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Davis NF, Cunnane EM, O'Brien FJ, Mulvihill JJ, Walsh MT. Tissue engineered extracellular matrices (ECMs) in urology: Evolution and future directions. Surgeon 2017; 16:55-65. [PMID: 28811169 DOI: 10.1016/j.surge.2017.07.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/18/2017] [Indexed: 12/21/2022]
Abstract
Autologous gastrointestinal tissue has remained the gold-standard reconstructive biomaterial in urology for >100 years. Mucus-secreting epithelium is associated with lifelong metabolic and neuromechanical complications when implanted into the urinary tract. Therefore, the availability of biocompatible tissue-engineered biomaterials such as extracellular matrix (ECM) scaffolds may provide an attractive alternative for urologists. ECMs are decellularised, biodegradable membranes that have shown promise for repairing defective urinary tract segments in vitro and in vivo by inducing a host-derived tissue remodelling response after implantation. In urology, porcine small intestinal submucosa (SIS) and porcine urinary bladder matrix (UBM) are commonly selected as ECMs for tissue regeneration. Both ECMs support ingrowth of native tissue and differentiation of multi-layered urothelial and smooth muscle cells layers while providing mechanical support in vivo. In their native acellular state, ECM scaffolds can repair small urinary tract defects. Larger urinary tract segments can be repaired when ECMs are manipulated by seeding them with various cell types prior to in vivo implantation. In the present review, we evaluate and summarise the clinical potential of tissue engineered ECMs in reconstructive urology with emphasis on their long-term outcomes in urological clinical trials.
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Mulvihill JJ, Capps B, Joly Y, Lysaght T, Zwart HAE, Chadwick R. Ethical issues of CRISPR technology and gene editing through the lens of solidarity. Br Med Bull 2017; 122:17-29. [PMID: 28334154 DOI: 10.1093/bmb/ldx002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 01/30/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND The avalanche of commentaries on CRISPR-Cas9 technology, a bacterial immune system modified to recognize any short DNA sequence, cut it out, and insert a new one, has rekindled hopes for gene therapy and other applications and raised criticisms of engineering genes in future generations. SOURCES OF DATA This discussion draws on articles that emphasize ethics, identified partly through PubMed and Google, 2014-2016. AREAS OF AGREEMENT CRISPR-Cas9 has taken the pace and prospects for genetic discovery and applications to a high level, stoking anticipation for somatic gene engineering to help patients. We support a moratorium on germ line manipulation. AREAS OF CONTROVERSY We place increased emphasis on the principle of solidarity and the public good. The genetic bases of some diseases are not thoroughly addressable with CRISPR-Cas9. We see no new ethical issues, compared with gene therapy and genetic engineering in general, apart from the explosive rate of findings. Other controversies include eugenics, patentability and unrealistic expectations of professionals and the public. GROWING POINTS Biggest issues are the void of research on human germ cell biology, the appropriate routes for oversight and transparency, and the scientific and ethical areas of reproductive medicine. AREAS TIMELY FOR DEVELOPING RESEARCH The principle of genomic solidarity and priority on public good should be a lens for bringing clarity to CRISPR debates. The valid claim of genetic exceptionalism supports restraint on experimentation in human germ cells, given the trans-generational dangers and the knowledge gap in germ cell biology.
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Ramoni RB, Mulvihill JJ, Adams DR, Allard P, Ashley EA, Bernstein JA, Gahl WA, Hamid R, Loscalzo J, McCray AT, Shashi V, Tifft CJ, Wise AL. The Undiagnosed Diseases Network: Accelerating Discovery about Health and Disease. Am J Hum Genet 2017; 100:185-192. [PMID: 28157539 PMCID: PMC5294757 DOI: 10.1016/j.ajhg.2017.01.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 12/30/2016] [Indexed: 01/07/2023] Open
Abstract
Diagnosis at the edges of our knowledge calls upon clinicians to be data driven, cross-disciplinary, and collaborative in unprecedented ways. Exact disease recognition, an element of the concept of precision in medicine, requires new infrastructure that spans geography, institutional boundaries, and the divide between clinical care and research. The National Institutes of Health (NIH) Common Fund supports the Undiagnosed Diseases Network (UDN) as an exemplar of this model of precise diagnosis. Its goals are to forge a strategy to accelerate the diagnosis of rare or previously unrecognized diseases, to improve recommendations for clinical management, and to advance research, especially into disease mechanisms. The network will achieve these objectives by evaluating patients with undiagnosed diseases, fostering a breadth of expert collaborations, determining best practices for translating the strategy into medical centers nationwide, and sharing findings, data, specimens, and approaches with the scientific and medical communities. Building the UDN has already brought insights to human and medical geneticists. The initial focus has been on data sharing, establishing common protocols for institutional review boards and data sharing, creating protocols for referring and evaluating patients, and providing DNA sequencing, metabolomic analysis, and functional studies in model organisms. By extending this precision diagnostic model nationally, we strive to meld clinical and research objectives, improve patient outcomes, and contribute to medical science.
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Chao HT, Davids M, Burke E, Pappas JG, Rosenfeld JA, McCarty AJ, Davis T, Wolfe L, Toro C, Tifft C, Xia F, Stong N, Johnson TK, Warr CG, Yamamoto S, Adams DR, Markello TC, Gahl WA, Bellen HJ, Wangler MF, Malicdan MCV, Adams DR, Adams CJ, Alejandro ME, Allard P, Ashley EA, Bacino CA, Balasubramanyam A, Barseghyan H, Beggs AH, Bellen HJ, Bernstein JA, Bick DP, Birch CL, Boone BE, Briere LC, Brown DM, Brush M, Burrage LC, Chao KR, Clark GD, Cogan JD, Cooper CM, Craigen WJ, Davids M, Dayal JG, Dell'Angelica EC, Dhar SU, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Draper DD, Dries AM, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fisher PG, Frisby TS, Frost K, Gahl WA, Gartner V, Godfrey RA, Goheen M, Golas GA, Goldstein DB, Gordon M“GG, Gould SE, Gourdine JPF, Graham BH, Groden CA, Gropman AL, Hackbarth ME, Haendel M, Hamid R, Hanchard NA, Handley LH, Hardee I, Herzog MR, Holm IA, Howerton EM, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Koehler AE, Koeller DM, Kohane IS, Kohler JN, Krasnewich DM, Krieg EL, Krier JB, Kyle JE, Lalani SR, Latham L, Latour YL, Lau CC, Lazar J, Lee BH, Lee H, Lee PR, Levy SE, Levy DJ, Lewis RA, Liebendorder AP, Lincoln SA, Loomis CR, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Mashid AS, Mazur P, McCarty AJ, McConkie-Rosell A, McCray AT, Metz TO, Might M, Moretti PM, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Ramoni RB, Rodan LH, Sadozai S, Schaffer KE, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Silverman EK, Sinsheimer JS, Soldatos AG, Spillmann RC, Splinter K, Stoler JM, Stong N, Strong KA, Sullivan JA, Sweetser DA, Thomas SP, Tift CJ, Tolman NJ, Toro C, Tran AA, Valivullah ZM, Vilain E, Waggott DM, Wahl CE, Walley NM, Walsh CA, Wangler MF, Warburton M, Ward PA, Waters KM, Webb-Robertson BJM, Weech AA, Westerfield M, Wheeler MT, Wise AL, Worthe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zornio PA. A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3. Am J Hum Genet 2017; 100:128-137. [PMID: 28017372 PMCID: PMC5223093 DOI: 10.1016/j.ajhg.2016.11.018] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
Early B cell factor 3 (EBF3) is a member of the highly evolutionarily conserved Collier/Olf/EBF (COE) family of transcription factors. Prior studies on invertebrate and vertebrate animals have shown that EBF3 homologs are essential for survival and that loss-of-function mutations are associated with a range of nervous system developmental defects, including perturbation of neuronal development and migration. Interestingly, aristaless-related homeobox (ARX), a homeobox-containing transcription factor critical for the regulation of nervous system development, transcriptionally represses EBF3 expression. However, human neurodevelopmental disorders related to EBF3 have not been reported. Here, we describe three individuals who are affected by global developmental delay, intellectual disability, and expressive speech disorder and carry de novo variants in EBF3. Associated features seen in these individuals include congenital hypotonia, structural CNS malformations, ataxia, and genitourinary abnormalities. The de novo variants affect a single conserved residue in a zinc finger motif crucial for DNA binding and are deleterious in a fly model. Our findings indicate that mutations in EBF3 cause a genetic neurodevelopmental syndrome and suggest that loss of EBF3 function might mediate a subset of neurologic phenotypes shared by ARX-related disorders, including intellectual disability, abnormal genitalia, and structural CNS malformations.
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Shashi V, Pena LD, Kim K, Burton B, Hempel M, Schoch K, Walkiewicz M, McLaughlin HM, Cho M, Stong N, Hickey SE, Shuss CM, Freemark MS, Bellet JS, Keels MA, Bonner MJ, El-Dairi M, Butler M, Kranz PG, Stumpel CT, Klinkenberg S, Oberndorff K, Alawi M, Santer R, Petrovski S, Kuismin O, Korpi-Heikkilä S, Pietilainen O, Aarno P, Kurki MI, Hoischen A, Need AC, Goldstein DB, Kortüm F, Bacino A, Lee BH, Balasubramanyam A, Burrage LC, Clark GD, Craigen WJ, Dhar SU, Emrick LT, Graham BH, Jain M, Lalani SR, Lewis RA, Moretti PM, Nicholas SK, Orange JS, Posey JE, Potocki L, Rosenfeld JA, Scott DA, Hanchard NA, Alyssa TA, Mercedes AE, Mashid AS, Bellen HJ, Yamamoto S, Wangler MF, Westerfield M, Postlethwait JH, Eng CM, Yang Y, Muzny DM, Ward PA, Ramoni RB, McCray AT, Kohane IS, Holm IA, Might M, Mazur P, Splinter K, Esteves C, Shashi V, Jiang YH, Pena LD, McConkie-Rosell A, Schoch K, Spillmann RC, Sullivan JA, Walley NM, Goldstein DB, Stong N, Beggs AH, Loscalzo J, MacRae CA, Silverman EK, Stoler JM, Sweetser DA, Maas RL, Krier JB, Rodan LH, Walsh CA, Cooper CM, Pallais JC, Donnell-Fink LA, Krieg EL, Lincoln SA, Briere LC, Jacob HJ, Worthey EA, Lazar J, Strong KA, Handley LH, Newberry JS, Bick DP, Schroeder MC, Brown DM, Birch CL, Levy SE, Boone BE, Dorset DC, Jones AL, Manolio TA, Mulvihill JJ, Wise AL, Dayal JG, Eckstein DJ, Krasnewich DM, Loomis CR, Mamounas LA, Iglesias B, Martin C, Koeller DM, Metz TO, Ashley EA, Fisher PG, Bernstein JA, Wheeler MT, Zornio PA, Waggott DM, Dries AM, Kohler JN, Dipple KM, Nelson SF, Palmer CG, Vilain E, Allard P, Dell Angelica EC, Lee H, Sinsheimer JS, Papp JC, Dorrani N, Herzog MR, Barseghyan H, Adams DR, Adams CJ, Burke EA, Chao KR, Davids M, Draper DD, Estwick T, Frisby TS, Frost K, Gahl WA, Gartner V, Godfrey RA, Goheen M, Golas GA, Gordon MG, Groden CA, Gropman AL, Hackbarth ME, Hardee I, Johnston JM, Koehler AE, Latham L, Latour YL, Lau CYC, Lee PR, Levy DJ, Liebendorder AP, Macnamara EF, Maduro VV, Malicdan MV, Markello TC, McCarty AJ, Murphy JL, Nehrebecky ME, Novacic D, Pusey BN, Sadozai S, Schaffer KE, Sharma P, Soldatos AG, Thomas SP, Tifft CJ, Tolman NJ, Toro C, Valivullah ZM, Wahl CE, Warburton M, Weech AA, Wolfe LA, Yu G, Hamid R, Newman JH, Phillips JA, Cogan JD. De Novo Truncating Variants in ASXL2 Are Associated with a Unique and Recognizable Clinical Phenotype. Am J Hum Genet 2016; 99:991-999. [PMID: 27693232 PMCID: PMC5065681 DOI: 10.1016/j.ajhg.2016.08.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/24/2016] [Indexed: 12/14/2022] Open
Abstract
The ASXL genes (ASXL1, ASXL2, and ASXL3) participate in body patterning during embryogenesis and encode proteins involved in epigenetic regulation and assembly of transcription factors to specific genomic loci. Germline de novo truncating variants in ASXL1 and ASXL3 have been respectively implicated in causing Bohring-Opitz and Bainbridge-Ropers syndromes, which result in overlapping features of severe intellectual disability and dysmorphic features. ASXL2 has not yet been associated with a human Mendelian disorder. In this study, we performed whole-exome sequencing in six unrelated probands with developmental delay, macrocephaly, and dysmorphic features. All six had de novo truncating variants in ASXL2. A careful review enabled the recognition of a specific phenotype consisting of macrocephaly, prominent eyes, arched eyebrows, hypertelorism, a glabellar nevus flammeus, neonatal feeding difficulties, hypotonia, and developmental disabilities. Although overlapping features with Bohring-Opitz and Bainbridge-Ropers syndromes exist, features that distinguish the ASXL2-associated condition from ASXL1- and ASXL3-related disorders are macrocephaly, absence of growth retardation, and more variability in the degree of intellectual disabilities. We were also able to demonstrate with mRNA studies that these variants are likely to exert a dominant-negative effect, given that both alleles are expressed in blood and the mutated ASXL2 transcripts escape nonsense-mediated decay. In conclusion, de novo truncating variants in ASXL2 underlie a neurodevelopmental syndrome with a clinically recognizable phenotype. This report expands the germline disorders that are linked to the ASXL genes.
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Pathak A, Seipel K, Pemov A, Dewan R, Brown C, Ravichandran S, Luke BT, Malasky M, Suman S, Yeager M, Gatti RA, Caporaso NE, Mulvihill JJ, Goldin LR, Pabst T, McMaster ML, Stewart DR. Whole exome sequencing reveals a C-terminal germline variant in CEBPA-associated acute myeloid leukemia: 45-year follow up of a large family. Haematologica 2016; 101:846-52. [PMID: 26721895 PMCID: PMC5004464 DOI: 10.3324/haematol.2015.130799] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 12/29/2015] [Indexed: 11/09/2022] Open
Abstract
Familial acute myeloid leukemia is rare and linked to germline mutations in RUNX1, GATA2 or CCAAT/enhancer binding protein-α (CEBPA). We re-evaluated a large family with acute myeloid leukemia originally seen at NIH in 1969. We used whole exome sequencing to study this family, and conducted in silico bioinformatics analysis, protein structural modeling and laboratory experiments to assess the impact of the identified CEBPA Q311P mutation. Unlike most previously identified germline mutations in CEBPA, which were N-terminal frameshift mutations, we identified a novel Q311P variant that was located in the C-terminal bZip domain of C/EBPα. Protein structural modeling suggested that the Q311P mutation alters the ability of the CEBPA dimer to bind DNA. Electrophoretic mobility shift assays showed that the Q311P mu-tant had attenuated binding to DNA, as predicted by the protein modeling. Consistent with these findings, we found that the Q311P mutation has reduced transactivation, consistent with a loss-of-function mutation. From 45 years of follow up, we observed incomplete penetrance (46%) of CEBPA Q311P. This study of a large multi-generational pedigree reveals that a germline mutation in the C-terminal bZip domain can alter the ability of C/EBP-α to bind DNA and reduces transactivation, leading to acute myeloid leukemia.
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Gahl WA, Mulvihill JJ, Toro C, Markello TC, Wise AL, Ramoni RB, Adams DR, Tifft CJ. The NIH Undiagnosed Diseases Program and Network: Applications to modern medicine. Mol Genet Metab 2016; 117:393-400. [PMID: 26846157 PMCID: PMC5560125 DOI: 10.1016/j.ymgme.2016.01.007] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 11/21/2022]
Abstract
INTRODUCTION The inability of some seriously and chronically ill individuals to receive a definitive diagnosis represents an unmet medical need. In 2008, the NIH Undiagnosed Diseases Program (UDP) was established to provide answers to patients with mysterious conditions that long eluded diagnosis and to advance medical knowledge. Patients admitted to the NIH UDP undergo a five-day hospitalization, facilitating highly collaborative clinical evaluations and a detailed, standardized documentation of the individual's phenotype. Bedside and bench investigations are tightly coupled. Genetic studies include commercially available testing, single nucleotide polymorphism microarray analysis, and family exomic sequencing studies. Selected gene variants are evaluated by collaborators using informatics, in vitro cell studies, and functional assays in model systems (fly, zebrafish, worm, or mouse). INSIGHTS FROM THE UDP In seven years, the UDP received 2954 complete applications and evaluated 863 individuals. Nine vignettes (two unpublished) illustrate the relevance of an undiagnosed diseases program to complex and common disorders, the coincidence of multiple rare single gene disorders in individual patients, newly recognized mechanisms of disease, and the application of precision medicine to patient care. CONCLUSIONS The UDP provides examples of the benefits expected to accrue with the recent launch of a national Undiagnosed Diseases Network (UDN). The UDN should accelerate rare disease diagnosis and new disease discovery, enhance the likelihood of diagnosing known diseases in patients with uncommon phenotypes, improve management strategies, and advance medical research.
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Pathak A, Seipel K, Pemov A, Dewan R, Brown C, Ravichandran S, Luke BT, Yeager M, Gatti RA, Caporaso N, Mulvihill JJ, Goldin L, Pabst TM, McMaster ML, Stewart DR. Abstract 2756: Whole-exome sequencing reveals a novel germline variant in CEBPA-associated familial acute myeloid leukemia: 45-year follow-up of a large family. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Familial acute myeloid leukemia (AML) is rare and linked to germline mutations in RUNX1 or CCAAT/enhancer binding protein-α (CEBPA). We conducted whole-exome sequencing on a large family with AML originally evaluated at NIH in 1969 and uncovered a CEBPA Q311P mutation in all tested, affected members. The Q311P variant, located in the C-terminal bZip domain of CEBPA, was predicted to be highly deleterious by in silico algorithms; the Q311 position was highly conserved among CEBPA orthologs and paralogs. This variant has not been observed in the NHLBI's Exome Sequencing Project or the Broad Institute's Exome Aggregation Consortium. Protein structural modeling suggested that the Q311P mutation alters the ability of the CEBPA dimer to bind DNA. Electrophoretic mobility shift assays showed that the Q311P mutant had attenuated binding to DNA, as predicted by the protein modeling. Consistent with these findings, we found that the Q311P mutation has reduced transactivation of a promoter with a tetramer of CEBP sites, consistent with a loss-of-function mutation. In addition, there was decreased colony survival in fibroblasts with CEBPA Q311P, associated with the clinical radiosensitivity postulated in one carrier. From 45 years of follow-up, we observed incomplete penetrance (46%) of CEBPA Q311P; we did not observe other cancers or leukemias segregating with the mutation. Thus, we present a comprehensive clinical and molecular characterization of a novel AML-associated variant in CEBPA in a NCI family with nearly half a century of follow-up. This study reveals that a germline mutation in the C-terminal bZip domain can alter the ability of CEBPA to bind DNA and reduces transactivation, leading to AML, though with lower penetrance than the canonical N-terminal frameshift germline mutations.
Citation Format: Anand Pathak, Katja Seipel, Alexander Pemov, Ramita Dewan, Christina Brown, Sarangan Ravichandran, Brian T. Luke, Meredith Yeager, Richard A. Gatti, Neil Caporaso, John J. Mulvihill, Lynn Goldin, Thomas Muller Pabst, Mary Lou McMaster, Douglas R. Stewart. Whole-exome sequencing reveals a novel germline variant in CEBPA-associated familial acute myeloid leukemia: 45-year follow-up of a large family. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2756. doi:10.1158/1538-7445.AM2015-2756
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Penles Stadler M, Mulvihill JJ. Cancer Risk Assessment and Genetic Counseling in an Academic Medical Center: Consultands' Satisfaction, Knowledge, and Behavior in the First Year. J Genet Couns 2015; 7:279-97. [PMID: 26141403 DOI: 10.1023/a:1022847323935] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In 1995, we formally established a multifaceted cancer genetics program of clinical services, research, and education at a general academic medical center. In the first year, 58 families, mostly physician referred, received cancer risk assessment and genetic counseling for a family and/or medical history of cancer. The primary reasons for seeking consultation were to determine their risk or their offspring's risk for developing certain cancers and to inquire about the availability of DNA testing for predisposition to breast, ovarian, or colon cancers. To assess the level of satisfaction with program services, 51 consultands (22% with a personal history of cancer) were interviewed independently by telephone 3-12 months after the session. One goal of the survey was to improve program service. Ninety percent of respondents reported that the consultation was worth their time and money. Forty-two percent stated that their anxiety related to their cancer risk had decreased following counseling and 56% indicated no change. Recall of exact numerical risk was poor and one-third could not remember hearing any risk estimate. More respondents would recommend the service to friends (90%) than to family members (75%). Overall, the service was positively received by the majority of patients.
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Mulvihill JJ. Familial Aspects of Pancreatic Cancer. Fam Cancer 2015. [DOI: 10.1159/000412540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Mulvihill JJ. Clinical Ecogenetics of Human Cancer. Fam Cancer 2015. [DOI: 10.1159/000412518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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S�rensen SA, Mulvihill JJ, Nielsen A. Malignancy in Neurofibromatosis. Fam Cancer 2015. [DOI: 10.1159/000412547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Mulvihill JJ. Familial Non-Melanotic Skin Cancer. Fam Cancer 2015. [DOI: 10.1159/000412548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Barrett HE, Mulvihill JJ, Cunnane EM, Walsh MT. Characterising human atherosclerotic carotid plaque tissue composition and morphology using combined spectroscopic and imaging modalities. Biomed Eng Online 2015; 14 Suppl 1:S5. [PMID: 25602176 PMCID: PMC4306117 DOI: 10.1186/1475-925x-14-s1-s5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Calcification is a marked pathological component in carotid artery plaque. Studies have suggested that calcification may induce regions of high stress concentrations therefore increasing the potential for rupture. However, the mechanical behaviour of the plaque under the influence of calcification is not fully understood. A method of accurately characterising the calcification coupled with the associated mechanical plaque properties is needed to better understand the impact of calcification on the mechanical behaviour of the plaque during minimally invasive treatments. This study proposes a comparison of biochemical and structural characterisation methods of the calcification in carotid plaque specimens to identify plaque mechanical behaviour. Biochemical analysis, by Fourier Transform Infrared (FTIR) spectroscopy, was used to identify the key components, including calcification, in each plaque sample. However, FTIR has a finite penetration depth which may limit the accuracy of the calcification measurement. Therefore, this FTIR analysis was coupled with the identification of the calcification inclusions located internally in the plaque specimen using micro x-ray computed tomography (μX-CT) which measures the calcification volume fraction (CVF) to total tissue content. The tissue characterisation processes were then applied to the mechanical material plaque properties acquired from experimental circumferential loading of human carotid plaque specimen for comparison of the methods. FTIR characterised the degree of plaque progression by identifying the functional groups associated with lipid, collagen and calcification in each specimen. This identified a negative relationship between stiffness and 'lipid to collagen' and 'calcification to collagen' ratios. However, μX-CT results suggest that CVF measurements relate to overall mechanical stiffness, while peak circumferential strength values may be dependent on specific calcification geometries. This study demonstrates the need to fully characterise the calcification structure of the plaque tissue and that a combination of FTIR and μX-CT provides the necessary information to fully understand the mechanical behaviour of the plaque tissue.
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Jupe ER, Dalessandri KM, Mulvihill JJ, Miike R, Knowlton NS, Pugh TW, Zhao LP, DeFreese DC, Manjeshwar S, Gramling BA, Wiencke JK, Benz CC. A steroid metabolizing gene variant in a polyfactorial model improves risk prediction in a high incidence breast cancer population. BBA CLINICAL 2014; 2:94-102. [PMID: 26673457 PMCID: PMC4633888 DOI: 10.1016/j.bbacli.2014.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 10/29/2014] [Accepted: 11/02/2014] [Indexed: 01/08/2023]
Abstract
Background We have combined functional gene polymorphisms with clinical factors to improve prediction and understanding of sporadic breast cancer risk, particularly within a high incidence Caucasian population. Methods A polyfactorial risk model (PFRM) was built from both clinical data and functional single nucleotide polymorphism (SNP) gene candidates using multivariate logistic regression analysis on data from 5022 US Caucasian females (1671 breast cancer cases, 3351 controls), validated in an independent set of 1193 women (400 cases, 793 controls), and reassessed in a unique high incidence breast cancer population (165 cases, 173 controls) from Marin County, CA. Results The optimized PFRM consisted of 22 SNPs (19 genes, 6 regulating steroid metabolism) and 5 clinical risk factors, and its 5-year and lifetime risk prediction performance proved significantly superior (~ 2-fold) over the Gail model (Breast Cancer Risk Assessment Tool, BCRAT), whether assessed by odds (OR) or positive likelihood (PLR) ratios over increasing model risk levels. Improved performance of the PFRM in high risk Marin women was due in part to genotype enrichment by a CYP11B2 (-344T/C) variant. Conclusions and general significance Since the optimized PFRM consistently outperformed BCRAT in all Caucasian study populations, it represents an improved personalized risk assessment tool. The finding of higher Marin County risk linked to a CYP11B2 aldosterone synthase SNP associated with essential hypertension offers a new genetic clue to sporadic breast cancer predisposition. A polyfactorial breast cancer risk assessment model (PFRM) was built and validated. The optimized PFRM incorporates both genetic (22 SNPs/19 genes) and clinical risk factors. The PFRM was further validated in a high risk USA/Marin breast cancer population. This PFRM consistently performed significantly better than the BCRAT (Gail model). A functional aldosterone synthase SNP in PFRM improved predictive performance in Marin.
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Holzapfel GA, Mulvihill JJ, Cunnane EM, Walsh MT. Computational approaches for analyzing the mechanics of atherosclerotic plaques: a review. J Biomech 2014; 47:859-69. [PMID: 24491496 DOI: 10.1016/j.jbiomech.2014.01.011] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2014] [Indexed: 11/18/2022]
Abstract
Vulnerable and stable atherosclerotic plaques are heterogeneous living materials with peculiar mechanical behaviors depending on geometry, composition, loading and boundary conditions. Computational approaches have the potential to characterize the three-dimensional stress/strain distributions in patient-specific diseased arteries of different types and sclerotic morphologies and to estimate the risk of plaque rupture which is the main trigger of acute cardiovascular events. This review article attempts to summarize a few finite element (FE) studies for different vessel types, and how these studies were performed focusing on the used stress measure, inclusion of residual stress, used imaging modality and material model. In addition to histology the most used imaging modalities are described, the most common nonlinear material models and the limited number of models for plaque rupture used for such studies are provided in more detail. A critical discussion on stress measures and threshold stress values for plaque rupture used within the FE studies emphasizes the need to develop a more location and tissue-specific threshold value, and a more appropriate failure criterion. With this addition future FE studies should also consider more advanced strain-energy functions which then fit better to location and tissue-specific experimental data.
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Walsh MT, Cunnane EM, Mulvihill JJ, Akyildiz AC, Gijsen FJH, Holzapfel GA. Uniaxial tensile testing approaches for characterisation of atherosclerotic plaques. J Biomech 2014; 47:793-804. [PMID: 24508324 DOI: 10.1016/j.jbiomech.2014.01.017] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2014] [Indexed: 01/19/2023]
Abstract
The pathological changes associated with the development of atherosclerotic plaques within arterial vessels result in significant alterations to the mechanical properties of the diseased arterial wall. There are several methods available to characterise the mechanical behaviour of atherosclerotic plaque tissue, and it is the aim of this paper to review the use of uniaxial mechanical testing. In the case of atherosclerotic plaques, there are nine studies that employ uniaxial testing to characterise mechanical behaviour. A primary concern regarding this limited cohort of published studies is the wide range of testing techniques that are employed. These differing techniques have resulted in a large variance in the reported data making comparison of the mechanical behaviour of plaques from different vasculatures, and even the same vasculature, difficult and sometimes impossible. In order to address this issue, this paper proposes a more standardised protocol for uniaxial testing of diseased arterial tissue that allows for better comparisons and firmer conclusions to be drawn between studies. To develop such a protocol, this paper reviews the acquisition and storage of the tissue, the testing approaches, the post-processing techniques and the stress-strain measures employed by each of the nine studies. Future trends are also outlined to establish the role that uniaxial testing can play in the future of arterial plaque mechanical characterisation.
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Zhao W, Niu G, Shen B, Zheng Y, Gong F, Wang X, Lee J, Mulvihill JJ, Chen X, Li S. High-resolution analysis of copy number variants in adults with simple-to-moderate congenital heart disease. Am J Med Genet A 2013; 161A:3087-94. [PMID: 24115576 DOI: 10.1002/ajmg.a.36177] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Accepted: 07/16/2013] [Indexed: 01/09/2023]
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Saxena R, Saleheen D, Been LF, Garavito ML, Braun T, Bjonnes A, Young R, Ho WK, Rasheed A, Frossard P, Sim X, Hassanali N, Radha V, Chidambaram M, Liju S, Rees SD, Ng DPK, Wong TY, Yamauchi T, Hara K, Tanaka Y, Hirose H, McCarthy MI, Morris AP, Basit A, Barnett AH, Katulanda P, Matthews D, Mohan V, Wander GS, Singh JR, Mehra NK, Ralhan S, Kamboh MI, Mulvihill JJ, Maegawa H, Tobe K, Maeda S, Cho YS, Tai ES, Kelly MA, Chambers JC, Kooner JS, Kadowaki T, Deloukas P, Rader DJ, Danesh J, Sanghera DK. Genome-wide association study identifies a novel locus contributing to type 2 diabetes susceptibility in Sikhs of Punjabi origin from India. Diabetes 2013; 62:1746-55. [PMID: 23300278 PMCID: PMC3636649 DOI: 10.2337/db12-1077] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We performed a genome-wide association study (GWAS) and a multistage meta-analysis of type 2 diabetes (T2D) in Punjabi Sikhs from India. Our discovery GWAS in 1,616 individuals (842 case subjects) was followed by in silico replication of the top 513 independent single nucleotide polymorphisms (SNPs) (P < 10⁻³) in Punjabi Sikhs (n = 2,819; 801 case subjects). We further replicated 66 SNPs (P < 10⁻⁴) through genotyping in a Punjabi Sikh sample (n = 2,894; 1,711 case subjects). On combined meta-analysis in Sikh populations (n = 7,329; 3,354 case subjects), we identified a novel locus in association with T2D at 13q12 represented by a directly genotyped intronic SNP (rs9552911, P = 1.82 × 10⁻⁸) in the SGCG gene. Next, we undertook in silico replication (stage 2b) of the top 513 signals (P < 10⁻³) in 29,157 non-Sikh South Asians (10,971 case subjects) and de novo genotyping of up to 31 top signals (P < 10⁻⁴) in 10,817 South Asians (5,157 case subjects) (stage 3b). In combined South Asian meta-analysis, we observed six suggestive associations (P < 10⁻⁵ to < 10⁻⁷), including SNPs at HMG1L1/CTCFL, PLXNA4, SCAP, and chr5p11. Further evaluation of 31 top SNPs in 33,707 East Asians (16,746 case subjects) (stage 3c) and 47,117 Europeans (8,130 case subjects) (stage 3d), and joint meta-analysis of 128,127 individuals (44,358 case subjects) from 27 multiethnic studies, did not reveal any additional loci nor was there any evidence of replication for the new variant. Our findings provide new evidence on the presence of a population-specific signal in relation to T2D, which may provide additional insights into T2D pathogenesis.
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Kim YM, Lee JY, Xia L, Mulvihill JJ, Li S. Trisomy 8: a common finding in mouse embryonic stem (ES) cell lines. Mol Cytogenet 2013; 6:3. [PMID: 23320952 PMCID: PMC3564830 DOI: 10.1186/1755-8166-6-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 12/06/2012] [Indexed: 11/18/2022] Open
Abstract
Background Obtaining a germ cell line is one of the most important steps in developing a transgenic or knockout mouse with a targeted mutated gene of interest. A common problem with this technology is that embryonic stem (ES) cells often lack, or are extremely inefficient at, germ line transmission. Results To determine whether chromosomal anomalies are correlated with inefficient ES cell germ line transmission, we examined 97 constructed ES cell lines using conventional cytogenetic analysis, and fluorescence in situ hybridization (FISH). Chromosomal abnormalities occurred in 44 (45%) out of the 97 specimens analyzed: 31 specimens had trisomy 8 or mosaic trisomy 8, eight specimens had partial trisomy 8 resulting from unbalanced translocations, and five specimens had other chromosomal anomalies. Conclusions Our data suggest that chromosomal analysis is an important tool for improving the yield and quality of gene targeting experiments.
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Yauk CL, Lucas Argueso J, Auerbach SS, Awadalla P, Davis SR, DeMarini DM, Douglas GR, Dubrova YE, Elespuru RK, Glover TW, Hales BF, Hurles ME, Klein CB, Lupski JR, Manchester DK, Marchetti F, Montpetit A, Mulvihill JJ, Robaire B, Robbins WA, Rouleau GA, Shaughnessy DT, Somers CM, Taylor JG, Trasler J, Waters MD, Wilson TE, Witt KL, Bishop JB. Harnessing genomics to identify environmental determinants of heritable disease. Mutat Res 2012; 752:6-9. [PMID: 22935230 DOI: 10.1016/j.mrrev.2012.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 08/17/2012] [Accepted: 08/19/2012] [Indexed: 12/27/2022]
Abstract
Next-generation sequencing technologies can now be used to directly measure heritable de novo DNA sequence mutations in humans. However, these techniques have not been used to examine environmental factors that induce such mutations and their associated diseases. To address this issue, a working group on environmentally induced germline mutation analysis (ENIGMA) met in October 2011 to propose the necessary foundational studies, which include sequencing of parent-offspring trios from highly exposed human populations, and controlled dose-response experiments in animals. These studies will establish background levels of variability in germline mutation rates and identify environmental agents that influence these rates and heritable disease. Guidance for the types of exposures to examine come from rodent studies that have identified agents such as cancer chemotherapeutic drugs, ionizing radiation, cigarette smoke, and air pollution as germ-cell mutagens. Research is urgently needed to establish the health consequences of parental exposures on subsequent generations.
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Hassed SJ, Wiley GB, Wang S, Lee JY, Li S, Xu W, Zhao ZJ, Mulvihill JJ, Robertson J, Warner J, Gaffney PM. RBPJ mutations identified in two families affected by Adams-Oliver syndrome. Am J Hum Genet 2012; 91:391-5. [PMID: 22883147 DOI: 10.1016/j.ajhg.2012.07.005] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 05/21/2012] [Accepted: 07/01/2012] [Indexed: 01/17/2023] Open
Abstract
Through exome resequencing, we identified two unique mutations in recombination signal binding protein for immunoglobulin kappa J (RBPJ) in two independent families affected by Adams-Oliver syndrome (AOS), a rare multiple-malformation disorder consisting primarily of aplasia cutis congenita of the vertex scalp and transverse terminal limb defects. These identified mutations link RBPJ, the primary transcriptional regulator for the Notch pathway, with AOS, a human genetic disorder. Functional assays confirmed impaired DNA binding of mutated RBPJ, placing it among other notch-pathway proteins altered in human genetic syndromes.
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Selig BP, Furr JR, Huey RW, Moran C, Alluri VN, Medders GR, Mumm CD, Hallford HG, Mulvihill JJ. Cancer chemotherapeutic agents as human teratogens. ACTA ACUST UNITED AC 2012; 94:626-50. [DOI: 10.1002/bdra.23063] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 06/29/2012] [Accepted: 07/04/2012] [Indexed: 12/11/2022]
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Mulvihill JJ. Preconception exposure to mutagens: medical and other exposures to radiation and chemicals. J Community Genet 2012; 3:205-11. [PMID: 22752838 PMCID: PMC3419286 DOI: 10.1007/s12687-012-0104-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 06/01/2012] [Indexed: 12/14/2022] Open
Abstract
Contrary to intuition, no environmental exposure has been proved to cause human germ line mutations that manifest as heritable disease in the offspring, not among the children born to survivors of the American atomic bombs in Japan nor in survivors of cancer in childhood, adolescence, or young adulthood who receive intensive chemotherapy, radiotherapy, or both. Even the smallest of recent case series had sufficient statistical power to exclude, with the usual assumptions, an increase as small as 20 % over baseline rates. One positive epidemiologic study of a localized epidemic of Down syndrome in Hungary found an association with periconceptual exposure to a pesticide used in fish farming, trichlorfon. Current population and occupational guidelines to protect against genetic effects of ionizing radiation should continue, with the understanding they are based on extrapolations from mouse experiments and mostly on males. Presently, pre-conceptual counseling for possible germ cell mutation due to the environment can be very reassuring, at least based on, in a sense, the worst-case exposures of cancer survivors. Prudence demands further study. Future work will address the issue with total genomic sequencing and epigenomic analysis.
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Signorello LB, Mulvihill JJ, Green DM, Munro HM, Stovall M, Weathers RE, Mertens AC, Whitton JA, Robison LL, Boice JD. Congenital anomalies in the children of cancer survivors: a report from the childhood cancer survivor study. J Clin Oncol 2011; 30:239-45. [PMID: 22162566 DOI: 10.1200/jco.2011.37.2938] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Children with cancer receive mutagenic treatments, which raises concern about the potential transmissibility of germline damage to their offspring. This question has been inadequately studied to date because of a lack of detailed individual treatment exposure assessment such as gonadal radiation doses. METHODS Within the Childhood Cancer Survivor Study, we performed a retrospective cohort analysis of validated cases of congenital anomalies among 4,699 children of 1,128 male and 1,627 female childhood cancer survivors. We quantified chemotherapy with alkylating agents and radiotherapy doses to the testes and ovaries and related these exposures to risk of congenital anomalies using logistic regression. RESULTS One hundred twenty-nine children had at least one anomaly (prevalence = 2.7%). For children whose mothers were exposed to radiation or alkylating agents versus neither, the prevalence of anomalies was 3.0% versus 3.5% (P = .51); corresponding figures were 1.9% versus 1.7% (P = .79) for the children of male survivors. Neither ovarian radiation dose (mean, 1.19 Gy; odds ratio [OR] = 0.59; 95% CI, 0.20 to 1.75 for 2.50+ Gy) nor testicular radiation dose (mean, 0.48 Gy; OR = 1.01; 95% CI, 0.36 to 2.83 for 0.50+ Gy) was related to risk of congenital anomalies. Treatment with alkylating agents also was not significantly associated with anomalies in the children of male or female survivors. CONCLUSION Our findings offer strong evidence that the children of cancer survivors are not at significantly increased risk for congenital anomalies stemming from their parent's exposure to mutagenic cancer treatments. This information is important for counseling cancer survivors planning to have children.
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