1
|
Li BZ, Yuan YJ. Enhancing whole yeast genome rearrangements through multiple LoxPsym sequences. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2617-1. [PMID: 38856790 DOI: 10.1007/s11427-024-2617-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024]
Affiliation(s)
- Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China.
| |
Collapse
|
2
|
Kumari N, Das K, Sharma S, Dahal S, Desai SS, Roy U, Sharma A, Manjunath M, Gopalakrishnan V, Retheesh ST, Javadekar SM, Choudhary B, Raghavan SC. Evaluation of potential role of R-loop and G-quadruplex DNA in the fragility of c-MYC during chromosomal translocation associated with Burkitt's lymphoma. J Biol Chem 2023; 299:105431. [PMID: 37926284 PMCID: PMC10704377 DOI: 10.1016/j.jbc.2023.105431] [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: 08/15/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023] Open
Abstract
t(8;14) translocation is the hallmark of Burkitt's lymphoma and results in c-MYC deregulation. During the translocation, c-MYC gene on chromosome 8 gets juxtaposed to the Ig switch regions on chromosome 14. Although the promoter of c-MYC has been investigated for its mechanism of fragility, little is known about other c-MYC breakpoint regions. We have analyzed the translocation break points at the exon 1/intron 1 of c-MYC locus from patients with Burkitt's lymphoma. Results showed that the breakpoint region, when present on a plasmid, could fold into an R-loop confirmation in a transcription-dependent manner. Sodium bisulfite modification assay revealed significant single-strandedness on chromosomal DNA of Burkitt's lymphoma cell line, Raji, and normal lymphocytes, revealing distinct R-loops covering up to 100 bp region. Besides, ChIP-DRIP analysis reveals that the R-loop antibody can bind to the breakpoint region. Further, we show the formation of stable parallel intramolecular G-quadruplex on non-template strand of the genome. Finally, incubation of purified AID in vitro or overexpression of AID within the cells led to enhanced mutation frequency at the c-MYC breakpoint region. Interestingly, anti-γH2AX can bind to DSBs generated at the c-MYC breakpoint region within the cells. The formation of R-loop and G-quadruplex was found to be mutually exclusive. Therefore, our results suggest that AID can bind to the single-stranded region of the R-loop and G4 DNA, leading to the deamination of cytosines to uracil and induction of DNA breaks in one of the DNA strands, leading to double-strand break, which could culminate in t(8;14) chromosomal translocation.
Collapse
Affiliation(s)
- Nitu Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Kohal Das
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Shivangi Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, India; Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Sumedha Dahal
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Urbi Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Anju Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Vidya Gopalakrishnan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India; Department of Zoology, St Joseph's College, Irinjalakuda, Kerala, India
| | - S T Retheesh
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Saniya M Javadekar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
| |
Collapse
|
3
|
Polat S, Karaburgu S, Unluhizarci K, Dundar M, Ozkul Y, Arslan YK, Karaca Z, Kelestimur F. Unexpectedly high mutation rate of cyp11b1 compared to cyp21a2 in randomly-selected turkish women: a large screening study. J Endocrinol Invest 2023; 46:2367-2377. [PMID: 37055708 DOI: 10.1007/s40618-023-02093-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/06/2023] [Indexed: 04/15/2023]
Abstract
PURPOSE Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive disorders resulting from enzyme deficiencies associated with steroidogenesis. The clinical presentation of non-classic CAH (NCAH) in females is often indistinguishable from other hyperandrogenic disorders like polycystic ovary syndrome (PCOS). The data on the prevalence of NCAH in unselected women in the literature is scanty. The research aimed to evaluate the prevalence of NCAH, carrier frequencies, and the correlation between clinical symptoms and genotype in Turkish women. METHODS The study group comprised two hundred and seventy randomly-selected unrelated asymptomatic women of reproductive age (18-45). Subjects were recruited from female blood donors. All volunteers underwent clinical examination and hormone measurements. The protein-encoding exons and exon-intron boundaries of the CYP21A2, CYP11B1, HSD3β2 and CYP21A2 promoter were sequenced by direct DNA sequencing. RESULTS After genotyping, seven (2.2%) individuals were diagnosed with NCAH. The heterozygous carrier frequencies of CYP21A2, CYP21A2 promoter, CYP11B1, and HSD3β2 genes with 34, 34, 41, and 1 pathologic mutation were determined at 12.6%, 12.6%, 15.2%, and 0.37% of volunteers, respectively. Gene-conversion (GC) frequencies between CYP21A2/CYP21A1P and CYP11B1/CYP11B2 were determined as 10.4% and 14.8%, respectively. CONCLUSION Despite GC-derived higher mutation frequency determined in the CYP11B1 gene, the reason for the low frequency of NCAH due to 11OHD compared to 21OHD might be that gene-conversion arises with active CYP11B2 rather than an inactive pseudogene. HSD3β1 exhibits high homology with HSD3β2 located on the same chromosome; remarkably, it demonstrates low heterozygosity and no GC, most probably the outcome of a tissue-specific expression pattern.
Collapse
Affiliation(s)
- S Polat
- Department of Medical Genetics, Medical Faculty, Erzincan Binali Yıldırım University, Basbaglar Mah., 24100, Erzincan, Merkez, Turkey.
| | - S Karaburgu
- Department of Endocrinology, Medical Faculty, Erciyes University, Kayseri, Turkey
| | - K Unluhizarci
- Department of Endocrinology, Medical Faculty, Erciyes University, Kayseri, Turkey
| | - M Dundar
- Department of Medical Genetics, Medical Faculty, Erciyes University, Kayseri, Turkey
| | - Y Ozkul
- Department of Medical Genetics, Medical Faculty, Erciyes University, Kayseri, Turkey
| | - Y K Arslan
- Department of Biostatistics, Medical Faculty, Çukurova University, Adana, Turkey
| | - Z Karaca
- Department of Endocrinology, Medical Faculty, Erciyes University, Kayseri, Turkey
| | - F Kelestimur
- Department of Endocrinology, Medical Faculty, Erciyes University, Kayseri, Turkey
- Department of Endocrinology, Medical Faculty, Yeditepe University, Istanbul, Turkey
| |
Collapse
|
4
|
Zhao Z, Shang P, Mohanraju P, Geijsen N. Prime editing: advances and therapeutic applications. Trends Biotechnol 2023; 41:1000-1012. [PMID: 37002157 DOI: 10.1016/j.tibtech.2023.03.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/24/2023] [Accepted: 03/03/2023] [Indexed: 04/01/2023]
Abstract
Clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR-Cas)-mediated genome editing has revolutionized biomedical research and will likely change the therapeutic and diagnostic landscape. However, CRISPR-Cas9, which edits DNA by activating DNA double-strand break (DSB) repair pathways, is not always sufficient for gene therapy applications where precise mutation repair is required. Prime editing, the latest revolution in genome-editing technologies, can achieve any possible base substitution, insertion, or deletion without the requirement for DSBs. However, prime editing is still in its infancy, and further development is needed to improve editing efficiency and delivery strategies for therapeutic applications. We summarize latest developments in the optimization of prime editor (PE) variants with improved editing efficiency and precision. Moreover, we highlight some potential therapeutic applications.
Collapse
Affiliation(s)
- Zhihan Zhao
- Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, The Netherlands
| | - Peng Shang
- Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, The Netherlands
| | - Prarthana Mohanraju
- Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, The Netherlands.
| | - Niels Geijsen
- Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, The Netherlands.
| |
Collapse
|
5
|
Chen XZ, Guo R, Zhao C, Xu J, Song H, Yu H, Pilarsky C, Nainu F, Li JQ, Zhou XK, Zhang JY. A Novel Anti-Cancer Therapy: CRISPR/Cas9 Gene Editing. Front Pharmacol 2022; 13:939090. [PMID: 35935840 PMCID: PMC9353945 DOI: 10.3389/fphar.2022.939090] [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: 05/08/2022] [Accepted: 06/14/2022] [Indexed: 11/27/2022] Open
Abstract
Cancer becomes one of the main causes of human deaths in the world due to the high incidence and mortality rate and produces serious economic burdens. With more and more attention is paid on cancer, its therapies are getting more of a concern. Previous research has shown that the occurrence, progression, and treatment prognosis of malignant tumors are closely related to genetic and gene mutation. CRISPR/Cas9 has emerged as a powerful method for making changes to the genome, which has extensively been applied in various cell lines. Establishing the cell and animal models by CRISPR/Cas9 laid the foundation for the clinical trials which possibly treated the tumor. CRISPR-Cas9-mediated genome editing technology brings a great promise for inhibiting migration, invasion, and even treatment of tumor. However, the potential off-target effect limits its clinical application, and the effective ethical review is necessary. The article reviews the molecular mechanisms of CRISPR/Cas9 and discusses the research and the limitation related to cancer clinical trials.
Collapse
Affiliation(s)
- Xin-Zhu Chen
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
- The First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Rong Guo
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Cong Zhao
- Department of Cellular and Molecular Biology, Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Beijing, China
| | - Jing Xu
- Department of Biochemistry and Molecular Biology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Hang Song
- Department of Biochemistry and Molecular Biology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Hua Yu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Christian Pilarsky
- Department of Surgery, University Hospital of Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg (FAU), Erlangen, Germany
| | - Firzan Nainu
- Faculty of Pharmacy, Hasanuddin University, Makassar, Indonesia
| | - Jing-Quan Li
- The First Affiliated Hospital, Hainan Medical University, Haikou, China
- *Correspondence: Jing-Quan Li, ; Xin-Ke Zhou, ; Jian-Ye Zhang,
| | - Xin-Ke Zhou
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Jing-Quan Li, ; Xin-Ke Zhou, ; Jian-Ye Zhang,
| | - Jian-Ye Zhang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Jing-Quan Li, ; Xin-Ke Zhou, ; Jian-Ye Zhang,
| |
Collapse
|
6
|
Li Z, Sun Q, Shi Y. Somatic structural variations in pediatric brain tumors. Minerva Pediatr (Torino) 2022; 74:358-364. [DOI: 10.23736/s2724-5276.17.04830-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
7
|
Li Q, Lindtke D, Rodríguez-Ramírez C, Kakioka R, Takahashi H, Toyoda A, Kitano J, Ehrlich RL, Chang Mell J, Yeaman S. Local Adaptation and the Evolution of Genome Architecture in Threespine Stickleback. Genome Biol Evol 2022; 14:6589818. [PMID: 35594844 PMCID: PMC9178229 DOI: 10.1093/gbe/evac075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 12/11/2022] Open
Abstract
Theory predicts that local adaptation should favor the evolution of a concentrated genetic architecture, where the alleles driving adaptive divergence are tightly clustered on chromosomes. Adaptation to marine versus freshwater environments in threespine stickleback has resulted in an architecture that seems consistent with this prediction: divergence among populations is mainly driven by a few genomic regions harboring multiple quantitative trait loci for environmentally adapted traits, as well as candidate genes with well-established phenotypic effects. One theory for the evolution of these "genomic islands" is that rearrangements remodel the genome to bring causal loci into tight proximity, but this has not been studied explicitly. We tested this theory using synteny analysis to identify micro- and macro-rearrangements in the stickleback genome and assess their potential involvement in the evolution of genomic islands. To identify rearrangements, we conducted a de novo assembly of the closely related tubesnout (Aulorhyncus flavidus) genome and compared this to the genomes of threespine stickleback and two other closely related species. We found that small rearrangements, within-chromosome duplications, and lineage-specific genes (LSGs) were enriched around genomic islands, and that all three chromosomes harboring large genomic islands have experienced macro-rearrangements. We also found that duplicates and micro-rearrangements are 9.9× and 2.9× more likely to involve genes differentially expressed between marine and freshwater genotypes. While not conclusive, these results are consistent with the explanation that strong divergent selection on candidate genes drove the recruitment of rearrangements to yield clusters of locally adaptive loci.
Collapse
Affiliation(s)
- Qiushi Li
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Canada T2N 1N4
| | - Dorothea Lindtke
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Canada T2N 1N4
| | - Carlos Rodríguez-Ramírez
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Nakagami-gun, Okinawa 903-0213, Japan
| | - Hiroshi Takahashi
- National Fisheries University, 2-7-1 Nagata-honmachi, Shimonoseki, Yamaguchi 759-6595, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Rachel L Ehrlich
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia 19102, PA, USA
| | - Joshua Chang Mell
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia 19102, PA, USA
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Canada T2N 1N4
| |
Collapse
|
8
|
Li X, Baek G, Carreira S, Yuan W, Ma S, Hofstad M, Lee S, Gao Y, Bertan C, Fenor de la Maza MDLD, Alluri PG, Burma S, Chen BP, Raj GV, de Bono J, Pommier Y, Mani RS. Targeting radioresistance and replication fork stability in prostate cancer. JCI Insight 2022; 7:152955. [PMID: 35349486 PMCID: PMC9090241 DOI: 10.1172/jci.insight.152955] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
The bromodomain and extraterminal (BET) family of chromatin reader proteins bind to acetylated histones and regulate gene expression. The development of BET inhibitors (BETi) has expanded our knowledge of BET protein function beyond transcriptional regulation and has ushered several prostate cancer (PCa) clinical trials. However, BETi as a single agent is not associated with antitumor activity in patients with castration-resistant prostate cancer (CRPC). We hypothesized novel combinatorial strategies are likely to enhance the efficacy of BETi. By using PCa patient-derived explants and xenograft models, we show that BETi treatment enhanced the efficacy of radiation therapy (RT) and overcame radioresistance. Mechanistically, BETi potentiated the activity of RT by blocking DNA repair. We also report a synergistic relationship between BETi and topoisomerase I (TOP1) inhibitors (TOP1i). We show that the BETi OTX015 synergized with the new class of synthetic noncamptothecin TOP1i, LMP400 (indotecan), to block tumor growth in aggressive CRPC xenograft models. Mechanistically, BETi potentiated the antitumor activity of TOP1i by disrupting replication fork stability. Longitudinal analysis of patient tumors indicated that TOP1 transcript abundance increased as patients progressed from hormone-sensitive prostate cancer to CRPC. TOP1 was highly expressed in metastatic CRPC, and its expression correlated with the expression of BET family genes. These studies open new avenues for the rational combinatorial treatment of aggressive PCa.
Collapse
Affiliation(s)
- Xiangyi Li
- Department of Pathology, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - GuemHee Baek
- Department of Pathology, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Suzanne Carreira
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, The Institute of Cancer Research and The Royal Marsden National Health Service (NHS) Foundation Trust, Sutton, United Kingdom
| | - Wei Yuan
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, The Institute of Cancer Research and The Royal Marsden National Health Service (NHS) Foundation Trust, Sutton, United Kingdom
| | | | | | - Sora Lee
- Department of Pathology, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Yunpeng Gao
- Department of Pathology, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Claudia Bertan
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, The Institute of Cancer Research and The Royal Marsden National Health Service (NHS) Foundation Trust, Sutton, United Kingdom
| | - Maria de los Dolores Fenor de la Maza
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, The Institute of Cancer Research and The Royal Marsden National Health Service (NHS) Foundation Trust, Sutton, United Kingdom
| | - Prasanna G. Alluri
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology and Department of Neurosurgery, UT Health Science Center, San Antonio, Texas, USA
| | - Benjamin P.C. Chen
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas, USA
| | | | - Johann de Bono
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, The Institute of Cancer Research and The Royal Marsden National Health Service (NHS) Foundation Trust, Sutton, United Kingdom
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Ram S. Mani
- Department of Pathology, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
- Department of Urology and
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
9
|
Shohat S, Vol E, Shifman S. Gene essentiality in cancer cell lines is modified by the sex chromosomes. Genome Res 2022; 32:1993-2002. [PMID: 36418059 PMCID: PMC9808629 DOI: 10.1101/gr.276488.121] [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: 12/14/2021] [Accepted: 11/16/2022] [Indexed: 11/27/2022]
Abstract
Human sex differences arise from gonadal hormones and sex chromosomes. Studying the direct effects of sex chromosomes in humans is still challenging. Here we studied how the sex chromosomes can modulate gene expression and the outcome of mutations across the genome by exploiting the tendency of cancer cell lines to lose or gain sex chromosomes. We inferred the dosage of the sex chromosomes in 355 female and 408 male cancer cell lines and used it to dissect the contributions of the Y and X Chromosomes to sex-biased gene expression. Furthermore, based on genome-wide CRISPR screens, we identified genes whose essentiality is different between male and female cells depending on the sex chromosomes. The most significant genes were X-linked genes compensated by Y-linked paralogs. Our sex-based analysis identifies genes that, when mutated, can affect male and female cells differently and reinforces the roles of the X and Y Chromosomes in sex-specific cell function.
Collapse
|
10
|
Mechanisms Underlying the Suppression of Chromosome Rearrangements by Ataxia-Telangiectasia Mutated. Genes (Basel) 2021; 12:genes12081232. [PMID: 34440406 PMCID: PMC8392746 DOI: 10.3390/genes12081232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 02/07/2023] Open
Abstract
Chromosome rearrangements are structural variations in chromosomes, such as inversions and translocations. Chromosome rearrangements have been implicated in a variety of human diseases. Ataxia-telangiectasia (A-T) is an autosomal recessive disorder characterized by a broad range of clinical and cellular phenotypes. At the cellular level, one of the most prominent features of A-T cells is chromosome rearrangement, especially that in T lymphocytes. The gene that is defective in A-T is ataxia-telangiectasia mutated (ATM). The ATM protein is a serine/threonine kinase and plays a central role in the cellular response to DNA damage, particularly DNA double-strand breaks. In this review, the mechanisms by which ATM suppresses chromosome rearrangements are discussed.
Collapse
|
11
|
He F, Song K, Guan G, Huo J, Xin Y, Li T, Liu C, Zhu Q, Fan N, Guo Y, Wu L. The Phenomenon of Gene Rearrangement is Frequently Associated with TP53 Mutations and Poor Disease-Free Survival in Hepatocellular Carcinoma. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:723-736. [PMID: 34188519 PMCID: PMC8233541 DOI: 10.2147/pgpm.s313848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/03/2021] [Indexed: 01/05/2023]
Abstract
Purpose Gene rearrangements (GRs) have been reported to be related to adverse prognosis in some tumours, but the relationship in hepatocellular carcinoma (HCC) remains less studied. The objective of our study was to explore the clinicopathological characteristics and prognosis of HCC patients (HCCs) with GRs (GR-HCCs). Patients and Methods This retrospective study included 297 HCCs who underwent hepatectomy and had their tumours sequenced by next-generation sequencing. Categorical variables between groups were compared by the chi-square test. The impact of variables on disease-free survival (DFS) and survival after relapse (SAR) was analysed by the Kaplan–Meier method and Cox regression. Results We observed four repetitive GR events in 297 HCCs: BRD9/TERT, ARID2/intergenic, CDKN2A/intergenic and OBSCN truncation. GR-HCCs frequently presented with low tumour differentiation, tumour necrosis, microvascular invasion, elevated AFP and gene mutations (TP53, NTRK3 and BRD9). The 1-, 2-, and 3-year cumulative DFS rates in GR-HCCs were 45.1%, 31.9%, 31.9%, respectively, which were significantly lower than those of GR-negative HCCs (NGR-HCCs) (72.5%, 57.9%, and 49.0%, respectively; P = 0.001). GR was identified as an independent risk factor for inferior DFS in HCCs (HR = 1.980, 95% CI = 1.246–3.147; P = 0.004). However, there was no significant difference in SAR between GR-HCCs and NGR-HCCs receiving targeted therapy or immunotherapy. Conclusion GR is frequently associated with TP53 mutations and significantly affects DFS following radical resection for HCC. We recommend that GR-HCCs should be closely followed up as a high-risk group for postoperative recurrence.
Collapse
Affiliation(s)
- Fu He
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China.,Department of Clinical Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Kangjian Song
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China.,Department of Clinical Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Ge Guan
- Organ Transplant Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Junyu Huo
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China.,Department of Clinical Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Yang Xin
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Tianxiang Li
- Organ Transplant Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Chao Liu
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Qingwei Zhu
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China.,Department of Clinical Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Ning Fan
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Yuan Guo
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Liqun Wu
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| |
Collapse
|
12
|
Karpinets TV, Mitani Y, Liu B, Zhang J, Pytynia KB, Sellen LD, Karagiannis DT, Ferrarotto R, Futreal AP, El-Naggar AK. Whole-Genome Sequencing of Common Salivary Gland Carcinomas: Subtype-Restricted and Shared Genetic Alterations. Clin Cancer Res 2021; 27:3960-3969. [PMID: 34011559 DOI: 10.1158/1078-0432.ccr-20-4071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/27/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Salivary gland carcinomas (SGCs) are pathologically classified into several widely diverse subtypes, of which adenoid cystic carcinoma (ACC), mucoepidermoid carcinoma (MEC), and salivary duct carcinoma (SDC) are the most commonly encountered. A comparative genetic analysis of these subtypes provides detailed information on the genetic alterations that are associated with their tumorigenesis and may lead to the identification of biomarkers to guide tumor-specific clinical trials. EXPERIMENTAL DESIGN Whole-genome sequencing of 58 common SGCs (20 ACCs, 20 SDCs, and 18 MECs) was performed to catalog structural variations, copy number, rearrangements, and driver mutations. Data were bioinformatically analyzed and correlated with clinicopathologic parameters, and selected targets were validated. RESULTS Novel and recurrent type-specific and shared genetic alterations were identified within and among 3 subtypes. Mutually exclusive canonical fusion and nonfusion genomic alterations were identified in both ACC and MEC. In ACCs, loss of chromosome 12q was dominant in MYB or MYBL1 fusion-positive tumors and mutations of NOTCH pathway were more common in these fusion negatives. In MECs, CRTC1-MAML2 fusion-positive tumors showed frequent BAP1 mutation, and tumors lacking this fusion were enriched with LRFN1 mutation. SDCs displayed considerable genetic instability, lacked recurrent chromosomal rearrangements, and demonstrated nonoverlapping TP53 mutation and ERBB2 amplification in a subset of tumors. Limited genetic alterations, including focal amplifications of 8q21-q23, were shared by all subtypes and were associated with poor survival. CONCLUSIONS This study delineates type-specific and shared genetic alterations that are associated with early phenotypic commitment and the biologic progression of common SGCs. These alterations, upon validation, could serve as biomarkers in tumor-specific clinical trials.
Collapse
Affiliation(s)
- Tatiana V Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yoshitsugu Mitani
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kristen B Pytynia
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Linton D Sellen
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Danice T Karagiannis
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Renata Ferrarotto
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Andrew P Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Adel K El-Naggar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| |
Collapse
|
13
|
Yip HYK, Papa A. Signaling Pathways in Cancer: Therapeutic Targets, Combinatorial Treatments, and New Developments. Cells 2021; 10:659. [PMID: 33809714 PMCID: PMC8002322 DOI: 10.3390/cells10030659] [Citation(s) in RCA: 203] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 12/13/2022] Open
Abstract
Molecular alterations in cancer genes and associated signaling pathways are used to inform new treatments for precision medicine in cancer. Small molecule inhibitors and monoclonal antibodies directed at relevant cancer-related proteins have been instrumental in delivering successful treatments of some blood malignancies (e.g., imatinib with chronic myelogenous leukemia (CML)) and solid tumors (e.g., tamoxifen with ER positive breast cancer and trastuzumab for HER2-positive breast cancer). However, inherent limitations such as drug toxicity, as well as acquisition of de novo or acquired mechanisms of resistance, still cause treatment failure. Here we provide an up-to-date review of the successes and limitations of current targeted therapies for cancer treatment and highlight how recent technological advances have provided a new level of understanding of the molecular complexity underpinning resistance to cancer therapies. We also raise three basic questions concerning cancer drug discovery based on molecular markers and alterations of selected signaling pathways, and further discuss how combination therapies may become the preferable approach over monotherapy for cancer treatments. Finally, we consider novel therapeutic developments that may complement drug delivery and significantly improve clinical response and outcomes of cancer patients.
Collapse
Affiliation(s)
| | - Antonella Papa
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia;
| |
Collapse
|
14
|
Kumari N, Raghavan SC. G-quadruplex DNA structures and their relevance in radioprotection. Biochim Biophys Acta Gen Subj 2021; 1865:129857. [PMID: 33508382 DOI: 10.1016/j.bbagen.2021.129857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND DNA, the genetic material of most of the organisms, is the crucial element of life. Integrity of DNA needs to be maintained for transmission of genetic material from one generation to another. All organisms are constantly challenged by the environmental conditions which can lead to the induction of DNA damage. Ionizing radiation (IR) has been known to induce DNA damage and IR sensitivity varies among different organisms. The causes for differential radiosensitivity among various organisms have not been studied in great detail. SCOPE OF REVIEW We discuss DNA secondary structure formation, GC content of the genome, role of G-quadruplex formation, and its relationship with radiosensitivity of the genome. MAJOR CONCLUSION In Deinococcus radiodurans, the bacterium that exhibits maximum radio resistance, multiple G-quadruplex forming motifs are reported. In human cells, G-quadruplex formation led to differential radiosensitivity. In this article, we have discussed, the role of secondary DNA structure formation like G-quadruplex in shielding the genome from radiation and its implications in understanding evolution of radio protective effect of an organism. We also discuss role of GC content and its correlation with radio resistance. GENERAL SIGNIFICANCE This review provides an insight into the role of G-quadruplexes in providing differential radiosensitivity at different site of the genome and in different organisms. It further discusses the possibility of higher GC content contributing towards reduced radiosensitivity in different organisms, evolution of radiosensitivity, and regulation of multiple cellular processes.
Collapse
Affiliation(s)
- Nitu Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
15
|
Karageorgiou C, Tarrío R, Rodríguez-Trelles F. The Cyclically Seasonal Drosophila subobscura Inversion O 7 Originated From Fragile Genomic Sites and Relocated Immunity and Metabolic Genes. Front Genet 2020; 11:565836. [PMID: 33193649 PMCID: PMC7584159 DOI: 10.3389/fgene.2020.565836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/09/2020] [Indexed: 11/28/2022] Open
Abstract
Chromosome inversions are important contributors to standing genetic variation in Drosophila subobscura. Presently, the species is experiencing a rapid replacement of high-latitude by low-latitude inversions associated with global warming. Yet not all low-latitude inversions are correlated with the ongoing warming trend. This is particularly unexpected in the case of O7 because it shows a regular seasonal cycle that peaks in summer and rose with a heatwave. The inconsistent behavior of O7 across components of the ambient temperature suggests that is causally more complex than simply due to temperature alone. In order to understand the dynamics of O7, high-quality genomic data are needed to determine both the breakpoints and the genetic content. To fill this gap, here we generated a PacBio long read-based chromosome-scale genome assembly, from a highly homozygous line made isogenic for an O3 + 4 + 7 chromosome. Then we isolated the complete continuous sequence of O7 by conserved synteny analysis with the available reference genome. Main findings include the following: (i) the assembled O7 inversion stretches 9.936 Mb, containing > 1,000 annotated genes; (ii) O7 had a complex origin, involving multiple breaks associated with non-B DNA-forming motifs, formation of a microinversion, and ectopic repair in trans with the two homologous chromosomes; (iii) the O7 breakpoints carry a pre-inversion record of fragility, including a sequence insertion, and transposition with later inverted duplication of an Attacin immunity gene; and (iv) the O7 inversion relocated the major insulin signaling forkhead box subgroup O (foxo) gene in tight linkage with its antagonistic regulatory partner serine/threonine-protein kinase B (Akt1) and disrupted concerted evolution of the two inverted Attacin duplicates, reattaching them to dFOXO metabolic enhancers. Our findings suggest that O7 exerts antagonistic pleiotropic effects on reproduction and immunity, setting a framework to understand its relationship with climate change. Furthermore, they are relevant for fragility in genome rearrangement evolution and for current views on the contribution of breakage versus repair in shaping inversion-breakpoint junctions.
Collapse
Affiliation(s)
- Charikleia Karageorgiou
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Barcelona, Spain
| | - Rosa Tarrío
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Barcelona, Spain
| | - Francisco Rodríguez-Trelles
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Barcelona, Spain
| |
Collapse
|
16
|
Anzalone AV, Koblan LW, Liu DR. Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors. Nat Biotechnol 2020; 38:824-844. [PMID: 32572269 DOI: 10.1038/s41587-020-0561-9] [Citation(s) in RCA: 1094] [Impact Index Per Article: 273.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022]
Abstract
The development of new CRISPR-Cas genome editing tools continues to drive major advances in the life sciences. Four classes of CRISPR-Cas-derived genome editing agents-nucleases, base editors, transposases/recombinases and prime editors-are currently available for modifying genomes in experimental systems. Some of these agents have also moved rapidly into the clinic. Each tool comes with its own capabilities and limitations, and major efforts have broadened their editing capabilities, expanded their targeting scope and improved editing specificity. We analyze key considerations when choosing genome editing agents and identify opportunities for future improvements and applications in basic research and therapeutics.
Collapse
Affiliation(s)
- Andrew V Anzalone
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Luke W Koblan
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
17
|
Felipe C, Shin J, Loginova Y, Kolomeisky AB. The effect of obstacles in multi-site protein target search with DNA looping. J Chem Phys 2020; 152:025101. [PMID: 31941320 DOI: 10.1063/1.5135917] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Many fundamental biological processes are regulated by protein-DNA complexes called synaptosomes, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation are not well understood. Because of the multisite nature of participating proteins, it is widely believed that their search for specific sites on DNA involves the formation and breaking of DNA loops and sliding in the looped configurations. In reality, DNA in live cells is densely covered by other biological molecules that might interfere with the formation of synaptosomes. In this work, we developed a theoretical approach to evaluate the role of obstacles in the target search of multisite proteins when the formation of DNA loops and the sliding in looped configurations are possible. Our theoretical method is based on analysis of a discrete-state stochastic model that uses a master equations approach and extensive computer simulations. It is found that the obstacle slows down the search dynamics in the system when DNA loops are long-lived, but the effect is minimal for short-lived DNA loops. In addition, the relative positions of the target and the obstacle strongly influence the target search kinetics. Furthermore, the presence of the obstacle might increase the noise in the system. These observations are discussed using physical-chemical arguments. Our theoretical approach clarifies the molecular mechanisms of formation of protein-DNA complexes with multiple interactions sites.
Collapse
Affiliation(s)
- Cayke Felipe
- Department of Physics, Rice University, Houston, Texas 77005, USA
| | - Jaeoh Shin
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
| | - Yulia Loginova
- Department of Chemistry, Moscow State University, Moscow, Russia
| | | |
Collapse
|
18
|
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 2020; 578:102-111. [PMID: 32025015 PMCID: PMC7054214 DOI: 10.1038/s41586-020-1965-x] [Citation(s) in RCA: 346] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 12/02/2019] [Indexed: 01/28/2023]
Abstract
The discovery of drivers of cancer has traditionally focused on protein-coding genes1-4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5' region of TP53, in the 3' untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.
Collapse
Affiliation(s)
- Esther Rheinbay
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Morten Muhlig Nielsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | | | - Jeremiah A Wala
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA
| | - Ofer Shapira
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Grace Tiao
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Henrik Hornshøj
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Julian M Hess
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Randi Istrup Juul
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Ziao Lin
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard University, Cambridge, MA, USA
| | - Lars Feuerbach
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Radhakrishnan Sabarinathan
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Tobias Madsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Jaegil Kim
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Loris Mularoni
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Shimin Shuai
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Andrés Lanzós
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Department of Medical Oncology, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Carl Herrmann
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bioquant Center, Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Yosef E Maruvka
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Ciyue Shen
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- cBio Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Samirkumar B Amin
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Pratiti Bandopadhayay
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Johanna Bertl
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Keith A Boroevich
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - John Busanovich
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joana Carlevaro-Fita
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Department of Medical Oncology, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Dimple Chakravarty
- Department of Genitourinary Medical Oncology - Research, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Urology, Icahn school of Medicine at Mount Sinai, New York, NY, USA
| | - Calvin Wing Yiu Chan
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - David Craft
- Department of Radiation Oncology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Priyanka Dhingra
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Klev Diamanti
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Nuno A Fonseca
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Qianyun Guo
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Mark P Hamilton
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nicholas J Haradhvala
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Chen Hong
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Keren Isaev
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Todd A Johnson
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Malene Juul
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Andre Kahles
- Division of Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Abdullah Kahraman
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Youngwook Kim
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jan Komorowski
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland
| | - Kiran Kumar
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sushant Kumar
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Donghoon Lee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Kjong-Van Lehmann
- Division of Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yilong Li
- SBGD Inc, Cambridge, MA, USA
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Eric Minwei Liu
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Lucas Lochovsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Keunchil Park
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Oriol Pich
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nicola D Roberts
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Gordon Saksena
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven E Schumacher
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nikos Sidiropoulos
- Biotech Research & Innovation Centre (BRIC), The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lina Sieverling
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | | | - Chip Stewart
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Tamborero
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jose M C Tubio
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- The Biomedical Research Centre (CINBIO), Universidade de Vigo, Vigo, Spain
| | - Husen M Umer
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Liis Uusküla-Reimand
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, Ontario, Canada
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Lina Wadi
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Cheng-Zhong Zhang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jing Zhang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA
| | - Asger Hobolth
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Marcin Imielinski
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, and Englander Institute for Precision Medicine, and Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Manolis Kellis
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Michael S Lawrence
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Chris Sander
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- cBio Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Lincoln D Stein
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Joshua M Stuart
- Center for Biomolecular Science and Engineering, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Tatsuhiko Tsunoda
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Laboratory for Medical Science Mathematics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Rory Johnson
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Medical Oncology, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jüri Reimand
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Ekta Khurana
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Joachim Weischenfeldt
- Biotech Research & Innovation Centre (BRIC), The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| | - Rameen Beroukhim
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | | | - Jakob Skou Pedersen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark.
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark.
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
| |
Collapse
|
19
|
G-quadruplex Structures Contribute to Differential Radiosensitivity of the Human Genome. iScience 2019; 21:288-307. [PMID: 31678912 PMCID: PMC6838516 DOI: 10.1016/j.isci.2019.10.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 06/12/2019] [Accepted: 10/16/2019] [Indexed: 02/04/2023] Open
Abstract
DNA, the fundamental unit of human cell, generally exists in Watson-Crick base-paired B-DNA form. Often, DNA folds into non-B forms, such as four-stranded G-quadruplexes. It is generally believed that ionizing radiation (IR) induces DNA strand-breaks in a random manner. Here, we show that regions of DNA enriched in G-quadruplex structures are less sensitive to IR compared with B-DNA in vitro and inside cells. Planar G-quartet of G4-DNA is shielded from IR-induced free radicals, unlike single- and double-stranded DNA. Whole-genome sequence analysis and real-time PCR reveal that genomic regions abundant in G4-DNA are protected from radiation-induced breaks and can be modulated by G4 stabilizers. Thus, our results reveal that formation of G4 structures contribute toward differential radiosensitivity of the human genome. G4 DNA contributes to genome-wide radioprotection and is modulated by G4 resolvases Radiation causes minimal damage at the G4 structures at telomeres Formation of G4 DNA contributes toward differential radiosensitivity of human genome Planar quartet of G4 DNA is shielded from IR-induced free radicals and thus DNA breaks
Collapse
|
20
|
Shin J, Kolomeisky AB. Facilitation of DNA loop formation by protein-DNA non-specific interactions. SOFT MATTER 2019; 15:5255-5263. [PMID: 31204761 DOI: 10.1039/c9sm00671k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these systems remain not well understood. Existing theoretical studies focus only on specific interactions between protein and DNA molecules at target sequences. However, the electrostatic origin of primary protein-DNA interactions suggests that interactions of proteins with all DNA segments should be considered. Here we theoretically investigate the role of non-specific interactions between protein and DNA molecules on the dynamics of loop formation. Our approach is based on analyzing a discrete-state stochastic model via a method of first-passage probabilities supplemented by Monte Carlo computer simulations. It is found that depending on a protein sliding length during the non-specific binding event three different dynamic regimes of the DNA loop formation might be observed. In addition, the loop formation time might be optimized by varying the protein sliding length, the size of the DNA molecule, and the position of the specific target sequences on DNA. Our results demonstrate the importance of non-specific protein-DNA interactions in the dynamics of DNA loop formations.
Collapse
Affiliation(s)
- Jaeoh Shin
- Department of Chemistry, Rice University, Houston, Texas 77005, USA.
| | - Anatoly B Kolomeisky
- Department of Chemistry, Rice University, Houston, Texas 77005, USA. and Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| |
Collapse
|
21
|
Mechanisms of Genomic Instability in Breast Cancer. Trends Mol Med 2019; 25:595-611. [DOI: 10.1016/j.molmed.2019.04.004] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/29/2019] [Accepted: 04/04/2019] [Indexed: 12/22/2022]
|
22
|
Abstract
Among the various genes that can be rearranged in soft tissue neoplasms associated with nonrandom chromosomal translocations, EWSR1 is the most frequent one to partner with other genes to generate recurrent fusion genes. This leads to a spectrum of clinically and pathologically diverse mesenchymal and nonmesenchymal neoplasms, variably manifesting as small round cell, spindle cell, clear cell or adipocytic tumors, or tumors with distinctive myxoid stroma. This review summarizes the growing list of mesenchymal neoplasms that are associated with EWSR1 gene rearrangements.
Collapse
Affiliation(s)
- Khin Thway
- Sarcoma Unit, Royal Marsden Hospital, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK.
| | - Cyril Fisher
- Department of Musculoskeletal Pathology, Royal Orthopaedic Hospital NHS Foundation Trust, Robert Aitken Institute for Clinical Research, University of Birmingham, Birmingham B15 2TT, UK
| |
Collapse
|
23
|
Nguyen KV. Potential epigenomic co-management in rare diseases and epigenetic therapy. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:752-780. [PMID: 31079569 DOI: 10.1080/15257770.2019.1594893] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The purpose of this review is to highlight the impact of the alternative splicing process on human disease. Epigenetic regulation determines not only what parts of the genome are expressed but also how they are spliced. The recent progress in the field of epigenetics has important implications for the study of rare diseases. The role of epigenetics in rare diseases is a key issue in molecular physiology and medicine because not only rare diseases can benefit from epigenetic research, but can also provide useful principles for other common and complex disorders such as cancer, cardiovascular, type 2 diabetes, obesity, and neurological diseases. Predominantly, epigenetic modifications include DNA methylation, histone modification, and RNA-associated silencing. These modifications in the genome regulate numerous cellular activities. Disruption of epigenetic regulation process can contribute to the etiology of numerous diseases during both prenatal and postnatal life. Here, I discuss current knowledge about this matter including some current epigenetic therapies and future directions in the field by emphasizing on the RNA-based therapy via antisense oligonucleotides to correct splicing defects.
Collapse
Affiliation(s)
- Khue Vu Nguyen
- a Department of Medicine, Biochemical Genetics and Metabolism, The Mitochondrial and Metabolic Disease Center, School of Medicine, University of California, San Diego , San Diego , CA , USA.,b Department of Pediatrics, UC San Diego School of Medicine , La Jolla , CA , USA
| |
Collapse
|
24
|
Oncogenic Effect of the Novel Fusion Gene VAPA-Rab31 in Lung Adenocarcinoma. Int J Mol Sci 2019; 20:ijms20092309. [PMID: 31083279 PMCID: PMC6539523 DOI: 10.3390/ijms20092309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 12/24/2022] Open
Abstract
Fusion genes have been identified as oncogenes in several solid tumors including lung, colorectal, and stomach cancers. Here, we characterized the fusion gene, VAPA-Rab31, discovered from RNA-sequencing data of a patient with lung adenocarcinoma who did not harbor activating mutations in EGFR, KRAS and ALK. This fusion gene encodes a protein comprising the N-terminal region of vesicle-associated membrane protein (VAMP)-associated protein A (VAPA) fused to the C-terminal region of Ras-related protein 31 (Rab31). Exogenous expression of VAPA-Rab31 in immortalized normal bronchial epithelial cells demonstrated the potential transforming effects of this fusion gene, including increased colony formation and cell proliferation in vitro. Also, enhanced tumorigenicity upon VAPA-Rab31 was confirmed in vivo using a mouse xenograft model. Metastatic tumors were also detected in the liver and lungs of xenografted mice. Overexpression of VAPA-Rab31 upregulated anti-apoptotic protein Bcl-2 and phosphorylated CREB both in cells and xenograft tumors. Reduced apoptosis and increased phosphorylation of CREB and Erk were observed in VAPA-Rab31-overexpressing cells after bortezomib treatment. Elevated Bcl-2 level via activated CREB contributed to the resistance to the bortezomib-induced apoptosis. Our data suggest the oncogenic function of the novel fusion gene VAPA-Rab31 via upregulated Bcl-2 and activated CREB in lung cancer.
Collapse
|
25
|
Tuna M, Amos CI, Mills GB. Molecular mechanisms and pathobiology of oncogenic fusion transcripts in epithelial tumors. Oncotarget 2019; 10:2095-2111. [PMID: 31007851 PMCID: PMC6459343 DOI: 10.18632/oncotarget.26777] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/22/2019] [Indexed: 02/07/2023] Open
Abstract
Recurrent fusion transcripts, which are one of the characteristic hallmarks of cancer, arise either from chromosomal rearrangements or from transcriptional errors in splicing. DNA rearrangements include intrachromosomal or interchromosomal translocation, tandem duplication, deletion, inversion, or result from chromothripsis, which causes complex rearrangements. In addition, fusion proteins can be created through transcriptional read-through. Fusion genes can be transcribed to fusion transcripts and translated to chimeric proteins, with many having demonstrated transforming activities through multiple mechanisms in cells. Fusion proteins represent novel therapeutic targets and diagnostic biomarkers of diagnosis, disease status, or progression. This review focuses on the mechanisms underlying the formation of oncogenic fusion genes and transcripts and their impact on the pathobiology of epithelial tumors.
Collapse
Affiliation(s)
- Musaffe Tuna
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Christopher I. Amos
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Gordon B. Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Cell, Developmental and Cancer Biology, School of Medicine, Oregon Health Science University, Portland, OR, USA
- Precision Oncology, Knight Cancer Institute, Portland, OR, USA
| |
Collapse
|
26
|
Abstract
The genomics of prostate cancer (PCA) has been difficult to study compared with some other cancer types for a multitude of reasons, despite significant efforts since the early 1980s. Overcoming some of these obstacles has paved the way for greater insight into the genomics of PCA. The advent of high-throughput technologies coming from the initial use of microsatellite and oligonucleotide probes gave rise to techniques like comparative genomic hybridization (CGH). With the introduction of massively parallel genomic sequencing, referred to as next-generation sequencing (NGS), a deeper understanding of cancer genomics in general has occurred. Along with these technologic advances, there has been the development of computational biology and statistical approaches to address novel large data sets characterized by single base resolution. This review will provide a historic perspective of PCA genomics with an emphasis on the cardinal mutations and alterations observed to be consistently seen in PCA for both hormone-naïve localized PCA and castration-resistant prostate cancer (CRPC). There will be a focus on alterations that have the greatest potential to play a role in disease progression and therapy management.
Collapse
Affiliation(s)
- Mark A Rubin
- Englander Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, New York 10065
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medical College, New York, New York 10021
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York 10021
- Department of BioMedical Research, University of Bern, 3012 Bern, Switzerland
| | - Francesca Demichelis
- Englander Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, New York 10065
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| |
Collapse
|
27
|
Donati B, Lorenzini E, Ciarrocchi A. BRD4 and Cancer: going beyond transcriptional regulation. Mol Cancer 2018; 17:164. [PMID: 30466442 PMCID: PMC6251205 DOI: 10.1186/s12943-018-0915-9] [Citation(s) in RCA: 400] [Impact Index Per Article: 66.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/07/2018] [Indexed: 12/18/2022] Open
Abstract
BRD4, member of the Bromodomain and Extraterminal (BET) protein family, is largely acknowledged in cancer for its role in super-enhancers (SEs) organization and oncogenes expression regulation. Inhibition of BRD4 shortcuts the communication between SEs and target promoters with a subsequent cell-specific repression of oncogenes to which cancer cells are addicted and cell death. To date, this is the most credited mechanism of action of BET inhibitors, a class of small molecules targeting BET proteins which are currently in clinical trials in several cancer settings. However, recent evidence indicates that BRD4 relevance in cancer goes beyond its role in transcription regulation and identifies this protein as a keeper of genome stability. Indeed, a non-transcriptional role of BRD4 in controlling DNA damage checkpoint activation and repair as well as telomere maintenance has been proposed, throwing new lights into the multiple functions of this protein and opening new perspectives on the use of BETi in cancer. Here we discuss the current available information on non-canonical, non-transcriptional functions of BRD4 and on their implications in cancer biology. Integrating this information with the already known BRD4 role in gene expression regulation, we propose a “common” model to explain BRD4 genomic function. Furthermore, in light of the transversal function of BRD4, we provide new interpretation for the cytotoxic activity of BETi and we discuss new possibilities for a wide and focused employment of these drugs in clinical settings.
Collapse
Affiliation(s)
- Benedetta Donati
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Eugenia Lorenzini
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy.
| |
Collapse
|
28
|
Hamaker NK, Lee KH. Site-specific Integration Ushers in a New Era of Precise CHO Cell Line Engineering. Curr Opin Chem Eng 2018; 22:152-160. [PMID: 31086757 DOI: 10.1016/j.coche.2018.09.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Chinese hamster ovary (CHO) cells are widely used for the production of therapeutic proteins. Customarily, CHO production cell lines are established through random integration, which requires laborious screening of many clones to isolate suitable producers. In contrast, site-specific integration (SSI) accelerates cell line development by targeting integration of transgenes to pre-validated genomic loci capable of supporting high and stable expression. To date, a relatively small number of these so called 'hot spots' have been identified, mainly through empirical methods. Nevertheless, nuclease-mediated and recombinase-mediated SSI have revolutionized cell line engineering by enabling rational and reproducible transgene targeting.
Collapse
Affiliation(s)
- Nathaniel K Hamaker
- Delaware Biotechnology Institute, Newark, DE.,Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
| | - Kelvin H Lee
- Delaware Biotechnology Institute, Newark, DE.,Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
| |
Collapse
|
29
|
Pernar CH, Ebot EM, Pettersson A, Graff RE, Giunchi F, Ahearn TU, Gonzalez-Feliciano AG, Markt SC, Wilson KM, Stopsack KH, Gazeeva E, Lis RT, Parmigiani G, Rimm EB, Finn SP, Giovannucci EL, Fiorentino M, Mucci LA. A Prospective Study of the Association between Physical Activity and Risk of Prostate Cancer Defined by Clinical Features and TMPRSS2:ERG. Eur Urol 2018; 76:33-40. [PMID: 30301696 DOI: 10.1016/j.eururo.2018.09.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/21/2018] [Indexed: 01/07/2023]
Abstract
BACKGROUND Growing evidence shows that clinical and molecular subtypes of prostate cancer (PCa) have specific risk factors. Observational studies suggest that physical activity may lower the risk of aggressive PCa. To our knowledge, the association between physical activity and PCa defined by TMPRSS2:ERG has not been evaluated. OBJECTIVE To prospectively examine the association between physical activity and risk of PCa defined by clinical features and TMPRSS2:ERG. DESIGN, SETTING, AND PARTICIPANTS We studied 49160 men aged 40-75 yr in the Health Professionals Follow-up Study from 1986 to 2012. Data was collected at baseline and every 2 yr with >90% follow-up. Total and vigorous physical activity were measured in metabolic equivalent of task (MET)-h/wk. OUTCOME MEASURES AND STATISTICAL ANALYSIS Advanced PCa was defined as stage T3b, T4, N1, or M1 at diagnosis and lethal PCa as distant metastases or death due to disease over follow-up. Presence of TMPRSS2:ERG was estimated by immunohistochemistry of ERG protein expression. Cox proportional hazards models were used to obtain multivariable hazard ratios (HRs) and 95% confidence intervals (CIs) for incidence of subtype-specific PCa. RESULTS AND LIMITATIONS During 26 yr of follow-up, 6411 developed PCa overall and 888 developed lethal disease. There were no significant associations between total physical activity and risk of PCa in the overall cohort. In multivariable-adjusted models, men in the highest quintile of vigorous activity had a significant 30% lower risk of advanced PCa (HR: 0.70, 95% CI: 0.53-0.92) and 25% lower risk of lethal PCa (HR: 0.75, 95% CI: 0.59-0.94) than men in the lowest quintile of vigorous activity. The association was independent of screening history. Vigorous activity was not associated with total PCa in the overall cohort but was inversely associated among highly screened men (top vs bottom quintile, HR: 0.83, 95% CI: 0.70-0.97). Of all cases, 945 were assayed for ERG (48% ERG-positive). Men with higher vigorous activity had a lower risk of ERG-positive PCa (top vs bottom quintile, HR: 0.71, 95% CI: 0.52-0.97). There was no significant association with the risk of ERG-negative disease (p heterogeneity=0.09). CONCLUSIONS Our study confirms that vigorous physical activity is associated with lower risk of advanced and lethal PCa and provides novel evidence for a lower risk of TMPRSS2:ERG-positive disease. PATIENT SUMMARY The identification of modifiable lifestyle factors for prevention of clinically important prostate cancer (PCa) is needed. In this report, we compared risk of PCa in men with different levels of physical activity. Men with higher vigorous activity had a lower risk of developing advanced and lethal PCa and PCa with the common TMPRSS2:ERG gene fusion.
Collapse
Affiliation(s)
- Claire H Pernar
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Ericka M Ebot
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andreas Pettersson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Rebecca E Graff
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Francesca Giunchi
- Pathology Unit, Addarii Institute, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Thomas U Ahearn
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Sarah C Markt
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kathryn M Wilson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Konrad H Stopsack
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizaveta Gazeeva
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rosina T Lis
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Giovanni Parmigiani
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eric B Rimm
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stephen P Finn
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Histopathology, Trinity College, Dublin, Ireland
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Michelangelo Fiorentino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Pathology Unit, Addarii Institute, S. Orsola-Malpighi Hospital, Bologna, Italy; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| |
Collapse
|
30
|
Abstract
53BP1 restrains DNA end resection, and its dosage imbalance upsets DNA double-strand break (DSB) repair pathway choice. Here, by monitoring 53BP1 distribution on DSB-flanking chromatin, we have established a dose-dependent role of the RING finger protein RNF169 in limiting 53BP1 DSB deposition. Moreover, we found that forced expression of RNF169 overcomes 53BP1 activity and stimulates mutagenic DSB repair via the single-strand annealing pathway. Our findings suggest that aberrant expression of RNF169 may represent a deleterious factor in DSB repair control and in maintenance of genome stability. Unrestrained 53BP1 activity at DNA double-strand breaks (DSBs) hampers DNA end resection and upsets DSB repair pathway choice. RNF169 acts as a molecular rheostat to limit 53BP1 deposition at DSBs, but how this fine balance translates to DSB repair control remains undefined. In striking contrast to 53BP1, ChIP analyses of AsiSI-induced DSBs unveiled that RNF169 exhibits robust accumulation at DNA end-proximal regions and preferentially targets resected, RPA-bound DSBs. Accordingly, we found that RNF169 promotes CtIP-dependent DSB resection and favors homology-mediated DSB repair, and further showed that RNF169 dose-dependently stimulates single-strand annealing repair, in part, by alleviating the 53BP1-imposed barrier to DSB end resection. Our results highlight the interplay of RNF169 with 53BP1 in fine-tuning choice of DSB repair pathways.
Collapse
|
31
|
Simonaitis P, Swenson KM. Finding local genome rearrangements. Algorithms Mol Biol 2018; 13:9. [PMID: 29755580 PMCID: PMC5934872 DOI: 10.1186/s13015-018-0127-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 04/16/2018] [Indexed: 11/24/2022] Open
Abstract
Background The double cut and join (DCJ) model of genome rearrangement is well studied due to its mathematical simplicity and power to account for the many events that transform gene order. These studies have mostly been devoted to the understanding of minimum length scenarios transforming one genome into another. In this paper we search instead for rearrangement scenarios that minimize the number of rearrangements whose breakpoints are unlikely due to some biological criteria. One such criterion has recently become accessible due to the advent of the Hi-C experiment, facilitating the study of 3D spacial distance between breakpoint regions. Results We establish a link between the minimum number of unlikely rearrangements required by a scenario and the problem of finding a maximum edge-disjoint cycle packing on a certain transformed version of the adjacency graph. This link leads to a 3/2-approximation as well as an exact integer linear programming formulation for our problem, which we prove to be NP-complete. We also present experimental results on fruit flies, showing that Hi-C data is informative when used as a criterion for rearrangements. Conclusions A new variant of the weighted DCJ distance problem is addressed that ignores scenario length in its objective function. A solution to this problem provides a lower bound on the number of unlikely moves necessary when transforming one gene order into another. This lower bound aids in the study of rearrangement scenarios with respect to chromatin structure, and could eventually be used in the design of a fixed parameter algorithm with a more general objective function.
Collapse
|
32
|
Msaouel P, Tannir NM, Walker CL. A Model Linking Sickle Cell Hemoglobinopathies and SMARCB1 Loss in Renal Medullary Carcinoma. Clin Cancer Res 2018; 24:2044-2049. [DOI: 10.1158/1078-0432.ccr-17-3296] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/13/2018] [Accepted: 02/05/2018] [Indexed: 11/16/2022]
|
33
|
Li X, Baek G, Ramanand SG, Sharp A, Gao Y, Yuan W, Welti J, Rodrigues DN, Dolling D, Figueiredo I, Sumanasuriya S, Crespo M, Aslam A, Li R, Yin Y, Mukherjee B, Kanchwala M, Hughes AM, Halsey WS, Chiang CM, Xing C, Raj GV, Burma S, de Bono J, Mani RS. BRD4 Promotes DNA Repair and Mediates the Formation of TMPRSS2-ERG Gene Rearrangements in Prostate Cancer. Cell Rep 2018; 22:796-808. [PMID: 29346775 PMCID: PMC5843368 DOI: 10.1016/j.celrep.2017.12.078] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/06/2017] [Accepted: 12/21/2017] [Indexed: 11/28/2022] Open
Abstract
BRD4 belongs to the bromodomain and extraterminal (BET) family of chromatin reader proteins that bind acetylated histones and regulate gene expression. Pharmacological inhibition of BRD4 by BET inhibitors (BETi) has indicated antitumor activity against multiple cancer types. We show that BRD4 is essential for the repair of DNA double-strand breaks (DSBs) and mediates the formation of oncogenic gene rearrangements by engaging the non-homologous end joining (NHEJ) pathway. Mechanistically, genome-wide DNA breaks are associated with enhanced acetylation of histone H4, leading to BRD4 recruitment, and stable establishment of the DNA repair complex. In support of this, we also show that, in clinical tumor samples, BRD4 protein levels are negatively associated with outcome after prostate cancer (PCa) radiation therapy. Thus, in addition to regulating gene expression, BRD4 is also a central player in the repair of DNA DSBs, with significant implications for cancer therapy.
Collapse
Affiliation(s)
- Xiangyi Li
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - GuemHee Baek
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Susmita G Ramanand
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adam Sharp
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Yunpeng Gao
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wei Yuan
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Jon Welti
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Daniel N Rodrigues
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - David Dolling
- Clinical Trials and Statistics Unit, Institute of Cancer Research, London SM2 5NG, UK
| | - Ines Figueiredo
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Semini Sumanasuriya
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Mateus Crespo
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Adam Aslam
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rui Li
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yi Yin
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bipasha Mukherjee
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mohammed Kanchwala
- Eugene McDermott Center for Human Growth & Development, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashley M Hughes
- Target Sciences, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - Wendy S Halsey
- Target Sciences, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - Cheng-Ming Chiang
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth & Development, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ganesh V Raj
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sandeep Burma
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Johann de Bono
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Ram S Mani
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
34
|
Exploration of the Germline Genome of the Ciliate Chilodonella uncinata through Single-Cell Omics (Transcriptomics and Genomics). mBio 2018; 9:mBio.01836-17. [PMID: 29317511 PMCID: PMC5760741 DOI: 10.1128/mbio.01836-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Separate germline and somatic genomes are found in numerous lineages across the eukaryotic tree of life, often separated into distinct tissues (e.g., in plants, animals, and fungi) or distinct nuclei sharing a common cytoplasm (e.g., in ciliates and some foraminifera). In ciliates, germline-limited (i.e., micronuclear-specific) DNA is eliminated during the development of a new somatic (i.e., macronuclear) genome in a process that is tightly linked to large-scale genome rearrangements, such as deletions and reordering of protein-coding sequences. Most studies of germline genome architecture in ciliates have focused on the model ciliates Oxytricha trifallax, Paramecium tetraurelia, and Tetrahymena thermophila, for which the complete germline genome sequences are known. Outside of these model taxa, only a few dozen germline loci have been characterized from a limited number of cultivable species, which is likely due to difficulties in obtaining sufficient quantities of “purified” germline DNA in these taxa. Combining single-cell transcriptomics and genomics, we have overcome these limitations and provide the first insights into the structure of the germline genome of the ciliate Chilodonella uncinata, a member of the understudied class Phyllopharyngea. Our analyses reveal the following: (i) large gene families contain a disproportionate number of genes from scrambled germline loci; (ii) germline-soma boundaries in the germline genome are demarcated by substantial shifts in GC content; (iii) single-cell omics techniques provide large-scale quality germline genome data with limited effort, at least for ciliates with extensively fragmented somatic genomes. Our approach provides an efficient means to understand better the evolution of genome rearrangements between germline and soma in ciliates. Our understanding of the distinctions between germline and somatic genomes in ciliates has largely relied on studies of a few model genera (e.g., Oxytricha, Paramecium, Tetrahymena). We have used single-cell omics to explore germline-soma distinctions in the ciliate Chilodonella uncinata, which likely diverged from the better-studied ciliates ~700 million years ago. The analyses presented here indicate that developmentally regulated genome rearrangements between germline and soma are demarcated by rapid transitions in local GC composition and lead to diversification of protein families. The approaches used here provide the basis for future work aimed at discerning the evolutionary impacts of germline-soma distinctions among diverse ciliates.
Collapse
|
35
|
Rubin MA, Demichelis F. The Genomics of Prostate Cancer: emerging understanding with technologic advances. Mod Pathol 2018; 31:S1-11. [PMID: 29297493 DOI: 10.1038/modpathol.2017.166] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 10/10/2017] [Accepted: 10/10/2017] [Indexed: 01/06/2023]
Abstract
With the advent of next-generation sequencing technologies and large whole-exome and genome studies in prostate and other cancers, our understanding of the landscape of genomic alterations has dramatically been refined. In additional to well-known alterations in genomic regions involving 8p, 8q, 10q23, common ETS translocations and androgen receptor amplifications, newer technology have uncovered recurrent mutations in SPOP, FOXA1, MED12, IDH and complex large scale genomic alterations (eg, chromoplexy). This review surveys the enhanced landscape of genomic alterations in clinically localized and advanced prostate cancer.
Collapse
Affiliation(s)
- Mark A Rubin
- Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, NY, USA.,Sandra and Edward Meyer Cancer Center at Weill Cornell Medical College, New York, NY, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA.,Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Francesca Demichelis
- Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, NY, USA.,Centre of Integrative Biology, University of Trento, Trento, Italy
| |
Collapse
|
36
|
Brunet E, Jasin M. Induction of Chromosomal Translocations with CRISPR-Cas9 and Other Nucleases: Understanding the Repair Mechanisms That Give Rise to Translocations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:15-25. [PMID: 29956288 DOI: 10.1007/978-981-13-0593-1_2] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Chromosomal translocations are associated with several tumor types, including hematopoietic malignancies, sarcomas, and solid tumors of epithelial origin, due to their activation of a proto-oncogene or generation of a novel fusion protein with oncogenic potential. In many cases, the availability of suitable human models has been lacking because of the difficulty in recapitulating precise expression of the fusion protein or other reasons. Further, understanding how translocations form mechanistically has been a goal, as it may suggest ways to prevent their occurrence. Chromosomal translocations arise when DNA ends from double-strand breaks (DSBs) on two heterologous chromosomes are improperly joined. This review provides a summary of DSB repair mechanisms and their contribution to translocation formation, the various programmable nuclease platforms that have been used to generate translocations, and the successes that have been achieved in this area.
Collapse
Affiliation(s)
- Erika Brunet
- Genome Dynamics in the Immune System Laboratory, Institut Imagine, INSERM UMR 1163, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
37
|
Reczek CR, Shakya R, Miteva Y, Szabolcs M, Ludwig T, Baer R. The DNA resection protein CtIP promotes mammary tumorigenesis. Oncotarget 2017; 7:32172-83. [PMID: 27058754 PMCID: PMC5078005 DOI: 10.18632/oncotarget.8605] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/14/2016] [Indexed: 01/15/2023] Open
Abstract
Many DNA repair factors act to suppress tumor formation by preserving genomic stability. Similarly, the CtIP protein, which interacts with the BRCA1 tumor suppressor, is also thought to have tumor suppression activity. Through its role in DNA end resection, CtIP facilitates DNA double-strand break (DSB) repair by homologous recombination (DSBR-HR) and microhomology-mediated end joining (MMEJ). In addition, however, CtIP has also been implicated in the formation of aberrant chromosomal rearrangements in an MMEJ-dependent manner, an activity that could potentially promote tumor development by increasing genome instability. To clarify whether CtIP acts in vivo to suppress or promote tumorigenesis, we have examined its oncogenic potential in mouse models of human breast cancer. Surprisingly, mice heterozygous for a null Ctip allele did not display an increased susceptibility to tumor formation. Moreover, mammary-specific biallelic CtIP ablation did not elicit breast tumors in a manner reminiscent of BRCA1 loss. Instead, CtIP inactivation dramatically reduced the kinetics of mammary tumorigenesis in mice bearing mammary-specific lesions of the p53 gene. Thus, unlike other repair factors, CtIP is not a tumor suppressor, but has oncogenic properties that can promote tumorigenesis, consistent with its ability to facilitate MMEJ-dependent chromosomal instability. Consequently, inhibition of CtIP-mediated MMEJ may prove effective against tumor types, such as human breast cancer, that display MMEJ-dependent chromosomal rearrangements.
Collapse
Affiliation(s)
- Colleen R Reczek
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Reena Shakya
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA.,Current address: Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Wexner Medical Center and Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Yana Miteva
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Matthias Szabolcs
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Thomas Ludwig
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA.,Current address: Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Wexner Medical Center and Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Richard Baer
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| |
Collapse
|
38
|
TDP2 suppresses chromosomal translocations induced by DNA topoisomerase II during gene transcription. Nat Commun 2017; 8:233. [PMID: 28794467 PMCID: PMC5550487 DOI: 10.1038/s41467-017-00307-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/19/2017] [Indexed: 11/18/2022] Open
Abstract
DNA double-strand breaks (DSBs) induced by abortive topoisomerase II (TOP2) activity are a potential source of genome instability and chromosome translocation. TOP2-induced DNA double-strand breaks are rejoined in part by tyrosyl-DNA phosphodiesterase 2 (TDP2)-dependent non-homologous end-joining (NHEJ), but whether this process suppresses or promotes TOP2-induced translocations is unclear. Here, we show that TDP2 rejoins DSBs induced during transcription-dependent TOP2 activity in breast cancer cells and at the translocation ‘hotspot’, MLL. Moreover, we find that TDP2 suppresses chromosome rearrangements induced by TOP2 and reduces TOP2-induced chromosome translocations that arise during gene transcription. Interestingly, however, we implicate TDP2-dependent NHEJ in the formation of a rare subclass of translocations associated previously with therapy-related leukemia and characterized by junction sequences with 4-bp of perfect homology. Collectively, these data highlight the threat posed by TOP2-induced DSBs during transcription and demonstrate the importance of TDP2-dependent non-homologous end-joining in protecting both gene transcription and genome stability. DNA double-strand breaks (DSBs) induced by topoisomerase II (TOP2) are rejoined by TDP2-dependent non-homologous end-joining (NHEJ) but whether this promotes or suppresses translocations is not clear. Here the authors show that TDP2 suppresses chromosome translocations from DSBs introduced during gene transcription.
Collapse
|
39
|
|
40
|
Vanoli F, Jasin M. Generation of chromosomal translocations that lead to conditional fusion protein expression using CRISPR-Cas9 and homology-directed repair. Methods 2017; 121-122:138-145. [PMID: 28522325 PMCID: PMC5531069 DOI: 10.1016/j.ymeth.2017.05.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/24/2017] [Accepted: 05/10/2017] [Indexed: 10/19/2022] Open
Abstract
Recurrent chromosomal translocations often lead to expression of fusion proteins associated with oncogenic transformation. To study translocations and downstream events, genome editing techniques have been developed to generate chromosomal translocations through non-homologous end joining of DNA double-strand breaks introduced at the two participating endogenous loci. However, the frequencies at which these events occur is usually too low to efficiently clone cells carrying the translocation. This article provides a detailed method using CRISPR-Cas9 technology and homology-directed repair to efficiently isolate cells harboring a chromosomal translocation. For an additional level of control, the resulting fusion protein is conditionally expressed to allow early events in oncogenic transformation to be studied. We focus on the generation of the EWSR1-WT1 fusion using human mesenchymal cells, which is associated with the translocation found in desmoplastic small round cell tumors.
Collapse
MESH Headings
- Abdominal Neoplasms/genetics
- Abdominal Neoplasms/metabolism
- Abdominal Neoplasms/pathology
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- CRISPR-Associated Protein 9
- CRISPR-Cas Systems
- Cell Line
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Chromosomes, Human, Pair 11
- Chromosomes, Human, Pair 22
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA Breaks, Double-Stranded
- Desmoplastic Small Round Cell Tumor/genetics
- Desmoplastic Small Round Cell Tumor/metabolism
- Desmoplastic Small Round Cell Tumor/pathology
- Endonucleases/genetics
- Endonucleases/metabolism
- Genome, Human
- Humans
- Mesenchymal Stem Cells/metabolism
- Mesenchymal Stem Cells/pathology
- Mutagenesis, Site-Directed/methods
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- RNA-Binding Protein EWS/genetics
- RNA-Binding Protein EWS/metabolism
- Recombinational DNA Repair
- Translocation, Genetic
- WT1 Proteins/genetics
- WT1 Proteins/metabolism
Collapse
Affiliation(s)
- Fabio Vanoli
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
41
|
Graff RE, Judson G, Ahearn TU, Fiorentino M, Loda M, Giovannucci EL, Mucci LA, Pettersson A. Circulating Antioxidant Levels and Risk of Prostate Cancer by TMPRSS2:ERG. Prostate 2017; 77:647-653. [PMID: 28102015 PMCID: PMC5354965 DOI: 10.1002/pros.23312] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/04/2017] [Indexed: 11/06/2022]
Abstract
BACKGROUND Few studies have considered etiological differences across molecular subtypes of prostate cancer, despite potential to improve opportunities for precision prevention of a disease for which modifiable risk factors have remained elusive. Factors that lead to DNA double-strand breaks, such as oxidative stress, may promote the formation of the TMPRSS2:ERG gene fusion in prostate cancer. We tested the hypothesis that increasing levels of pre-diagnostic circulating antioxidants, which may reduce oxidative stress, are associated with lower risk of developing TMPRSS2:ERG positive prostate cancer. METHODS We conducted a nested case-control study, including 370 cases and 2,470 controls, to evaluate associations between pre-diagnostic α- and β-carotene, α- and γ-tocopherol, β-cryptoxanthin, lutein, lycopene, retinol, and selenium with the risk of prostate cancer by ERG protein expression status (a marker of TMPRSS2:ERG). Multivariable unconditional polytomous logistic regression was used to calculate odds ratios and 95% confidence intervals. RESULTS We did not find any of the antioxidants to be significantly associated with the risk of prostate cancer according to ERG status. CONCLUSIONS The results do not support the hypothesis that circulating pre-diagnostic antioxidant levels protect against developing TMPRSS2:ERG positive prostate cancer. Additional studies are needed to explore mechanisms for the development of TMPRSS2:ERG positive disease. Prostate 77: 647-653, 2017. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Rebecca E. Graff
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Gregory Judson
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Thomas U. Ahearn
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Michelangelo Fiorentino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Pathology Unit, Addarii Institute, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Massimo Loda
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Edward L. Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Lorelei A. Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Andreas Pettersson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
42
|
CRISPR-Cas9-guided oncogenic chromosomal translocations with conditional fusion protein expression in human mesenchymal cells. Proc Natl Acad Sci U S A 2017; 114:3696-3701. [PMID: 28325870 DOI: 10.1073/pnas.1700622114] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Gene editing techniques have been extensively used to attempt to model recurrent genomic rearrangements found in tumor cells. These methods involve the induction of double-strand breaks at endogenous loci followed by the identification of breakpoint junctions within a population, which typically arise by nonhomologous end joining. The low frequency of these events, however, has hindered the cloning of cells with the desired rearrangement before oncogenic transformation. Here we present a strategy combining CRISPR-Cas9 technology and homology-directed repair to allow for the selection of human mesenchymal stem cells harboring the oncogenic translocation EWSR1-WT1 found in the aggressive desmoplastic small round cell tumor. The expression of the fusion transcript is under the control of the endogenous EWSR1 promoter and, importantly, can be conditionally expressed using Cre recombinase. This method is easily adapted to generate any cancer-relevant rearrangement.
Collapse
|
43
|
Germini D, Bou Saada Y, Tsfasman T, Osina K, Robin C, Lomov N, Rubtsov M, Sjakste N, Lipinski M, Vassetzky Y. A One-Step PCR-Based Assay to Evaluate the Efficiency and Precision of Genomic DNA-Editing Tools. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2017; 5:43-50. [PMID: 28480303 PMCID: PMC5415314 DOI: 10.1016/j.omtm.2017.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/03/2017] [Indexed: 12/16/2022]
Abstract
Despite rapid progress, many problems and limitations persist and limit the applicability of gene-editing techniques. Making use of meganucleases, TALENs, or CRISPR/Cas9-based tools requires an initial step of pre-screening to determine the efficiency and specificity of the designed tools. This step remains time consuming and material consuming. Here we propose a simple, cheap, reliable, time-saving, and highly sensitive method to evaluate a given gene-editing tool based on its capacity to induce chromosomal translocations when combined with a reference engineered nuclease. In the proposed technique, designated engineered nuclease-induced translocations (ENIT), a plasmid coding for the DNA-editing tool to be tested is co-transfected into carefully chosen target cells along with that for an engineered nuclease of known specificity and efficiency. If the new enzyme efficiently cuts within the desired region, then specific chromosomal translocations will be generated between the two targeted genomic regions and be readily detectable by a one-step PCR or qPCR assay. The PCR product thus obtained can be directly sequenced, thereby determining the exact position of the double-strand breaks induced by the gene-editing tools. As a proof of concept, ENIT was successfully tested in different cell types and with different meganucleases, TALENs, and CRISPR/Cas9-based editing tools.
Collapse
Affiliation(s)
- Diego Germini
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.,LIA 1066, French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France.,Department of Biophysics, Institute of Physics, Nanotechnology, and Telecommunications, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Yara Bou Saada
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.,LIA 1066, French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France
| | - Tatiana Tsfasman
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.,LIA 1066, French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France
| | - Kristina Osina
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.,University of Latvia, 1586 Riga, Latvia
| | - Chloé Robin
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France
| | - Nikolay Lomov
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.,LIA 1066, French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France.,M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Mikhail Rubtsov
- LIA 1066, French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France.,M.V. Lomonosov Moscow State University, Moscow 119991, Russia.,Department of Biochemistry and Strategic Management Department, I.M. Sechenov First Moscow State Medical University, Moscow 119048, Russia
| | | | - Mar Lipinski
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.,LIA 1066, French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France
| | - Yegor Vassetzky
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.,LIA 1066, French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France.,M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| |
Collapse
|
44
|
Shvets AA, Kolomeisky AB. The Role of DNA Looping in the Search for Specific Targets on DNA by Multisite Proteins. J Phys Chem Lett 2016; 7:5022-5027. [PMID: 27973894 DOI: 10.1021/acs.jpclett.6b02371] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Many cellular processes involve simultaneous interactions between DNA and protein molecules at several locations. They are regulated and controlled by special protein-DNA complexes, which are known as synaptic complexes or synaptosomes. Because of the multisite nature of involved proteins, it was suggested that during the formation of synaptic complexes DNA loops might appear, but their role is unclear. We developed a theoretical model that allowed us to evaluate the effect of transient DNA loop formation. It is based on a discrete-state stochastic method that explicitly takes into account the free-energy contributions due to the appearance of DNA loops. The formation of the synaptic complexes is viewed as a search for a specific binding site on DNA by the protein molecule already bound to DNA at another location. It was found that the search might be optimized by varying the position of the target and the total length of DNA. Furthermore, the formation of transient DNA loops leads to faster dynamics if it is associated with favorable enthalpic contributions to nonspecific protein-DNA interactions. It is also shown that DNA looping might reduce stochastic noise in the system.
Collapse
Affiliation(s)
- Alexey A Shvets
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
| | - Anatoly B Kolomeisky
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
| |
Collapse
|
45
|
|
46
|
Structural variation discovery in the cancer genome using next generation sequencing: computational solutions and perspectives. Oncotarget 2016; 6:5477-89. [PMID: 25849937 PMCID: PMC4467381 DOI: 10.18632/oncotarget.3491] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/04/2015] [Indexed: 01/03/2023] Open
Abstract
Somatic Structural Variations (SVs) are a complex collection of chromosomal mutations that could directly contribute to carcinogenesis. Next Generation Sequencing (NGS) technology has emerged as the primary means of interrogating the SVs of the cancer genome in recent investigations. Sophisticated computational methods are required to accurately identify the SV events and delineate their breakpoints from the massive amounts of reads generated by a NGS experiment. In this review, we provide an overview of current analytic tools used for SV detection in NGS-based cancer studies. We summarize the features of common SV groups and the primary types of NGS signatures that can be used in SV detection methods. We discuss the principles and key similarities and differences of existing computational programs and comment on unresolved issues related to this research field. The aim of this article is to provide a practical guide of relevant concepts, computational methods, software tools and important factors for analyzing and interpreting NGS data for the detection of SVs in the cancer genome.
Collapse
|
47
|
Abstract
The ciliate Oxytricha is a microbial eukaryote with two genomes, one of which experiences extensive genome remodeling during development. Each round of conjugation initiates a cascade of events that construct a transcriptionally active somatic genome from a scrambled germline genome, with considerable help from both long and small noncoding RNAs. This process of genome remodeling entails massive DNA deletion and reshuffling of remaining DNA segments to form functional genes from their interrupted and scrambled germline precursors. The use of Oxytricha as a model system provides an opportunity to study an exaggerated form of programmed genome rearrangement. Furthermore, studying the mechanisms that maintain nuclear dimorphism and mediate genome rearrangement has demonstrated a surprising plasticity and diversity of noncoding RNA pathways, with new roles that go beyond conventional gene silencing. Another aspect of ciliate genetics is their unorthodox patterns of RNA-mediated, epigenetic inheritance that rival Mendelian inheritance. This review takes the reader through the key experiments in a model eukaryote that led to fundamental discoveries in RNA biology and pushes the biological limits of DNA processing.
Collapse
|
48
|
Abstract
Much progress has been made in research for prostate cancer in the past decade. There is now greater understanding for the genetic basis of familial prostate cancer with identification of rare but high-risk mutations (eg, BRCA2, HOXB13) and low-risk but common alleles (77 identified so far by genome-wide association studies) that could lead to targeted screening of patients at risk. This is especially important because screening for prostate cancer based on prostate-specific antigen remains controversial due to the high rate of overdiagnosis and unnecessary prostate biopsies, despite evidence that it reduces mortality. Classification of prostate cancer into distinct molecular subtypes, including mutually exclusive ETS-gene-fusion-positive and SPINK1-overexpressing, CHD1-loss cancers, could allow stratification of patients for different management strategies. Presently, men with localised disease can have very different prognoses and treatment options, ranging from observation alone through to radical surgery, with few good-quality randomised trials to inform on the best approach for an individual patient. The survival of patients with metastatic prostate cancer progressing on androgen-deprivation therapy (castration-resistant prostate cancer) has improved substantially. In addition to docetaxel, which has been used for more than a decade, in the past 4 years five new drugs have shown efficacy with improvements in overall survival leading to licensing for the treatment of metastatic castration-resistant prostate cancer. Because of this rapid change in the therapeutic landscape, no robust data exist to inform on the selection of patients for a specific treatment for castration-resistant prostate cancer or the best sequence of administration. Moreover, the high cost of the newer drugs limits their widespread use in several countries. Data from continuing clinical and translational research are urgently needed to improve, and, crucially, to personalise management.
Collapse
Affiliation(s)
- Gerhardt Attard
- Division of Clinical Studies, The Institute of Cancer Research, London, UK; Prostate Cancer Targeted Therapy Group, Royal Marsden NHS Foundation Trust, Sutton, Surrey, UK
| | - Chris Parker
- Academic Urology Unit, Royal Marsden NHS Foundation Trust, Sutton, Surrey, UK
| | - Ros A Eeles
- Clinical Academic Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, Sutton, Surrey, UK; Oncogenetics Team, Division of Cancer Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Fritz Schröder
- Erasmus University Medical Center, Rotterdam, Netherlands
| | - Scott A Tomlins
- Departments of Pathology Urology, Comprehensive Cancer Center and Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ian Tannock
- Princess Margaret Cancer Centre and University of Toronto, Toronto, ON, Canada
| | - Charles G Drake
- Division of Medical Oncology, Johns Hopkins Hospital, Baltimore, MA, USA
| | - Johann S de Bono
- Division of Clinical Studies, The Institute of Cancer Research, London, UK; Prostate Cancer Targeted Therapy Group, Royal Marsden NHS Foundation Trust, Sutton, Surrey, UK.
| |
Collapse
|
49
|
Thums Konerat J, Bueno V, Margarido VP, Portela-Castro AL, Martins-Santos IC. Diversity of Sex Chromosome Systems in Ancistrini (Loricariidae, Hypostominae): ZZ/ZW in Ancistrus taunayi Miranda Ribeiro, 1918. Cytogenet Genome Res 2015; 146:306-10. [DOI: 10.1159/000441431] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2015] [Indexed: 11/19/2022] Open
Abstract
The karyotype of the Ancistrini catfish Ancistrus taunayi was analyzed by conventional (Giemsa staining, AgNOR staining and C-banding) and molecular cytogenetic (5S and 18S rDNA-FISH) methods. The diploid chromosome number was 2n = 50 (22 metacentrics + 10 submetacentrics + 10 subtelocentrics + 8 acrocentrics) for both sexes. A single NOR-bearing acrocentric chromosome pair (No. 24) was detected after Ag-staining and 18S rDNA-FISH, while 5S rDNA was found only in the subtelocentric pair No. 21. Conspicuous GC-rich heterochromatin blocks corresponded to the NOR sites and were also observed in the distal regions of the acrocentric chromosome pairs Nos. 22 and 25. Chromosome pair No. 22 differed between males and females; in males, only a small interstitial block of GC-rich heterochromatin was present in both chromosomes, whereas in females, 2 blocks of GC-rich heterochromatin flanked a euchromatic region in one of the homologues, suggesting the occurrence of a ZZ/ZW sex chromosome system. Two mechanisms for the origin and evolution of this simple ZZ/ZW sex chromosome system in A. taunayi are proposed: (1) a paracentric inversion followed by amplification of the proximal heterochromatin and (2) amplification of the interstitial heterochromatin followed by a paracentric inversion. Although ZZ/ZW systems have already been described for other Ancistrus species, our results do not show the same pattern, suggesting an independent origin.
Collapse
|
50
|
Burman B, Misteli T, Pegoraro G. Quantitative detection of rare interphase chromosome breaks and translocations by high-throughput imaging. Genome Biol 2015; 16:146. [PMID: 26313373 PMCID: PMC4531802 DOI: 10.1186/s13059-015-0718-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
We report a method for the sensitive detection of rare chromosome breaks and translocations in interphase cells. HiBA-FISH (High-throughput break-apart FISH) combines high-throughput imaging with the measurement of the spatial separation of FISH probes flanking target genome regions of interest. As proof-of-principle, we apply hiBA-FISH to detect with high sensitivity and specificity rare chromosome breaks and translocations in the anaplastic large cell lymphoma breakpoint regions of NPM1 and ALK. This method complements existing approaches to detect translocations by overcoming the need for precise knowledge of translocation breakpoints and it extends traditional FISH by its quantitative nature.
Collapse
Affiliation(s)
- Bharat Burman
- Cell Biology of Genomes, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Program in Cell, Molecular, and Developmental Biology, Tufts University Sackler School of Biomedical Sciences, Boston, MA, 02111, USA
| | - Tom Misteli
- Cell Biology of Genomes, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Gianluca Pegoraro
- NCI High-Throughput Imaging Facility, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|