Person: Talkowski, Michael
Loading...
Email Address
AA Acceptance Date
Birth Date
Research Projects
Organizational Units
Job Title
Last Name
Talkowski
First Name
Michael
Name
Talkowski, Michael
17 results
Search Results
Now showing 1 - 10 of 17
Publication Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy(SpringerNature, 2018-07-05) Kousi, Maria; Söylemez, Onuralp; Ozanturk, Aysegül; Akle, Sebastian; Jungreis, Irwin; Muller, Jean-Francois; Cassa, Christopher; Brand, Harrison; Mokry, Jill Anne; Wolf, Maxim; Sadeghpour, Azita; McFadden, Kelsey; Lewis, Richard A.; Talkowski, Michael; Dollfus, Hélène; Kellis, Manolis; Davis, Erica E.; Sunyaev, Shamil; Katsanis, NicholasThe influence of genetic background on driver mutations is well established; however, the mechanisms by which the background interacts with Mendelian loci remains unclear. We performed a systematic secondary-variant burden analysis of two independent Bardet-Biedl syndrome (BBS)1 cohorts with known recessive biallelic pathogenic mutations in one of 17 BBS genes for each individual. We observed a significant enrichment of trans-acting rare nonsynonymous secondary variants compared to either population controls or to a cohort of individuals with a non-BBS diagnosis and recessive variants in the same gene set. Strikingly, we found a significant over-representation of secondary alleles in chaperonin-encoding genes, a finding corroborated by the observation of epistatic interactions involving this complex in vivo. These data indicate a complex genetic architecture for BBS that informs the biological properties of disease modules and presents a model paradigm for secondary-variant burden analysis in recessive disorders.Publication Genome-Encoded Cytoplasmic Double-Stranded RNAs, Found in C9ORF72 ALS-FTD Brain, Propagate Neuronal Loss(Science Press / AAAS, 2021-07-07) Rodriguez, Steve; Sahin, Asli; Schrank, Benjamin R.; Al Lawati, Hawra; Costantino, Isabel; Benz, Eric; Fard, Darian; Albers, Alefiya; Cao, Luxiang; Gomez, Alexis; Evans, Kyle; Ratti, Elena; Cudkowicz, Merit; Frosch, Matthew; Talkowski, Michael; Sorger, Peter; Hyman, Bradley; Albers, MarkTriggers of innate immune signaling in the CNS of amyotrophic lateral sclerosis and frontotemporal degeneration (ALS/FTD) patients remain elusive. We report the presence of cytoplasmic double-stranded RNA (cdsRNA), an established trigger of innate immunity, in ALS-FTD brains carrying C9ORF72 intronic hexanucleotide expansions that included genomically encoded expansions of the G4C2 repeat sequences. Presence of cdsRNA in human brains was coincident with cytoplasmic TAR DNA-binding protein 43 (TDP-43) inclusions, a pathologic hallmark of ALS/FTD. Introducing cdsRNA into cultured human neural cells induced Type I interferon (IFN-I) signaling and death that was rescued by FDA-approved JAK inhibitors. In mice, genomically encoded dsRNAs expressed exclusively in a neuronal class induced IFN-I and death in connected neurons non-cell autonomously. Our findings establish that genomically encoded cdsRNAs trigger sterile, viral-mimetic IFN-I induction, and propagated death within neural circuits and may drive neuroinflammation and neurodegeneration in ALS/FTD patients.Publication Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome(BioMed Central, 2017) Collins, Ryan; Brand, Harrison; Redin, Claire; Hanscom, Carrie; Antolik, Caroline; Stone, Matthew R.; Glessner, Joseph; Mason, Tamara; Pregno, Giulia; Dorrani, Naghmeh; Mandrile, Giorgia; Giachino, Daniela; Perrin, Danielle; Walsh, Cole; Cipicchio, Michelle; Costello, Maura; Stortchevoi, Alexei; An, Joon-Yong; Currall, Benjamin B.; Seabra, Catarina M.; Ragavendran, Ashok; Margolin, Lauren; Martinez-Agosto, Julian A.; Lucente, Diane; Levy, Brynn; Sanders, Stephan J.; Wapner, Ronald J.; Quintero-Rivera, Fabiola; Kloosterman, Wigard; Talkowski, MichaelBackground: Structural variation (SV) influences genome organization and contributes to human disease. However, the complete mutational spectrum of SV has not been routinely captured in disease association studies. Results: We sequenced 689 participants with autism spectrum disorder (ASD) and other developmental abnormalities to construct a genome-wide map of large SV. Using long-insert jumping libraries at 105X mean physical coverage and linked-read whole-genome sequencing from 10X Genomics, we document seven major SV classes at ~5 kb SV resolution. Our results encompass 11,735 distinct large SV sites, 38.1% of which are novel and 16.8% of which are balanced or complex. We characterize 16 recurrent subclasses of complex SV (cxSV), revealing that: (1) cxSV are larger and rarer than canonical SV; (2) each genome harbors 14 large cxSV on average; (3) 84.4% of large cxSVs involve inversion; and (4) most large cxSV (93.8%) have not been delineated in previous studies. Rare SVs are more likely to disrupt coding and regulatory non-coding loci, particularly when truncating constrained and disease-associated genes. We also identify multiple cases of catastrophic chromosomal rearrangements known as chromoanagenesis, including somatic chromoanasynthesis, and extreme balanced germline chromothripsis events involving up to 65 breakpoints and 60.6 Mb across four chromosomes, further defining rare categories of extreme cxSV. Conclusions: These data provide a foundational map of large SV in the morbid human genome and demonstrate a previously underappreciated abundance and diversity of cxSV that should be considered in genomic studies of human disease. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1158-6) contains supplementary material, which is available to authorized users.Publication Indexcov: fast coverage quality control for whole-genome sequencing(Oxford University Press, 2017) Pedersen, Brent S; Collins, Ryan; Talkowski, Michael; Quinlan, Aaron RAbstract The BAM and CRAM formats provide a supplementary linear index that facilitates rapid access to sequence alignments in arbitrary genomic regions. Comparing consecutive entries in a BAM or CRAM index allows one to infer the number of alignment records per genomic region for use as an effective proxy of sequence depth in each genomic region. Based on these properties, we have developed indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample. Indexcov is available at https://github.com/brentp/goleft under the MIT license.Publication Traditional and systems biology based drug discovery for the rare tumor syndrome neurofibromatosis type 2(Public Library of Science, 2018) Allaway, Robert; Angus, Steve P.; Beauchamp, Roberta L.; Blakeley, Jaishri O.; Bott, Marga; Burns, Sarah S.; Carlstedt, Annemarie; Chang, Long-Sheng; Chen, Xin; Clapp, D. Wade; Desouza, Patrick A.; Erdin, Serkan; Fernandez-Valle, Cristina; Guinney, Justin; Gusella, James; Haggarty, Stephen; Johnson, Gary L.; La Rosa, Salvatore; Morrison, Helen; Petrilli, Alejandra M.; Plotkin, Scott; Pratap, Abhishek; Ramesh, Vijaya; Sciaky, Noah; Stemmer-Rachamimov, Anat; Stuhlmiller, Tim J.; Talkowski, Michael; Welling, Duane; Yates, Charles W.; Zawistowski, Jon S.; Zhao, Wen-NingNeurofibromatosis 2 (NF2) is a rare tumor suppressor syndrome that manifests with multiple schwannomas and meningiomas. There are no effective drug therapies for these benign tumors and conventional therapies have limited efficacy. Various model systems have been created and several drug targets have been implicated in NF2-driven tumorigenesis based on known effects of the absence of merlin, the product of the NF2 gene. We tested priority compounds based on known biology with traditional dose-concentration studies in meningioma and schwann cell systems. Concurrently, we studied functional kinome and gene expression in these cells pre- and post-treatment to determine merlin deficient molecular phenotypes. Cell viability results showed that three agents (GSK2126458, Panobinostat, CUDC-907) had the greatest activity across schwannoma and meningioma cell systems, but merlin status did not significantly influence response. In vivo, drug effect was tumor specific with meningioma, but not schwannoma, showing response to GSK2126458 and Panobinostat. In culture, changes in both the transcriptome and kinome in response to treatment clustered predominantly based on tumor type. However, there were differences in both gene expression and functional kinome at baseline between meningioma and schwannoma cell systems that may form the basis for future selective therapies. This work has created an openly accessible resource (www.synapse.org/SynodosNF2) of fully characterized isogenic schwannoma and meningioma cell systems as well as a rich data source of kinome and transcriptome data from these assay systems before and after treatment that enables single and combination drug discovery based on molecular phenotype.Publication Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR(2016) Tai, Derek J. C.; Ragavendran, Ashok; Manavalan, Poornima; Stortchevoi, Alexei; Seabra, Catarina M.; Erdin, Serkan; Collins, Ryan; Blumenthal, Ian; Chen, Xiaoli; Shen, Yiping; Sahin, Mustafa; Zhang, Chengsheng; Lee, Charles; Gusella, James; Talkowski, MichaelRecurrent, reciprocal genomic disorders resulting from non-allelic homologous recombination (NAHR) between near-identical segmental duplications (SDs) are a major cause of human disease, often producing phenotypically distinct syndromes. The genomic architecture of flanking SDs presents a significant challenge for modeling these syndromes; however, the capability to efficiently generate reciprocal copy number variants (CNVs) that mimic NAHR would represent an invaluable modeling tool. We describe here a CRISPR/Cas9 genome engineering method, Single-guide-CRISPR/Cas-targeting-Of-Repetitive-Elements (SCORE), to model reciprocal genomic disorders and demonstrate its capabilities by generating reciprocal CNVs of 16p11.2 and 15q13.3, including alteration of one copy-equivalent of the SDs that mediate NAHR in vivo. The method is reproducible and RNAseq reliably clusters transcriptional signatures from human subjects with in vivo CNV and their corresponding in vitro models. This new approach will provide broad applicability for the study of genomic disorders and, with further development, may also permit efficient correction of these defects.Publication Efficient Ablation of Genes in Human Hematopoietic Stem and Effector Cells using CRISPR/Cas9(Elsevier BV, 2014) Mandal, Pankaj; Ferreira, Leonardo Manuel Ramos; Collins, Ryan; Meissner, Torsten; Boutwell, C; Friesen, Max; Vrbanac, Vladimir; Garrison, Brian Scott; Stortchevoi, Alexei; Bryder, David; Musunuru, Kiran; Brand, Harrison; Tager, Andrew Martin; Allen, Todd; Talkowski, Michael; Rossi, Derrick; Cowan, ChadGenome editing via CRISPR/Cas9 has rapidly become the tool of choice by virtue of its efficacy and ease of use. However, CRISPR/Cas9-mediated genome editing in clinically relevant human somatic cells remains untested. Here, we report CRISPR/Cas9 targeting of two clinically relevant genes, B2M and CCR5, in primary human CD4+ T cells and CD34+ hematopoietic stem and progenitor cells (HSPCs). Use of single RNA guides led to highly efficient mutagenesis in HSPCs but not in T cells. A dual guide approach improved gene deletion efficacy in both cell types. HSPCs that had undergone genome editing with CRISPR/Cas9 retained multilineage potential. We examined predicted on- and off-target mutations via target capture sequencing in HSPCs and observed low levels of off-target mutagenesis at only one site. These results demonstrate that CRISPR/Cas9 can efficiently ablate genes in HSPCs with minimal off-target mutagenesis, which could have broad applicability for hematopoietic cell-based therapy.Publication Mutations in DCHS1 Cause Mitral Valve Prolapse(2015) Durst, Ronen; Sauls, Kimberly; Peal, David; deVlaming, Annemarieke; Toomer, Katelynn; Leyne, Maire; Salani, Monica; Talkowski, Michael; Brand, Harrison; Perrocheau, Maëlle; Simpson, Charles; Jett, Christopher; Stone, Matthew R.; Charles, Florie; Chiang, Colby; Lynch, Stacey N.; Bouatia-Naji, Nabila; Delling, Francesca N.; Freed, Lisa A.; Tribouilloy, Christophe; Le Tourneau, Thierry; LeMarec, Hervé; Fernandez-Friera, Leticia; Solis, Jorge; Trujillano, Daniel; Ossowski, Stephan; Estivill, Xavier; Dina, Christian; Bruneval, Patrick; Chester, Adrian; Schott, Jean-Jacques; Irvine, Kenneth D.; Mao, Yaopan; Wessels, Andy; Motiwala, Tahirali; Puceat, Michel; Tsukasaki, Yoshikazu; Menick, Donald R.; Kasiganesan, Harinath; Nie, Xingju; Broome, Ann-Marie; Williams, Katherine; Johnson, Amanda; Markwald, Roger R.; Jeunemaitre, Xavier; Hagege, Albert; Levine, Robert; Milan, David; Norris, Russell A.; Slaugenhaupt, SusanSUMMARY Mitral valve prolapse (MVP) is a common cardiac valve disease that affects nearly 1 in 40 individuals1–3. It can manifest as mitral regurgitation and is the leading indication for mitral valve surgery4,5. Despite a clear heritable component, the genetic etiology leading to non-syndromic MVP has remained elusive. Four affected individuals from a large multigenerational family segregating non-syndromic MVP underwent capture sequencing of the linked interval on chromosome 11. We report a missense mutation in the DCHS1 gene, the human homologue of the Drosophila cell polarity gene dachsous (ds) that segregates with MVP in the family. Morpholino knockdown of the zebrafish homolog dachsous1b resulted in a cardiac atrioventricular canal defect that could be rescued by wild-type human DCHS1, but not by DCHS1 mRNA with the familial mutation. Further genetic studies identified two additional families in which a second deleterious DCHS1 mutation segregates with MVP. Both DCHS1 mutations reduce protein stability as demonstrated in zebrafish, cultured cells, and, notably, in mitral valve interstitial cells (MVICs) obtained during mitral valve repair surgery of a proband. Dchs1+/− mice had prolapse of thickened mitral leaflets, which could be traced back to developmental errors in valve morphogenesis. DCHS1 deficiency in MVP patient MVICs as well as in Dchs1+/− mouse MVICs result in altered migration and cellular patterning, supporting these processes as etiological underpinnings for the disease. Understanding the role of DCHS1 in mitral valve development and MVP pathogenesis holds potential for therapeutic insights for this very common disease.Publication An eMERGE Clinical Center at Partners Personalized Medicine(MDPI AG, 2016) Smoller, Jordan; Karlson, Elizabeth; Green, Robert; Kathiresan, Sekar; MacArthur, Daniel; Talkowski, Michael; Murphy, Shawn; Weiss, ScottThe integration of electronic medical records (EMRs) and genomic research has become a major component of efforts to advance personalized and precision medicine. The Electronic Medical Records and Genomics (eMERGE) network, initiated in 2007, is an NIH-funded consortium devoted to genomic discovery and implementation research by leveraging biorepositories linked to EMRs. In its most recent phase, eMERGE III, the network is focused on facilitating implementation of genomic medicine by detecting and disclosing rare pathogenic variants in clinically relevant genes. Partners Personalized Medicine (PPM) is a center dedicated to translating personalized medicine into clinical practice within Partners HealthCare. One component of the PPM is the Partners Healthcare Biobank, a biorepository comprising broadly consented DNA samples linked to the Partners longitudinal EMR. In 2015, PPM joined the eMERGE Phase III network. Here we describe the elements of the eMERGE clinical center at PPM, including plans for genomic discovery using EMR phenotypes, evaluation of rare variant penetrance and pleiotropy, and a novel randomized trial of the impact of returning genetic results to patients and clinicians.Publication Loss of delta catenin function in severe autism(2015) Turner, Tychele N.; Sharma, Kamal; Oh, Edwin C.; Liu, Yangfan P.; Collins, Ryan L.; Sosa, Maria X.; Auer, Dallas R.; Brand, Harrison; Sanders, Stephan J.; Moreno-De-Luca, Daniel; Pihur, Vasyl; Plona, Teri; Pike, Kristen; Soppet, Daniel R.; Smith, Michael W.; Cheung, Sau Wai; Martin, Christa Lese; State, Matthew W.; Talkowski, Michael; Cook, Edwin; Huganir, Richard; Katsanis, Nicholas; Chakravarti, AravindaSUMMARY Autism is a multifactorial neurodevelopmental disorder affecting more males than females; consequently, under a multifactorial genetic hypothesis, females are affected only when they cross a higher biological threshold. We hypothesize that deleterious variants at conserved residues are enriched in severely affected patients arising from FEMFs (female-enriched multiplex families) with severe disease, enhancing the detection of key autism genes in modest numbers of cases. We show the utility of this strategy by identifying missense and dosage sequence variants in the gene encoding the adhesive junction-associated delta catenin protein (CTNND2) in FEMFs and demonstrating their loss-of-function effect by functional analyses in zebrafish embryos and cultured hippocampal neurons from wildtype and Ctnnd2 null mouse embryos. Finally, through gene expression and network analyses, we highlight a critical role for CTNND2 in neuronal development and an intimate connection to chromatin biology. Our data contribute to the understanding of the genetic architecture of autism and suggest that genetic analyses of phenotypic extremes, such as FEMFs, are of innate value in multifactorial disorders.