A gain-of-function variant in DIAPH1 causes dominant macrothrombocytopenia and hearing loss

Abstract

Key Points• A gain-of-function variant in DIAPH1 causes macrothrombocytopenia and hearing loss and extends the spectrum of DIAPH1-related disease.• Our findings of altered megakaryopoiesis and platelet cytoskeletal regulation highlight a critical role for DIAPH1 in platelet formation.Macrothrombocytopenia (MTP) is a heterogeneous group of disorders characterized by enlarged and reduced numbers of circulating platelets, sometimes resulting in abnormal bleeding. In most MTP, this phenotype arises because of altered regulation of platelet formation from megakaryocytes (MKs). We report the identification of DIAPH1, which encodes the Rho-effector diaphanous-related formin 1 (DIAPH1), as a candidate gene for MTP using exome sequencing, ontological phenotyping, and similarity regression. We describe 2 unrelated pedigrees with MTP and sensorineural hearing loss that segregate with a DIAPH1 R1213* variant predicting partial truncation of the DIAPH1 diaphanous autoregulatory domain. The R1213* variant was linked to reduced proplatelet formation from cultured MKs, cell clustering, and abnormal cortical filamentous actin. Similarly, in platelets, there was increased filamentous actin and stable microtubules, indicating constitutive activation of DIAPH1. Overexpression of DIAPH1 R1213* in cells reproduced the cytoskeletal alterations found in platelets. Our description of a novel disorder of platelet formation and hearing loss extends the repertoire of DIAPH1-related disease andprovides new insight into the autoregulation of DIAPH1 activity.

Inherited platelet disorders: toward DNA-based diagnosis

“…It has been shown that specific GOF variants in DIAPH1 and SRC can cause a defect in megakaryopoiesis, whereas this is not expected of LOF variants. 22,48 Similar observations can be made for SFLN14, where all variants are located in the ATPase-AAA-4 domain, and rare variants outside this domain seem not to result in an IPD. 54 There are publicly accessible databases such as ClinVar, 94 DECIPHER, 95 and Exome variant server 96 and access-for-a-fee databases such as the Human Gene Mutation Database (HGMD) 97 that record disease-associated variants.…”

“…This collaborative approach will provide the platform to evaluate existing and new interventions to gather evidence for the best approach to treatment. That such international approaches can be successful has been demonstrated by the BRIDGE-BPD and ThromboGenomics consortium efforts reported in this issue 22,82 and in other journals.…”

“…Indeed, genome sequencing combined with HPO coding supported the identification of the DIAPH1 variant in 2 unrelated pedigrees with similar phenotype terms thrombocytopenia and deafness. 22 It also allowed integration with existing phenotype databases, such as the one for mouse phenotype ontology terms, which aided the discovery of the SRC variant because cases and knockout mice shared HPO terms. 48 These discoveries are critically dependent on new statistical methods that exploit the power of HPO-based patient coding together with genotypes obtained by sequencing.…”

“…Genome sequencing results of the DNA samples of hundreds of probands with uncharacterized BPDs, analyzed using assigned human phenotype ontology (HPO) terms, 2 have helped identify pathogenic variants in known IPD genes in almost 20% of cases. New algorithms to compare cases with similar phenotypes 48,84 have been used to identify 2 novel IPD genes (DIAPH1 and SRC) 22,48 and several putative ones. This suggests that the majority of cases either harbor pathogenic variants in unknown genes or regulatory regions or are the result of a digenic mode of inheritance.…”

High-throughput sequencing for rapid diagnosis of inherited platelet disorders: a case for a European consensus

“…WES, and particularly WGS, offer the potential to identify new genes, especially when combined with selective approaches such as comparing patient phenotypes with those of knock-out mouse models or gene datasets; approaches that allowed us to identify TRPM7 (from an existing mouse model) and DIAPH1 (from a search of genes responsible for deafness) in patients belonging to the French cohort which we submitted to BRIDGE. 10,11 Recent advances in bioinformatic analysis of next-generation sequencing data are enhancing causal gene identification in IPDs, helped by HPO questioning and the study of variant penetrance within large families. 12 It would be interesting to now apply WGS to those cases in the Spanish cohort for whom disease-causing variants were not identified.…”