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Nakazawa MS, Silverman IM, Rimkunas V, Veloso A, Glodzik D, Johnson A, Ohsumi TK, Patel SR, Conley AP, Roland CL, Soliman PT, Beird HC, Wu CC, Ingram DR, Lazcano R, Song D, Wani KM, Lazar AJ, Yap TA, Wang WL, Livingston JA. Loss of the DNA Repair Gene RNase H2 Identifies a Unique Subset of DDR-Deficient Leiomyosarcomas. Mol Cancer Ther 2024:742109. [PMID: 38561019 DOI: 10.1158/1535-7163.mct-23-0761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/26/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Targeting the DNA damage response (DDR) pathway is an emerging therapeutic approach for leiomyosarcoma (LMS), and loss of RNase H2, a DDR pathway member, is a potentially actionable alteration for DDR targeted treatments. Therefore, we designed a protein and genomic based RNase H2 screening assay to determine its prevalence and prognostic significance. Using a selective RNase H2 antibody on a pan-tumor tissue microarray (TMA), RNase H2 loss was more common in LMS (11.5%, 9/78) than across all tumors (3.8%, 32/843). In a separate LMS cohort, RNase H2 deficiency was confirmed in uterine LMS (U-LMS, 21%, 23/108) and soft-tissue LMS (ST-LMS) (30%, 39/102). In the TCGA database, RNASEH2B homozygous deletions (HomDels) were found in 6% (5/80) of LMS cases, with a higher proportion in U-LMS (15%; 4/27) compared to ST-LMS (2%; 1/53). Using the SNiPDx targeted-NGS sequencing assay to detect biallelic loss of function in select DDR related genes, we found RNASEH2B HomDels in 54% (19/35) of U-LMS cases with RNase H2 loss by IHC, and 7% (3/43) HomDels in RNase H2 intact cases. No RNASEH2B HomDels were detected in ST-LMS. In U-LMS patient cohort (n = 109), no significant overall survival difference was seen in patients with RNase H2 loss versus intact, or RNASEH2B HomDel (n=12) vs Non-HomDel (n=37). The overall diagnostic accuracy, sensitivity, and specificity of RNase H2 IHC for detecting RNASEH2B HomDels in U-LMS was 76%, 93% and 71% respectively, and it is being developed for future predictive biomarker driven clinical trials targeting DDR in U-LMS.
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Affiliation(s)
- Michael S Nakazawa
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ian M Silverman
- Repare Therapeutics, Cambridge, Massachusetts, United States
| | | | | | | | | | | | - Shreyaskumar R Patel
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Anthony P Conley
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Christina L Roland
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Pamela T Soliman
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Hannah C Beird
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Chia-Chin Wu
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Davis R Ingram
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Rossana Lazcano
- The University of Texas MD Anderson Cancer Center, Houston, United States
| | - Dawon Song
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Khalida M Wani
- The University of Texas MD Anderson Cancer Center, Houston, Tx, United States
| | - Alexander J Lazar
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Timothy A Yap
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Wei-Lien Wang
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - J Andrew Livingston
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
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Harris EM, Chamseddine S, Chu A, Senkpeil L, Nikiciuk M, Al-Musa A, Woods B, Ozdogan E, Saker S, van Konijnenburg DPH, Yee CS, Nelson R, Lee P, Halyabar O, Hale RC, Day-Lewis M, Henderson LA, Nguyen AA, Elkins M, Ohsumi TK, Gutierrez-Arcelus M, Peyper JM, Platt CD, Grace RF, LaBere B, Chou J. Integrating circulating T follicular memory cells and autoantibody repertoires for characterization of autoimmune disorders. medRxiv 2024:2024.02.25.24303331. [PMID: 38464255 PMCID: PMC10925364 DOI: 10.1101/2024.02.25.24303331] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Introduction Autoimmune diseases are heterogeneous and often lack specific or sensitive diagnostic tests. Increased percentages of CD4+CXCR5+PD1+ circulating T follicular helper (cTfh) cells and skewed distributions of cTfh subtypes have been associated with autoimmunity. However, cTfh cell percentages can normalize with immunomodulatory treatment despite persistent disease activity, indicating the need for identifying additional cellular and/or serologic features correlating with autoimmunity. Methods The cohort included 50 controls and 56 patients with autoimmune cytopenias, gastrointestinal, pulmonary, and/or neurologic autoimmune disease. Flow cytometry was used to measure CD4+CXCR5+ T cell subsets expressing the chemokine receptors CXCR3 and/or CCR6: CXCR3+CCR6- Type 1, CXCR3-CCR6- Type 2, CXCR3+CCR6+ Type 1/17, and CXCR3- CCR6+ Type 17 T cells. IgG and IgA autoantibodies were quantified using a microarray featuring 1616 full-length, conformationally intact protein antigens. The 97.5th percentile in the control cohort defined normal limits for T cell subset percentages and total number (burden) of autoantibodies. Results This study focused on CD4+CXCR5+ T cells because CXCR5 upregulation occurs after cognate T-B cell interactions characteristic of autoimmune diseases. We refer to these cells as circulating T follicular memory (cTfm) cells to acknowledge the dynamic nature of antigen-experienced CXCR5+ T cells, which encompass progenitors of cTfh or Tfh cells as well as early effector memory T cells that have not yet lost CXCR5. Compared to controls, 57.1% of patients had increased CXCR5+CXCR3+CCR6+ cTfm1/17 and 25% had increased CXCR5+CXCR3-CCR6+ cTfm17 cell percentages. Patients had significantly more diverse IgG and IgA autoantibodies than controls and 44.6% had an increased burden of autoantibodies of either isotype. Unsupervised autoantibody clustering identified three clusters of patients with IgG autoantibody profiles distinct from those of controls, enriched for patients with active autoimmunity and monogenic diseases. An increased percentage of cTfm17 cells was most closely associated with an increased burden of high-titer IgG and IgA autoantibodies. A composite measure integrating increased cTfm1/17, cTfm17, and high-titer IgG and/or IgA autoantibodies had 91.1% sensitivity and 90.9% specificity for identifying patients with autoimmunity. Percentages of cTfm1/17 and cTfm17 percentages and numbers of high-titer autoantibodies in patients receiving immunomodulatory treatment did not differ from those in untreated patients, thus suggesting that measurements of cTfm can complement measurements of other cellular markers affected by treatment. Conclusions This study highlights two new approaches for assessing autoimmunity: measuring CD4+CXCR5+ cTfm subsets as well as total burden of autoantibodies. Our findings suggest that these approaches are particularly relevant to patients with rare autoimmune disorders for whom target antigens and prognosis are often unknown.
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Affiliation(s)
- Emily M. Harris
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Sarah Chamseddine
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Anne Chu
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Northeastern University, Boston, MA
| | - Leetah Senkpeil
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew Nikiciuk
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Northeastern University, Boston, MA
| | - Amer Al-Musa
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian Woods
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Sarife Saker
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Christina S.K. Yee
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ryan Nelson
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Pui Lee
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Olha Halyabar
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Rebecca C. Hale
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Megan Day-Lewis
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren A. Henderson
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Alan A. Nguyen
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Megan Elkins
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Craig D. Platt
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Rachael F. Grace
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Brenna LaBere
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Current affiliation: Division of Allergy and Immunology, Phoenix Children’s Hospital, Phoenix, AZ 85016
| | - Janet Chou
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
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Nguyen AA, Habiballah SB, LaBere B, Day-Lewis M, Elkins M, Al-Musa A, Chu A, Jones J, Fried AJ, McDonald D, Hoytema van Konijnenburg DP, Rockowitz S, Sliz P, Oettgen HC, Schneider LC, MacGinnitie A, Bartnikas LM, Platt CD, Ohsumi TK, Chou J. Rethinking Immunological Risk: A Retrospective Cohort Study of Severe SARS-Cov-2 Infections in Individuals With Congenital Immunodeficiencies. J Allergy Clin Immunol Pract 2023; 11:3391-3399.e3. [PMID: 37544429 PMCID: PMC10839118 DOI: 10.1016/j.jaip.2023.07.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 06/22/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
BACKGROUND Debates on the allocation of medical resources during the coronavirus disease 2019 (COVID-19) pandemic revealed the need for a better understanding of immunological risk. Studies highlighted variable clinical outcomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in individuals with defects in both adaptive and innate immunity, suggesting additional contributions from other factors. Notably, none of these studies controlled for variables linked with social determinants of health. OBJECTIVE To determine the contributions of determinants of health to risk of hospitalization for SARS-CoV-2 infection among individuals with inborn errors of immunodeficiencies. METHODS This is a retrospective, single-center cohort study of 166 individuals with inborn errors of immunity, aged 2 months through 69 years, who developed SARS-CoV-2 infections from March 1, 2020, through March 31, 2022. Risks of hospitalization were assessed using a multivariable logistic regression analysis. RESULTS The risk of SARS-CoV-2-related hospitalization was associated with underrepresented racial and ethnic populations (odds ratio [OR] 4.50; 95% confidence interval [95% CI] 1.57-13.4), a diagnosis of any genetically defined immunodeficiency (OR 3.32; 95% CI 1.24-9.43), obesity (OR 4.24; 95% CI 1.38-13.3), and neurological disease (OR 4.47; 95% CI 1.44-14.3). The COVID-19 vaccination was associated with reduced hospitalization risk (OR 0.52; 95% CI 0.31-0.81). Defects in T cell and innate immune function, immune-mediated organ dysfunction, and social vulnerability were not associated with increased risk of hospitalization after controlling for covariates. CONCLUSIONS The associations between race, ethnicity, and obesity with increased risk of hospitalization for SARS-CoV-2 infection indicate the importance of variables linked with social determinants of health as immunological risk factors for individuals with inborn errors of immunity.
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Affiliation(s)
- Alan A Nguyen
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Saddiq B Habiballah
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Brenna LaBere
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Megan Day-Lewis
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Megan Elkins
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Amer Al-Musa
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Anne Chu
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Jennifer Jones
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Ari J Fried
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Douglas McDonald
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | | | - Shira Rockowitz
- Research Computing, Information Technology, Boston Children's Hospital, Boston, Mass; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Mass
| | - Piotr Sliz
- Research Computing, Information Technology, Boston Children's Hospital, Boston, Mass; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Mass; Division of Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Hans C Oettgen
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Lynda C Schneider
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Andrew MacGinnitie
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Lisa M Bartnikas
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Craig D Platt
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | | | - Janet Chou
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass.
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4
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Nguyen AA, Habiballah SB, LaBere B, Day-Lewis M, Elkins M, Al-Musa A, Chu A, Jones J, Fried AJ, McDonald D, van Konijnenburg DPH, Rockowitz S, Sliz P, Oettgen HC, Schneider LC, MacGinnitie A, Bartnikas LM, Platt CD, Ohsumi TK, Chou J. Rethinking immunologic risk: a retrospective cohort study of severe SARS-CoV-2 infections in individuals with congenital immunodeficiencies. medRxiv 2023:2023.06.01.23290843. [PMID: 37333367 PMCID: PMC10275008 DOI: 10.1101/2023.06.01.23290843] [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: 06/20/2023]
Abstract
Background Debates on the allocation of medical resources during the COVID-19 pandemic revealed the need for a better understanding of immunologic risk. Studies highlighted variable clinical outcomes of SARS-CoV-2 infections in individuals with defects in both adaptive and innate immunity, suggesting additional contributions from other factors. Notably, none of these studies controlled for variables linked with social determinants of health. Objective To determine the contributions of determinants of health to risk of hospitalization for SARS-CoV-2 infection among individuals with inborn errors of immunodeficiencies. Methods This is a retrospective, single-center cohort study of 166 individuals with inborn errors of immunity, aged two months through 69 years, who developed SARS-CoV-2 infections from March 1, 2020 through March 31, 2022. Risks of hospitalization was assessed using a multivariable logistic regression analysis. Results The risk of SARS-CoV-2-related hospitalization was associated with underrepresented racial and ethnic populations (odds ratio [OR] 5.29; confidence interval [CI], 1.76-17.0), a diagnosis of any genetically-defined immunodeficiency (OR 4.62; CI, 1.60-14.8), use of B cell depleting therapy within one year of infection (OR 6.1; CI, 1.05-38.5), obesity (OR 3.74; CI, 1.17-12.5), and neurologic disease (OR 5.38; CI, 1.61-17.8). COVID-19 vaccination was associated with reduced hospitalization risk (OR 0.52; CI, 0.31-0.81). Defective T cell function, immune-mediated organ dysfunction, and social vulnerability were not associated with increased risk of hospitalization after controlling for covariates. Conclusions The associations between race, ethnicity, and obesity with increased risk of hospitalization for SARS-CoV-2 infection indicate the importance of variables linked with social determinants of health as immunologic risk factors for individuals with inborn errors of immunity. Highlights What is already known about this topic? Outcomes of SARS-CoV-2 infections in individuals with inborn errors of immunity (IEI) are highly variable. Prior studies of patients with IEI have not controlled for race or social vulnerability. What does this article add to our knowledge ? For individuals with IEI, hospitalizations for SARS-CoV-2 were associated with race, ethnicity, obesity, and neurologic disease. Specific types of immunodeficiency, organ dysfunction, and social vulnerability were not associated with increased risk of hospitalization. How does this study impact current management guidelines? Current guidelines for the management of IEIs focus on risk conferred by genetic and cellular mechanisms. This study highlights the importance of considering variables linked with social determinants of health and common comorbidities as immunologic risk factors.
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Adam S, Rossi SE, Moatti N, De Marco Zompit M, Xue Y, Ng TF, Álvarez-Quilón A, Desjardins J, Bhaskaran V, Martino G, Setiaputra D, Noordermeer SM, Ohsumi TK, Hustedt N, Szilard RK, Chaudhary N, Munro M, Veloso A, Melo H, Yin SY, Papp R, Young JTF, Zinda M, Stucki M, Durocher D. The CIP2A-TOPBP1 axis safeguards chromosome stability and is a synthetic lethal target for BRCA-mutated cancer. Nat Cancer 2021; 2:1357-1371. [PMID: 35121901 DOI: 10.1038/s43018-021-00266-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 09/10/2021] [Indexed: 05/26/2023]
Abstract
BRCA1/2-mutated cancer cells adapt to the genome instability caused by their deficiency in homologous recombination (HR). Identification of these adaptive mechanisms may provide therapeutic strategies to target tumors caused by the loss of these genes. In the present study, we report genome-scale CRISPR-Cas9 synthetic lethality screens in isogenic pairs of BRCA1- and BRCA2-deficient cells and identify CIP2A as an essential gene in BRCA1- and BRCA2-mutated cells. CIP2A is cytoplasmic in interphase but, in mitosis, accumulates at DNA lesions as part of a complex with TOPBP1, a multifunctional genome stability factor. Unlike PARP inhibition, CIP2A deficiency does not cause accumulation of replication-associated DNA lesions that require HR for their repair. In BRCA-deficient cells, the CIP2A-TOPBP1 complex prevents lethal mis-segregation of acentric chromosomes that arises from impaired DNA synthesis. Finally, physical disruption of the CIP2A-TOPBP1 complex is highly deleterious in BRCA-deficient tumors, indicating that CIP2A represents an attractive synthetic lethal therapeutic target for BRCA1- and BRCA2-mutated cancers.
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Affiliation(s)
- Salomé Adam
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Silvia Emma Rossi
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Nathalie Moatti
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Mara De Marco Zompit
- Department of Gynecology, University Hospital and University of Zurich, Schlieren, Switzerland
| | - Yibo Xue
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Timothy F Ng
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alejandro Álvarez-Quilón
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Repare Therapeutics, St-Laurent, Quebec, Canada
| | | | | | | | - Dheva Setiaputra
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Sylvie M Noordermeer
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Nicole Hustedt
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Lonza AG, Visp, Switzerland
| | - Rachel K Szilard
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Natasha Chaudhary
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Meagan Munro
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Henrique Melo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Robert Papp
- Repare Therapeutics, St-Laurent, Quebec, Canada
| | | | | | - Manuel Stucki
- Department of Gynecology, University Hospital and University of Zurich, Schlieren, Switzerland
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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Ward HN, Aregger M, Gonatopoulos-Pournatzis T, Billmann M, Ohsumi TK, Brown KR, Blencowe BJ, Moffat J, Myers CL. Analysis of combinatorial CRISPR screens with the Orthrus scoring pipeline. Nat Protoc 2021; 16:4766-4798. [PMID: 34508259 PMCID: PMC9084619 DOI: 10.1038/s41596-021-00596-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 08/26/2020] [Accepted: 06/03/2021] [Indexed: 02/08/2023]
Abstract
The continued improvement of combinatorial CRISPR screening platforms necessitates the development of new computational pipelines for scoring combinatorial screening data. Unlike for single-guide RNA (sgRNA) pooled screening platforms, combinatorial scoring for multiplexed systems is confounded by guide design parameters such as the number of gRNAs per construct, the position of gRNAs along constructs, and additional features that may impact gRNA expression, processing or capture. In this protocol we describe Orthrus, an R package for processing, scoring and analyzing combinatorial CRISPR screening data that addresses these challenges. This protocol walks through the application of Orthrus to previously published combinatorial screening data from the CHyMErA experimental system, a platform we recently developed that pairs Cas9 with Cas12a gRNAs and enables programmed targeting of multiple genomic sites. We demonstrate Orthrus' features for screen quality assessment and two distinct scoring modes for dual guide RNAs (dgRNAs) that target the same gene twice or dgRNAs that target two different genes. Running Orthrus requires basic R programming experience, ~5-10 min of computational time and 15-60 min total.
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Affiliation(s)
- Henry N Ward
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Michael Aregger
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Thomas Gonatopoulos-Pournatzis
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | | | - Kevin R Brown
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Institute for Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Chad L Myers
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
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Badran YR, Dedeoglu F, Leyva Castillo JM, Bainter W, Ohsumi TK, Bousvaros A, Goldsmith JD, Geha RS, Chou J. Human RELA haploinsufficiency results in autosomal-dominant chronic mucocutaneous ulceration. J Exp Med 2017; 214:1937-1947. [PMID: 28600438 PMCID: PMC5502421 DOI: 10.1084/jem.20160724] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 02/25/2017] [Accepted: 05/09/2017] [Indexed: 11/09/2022] Open
Abstract
Badran et al. demonstrate an essential contribution of biallelic RELA expression in protecting stromal and epithelial cells from TNF-mediated cell death in patients with chronic mucocutaneous ulceration. The treatment of chronic mucocutaneous ulceration is challenging, and only some patients respond selectively to inhibitors of tumor necrosis factor-α (TNF). TNF activates opposing pathways leading to caspase-8–mediated apoptosis as well as nuclear factor κB (NF-κB)–dependent cell survival. We investigated the etiology of autosomal-dominant, mucocutaneous ulceration in a family whose proband was dependent on anti-TNF therapy for sustained remission. A heterozygous mutation in RELA, encoding the NF-κB subunit RelA, segregated with the disease phenotype and resulted in RelA haploinsufficiency. The patients’ fibroblasts exhibited increased apoptosis in response to TNF, impaired NF-κB activation, and defective expression of NF-κB–dependent antiapoptotic genes. Rela+/− mice have similarly impaired NF-κB activation, develop cutaneous ulceration from TNF exposure, and exhibit severe dextran sodium sulfate–induced colitis, ameliorated by TNF inhibition. These findings demonstrate an essential contribution of biallelic RELA expression in protecting stromal cells from TNF-mediated cell death, thus delineating the mechanisms driving the effectiveness of TNF inhibition in this disease.
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Affiliation(s)
- Yousef R Badran
- Division of Immunology, Boston Children's Hospital, Boston, MA
| | - Fatma Dedeoglu
- Division of Immunology, Boston Children's Hospital, Boston, MA
| | | | - Wayne Bainter
- Division of Immunology, Boston Children's Hospital, Boston, MA
| | - Toshiro K Ohsumi
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
| | - Athos Bousvaros
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA
| | - Jeffrey D Goldsmith
- Department of Pathology, Boston Children's Hospital, Boston, MA.,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA
| | - Raif S Geha
- Division of Immunology, Boston Children's Hospital, Boston, MA
| | - Janet Chou
- Division of Immunology, Boston Children's Hospital, Boston, MA
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8
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Massaad MJ, Zhou J, Tsuchimoto D, Chou J, Jabara H, Janssen E, Glauzy S, Olson BG, Morbach H, Ohsumi TK, Schmitz K, Kyriacos M, Kane J, Torisu K, Nakabeppu Y, Notarangelo LD, Chouery E, Megarbane A, Kang PB, Al-Idrissi E, Aldhekri H, Meffre E, Mizui M, Tsokos GC, Manis JP, Al-Herz W, Wallace SS, Geha RS. Deficiency of base excision repair enzyme NEIL3 drives increased predisposition to autoimmunity. J Clin Invest 2016; 126:4219-4236. [PMID: 27760045 DOI: 10.1172/jci85647] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 09/06/2016] [Indexed: 12/17/2022] Open
Abstract
Alterations in the apoptosis of immune cells have been associated with autoimmunity. Here, we have identified a homozygous missense mutation in the gene encoding the base excision repair enzyme Nei endonuclease VIII-like 3 (NEIL3) that abolished enzymatic activity in 3 siblings from a consanguineous family. The NEIL3 mutation was associated with fatal recurrent infections, severe autoimmunity, hypogammaglobulinemia, and impaired B cell function in these individuals. The same homozygous NEIL3 mutation was also identified in an asymptomatic individual who exhibited elevated levels of serum autoantibodies and defective peripheral B cell tolerance, but normal B cell function. Further analysis of the patients revealed an absence of LPS-responsive beige-like anchor (LRBA) protein expression, a known cause of immunodeficiency. We next examined the contribution of NEIL3 to the maintenance of self-tolerance in Neil3-/- mice. Although Neil3-/- mice displayed normal B cell function, they exhibited elevated serum levels of autoantibodies and developed nephritis following treatment with poly(I:C) to mimic microbial stimulation. In Neil3-/- mice, splenic T and B cells as well as germinal center B cells from Peyer's patches showed marked increases in apoptosis and cell death, indicating the potential release of self-antigens that favor autoimmunity. These findings demonstrate that deficiency in NEIL3 is associated with increased lymphocyte apoptosis, autoantibodies, and predisposition to autoimmunity.
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9
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Dobbs K, Domínguez Conde C, Zhang SY, Parolini S, Audry M, Chou J, Haapaniemi E, Keles S, Bilic I, Okada S, Massaad MJ, Rounioja S, Alwahadneh AM, Serwas NK, Capuder K, Ciftci E, Felgentreff K, Ohsumi TK, Pedergnana V, Boisson B, Haskoloğlu S, Ensari A, Schuster M, Moretta A, Itan Y, Patrizi O, Rozenberg F, Lebon P, Saarela J, Knip M, Petrovski S, Goldstein DB, Parrott RE, Savas B, Schambach A, Tabellini G, Bock C, Chatila T, Comeau AM, Geha RS, Abel L, Buckley RH, Ikincioğullari A, Al-Herz W, Helminen M, Doğu F, Casanova JL, Boztuğ K, Notarangelo LD. Inherited DOCK2 Deficiency in Patients with Early-Onset Invasive Infections. N Engl J Med 2015; 372:2409-22. [PMID: 26083206 PMCID: PMC4480434 DOI: 10.1056/nejmoa1413462] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background Combined immunodeficiencies are marked by inborn errors of T-cell immunity in which the T cells that are present are quantitatively or functionally deficient. Impaired humoral immunity is also common. Patients have severe infections, autoimmunity, or both. The specific molecular, cellular, and clinical features of many types of combined immunodeficiencies remain unknown. Methods We performed genetic and cellular immunologic studies involving five unrelated children with early-onset invasive bacterial and viral infections, lymphopenia, and defective T-cell, B-cell, and natural killer (NK)-cell responses. Two patients died early in childhood; after allogeneic hematopoietic stem-cell transplantation, the other three had normalization of T-cell function and clinical improvement. Results We identified biallelic mutations in the dedicator of cytokinesis 2 gene (DOCK2) in these five patients. RAC1 activation was impaired in the T cells. Chemokine-induced migration and actin polymerization were defective in the T cells, B cells, and NK cells. NK-cell degranulation was also affected. Interferon-α and interferon-λ production by peripheral-blood mononuclear cells was diminished after viral infection. Moreover, in DOCK2-deficient fibroblasts, viral replication was increased and virus-induced cell death was enhanced; these conditions were normalized by treatment with interferon alfa-2b or after expression of wild-type DOCK2. Conclusions Autosomal recessive DOCK2 deficiency is a new mendelian disorder with pleiotropic defects of hematopoietic and nonhematopoietic immunity. Children with clinical features of combined immunodeficiencies, especially with early-onset, invasive infections, may have this condition. (Supported by the National Institutes of Health and others.).
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10
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Chou J, Badran YR, Yee CSK, Bainter W, Ohsumi TK, Al-Hammadi S, Pai SY, Feske S, Geha RS. A novel mutation in ORAI1 presenting with combined immunodeficiency and residual T-cell function. J Allergy Clin Immunol 2015; 136:479-482.e1. [PMID: 26070885 DOI: 10.1016/j.jaci.2015.03.050] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/16/2015] [Accepted: 03/23/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Janet Chou
- Division of Immunology, Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Yousef R Badran
- Division of Immunology, Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Christina S K Yee
- Division of Immunology, Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Wayne Bainter
- Division of Immunology, Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Toshiro K Ohsumi
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Suleiman Al-Hammadi
- Department of Pediatrics, United Arab Emirates University, United Arab Emirates
| | - Sung-Yun Pai
- Division of Hematology-Oncology, Boston Children's Hospital, Boston, MA and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Stefan Feske
- Department of Pathology, Langone Medical Center, New York University
| | - Raif S Geha
- Division of Immunology, Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA
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11
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Charbonnier LM, Janssen E, Chou J, Ohsumi TK, Keles S, Hsu JT, Massaad MJ, Garcia-Lloret M, Hanna-Wakim R, Dbaibo G, Alangari AA, Alsultan A, Al-Zahrani D, Geha RS, Chatila TA. Regulatory T-cell deficiency and immune dysregulation, polyendocrinopathy, enteropathy, X-linked-like disorder caused by loss-of-function mutations in LRBA. J Allergy Clin Immunol 2014; 135:217-27. [PMID: 25468195 DOI: 10.1016/j.jaci.2014.10.019] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [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: 05/07/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 01/26/2023]
Abstract
BACKGROUND A number of heritable immune dysregulatory diseases result from defects affecting regulatory T (Treg) cell development, function, or both. They include immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome, which is caused by mutations in forkhead box P3 (FOXP3), and IPEX-like disorders caused by mutations in IL-2 receptor α (IL2RA), signal transducer and activator of transcription 5b (STAT5b), and signal transducer and activator of transcription 1 (STAT1). However, the genetic defects underlying many cases of IPEX-like disorders remain unknown. OBJECTIVE We sought to identify the genetic abnormalities in patients with idiopathic IPEX-like disorders. METHODS We performed whole-exome and targeted gene sequencing and phenotypic and functional analyses of Treg cells. RESULTS A child who presented with an IPEX-like syndrome and severe Treg cell deficiency was found to harbor a nonsense mutation in the gene encoding LPS-responsive beige-like anchor (LRBA), which was previously implicated as a cause of common variable immunodeficiency with autoimmunity. Analysis of subjects with LRBA deficiency revealed marked Treg cell depletion; profoundly decreased expression of canonical Treg cell markers, including FOXP3, CD25, Helios, and cytotoxic T lymphocyte-associated antigen 4; and impaired Treg cell-mediated suppression. There was skewing in favor of memory T cells and intense autoantibody production, with marked expansion of T follicular helper and contraction of T follicular regulatory cells. Whereas the frequency of recent thymic emigrants and the differentiation of induced Treg cells were normal, LRBA-deficient T cells exhibited increased apoptosis and reduced activities of the metabolic sensors mammalian target of rapamycin complexes 1 and 2. CONCLUSION LRBA deficiency is a novel cause of IPEX-like syndrome and Treg cell deficiency associated with metabolic dysfunction and increased apoptosis of Treg cells.
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Affiliation(s)
- Louis-Marie Charbonnier
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Erin Janssen
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Janet Chou
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Toshiro K Ohsumi
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Mass
| | - Sevgi Keles
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Joyce T Hsu
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Michel J Massaad
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Maria Garcia-Lloret
- Division of Immunology, Department of Pediatrics, University of California at Los Angeles, Los Angeles, Calif
| | - Rima Hanna-Wakim
- Division of Pediatric Infectious Diseases, American University of Beirut, Beirut, Lebanon
| | - Ghassan Dbaibo
- Division of Pediatric Infectious Diseases, American University of Beirut, Beirut, Lebanon
| | - Abdullah A Alangari
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alsultan
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Daifulah Al-Zahrani
- Immunology and Allergy, Pediatric Department, King Abdulaziz Medical City-WR, Jeddah, Saudi Arabia
| | - Raif S Geha
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Talal A Chatila
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass.
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12
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Hedayat M, Massaad MJ, Lee YN, Conley ME, Orange JS, Ohsumi TK, Al-Herz W, Notarangelo LD, Geha RS, Chou J. Lessons in gene hunting: a RAG1 mutation presenting with agammaglobulinemia and absence of B cells. J Allergy Clin Immunol 2014; 134:983-5.e1. [PMID: 24985406 DOI: 10.1016/j.jaci.2014.04.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 04/06/2014] [Accepted: 04/14/2014] [Indexed: 10/25/2022]
Affiliation(s)
- Mona Hedayat
- Division of Immunology, Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Michel J Massaad
- Division of Immunology, Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Yu Nee Lee
- Division of Immunology, Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Mary Ellen Conley
- St Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY
| | - Jordan S Orange
- Immunology, Allergy, and Rheumatology, Baylor College of Medicine and the Texas Children's Hospital, Houston, Tex
| | - Toshiro K Ohsumi
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Mass
| | - Waleed Al-Herz
- Faculty of Medicine, Department of Pediatrics, Kuwait University, Kuwait City, Kuwait
| | - Luigi D Notarangelo
- Division of Immunology, Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Raif S Geha
- Division of Immunology, Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Janet Chou
- Division of Immunology, Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass.
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13
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Apostolou E, Ferrari F, Walsh RM, Bar-Nur O, Stadtfeld M, Cheloufi S, Stuart HT, Polo JM, Ohsumi TK, Borowsky ML, Kharchenko PV, Park PJ, Hochedlinger K. Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell 2013; 12:699-712. [PMID: 23665121 DOI: 10.1016/j.stem.2013.04.013] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 03/27/2013] [Accepted: 04/16/2013] [Indexed: 12/14/2022]
Abstract
The chromatin state of pluripotency genes has been studied extensively in embryonic stem cells (ESCs) and differentiated cells, but their potential interactions with other parts of the genome remain largely unexplored. Here, we identified a genome-wide, pluripotency-specific interaction network around the Nanog promoter by adapting circular chromosome conformation capture sequencing. This network was rearranged during differentiation and restored in induced pluripotent stem cells. A large fraction of Nanog-interacting loci were bound by Mediator or cohesin in pluripotent cells. Depletion of these proteins from ESCs resulted in a disruption of contacts and the acquisition of a differentiation-specific interaction pattern prior to obvious transcriptional and phenotypic changes. Similarly, the establishment of Nanog interactions during reprogramming often preceded transcriptional upregulation of associated genes, suggesting a causative link. Our results document a complex, pluripotency-specific chromatin "interactome" for Nanog and suggest a functional role for long-range genomic interactions in the maintenance and induction of pluripotency.
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Affiliation(s)
- Effie Apostolou
- Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, 185 Cambridge Street, Boston, MA 02114, USA
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14
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Chen L, Stuart L, Ohsumi TK, Burgess S, Varshney GK, Dastur A, Borowsky M, Benes C, Lacy-Hulbert A, Schmidt EV. Transposon activation mutagenesis as a screening tool for identifying resistance to cancer therapeutics. BMC Cancer 2013; 13:93. [PMID: 23442791 PMCID: PMC3598783 DOI: 10.1186/1471-2407-13-93] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 02/19/2013] [Indexed: 11/16/2022] Open
Abstract
Background The development of resistance to chemotherapies represents a significant barrier to successful cancer treatment. Resistance mechanisms are complex, can involve diverse and often unexpected cellular processes, and can vary with both the underlying genetic lesion and the origin or type of tumor. For these reasons developing experimental strategies that could be used to understand, identify and predict mechanisms of resistance in different malignant cells would be a major advance. Methods Here we describe a gain-of-function forward genetic approach for identifying mechanisms of resistance. This approach uses a modified piggyBac transposon to generate libraries of mutagenized cells, each containing transposon insertions that randomly activate nearby gene expression. Genes of interest are identified using next-gen high-throughput sequencing and barcode multiplexing is used to reduce experimental cost. Results Using this approach we successfully identify genes involved in paclitaxel resistance in a variety of cancer cell lines, including the multidrug transporter ABCB1, a previously identified major paclitaxel resistance gene. Analysis of co-occurring transposons integration sites in single cell clone allows for the identification of genes that might act cooperatively to produce drug resistance a level of information not accessible using RNAi or ORF expression screening approaches. Conclusion We have developed a powerful pipeline to systematically discover drug resistance in mammalian cells in vitro. This cost-effective approach can be readily applied to different cell lines, to identify canonical or context specific resistance mechanisms. Its ability to probe complex genetic context and non-coding genomic elements as well as cooperative resistance events makes it a good complement to RNAi or ORF expression based screens.
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Affiliation(s)
- Li Chen
- Center for Molecular Therapeutics, Center for Cancer Research, Massachusetts General Hospital, and Harvard Medical School, CNY 149-Rm7308, Thirteenth St. Charlestown, MA 02129, USA.
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15
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Yuan CC, Matthews AGW, Jin Y, Chen CF, Chapman BA, Ohsumi TK, Glass KC, Kutateladze TG, Borowsky ML, Struhl K, Oettinger MA. Histone H3R2 symmetric dimethylation and histone H3K4 trimethylation are tightly correlated in eukaryotic genomes. Cell Rep 2013; 1:83-90. [PMID: 22720264 DOI: 10.1016/j.celrep.2011.12.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The preferential in vitro interaction of the PHD finger of RAG2, a subunit of the V(D)J recombinase, with histone H3 tails simultaneously trimethylated at lysine 4 and symmetrically dimethylated at arginine 2 (H3R2me2sK4me3) predicted the existence of the previously unknown histone modification H3R2me2s. Here, we report the in vivo identification of H3R2me2s . Consistent with the binding specificity of the RAG2 PHD finger, high levels of H3R2me2sK4me3 are found at antigen receptor gene segments ready for rearrangement. However, this double modification is much more general; it is conserved throughout eukaryotic evolution. In mouse, H3R2me2s is tightly correlated with H3K4me3 at active promoters throughout the genome. Mutational analysis in S. cerevisiae reveals that deposition of H3R2me2s requires the same Set1 complex that deposits H3K4me3. Our work suggests that H3R2me2sK4me3, not simply H3K4me3 alone, is the mark of active promoters and that factors that recognize H3K4me3 will have their binding modulated by their preference for H3R2me2s.
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Affiliation(s)
- Chih-Chi Yuan
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
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16
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Pinter SF, Sadreyev RI, Yildirim E, Jeon Y, Ohsumi TK, Borowsky M, Lee JT. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. Genome Res 2012; 22:1864-76. [PMID: 22948768 PMCID: PMC3460182 DOI: 10.1101/gr.133751.111] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
X chromosome inactivation (XCI) achieves dosage balance in mammals by repressing one of two X chromosomes in females. During XCI, the long noncoding Xist RNA and Polycomb proteins spread along the inactive X (Xi) to initiate chromosome-wide silencing. Although inactivation is known to commence at the X-inactivation center (Xic), how it propagates remains unknown. Here, we examine allele-specific binding of Polycomb repressive complex 2 (PRC2) and chromatin composition during XCI and generate a chromosome-wide profile of Xi and Xa (active X) at nucleosome-resolution. Initially, Polycomb proteins are localized to ∼150 strong sites along the X and concentrated predominantly within bivalent domains coinciding with CpG islands (“canonical sites”). As XCI proceeds, ∼4000 noncanonical sites are recruited, most of which are intergenic, nonbivalent, and lack CpG islands. Polycomb sites are depleted of LINE repeats but enriched for SINEs and simple repeats. Noncanonical sites cluster around the ∼150 strong sites, and their H3K27me3 levels reflect a graded concentration originating from strong sites. This suggests that PRC2 and H3K27 methylation spread along a gradient unique to XCI. We propose that XCI is governed by a hierarchy of defined Polycomb stations that spread H3K27 methylation in cis.
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Affiliation(s)
- Stefan F Pinter
- Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
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17
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Abstract
Summary: We developed MolBioLib to address the need for adaptable next-generation sequencing analysis tools. The result is a compact, portable and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. MolBioLib is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib has been used to identify causative single-nucleotide polymorphisms in whole genome sequencing, detect balanced chromosomal rearrangements and compute enrichment of messenger RNAs (mRNAs) on microtubules, typically requiring applications of under 200 lines of code. MolBioLib includes programs to perform a wide variety of analysis tasks, such as computing read coverage, annotating genomic intervals and novel peak calling with a wavelet algorithm. Although MolBioLib was designed primarily for bioinformatics purposes, much of its functionality is applicable to a wide range of problems. Complete documentation and an extensive automated test suite are provided. Availability: MolBioLib is available for download at: http://sourceforge.net/projects/molbiolib Contact: ohsumit@molbio.mgh.harvard.edu
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Affiliation(s)
- Toshiro K Ohsumi
- Department of Molecular Biology, Massachusetts General Hospital, Richard B. Simches Research Center, Boston, MA 02114, USA.
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18
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Talkowski ME, Rosenfeld JA, Blumenthal I, Pillalamarri V, Chiang C, Heilbut A, Ernst C, Hanscom C, Rossin E, Lindgren A, Pereira S, Ruderfer D, Kirby A, Ripke S, Harris D, Lee JH, Ha K, Kim HG, Solomon BD, Gropman AL, Lucente D, Sims K, Ohsumi TK, Borowsky ML, Loranger S, Quade B, Lage K, Miles J, Wu BL, Shen Y, Neale B, Shaffer LG, Daly MJ, Morton CC, Gusella JF. Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries. Cell 2012; 149:525-37. [PMID: 22521361 PMCID: PMC3340505 DOI: 10.1016/j.cell.2012.03.028] [Citation(s) in RCA: 425] [Impact Index Per Article: 35.4] [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: 11/23/2011] [Revised: 02/27/2012] [Accepted: 03/28/2012] [Indexed: 01/18/2023]
Abstract
Balanced chromosomal abnormalities (BCAs) represent a relatively untapped reservoir of single-gene disruptions in neurodevelopmental disorders (NDDs). We sequenced BCAs in patients with autism or related NDDs, revealing disruption of 33 loci in four general categories: (1) genes previously associated with abnormal neurodevelopment (e.g., AUTS2, FOXP1, and CDKL5), (2) single-gene contributors to microdeletion syndromes (MBD5, SATB2, EHMT1, and SNURF-SNRPN), (3) novel risk loci (e.g., CHD8, KIRREL3, and ZNF507), and (4) genes associated with later-onset psychiatric disorders (e.g., TCF4, ZNF804A, PDE10A, GRIN2B, and ANK3). We also discovered among neurodevelopmental cases a profoundly increased burden of copy-number variants from these 33 loci and a significant enrichment of polygenic risk alleles from genome-wide association studies of autism and schizophrenia. Our findings suggest a polygenic risk model of autism and reveal that some neurodevelopmental genes are sensitive to perturbation by multiple mutational mechanisms, leading to variable phenotypic outcomes that manifest at different life stages.
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Affiliation(s)
- Michael E. Talkowski
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Department of Neurology, Harvard Medical School, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | | | - Ian Blumenthal
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Vamsee Pillalamarri
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Colby Chiang
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Adrian Heilbut
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Carl Ernst
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Carrie Hanscom
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Elizabeth Rossin
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Amelia Lindgren
- Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA
| | - Shahrin Pereira
- Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA
| | - Douglas Ruderfer
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Andrew Kirby
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Stephan Ripke
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - David Harris
- Division of Clinical Genetics, Children’s Hospital of Boston, Boston, MA
| | - Ji-Hyun Lee
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Kyungsoo Ha
- Cancer Research Center, Georgia Health Sciences University, Augusta, GA
| | - Hyung-Goo Kim
- Department of OB/GYN, IMMAG, Georgia Health Sciences University, Augusta, GA
| | - Benjamin D. Solomon
- Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Andrea L. Gropman
- Department of Neurology, Children’s National Medical Center, Washington, DC, USA
- Department of Neurology, George Washington University of Health Sciences, Washington, DC, USA
| | - Diane Lucente
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Katherine Sims
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Toshiro K. Ohsumi
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
| | - Mark L. Borowsky
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
| | | | - Bradley Quade
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Kasper Lage
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
- Pediatric Surgical Research Laboratories, MassGeneral Hospital for Children, Massachusetts General Hospital, Boston, MA, USA
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Judith Miles
- Departments of Pediatrics, Medical Genetics & Pathology, The Thompson Center for Autism & Neurodevelopmental Disorders, University of Missouri Hospitals and Clinics, Columbia, MO
| | - Bai-Lin Wu
- Department of Pathology, Massachusetts General Hospital, Boston, MA
- Department of Laboratory Medicine, Children’s Hospital Boston, Boston, MA
- Children’s Hospital and Institutes of Biomedical Science, Fudan University, Shanghai, China
| | - Yiping Shen
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
- Department of Laboratory Medicine, Children’s Hospital Boston, Boston, MA
- Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Benjamin Neale
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Lisa G. Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA
| | - Mark J. Daly
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
- Autism Consortium of Boston, Boston, MA
| | - Cynthia C. Morton
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - James F. Gusella
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Autism Consortium of Boston, Boston, MA
- Department of Genetics, Harvard Medical School, Boston, MA
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19
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Chiang C, Jacobsen JC, Ernst C, Hanscom C, Heilbut A, Blumenthal I, Mills RE, Kirby A, Lindgren AM, Rudiger SR, McLaughlan CJ, Bawden CS, Reid SJ, Faull RLM, Snell RG, Hall IM, Shen Y, Ohsumi TK, Borowsky ML, Daly MJ, Lee C, Morton CC, MacDonald ME, Gusella JF, Talkowski ME. Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration. Nat Genet 2012; 44:390-7, S1. [PMID: 22388000 PMCID: PMC3340016 DOI: 10.1038/ng.2202] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 01/17/2012] [Indexed: 12/17/2022]
Abstract
We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically-interpreted translocations and inversions. We confirm that the recently described phenomenon of “chromothripsis” (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline where it can resolve to a karyotypically balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign CNVs. We compared these results to experimentally-generated DNA breakage-repair by sequencing seven transgenic animals, and revealed extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion is the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations.
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Affiliation(s)
- Colby Chiang
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
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20
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Pinter SF, Pinter SF, Pinter SF, Jeon Y, Jeon Y, Jeon Y, Ohsumi TK, Ohsumi TK, Borowsky M, Borowsky M, Lee JT, Lee JT, Lee JT, Sadreyev RI, Sadreyev RI, Sadreyev RI, Yildirim E, Yildirim E, Yildirim E. Abstract IA10: Spreading of X-chromosome inactivation via a hierarchy of defined Polycomb stations. Cancer Res 2012. [DOI: 10.1158/1538-7445.nonrna12-ia10] [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
X-chromosome inactivation (XCI) achieves dosage balance in mammals by repressing one of two X-chromosomes in females. During XCI, the long noncoding Xist RNA and Polycomb proteins spread along the inactive X (Xi) to initiate chromosome-wide silencing. Although inactivation is known to commence at the X-inactivation center (Xic), how it propagates remains unknown. We have examined allele-specific binding of Polycomb repressive complex 2 (PRC2) and chromatin composition during XCI, and generate a chromosome-wide profile of Xi and Xa (active X) at nucleosome-resolution. Initially, Polycomb proteins are localized to a limited number of sites along the X. As Xist RNA spreads in cis during the XCI process, thousands of additional sites are recruited. PRC2 and H3K27 methylation spread along a gradient in an Xi-specific manner not seen on autosomes. Our findings suggest that XCI is governed by a hierarchy of defined Polycomb stations that spread H3K27 methylation in cis.
Citation Format: Stefan F. Pinter, Yesu Jeon, Toshiro K. Ohsumi, Mark Borowsky, Jeannie T. Lee, Ruslan I. Sadreyev, Eda Yildirim. Spreading of X-chromosome inactivation via a hierarchy of defined Polycomb stations [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr IA10.
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Affiliation(s)
- Stefan F. Pinter
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Stefan F. Pinter
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Stefan F. Pinter
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Yesu Jeon
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Yesu Jeon
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Yesu Jeon
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Toshiro K. Ohsumi
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Toshiro K. Ohsumi
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Mark Borowsky
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Mark Borowsky
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Jeannie T. Lee
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Jeannie T. Lee
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Jeannie T. Lee
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Ruslan I. Sadreyev
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Ruslan I. Sadreyev
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Ruslan I. Sadreyev
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Eda Yildirim
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Eda Yildirim
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
| | - Eda Yildirim
- 1Howard Hughes Medical Institute, Boston, MA, 2Massachusetts General Hospital, Boston, MA, 3Harvard Medical School, Boston, MA
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21
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Abstract
A combination of bioinformatic and RNA interference analysis of Xenopus tropicalis RNA-seq data shows that the identification of microtubule-associated (MT) mRNAs can be used for discovering novel factors in the processes of spindle pole organization and centrosome structure. MT-RNAs are likely to contribute to spindle-localized mitotic translation. RNA localization is an important mechanism for achieving precise control of posttranscriptional gene expression. Previously, we demonstrated that a subset of cellular mRNAs copurify with mitotic microtubules in egg extracts of Xenopus laevis. Due to limited genomic sequence information available for X. laevis, we used RNA-seq to comprehensively identify the microtubule-interacting transcriptome of the related frog Xenopus tropicalis. We identified ∼450 mRNAs that showed significant enrichment on microtubules (MT-RNAs). In addition, we demonstrated that the MT-RNAs incenp, xrhamm, and tpx2 associate with spindle microtubules in vivo. MT-RNAs are enriched with transcripts associated with cell division, spindle formation, and chromosome function, demonstrating an overrepresentation of genes involved in mitotic regulation. To test whether uncharacterized MT-RNAs have a functional role in mitosis, we performed RNA interference and discovered that several MT-RNAs are required for normal spindle pole organization and γ-tubulin distribution. Together, these data demonstrate that microtubule association is one mechanism for compartmentalizing functionally related mRNAs within the nucleocytoplasmic space of mitotic cells and suggest that MT-RNAs are likely to contribute to spindle-localized mitotic translation.
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Affiliation(s)
- Judith A Sharp
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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22
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Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, Warren RM, Hung DT, Birren BW, Lander ES, Jaffe DB. Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nat Methods 2008; 6:67-9. [PMID: 19079253 PMCID: PMC2613166 DOI: 10.1038/nmeth.1286] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 11/24/2008] [Indexed: 11/18/2022]
Abstract
Our variant ascertainment algorithm VAAL uses massively parallel DNA sequence data to identify differences between bacterial genomes at high sensitivity and specificity. VAAL found ~98% of differences (including large indels) between pairs of strains from three species while calling no false positives. Further, VAAL pinpointed a single mutation between Vibrio genomes, identifying an antibiotic’s site of action by finding the difference(s) between a drug sensitive strain and a resistant derivative.
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Affiliation(s)
- Chad Nusbaum
- Broad Institute of Massachusetts Institute of Technology and Harvard University, 320 Charles Street, Cambridge, MA 02141, USA
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23
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Ohsumi TK, Flaherty JE, Evans MC, Barocas VH. Three-dimensional simulation of anisotropic cell-driven collagen gel compaction. Biomech Model Mechanobiol 2007; 7:53-62. [PMID: 17354006 DOI: 10.1007/s10237-007-0075-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [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] [Received: 07/19/2005] [Accepted: 12/30/2006] [Indexed: 11/28/2022]
Abstract
Tissue equivalents (TEs), formed by entrapping cells in a collagen gel, are an important model system for studying cell behavior. We have previously (Barocas and Tranquillo in J Biomech Eng 117:161-170, 1997a) developed an anisotropic biphasic theory of TE mechanics, which comprises five coupled partial differential equations describing interaction among cells and collagen fibers in the TE. The model equations, previously solved in one or two dimensions, were solved in three dimensions using an adaptive finite-element platform. The model was applied to three systems: a rectangular isometric cell traction assay, an otherwise- acellular gel containing two islands of cells, and an idealized tissue-engineered cardiac valve leaflet. In the first two cases, published experimental data were available for comparison, and the model results were consistent with the experimental observations. Fibers and cells aligned in the fixed direction in the isometric assay, and a region of strong fiber alignment arose between the two cell islands. For the valve problem, the alignment predicted by the model was generally similar to that observed experimentally, but an asymmetry in the experiment was not captured by the model.
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Affiliation(s)
- Toshiro K Ohsumi
- Department of Computer Science, Colgate University, Hamilton, NY, USA
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24
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Caraco T, Glavanakov S, Chen G, Flaherty JE, Ohsumi TK, Szymanski BK. Stage‐Structured Infection Transmission and a Spatial Epidemic: A Model for Lyme Disease. Am Nat 2002; 160:348-59. [DOI: 10.1086/341518] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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