1
|
Young CC, Horton C, Grzybowski J, Abualkheir N, Ramirez Castano J, Molparia B, Karam R, Chao E, Richardson ME. Solving Missing Heritability in Patients With Familial Adenomatous Polyposis With DNA-RNA Paired Testing. JCO Precis Oncol 2024; 8:e2300404. [PMID: 38564685 DOI: 10.1200/po.23.00404] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 02/02/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
PURPOSE Patients with germline pathogenic variants (PVs) in APC develop tens (attenuated familial adenomatous polyposis [AFAP]) to innumerable (classic FAP) adenomatous polyps in their colon and are at significantly increased lifetime risk of colorectal cancer. Up to 10% of FAP and up to 50% of patients with AFAP who have undergone DNA-only multigene panel testing (MGPT) do not have an identified PV in APC. We seek to demonstrate how the addition of RNA sequencing run concurrently with DNA can improve detection of germline PVs in individuals with a clinical presentation of AFAP/FAP. METHODS We performed a retrospective query of individuals tested with paired DNA-RNA MGPT from 2021 to 2022 at a single laboratory and included those with a novel APC PV located in intronic regions infrequently covered by MGPT, a personal history of polyposis, and family medical history provided. All clinical data were deidentified in this institutional review board-exempt study. RESULTS Three novel APC variants were identified in six families and were shown to cause aberrant splicing because of the creation of a deep intronic cryptic splice site that leads to an RNA transcript subject nonsense-mediated decay. Several carriers had previously undergone DNA-only genetic testing and had received a negative result. CONCLUSION Here, we describe how paired DNA-RNA MGPT can be used to solve missing heritability in FAP families, which can have important implications in family planning and treatment decisions for patients and their families.
Collapse
|
2
|
Safonov A, Nomakuchi TT, Chao E, Horton C, Dolinsky JS, Yussuf A, Richardson M, Speare V, Li S, Bogus ZC, Bonanni M, Raper A, Kallish S, Ritchie MD, Nathanson KL, Drivas TG. A genotype-first approach identifies high incidence of NF1 pathogenic variants with distinct disease associations. medRxiv 2023:2023.08.08.23293676. [PMID: 37609227 PMCID: PMC10441497 DOI: 10.1101/2023.08.08.23293676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Loss of function variants in the NF1 gene cause neurofibromatosis type 1 (NF1), a genetic disorder characterized by complete penetrance, prevalence of 1 in 3,000, characteristic physical exam findings, and a substantially increased risk for malignancy. However, our understanding of the disorder is entirely based on patients ascertained through phenotype-first approaches. Leveraging a genotype-first approach in two large patient cohorts, we demonstrate unexpectedly high prevalence (1 in 450-750) of NF1 pathogenic variants. Half were identified in individuals lacking clinical features of NF1, with many appearing to have post-zygotic mosaicism for the identified variant. Incidentally discovered variants were not associated with classic NF1 features but were associated with an increased incidence of malignancy compared to a control population. Our findings suggest that NF1 pathogenic variants are substantially more common than previously thought, often characterized by somatic mosaicism and reduced penetrance, and are important contributors to cancer risk in the general population.
Collapse
|
3
|
Hu C, Nagaraj AB, Shimelis H, Montalban G, Lee KY, Huang H, Lumby CA, Na J, Susswein LR, Roberts ME, Marshall ML, Hiraki S, LaDuca H, Chao E, Yussuf A, Pesaran T, Neuhausen SL, Haiman CA, Kraft P, Lindstrom S, Palmer JR, Teras LR, Vachon CM, Yao S, Ong I, Nathanson KL, Weitzel JN, Boddicker N, Gnanaolivu R, Polley EC, Mer G, Cui G, Karam R, Richardson ME, Domchek SM, Yadav S, Hruska KS, Dolinsky J, Weroha SJ, Hart SN, Simard J, Masson JY, Pang YP, Couch FJ. Functional and Clinical Characterization of Variants of Uncertain Significance Identifies a Hotspot for Inactivating Missense Variants in RAD51C. Cancer Res 2023; 83:2557-2571. [PMID: 37253112 PMCID: PMC10390864 DOI: 10.1158/0008-5472.can-22-2319] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/07/2022] [Accepted: 05/25/2023] [Indexed: 06/01/2023]
Abstract
Pathogenic protein-truncating variants of RAD51C, which plays an integral role in promoting DNA damage repair, increase the risk of breast and ovarian cancer. A large number of RAD51C missense variants of uncertain significance (VUS) have been identified, but the effects of the majority of these variants on RAD51C function and cancer predisposition have not been established. Here, analysis of 173 missense variants by a homology-directed repair (HDR) assay in reconstituted RAD51C-/- cells identified 30 nonfunctional (deleterious) variants, including 18 in a hotspot within the ATP-binding region. The deleterious variants conferred sensitivity to cisplatin and olaparib and disrupted formation of RAD51C/XRCC3 and RAD51B/RAD51C/RAD51D/XRCC2 complexes. Computational analysis indicated the deleterious variant effects were consistent with structural effects on ATP-binding to RAD51C. A subset of the variants displayed similar effects on RAD51C activity in reconstituted human RAD51C-depleted cancer cells. Case-control association studies of deleterious variants in women with breast and ovarian cancer and noncancer controls showed associations with moderate breast cancer risk [OR, 3.92; 95% confidence interval (95% CI), 2.18-7.59] and high ovarian cancer risk (OR, 14.8; 95% CI, 7.71-30.36), similar to protein-truncating variants. This functional data supports the clinical classification of inactivating RAD51C missense variants as pathogenic or likely pathogenic, which may improve the clinical management of variant carriers. SIGNIFICANCE Functional analysis of the impact of a large number of missense variants on RAD51C function provides insight into RAD51C activity and information for classification of the cancer relevance of RAD51C variants.
Collapse
Affiliation(s)
| | | | | | - Gemma Montalban
- CHU de Quebec-Université Laval Research Center, Université Laval, Quebec City, Quebec, Canada
| | | | | | | | - Jie Na
- Mayo Clinic, Rochester, Minnesota
| | | | | | | | | | | | | | | | | | | | | | - Peter Kraft
- T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Sara Lindstrom
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Julie R. Palmer
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Lauren R. Teras
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | | | - Song Yao
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Irene Ong
- University of Wisconsin-Madison, Madison, Wisconsin
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jacques Simard
- CHU de Quebec-Université Laval Research Center, Université Laval, Quebec City, Quebec, Canada
| | - Jean Yves Masson
- CHU de Quebec-Université Laval Research Center, Université Laval, Quebec City, Quebec, Canada
| | | | | |
Collapse
|
4
|
Iversen ES, Lipton G, Hart SN, Lee KY, Hu C, Polley EC, Pesaran T, Yussuf A, LaDuca H, Chao E, Karam R, Goldgar DE, Couch FJ, Monteiro ANA. An integrative model for the comprehensive classification of BRCA1 and BRCA2 variants of uncertain clinical significance. NPJ Genom Med 2022; 7:35. [PMID: 35665744 PMCID: PMC9166814 DOI: 10.1038/s41525-022-00302-3] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/04/2022] [Indexed: 12/14/2022] Open
Abstract
Loss-of-function variants in the BRCA1 and BRCA2 susceptibility genes predispose carriers to breast and/or ovarian cancer. The use of germline testing panels containing these genes has grown dramatically, but the interpretation of the results has been complicated by the identification of many sequence variants of undefined cancer relevance, termed "Variants of Uncertain Significance (VUS)." We have developed functional assays and a statistical model called VarCall for classifying BRCA1 and BRCA2 VUS. Here we describe a multifactorial extension of VarCall, called VarCall XT, that allows for co-analysis of multiple forms of genetic evidence. We evaluated the accuracy of models defined by the combinations of functional, in silico protein predictors, and family data for VUS classification. VarCall XT classified variants of known pathogenicity status with high sensitivity and specificity, with the functional assays contributing the greatest predictive power. This approach could be used to identify more patients that would benefit from personalized cancer risk assessment and management.
Collapse
Affiliation(s)
- Edwin S. Iversen
- grid.26009.3d0000 0004 1936 7961Department of Statistical Science, Duke University, Durham, NC 27708 USA
| | - Gary Lipton
- grid.26009.3d0000 0004 1936 7961Department of Statistical Science, Duke University, Durham, NC 27708 USA
| | - Steven N. Hart
- grid.66875.3a0000 0004 0459 167XDepartment of Health Sciences Research, Mayo Clinic, Rochester, MN 55901 USA
| | - Kun Y. Lee
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902 USA
| | - Chunling Hu
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902 USA
| | - Eric C. Polley
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902 USA
| | - Tina Pesaran
- grid.465138.d0000 0004 0455 211XAmbry Genetics Corporation, Aliso Viejo, CA 92656 USA
| | - Amal Yussuf
- grid.465138.d0000 0004 0455 211XAmbry Genetics Corporation, Aliso Viejo, CA 92656 USA
| | - Holly LaDuca
- grid.465138.d0000 0004 0455 211XAmbry Genetics Corporation, Aliso Viejo, CA 92656 USA
| | - Elizabeth Chao
- grid.465138.d0000 0004 0455 211XAmbry Genetics Corporation, Aliso Viejo, CA 92656 USA
| | - Rachid Karam
- grid.465138.d0000 0004 0455 211XAmbry Genetics Corporation, Aliso Viejo, CA 92656 USA
| | - David E. Goldgar
- grid.223827.e0000 0001 2193 0096Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT 84132 USA
| | - Fergus J. Couch
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902 USA
| | - Alvaro N. A. Monteiro
- grid.468198.a0000 0000 9891 5233Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612 USA
| |
Collapse
|
5
|
Yadav S, Hu C, Nathanson KL, Weitzel JN, Goldgar DE, Kraft P, Gnanaolivu RD, Na J, Huang H, Boddicker NJ, Larson N, Gao C, Yao S, Weinberg C, Vachon CM, Trentham-Dietz A, Taylor JA, Sandler DR, Patel A, Palmer JR, Olson JE, Neuhausen S, Martinez E, Lindstrom S, Lacey JV, Kurian AW, John EM, Haiman C, Bernstein L, Auer PW, Anton-Culver H, Ambrosone CB, Karam R, Chao E, Yussuf A, Pesaran T, Dolinsky JS, Hart SN, LaDuca H, Polley EC, Domchek SM, Couch FJ. Germline Pathogenic Variants in Cancer Predisposition Genes Among Women With Invasive Lobular Carcinoma of the Breast. J Clin Oncol 2021; 39:3918-3926. [PMID: 34672684 PMCID: PMC8660003 DOI: 10.1200/jco.21.00640] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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] [Received: 03/09/2021] [Revised: 06/16/2021] [Accepted: 09/16/2021] [Indexed: 12/14/2022] Open
Abstract
PURPOSE To determine the contribution of germline pathogenic variants (PVs) in hereditary cancer testing panel genes to invasive lobular carcinoma (ILC) of the breast. MATERIALS AND METHODS The study included 2,999 women with ILC from a population-based cohort and 3,796 women with ILC undergoing clinical multigene panel testing (clinical cohort). Frequencies of germline PVs in breast cancer predisposition genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, PALB2, PTEN, RAD51C, RAD51D, and TP53) were compared between women with ILC and unaffected female controls and between women with ILC and infiltrating ductal carcinoma (IDC). RESULTS The frequency of PVs in breast cancer predisposition genes among women with ILC was 6.5% in the clinical cohort and 5.2% in the population-based cohort. In case-control analysis, CDH1 and BRCA2 PVs were associated with high risks of ILC (odds ratio [OR] > 4) and CHEK2, ATM, and PALB2 PVs were associated with moderate (OR = 2-4) risks. BRCA1 PVs and CHEK2 p.Ile157Thr were not associated with clinically relevant risks (OR < 2) of ILC. Compared with IDC, CDH1 PVs were > 10-fold enriched, whereas PVs in BRCA1 were substantially reduced in ILC. CONCLUSION The study establishes that PVs in ATM, BRCA2, CDH1, CHEK2, and PALB2 are associated with an increased risk of ILC, whereas BRCA1 PVs are not. The similar overall PV frequencies for ILC and IDC suggest that cancer histology should not influence the decision to proceed with genetic testing. Similar to IDC, multigene panel testing may be appropriate for women with ILC, but CDH1 should be specifically discussed because of low prevalence and gastric cancer risk.
Collapse
Affiliation(s)
| | | | - Katherine L. Nathanson
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Basser Center for BRCA, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | | | | | - Peter Kraft
- Harvard University T.H. Chan School of Public Health, Boston, MA
| | | | - Jie Na
- Mayo Clinic, Rochester, MN
| | - Hongyan Huang
- Harvard University T.H. Chan School of Public Health, Boston, MA
| | | | | | - Chi Gao
- Harvard University T.H. Chan School of Public Health, Boston, MA
| | - Song Yao
- Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | | | | | | | | | - Alpa Patel
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA
| | | | | | | | | | | | | | | | | | - Christopher Haiman
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | - Paul W. Auer
- UWM Joseph J. Zilber School of Public Health, Milwaukee, WI
| | | | | | | | | | | | | | | | | | | | | | - Susan M. Domchek
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Basser Center for BRCA, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | | |
Collapse
|
6
|
Boddicker NJ, Hu C, Weitzel JN, Kraft P, Nathanson KL, Goldgar DE, Na J, Huang H, Gnanaolivu RD, Larson N, Yussuf A, Yao S, Vachon CM, Trentham-Dietz A, Teras L, Taylor JA, Scott CE, Sandler DP, Pesaran T, Patel AV, Palmer JR, Ong IM, Olson JE, O'Brien K, Neuhausen S, Martinez E, Ma H, Lindstrom S, Le Marchand L, Kooperberg C, Karam R, Hunter DJ, Hodge JM, Haiman C, Gaudet MM, Gao C, LaDuca H, Lacey JV, Dolinsky JS, Chao E, Carter BD, Burnside ES, Bertrand KA, Bernstein L, Auer PW, Ambrosone C, Yadav S, Hart SN, Polley EC, Domchek SM, Couch FJ. Risk of Late-Onset Breast Cancer in Genetically Predisposed Women. J Clin Oncol 2021; 39:3430-3440. [PMID: 34292776 PMCID: PMC8547938 DOI: 10.1200/jco.21.00531] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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] [Received: 02/24/2021] [Revised: 05/07/2021] [Accepted: 06/29/2021] [Indexed: 12/14/2022] Open
Abstract
PURPOSE The prevalence of germline pathogenic variants (PVs) in established breast cancer predisposition genes in women in the general population over age 65 years is not well-defined. However, testing guidelines suggest that women diagnosed with breast cancer over age 65 years might have < 2.5% likelihood of a PV in a high-penetrance gene. This study aimed to establish the frequency of PVs and remaining risks of breast cancer for each gene in women over age 65 years. METHODS A total of 26,707 women over age 65 years from population-based studies (51.5% with breast cancer and 48.5% unaffected) were tested for PVs in germline predisposition gene. Frequencies of PVs and associations between PVs in each gene and breast cancer were assessed, and remaining lifetime breast cancer risks were estimated for non-Hispanic White women with PVs. RESULTS The frequency of PVs in predisposition genes was 3.18% for women with breast cancer and 1.48% for unaffected women over age 65 years. PVs in BRCA1, BRCA2, and PALB2 were found in 3.42% of women diagnosed with estrogen receptor (ER)-negative, 1.0% with ER-positive, and 3.01% with triple-negative breast cancer. Frequencies of PVs were lower among women with no first-degree relatives with breast cancer. PVs in CHEK2, PALB2, BRCA2, and BRCA1 were associated with increased risks (odds ratio = 2.9-4.0) of breast cancer. Remaining lifetime risks of breast cancer were ≥ 15% for those with PVs in BRCA1, BRCA2, and PALB2. CONCLUSION This study suggests that all women diagnosed with triple-negative breast cancer or ER-negative breast cancer should receive genetic testing and that women over age 65 years with BRCA1 and BRCA2 PVs and perhaps with PALB2 and CHEK2 PVs should be considered for magnetic resonance imaging screening.
Collapse
Affiliation(s)
| | | | | | - Peter Kraft
- Harvard University T.H. Chan School of Public Health, Boston, MA
| | - Katherine L. Nathanson
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Basser Center for BRCA, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | | | - Jie Na
- Mayo Clinic, Rochester, MN
| | - Hongyan Huang
- Harvard University T.H. Chan School of Public Health, Boston, MA
| | | | | | | | - Song Yao
- Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | | | - Lauren Teras
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA
| | | | | | | | | | - Alpa V. Patel
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA
| | | | | | | | | | | | | | - Huiyan Ma
- Beckman Research Institute of City of Hope, Duarte, CA
| | - Sara Lindstrom
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | | | | | | | - James M. Hodge
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA
| | - Christopher Haiman
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Mia M. Gaudet
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA
| | - Chi Gao
- Harvard University T.H. Chan School of Public Health, Boston, MA
| | | | | | | | | | - Brian D. Carter
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA
| | | | | | | | - Paul W. Auer
- UWM Joseph J. Zilber School of Public Health, Milwaukee, WI
| | | | | | | | | | - Susan M. Domchek
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Basser Center for BRCA, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | | |
Collapse
|
7
|
Hernandez F, Conner BR, Richardson ME, LaDuca H, Chao E, Pesaran T, Karam R. Classification of the canonical splice alteration MUTYH c.934-2A>G is likely benign based on RNA and clinical data. Cold Spring Harb Mol Case Stud 2021; 8:mcs.a006152. [PMID: 34716202 PMCID: PMC8744492 DOI: 10.1101/mcs.a006152] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/26/2021] [Indexed: 11/24/2022] Open
Abstract
MUTYH-associated polyposis (MAP) is an autosomal recessive disorder characterized by the development of multiple adenomatous colonic polyps and an increased lifetime risk of colorectal cancer. Germline biallelic pathogenic variants in MUTYH are responsible for MAP. The MUTYH c.934-2A > G (NM_001128425.1) variant, which is also known as c.850-2A > G for NM_001048174.2, has been identified in our laboratory in more than 800 patients, including homozygous and compound heterozygote carriers. The variant was initially classified as a variant of uncertain significance (VUS) because of lack of a MAP phenotype in biallelic carriers. In two unrelated female patients who were heterozygous carriers of this variant, further testing by RNA sequencing identified an aberrant transcript with a deletion of 9 nt at the start of exon 11 (MUTYH r.934_942del9). This event is predicted to lead to an in-frame loss of three amino acids in a noncritical domain of the protein. This was the only splice defect identified in these patients that was not present in the controls, and the aberrant transcript is derived exclusively from the variant allele, strongly supporting the cause of this splice defect as being the intronic variant, MUTYH c.934-2A > G. The splicing analysis demonstrating a small in-frame skipping of three amino acids in a noncritical domain, along with the absence of a MAP phenotype in our internal cohort of biallelic carriers, provides evidence that the variant is likely benign and not of clinical significance.
Collapse
|
8
|
Yadav S, Hu C, Domchek SM, Weitzel JN, Goldgar D, Kraft P, Nathanson KL, Karam R, Chao E, Yussuf A, Pesaran T, Dolinsky JS, Hart S, LaDuca H, Polley E, Couch F. Germline pathogenic variants in cancer predisposition genes among women with invasive lobular cancer of breast. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.10581] [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: 11/20/2022] Open
Abstract
10581 Background: The prevalence of germline pathogenic variants (PVs) in cancer predisposition genes among women with invasive lobular breast cancer (ILC) and the risk of ILC in PV carriers is not well-defined. Methods: The study included 2,999 women with ILC and 32,544 unaffected controls from a population-based cohort; 3,796 women with ILC and 20,323 women with invasive ductal carcinoma (IDC) undergoing clinical multigene panel testing (clinical cohort); and 125,748 exome sequences from unrelated women without a cancer diagnosis in the gnomAD 3.0 dataset. Frequencies of germline PVs in breast cancer predisposition genes ( ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, PALB2, PTEN, RAD51C, RAD51D, and TP53) were compared between women with ILC and unaffected controls in both cohorts and between women with ILC and IDC in the clinical cohort. Results: The frequency of PVs in breast cancer predisposition genes among women with ILC was 6.5% in the clinical cohort and 5.2% in the population-based cohort. In case-control analyses, CDH1 and BRCA2 PVs were associated with high risks of ILC (Odds ratio (OR) > 4), and CHEK2, ATM and PALB2 PVs were associated with moderate (OR = 2-4) risks. BRCA1 PVs and CHEK2 p.Ile157Thr were not associated with clinically relevant risks (OR < 2) of ILC. PV frequencies in these genes in ILC and IDC were similar except for PV frequencies in BRCA1 and CDH1. Conclusions: The study establishes that PVs in ATM, BRCA2, CDH1, CHEK2 and PALB2 are associated with an increased risk of ILC, whereas BRCA1 PVs are not. The similar overall PV frequencies for ILC and IDC suggest that cancer histology should not influence the decision to proceed with genetic testing. While, multigene panel testing may be appropriate for women with ILC, CDH1 should be specifically discussed in the context of low prevalence and attendant gastric cancer risk.
Collapse
Affiliation(s)
| | | | | | - Jeffrey N. Weitzel
- Oncogenetics for Precision Prevention, and Latin American School of Oncology, Sierra Madre, CA
| | | | | | | | | | | | | | | | | | | | | | | | - Fergus Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | |
Collapse
|
9
|
Rehder C, Bean LJH, Bick D, Chao E, Chung W, Das S, O'Daniel J, Rehm H, Shashi V, Vincent LM. Next-generation sequencing for constitutional variants in the clinical laboratory, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1399-1415. [PMID: 33927380 DOI: 10.1038/s41436-021-01139-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technologies are now established in clinical laboratories as a primary testing modality in genomic medicine. These technologies have reduced the cost of large-scale sequencing by several orders of magnitude. It is now cost-effective to analyze an individual with disease-targeted gene panels, exome sequencing, or genome sequencing to assist in the diagnosis of a wide array of clinical scenarios. While clinical validation and use of NGS in many settings is established, there are continuing challenges as technologies and the associated informatics evolve. To assist clinical laboratories with the validation of NGS methods and platforms, the ongoing monitoring of NGS testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics (ACMG) has developed the following technical standards.
Collapse
Affiliation(s)
| | - Lora J H Bean
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Elizabeth Chao
- Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, CA, USA
| | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Soma Das
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Julianne O'Daniel
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Heidi Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Lisa M Vincent
- Division of Pathology & Laboratory Medicine, Children's National Health System, Washington, DC, USA.,Departments of Pathology and Pediatrics, George Washington University, Washington, DC, USA
| | | |
Collapse
|
10
|
Horton C, LaDuca H, Hoang L, Chao E, Dolinsky J, Chen J, Chamberlin A, Karam R. QIM21-083: Quantitative Evaluation of Methods Designed to Improve the Accuracy and Quality of Multi-Gene Panel Testing for Hereditary Cancer. J Natl Compr Canc Netw 2021. [DOI: 10.6004/jnccn.2020.7791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
11
|
Richardson ME, Hu C, Lee KY, LaDuca H, Fulk K, Durda KM, Deckman AM, Goldgar DE, Monteiro AN, Gnanaolivu R, Hart SN, Polley EC, Chao E, Pesaran T, Couch FJ. Strong functional data for pathogenicity or neutrality classify BRCA2 DNA-binding-domain variants of uncertain significance. Am J Hum Genet 2021; 108:458-468. [PMID: 33609447 PMCID: PMC8008494 DOI: 10.1016/j.ajhg.2021.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/02/2021] [Indexed: 12/14/2022] Open
Abstract
Determination of the clinical relevance of rare germline variants of uncertain significance (VUSs) in the BRCA2 cancer predisposition gene remains a challenge as a result of limited availability of data for use in classification models. However, laboratory-based functional data derived from validated functional assays of known sensitivity and specificity may influence the interpretation of VUSs. We evaluated 252 missense VUSs from the BRCA2 DNA-binding domain by using a homology-directed DNA repair (HDR) assay and identified 90 as non-functional and 162 as functional. The functional assay results were integrated with other available data sources into an ACMG/AMP rules-based classification framework used by a hereditary cancer testing laboratory. Of the 186 missense variants observed by the testing laboratory, 154 were classified as VUSs without functional data. However, after applying protein functional data, 86% (132/154) of the VUSs were reclassified as either likely pathogenic/pathogenic (39/132) or likely benign/benign (93/132), which impacted testing results for 1,900 individuals. These results indicate that validated functional assay data can have a substantial impact on VUS classification and associated clinical management for many individuals with inherited alterations in BRCA2.
Collapse
|
12
|
Chao E, Dai L, Yu J. In Silico Investigations on Switching Promotor Recognition of Phage RNA Polymerase Variants Following Path Along Lab Directed Evolution. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1046] [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: 11/26/2022] Open
|
13
|
Affiliation(s)
- Rachid Karam
- Rachid Karam, MD, PhD; Holly LaDuca, MS; Marcy E. Richardson, PhD; and Tina Pesaran, MS, Ambry Genetics, Aliso Viejo, CA and Elizabeth Chao, MD, Ambry Genetics, Aliso Viejo, CA, and University of California, Irvine, CA
| | - Holly LaDuca
- Rachid Karam, MD, PhD; Holly LaDuca, MS; Marcy E. Richardson, PhD; and Tina Pesaran, MS, Ambry Genetics, Aliso Viejo, CA and Elizabeth Chao, MD, Ambry Genetics, Aliso Viejo, CA, and University of California, Irvine, CA
| | - Marcy E. Richardson
- Rachid Karam, MD, PhD; Holly LaDuca, MS; Marcy E. Richardson, PhD; and Tina Pesaran, MS, Ambry Genetics, Aliso Viejo, CA and Elizabeth Chao, MD, Ambry Genetics, Aliso Viejo, CA, and University of California, Irvine, CA
| | - Tina Pesaran
- Rachid Karam, MD, PhD; Holly LaDuca, MS; Marcy E. Richardson, PhD; and Tina Pesaran, MS, Ambry Genetics, Aliso Viejo, CA and Elizabeth Chao, MD, Ambry Genetics, Aliso Viejo, CA, and University of California, Irvine, CA
| | - Elizabeth Chao
- Rachid Karam, MD, PhD; Holly LaDuca, MS; Marcy E. Richardson, PhD; and Tina Pesaran, MS, Ambry Genetics, Aliso Viejo, CA and Elizabeth Chao, MD, Ambry Genetics, Aliso Viejo, CA, and University of California, Irvine, CA
| |
Collapse
|
14
|
Kimonis V, Al Dubaisi R, Maclean AE, Hall K, Weiss L, Stover AE, Schwartz PH, Berg B, Cheng C, Parikh S, Conner BR, Wu S, Hasso AN, Scott DA, Koenig MK, Karam R, Tang S, Smith M, Chao E, Balk J, Hatchwell E, Eis PS. NUBPL mitochondrial disease: new patients and review of the genetic and clinical spectrum. J Med Genet 2020; 58:314-325. [PMID: 32518176 DOI: 10.1136/jmedgenet-2020-106846] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/02/2020] [Accepted: 04/22/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND The nucleotide binding protein-like (NUBPL) gene was first reported as a cause of mitochondrial complex I deficiency (MIM 613621, 618242) in 2010. To date, only eight patients have been reported with this mitochondrial disorder. Five other patients were recently reported to have NUBPL disease but their clinical picture was different from the first eight patients. Here, we report clinical and genetic findings in five additional patients (four families). METHODS Whole exome sequencing was used to identify patients with compound heterozygous NUBPL variants. Functional studies included RNA-Seq transcript analyses, missense variant biochemical analyses in a yeast model (Yarrowia lipolytica) and mitochondrial respiration experiments on patient fibroblasts. RESULTS The previously reported c.815-27T>C branch-site mutation was found in all four families. In prior patients, c.166G>A [p.G56R] was always found in cis with c.815-27T>C, but only two of four families had both variants. The second variant found in trans with c.815-27T>C in each family was: c.311T>C [p.L104P] in three patients, c.693+1G>A in one patient and c.545T>C [p.V182A] in one patient. Complex I function in the yeast model was impacted by p.L104P but not p.V182A. Clinical features include onset of neurological symptoms at 3-18 months, global developmental delay, cerebellar dysfunction (including ataxia, dysarthria, nystagmus and tremor) and spasticity. Brain MRI showed cerebellar atrophy. Mitochondrial function studies on patient fibroblasts showed significantly reduced spare respiratory capacity. CONCLUSION We report on five new patients with NUBPL disease, adding to the number and phenotypic variability of patients diagnosed worldwide, and review prior reported patients with pathogenic NUBPL variants.
Collapse
Affiliation(s)
- Virginia Kimonis
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA
| | - Rehab Al Dubaisi
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA
| | - Andrew E Maclean
- Department of Biological Chemistry, John Innes Centre, Norwich, Norfolk, UK.,Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, Glasgow, UK
| | - Kathy Hall
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA
| | - Lan Weiss
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA
| | - Alexander E Stover
- CHOC National Human Neural Stem Cell Resource, Children's Hospital of Orange County Research Institute, Orange, California, USA
| | - Philip H Schwartz
- CHOC National Human Neural Stem Cell Resource, Children's Hospital of Orange County Research Institute, Orange, California, USA
| | - Bethany Berg
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA
| | - Cheng Cheng
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA
| | - Sumit Parikh
- Center for Pediatric Neurology, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Sitao Wu
- Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Anton N Hasso
- Radiological Sciences, University of California Irvine School of Medicine, Irvine, California, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
| | - Mary Kay Koenig
- Department of Pediatrics, University of Texas McGovern Medical School, Houston, Texas, USA
| | - Rachid Karam
- Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Sha Tang
- Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Moyra Smith
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA
| | - Elizabeth Chao
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA.,Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Janneke Balk
- Department of Biological Chemistry, John Innes Centre, Norwich, Norfolk, UK
| | | | - Peggy S Eis
- Population Bio, Inc, New York, New York, USA
| |
Collapse
|
15
|
Deignan JL, Chao E, Gannon JL, Greely HT, Hagman KDF, Mao R, Topper S. Points to consider when assessing relationships (or suspecting misattributed relationships) during family-based clinical genomic testing: a statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2020; 22:1285-1287. [PMID: 32404921 DOI: 10.1038/s41436-020-0821-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/25/2022] Open
Affiliation(s)
- Joshua L Deignan
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Elizabeth Chao
- Division of Genetics and Genomics, Department of Pediatrics, University of California Irvine School of Medicine, Irvine, CA, USA
| | - Jennifer L Gannon
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Henry T Greely
- Center for Law and the Biosciences, Stanford Law School, Stanford, CA, USA
| | | | - Rong Mao
- ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | | | | |
Collapse
|
16
|
Landrith T, Li B, Cass AA, Conner BR, LaDuca H, McKenna DB, Maxwell KN, Domchek S, Morman NA, Heinlen C, Wham D, Koptiuch C, Vagher J, Rivera R, Bunnell A, Patel G, Geurts JL, Depas MM, Gaonkar S, Pirzadeh-Miller S, Krukenberg R, Seidel M, Pilarski R, Farmer M, Pyrtel K, Milliron K, Lee J, Hoodfar E, Nathan D, Ganzak AC, Wu S, Vuong H, Xu D, Arulmoli A, Parra M, Hoang L, Molparia B, Fennessy M, Fox S, Charpentier S, Burdette J, Pesaran T, Profato J, Smith B, Haynes G, Dalton E, Crandall JRR, Baxter R, Lu HM, Tippin-Davis B, Elliott A, Chao E, Karam R. Splicing profile by capture RNA-seq identifies pathogenic germline variants in tumor suppressor genes. NPJ Precis Oncol 2020; 4:4. [PMID: 32133419 PMCID: PMC7039900 DOI: 10.1038/s41698-020-0109-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [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: 09/11/2019] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
Germline variants in tumor suppressor genes (TSGs) can result in RNA mis-splicing and predisposition to cancer. However, identification of variants that impact splicing remains a challenge, contributing to a substantial proportion of patients with suspected hereditary cancer syndromes remaining without a molecular diagnosis. To address this, we used capture RNA-sequencing (RNA-seq) to generate a splicing profile of 18 TSGs (APC, ATM, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MSH2, MSH6, MUTYH, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, and TP53) in 345 whole-blood samples from healthy donors. We subsequently demonstrated that this approach can detect mis-splicing by comparing splicing profiles from the control dataset to profiles generated from whole blood of individuals previously identified with pathogenic germline splicing variants in these genes. To assess the utility of our TSG splicing profile to prospectively identify pathogenic splicing variants, we performed concurrent capture DNA and RNA-seq in a cohort of 1000 patients with suspected hereditary cancer syndromes. This approach improved the diagnostic yield in this cohort, resulting in a 9.1% relative increase in the detection of pathogenic variants, demonstrating the utility of performing simultaneous DNA and RNA genetic testing in a clinical context.
Collapse
Affiliation(s)
| | - Bing Li
- Ambry Genetics, Aliso Viejo, CA USA
| | | | | | | | | | | | | | | | | | - Deborah Wham
- Aurora St. Luke’s Medical Center, Milwaukee, WI USA
| | | | | | - Ragene Rivera
- Texas Oncology, El Paso, Fort Worth, and Austin, TX USA
| | - Ann Bunnell
- Texas Oncology, El Paso, Fort Worth, and Austin, TX USA
| | - Gayle Patel
- Texas Oncology, El Paso, Fort Worth, and Austin, TX USA
| | | | | | | | | | | | | | - Robert Pilarski
- Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH USA
| | - Meagan Farmer
- University of Alabama at Birmingham, Birmingham, AL USA
| | | | | | - John Lee
- Cedars-Sinai Medical Center, Los Angeles, CA USA
| | | | | | | | - Sitao Wu
- Ambry Genetics, Aliso Viejo, CA USA
| | | | - Dong Xu
- Ambry Genetics, Aliso Viejo, CA USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Elizabeth Chao
- Ambry Genetics, Aliso Viejo, CA USA
- University of California at Irvine, Irvine, CA USA
| | | |
Collapse
|
17
|
Karam R, Conner B, LaDuca H, McGoldrick K, Krempely K, Richardson ME, Zimmermann H, Gutierrez S, Reineke P, Hoang L, Allen K, Yussuf A, Farber-Katz S, Rana HQ, Culver S, Lee J, Nashed S, Toppmeyer D, Collins D, Haynes G, Pesaran T, Dolinsky JS, Tippin Davis B, Elliott A, Chao E. Assessment of Diagnostic Outcomes of RNA Genetic Testing for Hereditary Cancer. JAMA Netw Open 2019; 2:e1913900. [PMID: 31642931 PMCID: PMC6820040 DOI: 10.1001/jamanetworkopen.2019.13900] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
IMPORTANCE Performing DNA genetic testing (DGT) for hereditary cancer genes is now a well-accepted clinical practice; however, the interpretation of DNA variation remains a challenge for laboratories and clinicians. Adding RNA genetic testing (RGT) enhances DGT by clarifying the clinical actionability of hereditary cancer gene variants, thus improving clinicians' ability to accurately apply strategies for cancer risk reduction and treatment. OBJECTIVE To evaluate whether RGT is associated with improvement in the diagnostic outcome of DGT and in the delivery of personalized cancer risk management for patients with hereditary cancer predisposition. DESIGN, SETTING, AND PARTICIPANTS Diagnostic study in which patients and/or families with inconclusive variants detected by DGT in genes associated with hereditary breast and ovarian cancer, Lynch syndrome, and hereditary diffuse gastric cancer sent blood samples for RGT from March 2016 to April 2018. Clinicians who ordered genetic testing and received a reclassification report for these variants were surveyed to assess whether RGT-related variant reclassifications changed clinical management of these patients. To quantify the potential number of tested individuals who could benefit from RGT, a cohort of 307 812 patients who underwent DGT for hereditary cancer were separately queried to identify variants predicted to affect splicing. Data analysis was conducted from March 2016 and September 2018. MAIN OUTCOMES AND MEASURES Variant reclassification outcomes following RGT, clinical management changes associated with RGT-related variant reclassifications, and the proportion of patients who would likely be affected by a concurrent DGT and RGT multigene panel testing approach. RESULTS In total, 93 if 909 eligible families (10.2%) submitted samples for RGT. Evidence from RGT clarified the interpretation of 49 of 56 inconclusive cases (88%) studied; 26 (47%) were reclassified as clinically actionable and 23 (41%) were clarified as benign. Variant reclassifications based on RGT results changed clinical management recommendations for 8 of 18 patients (44%) and 14 of 18 families (78%), based on responses from 18 of 45 clinicians (40%) surveyed. A total of 7265 of 307 812 patients who underwent DGT had likely pathogenic variants or variants of uncertain significance potentially affecting splicing, indicating that approximately 1 in 43 individuals could benefit from RGT. CONCLUSIONS AND RELEVANCE In this diagnostic study, conducting RNA testing resolved a substantial proportion of variants of uncertain significance in a cohort of individuals previously tested for cancer predisposition by DGT. Performing RGT might change the diagnostic outcome of at least 1 in 43 patients if performed in all individuals undergoing genetic evaluation for hereditary cancer.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Suzette Farber-Katz
- Ambry Genetics, Aliso Viejo, California
- now with Merck Research Laboratories, South San Francisco, California
| | - Huma Q. Rana
- Department of Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Samantha Culver
- Department of Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - John Lee
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Sarah Nashed
- Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick
| | - Deborah Toppmeyer
- Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick
| | | | | | | | | | | | | | - Elizabeth Chao
- Ambry Genetics, Aliso Viejo, California
- Department of Pediatrics, School of Medicine, University of California, Irvine
| |
Collapse
|
18
|
Walsh MF, Ritter DI, Kesserwan C, Sonkin D, Chakravarty D, Chao E, Ghosh R, Kemel Y, Wu G, Lee K, Kulkarni S, Hedges D, Mandelker D, Ceyhan-Birsoy O, Luo M, Drazer M, Zhang L, Offit K, Plon SE. Integrating somatic variant data and biomarkers for germline variant classification in cancer predisposition genes. Hum Mutat 2019; 39:1542-1552. [PMID: 30311369 DOI: 10.1002/humu.23640] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 05/09/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 12/20/2022]
Abstract
In its landmark paper about Standards and Guidelines for the Interpretation of Sequence Variants, the American College of Medical Genetics and Genomics (ACMG), and Association for Molecular Pathology (AMP) did not address how to use tumor data when assessing the pathogenicity of germline variants. The Clinical Genome Resource (ClinGen) established a multidisciplinary working group, the Germline/Somatic Variant Subcommittee (GSVS) with this focus. The GSVS implemented a survey to determine current practices of integrating somatic data when classifying germline variants in cancer predisposition genes. The GSVS then reviewed and analyzed available resources of relevant somatic data, and performed integrative germline variant curation exercises. The committee determined that somatic hotspots could be systematically integrated into moderate evidence of pathogenicity (PM1). Tumor RNA sequencing data showing altered splicing may be considered as strong evidence in support of germline pathogenicity (PVS1) and tumor phenotypic features such as mutational signatures be considered supporting evidence of pathogenicity (PP4). However, at present, somatic data such as focal loss of heterozygosity and mutations occurring on the alternative allele are not recommended to be systematically integrated, instead, incorporation of this type of data should take place under the advisement of multidisciplinary cancer center tumor-normal sequencing boards.
Collapse
Affiliation(s)
- Michael F Walsh
- Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | | | | | | | | | | | | | - Yelena Kemel
- Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Gang Wu
- St. Jude Children's Hospital, Memphis, Tennessee, USA
| | - Kristy Lee
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Dale Hedges
- St. Jude Children's Hospital, Memphis, Tennessee, USA
| | - Diana Mandelker
- Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | | | - Minjie Luo
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Liying Zhang
- Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | | |
Collapse
|
19
|
Yadav S, LaDuca H, Polley E, Shimelis H, Niguidula N, Hu C, Lilyquist J, Na J, Lee K, Gutierrez S, Yussuf A, Hart S, Tippin Davis B, Chao E, Pesaran T, Goldgar D, Dolinsky JS, Couch F. Racial and ethnic differences in the results of multigene panel testing of inherited cancer predisposition genes in breast cancer patients. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.1514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
1514 Background: The prevalence of germline mutations in non-white patients with breast cancer and the germline genetic drivers of breast cancer risk in non-white populations are largely unknown. Methods: The study population included 77,900 women with breast cancer (Non-Hispanic white: 57,003; Black: 6,722; Asian: 4,183; Hispanic: 5,194; Ashkenazi-Jewish: 4,798) who underwent germline multigene panel testing of cancer predisposition genes from March 2012 to December 2016. The prevalence of predisposition gene mutations in racial and ethnic populations relative to non-Hispanic Whites was assessed while accounting for age at diagnosis of breast cancer, family history of breast and ovarian cancer, and estrogen receptor status of breast tumors. Associations between mutations in each gene and breast cancer risk were evaluated using reference controls. Results: The overall frequency of pathogenic mutations in known breast cancer predisposition genes was 9.1% for non-Hispanic Whites, 9.8% for African Americans, 10.2% for Hispanics, 7.6% for Ashkenazi-Jewish, and 7.5% for Asians. BRCA1 mutations were enriched (p < 0.05) and CHEK2 mutations were under-represented in all racial and ethnic populations relative to non-Hispanic Whites. BRCA2 and BARD1 mutations were enriched in African Americans and Hispanics relative to non-Hispanic Whites, whereas PALB2 and RAD51C mutations were enriched in Hispanics. Among genes with mutation counts large enough for assessment, mutations in BARD1, BRCA1, BRCA2, PALB2 and TP53 were significantly associated with clinically relevant increased risks (odds ratio (OR) > 2) of breast cancer across all ethnicities and races. Rates of variants of uncertain significance were highest among Asians (29%), followed by blacks (27%), Hispanics (21%), non-Hispanic whites (16%) and Ashkenazi-Jews (14%). Conclusions: While there is some similarity across ethnic groups, substantial heterogeneity exists in the prevalence of mutations in breast cancer predisposition genes across major racial and ethnic groups in the US population. These findings contribute to our understanding of breast cancer risk and have significant implications for genetic testing, screening, and management of patients with an inherited predisposition to breast cancer, with a need for continued analysis with increased cohort size in ethnic minority groups.
Collapse
Affiliation(s)
| | | | | | - Hermela Shimelis
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN
| | | | | | | | - Jie Na
- Mayo Clinic, Department of Health Sciences Research, Rochester, MN
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Chao E, Sun HL, Huang SW, Liao JH, Ma PL, Chen HC. Metaraminol use during spinal anaesthesia for caesarean section: a meta-analysis of randomised controlled trials. Int J Obstet Anesth 2019; 39:42-50. [PMID: 30772119 DOI: 10.1016/j.ijoa.2019.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 01/12/2019] [Accepted: 01/18/2019] [Indexed: 10/27/2022]
Abstract
INTRODUCTION During caesarean section, the use of a vasopressor is often required to achieve haemodynamic stability of the parturient. Metaraminol is a vasopressor used in this context in some countries. However, the differences between metaraminol and other vasopressors remain unclear. METHODS A search of the PubMed, Cochrane Library, and Embase databases was performed to identify randomised controlled trials comparing the use of metaraminol with other vasopressors during spinal anaesthesia at caesarean section. The selected studies were subjected to meta-analysis and risk-of-bias assessment. RESULTS Four randomised, controlled trials met the selection criteria and 409 parturients who underwent an elective caesarean section were included in this meta-analysis. The quality of these trials was good. Metaraminol was associated with higher umbilical arterial pH (standardised mean difference [SMD] 0.82, 95% CI 0.01 to 1.62, P=0.05); a lower incidence of fetal acidosis (RR 0.08, 95% CI 0.01 to 0.63, P=0.02); and a lower incidence of nausea or vomiting (RR 0.16, 95% CI 0.04 to 0.57, P=0.0005) than was ephedrine. Metaraminol resulted in higher umbilical arterial pH (SMD 0.42, 95% CI 0.15 to 0.68, P=0.002) but a higher incidence of reactive hypertension (RR 1.80, 95% CI 1.32 to 2.46, P=0.0002) than did phenylephrine. CONCLUSION The results of this study showed that for spinal anaesthesia at elective caesarean section, metaraminol may be a more suitable vasopressor than ephedrine and its effects are at least not inferior to those of phenylephrine.
Collapse
Affiliation(s)
- E Chao
- Department of Anaesthesia, Sijhih Cathay General Hospital, New Taipei City, Taiwan
| | - H-L Sun
- Department of Anaesthesia, Sijhih Cathay General Hospital, New Taipei City, Taiwan; School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - S-W Huang
- Department of Physical Medicine and Rehabilitation, School of Medicine, College of Medicine, Taipei Medical University, Taipei City, Taiwan; Department of Physical Medicine and Rehabilitation, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - J-H Liao
- Department of Anaesthesia, Sijhih Cathay General Hospital, New Taipei City, Taiwan
| | - P-L Ma
- Department of Anaesthesia, Sijhih Cathay General Hospital, New Taipei City, Taiwan
| | - H-C Chen
- Department of Physical Medicine and Rehabilitation, School of Medicine, College of Medicine, Taipei Medical University, Taipei City, Taiwan; Department of Physical Medicine and Rehabilitation, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan; Center for Evidence-Based Health Care, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.
| |
Collapse
|
21
|
Muppidi A, Lee SJ, Hsu CH, Zou H, Lee C, Pflimlin E, Mahankali M, Yang P, Chao E, Ahmad I, Crameri A, Wang D, Woods A, Shen W. Design and Synthesis of Potent, Long-Acting Lipidated Relaxin-2 Analogs. Bioconjug Chem 2018; 30:83-89. [DOI: 10.1021/acs.bioconjchem.8b00764] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Avinash Muppidi
- Calibr at the Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sang Jun Lee
- Calibr at the Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Che-Hsiung Hsu
- Calibr at the Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Huafei Zou
- Calibr at the Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Candy Lee
- Calibr at the Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Elsa Pflimlin
- Calibr at the Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Madhupriya Mahankali
- Calibr at the Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Pengyu Yang
- Calibr at the Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Elizabeth Chao
- Calibr at the Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Insha Ahmad
- Calibr at the Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Andreas Crameri
- Calibr at the Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Danling Wang
- Calibr at the Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ashley Woods
- Calibr at the Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Weijun Shen
- Calibr at the Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| |
Collapse
|
22
|
Lee K, Krempely K, Roberts ME, Anderson MJ, Carneiro F, Chao E, Dixon K, Figueiredo J, Ghosh R, Huntsman D, Kaurah P, Kesserwan C, Landrith T, Li S, Mensenkamp AR, Oliveira C, Pardo C, Pesaran T, Richardson M, Slavin TP, Spurdle AB, Trapp M, Witkowski L, Yi CS, Zhang L, Plon SE, Schrader KA, Karam R. Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline CDH1 sequence variants. Hum Mutat 2018; 39:1553-1568. [PMID: 30311375 PMCID: PMC6188664 DOI: 10.1002/humu.23650] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [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: 04/30/2018] [Revised: 08/30/2018] [Accepted: 09/06/2018] [Indexed: 12/22/2022]
Abstract
The variant curation guidelines published in 2015 by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) provided the genetics community with a framework to assess variant pathogenicity; however, these rules are not gene specific. Germline pathogenic variants in the CDH1 gene cause hereditary diffuse gastric cancer and lobular breast cancer, a clinically challenging cancer predisposition syndrome that often requires a multidisciplinary team of experts to be properly managed. Given this challenge, the Clinical Genome Resource (ClinGen) Hereditary Cancer Domain prioritized the development of the CDH1 variant curation expert panel (VCEP) to develop and implement rules for CDH1 variant classifications. Here, we describe the CDH1 specifications of the ACMG/AMP guidelines, which were developed and validated after a systematic evaluation of variants obtained from a cohort of clinical laboratory data encompassing ∼827,000 CDH1 sequenced alleles. Comparing previously reported germline variants that were classified using the 2015 ACMG/AMP guidelines to the CDH1 VCEP recommendations resulted in reduced variants of uncertain significance and facilitated resolution of variants with conflicted assertions in ClinVar. The ClinGen CDH1 VCEP recommends the use of these CDH1-specific guidelines for the assessment and classification of variants identified in this clinically actionable gene.
Collapse
Affiliation(s)
- Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | | | - Fatima Carneiro
- Institute for Research and Innovation in Health of the University of Porto, Instituto de Investigação e Inovação em Saúde – (i3S), Faculty of Medicine – University of Porto, Porto, PRT
| | - Elizabeth Chao
- Ambry Genetics, Aliso Viejo, CA, USA
- University of California Irvine, Irvine, CA, USA
| | | | - Joana Figueiredo
- Institute for Research and Innovation in Health of the University of Porto, Instituto de Investigação e Inovação em Saúde – (i3S), Faculty of Medicine – University of Porto, Porto, PRT
| | | | | | | | | | | | - Shuwei Li
- Ambry Genetics, Aliso Viejo, CA, USA
| | | | - Carla Oliveira
- Institute for Research and Innovation in Health of the University of Porto, Instituto de Investigação e Inovação em Saúde – (i3S), Faculty of Medicine – University of Porto, Porto, PRT
| | | | | | | | - Thomas P. Slavin
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | | | - Mackenzie Trapp
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leora Witkowski
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA, USA
| | | | | | | | - Kasmintan A. Schrader
- Institute for Research and Innovation in Health of the University of Porto, Instituto de Investigação e Inovação em Saúde – (i3S), Faculty of Medicine – University of Porto, Porto, PRT
| | | |
Collapse
|
23
|
Yang PY, Zou H, Lee C, Muppidi A, Chao E, Fu Q, Luo X, Wang D, Schultz PG, Shen W. Stapled, Long-Acting Glucagon-like Peptide 2 Analog with Efficacy in Dextran Sodium Sulfate Induced Mouse Colitis Models. J Med Chem 2018. [PMID: 29528634 DOI: 10.1021/acs.jmedchem.7b00768] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Glucagon-like peptide 2 (GLP-2) is a hormone that has been shown to stimulate intestinal growth and attenuate intestinal inflammation. Despite being efficacious in a variety of animal models of disease, its therapeutic potential is hampered by the short half-life in vivo. We now describe a highly potent, stapled long-acting GLP-2 analog, peptide 10, that has a more than 10-fold longer half-life than teduglutide and improved intestinotrophic and anti-inflammatory effects in mouse models of DSS-induced colitis.
Collapse
Affiliation(s)
- Peng-Yu Yang
- California Institute for Biomedical Research , La Jolla , California 92037 , United States.,Department of Chemistry, The Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Huafei Zou
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
| | - Candy Lee
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
| | - Avinash Muppidi
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
| | - Elizabeth Chao
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
| | - Qiangwei Fu
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
| | - Xiaozhou Luo
- Department of Chemistry, The Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Danling Wang
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
| | - Peter G Schultz
- California Institute for Biomedical Research , La Jolla , California 92037 , United States.,Department of Chemistry, The Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Weijun Shen
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
| |
Collapse
|
24
|
Lowstuter K, Espenschied CR, Sturgeon D, Ricker C, Karam R, LaDuca H, Culver JO, Dolinsky JS, Chao E, Sturgeon J, Speare V, Ma Y, Kingham K, Melas M, Idos GE, McDonnell KJ, Gruber SB. Unexpected CDH1 Mutations Identified on Multigene Panels Pose Clinical Management Challenges. JCO Precis Oncol 2017; 1:1-12. [DOI: 10.1200/po.16.00021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose Mutations in the CDH1 gene confer up to an 80% lifetime risk of diffuse gastric cancer and up to a 60% lifetime risk of lobular breast cancer. Testing for CDH1 mutations is recommended for individuals who meet the International Gastric Cancer Linkage Consortium (IGCLC) guidelines. However, the interpretation of unexpected CDH1 mutations identified in patients who do not meet IGCLC criteria or do not have phenotypes suggestive of hereditary diffuse gastric cancer is clinically challenging. This study aims to describe phenotypes of CDH1 mutation carriers identified through multigene panel testing (MGPT) and to offer informed recommendations for medical management. Patients and Methods This cross-sectional prevalence study included all patients who underwent MGPT between March 2012 and September 2014 from a commercial laboratory (n = 26,936) and an academic medical center cancer genetics clinic (n = 318) to estimate CDH1 mutation prevalence and associated clinical phenotypes. CDH1 mutation carriers were classified as IGCLC positive (met criteria), IGCLC partial phenotype, and IGCLC negative. Results In the laboratory cohort, 16 (0.06%) of 26,936 patients were identified as having a pathogenic CDH1 mutation. In the clinic cohort, four (1.26%) of 318 had a pathogenic CDH1 mutation. Overall, 65% of mutation carriers did not meet the revised testing criteria published in 2015. All three CDH1 mutation carriers who had risk-reducing gastrectomy had pathologic evidence of diffuse gastric cancer despite not having met IGCLC criteria. Conclusion The majority of CDH1 mutations identified on MGPT are unexpected and found in individuals who do not fit the accepted diagnostic testing criteria. These test results alter the medical management of CDH1-positive patients and families and provide opportunities for early detection and risk reduction.
Collapse
Affiliation(s)
- Katrina Lowstuter
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Carin R. Espenschied
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Duveen Sturgeon
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Charité Ricker
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Rachid Karam
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Holly LaDuca
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Julie O. Culver
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Jill S. Dolinsky
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Elizabeth Chao
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Julia Sturgeon
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Virginia Speare
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Yanling Ma
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Kerry Kingham
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Marilena Melas
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Gregory E. Idos
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Kevin J. McDonnell
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| | - Stephen B. Gruber
- Katrina Lowstuter, Duveen Sturgeon, Charité Ricker, Julie O. Culver, Julia Sturgeon, Yanling Ma, Marilena Melas, Gregory E. Idos, Kevin J. McDonnell, and Stephen B. Gruber, University of Southern California, Los Angeles; Carin R. Espenschied, Rachid Karam, Holly LaDuca, Jill S. Dolinsky, Elizabeth Chao, and Virginia Speare, Ambry Genetics, Aliso Viejo; and Kerry Kingham, Stanford University School of Medicine, Stanford, CA
| |
Collapse
|
25
|
Liu Y, Wang Y, Zhang Y, Liu T, Jia H, Zou H, Fu Q, Zhang Y, Lu L, Chao E, Parker H, Nguyen-Tran V, Shen W, Wang D, Schultz PG, Wang F. Rational Design of Dual Agonist-Antibody Fusions as Long-acting Therapeutic Hormones. ACS Chem Biol 2016; 11:2991-2995. [PMID: 27704775 DOI: 10.1021/acschembio.6b00630] [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: 11/27/2022]
Abstract
Recent studies have suggested that modulation of two or more signaling pathways can achieve substantial weight loss and glycemic stability. We have developed an approach to the generation of bifunctional antibody agonists that activate leptin receptor and GLP-1 receptor. Leptin was fused into the complementarity determining region 3 loop of the light chain alone, or in combination with exendin-4 (EX4) fused at the N-terminus of the heavy chain of Herceptin. The antibody fusions exhibit similar or increased in vitro activities on their cognate receptors, but 50-100-fold longer circulating half-lives in rodents compared to the corresponding native peptides/proteins. The efficacy of the leptin/EX4 dual antibody fusion on weight loss, especially fat mass loss, was enhanced in ob/ob mice and DIO mice compared to the antibody fusion of either EX4 or leptin alone. This work demonstrates the versatility of this combinatorial fusion strategy for generating dual antibody agonists with long half-lives.
Collapse
Affiliation(s)
- Yan Liu
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Ying Wang
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Yong Zhang
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Tao Liu
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Haiqun Jia
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Huafei Zou
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Qiangwei Fu
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Yuhan Zhang
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Lucy Lu
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Elizabeth Chao
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Holly Parker
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Van Nguyen-Tran
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Weijun Shen
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Danling Wang
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Peter G. Schultz
- California Institute for Biomedical Research, La Jolla, California 92037, United States
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Feng Wang
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| |
Collapse
|
26
|
Wang Y, Du J, Zou H, Liu Y, Zhang Y, Gonzalez J, Chao E, Lu L, Yang P, Parker H, Nguyen-Tran V, Shen W, Wang D, Schultz PG, Wang F. Multifunctional Antibody Agonists Targeting Glucagon-like Peptide-1, Glucagon, and Glucose-Dependent Insulinotropic Polypeptide Receptors. Angew Chem Int Ed Engl 2016; 55:12475-8. [PMID: 27595986 DOI: 10.1002/anie.201606321] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 06/30/2016] [Revised: 08/05/2016] [Indexed: 01/04/2023]
Abstract
Glucagon-like peptide-1 (GLP-1) receptor (GLP-1R), glucagon (GCG) receptor (GCGR), and glucose-dependent insulinotropic polypeptide (GIP, also known as gastric inhibitory polypeptide) receptor (GIPR), are three metabolically related peptide hormone receptors. A novel approach to the generation of multifunctional antibody agonists that activate these receptors has been developed. Native or engineered peptide agonists for GLP-1R, GCGR, and GIPR were fused to the N-terminus of the heavy chain or light chain of an antibody, either alone or in pairwise combinations. The fusion proteins have similar in vitro biological activities on the cognate receptors as the corresponding peptides, but circa 100-fold longer plasma half-lives. The GLP-1R mono agonist and GLP-1R/GCGR dual agonist antibodies both exhibit potent effects on glucose control and body weight reduction in mice, with the dual agonist antibody showing enhanced activity in the latter.
Collapse
Affiliation(s)
- Ying Wang
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Jintang Du
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Huafei Zou
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Yan Liu
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Yuhan Zhang
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Jose Gonzalez
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Elizabeth Chao
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Lucy Lu
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Pengyu Yang
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Holly Parker
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Van Nguyen-Tran
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Weijun Shen
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Danling Wang
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter G Schultz
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA, 92037, USA.
| | - Feng Wang
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA, 92037, USA.
| |
Collapse
|
27
|
Wang Y, Du J, Zou H, Liu Y, Zhang Y, Gonzalez J, Chao E, Lu L, Yang P, Parker H, Nguyen-Tran V, Shen W, Wang D, Schultz PG, Wang F. Multifunctional Antibody Agonists Targeting Glucagon-like Peptide-1, Glucagon, and Glucose-Dependent Insulinotropic Polypeptide Receptors. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ying Wang
- California Institute for Biomedical Research (Calibr); 11119 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Jintang Du
- California Institute for Biomedical Research (Calibr); 11119 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Huafei Zou
- California Institute for Biomedical Research (Calibr); 11119 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Yan Liu
- California Institute for Biomedical Research (Calibr); 11119 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Yuhan Zhang
- California Institute for Biomedical Research (Calibr); 11119 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Jose Gonzalez
- California Institute for Biomedical Research (Calibr); 11119 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Elizabeth Chao
- California Institute for Biomedical Research (Calibr); 11119 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Lucy Lu
- California Institute for Biomedical Research (Calibr); 11119 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Pengyu Yang
- California Institute for Biomedical Research (Calibr); 11119 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Holly Parker
- California Institute for Biomedical Research (Calibr); 11119 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Van Nguyen-Tran
- California Institute for Biomedical Research (Calibr); 11119 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Weijun Shen
- California Institute for Biomedical Research (Calibr); 11119 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Danling Wang
- California Institute for Biomedical Research (Calibr); 11119 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Peter G. Schultz
- California Institute for Biomedical Research (Calibr); 11119 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Feng Wang
- California Institute for Biomedical Research (Calibr); 11119 N. Torrey Pines Road La Jolla CA 92037 USA
| |
Collapse
|
28
|
Couch FJ, Goldgar DE, Hart SN, Hallberg E, Moore R, Meeks H, Huether R, LaDuca H, Chao E, Dolinsky J. Abstract 2597: Breast and ovarian cancer risks associated with cancer predisposition gene mutations identified by multigene panel testing. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Multigene panel testing (MGPT) for hereditary cancer is increasing in popularity in the USA. Many panels include genes identified as hereditary breast and/or ovarian cancer (HBOC) genes despite limited data regarding the precise cancer risks associated with mutations in these genes. Here we report on results from BreastNext and OvaNext panel testing of 20 genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MRE11A, MSH2, MSH6, NBN, NF1, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, TP53) in a cohort of 15,083 individuals. The majority of individuals were from high-risk breast and/or ovarian (Br/Ov) cancer families, with 92.4% of all probands meeting National Comprehensive Cancer Network HBOC testing criteria. Pathogenic mutations were identified in 9.4% of the overall cohort.
To estimate gene-specific breast and ovarian cancer risks, case-control analyses were performed comparing the frequencies of pathogenic mutations from Caucasian breast or ovarian cancer cases from BreastNext and OvaNext with frequencies from Caucasian, non-Finnish, non-TCGA controls from the Exome Aggregation Consortium (ExAC) database. Mutations in the well studied ATM and CHEK2 genes were associated with moderate risks (OR>2) of breast cancer and mutations in PALB2 were associated with high-risks (OR>5) of breast cancer, consistent with previous reports. In addition, the study suggested that pathogenic mutations in MSH6, RAD51D, CDH1, and NF1 are associated with moderate to high risks of breast cancer. In contrast, RAD51C, RAD51D, and BRIP1 mutations were associated with high risks of ovarian cancer, PALB2 mutations were associated with moderate risks, but ATM and CHEK2 mutations were not associated with increased ovarian cancer risk. In addition, modeling of missense mutations in the predisposition genes using in silico prediction algorithms suggested that missense mutations in CDH1, CHEK2, MSH2, and MSH6 are associated with moderate risks of breast cancer and missense mutations in RAD51C increase risks of ovarian cancer. This large breast and ovarian cancer case-control analysis provides useful data for many predisposition genes previously lacking risk estimates, and should prove useful for clinical risk management of patients after clinical panel testing.
Citation Format: Fergus J. Couch, David E. Goldgar, Steven N. Hart, Emily Hallberg, Raymond Moore, Huong Meeks, Robert Huether, Holly LaDuca, Elizabeth Chao, Jill Dolinsky. Breast and ovarian cancer risks associated with cancer predisposition gene mutations identified by multigene panel testing. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2597.
Collapse
|
29
|
Price A, Chao E, Chang S, Matney J, Wang A, Lian J. MO-FG-BRA-07: Intrafractional Motion Effect Can Be Minimized in Tomotherapy Stereotactic Body Radiotherapy (SBRT). Med Phys 2016. [DOI: 10.1118/1.4957300] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
30
|
Chao E, Lucas D. SU-G-BRA-14: Dose in a Rigidly Moving Phantom with Jaw and MLC Compensation. Med Phys 2016. [DOI: 10.1118/1.4956938] [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: 11/07/2022] Open
|
31
|
de la Hoya M, Soukarieh O, López-Perolio I, Vega A, Walker LC, van Ierland Y, Baralle D, Santamariña M, Lattimore V, Wijnen J, Whiley P, Blanco A, Raponi M, Hauke J, Wappenschmidt B, Becker A, Hansen TVO, Behar R, Investigators KC, Niederacher D, Arnold N, Dworniczak B, Steinemann D, Faust U, Rubinstein W, Hulick PJ, Houdayer C, Caputo SM, Castera L, Pesaran T, Chao E, Brewer C, Southey MC, van Asperen CJ, Singer CF, Sullivan J, Poplawski N, Mai P, Peto J, Johnson N, Burwinkel B, Surowy H, Bojesen SE, Flyger H, Lindblom A, Margolin S, Chang-Claude J, Rudolph A, Radice P, Galastri L, Olson JE, Hallberg E, Giles GG, Milne RL, Andrulis IL, Glendon G, Hall P, Czene K, Blows F, Shah M, Wang Q, Dennis J, Michailidou K, McGuffog L, Bolla MK, Antoniou AC, Easton DF, Couch FJ, Tavtigian S, Vreeswijk MP, Parsons M, Meeks HD, Martins A, Goldgar DE, Spurdle AB. Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms. Hum Mol Genet 2016; 25:2256-2268. [PMID: 27008870 PMCID: PMC5081057 DOI: 10.1093/hmg/ddw094] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [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] [Received: 11/23/2015] [Revised: 02/10/2016] [Accepted: 03/17/2016] [Indexed: 12/13/2022] Open
Abstract
A recent analysis using family history weighting and co-observation classification modeling indicated that BRCA1 c.594-2A > C (IVS9-2A > C), previously described to cause exon 10 skipping (a truncating alteration), displays characteristics inconsistent with those of a high risk pathogenic BRCA1 variant. We used large-scale genetic and clinical resources from the ENIGMA, CIMBA and BCAC consortia to assess pathogenicity of c.594-2A > C. The combined odds for causality considering case-control, segregation and breast tumor pathology information was 3.23 × 10-8 Our data indicate that c.594-2A > C is always in cis with c.641A > G. The spliceogenic effect of c.[594-2A > C;641A > G] was characterized using RNA analysis of human samples and splicing minigenes. As expected, c.[594-2A > C; 641A > G] caused exon 10 skipping, albeit not due to c.594-2A > C impairing the acceptor site but rather by c.641A > G modifying exon 10 splicing regulatory element(s). Multiple blood-based RNA assays indicated that the variant allele did not produce detectable levels of full-length transcripts, with a per allele BRCA1 expression profile composed of ≈70-80% truncating transcripts, and ≈20-30% of in-frame Δ9,10 transcripts predicted to encode a BRCA1 protein with tumor suppression function.We confirm that BRCA1c.[594-2A > C;641A > G] should not be considered a high-risk pathogenic variant. Importantly, results from our detailed mRNA analysis suggest that BRCA-associated cancer risk is likely not markedly increased for individuals who carry a truncating variant in BRCA1 exons 9 or 10, or any other BRCA1 allele that permits 20-30% of tumor suppressor function. More generally, our findings highlight the importance of assessing naturally occurring alternative splicing for clinical evaluation of variants in disease-causing genes.
Collapse
Affiliation(s)
- Miguel de la Hoya
- Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos (IdISSC), Hospital Clinico San Carlos, Madrid, Spain
| | - Omar Soukarieh
- Inserm U1079-IRIB, University of Rouen, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Irene López-Perolio
- Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos (IdISSC), Hospital Clinico San Carlos, Madrid, Spain
| | - Ana Vega
- Fundacion Publica Galega de Medicina Xenómica-SERGAS Grupo de Medicina Xenómica-USC, IDIS, CIBERER, Santiago de Compostela 15706, Spain
| | - Logan C Walker
- Department of Pathology, University of Otago, Christchurch 8140, New Zealand
| | - Yvette van Ierland
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2300, The Netherlands
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton S016 5YA, UK
| | - Marta Santamariña
- CIBERER, Grupo de Medicina Xenómica-USC, Universidade de Santiago de Compostela, Fundacion Galega de Medicina Xenómica (SERGAS), Santiago de Compostela 15706, Spain
| | - Vanessa Lattimore
- Department of Pathology, University of Otago, Christchurch 8140, New Zealand
| | - Juul Wijnen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2300, The Netherlands Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2300, The Netherlands
| | - Philip Whiley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Ana Blanco
- Fundacion Publica Galega de Medicina Xenómica-SERGAS Grupo de Medicina Xenómica-USC, IDIS, CIBERER, Santiago de Compostela 15706, Spain
| | - Michela Raponi
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton S016 5YA, UK
| | - Jan Hauke
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hosptial Cologne, Cologne 50931, Germany
| | - Barbara Wappenschmidt
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hosptial Cologne, Cologne 50931, Germany
| | - Alexandra Becker
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hosptial Cologne, Cologne 50931, Germany
| | - Thomas V O Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen DK-2100, Denmark
| | - Raquel Behar
- Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos (IdISSC), Hospital Clinico San Carlos, Madrid, Spain
| | - KConFaB Investigators
- Peter MacCallum Cancer Center, University of Melbourne, Melbourne, VIC 3002, Australia
| | - Diether Niederacher
- Department of Gynaecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Kiel 24105, Germany
| | - Bernd Dworniczak
- Institute of Human Genetics, University of Münster, Münster 48149, Germany
| | - Doris Steinemann
- Institute of Human Genetics, Hannover Medical School, Hannover 30625, Germany
| | - Ulrike Faust
- Institute of Medical Genetics and Applied Genomics, University Hospital Tuebingen, Tuebingen 72076, Germany
| | | | - Peter J Hulick
- Center for Medical Genetics, NorthShore University Health System, University of Chicago Pritzker School of Medicine, Evanston, IL 60201, USA
| | - Claude Houdayer
- Service de Génétique, Department de Biologie des Tumeurs, Institut Curie and INSERM U830, Centre de Recherche de l'Institut Curie, Paris, and Universite Paris Descartes, Sorbonne Paris Cite, Paris 75248, France
| | - Sandrine M Caputo
- Service de Génétique, Department de Biologie des Tumeurs, Institut Curie, Paris 75248, France
| | - Laurent Castera
- Centre Francois Baclesse, Laboratoire de Biologie et de Genetique du Cancer, 14076 Caen, Paris 75248, France
| | | | | | - Carole Brewer
- Department of Clinical Genetics, Royal Devon and Exeter Hospital, Exeter, UK
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2300, The Netherlands
| | - Christian F Singer
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria, Waehringer Guertel 18-20, A 1090 Vienna, Austria
| | - Jan Sullivan
- Genetic Health Service NZ, South Island Hub, Christchurch Hospital, Christchurch 8140, New Zealand
| | - Nicola Poplawski
- Adult Genetics Unit, South Australian Clinical Genetics Service, SA Pathology at the Women's and Children's Hospital, North Adelaide, SA 5067, Australia University Department of Paediatrics, University of Adelaide, North Terrace, Adelaide, SA 5000, Australia
| | - Phuong Mai
- Clinical Genetics Branch, DCEG, NCI, NIH, Bethesda, MD, USA
| | - Julian Peto
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, UK Division of Breast Cancer Research, Institute of Cancer Research, London SW3 6JB, UK
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany Molecular Epidemiology Group, German Cancer Research Center, DKFZ, Heidelberg 69120, Germany
| | - Harald Surowy
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany Molecular Epidemiology Group, German Cancer Research Center, DKFZ, Heidelberg 69120, Germany
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen 2730, Denmark Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev 2730, Denmark Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730 Denmark
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Sara Margolin
- Department of Oncology Pathology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Paolo Radice
- Unit of "Molecular bases of genetic risk and genetic testing", Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano 20139, Italy
| | - Laura Galastri
- Associazione Volontari Italiani Sangue (AVIS) comunale di Milano, Milano 20139, Italy
| | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, VIC 3010, Australia Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC 3004, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, VIC 3010, Australia Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC 3004, Australia
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada Department of Molecular Genetics, University of Toronto, M5B 1W8, Canada
| | - Gord Glendon
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Fiona Blows
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, 1683, Nicosia, Cyprus
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Fergus J Couch
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Maaike P Vreeswijk
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2300, The Netherlands
| | - Michael Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | - Alexandra Martins
- Inserm U1079-IRIB, University of Rouen, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| |
Collapse
|
32
|
Couch FJ, Akinhanmi M, Shimelis H, Hallberg EJ, Hu C, Hart S, Moore R, Meeks H, Huether R, Laduca H, Chao E, Goldgar D, Dolinsky JS. Risks of triple negative breast cancer associated with cancer predisposition gene mutations. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.1513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
33
|
Milutinovic S, Heynen-Genel S, Chao E, Dewing A, Solano R, Milan L, Barron N, He M, Diaz PW, Matsuzawa SI, Reed JC, Hassig CA. Cardiac Glycosides Activate the Tumor Suppressor and Viral Restriction Factor Promyelocytic Leukemia Protein (PML). PLoS One 2016; 11:e0152692. [PMID: 27031987 PMCID: PMC4816303 DOI: 10.1371/journal.pone.0152692] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/17/2016] [Indexed: 02/05/2023] Open
Abstract
Cardiac glycosides (CGs), inhibitors of Na+/K+-ATPase (NKA), used clinically to treat heart failure, have garnered recent attention as potential anti-cancer and anti-viral agents. A high-throughput phenotypic screen designed to identify modulators of promyelocytic leukemia protein (PML) nuclear body (NB) formation revealed the CG gitoxigenin as a potent activator of PML. We demonstrate that multiple structurally distinct CGs activate the formation of PML NBs and induce PML protein SUMOylation in an NKA-dependent fashion. CG effects on PML occur at the post-transcriptional level, mechanistically distinct from previously described PML activators and are mediated through signaling events downstream of NKA. Curiously, genomic deletion of PML in human cancer cells failed to abrogate the cytotoxic effects of CGs and other apoptotic stimuli such as ceramide and arsenic trioxide that were previously shown to function through PML in mice. These findings suggest that alternative pathways can compensate for PML loss to mediate apoptosis in response to CGs and other apoptotic stimuli.
Collapse
Affiliation(s)
- Snezana Milutinovic
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Susanne Heynen-Genel
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Elizabeth Chao
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Antimone Dewing
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Ricardo Solano
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Loribelle Milan
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Nikki Barron
- Bemer USA, LLC, Carlsbad, CA, United States of America
| | - Min He
- National Cancer Institute (NCI), Bethesda, MD, United States of America
| | - Paul W. Diaz
- P.William Diaz, Pharmaceutical Consulting, Riverside, CA, United States of America
| | - Shu-ichi Matsuzawa
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - John C. Reed
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Christian A. Hassig
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, United States of America
- * E-mail:
| |
Collapse
|
34
|
Muppidi A, Zou H, Yang PY, Chao E, Sherwood L, Nunez V, Woods A, Schultz PG, Lin Q, Shen W. Design of Potent and Proteolytically Stable Oxyntomodulin Analogs. ACS Chem Biol 2016; 11:324-8. [PMID: 26727558 PMCID: PMC4861236 DOI: 10.1021/acschembio.5b00787] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [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: 01/24/2023]
Abstract
Incretin-based peptides are effective therapeutics for treating type 2 diabetes mellitus (T2DM). Oxyntomodulin (OXM), a dual agonist of GLP-1R and GCGR, has shown superior weight loss and glucose lowering effects, compared to single GLP-1R agonists. To overcome the short half-life and rapid renal clearance of OXM, which limit its therapeutic potential, both lipid and PEG modified OXM analogs have been reported. However, these approaches often result in reduced potency or PEG-associated toxicity. Herein, we report a new class of cross-linked OXM analogs that show increased plasma stability and higher potency in activating both GLP-1R and GCGR. Moreover, the extended in vivo half-life results in superior antihyperglycemic activity in mice compared to the wild-type OXM.
Collapse
Affiliation(s)
- Avinash Muppidi
- California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, La Jolla, California 92037, United States
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Huafei Zou
- California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peng Yu Yang
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United states
| | - Elizabeth Chao
- California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lance Sherwood
- California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Vanessa Nunez
- California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ashley Woods
- California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter G Schultz
- California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, La Jolla, California 92037, United States
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United states
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Weijun Shen
- California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| |
Collapse
|
35
|
Hernandez F, Huether R, Carter L, Johnston T, Thompson J, Gossage JR, Chao E, Elliott AM. Mutations in RASA1 and GDF2 identified in patients with clinical features of hereditary hemorrhagic telangiectasia. Hum Genome Var 2015; 2:15040. [PMID: 27081547 PMCID: PMC4785548 DOI: 10.1038/hgv.2015.40] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [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: 05/27/2015] [Revised: 09/02/2015] [Accepted: 09/09/2015] [Indexed: 01/18/2023] Open
Abstract
Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant vascular disorder caused by mutations in ENG, ACVRL1 and SMAD4, which function in regulating the transforming growth factor beta and bone morphogenetic protein signaling pathways. Symptoms of HHT can be present in individuals who test negative for mutations in these three genes indicating other genes may be involved. In this study, we tested for mutations in two genes, RASA1 and GDF2, which were recently reported to be involved in vascular disorders. To determine whether RASA1 and GDF2 have phenotypic overlap with HHT and should be included in diagnostic testing, we developed a next-generation sequencing assay to detect mutations in 93 unrelated individuals who previously tested negative for mutations in ENG, ACVRL1 and SMAD4, but were clinically suspected to have HHT. Pathogenic mutations in RASA1 were identified in two samples (2.15%) and a variant of unknown significance in GDF2 was detected in one sample. All three individuals experienced epistaxis with dermal lesions described in medical records as telangiectases. These results indicate that the inclusion of RASA1 and GDF2 screening in individuals suspected to have HHT will increase the detection rate and aid clinicians in making an accurate diagnosis.
Collapse
Affiliation(s)
- Felicia Hernandez
- Department of Research and Development, Ambry Genetics , Aliso Viejo, CA, USA
| | - Robert Huether
- Department of Bioinformatics, Ambry Genetics , Aliso Viejo, CA, USA
| | - Lester Carter
- Department of Bioinformatics, Ambry Genetics , Aliso Viejo, CA, USA
| | - Tami Johnston
- Department of Clinical Genetics, Ambry Genetics , Aliso Viejo, CA, USA
| | - Jennifer Thompson
- Department of Clinical Genetics, Ambry Genetics , Aliso Viejo, CA, USA
| | - James R Gossage
- Division of Pulmonary/Critical Care, Georgia Regents University , Augusta, GA, USA
| | - Elizabeth Chao
- Department of Clinical Genetics, Ambry Genetics , Aliso Viejo, CA, USA
| | - Aaron M Elliott
- Department of Research and Development, Ambry Genetics , Aliso Viejo, CA, USA
| |
Collapse
|
36
|
Abstract
The capability to sense and respond to external mechanical stimuli at various timescales is essential to many physiological aspects in plants, including self-protection, intake of nutrients and reproduction. Remarkably, some plants have evolved the ability to react to mechanical stimuli within a few seconds despite a lack of muscles and nerves. The fast movements of plants in response to mechanical stimuli have long captured the curiosity of scientists and engineers, but the mechanisms behind these rapid thigmonastic movements are still not understood completely. In this article, we provide an overview of such thigmonastic movements in several representative plants, including Dionaea, Utricularia, Aldrovanda, Drosera and Mimosa. In addition, we review a series of studies that present biomimetic structures inspired by fast-moving plants. We hope that this article will shed light on the current status of research on the fast movements of plants and bioinspired structures and also promote interdisciplinary studies on both the fundamental mechanisms of plants' fast movements and biomimetic structures for engineering applications, such as artificial muscles, multi-stable structures and bioinspired robots.
Collapse
Affiliation(s)
- Q Guo
- College of Materials Science and Engineering, Fujian University of Technology, Fuzhou 350108, China Fujian Provincial Key Laboratory of Advanced Materials Processing and Application, Fuzhou 350108, China
| | - E Dai
- Department of Biomedical Engineering, Washington University, St Louis, MO 63130, USA
| | - X Han
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - S Xie
- Department of Energy, Environmental, and Chemical Engineering, Washington University, St Louis, MO 63130, USA
| | - E Chao
- Department of Biomedical Engineering, Washington University, St Louis, MO 63130, USA
| | - Z Chen
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| |
Collapse
|
37
|
Alamillo CL, Powis Z, Farwell K, Shahmirzadi L, Weltmer EC, Turocy J, Lowe T, Kobelka C, Chen E, Basel D, Ashkinadze E, D'Augelli L, Chao E, Tang S. Exome sequencing positively identified relevant alterations in more than half of cases with an indication of prenatal ultrasound anomalies. Prenat Diagn 2015; 35:1073-8. [PMID: 26147564 DOI: 10.1002/pd.4648] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Exome sequencing is a successful option for diagnosing individuals with previously uncharacterized genetic conditions, however little has been reported regarding its utility in a prenatal setting. The goal of this study is to describe the results from a cohort of fetuses for which exome sequencing was performed. METHODS We performed a retrospective analysis of the first seven cases referred to our laboratory for exome sequencing following fetal demise or termination of pregnancy. All seven pregnancies had multiple congenital anomalies identified by level II ultrasound. Exome sequencing was performed on trios using cultured amniocytes or products of conception from the affected fetuses. RESULTS Relevant alterations were identified in more than half of the cases (4/7). Three of the four were categorized as 'positive' results, and one of the four was categorized as a 'likely positive' result. The provided diagnoses included osteogenesis imperfecta II (COL1A2), glycogen storage disease IV (GBE1), oral-facial-digital syndrome 1 (OFD1), and RAPSN-associated fetal akinesia deformation sequence. CONCLUSION This data suggests that exome sequencing is likely to be a valuable diagnostic testing option for pregnancies with multiple congenital anomalies detected by prenatal ultrasound; however, additional studies with larger cohorts of affected pregnancies are necessary to confirm these findings.
Collapse
Affiliation(s)
| | - Zöe Powis
- Ambry Genetics, Aliso Viejo, CA, USA
| | | | | | | | - John Turocy
- Genetics Department, Kaiser Permanente, Clovis, CA, USA
| | - Thomas Lowe
- Thomas Lowe, MD, Private Practice, Boca Raton, FL, USA
| | | | - Emily Chen
- Genetics Department, Kaiser Permanente, San Francisco, CA, USA
| | - Donald Basel
- Division of Genetics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Elena Ashkinadze
- Division of Maternal-Fetal Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | | | - Elizabeth Chao
- Ambry Genetics, Aliso Viejo, CA, USA.,Department of Pediatrics, University of California Irvine, Irvine, CA, USA
| | - Sha Tang
- Ambry Genetics, Aliso Viejo, CA, USA
| |
Collapse
|
38
|
Chao E, Lucas D, Beneke M, Casey D, Henderson D, Homp J, Kammeyer T, Lai S, Mauer C, O'Connell R, Schnarr E. SU-F-BRB-06: Validation of Dose Calculation for Helical Tomotherapy with a Rigidly Moving Object. Med Phys 2015. [DOI: 10.1118/1.4925201] [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: 11/07/2022] Open
|
39
|
Matney J, Lian J, Chao E, Chera B, Marks L, Das S. SU-E-T-657: Quantitative Assessment of Plan Robustness for Helical Tomotherapy for Head and Neck Cancer Radiotherapy. Med Phys 2015. [DOI: 10.1118/1.4925020] [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: 11/07/2022] Open
|
40
|
Lian J, Matney J, Chao E, Chang S, Zagar T, Wang A, Chera B, Das S, Schreiber E. SU-C-210-02: Impact of Intrafractional Motion On TomoTherapy Stereotactic Body Radiotherapy (SBRT) 4D Dosimetry. Med Phys 2015. [DOI: 10.1118/1.4923847] [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: 11/07/2022] Open
|
41
|
Brandt R, DelGiacco EJ, Nixon C, Chao E, Dolinsky JS, Speare V, Mushlin J, Carp NZ, McHugh TW. The genetic variation observed in BRCA 1/2 + families. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e12511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
42
|
Milam MR, Stany M, Li S, Fulk K, Chao E, Laduca H. Women with breast and uterine cancer in relation to genetic mutation risk: A case-control analysis. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.1549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Michael Stany
- Walter Reed National Military Medical Center, Bethesda, MD
| | | | | | | | | |
Collapse
|
43
|
Speare V, Dolinsky JS, Laduca H, Horton C, Panos L, Mason C, Dalton E, Chao E. Germline testing in hereditary cancer genes subsequent to the identification of mutations in tumor specimens. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.1527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
44
|
Panos L, Chao E, McFarland R, LaDuca H. Using multi-gene testing to broaden the understanding of inherited endometrial cancer. Gynecol Oncol 2015. [DOI: 10.1016/j.ygyno.2015.01.046] [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: 10/23/2022]
|
45
|
Zhang Y, Zou H, Wang Y, Caballero D, Gonzalez J, Chao E, Welzel G, Shen W, Wang D, Schultz PG, Wang F. Rational design of a humanized glucagon-like peptide-1 receptor agonist antibody. Angew Chem Int Ed Engl 2014; 54:2126-30. [PMID: 25556336 DOI: 10.1002/anie.201410049] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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: 10/13/2014] [Indexed: 11/09/2022]
Abstract
Bovine antibody BLV1H12 possesses a unique "stalk-knob" architecture in its ultralong heavy chain CDR3, allowing substitutions of the "knob" domain with protein agonists to generate functional antibody chimeras. We have generated a humanized glucagon-like peptide-1 (GLP-1) receptor agonist antibody by first introducing a coiled-coil "stalk" into CDR3H of the antibody herceptin. Exendin-4 (Ex-4), a GLP-1 receptor agonist, was then fused to the engineered stalk with flexible linkers, and a Factor Xa cleavage site was inserted immediately in front of Ex-4 to allow release of the N-terminus of the fused peptide. The resulting clipped herceptin-Ex-4 fusion protein is more potent in vitro in activating GLP-1 receptors than the Ex-4 peptide. The clipped herceptin-Ex-4 has an extended plasma half-life of approximately four days and sustained control of blood glucose levels for more than a week in mice. This work provides a novel approach to the development of human or humanized agonist antibodies as therapeutics.
Collapse
Affiliation(s)
- Yong Zhang
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Zhang Y, Zou H, Wang Y, Caballero D, Gonzalez J, Chao E, Welzel G, Shen W, Wang D, Schultz PG, Wang F. Rational Design of a Humanized Glucagon-Like Peptide-1 Receptor Agonist Antibody. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
47
|
Gau CL, LaDuca H, Lu H, Stuenkel AJ, Pesaran T, Chen E, Siegfried J, Mexal S, Hoiness R, Cook J, Copenhaver J, Chao E. Abstract 14: Identification of probands with multiple mutations in cancer susceptibility genes using a multigene panel approach. Cancer Res 2014. [DOI: 10.1158/1538-7445.cansusc14-14] [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
The multi-gene hereditary cancer panel testing approach allows for the identification of probands carrying multiple mutations in hereditary cancer predisposition genes. The purpose of this study is to assess the frequency and phenotypes of individuals in our hereditary cancer panel cohort carrying multiple mutations in hereditary cancer predisposition genes. From March 2012 through October 2013, results were reported for 4382 individuals who underwent hereditary cancer panel testing at our laboratory. Panels included comprehensive analysis of 14-24 genes, depending on the panel ordered. Genes analyzed on each panel included both genes associated with defined hereditary cancer syndromes and genes not yet associated with a defined hereditary cancer syndrome, with moderate to high penetrance estimates. Panel results were reviewed to determine the number of probands carrying multiple pathogenic mutations or likely pathogenic variants in the genes analyzed, and retrospective test requisition form review was used to obtain clinician-reported clinical history information. Biallelic MUTYH mutation carriers were not counted as multiple mutation cases, nor were individuals carrying a monoallelic MUTYH mutation in combination with a mutation in a different gene. Nine probands (0.2%) were identified to carry two cancer-predisposing mutations. Mutations included 7 small insertions/deletions, 1 nonsense, 4 missense, 3 splicing, and 3 gross deletions. Five individuals carried two mutations in moderately-penetrant cancer susceptibility genes not associated with a defined hereditary cancer syndrome. Mutated gene combinations included CHEK2/CHEK2 (confirmed to be in trans), ATM/RAD50, ATM/CHEK2 (identified in two probands), and MRE11A/PALB2. Two individuals carried one mutation in a moderately-penetrant gene and one mutation in a highly-penetrant gene associated with a defined hereditary cancer syndrome (ATM/MSH6 and MLH1/CHEK2). The remaining two individuals carried two mutations in highly-penetrant genes (MSH6/MSH6 (phase unknown) and MSH2/MSH6). The average age at first primary cancer diagnosis was 42 years (range 16-66 years). All probands had a history of cancer, including six of the nine probands with a reported history of more than one primary cancer diagnosis. Results from this study indicate that a minority of probands undergoing hereditary cancer panel testing are identified to carry multiple mutations in cancer susceptibility genes. This data highlights the need for further research to determine the clinical implications of carrying multiple mutations in cancer susceptibility genes, particularly for those with mutations in moderately-penetrant genes. Detailed pedigree analysis, co-segregation analysis, and longitudinal follow-up will be helpful in clarifying cancer risks in these probands and the significance of multiple mutations in cancer susceptibility genes.
Citation Format: Chia-Ling Gau, Holly LaDuca, Hong Lu, AJ Stuenkel, Tina Pesaran, Elaine Chen, Jill Siegfried, Sharon Mexal, Robert Hoiness, Jill Cook, John Copenhaver, Elizabeth Chao. Identification of probands with multiple mutations in cancer susceptibility genes using a multigene panel approach. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Susceptibility and Cancer Susceptibility Syndromes; Jan 29-Feb 1, 2014; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(23 Suppl):Abstract nr 14. doi:10.1158/1538-7445.CANSUSC14-14
Collapse
Affiliation(s)
| | | | - Hong Lu
- Ambry Genetics, Aliso Viejo, CA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Chao E, Dolinsky J, Pal T. Response to Cragun et al. Clin Genet 2014; 88:201. [PMID: 25381838 DOI: 10.1111/cge.12512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 09/23/2014] [Indexed: 11/28/2022]
Affiliation(s)
- E Chao
- Department of Pediatrics, University of California, Irvine, CA, USA.,Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA
| | - J Dolinsky
- Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA
| | - T Pal
- Department of Interdisciplinary Oncology, University of South Florida, Tampa, FL, USA
| |
Collapse
|
49
|
|
50
|
Haga A, Nakagawa K, Maurer C, Ruchala K, Chao E, Casey D, Ida S, Sakata D, Magome T, Nakano M, Masutani Y. SU-E-J-203: Reconstruction of the Treatment Area by Use of Sinogram in Helical Tomotherapy. Med Phys 2014. [DOI: 10.1118/1.4888256] [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: 11/07/2022] Open
|