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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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Marín-Aguilera M, Jares P, Sanfeliu E, Villacampa G, Hernández-Lllán E, Martínez-Puchol AI, Shankar S, González-Farré B, Waks AG, Brasó-Maristany F, Pardo F, Manning DK, Abery JA, Curaba J, Moon L, Gordon O, Galván P, Wachirakantapong P, Castillo O, Nee CM, Blasco P, Senevirathne TH, Sirenko V, Martínez-Sáez O, Aguirre A, Krop IE, Li Z, Spellman P, Metzger Filho O, Polyak K, Michaels P, Puig-Butillé JA, Vivancos A, Matito J, Buckingham W, Perou CM, Villagrasa-González P, Prat A, Parker JS, Paré L. Analytical validation of HER2DX genomic test for early-stage HER2-positive breast cancer. ESMO Open 2024; 9:102903. [PMID: 38452436 PMCID: PMC10937240 DOI: 10.1016/j.esmoop.2024.102903] [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: 12/24/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND HER2DX, a multianalyte genomic test, has been clinically validated to predict breast cancer recurrence risk (relapse risk score), the probability of achieving pathological complete response post-neoadjuvant therapy (pCR likelihood score), and individual ERBB2 messenger RNA (mRNA) expression levels in patients with early-stage human epidermal growth factor receptor 2 (HER2)-positive breast cancer. This study delves into the comprehensive analysis of HER2DX's analytical performance. MATERIALS AND METHODS Precision and reproducibility of HER2DX risk, pCR, and ERBB2 mRNA scores were assessed within and between laboratories using formalin-fixed paraffin-embedded (FFPE) tumor tissues and purified RNA. Robustness was appraised by analyzing the impact of tumor cell content and protocol variations including different instruments, reagent lots, and different RNA extraction kits. Variability was evaluated across intratumor biopsies and genomic platforms [RNA sequencing (RNAseq) versus nCounter], and according to protocol variations. RESULTS Precision analysis of 10 FFPE tumor samples yielded a maximal standard error of 0.94 across HER2DX scores (1-99 scale). High reproducibility of HER2DX scores across 29 FFPE tumors and 20 RNAs between laboratories was evident (correlation coefficients >0.98). The probability of identifying score differences >5 units was ≤5.2%. No significant variability emerged based on platform instruments, reagent lots, RNA extraction kits, or TagSet thaw/freeze cycles. Moreover, HER2DX displayed robustness at low tumor cell content (10%). Intratumor variability across 212 biopsies (106 tumors) was <4.0%. Concordance between HER2DX scores from 30 RNAs on RNAseq and nCounter platforms exceeded 90.0% (Cohen's κ coefficients >0.80). CONCLUSIONS The HER2DX assay is highly reproducible and robust for the quantification of recurrence risk, pCR likelihood, and ERBB2 mRNA expression in early-stage HER2-positive breast cancer.
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Affiliation(s)
| | - P Jares
- Pathology Department, Hospital Clínic of Barcelona, Barcelona, Spain; Molecular Biology Core, Hospital Clínic Barcelona, Barcelona, Spain
| | - E Sanfeliu
- Pathology Department, Hospital Clínic of Barcelona, Barcelona, Spain
| | - G Villacampa
- SOLTI Breast Cancer Research Group, Barcelona, Spain; Statistical Unit, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | | | - S Shankar
- Department of Pathology, Center for Advanced Medical Diagnostics, Brigham and Women's Hospital, Boston, USA
| | - B González-Farré
- Pathology Department, Hospital Clínic of Barcelona, Barcelona, Spain
| | - A G Waks
- Department of Pathology, Center for Advanced Medical Diagnostics, Brigham and Women's Hospital, Boston, USA
| | - F Brasó-Maristany
- Scientific Department, Reveal Genomics, S.L., Barcelona, Spain; Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - F Pardo
- Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - D K Manning
- Department of Pathology, Center for Advanced Medical Diagnostics, Brigham and Women's Hospital, Boston, USA
| | - J A Abery
- Eremid Genomic Services, LLC, Kannapolis, USA
| | - J Curaba
- Eremid Genomic Services, LLC, Kannapolis, USA
| | - L Moon
- Eremid Genomic Services, LLC, Kannapolis, USA
| | - O Gordon
- Eremid Genomic Services, LLC, Kannapolis, USA
| | - P Galván
- Scientific Department, Reveal Genomics, S.L., Barcelona, Spain; Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - P Wachirakantapong
- Department of Pathology, Center for Advanced Medical Diagnostics, Brigham and Women's Hospital, Boston, USA
| | - O Castillo
- Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - C M Nee
- Department of Pathology, Center for Advanced Medical Diagnostics, Brigham and Women's Hospital, Boston, USA
| | - P Blasco
- Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - T H Senevirathne
- Department of Pathology, Center for Advanced Medical Diagnostics, Brigham and Women's Hospital, Boston, USA
| | - V Sirenko
- Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - O Martínez-Sáez
- Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain; Medical Oncology Department, Hospital Clinic Barcelona, Barcelona, Spain; Department of Medicine, University of Barcelona, Barcelona, Spain
| | - A Aguirre
- Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - I E Krop
- Yale Cancer Center, New Haven, USA
| | - Z Li
- Dana-Farber Cancer Institute, Boston, USA; Harvard Medical School, Boston, USA
| | - P Spellman
- Oregon Health and Science University, Portland, USA
| | - O Metzger Filho
- Department of Pathology, Center for Advanced Medical Diagnostics, Brigham and Women's Hospital, Boston, USA; Harvard Medical School, Boston, USA
| | - K Polyak
- Dana-Farber Cancer Institute, Boston, USA; Harvard Medical School, Boston, USA
| | - P Michaels
- Department of Pathology, Center for Advanced Medical Diagnostics, Brigham and Women's Hospital, Boston, USA
| | - J A Puig-Butillé
- Molecular Biology Core, Hospital Clínic Barcelona, Barcelona, Spain
| | - A Vivancos
- Cancer Genomics Core, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - J Matito
- Scientific Department, Reveal Genomics, S.L., Barcelona, Spain; Cancer Genomics Core, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - W Buckingham
- Scientific Department, Reveal Genomics, S.L., Barcelona, Spain
| | - C M Perou
- Department of Genetics, Lineberger Comprehensive Cancer Center, Chapel Hill, USA
| | | | - A Prat
- Scientific Department, Reveal Genomics, S.L., Barcelona, Spain; Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain; Medical Oncology Department, Hospital Clinic Barcelona, Barcelona, Spain; Department of Medicine, University of Barcelona, Barcelona, Spain; Breast Cancer Unit, IOB-Quirón Salud, Barcelona, Spain
| | - J S Parker
- Department of Genetics, Lineberger Comprehensive Cancer Center, Chapel Hill, USA
| | - L Paré
- Scientific Department, Reveal Genomics, S.L., Barcelona, Spain.
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Rana HQ, Koeller DR, Walker M, Unal B, Levine AS, Chittenden A, Isidro RA, Hayes CP, Manam MD, Buehler RM, Manning DK, Barletta JA, Hornick JL, Garber JE, Ghazani AA. Advancing Precision Oncology in Hereditary Paraganglioma-Pheochromocytoma Syndromes: Integrated Interpretation and Data Sharing of the Germline and Tumor Genomes. Cancers (Basel) 2024; 16:947. [PMID: 38473309 PMCID: PMC10931192 DOI: 10.3390/cancers16050947] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/22/2024] [Accepted: 02/03/2024] [Indexed: 03/14/2024] Open
Abstract
Standard methods of variant assessment in hereditary cancer susceptibility genes are limited by the lack of availability of key supporting evidence. In cancer, information derived from tumors can serve as a useful source in delineating the tumor behavior and the role of germline variants in tumor progression. We have previously demonstrated the value of integrating tumor and germline findings to comprehensively assess germline variants in hereditary cancer syndromes. Building on this work, herein, we present the development and application of the INT2GRATE|HPPGL platform. INT2GRATE (INTegrated INTerpretation of GeRmline And Tumor gEnomes) is a multi-institution oncology consortium that aims to advance the integrated application of constitutional and tumor data and share the integrated variant information in publicly accessible repositories. The INT2GRATE|HPPGL platform enables automated parsing and integrated assessment of germline, tumor, and genetic findings in hereditary paraganglioma-pheochromocytoma syndromes (HPPGLs). Using INT2GRATE|HPPGL, we analyzed 8600 variants in succinate dehydrogenase (SDHx) genes and their associated clinical evidence. The integrated evidence includes germline variants in SDHx genes; clinical genetics evidence: personal and family history of HPPGL-related tumors; tumor-derived evidence: somatic inactivation of SDHx alleles, KIT and PDGFRA status in gastrointestinal stromal tumors (GISTs), multifocal or extra-adrenal tumors, and metastasis status; and immunohistochemistry staining status for SDHA and SDHB genes. After processing, 8600 variants were submitted programmatically from the INT2GRATE|HPPGL platform to ClinVar via a custom-made INT2GRATE|HPPGL variant submission schema and an application programming interface (API). This novel integrated variant assessment and data sharing in hereditary cancers aims to improve the clinical assessment of genomic variants and advance precision oncology.
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Affiliation(s)
- Huma Q. Rana
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA 02215, USA (A.C.)
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Diane R. Koeller
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA 02215, USA (A.C.)
| | - McKenzie Walker
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA (B.U.)
| | - Busra Unal
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA (B.U.)
| | - Alison Schwartz Levine
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA 02215, USA (A.C.)
| | - Anu Chittenden
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA 02215, USA (A.C.)
| | - Raymond A. Isidro
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Connor P. Hayes
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA (B.U.)
| | - Monica D. Manam
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ryan M. Buehler
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA 02215, USA (A.C.)
| | - Danielle K. Manning
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Justine A. Barletta
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jason L. Hornick
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Judy E. Garber
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA 02215, USA (A.C.)
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Arezou A. Ghazani
- Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA (B.U.)
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
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4
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Siegmund SE, Manning DK, Davineni PK, Dong F. Deriving tumor purity from cancer next generation sequencing data: applications for quantitative ERBB2 (HER2) copy number analysis and germline inference of BRCA1 and BRCA2 mutations. Mod Pathol 2022; 35:1458-1467. [PMID: 35902772 DOI: 10.1038/s41379-022-01083-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 03/30/2022] [Accepted: 04/03/2022] [Indexed: 11/09/2022]
Abstract
Tumor purity, or the relative contribution of tumor cells out of all cells in a pathological specimen, influences mutation identification and clinical interpretation of cancer panel next generation sequencing results. Here, we describe a method of calculating tumor purity using pathologist-guided copy number analysis from sequencing data. Molecular calculation of tumor purity showed strong linear correlation with purity derived from driver KRAS or BRAF variant allele fractions in colorectal cancers (R2 = 0.79) compared to histological estimation in the same set of colorectal cancers (R2 = 0.01) and in a broader dataset of cancers with various diagnoses (R2 = 0.35). We used calculated tumor purity to quantitate ERBB2 copy number in breast carcinomas with equivocal immunohistochemical staining and demonstrated strong correlation with fluorescence in situ hybridization (R2 = 0.88). Finally, we used calculated tumor purity to infer the germline status of variants in breast and ovarian carcinomas with concurrent germline testing. Tumor-only next generation sequencing correctly predicted the somatic versus germline nature of 26 of 26 (100%) pathogenic TP53, BRCA1 and BRCA2 variants. In this article, we describe a framework for calculating tumor purity from cancer next generation sequencing data. Accurate tumor purity assessment can be assimilated into interpretation pipelines to derive clinically useful information from cancer genomic panels.
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Affiliation(s)
| | | | - Phani K Davineni
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Fei Dong
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
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5
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Schwartz A, Manning DK, Koeller DR, Chittenden A, Isidro RA, Hayes CP, Abraamyan F, Manam MD, Dwan M, Barletta JA, Sholl LM, Yurgelun MB, Rana HQ, Garber JE, Ghazani AA. An integrated somatic and germline approach to aid interpretation of germline variants of uncertain significance in cancer susceptibility genes. Front Oncol 2022; 12:942741. [PMID: 36091175 PMCID: PMC9453486 DOI: 10.3389/fonc.2022.942741] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 05/12/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic profiles of tumors are often unique and represent characteristic mutational signatures defined by DNA damage or DNA repair response processes. The tumor-derived somatic information has been widely used in therapeutic applications, but it is grossly underutilized in the assessment of germline genetic variants. Here, we present a comprehensive approach for evaluating the pathogenicity of germline variants in cancer using an integrated interpretation of somatic and germline genomic data. We have previously demonstrated the utility of this integrated approach in the reassessment of pathogenic germline variants in selected cancer patients with unexpected or non-syndromic phenotypes. The application of this approach is presented in the assessment of rare variants of uncertain significance (VUS) in Lynch-related colon cancer, hereditary paraganglioma-pheochromocytoma syndrome, and Li-Fraumeni syndrome. Using this integrated method, germline VUS in PMS2, MSH6, SDHC, SHDA, and TP53 were assessed in 16 cancer patients after genetic evaluation. Comprehensive clinical criteria, somatic signature profiles, and tumor immunohistochemistry were used to re-classify VUS by upgrading or downgrading the variants to likely or unlikely actionable categories, respectively. Going forward, collation of such germline variants and creation of cross-institutional knowledgebase datasets that include integrated somatic and germline data will be crucial for the assessment of these variants in a larger cancer cohort.
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Affiliation(s)
- Alison Schwartz
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Danielle K. Manning
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Diane R. Koeller
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Anu Chittenden
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Raymond A. Isidro
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Connor P. Hayes
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Feruza Abraamyan
- Harvard Medical School, Boston, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Monica Devi Manam
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Meaghan Dwan
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Justine A. Barletta
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Matthew B. Yurgelun
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Huma Q. Rana
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Judy E. Garber
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Arezou A. Ghazani
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- *Correspondence: Arezou A. Ghazani,
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6
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Koeller DR, Manning DK, Schwartz A, Chittenden A, Hayes CP, Abraamyan F, Rana HQ, Lindeman NI, Garber JE, Ghazani AA. An optimized protocol for evaluating pathogenicity of VHL germline variants in patients suspected with von Hippel-Lindau syndrome: Using somatic genome to inform the role of germline variants. MethodsX 2022; 9:101761. [PMID: 35774415 PMCID: PMC9237939 DOI: 10.1016/j.mex.2022.101761] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/13/2022] [Indexed: 12/17/2022] Open
Abstract
The interpretation of hereditary genetic sequencing variants is often limited due to the absence of functional data and other key evidence to assess the role of variants in disease. Cancer genetics is unique, as two sets of genomic information are often available from a cancer patient: somatic and germline. Despite the progress made in the integrated analysis of somatic and germline findings, the assessment of pathogenicity of germline variants in high penetrance genes remains grossly underutilized. Indeed, standard ACMG/AMP guidelines for interpreting germline sequence variants do not address the evidence derived from tumor data in cancer. Previously, we have demonstrated the utility of somatic tumor data as supporting evidence to elucidate the role of germline variants in patients suspected with VHL syndrome and other cancers. We have leveraged the key elements of cancer genetics in these cases: genes with expected high disease penetrance and those with a known biallelic mechanism of tumorigenicity. Here we provide our optimized protocol for evaluating the pathogenicity of germline VHL variants using informative somatic profiling data. This protocol provides details of case selection, assessment of personal and family evidence, somatic tumor profiles, and loss of heterozygosity (LOH) as supporting evidence for the re-evaluation of germline variants.
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Affiliation(s)
- Diane R Koeller
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Danielle K Manning
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Alison Schwartz
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Anu Chittenden
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Connor P Hayes
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Feruza Abraamyan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Huma Q Rana
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Population Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Judy E Garber
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Population Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Arezou A Ghazani
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
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7
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Schienda J, Church AJ, Corson LB, Decker B, Clinton CM, Manning DK, Imamovic-Tuco A, Reidy D, Strand GR, Applebaum MA, Bagatell R, DuBois SG, Glade-Bender JL, Kang W, Kim A, Laetsch TW, Macy ME, Maese L, Pinto N, Sabnis AJ, Schiffman JD, Colace SI, Volchenboum SL, Weiser DA, Nowak JA, Lindeman NI, Janeway KA, Crompton BD, Kamihara J. Germline Sequencing Improves Tumor-Only Sequencing Interpretation in a Precision Genomic Study of Patients With Pediatric Solid Tumor. JCO Precis Oncol 2021; 5:PO.21.00281. [PMID: 34964003 PMCID: PMC8710335 DOI: 10.1200/po.21.00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/23/2021] [Revised: 10/14/2021] [Accepted: 11/09/2021] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Molecular tumor profiling is becoming a routine part of clinical cancer care, typically involving tumor-only panel testing without matched germline. We hypothesized that integrated germline sequencing could improve clinical interpretation and enhance the identification of germline variants with significant hereditary risks. MATERIALS AND METHODS Tumors from pediatric patients with high-risk, extracranial solid malignancies were sequenced with a targeted panel of cancer-associated genes. Later, germline DNA was analyzed for a subset of these genes. We performed a post hoc analysis to identify how an integrated analysis of tumor and germline data would improve clinical interpretation. RESULTS One hundred sixty participants with both tumor-only and germline sequencing reports were eligible for this analysis. Germline sequencing identified 38 pathogenic or likely pathogenic variants among 35 (22%) patients. Twenty-five (66%) of these were included in the tumor sequencing report. The remaining germline pathogenic or likely pathogenic variants were single-nucleotide variants filtered out of tumor-only analysis because of population frequency or copy-number variation masked by additional copy-number changes in the tumor. In tumor-only sequencing, 308 of 434 (71%) single-nucleotide variants reported were present in the germline, including 31% with suggested clinical utility. Finally, we provide further evidence that the variant allele fraction from tumor-only sequencing is insufficient to differentiate somatic from germline events. CONCLUSION A paired approach to analyzing tumor and germline sequencing data would be expected to improve the efficiency and accuracy of distinguishing somatic mutations and germline variants, thereby facilitating the process of variant curation and therapeutic interpretation for somatic reports, as well as the identification of variants associated with germline cancer predisposition.
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Affiliation(s)
- Jaclyn Schienda
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | | | - Laura B. Corson
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Brennan Decker
- Department of Pathology, Boston Children's Hospital, Boston, MA
| | - Catherine M. Clinton
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | | | - Alma Imamovic-Tuco
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Deirdre Reidy
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Gianna R. Strand
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | | | - Rochelle Bagatell
- Department of Pediatrics, Children's Hospital of Philadelphia/University of Pennsylvania, Philadelphia, PA
| | - Steven G. DuBois
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | | | - Wenjun Kang
- Center for Research Informatics, University of Chicago, Chicago, IL
| | - AeRang Kim
- Center for Cancer and Blood Disorders, Children's National Hospital, Washington, DC
| | - Theodore W. Laetsch
- Department of Pediatrics, Children's Hospital of Philadelphia/University of Pennsylvania, Philadelphia, PA
| | - Margaret E. Macy
- Children's Hospital Colorado and University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Luke Maese
- Division of Pediatrics (Pediatric Hematology and Oncology University of Utah), Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Navin Pinto
- Division of Pediatric Hematology/Oncology, University of Washington, Seattle, WA
| | - Amit J. Sabnis
- Department of Pediatrics, University of California, San Francisco, CA, San Francisco, CA
| | - Joshua D. Schiffman
- Division of Pediatrics (Pediatric Hematology and Oncology University of Utah), Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Susan I. Colace
- Division of Pediatric Hematology, Oncology, and BMT, Nationwide Children's Hospital, Columbus, OH
| | | | - Daniel A. Weiser
- Division of Pediatric Hematology, Oncology, and Cellular Therapy, Children's Hospital at Montefiore, Bronx, NY
| | | | - Neal I. Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Katherine A. Janeway
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Brian D. Crompton
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Junne Kamihara
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
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8
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Li YY, Schmidt RJ, Manning DK, Jia Y, Dong F. Contamination Assessment for Cancer Next-Generation Sequencing: Method Development and Clinical Implementation. Arch Pathol Lab Med 2021; 146:227-232. [PMID: 34015814 DOI: 10.5858/arpa.2020-0679-oa] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The presence of allogeneic contamination impacts clinical reporting in cancer next-generation sequencing specimens. Although consensus guidelines recommend the identification of contaminating DNA as a part of quality control, implementation of contamination assessment methods in clinical molecular diagnostic laboratories has not been reported in the literature. OBJECTIVE.— To develop and implement a method to assess allogeneic contamination in clinical cancer next-generation sequencing specimens. DESIGN.— We describe a method to detect contamination based on the evaluation of single-nucleotide polymorphic sites from tumor-only specimens. We validate this method and apply it to a large cohort of cancer sequencing specimens. RESULTS.— Identification of specimen contamination is validated via in silico and in vitro mixtures, and reference range and reproducibility are established in a panel of normal specimens. The algorithm accurately detects an episode of systemic contamination due to reagent impurity. We prospectively apply this algorithm across 7571 clinical cancer specimens from a targeted next-generation sequencing panel, in which 262 specimens (3.5%) are predicted to be affected by greater than 5% contamination. CONCLUSIONS.— Allogeneic contamination can be inferred from intrinsic cancer next-generation sequencing data without paired normal sequencing. The adoption of this approach can be useful as a quality control measure for laboratories performing clinical next-generation sequencing.
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Affiliation(s)
- Yvonne Y Li
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Li, Schmidt, Manning, Jia, Dong).,the Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts (Li)
| | - Ryan J Schmidt
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Li, Schmidt, Manning, Jia, Dong).,the Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine of USC, Los Angeles, California (Schmidt)
| | - Danielle K Manning
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Li, Schmidt, Manning, Jia, Dong)
| | - Yonghui Jia
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Li, Schmidt, Manning, Jia, Dong)
| | - Fei Dong
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Li, Schmidt, Manning, Jia, Dong)
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9
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Koeller DR, Schwartz A, Manning DK, Dong F, Lindeman NI, Garber JE, Ghazani AA. Novel Pathogenic Germline Variant of the Adenomatous Polyposis Coli (APC) Gene, p.S2627Gfs*12 Identified in a Mild Phenotype of APC-Associated Polyposis: A Case Report. Am J Case Rep 2020; 21:e927293. [PMID: 33303731 PMCID: PMC7737709 DOI: 10.12659/ajcr.927293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 12/31/2022]
Abstract
Patient: Male, 80-year-old Final Diagnosis: Attenuated APC-associated polyposis Symptoms: Colon polyps • renal carcinoma Medication: — Clinical Procedure: — Specialty: Genetics
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Affiliation(s)
- Diane R Koeller
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alison Schwartz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Fei Dong
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Arezou A Ghazani
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
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10
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Tsai HK, Brackett DG, Szeto D, Frazier R, MacLeay A, Davineni P, Manning DK, Garcia E, Lindeman NI, Le LP, Lennerz JK, Gibson CJ, Lindsley RC, Kim AS, Nardi V. Targeted Informatics for Optimal Detection, Characterization, and Quantification of FLT3 Internal Tandem Duplications Across Multiple Next-Generation Sequencing Platforms. J Mol Diagn 2020; 22:1162-1178. [PMID: 32603763 PMCID: PMC7479488 DOI: 10.1016/j.jmoldx.2020.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 12/11/2019] [Revised: 03/27/2020] [Accepted: 06/08/2020] [Indexed: 01/09/2023] Open
Abstract
Assessment of internal tandem duplications in FLT3 (FLT3-ITDs) and their allelic ratio (AR) is recommended by clinical guidelines for diagnostic workup of acute myeloid leukemia and traditionally performed through capillary electrophoresis (CE). Although significant progress has been made integrating FLT3-ITD detection within contemporary next-generation sequencing (NGS) panels, AR estimation is not routinely part of clinical NGS practice because of inherent biases and challenges. In this study, data from multiple NGS platforms—anchored multiplex PCR (AMP), amplicon [TruSeq Custom Amplicon (TSCA)], and hybrid-capture—were analyzed through a custom algorithm, including platform-specific measures of AR. Sensitivity and specificity of NGS for FLT3-ITD status relative to CE were 100% (42/42) and 99.4% (1076/1083), respectively, by AMP on an unselected cohort and 98.1% (53/54) and 100% (48/48), respectively, by TSCA on a selected cohort. Primer analysis identified criteria for ITDs to escape detection by TSCA, estimated to occur in approximately 9% of unselected ITDs. Allelic fractions under AMP or TSCA were highly correlated to CE, with linear regression slopes near 1 for ITDs not duplicating primers, and systematically underestimated for ITDs duplicating a primer. Bias was alleviated in AMP through simple adjustments. This article provides an approach for targeted computational FLT3-ITD analysis for NGS data from multiple platforms; AMP was found capable of near perfect sensitivity and specificity with relatively accurate estimates of ARs.
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Affiliation(s)
- Harrison K Tsai
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Diane G Brackett
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - David Szeto
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ryan Frazier
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Allison MacLeay
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Phani Davineni
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Danielle K Manning
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Elizabeth Garcia
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Long P Le
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Christopher J Gibson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - R Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.
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11
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Slevin MK, Wollison BM, Powers W, Burns RT, Patel N, Ducar MD, Starrett GJ, Garcia EP, Manning DK, Cheng J, Hanna GJ, Kaye KM, Van Hummelen P, Nag A, Thorner AR, DeCaprio JA, MacConaill LE. ViroPanel: Hybrid Capture and Massively Parallel Sequencing for Simultaneous Detection and Profiling of Oncogenic Virus Infection and Tumor Genome. J Mol Diagn 2020; 22:476-487. [PMID: 32068070 DOI: 10.1016/j.jmoldx.2019.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/03/2019] [Accepted: 12/24/2019] [Indexed: 12/17/2022] Open
Abstract
Precision cancer medicine aims to classify tumors by site, histology, and molecular testing to determine an individualized profile of cancer alterations. Viruses are a major contributor to oncogenesis, causing 12% to 20% of all human cancers. Several viruses are causal of specific types of cancer, promoting dysregulation of signaling pathways and resulting in carcinogenesis. In addition, integration of viral DNA into the host (human) genome is a hallmark of some viral species. Tests for the presence of viral infection used in the clinical setting most often use quantitative PCR or immunohistochemical staining. Both approaches have limitations and need to be interpreted/scored appropriately. In some cases, results are not binary (virus present/absent), and it is unclear what to do with a weakly or partially positive result. In addition, viral testing of cancers is performed separately from tests to detect human genomic alterations and can thus be time-consuming and use limited valuable specimen. We present a hybrid-capture and massively parallel sequencing approach to detect viral infection that is integrated with targeted genomic analysis to provide a more complete tumor profile from a single sample.
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Affiliation(s)
- Michael K Slevin
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Bruce M Wollison
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Winslow Powers
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Robert T Burns
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Neil Patel
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew D Ducar
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gabriel J Starrett
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Elizabeth P Garcia
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Danielle K Manning
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jingwei Cheng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Glenn J Hanna
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kenneth M Kaye
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Paul Van Hummelen
- Division of Oncology, Department of Medicine, Genome Technology Center, Stanford University, Stanford, California
| | - Anwesha Nag
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Aaron R Thorner
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Laura E MacConaill
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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12
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Slevin MK, Powers WT, Burns RT, Wollison BM, Coleman HA, Paskavitz AL, Nag A, Manning DK, Garcia E, Ducar MD, Thorner AR, MacConaill LE. Abstract 3417: Detection and analysis of oncovirus integration sites in FFPE-derived human tumor samples using hybrid capture and massively parallel sequencing. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Viral genome integration into the host's genetic material can provide cells with selective advantages that make critical contributions to unregulated growth, cell division, and genomic instability. Current clinical tests include in situ hybridization, immunohistochemical, and real-time PCR assays that are unable to identify viral integration points in relation to oncongenic somatic mutations. This precludes a complete picture of how such mutations work together to promote, maintain, and disperse tumor progression. Precision cancer medicine employs genomic technologies (e.g., massively parallel sequencing) for high-throughput genomic profiling to molecularly define patient tumors, allowing identification of clinically actionable mutations. We created a custom probe set for targeted hybrid capture enrichment of several oncoviruses and have tested it in combination with our clinical tumor DNA profiling probe set, OncoPanel v3.
Selected viruses were chosen due to their serving as causative cancer agents that disrupt tumor suppressors, facilitate genomic instability, and increase oncogene expression. The full viral genomes of hepatitis B virus and high-risk human papilloma virus (HPV) strains, 16, 18, 33, and 45 were targeted. Additionally, regions coding for E6 and E7 oncoproteins were targeted for several of the low-risk HPV strains, as was the LANA region of Kaposi's sarcoma-associated virus.
FFPE-derived human tumor samples of known infection status were fragmented to 250 bp and converted into Illumina libraries. Pooled libraries underwent hybrid capture with custom, Agilent-designed OncoPanel and viral probes, and resulting captures were sequenced on an Illumina HiSeq2500 sequencer.
SvABA (Structural variation and indel analysis by assembly) was used to perform de novo sequence assembly on soft-clipped and discordant aligned reads, and viral integration sites were identified by realigning contigs to the host genome to obtain breakpoint coordinates. Reduction of false positives was facilitated using dual-matched sample barcodes (IDT), which virtually eliminate barcode cross-talk, allowing for confident detection of low allele frequency events. Furthermore, inclusion of unique molecular identifiers (UMI) permitted discrimination of PCR duplicates and errors.
Our results demonstrate high concordance with clinical samples of known infection status and provide viral integration break point locations in association with genomic tumor mutations. Viral integration sites are often associated with deletions or amplifications of the host's flanking genomic regions. Furthermore, viral integration may disrupt or enhance expression of tumor suppressors and oncogenes, respectively. Coupled with tumor molecular profiling, this information will better inform patient treatment.
Citation Format: Michael K. Slevin, Winslow T. Powers, Robert T. Burns, Bruce M. Wollison, Haley A. Coleman, Amanda L. Paskavitz, Anwesha Nag, Danielle K. Manning, Elizabeth Garcia, Matthew D. Ducar, Aaron R. Thorner, Laura E. MacConaill. Detection and analysis of oncovirus integration sites in FFPE-derived human tumor samples using hybrid capture and massively parallel sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3417.
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13
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Czarnecki PG, Gabriel GC, Manning DK, Sergeev M, Lemke K, Klena NT, Liu X, Chen Y, Li Y, San Agustin JT, Garnaas MK, Francis RJ, Tobita K, Goessling W, Pazour GJ, Lo CW, Beier DR, Shah JV. ANKS6 is the critical activator of NEK8 kinase in embryonic situs determination and organ patterning. Nat Commun 2015; 6:6023. [PMID: 25599650 PMCID: PMC4361001 DOI: 10.1038/ncomms7023] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [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: 05/15/2014] [Accepted: 12/02/2014] [Indexed: 11/09/2022] Open
Abstract
The ciliary kinase NEK8 plays a critical role in situs determination and cystic kidney disease, yet its exact function remains unknown. In this study, we identify ANKS6 as a target and activator of NEK8. ANKS6 requires NEK8 for localizing to the ciliary inversin compartment (IC) and activates NEK8 by binding to its kinase domain. Here we demonstrate the functional importance of this interaction through the analysis of two novel mouse mutations, Anks6(Streaker) and Nek8(Roc). Both display heterotaxy, cardiopulmonary malformations and cystic kidneys, a syndrome also characteristic of mutations in Invs and Nphp3, the other known components of the IC. The Anks6(Strkr) mutation decreases ANKS6 interaction with NEK8, precluding NEK8 activation. The Nek8(Roc) mutation inactivates NEK8 kinase function while preserving ANKS6 localization to the IC. Together, these data reveal the crucial role of NEK8 kinase activation within the IC, promoting proper left-right patterning, cardiopulmonary development and renal morphogenesis.
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Affiliation(s)
- Peter G Czarnecki
- 1] Department of Systems Biology, Harvard Medical School, 4 Blackfan Circle, HIM 568, Boston, Massachussetts 02115, USA [2] Renal Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA [3] Renal Division, Beth Israel Deaconess Medical Center, Boston, Massachussetts 02215, USA
| | - George C Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Danielle K Manning
- Genetics Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA
| | - Mikhail Sergeev
- 1] Department of Systems Biology, Harvard Medical School, 4 Blackfan Circle, HIM 568, Boston, Massachussetts 02115, USA [2] Renal Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA
| | - Kristi Lemke
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Nikolai T Klena
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Xiaoqin Liu
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Yu Chen
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - You Li
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Jovenal T San Agustin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachussetts 01655, USA
| | - Maija K Garnaas
- Genetics Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA
| | - Richard J Francis
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Kimimasa Tobita
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Wolfram Goessling
- Genetics Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachussetts 01655, USA
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - David R Beier
- 1] Genetics Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA [2] Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington 98101, USA
| | - Jagesh V Shah
- 1] Department of Systems Biology, Harvard Medical School, 4 Blackfan Circle, HIM 568, Boston, Massachussetts 02115, USA [2] Renal Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA
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14
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Choi HJC, Lin JR, Vannier JB, Slaats GG, Kile AC, Paulsen RD, Manning DK, Beier DR, Giles RH, Boulton SJ, Cimprich KA. NEK8 links the ATR-regulated replication stress response and S phase CDK activity to renal ciliopathies. Mol Cell 2013; 51:423-39. [PMID: 23973373 PMCID: PMC3790667 DOI: 10.1016/j.molcel.2013.08.006] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [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: 02/27/2013] [Revised: 06/09/2013] [Accepted: 07/24/2013] [Indexed: 01/03/2023]
Abstract
Renal ciliopathies are a leading cause of kidney failure, but their exact etiology is poorly understood. NEK8/NPHP9 is a ciliary kinase associated with two renal ciliopathies in humans and mice, nephronophthisis (NPHP) and polycystic kidney disease. Here, we identify NEK8 as a key effector of the ATR-mediated replication stress response. Cells lacking NEK8 form spontaneous DNA double-strand breaks (DSBs) that further accumulate when replication forks stall, and they exhibit reduced fork rates, unscheduled origin firing, and increased replication fork collapse. NEK8 suppresses DSB formation by limiting cyclin A-associated CDK activity. Strikingly, a mutation in NEK8 that is associated with renal ciliopathies affects its genome maintenance functions. Moreover, kidneys of NEK8 mutant mice accumulate DNA damage, and loss of NEK8 or replication stress similarly disrupts renal cell architecture in a 3D-culture system. Thus, NEK8 is a critical component of the DNA damage response that links replication stress with cystic kidney disorders.
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Affiliation(s)
- Hyo Jei Claudia Choi
- Stanford University School of Medicine, Department of Chemical and Systems Biology, Stanford, CA 94025
| | - Jia-Ren Lin
- Stanford University School of Medicine, Department of Chemical and Systems Biology, Stanford, CA 94025
| | - Jean-Baptiste Vannier
- London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Gisela G. Slaats
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, the Netherlands
| | - Andrew C. Kile
- Stanford University School of Medicine, Department of Chemical and Systems Biology, Stanford, CA 94025
| | - Renee D. Paulsen
- Stanford University School of Medicine, Department of Chemical and Systems Biology, Stanford, CA 94025
| | | | - David R. Beier
- Brigham and Women's Hospital, Division of Genetics, Boston MA, 02115
| | - Rachel H. Giles
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, the Netherlands
| | - Simon J. Boulton
- London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Karlene A. Cimprich
- Stanford University School of Medicine, Department of Chemical and Systems Biology, Stanford, CA 94025
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15
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Manning DK, Sergeev M, van Heesbeen RG, Wong MD, Oh JH, Liu Y, Henkelman RM, Drummond I, Shah JV, Beier DR. Loss of the ciliary kinase Nek8 causes left-right asymmetry defects. J Am Soc Nephrol 2013; 24:100-12. [PMID: 23274954 DOI: 10.1681/asn.2012050490] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A missense mutation in mouse Nek8, which encodes a ciliary kinase, produces the juvenile cystic kidneys (jck) model of polycystic kidney disease, but the functions of Nek8 are incompletely understood. Here, we generated a Nek8-null allele and found that homozygous mutant mice die at birth and exhibit randomization of left-right asymmetry, cardiac anomalies, and glomerular kidney cysts. The requirement for Nek8 in left-right patterning is conserved, as knockdown of the zebrafish ortholog caused randomized heart looping. Ciliogenesis was intact in Nek8-deficient embryos and cells, but we observed misexpression of left-sided marker genes early in development, suggesting that nodal ciliary signaling was perturbed. We also generated jck/Nek8 compound heterozygotes; these mutants developed less severe cystic disease than jck homozygotes and provided genetic evidence that the jck allele may encode a gain-of-function protein. Notably, NEK8 and polycystin-2 (PC2) proteins interact, and we found that Nek8(-/-) and Pkd2(-/-) embryonic phenotypes are strikingly similar. Nek8-deficient embryos and cells did express PC2 normally, which localized properly to the cilia. However, similar to cells lacking PC2, NEK8-depleted inner medullary collecting duct cells exhibited a defective response to fluid shear, suggesting that NEK8 may play a role in mediating PC2-dependent signaling.
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Affiliation(s)
- Danielle K Manning
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
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16
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Dwyer ND, Manning DK, Moran JL, Mudbhary R, Fleming MS, Favero CB, Vock VM, O'Leary DDM, Walsh CA, Beier DR. A forward genetic screen with a thalamocortical axon reporter mouse yields novel neurodevelopment mutants and a distinct emx2 mutant phenotype. Neural Dev 2011; 6:3. [PMID: 21214893 PMCID: PMC3024922 DOI: 10.1186/1749-8104-6-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [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: 08/20/2010] [Accepted: 01/07/2011] [Indexed: 12/02/2022] Open
Abstract
Background The dorsal thalamus acts as a gateway and modulator for information going to and from the cerebral cortex. This activity requires the formation of reciprocal topographic axon connections between thalamus and cortex. The axons grow along a complex multistep pathway, making sharp turns, crossing expression boundaries, and encountering intermediate targets. However, the cellular and molecular components mediating these steps remain poorly understood. Results To further elucidate the development of the thalamocortical system, we first created a thalamocortical axon reporter line to use as a genetic tool for sensitive analysis of mutant mouse phenotypes. The TCA-tau-lacZ reporter mouse shows specific, robust, and reproducible labeling of thalamocortical axons (TCAs), but not the overlapping corticothalamic axons, during development. Moreover, it readily reveals TCA pathfinding abnormalities in known cortical mutants such as reeler. Next, we performed an unbiased screen for genes involved in thalamocortical development using random mutagenesis with the TCA reporter. Six independent mutant lines show aberrant TCA phenotypes at different steps of the pathway. These include ventral misrouting, overfasciculation, stalling at the corticostriatal boundary, and invasion of ectopic cortical cell clusters. An outcross breeding strategy coupled with a genomic panel of single nucleotide polymorphisms facilitated genetic mapping with small numbers of mutant mice. We mapped a ventral misrouting mutant to the Emx2 gene, and discovered that some TCAs extend to the olfactory bulbs in this mutant. Mapping data suggest that other lines carry mutations in genes not previously known for roles in thalamocortical development. Conclusions These data demonstrate the feasibility of a forward genetic approach to understanding mammalian brain morphogenesis and wiring. A robust axonal reporter enabled sensitive analysis of a specific axon tract inside the mouse brain, identifying mutant phenotypes at multiple steps of the pathway, and revealing a new aspect of the Emx2 mutant. The phenotypes highlight vulnerable choice points and latent tendencies of TCAs, and will lead to a refined understanding of the elements and interactions required to form the thalamocortical system. See Commentary: http://www.biomedcentral.com/1741-7007/9/1
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Affiliation(s)
- Noelle D Dwyer
- Howard Hughes Medical Institute, Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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Shiba D, Manning DK, Koga H, Beier DR, Yokoyama T. Inv acts as a molecular anchor for Nphp3 and Nek8 in the proximal segment of primary cilia. Cytoskeleton (Hoboken) 2010; 67:112-9. [PMID: 20169535 DOI: 10.1002/cm.20428] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A primary cilium is an antenna-like structure extending from the surface of most vertebrate cells. It is structurally divided along its vertical axis into sub-compartments that include the ciliary tip, the shaft, the ciliary necklace segment, the transitional zone and the basal body. We recently discovered that the shaft of the primary cilia has a distinct molecular compartment, termed the "Inv compartment", which is characterized by the accumulation of Inv at the base of primary cilia. Inv was discovered as a causative gene in inv mutant mice. It was later found to be responsible for the infantile type of nephronophthisis (NPHP2). Nephronophthisis (NPHP) is an autosomal recessive kidney disease. Nine causative genes have been identified, with all examined products thought to function in cilia, basal body and/or centrioles. However, their exact intra-ciliary localization and relationship have not been clear. Here, we report that products of Nphp3 and Nek8 (the mouse orthologs of the causative genes for NPHP3 and NPHP9, respectively) localize to the Inv compartment. We also show that Inv is essential for the compartmental localization of Nphp3 and Nek8, whereas localization of Inv does not require Nphp3 or Nek8. Nphp1 and Nphp4 also localize at the proximal region of the cilium, but not in Inv compartment. Our results indicate that Inv acts as an anchor for Nphp3 and Nek8 in the Inv compartment, and suggest that Inv compartment is a candidate site for intra-ciliary interaction of Inv, Nphp3 and Nek8.
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Affiliation(s)
- Dai Shiba
- Department of Anatomy and Developmental Biology, Kyoto Prefectural University of Medicine, Japan
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Smits P, Bolton AD, Funari V, Hong M, Boyden ED, Lu L, Manning DK, Dwyer ND, Moran JL, Prysak M, Merriman B, Nelson SF, Bonafé L, Superti-Furga A, Ikegawa S, Krakow D, Cohn DH, Kirchhausen T, Warman ML, Beier DR. Lethal skeletal dysplasia in mice and humans lacking the golgin GMAP-210. N Engl J Med 2010; 362:206-16. [PMID: 20089971 PMCID: PMC3108191 DOI: 10.1056/nejmoa0900158] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Establishing the genetic basis of phenotypes such as skeletal dysplasia in model organisms can provide insights into biologic processes and their role in human disease. METHODS We screened mutagenized mice and observed a neonatal lethal skeletal dysplasia with an autosomal recessive pattern of inheritance. Through genetic mapping and positional cloning, we identified the causative mutation. RESULTS Affected mice had a nonsense mutation in the thyroid hormone receptor interactor 11 gene (Trip11), which encodes the Golgi microtubule-associated protein 210 (GMAP-210); the affected mice lacked this protein. Golgi architecture was disturbed in multiple tissues, including cartilage. Skeletal development was severely impaired, with chondrocytes showing swelling and stress in the endoplasmic reticulum, abnormal cellular differentiation, and increased cell death. Golgi-mediated glycosylation events were altered in fibroblasts and chondrocytes lacking GMAP-210, and these chondrocytes had intracellular accumulation of perlecan, an extracellular matrix protein, but not of type II collagen or aggrecan, two other extracellular matrix proteins. The similarities between the skeletal and cellular phenotypes in these mice and those in patients with achondrogenesis type 1A, a neonatal lethal form of skeletal dysplasia in humans, suggested that achondrogenesis type 1A may be caused by GMAP-210 deficiency. Sequence analysis revealed loss-of-function mutations in the 10 unrelated patients with achondrogenesis type 1A whom we studied. CONCLUSIONS GMAP-210 is required for the efficient glycosylation and cellular transport of multiple proteins. The identification of a mutation affecting GMAP-210 in mice, and then in humans, as the cause of a lethal skeletal dysplasia underscores the value of screening for abnormal phenotypes in model organisms and identifying the causative mutations.
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Affiliation(s)
- Patrick Smits
- Orthopedic Research Laboratories, Department of Orthopedic Surgery, Children's Hospital, Boston, MA 02115, USA
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Trapp ML, Galtseva A, Manning DK, Beier DR, Rosenblum ND, Quarmby LM. Defects in ciliary localization of Nek8 is associated with cystogenesis. Pediatr Nephrol 2008; 23:377-87. [PMID: 18189147 PMCID: PMC6890203 DOI: 10.1007/s00467-007-0692-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 10/08/2007] [Accepted: 10/10/2007] [Indexed: 01/01/2023]
Abstract
Mutations in the human NIMA (Never in Mitosis gene A)-related kinase 8 (Nek8) are associated with a rare form of the juvenile renal cystic disease, nephronophthisis type 9, and mutations in murine Nek8 cause renal cysts in jck mice. Cystogenesis involves dysfunctional ciliary signaling, and we have previously reported that Nek8 localizes to the primary cilium in mouse kidney epithelial cells. We now report that in developing mouse kidney, Nek8 is detected in the cilia of a subset of ureteric-bud-derived tubules at embryonic day (E)15.5. An increasing proportion of ureteric-bud-derived tubules express ciliary Nek8 until E18.5. Postnatal day 1 and 7 Nek8 is observed with equal frequency in both ureteric-bud and non-ureteric-bud-derived tubules. To investigate the cell biological consequences of kinase-deficient and jck mutant forms of Nek8, we transiently expressed green fluorescent protein (GFP)-tagged constructs in vitro. Mutations in the kinase and C-terminal domains of Nek8 adversely affected ciliary targeting but did not affect ciliogenesis or ciliary length. Consistent with these in vitro observations, kidneys from homozygous jck mice revealed reduced ciliary expression of Nek8 compared with kidneys from heterozygous (unaffected) mice. These data indicate that the ciliary localization of Nek8 in a subset of ureteric-bud-derived kidney tubules is essential for maintaining the integrity of those tubules in the mammalian kidney.
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Affiliation(s)
- Melissa L Trapp
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Dr., Burnaby, BC V5A1S6, Canada
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Sohara E, Luo Y, Zhang J, Manning DK, Beier DR, Zhou J. Nek8 regulates the expression and localization of polycystin-1 and polycystin-2. J Am Soc Nephrol 2008; 19:469-76. [PMID: 18235101 DOI: 10.1681/asn.2006090985] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Nek8 is a serine/threonine kinase that is mutated in the jck (juvenile cystic kidneys) mouse, a model of autosomal recessive juvenile polycystic kidney disease, but its function is poorly understood. We used the jck mouse to study the functional relationship between Nek8 and other proteins that have been implicated in polycystic kidney diseases. In the collecting tubules and collecting ducts of wild-type mice, we found that Nek8 was localized to the proximal portion of primary cilia and was weakly detected in the cytosol. In the jck mutant, however, Nek8 was found along the entire length of cilia. Coimmunoprecipitation experiments demonstrated that Nek8 interacted with polycystin-2, but not with polycystin-1, and that the jck mutation did not affect this interaction. Western blot analysis and real-time reverse transcriptase PCR revealed that the protein and mRNA expression of polycystin-1 (PC1) and polycystin-2 (PC2) were increased in jck mouse kidneys. The jck mutation also led to abnormal phosphorylatin of PC2, and this was associated with longer cilia and ciliary accumulation of PC1 and PC2. Our data suggests that Nek8 interacts with the signal transduction pathways of the polycystins and may control the targeting of these ciliary proteins. Dysfunction Nek8 may lead to cystogenesis by altering the structure and function of cilia in the distal nephron.
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Affiliation(s)
- Eisei Sohara
- Harvard Institutes of Medicine, Room 522, Brigham and Women's Hospital and Harvard Medical School, 4 Blackfan Circle, Boston, MA 02115, USA
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Moran JL, Bolton AD, Tran PV, Brown A, Dwyer ND, Manning DK, Bjork BC, Li C, Montgomery K, Siepka SM, Vitaterna MH, Takahashi JS, Wiltshire T, Kwiatkowski DJ, Kucherlapati R, Beier DR. Utilization of a whole genome SNP panel for efficient genetic mapping in the mouse. Genome Res 2006; 16:436-40. [PMID: 16461637 PMCID: PMC1415208 DOI: 10.1101/gr.4563306] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Phenotype-driven genetics can be used to create mouse models of human disease and birth defects. However, the utility of these mutant models is limited without identification of the causal gene. To facilitate genetic mapping, we developed a fixed single nucleotide polymorphism (SNP) panel of 394 SNPs as an alternative to analyses using simple sequence length polymorphism (SSLP) marker mapping. With the SNP panel, chromosomal locations for 22 monogenic mutants were identified. The average number of affected progeny genotyped for mapped monogenic mutations is nine. Map locations for several mutants have been obtained with as few as four affected progeny. The average size of genetic intervals obtained for these mutants is 43 Mb, with a range of 17-83 Mb. Thus, our SNP panel allows for identification of moderate resolution map position with small numbers of mice in a high-throughput manner. Importantly, the panel is suitable for mapping crosses from many inbred and wild-derived inbred strain combinations. The chromosomal localizations obtained with the SNP panel allow one to quickly distinguish between potentially novel loci or remutations in known genes, and facilitates fine mapping and positional cloning. By using this approach, we identified DNA sequence changes in two ethylnitrosourea-induced mutants.
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Affiliation(s)
- Jennifer L Moran
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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