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Neil AJ, Chukwueke UN, Hoover N, Marris SRN, Rojas-Rudilla V, Manning DK, Mito JK, Cibas ES, Sholl LM. Validation of targeted next-generation sequencing of cell-free DNA from archival cerebrospinal fluid specimens for the detection of somatic variants in cancer involving the leptomeninges: Cytopathologic and radiographic correlation. Cancer Cytopathol 2024; 132:214-223. [PMID: 37812603 DOI: 10.1002/cncy.22768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/28/2023] [Accepted: 08/21/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND Leptomeningeal metastases occur across multiple solid and lymphoid cancers, and patients typically undergo cytopathologic assessment of cerebrospinal fluid (CSF) in this setting. For patients diagnosed with metastatic cancer, the detection of actionable somatic mutations in CSF can provide clinically valuable information for treatment without the need for additional tissue collection. METHODS The authors validated a targeted next-generation sequencing assay for the detection of somatic variants in cancer (OncoPanel) on cell-free DNA (cfDNA) isolated from archival CSF specimens in a cohort of 25 patients who had undergone molecular testing of a prior tumor specimen. RESULTS CSF storage time and volume had no impact on cfDNA concentration or mean target coverage of the assay. Previously identified somatic variants in CSF cfDNA were detected in 88%, 50%, and 27% of specimens diagnosed cytologically as positive, suspicious/atypical, and negative for malignancy, respectively. Somatic variants were identified in 81% of CSF specimens from patients who had leptomeningeal enhancement on magnetic resonance imaging compared with 31% from patients without such enhancement. CONCLUSIONS These data highlight the stability of cfDNA in CSF, which allows for cytopathologic evaluation before triage for next-generation sequencing assays. For a subset of cases in which clinical suspicion is high but cytologic or radiographic studies are inconclusive, the detection of pathogenic somatic variants in CSF cfDNA may aid in the diagnosis of leptomeningeal metastases.
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Affiliation(s)
- Alexander J Neil
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ugonma N Chukwueke
- Center for Neuro-Oncology, Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas Hoover
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sean R N Marris
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Vanesa Rojas-Rudilla
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Danielle K Manning
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey K Mito
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Edmund S Cibas
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Neil AJ, Li YY, Hakam A, Nucci MR, Parra-Herran C. Pattern A endocervical adenocarcinomas with ovarian metastasis are indolent and molecularly distinct from destructively invasive adenocarcinomas. Histopathology 2024; 84:369-380. [PMID: 37920148 DOI: 10.1111/his.15069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 11/04/2023]
Abstract
AIMS The invasive pattern in HPV-associated endocervical adenocarcinoma (HPVA) has prognostic value. Non-destructive (pattern A) HPVA has excellent prognosis mirroring adenocarcinoma in-situ (AIS). However, the rare occurrence of ovarian spread in these tumours suggests aggressiveness in a subset of patients with these otherwise indolent lesions. We hypothesise that AIS/pattern A HPVA with ovarian metastases are biologically different than metastatic destructively invasive HPVA. METHODS AND RESULTS Samples from patients with HPVA and synchronous or metachronous metastases were retrieved and reviewed to confirm diagnosis and determine the Silva pattern in the primary lesion. For each case, normal tissue, cervical tumour and at least one metastasis underwent comprehensive sequencing using a 447-gene panel. Pathogenic single-nucleotide variants and segmental copy-number alterations (CNA), tumour mutational burden and molecular signatures were evaluated and compared between primary and metastases and among invasive pattern categories. We identified 13 patients: four had AIS/pattern A primaries, while nine had pattern B/C tumours. All AIS/pattern A lesions had metastasis only to ovary; 50% of patients with ovarian involvement, regardless of invasive pattern, also had involvement of the endometrium and/or fallopian tube mucosa by HPVA. In the ovary, AIS/pattern A HPVA showed deceptive well-differentiated glands, often with adenofibroma-like appearance. Conversely, pattern C HPVAs consistently showed overt infiltrative features in the ovary. Sequencing confirmed the genetic relationship between primary and metastatic tumours in each case. PIK3CA alterations were identified in three of four AIS/pattern A HPVAs and three of eight pattern B/C tumours with sequenced metastases. Pattern C tumours showed a notably higher number of CNA in primary tumours compared to pattern A/B tumours. Only one metastatic AIS/pattern A HPVA had a novel pathogenic variant compared to the primary. Conversely, five of eight pattern B/C tumours with sequenced metastases developed novel pathogenic variants in the metastasis not seen in the primary. All four AIS/pattern A patients were alive and free of disease at 31, 47, 58 and 212 months after initial diagnosis. Conversely, cancer-related death was documented in five of nine pattern B/C patients with follow-up at 7, 20, 20, 43 and 87 months. CONCLUSION Morphologically and genomically, AIS/pattern A HPVA with secondary ovarian involvement appears distinct from destructively invasive tumours. In at least a subset of these cases, ovarian spread appears to occur via trans-Mullerian superficial extension, different from the stromal and lymphatic vascular spread typical of more aggressive tumours (pattern C). These differences may explain the indolent outcome observed in the rare subset of patients with AIS/pattern A HPVA and ovarian metastasis. Our data underscore the potential for conservative surgical management approaches to pattern A HPVA.
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Affiliation(s)
- Alexander J Neil
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yvonne Y Li
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Ardeshir Hakam
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, FL, USA
| | - Marisa R Nucci
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Carlos Parra-Herran
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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Zhou Y, Börcsök J, Adib E, Kamran SC, Neil AJ, Stawiski K, Freeman D, Stormoen DR, Sztupinszki Z, Samant A, Nassar A, Bekele RT, Hanlon T, Valentine H, Epstein I, Sharma B, Felt K, Abbosh P, Wu CL, Efstathiou JA, Miyamoto DT, Anderson W, Szallasi Z, Mouw KW. ATM deficiency confers specific therapeutic vulnerabilities in bladder cancer. Sci Adv 2023; 9:eadg2263. [PMID: 37992168 PMCID: PMC10664985 DOI: 10.1126/sciadv.adg2263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 10/19/2023] [Indexed: 11/24/2023]
Abstract
Ataxia-telangiectasia mutated (ATM) plays a central role in the cellular response to DNA damage and ATM alterations are common in several tumor types including bladder cancer. However, the specific impact of ATM alterations on therapy response in bladder cancer is uncertain. Here, we combine preclinical modeling and clinical analyses to comprehensively define the impact of ATM alterations on bladder cancer. We show that ATM loss is sufficient to increase sensitivity to DNA-damaging agents including cisplatin and radiation. Furthermore, ATM loss drives sensitivity to DNA repair-targeted agents including poly(ADP-ribose) polymerase (PARP) and Ataxia telangiectasia and Rad3 related (ATR) inhibitors. ATM loss alters the immune microenvironment and improves anti-PD1 response in preclinical bladder models but is not associated with improved anti-PD1/PD-L1 response in clinical cohorts. Last, we show that ATM expression by immunohistochemistry is strongly correlated with response to chemoradiotherapy. Together, these data define a potential role for ATM as a predictive biomarker in bladder cancer.
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Affiliation(s)
- Yuzhen Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Judit Börcsök
- Danish Cancer Institute, Copenhagen, Denmark
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Elio Adib
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Sophia C. Kamran
- Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander J. Neil
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Konrad Stawiski
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland
| | - Dory Freeman
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dag Rune Stormoen
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Zsofia Sztupinszki
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Amruta Samant
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amin Nassar
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT, USA
| | - Raie T. Bekele
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Timothy Hanlon
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Henkel Valentine
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Ilana Epstein
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bijaya Sharma
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kristen Felt
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Philip Abbosh
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Albert Einstein Medical Center, Philadelphia, PA, USA
| | - Chin-Lee Wu
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Jason A. Efstathiou
- Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - David T. Miyamoto
- Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William Anderson
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Zoltan Szallasi
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group and Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Kent W. Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Radiation Oncology, Brigham and Women’s Hospital, Boston, MA, USA
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Neil AJ, Muto MG, Kolin DL, Konstantinopoulos PA. Durable remission in a patient with ERBB2-amplified recurrent mucinous ovarian carcinoma treated with Trastuzumab-Carboplatin-Paclitaxel. Gynecol Oncol Rep 2023; 48:101237. [PMID: 37449085 PMCID: PMC10336730 DOI: 10.1016/j.gore.2023.101237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/01/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Patients with advanced stage or recurrent mucinous ovarian carcinoma exhibit poor response to standard platinum- and taxane-based chemotherapy and poor prognosis. We report a 29-year-old patient with recurrent ERBB2-amplified mucinous ovarian carcinoma (with expansile growth pattern at initial diagnosis and previously treated with adjuvant capecitabine/oxaliplatin) who underwent optimal secondary cytoreduction followed by 6 cycles of carboplatin/paclitaxel/trastuzumab and 1-year maintenance trastuzumab. This patient remains without radiologic or biochemical evidence of disease for more than 3 years after secondary cytoreduction. This case supports routine assessment of HER2 status in patients with advanced or recurrent mucinous ovarian carcinoma and highlights the potential of HER2-targeted therapy with trastuzumab in combination with standard carboplatin and paclitaxel in this disease. This case also raises the possibility that expansile mucinous ovarian carcinomas with ERBB2 amplification and p53 mutant immunohistochemical staining pattern (as this patient had) may be associated with a more aggressive behavior and higher risk of relapse.
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Affiliation(s)
- Alexander J. Neil
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Michael G. Muto
- Division of Gynecologic Oncology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA
| | - David L. Kolin
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
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Neil AJ, Zhao L, Isidro RA, Srivastava A, Cleary JM, Dong F. SMARCA4 Mutations in Carcinomas of the Esophagus, Esophagogastric Junction, and Stomach. Mod Pathol 2023; 36:100183. [PMID: 37054973 DOI: 10.1016/j.modpat.2023.100183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/08/2023] [Accepted: 03/29/2023] [Indexed: 04/15/2023]
Abstract
Deficiency of SMARCA4, a member of the SWI/SNF chromatin remodeling complex, has been described in a subset of undifferentiated gastroesophageal carcinomas with an aggressive clinical course. The full spectrum and frequency of SMARCA4 mutations in gastroesophageal cancer are unknown. We interrogated our institutional database and identified patients with gastroesophageal carcinomas who underwent cancer next-generation sequencing. We classified SMARCA4 mutations, assessed histologic features, and correlated SMARCA4 mutations with SMARCA4 protein expression by immunohistochemistry. SMARCA4 mutations were identified in gastroesophageal carcinomas from 107 (9.1%) of 1174 patients. Forty-nine SMARCA4 mutations, including 26 missense variants and 23 protein-truncating variants, were interpreted as pathogenic in 42 (3.6%) of 1174 patients. Thirty (71%) of 42 cancers with pathogenic SMARCA4 mutations were located in the esophagus or esophagogastric junction, and 12 cancers (29%) were located in the stomach. Sixty-four percent of carcinomas with pathogenic truncating SMARCA4 variants were poorly differentiated or undifferentiated compared with 25% of carcinomas with pathogenic missense variants. Eight of 12 carcinomas with truncating SMARCA4 variants and none of the 7 carcinomas with pathogenic SMARCA4 missense variants showed loss of SMARCA4 expression by immunohistochemistry. Four carcinomas with pathogenic truncating SMARCA4 variants were associated with Barrett esophagus. SMARCA4-mutated gastroesophageal cancers were enriched for APC (31%) and CTNNB1 (14%) mutations and exhibited similar frequency of TP53 (76%) and ARID1A (31%) mutations compared with gastroesophageal cancers without pathogenic SMARCA4 mutations. The median overall survival was 13.6 months for patients who presented with metastasis at diagnosis and 22.7 months for patients without metastasis. Overall, SMARCA4-mutated gastroesophageal cancers exhibit a spectrum of histologic grade, an association with Barrett esophagus, and a concurrent mutational pattern similar to SMARCA4-wild-type gastroesophageal adenocarcinomas. Although SMARCA4-deficient gastroesophageal carcinomas are associated with poorly differentiated and undifferentiated histology, the spectrum of histologic and molecular features suggests overlapping pathogenic pathways with conventional gastroesophageal adenocarcinomas.
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Affiliation(s)
- Alexander J Neil
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lei Zhao
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Raymond A Isidro
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Amitabh Srivastava
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Now with Department of Pathology, Memorial Sloan Kettering Cancer Center, New York
| | - James M Cleary
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Fei Dong
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.
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Santos A, Sauer M, Neil AJ, Solomon IH, Hornick JL, Roberts DJ, Quade BJ, Parra-Herran C. Absence of SARS-CoV-2 Spike glycoprotein expression in placentas from individuals after mRNA SARS-CoV-2 vaccination. Mod Pathol 2022; 35:1175-1180. [PMID: 35361888 PMCID: PMC8967927 DOI: 10.1038/s41379-022-01061-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 02/16/2022] [Accepted: 02/16/2022] [Indexed: 01/09/2023]
Abstract
Current public health initiatives to contain the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) global pandemic focus on expanding vaccination efforts to include vulnerable populations such as pregnant people. Vaccines using messenger ribonucleic acid (mRNA) technology rely on translation by immune cells, primarily at the injection site. Hesitancy remains among the general population regarding the safety of mRNA vaccines during gestation, and it remains unknown whether the SARS-CoV-2 Spike protein (the product of mRNA vaccines available) accumulates in the placenta after vaccination. Objective: To determine whether Spike protein translation and accumulation occurs in placental tissue in the context of recent mRNA SARC-CoV-2 vaccination during pregnancy. We identified 48 patients receiving one or two doses of mRNA SARS-CoV-2 vaccine during gestation and used immunohistochemistry against SARS-CoV-2 Spike protein in formalin-fixed, paraffin-embedded placental tissue. One placenta, positive for SARS-CoV-2 RNA by in situ hybridization (ISH) was used as positive control. Seven term placentas collected prior to the emergence of SARS-CoV-2 served as negative controls. Eighty one percent of patients in the study group underwent third-trimester delivery; remaining had a first-trimester spontaneous abortion or elective second-trimester termination. Patients received two (52%) or one (48%) vaccine doses during pregnancy, with a median interval between latest dose and delivery of 13 days (range 2-79 days). Most (63%) cases had their latest dose within 15 days prior to delivery. All the placentas in the study and negative control groups were negative for SARS-CoV-2 immunohistochemistry. Six study cases with short vaccine-delivery intervals (2-7 days) were subjected to SARS-CoV-2 ISH and were negative. Our findings suggest that mRNA vaccines do not reach significant concentrations in the placenta given the absence of definitive SARS-CoV-2 Spike protein accumulation in placental tissue. This observation provides evidence supporting the safety of mRNA vaccines to the placental-fetal unit.
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Affiliation(s)
- Andres Santos
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Madeline Sauer
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA,Faculty of Medicine, University of Missouri, Columbia, USA
| | - Alexander J. Neil
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Isaac H. Solomon
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Jason L. Hornick
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Drucilla J. Roberts
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, USA
| | - Bradley J. Quade
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Carlos Parra-Herran
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA.
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Acosta AM, Neil AJ, Hirsch MS. Primary mucinous adenocarcinoma of the seminal vesicle associated with intestinal metaplasia: a radiation-induced tumour? Histopathology 2021; 79:444-448. [PMID: 34096663 DOI: 10.1111/his.14425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Andres M Acosta
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexander J Neil
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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8
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Neil AJ, Liang MU, Khristich AN, Shah KA, Mirkin SM. RNA-DNA hybrids promote the expansion of Friedreich's ataxia (GAA)n repeats via break-induced replication. Nucleic Acids Res 2019; 46:3487-3497. [PMID: 29447396 PMCID: PMC5909440 DOI: 10.1093/nar/gky099] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/05/2018] [Indexed: 12/21/2022] Open
Abstract
Expansion of simple DNA repeats is responsible for numerous hereditary diseases in humans. The role of DNA replication, repair and transcription in the expansion process has been well documented. Here we analyzed, in a yeast experimental system, the role of RNA–DNA hybrids in genetic instability of long (GAA)n repeats, which cause Friedreich’s ataxia. Knocking out both yeast RNase H enzymes, which counteract the formation of RNA–DNA hybrids, increased (GAA)n repeat expansion and contraction rates when the repetitive sequence was transcribed. Unexpectedly, we observed a similar increase in repeat instability in RNase H-deficient cells when we either changed the direction of transcription-replication collisions, or flipped the repeat sequence such that the (UUC)n run occurred in the transcript. The increase in repeat expansions in RNase H-deficient strains was dependent on Rad52 and Pol32 proteins, suggesting that break-induced replication (BIR) is responsible for this effect. We conclude that expansions of (GAA)n repeats are induced by the formation of RNA–DNA hybrids that trigger BIR. Since this stimulation is independent of which strand of the repeat (homopurine or homopyrimidine) is in the RNA transcript, we hypothesize that triplex H-DNA structures stabilized by an RNA–DNA hybrid (H-loops), rather than conventional R-loops, could be responsible.
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Affiliation(s)
- Alexander J Neil
- Department of Biology, Tufts University, Medford, MA 02155, USA.,Genetics Program, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Miranda U Liang
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | | | - Kartik A Shah
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
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McGinty RJ, Rubinstein RG, Neil AJ, Dominska M, Kiktev D, Petes TD, Mirkin SM. Nanopore sequencing of complex genomic rearrangements in yeast reveals mechanisms of repeat-mediated double-strand break repair. Genome Res 2017; 27:2072-2082. [PMID: 29113982 PMCID: PMC5741057 DOI: 10.1101/gr.228148.117] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/26/2017] [Indexed: 01/25/2023]
Abstract
Improper DNA double-strand break (DSB) repair results in complex genomic rearrangements (CGRs) in many cancers and various congenital disorders in humans. Trinucleotide repeat sequences, such as (GAA)n repeats in Friedreich's ataxia, (CTG)n repeats in myotonic dystrophy, and (CGG)n repeats in fragile X syndrome, are also subject to double-strand breaks within the repetitive tract followed by DNA repair. Mapping the outcomes of CGRs is important for understanding their causes and potential phenotypic effects. However, high-resolution mapping of CGRs has traditionally been a laborious and highly skilled process. Recent advances in long-read DNA sequencing technologies, specifically Nanopore sequencing, have made possible the rapid identification of CGRs with single base pair resolution. Here, we have used whole-genome Nanopore sequencing to characterize several CGRs that originated from naturally occurring DSBs at (GAA)n microsatellites in Saccharomyces cerevisiae. These data gave us important insights into the mechanisms of DSB repair leading to CGRs.
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Affiliation(s)
- Ryan J McGinty
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | | | - Alexander J Neil
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Denis Kiktev
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
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Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw SJ, Algasaier SI, Kim JC, Finger LD, Jardine E, Gotham VJB, Sarker AH, Her MZ, Rashid F, Hamdan SM, Mirkin SM, Grasby JA, Tainer JA. Corrigendum: Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability. Nat Commun 2017; 8:16145. [PMID: 31305777 PMCID: PMC5603723 DOI: 10.1038/ncomms16145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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Abstract
In this review, we discuss how two evolutionarily conserved pathways at the interface of DNA replication and repair, template switching and break-induced replication, lead to the deleterious large-scale expansion of trinucleotide DNA repeats that cause numerous hereditary diseases. We highlight that these pathways, which originated in prokaryotes, may be subsequently hijacked to maintain long DNA microsatellites in eukaryotes. We suggest that the negative mutagenic outcomes of these pathways, exemplified by repeat expansion diseases, are likely outweighed by their positive role in maintaining functional repetitive regions of the genome such as telomeres and centromeres.
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Affiliation(s)
| | - Jane C Kim
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA, USA
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Belotserkovskii BP, Neil AJ, Saleh SS, Shin JHS, Mirkin SM, Hanawalt PC. 130 Transcription blockage by single-strand breaks in various sequences and the general model for transcription blockage by R-loop formation. J Biomol Struct Dyn 2013. [DOI: 10.1080/07391102.2013.786372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Belotserkovskii BP, Neil AJ, Saleh SS, Shin JHS, Mirkin SM, Hanawalt PC. Transcription blockage by homopurine DNA sequences: role of sequence composition and single-strand breaks. Nucleic Acids Res 2012; 41:1817-28. [PMID: 23275544 PMCID: PMC3561996 DOI: 10.1093/nar/gks1333] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The ability of DNA to adopt non-canonical structures can affect transcription and has broad implications for genome functioning. We have recently reported that guanine-rich (G-rich) homopurine-homopyrimidine sequences cause significant blockage of transcription in vitro in a strictly orientation-dependent manner: when the G-rich strand serves as the non-template strand [Belotserkovskii et al. (2010) Mechanisms and implications of transcription blockage by guanine-rich DNA sequences., Proc. Natl Acad. Sci. USA, 107, 12816–12821]. We have now systematically studied the effect of the sequence composition and single-stranded breaks on this blockage. Although substitution of guanine by any other base reduced the blockage, cytosine and thymine reduced the blockage more significantly than adenine substitutions, affirming the importance of both G-richness and the homopurine-homopyrimidine character of the sequence for this effect. A single-strand break in the non-template strand adjacent to the G-rich stretch dramatically increased the blockage. Breaks in the non-template strand result in much weaker blockage signals extending downstream from the break even in the absence of the G-rich stretch. Our combined data support the notion that transcription blockage at homopurine-homopyrimidine sequences is caused by R-loop formation.
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Neil AJ, Belotserkovskii BP, Hanawalt PC. Transcription blockage by bulky end termini at single-strand breaks in the DNA template: differential effects of 5' and 3' adducts. Biochemistry 2012; 51:8964-70. [PMID: 23066636 DOI: 10.1021/bi301240y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RNA polymerases from phage-infected bacteria and mammalian cells have been shown to bypass single-strand breaks (SSBs) with a single-nucleotide gap in the template DNA strand during transcription elongation; however, the SSB bypass efficiency varies significantly depending upon the backbone end chemistries at the break. Using a reconstituted T7 phage transcription system (T7 RNAP) and RNA polymerase II (RNAPII) in HeLa cell nuclear extracts, we observe a slight reduction in the level of transcription arrest at SSBs with no gap as compared to those with a single-nucleotide gap. We have shown that biotin and carbon-chain moieties linked to the 3' side, and in select cases the 5' side, of an SSB in the template strand strongly increase the level of transcription arrest when compared to unmodified SSBs. We also find that a small carbon-chain moiety linked to the upstream side of an SSB aids transcriptional bypass of SSBs for both T7 RNAP and RNAP II. Analysis of transcription across SSBs flanked by bulky 3' adducts reveals the ability of 3' end chemistries to arrest T7 RNAP in a size-dependent manner. T7 RNAP is also completely arrested when 3' adducts or 3'-phosphate groups are placed opposite 5'-phosphate groups at an SSB. We have also observed that a biotinylated thymine in the template strand (without a break) does not pose a strong block to transcription. Taken together, these results emphasize the importance of the size of 3', but usually not 5', end chemistries in arresting transcription at SSBs, substantiating the notion that bulky 3' lesions (e.g., topoisomerase cleavable complexes, 3'-phosphoglycolates, and 3'-unsaturated aldehydes) pose very strong blocks to transcribing RNA polymerases. These findings have implications for the processing of DNA damage through SSB intermediates and the mechanism of SSB bypass by T7 RNAP and mammalian RNAPII.
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Affiliation(s)
- Alexander J Neil
- Department of Biology, Stanford University, Stanford, California 94305, United States
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