Inherited Macrothrombocytopenia: Correlating Morphology, Epidemiology, Molecular Pathology and Clinical Features

Sparse matrix factorization robust to sample sharing across GWAS reveals interpretable genetic components

Complex trait-associated genetic variation is highly pleiotropic. This extensive pleiotropy implies that multi-phenotype analyses are informative for characterizing genetic associations, as they facilitate the discovery of trait-shared and trait-specific variants and pathways ("genetic factors"). Previous efforts have estimated genetic factors using matrix factorization (MF) applied to numerous GWAS. However, existing methods are susceptible to spurious factors arising from residual confounding due to sample-sharing in biobank GWAS. Furthermore, MF approaches have historically estimated dense factors, loaded on most traits and variants, that are challenging to map onto interpretable biological pathways. To address these shortcomings, we introduce "GWAS latent embeddings accounting for noise and regularization" (GLEANR), a MF method for detection of sparse genetic factors from summary statistics. GLEANR accounts for sample sharing between studies and uses regularization to estimate a data-driven number of interpretable factors. GLEANR is robust to confounding induced by shared samples and improves the replication of genetic factors derived from distinct biobanks. We used GLEANR to evaluate 137 diverse GWAS from the UK Biobank, identifying 58 factors that decompose the genetic architecture of input traits and have distinct signatures of negative selection and degrees of polygenicity. These sparse factors can be interpreted with respect to disease, cell-type, and pathway enrichment. We highlight three such factors capturing platelet measure phenotypes and enriched for disease-relevant markers corresponding to distinct stages of platelet differentiation. Overall, GLEANR is a powerful tool for discovering both trait-specific and trait-shared pathways underlying complex traits from GWAS summary statistics.

A circle of life: platelet and megakaryocyte cytoskeleton dynamics in health and disease

Platelets are blood cells derived from megakaryocytes that play a central role in regulating haemostasis and vascular integrity. The microtubule cytoskeleton of megakaryocytes undergoes a critical dynamic reorganization during cycles of endomitosis and platelet biogenesis. Quiescent platelets have a discoid shape maintained by a marginal band composed of microtubule bundles, which undergoes remarkable remodelling during platelet activation, driving shape change and platelet function. Disrupting or enhancing this process can cause platelet dysfunction such as bleeding disorders or thrombosis. However, little is known about the molecular mechanisms underlying the reorganization of the cytoskeleton in the platelet lineage. Recent studies indicate that the emergence of a unique platelet tubulin code and specific pathogenic tubulin mutations cause platelet defects and bleeding disorders. Frequently, these mutations exhibit dominant negative effects, offering valuable insights into both platelet disease mechanisms and the functioning of tubulins. This review will highlight our current understanding of the role of the microtubule cytoskeleton in the life and death of platelets, along with its relevance to platelet disorders.

Structural impact of pathogenic SNPs on β-tubulin using molecular dynamics study

Single nucleotide polymorphisms (SNPs) in the TUBB1 (β-tubulin) gene have been implicated as the primary cause of macro thrombocytopenia. Therefore it is essential to identify the potential SNPs which are harmful to cause diseases such as macro thrombocytopenia. The impact caused by these variants on β-tubulin is twofold, both structural and functional. Multiple in-silico tools were used to scrutinise the most deleterious nsSNPs (non-synonymous SNPs) via sequence and structure-based approaches. Further, the β-tubulin protein model incorporating identified mutants was subjected to MD (molecular dynamic) simulations to analyse the impact on protein structure. A total of 2974 SNPs of TUBB1 were retrieved from various sources, and 32 nsSNPs were identified. By screening through sequence-based technique, 13 variants were detected as deleterious and further structure-based filtration was carried out to find thermally destabilising variants. Finally, three variants have been detected as highly destabilising by the mCSM server and chosen for the MD study. All three variants are present in the N-terminal, Intermediate, and C-terminal regions, breaking the spatial arrangement required for microtubule assembly. The spatial arrangement of these variants is in deviation with respect to WT (wild type) β-tubulin. The protein model was subjected to a simulation period of 100 ns. The FEL analysis revealed multiple clusters with minor populations indicating the unstable conformation adapted by the β-tubulin. The normal mode vector analysis exhibited high-intensity flexible motions at the C-terminal end, responsible for binding with MAPs (microtubule-associated proteins), an essential region in microtubule assembly. All these results reveal that the SNP's predicted eventually influence the spatial arrangement of β-tubulin, which would disturb the stacking arrangement of αβ tubulin dimer in microtubule assembly. The present study may set a path to cure the diseases like macro thrombocytopenia.Communicated by Ramaswamy H. Sarma.

Macrothrombocytopenia: Role of Automated Platelet Data in Diagnosis

Purpose

Inherited macrothrombocytopenia is an underdiagnosed condition and may result in misdiagnosis and inappropriate management. This research was done to study this condition in a hospital setting.

Materials and Methods

This study was conducted over 6 months in a teaching hospital. Patients whose complete blood count (CBC) samples were sent to the hematology laboratory were included. Patients were suspected to have inherited macrothrombocytopenia according to pre-defined criteria. Demographic information, automated CBC and peripheral smear examination was carried out. Seventy five healthy individuals and 50 patients with secondary thrombocytopenia were also analyzed.

Results

Likely inherited macrothrombocytopenia was identified in 75 patients. Automated platelet count in these patients ranged from 26 × 10^9/L to 106 × 10^9/L while MPV ranged from 11.0 to 13.6 fL. There was significant difference (p < .001) in mean platelet volume (MPV) and platelet large cell ratio (P-LCR) amongst patients with likely inherited macrothrombocytopenia, those with secondary thrombocytopenia and the control group. Mean platelet diameter was significantly higher (3.5 ± 1.1μm) in patients with likely inherited macrothromboctopenia compared to those with secondary thrombocytopenia (2.4 ± 0.7μm) and control group (1.9 ± 0.7μm). All patients with suspected inherited macrothrombocytopenia showed abnormal platelet histograms with descending limb in the high volume and red cell zone. Four distinct histogram patterns were identified.

Conclusion

Inherited macrothrombocytopenia is an underdiagnosed condition. The patient's history, clinical examination, judicious use of automated CBC data including platelet histograms and careful review of the peripheral blood smear are useful tools to suspect this condition.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12288-022-01590-6.

Case Report: Exome Sequencing Identified a Novel Frameshift Mutation of α-Actin 1 in a Chinese Family With Macrothrombocytopenia and Mild Bleeding

Inherited macrothrombocytopenia (IMTP) is a rare disorder characterized by a reduced platelet count and abnormally large platelets. The main clinical symptom of IMTP is mild bleeding in some patients. At present, more than 30 genes have been identified in patients with syndromic and non-syndromic IMTP. In this study, a 3-year-old boy and his mother who presented with mild epistaxis and/or gingival bleeding were diagnosed as having IMTP. Wen then selected whole sequencing to explore the genetic lesion of the patients. After data filtering and mutation validation, a novel frameshift mutation (NM_001130004: c.398_399insTGCG, p.F134AfsX60) of α-actin 1 (ACTN1) was identified in the proband and his mother but absent in other unaffected individuals. Previous studies have proven that mutations in ACTN1 may lead to IMTP with mild to absent bleeding phenotype. The novel mutation, resulting in a truncated protein in exon 4 of the ACTN1 gene, was absent in the public database, such as 1000G and genomAD. Further Western blot revealed that the expression of α-actin 1 in the proband was decreased overtly, which indicated that the novel frameshift mutation may induce non-sense-mediated mRNA decay. In summary, this study not only broadened the variants spectrum of ACTN1 gene, which may contribute to the genetic counseling of IMTP, but also confirmed the diagnosis of IMTP, which may help the management and prognosis for the family members.

Summary and Review of the Abstracts on Hemostasis/Thrombosis Presented at Haematocon 2018, Kochi

The hemostatic pathways involve a complex interplay of a vast array of inherited and acquired factors. Derangements of these pathways lead to several disorders that are complex and challenging not just for laboratory and clinical hematologists but also of concern to public health officials and policy makers. The past decade has seen an increased focus on research in this area with several recent meetings focusing on the diagnosis and management of persons afflicted with these disorders. Haematocon 2018 is the national conference of the Indian Society of Haematology and Blood Transfusion, and papers presented at this year's event offered a glimpse of the contemporary research efforts in India. This mini-review summarizes and places in perspective, salient results from this meeting. The papers are divided into broad subsections of hemophilia, rare clotting factor deficiencies, platelet function defects, macrothrombocytopenia syndromes, thromboelastography, inherited and acquired prothrombotic states, and finally a miscellaneous section. Relevant recent Indian publications on the theme are also discussed.