Ongoing Projects

Shivangi Shah, MS
Shivangi Shah, MS examining stem cell models of XDP

A synthetic genomics approach to investigate the XDP/TAF1 locus
Jef Boeke, PhD, NYU

Identifying Shared Disease Pathways via Genomics and Transcriptomics in Cellular Models of XDP and Related Dystonias
Aloysius Domingo, MD, PhD, Mass General Brigham

Developmental, Behavioral, and Transcriptomic Characterization of the Postnatal and Adult Striatum Following Selective Total- or N-Taf1 knockdown
Michelle Ehrlich, MD, Mt. Sinai School of Medicine

Creating a Novel Knock In Control and XDP Mouse Models
Elizabeth Fisher, PhD University College of London

Identifying Physiological Markers of Speech and Swallowing Impairment Across Phenotypes in Individuals With XDP: A Longitudinal Study
Jordan Green, PhD, SSS-CLP, MGH Institute for Health Professions

Structural, Functional, and Electrophysiological Network Connectivity of Effective Deep Brain Stimulation in XDP
Todd Herrington, MD, PhD, Mass General Brigham
Ziv Williams, MD, Mass General Brigham

Towards Targeted Neutralization of the Disease-Causing SVA in XDP Brain Organoids
Frank Jacobs, PhD, University of Amsterdam, The Netherlands

SVA-mediated chromatin re-organisation in XDP
Johan Jakobsson, PhD, Lund University Stem Cell Center, Sweden

Rapid drug discovery of TAF1 deficiency therapeutics in vivo
Rajesh Khanna, PhD, University of Arizona
Mark Nelson, PhD, University of Arizona

Biostatistical analysis of X-linked Dystonia Parkinsonism
Casey Maguire, PhD,  Mass General Brigham

Biostatistical analysis of X-linked Dystonia Parkinsonism
Jeffrey Miller, PhD, Harvard T.H. Chan School of Public Health

Identification of a Network Biomarker in XDP
Martin Niethammer, MD, Feinstein Institute
Chris Tang, MD, PhD, Feinstein Institute
Jeffrey Waugh, MD, PhD, UT Southwestern
Dominic Jamora, MD, FPNA, University of the Philippines, Manila

Rapid drug discovery of TAF1 deficiency therapeutics in vivo
Richard Novak, PhD, Harvard University
Donald Ingber, MD, PhD, Harvard University
Naoto Ito, PhD, UT Mass General Brigham

Presence and role of DNA and RNA G- and C-quadraplex structures in the pathogenesis of XDP
Sara Richter, PhD, University of Padua, Italy

Deciphering the role of histone cirtullination and inflammation in XDP
Ghazaleh Sadri-Vakili, PhD, Mass General Brigham

Identification of New Modifier Genes of TAF1 Protein Expression
Philip Seibler, PhD, University of Luebeck, Germany
Aleksander Rakovic, PhD, University of Luebeck, Germany

Dissecting the influence of the XDP-linked SVA insertion in the TAF1 locus on promoter-proximal pausing
Matthew Simon, PhD, Yale School of Medicine

Molecular and Cellular Mechanisms of XDP Using Patient-derived Neuronal Models
Leslie Thompson, PhD, University of CA-Irvine
Steven Finkbeiner, PhD, University of California, San Francisco, The Gladstone Institutes

Developing a cell-based system to screen compounds countering XDP-SVA mediated transcriptional repression
Marc Timmers, PhD, German Cancer Research Center (DKFZ), University Medical Center Freiburg

Proteomic Analysis of XDP Medium Spiny Neurons Derived From Human iPSCs to Identify Key Molecular Determinants of XDP Neuropathogenesis
Kizito-Tshitoko Tshilenge, PhD, The Buck Institute for Aging Research

Probing XDP Phenotype Using High-Content Imaging in iPSC-Derived Neurons
Brian Wainger, MD, PhD, Massachusetts General Hospital

The Neurochemistry and Neuropathology in the Basal Ganglia of XDP brains
Henry Waldvogel, PhD, University of Auckland, New Zealand
Sir Richard Faull, MBChB, PhD, Dsc, FRSNZ, University of Auckland, New Zealand
Malvindar Singh-Bains, PhD, University of Auckland, New Zealand
Edwin Munoz, PhD, University of the Philippines
Mark Ang, MD, University of the Philippines

The Role of Hexanucleotide Repeat Instability in the Pathogenesis of XDP
Vanessa Wheeler, PhD, Massachusetts General Hospital

Mechanistic insights into the role of a proposed novel genetic modifier of X-linked dystonia-parkinsonism
Ana Westernberger, PhD, University of Luebeck
Christine Klein, MD,  University of Luebeck
Aleksandar Rakovic, University of Luebeck

Identification of pathogenic mechanisms underlying neurodegeneration of XDP neurons generated by direct conversion of fibroblasts
Andrew Yoo, PhD, Washington University


Completed Projects

PET imaging
PET Images of an XDP patient courtesy of Martin Niethammer, MD and Roland Dominic Jamora, MD

Does SVA Polymorphism Reduce Expression of TAF1 During Neural Development of XDP Patients Through KRAB-ZNF/TRIM28-mediated Heterochromatinization?
Johan Jakobsson, PhD, Lund University Stem Cell Center, Sweden

Presence and Role of DNA and RNA G- and C-quadruplex Structures in the Pathogenesis of XDP
Sara Richter, PhD, University of Padua, Italy

Comprehensive Characterization of XDP-specific Changes in RNA Metabolism Using TimeLapse-Seq
Matthew Simon, PhD, Yale School of Medicine

Harnessing X-Chromosome Inactivation and Retrotransposon Biology To Gain Insights Into XDP
Jennifer Erwin, PhD, Lieber Institute for Brain Discovery
Apua Paquola, PhD, Lieber Institute for Brain Discovery

Connecting Aberrant Splicing and Transcription of the TAF1 Gene to the SVA-F Retrotransposon in XDP
Marc Timmers, PhD, German Cancer Research Center (DKFZ), University Medical Center Freiburg

Modeling X-Linked Dystonia–Parkinsonism Using Patient-derived Neurons through Direct Neuronal Reprogramming of Dermal Fibroblasts
Andrew Yoo, PhD, Washington University

Assessing histone modifications in XDP
Ghazaleh Sadri-Vakili, PhD, Massachusetts General Hospital

Characterization of Striatal Compartmental Transcriptomes and Transcription Factors in vivo and Application to XDP iPSC Biology
Michelle Ehrlich, MD, Icahn School of Medicine at Mt. Sinai
Lisa Ellerby, PhD, Buck Institute for Research on Aging

DTI Tractography of Striatal Connectivity in XDP: Relationship to Striatal Compartments and Disease Characteristics
Anne J. Blood, PhD Massachusetts General Hospital
Norbert Brueggemann, MD University of Luebeck, Germany

Exploring Noncoding RNAs in XDP Using RNA-seq in Various Endogenous Models
Aloysius Domingo, MD, PhD, University of Luebeck, Germany
Christine Klein, MD University of Luebeck, Germany
Manuela Marz, PhD, University of Jena

Harnessing X-chromosome Inactivation to Gain Insights into XDP
Jennifer Erwin, PhD, Salk Institute

Creating a Novel Mouse Model with Human XDP Haplotype Towards Identifying and Characterizing the Causative Mutation
Elizabeth Fisher, PhD, University College of London

Response of DYT3 iPSC-derived Neurons to ER and Metabolic Stressors
Paul J. Gadue, PhD, Children's Hospital of Pennsylvania
Pedro Gonzalez-Alegre, MD, PhD, University of Pennsylvania

Modeling XDP Using BAC Transgenesis
Michelle Gray, PhD, University of Alabama, Birmingham

Next Generation RNA Sequencing to Identify TAF-1 Splice Forms and Striosome-Enriched mRNAs
Ann Graybiel, PhD, Massachusetts Institute of Technology
Jill Crittenden, PhD, Massachusetts Institute of Technology

Advancing Genome Editing Technologies to Engineer Cell-based Models of XDP
J. Keith Joung, MD, PhD Massachusetts General Hospital

Building up a Collaborative Resource of Biomaterials to Unravel the Genetic Cause and Molecular Pathways of XDP and to Enable Comprehensive –omics Approaches and Drug Screening
Christine Klein, MD and Philip Seibler, PhD University of Luebeck, Germany
Eva Cutiongco-de la Paz, MD, University of the Philippines, Manila, National Institutes of Health Manila, Philippines
Mike Talkowski, PhD Massachusetts General Hospital

Exploring Transcriptomopathy Syndromes Related to X-liked Dystonia Parkinsonism and TAF1
Gholson Lyon, MD, PhD, Cold Spring Harbor Laboratory
Jesse Gillis, PhD Cold Spring Harbor Laboratory

Evaluating the Role of Chromatin Modification and Altered Transcription as an Underlying Mechanism in X-linked Dystonia-Parkinsonism
Ghazaleh Sadri-Vakili, PhD, Massachusetts General Hospital

Novel Reference Free Assembly of the Panay Island Genome to Delineate the Genetic Architecture of XDP
Michael Talkowski, PhD, Massachusetts General Hospital
David B. Jaffe, PhD, Broad Institute of Harvard and MIT
Neil Weisenfeld, PhD, Broad Institute of Harvard and MIT

The International XDP Genomics Consortium: Integrative Genomic Studies of X-Linked Dystonia Parkinsonism
Michael Talkowski, PhD, Massachusetts General Hospital
David B. Jaffe, PhD, Broad Institute of Harvard and MIT
Christine Klein, MD, University of Luebeck, Germany
Cristopher Bragg, PhD, Massachusetts General Hospital

Understanding the Molecular Basis of XDP
Marc Timmers, PhD, University Medical Center, Utrecht

iPSC-based Physiological Modeling in X-linked Dystonia-Parkinsonism (XDP)
Brian J. Wainger, MD, PhD, Massachusetts General Hospital

Assessment of Presymptomatic Stages of XDP
Anne J. Blood, PhD, Massachusetts General Hospital
Cid Diesta, MD, Makati Medical Center
Norbert Brueggemann, MD, University of Luebeck, Germany
Jeff Waugh, MD, PhD, UT Southwestern

Pallidal Neurostimulation in XDP
Norbert Brueggemann, MD
Christine Klein, MD, University of Luebeck, Germany
Dominic Jamora, MD, FPNA, University of the Philippines, Manila

Evaluating the Role of Chromatin Modification and Altered Transcription as an Underlying Mechanism in XDP
Ghazaleh Sadri-Vakili, PhD, Massachusetts General Hospital

Cell-Type Specific Basis of Striatal Degeneration Patterns in XDP
Jill Crittenden, PhD, MIT

Identifying Shared Disease Pathways via Genomics and Transcriptomics in Cellular Models of XPD and Related Dystonias
Jill Crittenden, PhD, MIT
Sir Richard Faull, KNZM, FRSNZ, University of Auckland
Henry Waldvogel, PhD, University of Auckland

Exploring the Interaction Between N-TAF Function and Neuronal Stress in Cultured Neurons and in vivo
Pedro Gonzalez, MD, PhD University of Pennsylvania, Children's Hospital of Philadelphia

Development of Epigenetic Editing Technologies for Research and Therapy of XDP
J. Keith Joung, MD, PhD, Massachusetts General Hospital

Examination of Hexanucleotide Repeat Instability and Modifiers of Age of Onset in XDP
Laurie Ozelius, PhD, Massachusetts General Hospital
Vanessa Wheeler, PhD, Massachusetts General Hospital

A Genomics Hub for Collaborative Studies of XDP
Michael Talkowski, PhD, Massachusetts General Hospital
Laurie Ozelius, PhD, Massachusetts General Hospital
Cristopher Bragg, PhD, Massachusetts General Hospital

Dynamics of the in vivo RNA Transcriptional/Translational Landscape in XDP Patient-specific Cells
Sherman M. Weissman, MD, Yale University School of Medicine
Anna M. Szekely, MD, Yale University School of Medicine