OC 68.1 - Identification of non-coding genomic regions involved in the aetiology of bleeding, platelet, and thrombotic disorders.

Tuesday, July 12, 2022

2:45 PM – 3:00 PM

Location: ExCel Center, ICC Capital Suite Room 17

Presentation Format: In-Person

Presenting Author(s)

LS

Luca Stefanucci, PhD

postdoc
Wellcome Sanger Institute
Cambridge, England, United Kingdom

Co-Author(s)

MS

Matthew Sims

PhD fellow
Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
Cambridge, England, United Kingdom
JL

Jonathan Lambourne

Postdoctoral fellow
Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
cambridge, England, United Kingdom
FB

Frances Burden

RA
Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
Cambridge, England, United Kingdom
LG

Luigi Grassi

Postdoc
Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
Cambridge, England, United Kingdom
DS

Denis Seyres

Postdoc
University of Cambridge
Cambridge, England, United Kingdom
JS

Jonathan Stephens

RA
University of Cambridge
Cambridge, England, United Kingdom
RT

Rute Tomaz

Postdoc
University of Cambridge
Cambridge, England, United Kingdom
FL

Fatima Lugtu

RA
University of Cambridge
Cambridge, England, United Kingdom
DG

Daniel Greene

Postdoc
University of Cambridge
Cambridge, England, United Kingdom
NO

Nick Owens

PI
University of Exeter
Exeter, England, United Kingdom
KM

Karyn Megy

Postdoc
University of Cambridge
Cambridge, England, United Kingdom
SS

Suthesh Sivapalaratnam

Consultant in Haemostasis and Thrombosis
Barts NHS Trust
London, England, United Kingdom
Kathleen Freson, PhD

Professor
Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium.
Leuven, Vlaams-Brabant, Belgium
LV

Ludovic Vallier

Professor
University of Cambridge
Cambridge, England, United Kingdom
Ernest Turro, PhD

Associate Professor
Icahn School of Medicine at Mount Sinai
New York, New York, United States
WO

Willem H. Ouwehand

Group Coordinator and Principal Investigator
University of Cambridge
Cambridge, England, United Kingdom
MF

Mattia Frontini

Associate Professor
University of Exeter
Exeter, England, United Kingdom

Background: There is an increasing understanding of the relationship between rare coding pathogenic variants and their clinical sequelae. However, for bleeding, platelet, and thrombotic disorders (BPD) a large portion of heritable cases remain without a molecular diagnosis. We have shown that some of these unexplained cases are caused by non-coding variants in the gene-regulatory space (Turro et al., 2020).

Aims: This study aims to identify the regulatory regions of 93 diagnostic-grade BPD genes (Megy et al. 2019) in relevant cell types to increase the heritable-BPD diagnostic yield.

Methods: We differentiated human induced pluripotent stem cells into megakaryocytes, endothelial cells and hepatocytes. A capture Hi-C approach was used to identify regulatory regions of the 93 BPD genes (BPD-regulome hereafter) in these cells. The BPD-regulome was further constrained using statistical and experimental methods. We overlaid epigenetic features, RedPop and applied the BeviMed statistical approach (Greene et al., 2016; Turro et al., 2020). We searched the whole-genome-sequencing (WGS) data of 838 unexplained heritable BPD cases for putative pathogenic variants in the BPD-regulome, and measured their effects on transcription in reporter assays.

Results: We produced the highest resolution interaction maps to date for the 93 BPD genes, identifying 62,027 interactions to putative regulatory elements. This framework identified 31 possible associations between rare variants in the BPD-regulome of unexplained cases at a posterior probability >0.7. Moreover, a visual review of structural variants overlapping the BPD-regulome identified three possibly explanatory aberrations, including the recently described pathogenic deletion in the HDAC6-GATA1 locus (Turro et al. 2020). Finally, we showed that seven of these variants in the BPD-regulome alter gene expression in reporter assays.

Conclusion(s): We generated a high-resolution map of the BPD-regulome in the relevant cell types. The regulatory regions defined in this study lay the foundation to explore WGS-data from unexplained BPD cases for causal variants.