)
| | - Raffaele Armentano
- Histopathology Unit, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (A.M.V.); (R.A.)
| | - Gianluigi Giannelli
- Scientific Direction, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy;
| | - Claudio Lotesoriere
- Medical Oncology Unit, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (A.D.R.); (S.V.); (C.O.)
| | - Rosalba D’Alessandro
- Laboratory of Experimental Oncology, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (A.S.); (G.D.L.); (C.M.)
| |
Collapse
|
8
|
Gao F, Liu H, Meng X, Liu J, Wang J, Yu J, Liu X, Liu X, Li L, Qiu L, Qian Z, Zhou S, Gong W, Meng B, Ren X, Golchehre Z, Chavoshzadeh Z, He J, Zhang H, Wang X. Integrative genomic and transcriptomic analysis reveals genetic alterations associated with the early progression of follicular lymphoma. Br J Haematol 2023; 202:1151-1164. [PMID: 37455019 DOI: 10.1111/bjh.18974] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/25/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Follicular lymphoma (FL), the most common indolent lymphoma, is a clinically and genetically heterogeneous disease. However, the prognostic value of driver gene mutations and copy number alterations has not been systematically assessed. Here, we analysed the clinical-biological features of 415 FL patients to identify variables associated with disease progression within 24 months of first-line therapy (POD24). Patients with B symptoms, elevated lactate dehydrogenase and β2-microglobulin levels, unfavourable baseline haemoglobin levels, advanced stage, and high-risk FL International Prognostic Index (FLIPI) scores had an increased risk of POD24, with FLIPI being the most important factor in logistic regression. HIST1H1D, identified as a driver mutation, was correlated with POD24. Gains of 6p22.2 (HIST1H1D) and 18q21.33 (BCL2) and loss of 1p36.13 (NBPF1) predicted POD24 independent of FLIPI. Gene expression profiling of FL samples showed that the POD24 cohort was significantly enriched in the inflammatory response (mediated by interferon and tumour necrosis factor), cell cycle regulation (transcription, replication and proliferation) sets and PI3K-AKT-mTOR signalling. This result was further validated with transcriptome-wide information provided by RNA-seq at single-cell resolution. Our study, performed on a large cohort of FL patients, highlights the importance of distinctive genetic alterations and gene expression relevant to disease diagnosis and early progression.
Collapse
Affiliation(s)
- Fenghua Gao
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Hengqi Liu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Xiangrui Meng
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Jing Liu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Jiesong Wang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
- Department of Lymphoma & Head and Neck Oncology, College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, China
| | - Jingwei Yu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Xia Liu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Xianming Liu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Lanfang Li
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Lihua Qiu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Zhengzi Qian
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Shiyong Zhou
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Wenchen Gong
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Bin Meng
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Xiubao Ren
- Department of Immunology/Biotherapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zahra Golchehre
- Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Chavoshzadeh
- Department of Immunology/Allergy, Pediatric Infections Research Center, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jin He
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Huilai Zhang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Xianhuo Wang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| |
Collapse
|
9
|
Pires SF, de Barros JS, da Costa SS, de Oliveira Scliar M, Van Helvoort Lengert A, Boldrini É, da Silva SRM, Tasic L, Vidal DO, Krepischi ACV, Maschietto M. DNA methylation patterns suggest the involvement of DNMT3B and TET1 in osteosarcoma development. Mol Genet Genomics 2023; 298:721-733. [PMID: 37020053 DOI: 10.1007/s00438-023-02010-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/24/2023] [Indexed: 04/07/2023]
Abstract
DNA methylation may be involved in the development of osteosarcomas. Osteosarcomas commonly arise during the bone growth and remodeling in puberty, making it plausible to infer the involvement of epigenetic alterations in their development. As a highly studied epigenetic mechanism, we investigated DNA methylation and related genetic variants in 28 primary osteosarcomas aiming to identify deregulated driver alterations. Methylation and genomic data were obtained using the Illumina HM450K beadchips and the TruSight One sequencing panel, respectively. Aberrant DNA methylation was spread throughout the osteosarcomas genomes. We identified 3146 differentially methylated CpGs comparing osteosarcomas and bone tissue samples, with high methylation heterogeneity, global hypomethylation and focal hypermethylation at CpG islands. Differentially methylated regions (DMR) were detected in 585 loci (319 hypomethylated and 266 hypermethylated), mapped to the promoter regions of 350 genes. These DMR genes were enriched for biological processes related to skeletal system morphogenesis, proliferation, inflammatory response, and signal transduction. Both methylation and expression data were validated in independent groups of cases. Six tumor suppressor genes harbored deletions or promoter hypermethylation (DLEC1, GJB2, HIC1, MIR149, PAX6, and WNT5A), and four oncogenes presented gains or hypomethylation (ASPSCR1, NOTCH4, PRDM16, and RUNX3). Our analysis also revealed hypomethylation at 6p22, a region that contains several histone genes. Copy-number changes in DNMT3B (gain) and TET1 (loss), as well as overexpression of DNMT3B in osteosarcomas provide a possible explanation for the observed phenotype of CpG island hypermethylation. While the detected open-sea hypomethylation likely contributes to the well-known osteosarcoma genomic instability, enriched CpG island hypermethylation suggests an underlying mechanism possibly driven by overexpression of DNMT3B likely resulting in silencing of tumor suppressors and DNA repair genes.
Collapse
Affiliation(s)
- Sara Ferreira Pires
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Juliana Sobral de Barros
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Marília de Oliveira Scliar
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | | | | | - Ljubica Tasic
- Laboratory of Biological Chemistry, Institute of Chemistry, University of Campinas, Campinas, Brazil
| | - Daniel Onofre Vidal
- Molecular Oncology Research Center (CPOM), Barretos Cancer Hospital, Barretos, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Mariana Maschietto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.
- Research Center, Boldrini Children's Hospital, Campinas, SP, Brazil.
| |
Collapse
|
10
|
Wang Z, Xie W, Guan H. The diagnostic, prognostic role and molecular mechanism of miR-328 in human cancer. Biomed Pharmacother 2023; 157:114031. [PMID: 36413837 DOI: 10.1016/j.biopha.2022.114031] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/06/2022] [Accepted: 11/17/2022] [Indexed: 11/20/2022] Open
Abstract
MicroRNA are non-coding small RNAs that bind to their target mRNA and cause mRNA degradation or translation inhibition. MiRNA dysregulation is linked to a variety of human cancers and has a role in the genesis and development of cancer pathology. MiR-328 has been reported to be involved in various human cancers. And miR-328 is considered a key regulator in human cancer. It participates in biological processes such as proliferation, apoptosis, invasion, migration, and EMT. The present review will combine the basic and clinical studies to find that miR-328 promotes tumorigenesis and metastasis in human cancer. And we will describe the diagnostic, prognostic, and therapeutic value of miR-328 in various human cancers.
Collapse
Affiliation(s)
- Zhichao Wang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China.
| | - Wenjie Xie
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China.
| | - Hongzai Guan
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China.
| |
Collapse
|
11
|
The Role of PPARs in Breast Cancer. Cells 2022; 12:cells12010130. [PMID: 36611922 PMCID: PMC9818187 DOI: 10.3390/cells12010130] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/07/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Breast cancer is a malignant tumor with high morbidity and lethality. Its pathogenesis is related to the abnormal expression of many genes. The peroxisome proliferator-activated receptors (PPARs) are a class of ligand-dependent transcription factors in the nuclear receptor superfamily. They can regulate the transcription of a large number of target genes, which are involved in life activities such as cell proliferation, differentiation, metabolism, and apoptosis, and regulate physiological processes such as glucose metabolism, lipid metabolism, inflammation, and wound healing. Further, the changes in its expression are associated with various diseases, including breast cancer. The experimental reports related to "PPAR" and "breast cancer" were retrieved from PubMed since the discovery of PPARs and summarized in this paper. This review (1) analyzed the roles and potential molecular mechanisms of non-coordinated and ligand-activated subtypes of PPARs in breast cancer progression; (2) discussed the correlations between PPARs and estrogen receptors (ERs) as the nuclear receptor superfamily; and (3) investigated the interaction between PPARs and key regulators in several signaling pathways. As a result, this paper identifies PPARs as targets for breast cancer prevention and treatment in order to provide more evidence for the synthesis of new drugs targeting PPARs or the search for new drug combination treatments.
Collapse
|
12
|
Özçelik E, Kalaycı A, Çelik B, Avcı A, Akyol H, Kılıç İB, Güzel T, Çetin M, Öztürk MT, Çalışkaner ZO, Tombaz M, Yoleri D, Konu Ö, Kandilci A. Doxorubicin induces prolonged DNA damage signal in cells overexpressing DEK isoform-2. PLoS One 2022; 17:e0275476. [PMID: 36190960 PMCID: PMC9529144 DOI: 10.1371/journal.pone.0275476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/17/2022] [Indexed: 11/06/2022] Open
Abstract
DEK has a short isoform (DEK isoform-2; DEK2) that lacks amino acid residues between 49–82. The full-length DEK (DEK isoform-1; DEK1) is ubiquitously expressed and plays a role in different cellular processes but whether DEK2 is involved in these processes remains elusive. We stably overexpressed DEK2 in human bone marrow stromal cell line HS-27A, in which endogenous DEKs were intact or suppressed via short hairpin RNA (sh-RNA). We have found that contrary to ectopic DEK1, DEK2 locates in the nucleus and nucleolus, causes persistent γH2AX signal upon doxorubicin treatment, and couldn’t functionally compensate for the loss of DEK1. In addition, DEK2 overexpressing cells were more sensitive to doxorubicin than DEK1-cells. Expressions of DEK1 and DEK2 in cell lines and primary tumors exhibit tissue specificity. DEK1 is upregulated in cancers of the colon, liver, and lung compared to normal tissues while both DEK1 and DEK2 are downregulated in subsets of kidney, prostate, and thyroid carcinomas. Interestingly, only DEK2 was downregulated in a subset of breast tumors suggesting that DEK2 can be modulated differently than DEK1 in specific cancers. In summary, our findings show distinct expression patterns and subcellular location and suggest non-overlapping functions between the two DEK isoforms.
Collapse
Affiliation(s)
- Emrah Özçelik
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Ahmet Kalaycı
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Büşra Çelik
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Açelya Avcı
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Hasan Akyol
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - İrfan Baki Kılıç
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Türkan Güzel
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Metin Çetin
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Merve Tuzlakoğlu Öztürk
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Zihni Onur Çalışkaner
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Melike Tombaz
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Dilan Yoleri
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Özlen Konu
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Ayten Kandilci
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
- * E-mail:
| |
Collapse
|
13
|
Pancancer Analysis of the Oncogenic and Prognostic Role of NOL7: A Potential Target for Carcinogenesis and Survival. Int J Mol Sci 2022; 23:ijms23179611. [PMID: 36077008 PMCID: PMC9455868 DOI: 10.3390/ijms23179611] [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: 07/24/2022] [Revised: 08/16/2022] [Accepted: 08/23/2022] [Indexed: 11/18/2022] Open
Abstract
Despite growing evidence suggesting the critical function of NOL7 in cancer initiation and development, a systematic pancancer analysis of NOL7 is lacking. Herein, we present a comprehensive study of NOL7 which aimed to explore its potential role and detailed mechanisms across 33 human tumors based on The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CATPAC) databases. As a result, both gene and protein levels of NOL7 were found to be increased in various tumor tissues, including breast invasive carcinoma (BRCA), colon adenocarcinoma (COAD), hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), and head and neck squamous cell carcinoma (HNSC) as compared with corresponding normal tissues. Meanwhile, dysregulated NOL7 expression was found to be closely related to pathological stage and prognosis in several cancers, including LIHC, ovarian serous cystadenocarcinoma (OV), and bladder urothelial carcinoma (BLCA). The DNA methylation level of NOL7 was found to be decreased in most cancers and to be negatively associated with NOL7 expression. Furthermore, NOL7 expression was determined to be significantly associated with levels of infiltrating cells and immune checkpoint genes, including HMGB1. Analysis of NOL7-related genes revealed that RNA metabolism pathways, including “ribosome biogenesis”, “spliceosome”, and “RNA transport”, were mainly involved in the functional mechanism of NOL7 in human cancers. In summary, this pancancer study characterized the relationship between NOL7 expression and clinicopathologic features in multiple cancer types and further showed its potential regulatory network in human cancers. It represents a systemic analysis for further functional and therapeutic studies of NOL7 and highlights its predictive value with respect to the carcinogenesis and prognosis of various cancers, especially LIHC.
Collapse
|
14
|
Stålhammar G, Yeung A, Mendoza P, Dubovy SR, William Harbour J, Grossniklaus HE. Gain of Chromosome 6p Correlates with Severe Anaplasia, Cellular Hyperchromasia, and Extraocular Spread of Retinoblastoma. OPHTHALMOLOGY SCIENCE 2022; 2:100089. [PMID: 36246172 PMCID: PMC9560556 DOI: 10.1016/j.xops.2021.100089] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/03/2021] [Accepted: 12/03/2021] [Indexed: 06/16/2023]
Abstract
PURPOSE Gain of chromosome 6p has been associated with poor ocular survival in retinoblastoma and histopathologic grading of anaplasia with increased risk of metastatic spread and death. This study examined the correlation between these factors and other chromosomal abnormalities as well as results of whole genome sequencing, digital morphometry, and progression-free survival. DESIGN Retrospective cohort study from 2 United States tertiary referral centers. PARTICIPANTS Forty-two children who had undergone enucleation for retinoblastoma from January 2000 through December 2017. METHODS Status of chromosomes 6p, 1q, 9q, and 16q was evaluated with fluorescence in situ hybridization, the degree of anaplasia and presence of histologic high-risk features were assessed by ocular pathologists, digital morphometry was performed on scanned tumor slides, and whole genome sequencing was performed on a subset of tumors. Progression-free survival was defined as absence of distant or local metastases or tumor growth beyond the cut end of the optic nerve. MAIN OUTCOME MEASURES Correlation between each of chromosomal abnormalities, anaplasia, morphometry and sequencing results, and survival. RESULTS Forty-one of 42 included patients underwent primary enucleation and 1 was treated first with intra-arterial chemotherapy. Seven tumors showed mild anaplasia, 19 showed moderate anaplasia, and 16 showed severe anaplasia. All tumors had gain of 1q, 18 tumors had gain of 6p, 6 tumors had gain of 9q, and 36 tumors had loss of 16q. Tumors with severe anaplasia were significantly more likely to harbor 6p gains than tumors with nonsevere anaplasia (P < 0.001). Further, the hematoxylin staining intensity was significantly greater and that of eosin staining significantly lower in tumors with severe anaplasia (P < 0.05). Neither severe anaplasia (P = 0.10) nor gain of 6p (P = 0.21) correlated with histologic high-risk features, and severe anaplasia did not correlate to RB1, CREBBP, NSD1, or BCOR mutations in a subset of 14 tumors (P > 0.5). Patients with gain of 6p showed significantly shorter progression-free survival (P = 0.03, Wilcoxon test). CONCLUSIONS Gain of chromosome 6p emerges as a strong prognostic biomarker in retinoblastoma because it correlates with severe anaplasia, quantifiable changes in tumor cell staining characteristics, and extraocular spread.
Collapse
Affiliation(s)
- Gustav Stålhammar
- Ocular Pathology Service, St. Erik Eye Hospital, Stockholm, Sweden
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Aaron Yeung
- Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Departments of Ophthalmology and Pathology, Emory University School of Medicine, Atlanta, Georgia
| | - Pia Mendoza
- Departments of Ophthalmology and Pathology, Emory University School of Medicine, Atlanta, Georgia
| | - Sander R. Dubovy
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - J. William Harbour
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Hans E. Grossniklaus
- Departments of Ophthalmology and Pathology, Emory University School of Medicine, Atlanta, Georgia
| |
Collapse
|
15
|
Comprehensive patient-level classification and quantification of driver events in TCGA PanCanAtlas cohorts. PLoS Genet 2022; 18:e1009996. [PMID: 35030162 PMCID: PMC8759692 DOI: 10.1371/journal.pgen.1009996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 12/14/2021] [Indexed: 12/14/2022] Open
Abstract
There is a growing need to develop novel therapeutics for targeted treatment of cancer. The prerequisite to success is the knowledge about which types of molecular alterations are predominantly driving tumorigenesis. To shed light onto this subject, we have utilized the largest database of human cancer mutations–TCGA PanCanAtlas, multiple established algorithms for cancer driver prediction (2020plus, CHASMplus, CompositeDriver, dNdScv, DriverNet, HotMAPS, OncodriveCLUSTL, OncodriveFML) and developed four novel computational pipelines: SNADRIF (Single Nucleotide Alteration DRIver Finder), GECNAV (Gene Expression-based Copy Number Alteration Validator), ANDRIF (ANeuploidy DRIver Finder) and PALDRIC (PAtient-Level DRIver Classifier). A unified workflow integrating all these pipelines, algorithms and datasets at cohort and patient levels was created. We have found that there are on average 12 driver events per tumour, of which 0.6 are single nucleotide alterations (SNAs) in oncogenes, 1.5 are amplifications of oncogenes, 1.2 are SNAs in tumour suppressors, 2.1 are deletions of tumour suppressors, 1.5 are driver chromosome losses, 1 is a driver chromosome gain, 2 are driver chromosome arm losses, and 1.5 are driver chromosome arm gains. The average number of driver events per tumour increases with age (from 7 to 15) and cancer stage (from 10 to 15) and varies strongly between cancer types (from 1 to 24). Patients with 1 and 7 driver events per tumour are the most frequent, and there are very few patients with more than 40 events. In tumours having only one driver event, this event is most often an SNA in an oncogene. However, with increasing number of driver events per tumour, the contribution of SNAs decreases, whereas the contribution of copy-number alterations and aneuploidy events increases. By analysing genomic and transcriptomic data from 10000 cancer patients through our custom-built computational pipelines and previously established third-party algorithms, we have found that half of all driver events in a patient’s tumour appear to be gains and losses of chromosomal arms and whole chromosomes. We therefore suggest that future therapeutics development efforts should be focused on targeting aneuploidy. We have also found that approximately a third of driver events in a patient are whole gene amplifications and deletions. Thus, therapies aimed at copy-number alterations also appear very promising. On the other hand, drugs aiming at point mutations are predicted to be less successful, as these alterations are responsible for just a couple of drivers per tumour. One notable exception are patients having only one driver event in their tumours, as this event is almost always a single nucleotide alteration in an oncogene.
Collapse
|
16
|
Ibrahim J, Op de Beeck K, Fransen E, Peeters M, Van Camp G. Genome-wide DNA methylation profiling and identification of potential pan-cancer and tumor-specific biomarkers. Mol Oncol 2022; 16:2432-2447. [PMID: 34978357 PMCID: PMC9208075 DOI: 10.1002/1878-0261.13176] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/28/2021] [Accepted: 12/31/2021] [Indexed: 12/22/2022] Open
Abstract
DNA methylation alterations have already been linked to cancer, and their usefulness for therapy and diagnosis has encouraged research into the human epigenome. Several biomarker studies have focused on identifying cancer types individually, yet common cancer and multi-cancer markers are still underexplored. We used The Cancer Genome Atlas (TCGA) to investigate genome-wide methylation profiles of 14 different cancer types and developed a three-step computational approach to select candidate biomarker CpG sites. In total, 1,991 pan-cancer and between 75 and 1,803 cancer-specific differentially methylated CpG sites were discovered. Differentially methylated blocks and regions were also discovered for the first time on such a large-scale. Through a three-step computational approach, a combination of four pan-cancer CpG markers was identified from these sites and externally validated (AUC = 0.90), maintaining comparable performance across tumor stages. Additionally, 20 tumor-specific CpG markers were identified and made up the final type-specific prediction model, which could accurately differentiate tumor types (AUC = 0.87-0.99). Our study highlights the power of the methylome as a rich source of cancer biomarkers, and the signatures we identified provide a new resource for understanding cancer mechanisms on the wider genomic scale with strong applicability in the context of new minimally invasive cancer detection assays.
Collapse
Affiliation(s)
- Joe Ibrahim
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650, Edegem, Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650, Edegem, Belgium
| | - Ken Op de Beeck
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650, Edegem, Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650, Edegem, Belgium
| | - Erik Fransen
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650, Edegem, Belgium.,StatUa Center for Statistics, University of Antwerp, Prinsstraat 13, 2000, Antwerp, Belgium
| | - Marc Peeters
- Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650, Edegem, Belgium.,Department of Medical Oncology, Antwerp University Hospital, Wilrijkstraat 10, 2650, Edegem, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650, Edegem, Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650, Edegem, Belgium
| |
Collapse
|
17
|
Bhattarai S, Sugita BM, Bortoletto SM, Fonseca AS, Cavalli LR, Aneja R. QNBC Is Associated with High Genomic Instability Characterized by Copy Number Alterations and miRNA Deregulation. Int J Mol Sci 2021; 22:11548. [PMID: 34768979 PMCID: PMC8584247 DOI: 10.3390/ijms222111548] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/12/2022] Open
Abstract
Triple-negative breast cancer (TNBC) can be further classified into androgen receptor (AR)-positive TNBC and AR-negative TNBC or quadruple-negative breast cancer (QNBC). Here, we investigated genomic instability in 53 clinical cases by array-CGH and miRNA expression profiling. Immunohistochemical analysis revealed that 64% of TNBC samples lacked AR expression. This group of tumors exhibited a higher level of copy number alterations (CNAs) and a higher frequency of cases affected by CNAs than TNBCs. CNAs in genes of the chromosome instability 25 (CIN25) and centrosome amplification (CA) signatures were more frequent in the QNBCs and were similar between the groups, respectively. However, expression levels of CIN25 and CA20 genes were higher in QNBCs. miRNA profiling revealed 184 differentially expressed miRNAs between the groups. Fifteen of these miRNAs were mapped at cytobands with CNAs, of which eight (miR-1204, miR-1265, miR-1267, miR-23c, miR-548ai, miR-567, miR-613, and miR-943), and presented concordance of expression and copy number levels. Pathway enrichment analysis of these miRNAs/mRNAs pairings showed association with genomic instability, cell cycle, and DNA damage response. Furthermore, the combined expression of these eight miRNAs robustly discriminated TNBCs from QNBCs (AUC = 0.946). Altogether, our results suggest a significant loss of AR in TNBC and a profound impact in genomic instability characterized by CNAs and deregulation of miRNA expression.
Collapse
Affiliation(s)
- Shristi Bhattarai
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA;
| | - Bruna M. Sugita
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba 80250-060, Brazil; (B.M.S.); (S.M.B.); (A.S.F.)
| | - Stefanne M. Bortoletto
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba 80250-060, Brazil; (B.M.S.); (S.M.B.); (A.S.F.)
| | - Aline S. Fonseca
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba 80250-060, Brazil; (B.M.S.); (S.M.B.); (A.S.F.)
| | - Luciane R. Cavalli
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba 80250-060, Brazil; (B.M.S.); (S.M.B.); (A.S.F.)
- Lombardi Comprehensive Cancer Center, Oncology Department, Georgetown University, Washington, DC 20007, USA
| | - Ritu Aneja
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA;
| |
Collapse
|
18
|
Li Y, Zhong C, Wang J, Chen F, Shen W, Li B, Zheng N, Lu Y, Katanaev VL, Jia L. NOL7 facilitates melanoma progression and metastasis. Signal Transduct Target Ther 2021; 6:352. [PMID: 34642294 PMCID: PMC8511122 DOI: 10.1038/s41392-021-00676-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/18/2021] [Accepted: 06/12/2021] [Indexed: 11/22/2022] Open
Affiliation(s)
- Yumei Li
- Institution of Oceanography, Minjiang University, Fuzhou, Fujian, China.,Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou, Fujian, China.,School of Basic Medicine, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Chunlian Zhong
- Institution of Oceanography, Minjiang University, Fuzhou, Fujian, China
| | - Jie Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou, Fujian, China.,School of Pharmacy, Anhui Medical University, Hefei, Anhui, China
| | - Fan Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou, Fujian, China
| | - Weiyu Shen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou, Fujian, China
| | - Bifei Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou, Fujian, China
| | - Ning Zheng
- Department of Pharmacology, Fujian Key Laboratory of Natural Medicine Pharmacology, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian, China
| | - Yusheng Lu
- Institution of Oceanography, Minjiang University, Fuzhou, Fujian, China
| | - Vladimir L Katanaev
- Institution of Oceanography, Minjiang University, Fuzhou, Fujian, China. .,Natural Products Drug Discovery Laboratory, School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia. .,Department of Cell Physiology and Metabolism, Translational Research Center in Oncohaematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
| | - Lee Jia
- Institution of Oceanography, Minjiang University, Fuzhou, Fujian, China. .,Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou, Fujian, China.
| |
Collapse
|
19
|
Giblin W, Bringman-Rodenbarger L, Guo AH, Kumar S, Monovich AC, Mostafa AM, Skinner ME, Azar M, Mady AS, Chung CH, Kadambi N, Melong KA, Lee HJ, Zhang L, Sajjakulnukit P, Trefely S, Varner EL, Iyer S, Wang M, Wilmott JS, Soyer HP, Sturm RA, Pritchard AL, Andea AA, Scolyer RA, Stark MS, Scott DA, Fullen DR, Bosenberg MW, Chandrasekaran S, Nikolovska-Coleska Z, Verhaegen ME, Snyder NW, Rivera MN, Osterman AL, Lyssiotis CA, Lombard DB. The deacylase SIRT5 supports melanoma viability by influencing chromatin dynamics. J Clin Invest 2021; 131:138926. [PMID: 33945506 PMCID: PMC8203465 DOI: 10.1172/jci138926] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/29/2021] [Indexed: 12/13/2022] Open
Abstract
Cutaneous melanoma remains the most lethal skin cancer, and ranks third among all malignancies in terms of years of life lost. Despite the advent of immune checkpoint and targeted therapies, only roughly half of patients with advanced melanoma achieve a durable remission. Sirtuin 5 (SIRT5) is a member of the sirtuin family of protein deacylases that regulates metabolism and other biological processes. Germline Sirt5 deficiency is associated with mild phenotypes in mice. Here we showed that SIRT5 was required for proliferation and survival across all cutaneous melanoma genotypes tested, as well as uveal melanoma, a genetically distinct melanoma subtype that arises in the eye and is incurable once metastatic. Likewise, SIRT5 was required for efficient tumor formation by melanoma xenografts and in an autochthonous mouse Braf Pten-driven melanoma model. Via metabolite and transcriptomic analyses, we found that SIRT5 was required to maintain histone acetylation and methylation levels in melanoma cells, thereby promoting proper gene expression. SIRT5-dependent genes notably included MITF, a key lineage-specific survival oncogene in melanoma, and the c-MYC proto-oncogene. SIRT5 may represent a druggable genotype-independent addiction in melanoma.
Collapse
Affiliation(s)
- William Giblin
- Department of Pathology and
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | - Ahmed M. Mostafa
- Department of Pathology and
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | | | | | | | | | | | | | - Ho-Joon Lee
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Li Zhang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter Sajjakulnukit
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sophie Trefely
- Department of Cancer Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Temple University, Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
| | - Erika L. Varner
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Temple University, Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
| | - Sowmya Iyer
- Department of Pathology and MGH Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - James S. Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - H. Peter Soyer
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Australia
- Department of Dermatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Richard A. Sturm
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Antonia L. Pritchard
- Institute of Health Research and Innovation, University of the Highlands and Islands, An Lóchran, Inverness, United Kingdom
- Oncogenomics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Aleodor A. Andea
- Department of Pathology and
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Richard A. Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, and NSW Pathology, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Mitchell S. Stark
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - David A. Scott
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Douglas R. Fullen
- Department of Pathology and
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Marcus W. Bosenberg
- Departments of Pathology and Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering and
- Program in Chemical Biology
- Center for Computational Medicine and Bioinformatics, and
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Zaneta Nikolovska-Coleska
- Department of Pathology and
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | - Nathaniel W. Snyder
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Temple University, Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
| | - Miguel N. Rivera
- Department of Pathology and MGH Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Andrei L. Osterman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Division of Gastroenterology, Department of Internal Medicine and
| | - David B. Lombard
- Department of Pathology and
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Institute of Gerontology, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
20
|
Vargas AC, Ardakani NM, Wong DD, Maclean FM, Kattampallil J, Boyle R, Santos L, Gill AJ. Chromosomal imbalances detected in NTRK-rearranged sarcomas by the use of comparative genomic hybridisation. Histopathology 2021; 78:932-942. [PMID: 33128780 DOI: 10.1111/his.14295] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/29/2020] [Indexed: 12/25/2022]
Abstract
AIMS NTRK-rearranged sarcomas are emerging as a distinct class of sarcomas of particular importance in the era of targeted therapy. The aim of this study was to use array comparative genomic hybridisation (aCGH) to explore the cytogenetic profile of six adult soft tissue sarcomas harbouring NTRK gene fusions. METHODS AND RESULTS aCGH was performed on six adult soft tissue sarcomas with proven NTRK rearrangements [NTRK1, n = 1 (TPM3-NTRK1); NTRK2, n = 1 (MTMR2-NTRK2); NTRK3, n = 4 (two ETV6-NTRK3; two with unknown partners). The morphological patterns of these cases included inflammatory myofibroblastic tumour-like, fibrosarcoma/malignant peripheral nerve sheath tumour-like, and Ewing sarcoma-like. On the basis of the number of chromosomal copy number variations (CNVs), ranging from two to 15 per sample, NTRK-associated sarcomas could be subdivided into two groups: one with a relatively simple karyotype (n = 2; median of three genomic alterations), and those with a more complex karyotype (n = 4; median of 11 genomic imbalances). Recurrent chromosomal CNVs included gains at chromosomes 6p, 1q, 7 (whole chromosome), and 12p, and losses at chromosomes 10q, 13q, 19q, and 9p. CONCLUSIONS NTRK-rearranged sarcomas constitute a heterogeneous group of tumours that can show a relatively simple or a complex karyotype. Although there were some, but inconsistent, associations between karyotype complexity and morphology, our study showed that a more complex karyotype in this group of tumours appeared to correlate with more aggressive clinical behaviour. Gains at chromosome 6p and 1q were the most common recurrent genomic alterations, being present in 67% of the samples (4/6), followed by gains at chromosome 7, which were present in 50% of the samples (3/6).
Collapse
Affiliation(s)
- Ana Cristina Vargas
- Anatomical Pathology, Douglass Hanly Moir Pathology, Macquarie Park, NSW, Australia.,Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Nima M Ardakani
- Anatomical Pathology, PathWest, QEII Medical Centre, Nedlands, WA, Australia.,School of Medicine, The University of Western Australia, Crawley, WA, Australia
| | - Daniel D Wong
- Anatomical Pathology, PathWest, QEII Medical Centre, Nedlands, WA, Australia.,School of Medicine, The University of Western Australia, Crawley, WA, Australia
| | - Fiona M Maclean
- Anatomical Pathology, Douglass Hanly Moir Pathology, Macquarie Park, NSW, Australia.,Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, NSW, Australia.,Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | | | - Richard Boyle
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Chris O'Brien Lifehouse, Sydney, NSW, Australia
| | - Leonardo Santos
- Anatomical Pathology, Liverpool Hospital, Liverpool, NSW, Australia
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, NSW, Australia
| |
Collapse
|
21
|
Muniz TP, Sorotsky H, Kanjanapan Y, Rose AAN, Araujo DV, Fortuna A, Ghazarian D, Kamil ZS, Pugh T, Mah M, Thiagarajah M, Torti D, Spreafico A, Hogg D. Genomic Landscape of Malignant Peripheral Nerve Sheath Tumor‒Like Melanoma. J Invest Dermatol 2021; 141:2470-2479. [PMID: 33831431 DOI: 10.1016/j.jid.2021.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 10/21/2022]
Abstract
Malignant peripheral nerve sheath tumor (MPNST)-like melanoma is a rare malignancy with overlapping characteristics of both neural sarcoma and melanoma. Although the genomics of cutaneous melanoma has been extensively studied, those of MPNST-like melanoma have not. To characterize the genomic landscape of MPNST-like melanoma, we performed a single-center, retrospective cohort study at a tertiary academic cancer center. Consecutive patients with a confirmed histologic diagnosis of MPNST-like melanoma were screened, and those whose tissues were locally available were included in this analysis. Archival tissue from six patients (eight samples) was submitted for whole-exome and transcriptome sequencing analysis. We compared these data with available genomic studies of cutaneous melanoma and MPNST. NF1 was altered (mutated, deleted, or amplified) in 67% of patients. Genes related to cell cycle regulation were frequently altered, with frequent deletion of ZNF331, which, to the best of our knowledge, has not been previously described in cutaneous melanoma. The serine protease inhibitor SERPINB4 was deleted in 100% of the patients. We show that MPNST-like melanoma presents overlapping genomic features with cutaneous melanoma and MPNST, but it is unique by the frequency of loss of function of ZNF331 and SERPINB4.
Collapse
Affiliation(s)
- Thiago P Muniz
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada.
| | - Hadas Sorotsky
- Institute of Oncology, Chaim Sheba Medical Center at Tel-Hashomer, Ramant Gan, Israel
| | - Yada Kanjanapan
- Department of Medical Oncology, Canberra Region Cancer Centre, Canberra, Australia
| | - April A N Rose
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Gerald Bronfman Department of Oncology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada; Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Daniel V Araujo
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Department of Medical Oncology, Hospital de Base, Sao Jose do Rio Preto, Brazil
| | - Alexander Fortuna
- Translational Genomics Laboratory, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Danny Ghazarian
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine & Pathobiology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Zaid Saeed Kamil
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine & Pathobiology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Trevor Pugh
- Translational Genomics Laboratory, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Michelle Mah
- Translational Genomics Laboratory, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Trillium Health Partners, Genetics Laboratory, Mississauga, Ontario, Canada
| | - Madhuran Thiagarajah
- Translational Genomics Laboratory, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Laboratory Medicine, Unity Health Toronto, Toronto, Ontario, Canada
| | - Dax Torti
- Translational Genomics Laboratory, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Anna Spreafico
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Phase 1 Drug Development Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - David Hogg
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
22
|
Gerrish A, Jenkinson H, Cole T. The Impact of Cell-Free DNA Analysis on the Management of Retinoblastoma. Cancers (Basel) 2021; 13:cancers13071570. [PMID: 33805427 PMCID: PMC8037190 DOI: 10.3390/cancers13071570] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Retinoblastoma is a childhood eye cancer, mainly caused by mutations in the RB1 gene, which can be somatic or constitutional. Unlike many other cancers, tumour biopsies are not performed due to the risk of tumour dissemination. As a result, until recently, somatic genetic analysis was only possible if an affected eye was removed as part of a treatment. Several recent proof of principle studies have demonstrated that the analysis of tumour-derived cell-free DNA, either obtained from ocular fluid or blood plasma, has the potential to advance the diagnosis and influence the prognosis of retinoblastoma patients. It has been shown that a confirmed diagnosis is possible in retinoblastoma patients undergoing conservative treatment. In vivo genetic analysis of retinoblastoma tumours is also now possible, allowing the potential identification of secondary genetic events as prognostic biomarkers. In addition, noninvasive prenatal diagnosis in children at risk of inheriting retinoblastoma has been developed. Here, we review the current literature and discuss the potential impact of cell-free DNA analysis on both the diagnosis and treatment of retinoblastoma patients and their families.
Collapse
Affiliation(s)
- Amy Gerrish
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK;
- Correspondence:
| | - Helen Jenkinson
- Department of Paediatric Oncology, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK;
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK;
| |
Collapse
|
23
|
Couto Oliveira A, Ribeiro IP, Pires LM, Gonçalves AC, Paiva A, Geraldes C, Roque A, Sarmento-Ribeiro AB, Barbosa de Melo J, Carreira IM. Genomic characterisation of multiple myeloma: study of a Portuguese cohort. J Clin Pathol 2021; 75:422-425. [PMID: 33653728 DOI: 10.1136/jclinpath-2020-207204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/21/2020] [Accepted: 02/18/2021] [Indexed: 11/04/2022]
Abstract
Multiple myeloma (MM) genomic complexity reflects in the variable patients' clinical presentation. Genome-wide studies seem to be a reasonable alternative to identify critical genomic lesions. In the current study, we have performed the genomic characterisation of a Portuguese cohort of patients with MM by array comparative genomic hybridisation. Overall, the most frequently detected alterations were 13q deletions, gains of 1q, 19p, 15q, 5p and 7p and trisomy 9. Even though some identified genomic alterations were previously associated with a prognostic value, other abnormalities remain with unknown, but putative significance for patients' clinical practice. These genomic alterations should be further assessed as possible biomarkers.
Collapse
Affiliation(s)
- Alexandra Couto Oliveira
- University of Coimbra, Cytogenetics and Genomics Laboratory, Faculty of Medicine, Coimbra, Portugal
| | - Ilda Patrícia Ribeiro
- University of Coimbra, Cytogenetics and Genomics Laboratory, Faculty of Medicine, Coimbra, Portugal.,University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
| | - Luís Miguel Pires
- University of Coimbra, Cytogenetics and Genomics Laboratory, Faculty of Medicine, Coimbra, Portugal
| | - Ana Cristina Gonçalves
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.,University of Coimbra, Laboratory of Oncobiology and Haematology and University Clinic of Haematology, Faculty of Medicine, Coimbra, Portugal
| | - Artur Paiva
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal.,Cytometry Operational Management Unit, Clinical Pathology Service, Centro Hospitalar e Universitário de Coimbra EPE, Coimbra, Portugal
| | - Catarina Geraldes
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.,University of Coimbra, Laboratory of Oncobiology and Haematology and University Clinic of Haematology, Faculty of Medicine, Coimbra, Portugal.,Clinical Haematology Department, Centro Hospitalar e Universitário de Coimbra EPE, Coimbra, Portugal
| | - Adriana Roque
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.,Clinical Haematology Department, Centro Hospitalar e Universitário de Coimbra EPE, Coimbra, Portugal
| | - Ana Bela Sarmento-Ribeiro
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.,University of Coimbra, Laboratory of Oncobiology and Haematology and University Clinic of Haematology, Faculty of Medicine, Coimbra, Portugal.,Clinical Haematology Department, Centro Hospitalar e Universitário de Coimbra EPE, Coimbra, Portugal
| | - Joana Barbosa de Melo
- University of Coimbra, Cytogenetics and Genomics Laboratory, Faculty of Medicine, Coimbra, Portugal.,University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
| | - Isabel Marques Carreira
- University of Coimbra, Cytogenetics and Genomics Laboratory, Faculty of Medicine, Coimbra, Portugal .,University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
| |
Collapse
|
24
|
Zhou Y, Bastian IN, Long MD, Dow M, Li W, Liu T, Ngu RK, Antonucci L, Huang JY, Phung QT, Zhao XH, Banerjee S, Lin XJ, Wang H, Dang B, Choi S, Karin D, Su H, Ellisman MH, Jamieson C, Bosenberg M, Cheng Z, Haybaeck J, Kenner L, Fisch KM, Bourgon R, Hernandez G, Lill JR, Liu S, Carter H, Mellman I, Karin M, Shalapour S. Activation of NF-κB and p300/CBP potentiates cancer chemoimmunotherapy through induction of MHC-I antigen presentation. Proc Natl Acad Sci U S A 2021; 118:e2025840118. [PMID: 33602823 PMCID: PMC7923353 DOI: 10.1073/pnas.2025840118] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Many cancers evade immune rejection by suppressing major histocompatibility class I (MHC-I) antigen processing and presentation (AgPP). Such cancers do not respond to immune checkpoint inhibitor therapies (ICIT) such as PD-1/PD-L1 [PD-(L)1] blockade. Certain chemotherapeutic drugs augment tumor control by PD-(L)1 inhibitors through potentiation of T-cell priming but whether and how chemotherapy enhances MHC-I-dependent cancer cell recognition by cytotoxic T cells (CTLs) is not entirely clear. We now show that the lysine acetyl transferases p300/CREB binding protein (CBP) control MHC-I AgPPM expression and neoantigen amounts in human cancers. Moreover, we found that two distinct DNA damaging drugs, the platinoid oxaliplatin and the topoisomerase inhibitor mitoxantrone, strongly up-regulate MHC-I AgPP in a manner dependent on activation of nuclear factor kappa B (NF-κB), p300/CBP, and other transcription factors, but independently of autocrine IFNγ signaling. Accordingly, NF-κB and p300 ablations prevent chemotherapy-induced MHC-I AgPP and abrogate rejection of low MHC-I-expressing tumors by reinvigorated CD8+ CTLs. Drugs like oxaliplatin and mitoxantrone may be used to overcome resistance to PD-(L)1 inhibitors in tumors that had "epigenetically down-regulated," but had not permanently lost MHC-I AgPP activity.
Collapse
Affiliation(s)
- Yixuan Zhou
- Department of Pharmacology, School of Medicine, University of California San Diego, CA 92093
| | - Ingmar Niels Bastian
- Department of Pharmacology, School of Medicine, University of California San Diego, CA 92093
| | - Mark D Long
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263
| | - Michelle Dow
- Division of Medical Genetics, Health Sciences, Department of Biomedical Informatics, University of California San Diego, La Jolla, CA 92093
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Weihua Li
- Department of Pharmacology, School of Medicine, University of California San Diego, CA 92093
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Tao Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263
| | - Rachael Katie Ngu
- Department of Pharmacology, School of Medicine, University of California San Diego, CA 92093
| | - Laura Antonucci
- Department of Pharmacology, School of Medicine, University of California San Diego, CA 92093
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Jian Yu Huang
- Department of Pharmacology, School of Medicine, University of California San Diego, CA 92093
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Qui T Phung
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA 94080
| | - Xi-He Zhao
- Department of Pharmacology, School of Medicine, University of California San Diego, CA 92093
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093
- Oncology Department, China Medical University Shengjing Hospital, 110004 Shenyang City, China
| | - Sourav Banerjee
- Department of Pharmacology, School of Medicine, University of California San Diego, CA 92093
- Department of Cellular Medicine, Jacqui Wood Cancer Centre, University of Dundee, Dundee DD1 9SY, United Kingdom
| | - Xue-Jia Lin
- Department of Pharmacology, School of Medicine, University of California San Diego, CA 92093
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093
- Biomedical Translational Research Institute and the First Affiliated Hospital, Jinan University, 510632 Guangzhou, Guangdong, China
| | - Hongxia Wang
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 100850 Beijing, China
| | - Brian Dang
- Department of Pharmacology, School of Medicine, University of California San Diego, CA 92093
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Sylvia Choi
- Department of Pharmacology, School of Medicine, University of California San Diego, CA 92093
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Daniel Karin
- Department of Pharmacology, School of Medicine, University of California San Diego, CA 92093
| | - Hua Su
- Department of Pharmacology, School of Medicine, University of California San Diego, CA 92093
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093
| | - Christina Jamieson
- Department of Urology, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093
| | - Marcus Bosenberg
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510
- Department of Dermatology, Yale School of Medicine, New Haven, CT 06510
| | - Zhang Cheng
- Center for Epigenomics, Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Johannes Haybaeck
- Institute of Pathology, Medical University of Graz, A-8036 Graz, Austria
- Department of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, A-6020 Innsbruck, Austria
| | - Lukas Kenner
- Department of Pathology, Christian Doppler Laboratory, Medical University of Vienna, 1090 Vienna, Austria
- Unit of Pathology of Laboratory Animals, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Richard Bourgon
- Department of Cancer Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Genevive Hernandez
- Department of Cancer Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Jennie R Lill
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA 94080
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263
| | - Hannah Carter
- Division of Medical Genetics, Health Sciences, Department of Biomedical Informatics, University of California San Diego, La Jolla, CA 92093
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Ira Mellman
- Department of Cancer Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Michael Karin
- Department of Pharmacology, School of Medicine, University of California San Diego, CA 92093;
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Shabnam Shalapour
- Department of Pharmacology, School of Medicine, University of California San Diego, CA 92093;
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054
| |
Collapse
|
25
|
Bruhn C, Ajazi A, Ferrari E, Lanz MC, Batrin R, Choudhary R, Walvekar A, Laxman S, Longhese MP, Fabre E, Smolka MB, Foiani M. The Rad53 CHK1/CHK2-Spt21 NPAT and Tel1 ATM axes couple glucose tolerance to histone dosage and subtelomeric silencing. Nat Commun 2020; 11:4154. [PMID: 32814778 PMCID: PMC7438486 DOI: 10.1038/s41467-020-17961-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 07/23/2020] [Indexed: 12/14/2022] Open
Abstract
The DNA damage response (DDR) coordinates DNA metabolism with nuclear and non-nuclear processes. The DDR kinase Rad53CHK1/CHK2 controls histone degradation to assist DNA repair. However, Rad53 deficiency causes histone-dependent growth defects in the absence of DNA damage, pointing out unknown physiological functions of the Rad53-histone axis. Here we show that histone dosage control by Rad53 ensures metabolic homeostasis. Under physiological conditions, Rad53 regulates histone levels through inhibitory phosphorylation of the transcription factor Spt21NPAT on Ser276. Rad53-Spt21 mutants display severe glucose dependence, caused by excess histones through two separable mechanisms: dampening of acetyl-coenzyme A-dependent carbon metabolism through histone hyper-acetylation, and Sirtuin-mediated silencing of starvation-induced subtelomeric domains. We further demonstrate that repression of subtelomere silencing by physiological Tel1ATM and Rpd3HDAC activities coveys tolerance to glucose restriction. Our findings identify DDR mutations, histone imbalances and aberrant subtelomeric chromatin as interconnected causes of glucose dependence, implying that DDR kinases coordinate metabolism and epigenetic changes.
Collapse
Affiliation(s)
- Christopher Bruhn
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy.
| | - Arta Ajazi
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy
| | - Elisa Ferrari
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy
| | - Michael Charles Lanz
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Renaud Batrin
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Centre de Recherche St Louis, F-75010, Paris, France
| | - Ramveer Choudhary
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy
| | - Adhish Walvekar
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Edificio U3, Piazza della Scienza 2, 20126, Milan, Italy
| | - Emmanuelle Fabre
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Centre de Recherche St Louis, F-75010, Paris, France
| | - Marcus Bustamente Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Marco Foiani
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy.
- Università degli Studi di Milano, Via Festa del Perdono 7, 20122, Milan, Italy.
| |
Collapse
|
26
|
Xu L, Polski A, Prabakar RK, Reid MW, Chevez-Barrios P, Jubran R, Kim JW, Kuhn P, Cobrinik D, Hicks J, Berry JL. Chromosome 6p Amplification in Aqueous Humor Cell-Free DNA Is a Prognostic Biomarker for Retinoblastoma Ocular Survival. Mol Cancer Res 2020; 18:1166-1175. [PMID: 32434859 PMCID: PMC7415535 DOI: 10.1158/1541-7786.mcr-19-1262] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/10/2020] [Accepted: 05/18/2020] [Indexed: 11/16/2022]
Abstract
Aqueous humor contains tumor-derived cell-free DNA (cfDNA) and can serve as a liquid biopsy for retinoblastoma. We previously associated somatic copy-number alteration (SCNA) 6p gain with a 10-fold increased risk of enucleation. Here we provide a 2-year update to further explore 6p gain as a prognostic biomarker for ocular survival. Patients diagnosed with retinoblastoma from December 2014 to July 2019 from whom aqueous humor was sampled were included. cfDNA was extracted and shallow whole-genome sequencing performed to identify highly recurrent retinoblastoma SCNAs (gain of 1q, 2p, 6p, loss of 13q, 16q). 116 aqueous humor samples from 50 eyes of 46 patients were included: 27 eyes were salvaged, 23 were enucleated. Highly recurrent retinoblastoma SCNAs were found in 66% eyes. 6p gain was the most prevalent SCNA (50% eyes). It was particularly more prevalent in enucleated eyes (73.9%) than in salvaged eyes (29.6%; P = 0.004). 6p gain in aqueous humor cfDNA portended nearly 10-fold increased odds of enucleation (OR = 9.87; 95% confidence interval = 1.75-55.65; P = 0.009). In the enucleated eyes, 6p gain was associated with aggressive histopathologic features, including necrosis, higher degrees of anaplasia, and focal invasion of ocular structures. With extended follow-up and nearly double the aqueous humor samples, we continue to demonstrate 6p gain as a potential prognostic biomarker for retinoblastoma. IMPLICATIONS: Aqueous humor is a high-yield source of tumor-derived DNA in retinoblastoma eyes. Detection of 6p gain in the aqueous humor allows for targeted, patient-centered therapies based on this molecular prognostic marker. Prospective, multicenter studies with aqueous humor sampled from all eyes at diagnosis are warranted to validate these findings.
Collapse
Affiliation(s)
- Liya Xu
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - Ashley Polski
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck Medical School of the University of Southern California, Los Angeles, California
| | - Rishvanth K Prabakar
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California
| | - Mark W Reid
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California
| | - Patricia Chevez-Barrios
- Departments of Pathology and Genomic Medicine and Ophthalmology, Houston Methodist, Weill Cornell Medical College, Houston, Texas
| | - Rima Jubran
- Department of Hematology-Oncology, Children's Hospital Los Angeles, Los Angeles, California
| | - Jonathan W Kim
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck Medical School of the University of Southern California, Los Angeles, California
| | - Peter Kuhn
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California
| | - David Cobrinik
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck Medical School of the University of Southern California, Los Angeles, California
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - James Hicks
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jesse L Berry
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California.
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck Medical School of the University of Southern California, Los Angeles, California
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| |
Collapse
|
27
|
More DA, Kumar A. SRSF3: Newly discovered functions and roles in human health and diseases. Eur J Cell Biol 2020; 99:151099. [PMID: 32800280 DOI: 10.1016/j.ejcb.2020.151099] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/15/2020] [Accepted: 06/29/2020] [Indexed: 12/21/2022] Open
Abstract
The serine/arginine rich proteins (SR proteins) are members of a family of RNA binding proteins involved in regulating various features of RNA metabolism, including pre-mRNA constitutive and alternative splicing. In humans, a total of 12 SR splicing factors (SRSFs) namely SRSF1-SRSF12 have been reported. SRSF3, the smallest member of the SR family and the focus of this review, regulates critical steps in mRNA metabolism and has been shown to have mRNA-independent functions as well. Recent studies on SRSF3 have uncovered its role in a wide array of complex biological processes. We have also reviewed the involvement of SRSF3 in disease conditions like cancer, ageing, neurological and cardiac disorders. Finally, we have discussed in detail the autoregulation of SRSF3 and its implications in cancer and commented on the potential of SRSF3 as a therapeutic target, especially in the context of cancer.
Collapse
Affiliation(s)
- Dhanashree Anil More
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Arun Kumar
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India.
| |
Collapse
|
28
|
Xiao F, Luo X, Hao N, Niu YS, Xiao X, Cai G, Amos CI, Zhang H. An accurate and powerful method for copy number variation detection. Bioinformatics 2020; 35:2891-2898. [PMID: 30649252 DOI: 10.1093/bioinformatics/bty1041] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/28/2018] [Accepted: 01/09/2019] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Integration of multiple genetic sources for copy number variation detection (CNV) is a powerful approach to improve the identification of variants associated with complex traits. Although it has been shown that the widely used change point based methods can increase statistical power to identify variants, it remains challenging to effectively detect CNVs with weak signals due to the noisy nature of genotyping intensity data. We previously developed modSaRa, a normal mean-based model on a screening and ranking algorithm for copy number variation identification which presented desirable sensitivity with high computational efficiency. To boost statistical power for the identification of variants, here we present a novel improvement that integrates the relative allelic intensity with external information from empirical statistics with modeling, which we called modSaRa2. RESULTS Simulation studies illustrated that modSaRa2 markedly improved both sensitivity and specificity over existing methods for analyzing array-based data. The improvement in weak CNV signal detection is the most substantial, while it also simultaneously improves stability when CNV size varies. The application of the new method to a whole genome melanoma dataset identified novel candidate melanoma risk associated deletions on chromosome bands 1p22.2 and duplications on 6p22, 6q25 and 19p13 regions, which may facilitate the understanding of the possible roles of germline copy number variants in the etiology of melanoma. AVAILABILITY AND IMPLEMENTATION http://c2s2.yale.edu/software/modSaRa2 or https://github.com/FeifeiXiaoUSC/modSaRa2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Feifei Xiao
- Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC, USA
| | - Xizhi Luo
- Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC, USA
| | - Ning Hao
- Department of Mathematics, University of Arizona, Tucson, AZ, USA
| | - Yue S Niu
- Department of Mathematics, University of Arizona, Tucson, AZ, USA
| | - Xiangjun Xiao
- Department of Quantitative Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Guoshuai Cai
- Department of Environmental Health Science, University of South Carolina, Columbia, SC, USA
| | - Christopher I Amos
- Department of Quantitative Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Heping Zhang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| |
Collapse
|
29
|
Adwal A, Kalita-de Croft P, Shakya R, Lim M, Kalaw E, Taege LD, McCart Reed AE, Lakhani SR, Callen DF, Saunus JM. Tradeoff between metabolic i-proteasome addiction and immune evasion in triple-negative breast cancer. Life Sci Alliance 2020; 3:3/7/e201900562. [PMID: 32423906 PMCID: PMC7240743 DOI: 10.26508/lsa.201900562] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
In vitro studies have suggested proteasome inhibitors could be effective in triple-negative breast cancer (TNBC). We found that bortezomib and carfilzomib induce proteotoxic stress and apoptosis via the unfolded protein response (UPR) in TNBC cell lines, with sensitivity correlated with expression of immuno-(PSMB8/9/10) but not constitutive-(PSMB5/6/7) proteasome subunits. Equally, the transcriptomes of i-proteasome-high human TNBCs are enriched with UPR gene sets, and the genomic copy number landscape reflects positive selection pressure favoring i-proteasome activity, but in the setting of adjuvant treatment, this is actually associated with favorable prognosis. Tumor expression of PSMB8 protein (β5i) is associated with levels of MHC-I, interferon-γ-inducible proteasome activator PA28β, and the densities of stromal antigen-presenting cells and lymphocytes (TILs). Crucially, TILs were protective among TNBCs that maintain high β5i but did not stratify survival amongst β5i-low TNBCs. Moreover, β5i expression was lower in brain metastases than in patient-matched primary breast tumors (n = 34; P = 0.007), suggesting that suppression contributes to immune evasion and metastatic progression. Hence, inhibiting proteasome activity could be counterproductive in the adjuvant treatment setting because it potentiates anti-TNBC immunity.
Collapse
Affiliation(s)
- Alaknanda Adwal
- The Robinson Research Institute, Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Priyakshi Kalita-de Croft
- The University of Queensland (UQ) Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Reshma Shakya
- QIMR Centre for Immunotherapy and Vaccine Development, Tumour Immunology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Malcolm Lim
- The University of Queensland (UQ) Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Emarene Kalaw
- The University of Queensland (UQ) Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Lucinda D Taege
- The University of Queensland (UQ) Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia.,Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Amy E McCart Reed
- The University of Queensland (UQ) Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Sunil R Lakhani
- The University of Queensland (UQ) Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia.,Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - David F Callen
- School of Medicine, Faculty of Health Sciences, The University of Adelaide, Adelaide, Australia
| | - Jodi M Saunus
- The University of Queensland (UQ) Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| |
Collapse
|
30
|
Starrett GJ, Thakuria M, Chen T, Marcelus C, Cheng J, Nomburg J, Thorner AR, Slevin MK, Powers W, Burns RT, Perry C, Piris A, Kuo FC, Rabinowits G, Giobbie-Hurder A, MacConaill LE, DeCaprio JA. Clinical and molecular characterization of virus-positive and virus-negative Merkel cell carcinoma. Genome Med 2020; 12:30. [PMID: 32188490 PMCID: PMC7081548 DOI: 10.1186/s13073-020-00727-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/27/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Merkel cell carcinoma (MCC) is a highly aggressive neuroendocrine carcinoma of the skin caused by either the integration of Merkel cell polyomavirus (MCPyV) and expression of viral T antigens or by ultraviolet-induced damage to the tumor genome from excessive sunlight exposure. An increasing number of deep sequencing studies of MCC have identified significant differences between the number and types of point mutations, copy number alterations, and structural variants between virus-positive and virus-negative tumors. However, it has been challenging to reliably distinguish between virus positive and UV damaged MCC. METHODS In this study, we assembled a cohort of 71 MCC patients and performed deep sequencing with OncoPanel, a clinically implemented, next-generation sequencing assay targeting over 400 cancer-associated genes. To improve the accuracy and sensitivity for virus detection compared to traditional PCR and IHC methods, we developed a hybrid capture baitset against the entire MCPyV genome and software to detect integration sites and structure. RESULTS Sequencing from this approach revealed distinct integration junctions in the tumor genome and generated assemblies that strongly support a model of microhomology-initiated hybrid, virus-host, circular DNA intermediate that promotes focal amplification of host and viral DNA. Using the clear delineation between virus-positive and virus-negative tumors from this method, we identified recurrent somatic alterations common across MCC and alterations specific to each class of tumor, associated with differences in overall survival. Finally, comparing the molecular and clinical data from these patients revealed a surprising association of immunosuppression with virus-negative MCC and significantly shortened overall survival. CONCLUSIONS These results demonstrate the value of high-confidence virus detection for identifying molecular mechanisms of UV and viral oncogenesis in MCC. Furthermore, integrating these data with clinical data revealed features that could impact patient outcome and improve our understanding of MCC risk factors.
Collapse
Affiliation(s)
| | - Manisha Thakuria
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Merkel Cell Carcinoma Center of Excellence, Dana-Farber/Brigham Cancer Center, Boston, MA, USA
| | - Tianqi Chen
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christina Marcelus
- Department of Medical Oncology, Dana-Farber Cancer Institute, Mayer 440, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Jingwei Cheng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Mayer 440, 450 Brookline Avenue, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason Nomburg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Mayer 440, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Aaron R Thorner
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael K Slevin
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Winslow Powers
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Robert T Burns
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Caitlin Perry
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adriano Piris
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Frank C Kuo
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Guilherme Rabinowits
- Merkel Cell Carcinoma Center of Excellence, Dana-Farber/Brigham Cancer Center, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Mayer 440, 450 Brookline Avenue, Boston, MA, 02215, USA
- Present Address: Miami Cancer Institute, Miami, FL, USA
| | | | - Laura E MacConaill
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - James A DeCaprio
- Merkel Cell Carcinoma Center of Excellence, Dana-Farber/Brigham Cancer Center, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Mayer 440, 450 Brookline Avenue, Boston, MA, 02215, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
31
|
Palombo R, Verdile V, Paronetto MP. Poison-Exon Inclusion in DHX9 Reduces Its Expression and Sensitizes Ewing Sarcoma Cells to Chemotherapeutic Treatment. Cells 2020; 9:cells9020328. [PMID: 32023846 PMCID: PMC7072589 DOI: 10.3390/cells9020328] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing is a combinatorial mechanism by which exons are joined to produce multiple mRNA variants, thus expanding the coding potential and plasticity of eukaryotic genomes. Defects in alternative splicing regulation are associated with several human diseases, including cancer. Ewing sarcoma is an aggressive tumor of bone and soft tissue, mainly affecting adolescents and young adults. DHX9 is a key player in Ewing sarcoma malignancy, and its expression correlates with worse prognosis in patients. In this study, by screening a library of siRNAs, we have identified splicing factors that regulate the alternative inclusion of a poison exon in DHX9 mRNA, leading to its downregulation. In particular, we found that hnRNPM and SRSF3 bind in vivo to this poison exon and suppress its inclusion. Notably, DHX9 expression correlates with that of SRSF3 and hnRNPM in Ewing sarcoma patients. Furthermore, downregulation of SRSF3 or hnRNPM inhibited DHX9 expression and Ewing sarcoma cell proliferation, while sensitizing cells to chemotherapeutic treatment. Hence, our study suggests that inhibition of hnRNPM and SRSF3 expression or activity could be exploited as a therapeutic tool to enhance the efficacy of chemotherapy in Ewing sarcoma.
Collapse
Affiliation(s)
- Ramona Palombo
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy; (R.P.); (V.V.)
| | - Veronica Verdile
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy; (R.P.); (V.V.)
- Department of Movement, Human and Health Sciences, Università degli Studi di Roma “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
| | - Maria Paola Paronetto
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy; (R.P.); (V.V.)
- Department of Movement, Human and Health Sciences, Università degli Studi di Roma “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
- Correspondence: ; Tel.:+39-0636733576
| |
Collapse
|
32
|
Simbulan-Rosenthal CM, Dougherty R, Vakili S, Ferraro AM, Kuo LW, Alobaidi R, Aljehane L, Gaur A, Sykora P, Glasgow E, Agarwal S, Rosenthal DS. CRISPR-Cas9 Knockdown and Induced Expression of CD133 Reveal Essential Roles in Melanoma Invasion and Metastasis. Cancers (Basel) 2019; 11:cancers11101490. [PMID: 31623313 PMCID: PMC6827046 DOI: 10.3390/cancers11101490] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 09/26/2019] [Accepted: 10/01/2019] [Indexed: 02/07/2023] Open
Abstract
CD133, known as prominin1, is a penta-span transmembrane glycoprotein presumably a cancer stem cell marker for carcinomas, glioblastomas, and melanomas. We showed that CD133(+) ‘melanoma-initiating cells’ are associated with chemoresistance, contributing to poor patient outcome. The current study investigates the role(s) of CD133 in invasion and metastasis. Magnetic-activated cell sorting of a melanoma cell line (BAKP) followed by transwell invasion assays revealed that CD133(+) cells are significantly more invasive than CD133(−) cells. Conditional reprogramming of BAKP CD133(+) cells maintained stable CD133 overexpression (BAK-R), and induced cancer stem cell markers, melanosphere formation, and chemoresistance to kinase inhibitors. BAK-R cells showed upregulated CD133 expression, and consequently were more invasive and metastatic than BAK-P cells in transwell and zebrafish assays. CD133 knockdown by siRNA or CRISPR-Cas9 (BAK-R-T3) in BAK-R cells reduced invasion and levels of matrix metalloproteinases MMP2/MMP9. BAK-R-SC cells, but not BAK-R-T3, were metastatic in zebrafish. While CD133 knockdown by siRNA or CRISPR-Cas9 in BAK-P cells attenuated invasion and diminished MMP2/MMP9 levels, doxycycline-induced CD133 expression in BAK-P cells enhanced invasion and MMP2/MMP9 concentrations. CD133 may therefore play an essential role in invasion and metastasis via upregulation of MMP2/MMP9, leading to tumor progression, and represents an attractive target for intervention in melanoma.
Collapse
Affiliation(s)
- Cynthia M Simbulan-Rosenthal
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University School of Medicine, Washington, DC 20007, USA.
| | - Ryan Dougherty
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University School of Medicine, Washington, DC 20007, USA.
| | - Sahar Vakili
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University School of Medicine, Washington, DC 20007, USA.
| | - Alexandra M Ferraro
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University School of Medicine, Washington, DC 20007, USA.
| | - Li-Wei Kuo
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University School of Medicine, Washington, DC 20007, USA.
| | - Ryyan Alobaidi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University School of Medicine, Washington, DC 20007, USA.
| | - Leala Aljehane
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University School of Medicine, Washington, DC 20007, USA.
| | - Anirudh Gaur
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University School of Medicine, Washington, DC 20007, USA.
| | | | - Eric Glasgow
- Department of Oncology, Georgetown University School of Medicine, Washington, DC 20007, USA.
| | - Seema Agarwal
- Department of Pathology, Georgetown University School of Medicine, Washington, DC 20007, USA.
| | - Dean S Rosenthal
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University School of Medicine, Washington, DC 20007, USA.
| |
Collapse
|
33
|
Histone stress: an unexplored source of chromosomal instability in cancer? Curr Genet 2019; 65:1081-1088. [DOI: 10.1007/s00294-019-00967-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 02/27/2019] [Accepted: 04/03/2019] [Indexed: 01/24/2023]
|
34
|
Wang F, Zhu S, Fisher LA, Wang L, Eurek NJ, Wahl JK, Lan L, Peng A. Phosphatase 1 Nuclear Targeting Subunit Mediates Recruitment and Function of Poly (ADP-Ribose) Polymerase 1 in DNA Repair. Cancer Res 2019; 79:2526-2535. [PMID: 30733193 DOI: 10.1158/0008-5472.can-18-1673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/26/2018] [Accepted: 01/31/2019] [Indexed: 12/17/2022]
Abstract
PARP, particularly PARP1, plays an essential role in the detection and repair of DNA single-strand breaks and double-strand breaks. PARP1 accumulates at DNA damage sites within seconds after DNA damage to catalyze the massive induction of substrate protein poly ADP-ribosylation (PARylation). However, the molecular mechanisms underlying the recruitment and activation of PARP1 in DNA repair are not fully understood. Here we show that phosphatase 1 nuclear targeting subunit 1 (PNUTS) is a robust binding partner of PARP1. Inhibition of PNUTS led to strong accumulation of endogenous DNA damage and sensitized the cellular response to a wide range of DNA-damaging agents, implicating PNUTS as an essential and multifaceted regulator of DNA repair. Recruitment of PNUTS to laser-induced DNA damage was similar to that of PARP1, and depletion or inhibition of PARP1 abrogated recruitment of PNUTS to sites of DNA damage. Conversely, PNUTS was required for efficient induction of substrate PARylation after DNA damage. PNUTS bound the BRCA1 C-terminal (BRCT) domain of PARP1 and was required for the recruitment of PARP1 to sites of DNA damage. Finally, depletion of PNUTS rendered cancer cells hypersensitive to PARP inhibition. Taken together, our study characterizes PNUTS as an essential partner of PARP1 in DNA repair and a potential drug target in cancer therapy. SIGNIFICANCE: These findings reveal PNUTS as an essential functional partner of PARP1 in DNA repair and suggest its inhibition as a potential therapeutic strategy in conjunction with DNA-damaging agents or PARP inhibitors.See related commentary by Murai and Pommier, p. 2460.
Collapse
Affiliation(s)
- Feifei Wang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, P.R. China.,Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Songli Zhu
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Laura A Fisher
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Ling Wang
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Nicholas J Eurek
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - James K Wahl
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Li Lan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Aimin Peng
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska.
| |
Collapse
|
35
|
Fiedler D, Heselmeyer-Haddad K, Hirsch D, Hernandez LS, Torres I, Wangsa D, Hu Y, Zapata L, Rueschoff J, Belle S, Ried T, Gaiser T. Single-cell genetic analysis of clonal dynamics in colorectal adenomas indicates CDX2 gain as a predictor of recurrence. Int J Cancer 2018; 144:1561-1573. [PMID: 30229897 DOI: 10.1002/ijc.31869] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/11/2018] [Accepted: 08/13/2018] [Indexed: 12/19/2022]
Abstract
Colorectal adenomas are common precancerous lesions with the potential for malignant transformation to colorectal adenocarcinoma. Endoscopic polypectomy provides an opportunity for cancer prevention; however, recurrence rates are high. We collected formalin-fixed paraffin-embedded tissue of 15 primary adenomas with recurrence, 15 adenomas without recurrence, and 14 matched pair samples (primary adenoma and the corresponding recurrent adenoma). The samples were analysed by array-comparative genomic hybridisation (aCGH) and single-cell multiplex interphase fluorescence in situ hybridisation (miFISH) to understand clonal evolution, to examine the dynamics of copy number alterations (CNAs) and to identify molecular markers for recurrence prediction. The miFISH probe panel consisted of 14 colorectal carcinogenesis-relevant genes (COX2, PIK3CA, APC, CLIC1, EGFR, MYC, CCND1, CDX2, CDH1, TP53, HER2, SMAD7, SMAD4 and ZNF217), and a centromere probe (CEP10). The aCGH analysis confirmed the genetic landscape typical for colorectal tumorigenesis, that is, CNAs of chromosomes 7, 13q, 18 and 20q. Focal aberrations (≤10 Mbp) were mapped to chromosome bands 6p22.1-p21.33 (33.3%), 7q22.1 (31.4%) and 16q21 (29.4%). MiFISH detected gains of EGFR (23.6%), CDX2 (21.8%) and ZNF217 (18.2%). Most adenomas exhibited a major clone population which was accompanied by multiple smaller clone populations. Gains of CDX2 were exclusively seen in primary adenomas with recurrence (25%) compared to primary adenomas without recurrence (0%). Generation of phylogenetic trees for matched pair samples revealed four distinct patterns of clonal dynamics. In conclusion, adenoma development and recurrence are complex genetic processes driven by multiple CNAs whose evaluations by miFISH, with emphasis on CDX2, might serve as a predictor of recurrence.
Collapse
Affiliation(s)
- David Fiedler
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Daniela Hirsch
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Leanora S Hernandez
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Irianna Torres
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yue Hu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom.,Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CGR), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Sebastian Belle
- Department of Internal Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Central Interdisciplinary Endoscopy Unit, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Timo Gaiser
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| |
Collapse
|
36
|
Bellmunt J. Stem-Like Signature Predicting Disease Progression in Early Stage Bladder Cancer. The Role of E2F3 and SOX4. Biomedicines 2018; 6:biomedicines6030085. [PMID: 30072631 PMCID: PMC6164884 DOI: 10.3390/biomedicines6030085] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022] Open
Abstract
The rapid development of the cancer stem cells (CSC) field, together with powerful genome-wide screening techniques, have provided the basis for the development of future alternative and reliable therapies aimed at targeting tumor-initiating cell populations. Urothelial bladder cancer stem cells (BCSCs) that were identified for the first time in 2009 are heterogenous and originate from multiple cell types; including urothelial stem cells and differentiated cell types—basal, intermediate stratum and umbrella cells Some studies hypothesize that BCSCs do not necessarily arise from normal stem cells but might derive from differentiated progenies following mutational insults and acquisition of tumorigenic properties. Conversely, there is data that normal bladder tissues can generate CSCs through mutations. Prognostic risk stratification by identification of predictive markers is of major importance in the management of urothelial cell carcinoma (UCC) patients. Several stem cell markers have been linked to recurrence or progression. The CD44v8-10 to standard CD44-ratio (total ratio of all CD44 alternative splicing isoforms) in urothelial cancer has been shown to be closely associated with tumor progression and aggressiveness. ALDH1, has also been reported to be associated with BCSCs and a worse prognosis in a large number of studies. UCC include low-grade and high-grade non-muscle invasive bladder cancer (NMIBC) and high-grade muscle invasive bladder cancer (MIBC). Important genetic defects characterize the distinct pathways in each one of the stages and probably grades. As an example, amplification of chromosome 6p22 is one of the most frequent changes seen in MIBC and might act as an early event in tumor progression. Interestingly, among NMIBC there is a much higher rate of amplification in high-grade NMIBC compared to low grade NMIBC. CDKAL1, E2F3 and SOX4 are highly expressed in patients with the chromosomal 6p22 amplification aside from other six well known genes (ID4, MBOAT1, LINC00340, PRL, and HDGFL1). Based on that, SOX4, E2F3 or 6q22.3 amplifications might represent potential targets in this tumor type. Focusing more in SOX4, it seems to exert its critical regulatory functions upstream of the Snail, Zeb, and Twist family of transcriptional inducers of EMT (epithelial–mesenchymal transition), but without directly affecting their expression as seen in several cell lines of the Cancer Cell Line Encyclopedia (CCLE) project. SOX4 gene expression correlates with advanced cancer stages and poor survival rate in bladder cancer, supporting a potential role as a regulator of the bladder CSC properties. SOX4 might serve as a biomarker of the aggressive phenotype, also underlying progression from NMIBC to MIBC. The amplicon in chromosome 6 contains SOX4 and E2F3 and is frequently found amplified in bladder cancer. These genes/amplicons might be a potential target for therapy. As an existing hypothesis is that chromatin deregulation through enhancers or super-enhancers might be the underlying mechanism responsible of this deregulation, a potential way to target these transcription factors could be through epigenetic modifiers.
Collapse
Affiliation(s)
- Joaquim Bellmunt
- Department of Medical Oncology, Hospital del Mar, IMIM (PSMAR-Hospital del Mar Research Institute), 08003 Barcelona, Spain.
- Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
37
|
Chi Y, Xu H, Wang F, Chen X, Shan Z, Sun Y, Fan Q. ZKSCAN3 promotes breast cancer cell proliferation, migration and invasion. Biochem Biophys Res Commun 2018; 503:2583-2589. [PMID: 30049438 DOI: 10.1016/j.bbrc.2018.07.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 01/06/2023]
Abstract
ZKSCAN3, a zinc-finger transcription factor, which has been shown to be upregulated in several human cancer. However, the expression level, function and mechanism of ZKSCAN3 in breast cancer remains unknown. In the current study, immunohistochemistry, western blot and quantitative real time polymerase chain reaction (qRT-PCR) results showed that ZKSCAN3 was overexpressed in breast cancer tissue compared with normal breast tissue. Through analyzing the clinicopathological characteristics, we demonstrated that positive ZKSCAN3 expression predicted poor prognosis of patients with breast cancer. The expression level of ZKSCAN3 protein/mRNA in breast cancer cells (MCF-7 and MDA-MB-231) was higher than its expression in normal breast cells (HBL-100). Knocking down ZKSCAN3 via its short hairpin RNA (shRNA) in MCF-7 and MDA-MB-231 inhibited cell viability, migration and invasion. Western blot analysis showed that ZKSCAN3 silencing lead to significant decreases in the expression of Cyclin D1, B-cell lymphoma-2 (Bcl-2), and matrix metalloproteinase (MMP)-2/MMP-9, as well as increases in the expression of Bcl2 Associated X Protein (Bax) in breast cancer cells. Additionally, ZKSCAN3-shRNA expression markedly suppressed tumor growth in breast cancer xenograft mice. Finally, we demonstrated that silencing of ZKSCAN3 was able to inhibit Akt/mTOR signaling pathway by blocking p-Akt and p-mTOR protein expression in breast cancer cells. These results demonstrate that ZKSCAN3 plays a significant role in the progression of breast cancer. Therefore, ZKSCAN3 is a potential therapeutic target for breast cancer.
Collapse
Affiliation(s)
- Yanyan Chi
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Han Xu
- Department of Breast Disease Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Feng Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Xiaoling Chen
- Zhejiang Provincial Key Laboratory of Medical Genetics, School of Life Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Zhengzheng Shan
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yan Sun
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Qingxia Fan
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| |
Collapse
|
38
|
Rose AM, Radia UK, Luo R, Kalirai H, Jayasena CN, Luthert P, Coupland SE, Rose GE. Multiple primary malignancies and prolonged survival in a patient with widespread metastatic cutaneous melanoma. Melanoma Res 2018; 28:163-166. [PMID: 29346178 PMCID: PMC5832011 DOI: 10.1097/cmr.0000000000000426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/08/2017] [Indexed: 11/25/2022]
Affiliation(s)
- Anna M. Rose
- UCL Institute of Ophthalmology, University College
- Department of Medicine, Imperial College
| | | | - Rong Luo
- Department of Medicine, Imperial College
| | - Helen Kalirai
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | | | | | - Sarah E. Coupland
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Geoffrey E. Rose
- UCL Institute of Ophthalmology, University College
- Orbital Service, Moorfields Eye Hospital, London
| |
Collapse
|
39
|
Maya Miles D, Peñate X, Sanmartín Olmo T, Jourquin F, Muñoz Centeno MC, Mendoza M, Simon MN, Chavez S, Geli V. High levels of histones promote whole-genome-duplications and trigger a Swe1 WEE1-dependent phosphorylation of Cdc28 CDK1. eLife 2018; 7:35337. [PMID: 29580382 PMCID: PMC5871333 DOI: 10.7554/elife.35337] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/05/2018] [Indexed: 12/13/2022] Open
Abstract
Whole-genome duplications (WGDs) have played a central role in the evolution of genomes and constitute an important source of genome instability in cancer. Here, we show in Saccharomyces cerevisiae that abnormal accumulations of histones are sufficient to induce WGDs. Our results link these WGDs to a reduced incorporation of the histone variant H2A.Z to chromatin. Moreover, we show that high levels of histones promote Swe1WEE1 stabilisation thereby triggering the phosphorylation and inhibition of Cdc28CDK1 through a mechanism different of the canonical DNA damage response. Our results link high levels of histones to a specific type of genome instability that is quite frequently observed in cancer and uncovers a new mechanism that might be able to respond to high levels of histones.
Collapse
Affiliation(s)
- Douglas Maya Miles
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Equipe Labellisée Ligue, Marseille, France
| | - Xenia Peñate
- Instituto de Biomedicina de Sevilla, Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Trinidad Sanmartín Olmo
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Frederic Jourquin
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Equipe Labellisée Ligue, Marseille, France
| | - Maria Cruz Muñoz Centeno
- Instituto de Biomedicina de Sevilla, Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Manuel Mendoza
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Marie-Noelle Simon
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Equipe Labellisée Ligue, Marseille, France
| | - Sebastian Chavez
- Instituto de Biomedicina de Sevilla, Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Vincent Geli
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Equipe Labellisée Ligue, Marseille, France
| |
Collapse
|
40
|
Wilson AJ, Stubbs M, Liu P, Ruggeri B, Khabele D. The BET inhibitor INCB054329 reduces homologous recombination efficiency and augments PARP inhibitor activity in ovarian cancer. Gynecol Oncol 2018; 149:575-584. [PMID: 29567272 DOI: 10.1016/j.ygyno.2018.03.049] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/12/2018] [Accepted: 03/14/2018] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Homologous recombination (HR)-proficient ovarian tumors have poorer clinical outcomes and show resistance to poly ADP ribose polymerase inhibitors (PARPi). A subset of HR-proficient ovarian tumors show amplification in bromodomain and extra-terminal (BET) genes such as BRD4. We aimed to test the hypothesis that BRD4 inhibition sensitizes ovarian cancer cells to PARPi by reducing HR efficiency and increasing DNA damage. METHODS HR-proficient ovarian cancer cell lines (OVCAR-3, OVCAR-4, SKOV-3, UWB1.289+BRCA1) were treated with BRD4-targeting siRNA, novel (INB054329, INCB057643) and established (JQ1) BET inhibitors (BETi) and PARPi (olaparib, rucaparib). Cell growth and viability were assessed by sulforhodamine B assays in vitro, and in SKOV-3 and ovarian cancer patient-derived xenografts in vivo. DNA damage and repair (pH2AX, RAD51 and BRCA1 foci formation, and DRGFP HR reporter activity), apoptosis markers (cleaved PARP, cleaved caspase-3, Bax) and proliferation markers (PCNA, Ki67) were assessed by immunofluorescence and western blot. RESULTS In cultured cells, inhibition of BRD4 by siRNA or INCB054329 reduced expression and function of BRCA1 and RAD51, reduced HR reporter activity, and sensitized the cells to olaparib-induced growth inhibition, DNA damage induction and apoptosis. Synergy was observed between all BETi tested and PARPi. INCB054329 and olaparib also co-operatively inhibited xenograft tumor growth, accompanied by reduced BRCA1 expression and proliferation, and increased apoptosis and DNA damage. CONCLUSIONS These results provide strong rationale for using BETi to extend therapeutic efficacy of PARPi to HR-proficient ovarian tumors and could benefit a substantial number of women diagnosed with this devastating disease.
Collapse
Affiliation(s)
- Andrew J Wilson
- Department of Obstetrics & Gynecology, Vanderbilt University Medical Center, Nashville, TN, United States; Vanderbilt-Ingram Cancer Center, Nashville, TN, United States
| | | | - Phillip Liu
- Incyte Corporation, Wilmington, DE, United States
| | | | - Dineo Khabele
- The University of Kansas Medical Center, Kansas City, KS, United States; The University of Kansas Cancer Center, Kansas City, KS, United States.
| |
Collapse
|
41
|
Ammonium tetrathiomolybdate treatment targets the copper transporter ATP7A and enhances sensitivity of breast cancer to cisplatin. Oncotarget 2018; 7:84439-84452. [PMID: 27806319 PMCID: PMC5341295 DOI: 10.18632/oncotarget.12992] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/12/2016] [Indexed: 11/25/2022] Open
Abstract
Cisplatin is an effective breast cancer drug but resistance often develops over prolonged chemotherapy. Therefore, we performed a candidate approach RNAi screen in combination with cisplatin treatment to identify molecular pathways conferring survival advantages. The screen identified ATP7A as a therapeutic target. ATP7A is a copper ATPase transporter responsible for intercellular movement and sequestering of cisplatin. Pharmaceutical replacement for ATP7A by ammonium tetrathiomolybdate (TM) enhanced cisplatin treatment in breast cancer cells. Allograft and xenograft models in athymic nude mice treated with cisplatin/TM exhibited retarded tumor growth, reduced accumulation of cancer stem cells and decreased cell proliferation as compared to mono-treatment with cisplatin or TM. Cisplatin/TM treatment of cisplatin-resistant tumors reduced ATP7A protein levels, attenuated cisplatin sequestering by ATP7A, increased nuclear availability of cisplatin, and subsequently enhanced DNA damage and apoptosis. Microarray analysis of gene ontology pathways that responded uniquely to cisplatin/TM double treatment depicted changes in cell cycle regulation, specifically in the G1/S transition. These findings offer the potential to combat platinum-resistant tumors and sensitize patients to conventional breast cancer treatment by identifying and targeting the resistant tumors' unique molecular adaptations.
Collapse
|
42
|
Costa RA, Seuánez HN. Investigation of major genetic alterations in neuroblastoma. Mol Biol Rep 2018; 45:287-295. [PMID: 29455316 DOI: 10.1007/s11033-018-4161-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 02/08/2018] [Indexed: 12/11/2022]
Abstract
Neuroblastoma (NB) is the most common extracranial solid tumor in childhood. This malignancy shows a wide spectrum of clinical outcome and its prognosis is conditioned by manifold biological and genetic factors. We investigated the tumor genetic profile and clinical data of 29 patients with NB by multiplex ligation-dependent probe amplification (MLPA) to assess therapeutic risk. In 18 of these tumors, MYCN status was assessed by fluorescence in situ hybridization (FISH). Copy number variation was also determined for confirming MLPA findings in two 6p loci. We found 2p, 7q and 17q gains, and 1p and 11q losses as the most frequent chromosome alterations in this cohort. FISH confirmed all cases of MYCN amplification detected by MLPA. In view of unexpected 6p imbalance, copy number variation of two 6p loci was assessed for validating MLPA findings. Based on clinical data and genetic profiles, patients were stratified in pretreatment risk groups according to international consensus. MLPA proved to be effective for detecting multiple genetic alterations in all chromosome regions as requested by the International Neuroblastoma Risk Group (INRG) for therapeutic stratification. Moreover, this technique proved to be cost effective, reliable, only requiring standard PCR equipment, and attractive for routine analysis. However, the observed 6p imbalances made PKHD1 and DCDC2 inadequate for control loci. This must be considered when designing commercial MLPA kits for NB. Finally, four patients showed a normal MLPA profile, suggesting that NB might have a more complex genetic pattern than the one assessed by presently available MLPA kits.
Collapse
Affiliation(s)
- Régis Afonso Costa
- Genetics Program, Instituto Nacional de Câncer, Rua André Cavalcanti 37, Rio de Janeiro, RJ, 20231-050, Brazil.,Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Héctor N Seuánez
- Genetics Program, Instituto Nacional de Câncer, Rua André Cavalcanti 37, Rio de Janeiro, RJ, 20231-050, Brazil. .,Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| |
Collapse
|
43
|
ZKSCAN3 promotes bladder cancer cell proliferation, migration, and invasion. Oncotarget 2018; 7:53599-53610. [PMID: 27447553 PMCID: PMC5288208 DOI: 10.18632/oncotarget.10679] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/09/2016] [Indexed: 11/25/2022] Open
Abstract
The expression status of ZKSCAN3, a zinc-finger transcription factor containing KRAB and SCAN domains, as well as its biological significance, in human bladder cancer remains largely unknown. In the current study, we aimed to determine the functional role of ZKSCAN3 in bladder cancer progression. Immunohistochemistry in tissue specimens detected ZKSCAN3 signals in 138 (93.2%) of 148 urothelial neoplasms, which was significantly higher than in non-neoplastic urothelial tissues [76 (84.4%) of 90; P=0.044]. Correspondingly, the levels of ZKSCAN3 gene were significantly elevated in bladder tumors, compared with those in adjacent normal-appearing bladder mucosae (P=0.008). In a validation set of tissue microarray, significantly higher ZKSCAN3 expression was observed in high-grade and/or muscle-invasive urothelial carcinomas than in low-grade and/or non-muscle-invasive tumors. Two bladder cancer cell lines, UMUC3 and 647V, were found to strongly express ZKSCAN3 protein/mRNA, whereas its expression in 5637 bladder cancer and SVHUC normal urothelium cell lines was very weak. ZKSCAN3 silencing via its short hairpin RNA (shRNA) in UMUC3 and 647V resulted in significant decreases in cell viability/colony formation, cell migration/invasion, and the expression of matrix metalloproteinase (MMP)-2/MMP-9 and oncogenes c-myc/FGFR3, as well as significant increases in apoptosis and the expression of tumor suppressor genes p53/PTEN. ZKSCAN3 overexpression in 5637 also induced cell growth and migration. In addition, ZKSCAN3-shRNA expression considerably retarded tumor formation as well as its subsequent growth in xenograft-bearing mice. These results suggest that ZKSCAN3 plays an important role in bladder cancer outgrowth. Thus, ZKSCAN3 inhibition has the potential of being a therapeutic approach for bladder cancer.
Collapse
|
44
|
Renal Cell Carcinoma With Chromosome 6p Amplification Including the TFEB Gene: A Novel Mechanism of Tumor Pathogenesis? Am J Surg Pathol 2017; 41:287-298. [PMID: 28009604 DOI: 10.1097/pas.0000000000000776] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Amplification of chromosome 6p has been implicated in aggressive behavior in several cancers, but has not been characterized in renal cell carcinoma (RCC). We identified 9 renal tumors with amplification of chromosome 6p including the TFEB gene, 3 by fluorescence in situ hybridization, and 6 from the Cancer Genome Atlas (TCGA) databases. Patients' ages were 28 to 78 years (median, 61 y). Most tumors were high stage (7/9 pT3a, 2/9 pN1). Using immunohistochemistry, 2/4 were positive for melanocytic markers and cathepsin K. Novel TFEB fusions were reported by TCGA in 2; however, due to a small composition of fusion transcripts compared with full-length transcripts (0.5/174 and 3.3/132 FPKM), we hypothesize that these represent secondary fusions due to amplification. Five specimens (4 TCGA, 1 fluorescence in situ hybridization) had concurrent chromosome 3p copy number loss or VHL deletion. However, these did not resemble clear cell RCC, had negative carbonic anhydrase IX labeling, lacked VHL mutation, and had papillary or unclassified histology (2/4 had gain of chromosome 7 or 17). One tumor each had somatic FH mutation and SMARCB1 mutation. Chromosome 6p amplification including TFEB is a previously unrecognized cytogenetic alteration in RCC, associated with heterogenous tubulopapillary eosinophilic and clear cell histology. The combined constellation of features does not fit cleanly into an existing tumor category (unclassified), most closely resembling papillary or translocation RCC. The tendency for high tumor stage, varied tubulopapillary morphology, and a subset with melanocytic marker positivity suggests the possibility of a unique tumor type, despite some variation in appearance and genetics.
Collapse
|
45
|
Smith EA, Kumar B, Komurov K, Smith SM, Brown NV, Zhao S, Kumar P, Teknos TN, Wells SI. DEK associates with tumor stage and outcome in HPV16 positive oropharyngeal squamous cell carcinoma. Oncotarget 2017; 8:23414-23426. [PMID: 28423581 PMCID: PMC5410314 DOI: 10.18632/oncotarget.15582] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 02/12/2017] [Indexed: 01/25/2023] Open
Abstract
Oropharyngeal squamous cell carcinomas (OPSCC) are common, have poor outcomes, and comprise two biologically and clinically distinct diseases. While OPSCC that arise from human papillomavirus infections (HPV+) have better overall survival than their HPV- counterparts, the incidence of HPV+ OPSCC is increasing dramatically, affecting younger individuals which are often left with life-long co-morbidities from aggressive treatment. To identify patients which do poorly versus those who might benefit from milder regimens, risk-stratifying biomarkers are now needed within this population. One potential marker is the DEK oncoprotein, whose transcriptional upregulation in most malignancies is associated with chemotherapy resistance, advanced tumor stage, and worse outcomes. Herein, a retrospective case study was performed on DEK protein expression in therapy-naïve surgical resections from 194 OPSCC patients. We found that DEK was associated with advanced tumor stage, increased hazard of death, and interleukin IL6 expression in HPV16+ disease. Surprisingly, DEK levels in HPV16- OPSCC were not associated with advanced tumor stage or increased hazard of death. Overall, these findings mark HPV16- OPSCC as an exceptional malignancy were DEK expression does not correlate with outcome, and support the potential prognostic utility of DEK to identify aggressive HPV16+ disease.
Collapse
Affiliation(s)
- Eric A. Smith
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Bhavna Kumar
- Department of Otolaryngology–Head and Neck Surgery, The Ohio State University, Columbus, OH, 43210, USA
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Kakajan Komurov
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Stephen M. Smith
- Department of Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Nicole V. Brown
- Center for Biostatistics, The Ohio State University, Columbus, OH, 43210, USA
| | - Songzhu Zhao
- Center for Biostatistics, The Ohio State University, Columbus, OH, 43210, USA
| | - Pawan Kumar
- Department of Otolaryngology–Head and Neck Surgery, The Ohio State University, Columbus, OH, 43210, USA
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Theodoros N. Teknos
- Department of Otolaryngology–Head and Neck Surgery, The Ohio State University, Columbus, OH, 43210, USA
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Susanne I. Wells
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| |
Collapse
|
46
|
Mahas A, Potluri K, Kent MN, Naik S, Markey M. Copy number variation in archival melanoma biopsies versus benign melanocytic lesions. Cancer Biomark 2017; 16:575-97. [PMID: 27002761 DOI: 10.3233/cbm-160600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Skin melanocytes can give rise to benign and malignant neoplasms. Discrimination of an early melanoma from an unusual/atypical benign nevus can represent a significant challenge. However, previous studies have shown that in contrast to benign nevi, melanoma demonstrates pervasive chromosomal aberrations. OBJECTIVE This substantial difference between melanoma and benign nevi can be exploited to discriminate between melanoma and benign nevi. METHODS Array-comparative genomic hybridization (aCGH) is an approach that can be used on DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues to assess the entire genome for the presence of changes in DNA copy number. In this study, high resolution, genome-wide single-nucleotide polymorphism (SNP) arrays were utilized to perform comprehensive and detailed analyses of recurrent copy number aberrations in 41 melanoma samples in comparison with 21 benign nevi. RESULTS We found statistically significant copy number gains and losses within melanoma samples. Some of the identified aberrations are previously implicated in melanoma. Moreover, novel regions of copy number alterations were identified, revealing new candidate genes potentially involved in melanoma pathogenesis. CONCLUSIONS Taken together, these findings can help improve melanoma diagnosis and introduce novel melanoma therapeutic targets.
Collapse
Affiliation(s)
- Ahmed Mahas
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Keerti Potluri
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Michael N Kent
- Department of Dermatology, Wright State University Boonshoft School of Medicine, Dayton, OH, USA.,Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Sameep Naik
- Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Michael Markey
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| |
Collapse
|
47
|
García-Fernández M, Karras P, Checinska A, Cañón E, Calvo GT, Gómez-López G, Cifdaloz M, Colmenar A, Espinosa-Hevia L, Olmeda D, Soengas MS. Metastatic risk and resistance to BRAF inhibitors in melanoma defined by selective allelic loss of ATG5. Autophagy 2016; 12:1776-1790. [PMID: 27464255 DOI: 10.1080/15548627.2016.1199301] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Melanoma is a paradigm of aggressive tumors with a complex and heterogeneous genetic background. Still, melanoma cells frequently retain developmental traits that trace back to lineage specification programs. In particular, lysosome-associated vesicular trafficking is emerging as a melanoma-enriched lineage dependency. However, the contribution of other lysosomal functions such as autophagy to melanoma progression is unclear, particularly in the context of metastasis and resistance to targeted therapy. Here we mined a broad spectrum of cancers for a meta-analysis of mRNA expression, copy number variation and prognostic value of 13 core autophagy genes. This strategy identified heterozygous loss of ATG5 at chromosome band 6q21 as a distinctive feature of advanced melanomas. Importantly, partial ATG5 loss predicted poor overall patient survival in a manner not shared by other autophagy factors and not recapitulated in other tumor types. This prognostic relevance of ATG5 copy number was not evident for other 6q21 neighboring genes. Melanocyte-specific mouse models confirmed that heterozygous (but not homozygous) deletion of Atg5 enhanced melanoma metastasis and compromised the response to targeted therapy (exemplified by dabrafenib, a BRAF inhibitor in clinical use). Collectively, our results support ATG5 as a therapeutically relevant dose-dependent rheostat of melanoma progression. Moreover, these data have important translational implications in drug design, as partial blockade of autophagy genes may worsen (instead of counteracting) the malignant behavior of metastatic melanomas.
Collapse
Affiliation(s)
- María García-Fernández
- a Melanoma Laboratory , Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO) , Madrid , Spain
| | - Panagiotis Karras
- a Melanoma Laboratory , Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO) , Madrid , Spain
| | - Agnieszka Checinska
- a Melanoma Laboratory , Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO) , Madrid , Spain
| | - Estela Cañón
- a Melanoma Laboratory , Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO) , Madrid , Spain
| | - Guadalupe T Calvo
- a Melanoma Laboratory , Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO) , Madrid , Spain
| | - Gonzalo Gómez-López
- b Bioinformatics Unit , Spanish National Cancer Research Centre (CNIO) , Madrid , Spain
| | - Metehan Cifdaloz
- a Melanoma Laboratory , Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO) , Madrid , Spain
| | - Angel Colmenar
- a Melanoma Laboratory , Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO) , Madrid , Spain
| | - Luis Espinosa-Hevia
- c Cytogenetics Unit , Spanish National Cancer Research Center (CNIO) , Madrid , Spain
| | - David Olmeda
- a Melanoma Laboratory , Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO) , Madrid , Spain
| | - María S Soengas
- a Melanoma Laboratory , Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO) , Madrid , Spain
| |
Collapse
|
48
|
Mohanty V, Akmamedova O, Komurov K. Selective DNA methylation in cancers controls collateral damage induced by large structural variations. Oncotarget 2016; 8:71385-71392. [PMID: 29069713 PMCID: PMC5641056 DOI: 10.18632/oncotarget.10487] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/06/2016] [Indexed: 01/10/2023] Open
Abstract
Chromosomal instability is a hallmark of human cancers, and is characterized by large structural variations in the genome. Such large structural variations are expected to create intrinsic collateral stress due to gene dosage changes in many genes that are co-deleted or co-amplified in large chromosomal segments (onco-passenger genes). We show that the tumor-toxic effects of gene dosage changes of onco-passenger genes are compensated by the uncoupling of their copy number variations from their expression by means of selective DNA methylation. For example, collateral co-amplification of genes in tumor suppressor pathways, such as the TGF-β and inflammatory signaling pathways, are compensated by DNA hypermethylation to suppress their overexpression, while collateral deletion of pro-oncogenic genes are compensated by DNA hypomethylation to promote their expression from the single remaining allele. Our work reveals an important tumorigenic mechanism of regulation of toxic gene copy number imbalance in tumor cells arising from chromosomal instability, and suggests that targeting the DNA methylation machinery may prevent compensatory regulation of onco-passenger gene expression in chromosomally unstable cancers, and re-activate dormant tumor suppressor pathways for effective therapy.
Collapse
Affiliation(s)
- Vakul Mohanty
- Systems Biology and Physiology Graduate Program, University of Cincinnati, OH, USA
| | | | - Kakajan Komurov
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, OH, USA
| |
Collapse
|
49
|
Wang X, Wang G, Shi Y, Sun L, Gorczynski R, Li YJ, Xu Z, Spaner DE. PPAR-delta promotes survival of breast cancer cells in harsh metabolic conditions. Oncogenesis 2016; 5:e232. [PMID: 27270614 PMCID: PMC4945742 DOI: 10.1038/oncsis.2016.41] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/03/2016] [Indexed: 12/27/2022] Open
Abstract
Expression of the nuclear receptor peroxisome proliferator activated receptor delta (PPARδ) in breast cancer cells is negatively associated with patient survival, but the underlying mechanisms are not clear. High PPARδ protein levels in rat breast adenocarcinomas were found to be associated with increased growth in soft agar and mice. Transgenic expression of PPARδ increased the ability of human breast cancer cell lines to migrate in vitro and form lung metastases in mice. PPARδ also conferred the ability to grow in exhausted tissue culture media and survive in low-glucose and other endoplasmic reticulum stress conditions such as hypoxia. Upregulation of PPARδ by glucocorticoids or synthetic agonists also protected human breast cancer cells from low glucose. Survival in low glucose was related to increased antioxidant defenses mediated in part by catalase and also to late AKT phosphorylation, which is associated with the prolonged glucose-deprivation response. Synthetic antagonists reversed the survival benefits conferred by PPARδ in vitro. These findings suggest that PPARδ conditions breast cancer cells to survive in harsh microenvironmental conditions by reducing oxidative stress and enhancing survival signaling responses. Drugs that target PPARδ may have a role in the treatment of breast cancer.
Collapse
Affiliation(s)
- X Wang
- Biology Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Department of Breast Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - G Wang
- Biology Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Y Shi
- Biology Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - L Sun
- Biology Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Department of Breast Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - R Gorczynski
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Transplant Research Division, Toronto General Hospital, Toronto, Ontario, Canada
| | - Y-J Li
- Biology Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Department of Anatomy, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Z Xu
- Department of Breast Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - D E Spaner
- Biology Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Sunnybrook Odette Cancer Center, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
50
|
Jiang Y, Shi X, Zhao Q, Krauthammer M, Rothberg BEG, Ma S. Integrated analysis of multidimensional omics data on cutaneous melanoma prognosis. Genomics 2016; 107:223-30. [PMID: 27141884 PMCID: PMC4893887 DOI: 10.1016/j.ygeno.2016.04.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/05/2016] [Accepted: 04/23/2016] [Indexed: 01/09/2023]
Abstract
Multiple types of genetic, epigenetic, and genomic changes have been implicated in cutaneous melanoma prognosis. Many of the existing studies are limited in analyzing a single type of omics measurement and cannot comprehensively describe the biological processes underlying prognosis. As a result, the obtained prognostic models may be less satisfactory, and the identified prognostic markers may be less informative. The recently collected TCGA (The Cancer Genome Atlas) data have a high quality and comprehensive omics measurements, making it possible to more comprehensively and more accurately model prognosis. In this study, we first describe the statistical approaches that can integrate multiple types of omics measurements with the assistance of variable selection and dimension reduction techniques. Data analysis suggests that, for cutaneous melanoma, integrating multiple types of measurements leads to prognostic models with an improved prediction performance. Informative individual markers and pathways are identified, which can provide valuable insights into melanoma prognosis.
Collapse
Affiliation(s)
- Yu Jiang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA; VA Cooperative Studies Program Coordinating Center, West Haven, CT 06516, USA
| | - Xingjie Shi
- Department of Statistics, Nanjing University of Finance and Economics, Nanjing, China
| | - Qing Zhao
- Merck Research Laboratories, 126 East Lincoln Avenue, RY34, Rahway, NJ 07065, USA
| | | | - Bonnie E Gould Rothberg
- Cancer Center, Department of Internal Medicine, Pathology, Chronic Disease Epidemiology, Yale University, New Haven, CT 06520, USA
| | - Shuangge Ma
- VA Cooperative Studies Program Coordinating Center, West Haven, CT 06516, USA; Department of Biostatistics, Yale University, New Haven, CT 06520, USA.
| |
Collapse
|