Characteristic craniofacial defects associated with a novel USP9X truncation mutation
HGV database
The relevant data from this Data Report are hosted at the Human Genome Variation Database at https://doi.org/10.6084/m9.figshare.hgv.3402.
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Selection for somatic escape variants in SERPINA1 in the liver of patients with alpha-1 antitrypsin deficiency
Somatic variants accumulate in non-malignant tissues with age. Functional variants, leading to clonal advantage of hepatocytes, accumulate in the liver of patients with acquired chronic liver disease (CLD). Whether somatic variants are common to CLD from differing etiologies is unknown. We analyzed liver somatic variants in patients with genetic CLD from alpha-1 antitrypsin (A1AT) deficiency or hemochromatosis. We show that somatic variants in SERPINA1, the gene encoding A1AT, are strongly selected for in A1AT deficiency, with evidence of convergent evolution. Acquired SERPINA1 variants are clustered at the carboxyl terminus of A1AT, leading to truncation. In vitro and in vivo, C-terminal truncation variants reduce disease-associated Z-A1AT polymer accumulation and disruption of the endoplasmic reticulum, supporting the C-terminal domain swap mechanism. Therefore, somatic escape variants from a deleterious germline variant are selected for in A1AT deficiency, suggesting that functional somatic variants are disease-specific in CLD and point to disease-associated mechanisms.
The Marchantia polymorpha pangenome reveals ancient mechanisms of plant adaptation to the environment
Plant adaptation to terrestrial life started 450 million years ago and has played a major role in the evolution of life on Earth. The genetic mechanisms allowing this adaptation to a diversity of terrestrial constraints have been mostly studied by focusing on flowering plants. Here, we gathered a collection of 133 accessions of the model bryophyte Marchantia polymorpha and studied its intraspecific diversity using selection signature analyses, a genome–environment association study and a pangenome. We identified adaptive features, such as peroxidases or nucleotide-binding and leucine-rich repeats (NLRs), also observed in flowering plants, likely inherited from the first land plants. The M. polymorpha pangenome also harbors lineage-specific accessory genes absent from seed plants. We conclude that different land plant lineages still share many elements from the genetic toolkit evolved by their most recent common ancestor to adapt to the terrestrial habitat, refined by lineage-specific polymorphisms and gene family evolution.
Extreme shape coexistence observed in 70Co
The shape of the atomic nucleus is a property that underpins our understanding of nuclear systems, impacts the limits of nuclear existence, and enables probes of physics beyond the Standard Model. Nuclei can adopt a variety of shapes, including spheres, axially deformed spheroids, and pear shapes. In some regions of the nuclear chart where a spherical nucleus would naively be expected, deformed nuclear states can result from the collective action of constituent protons and neutrons. In a small subset of nuclei both spherical and deformed nuclear states have been experimentally observed, a phenomenon termed shape coexistence. We present spectroscopic evidence for the coexistence of Jπ = 1+ spherical and deformed states in 70Co, separated by less than 275 keV. This close degeneracy of levels with the same Jπ and different shapes demonstrates an extreme example of shape coexistence resulting from the interplay of independent particle motion and collective behavior in highly unstable nuclear systems and identifies the Co isotopes as a transition point between deformed ground states observed in the Cr isotopes and spherical configurations observed in the closed-shell Ni isotopes.
Wilson disease (novel ATP7B variants) with concomitant FLNC-related cardiomyopathy
We report a case of Wilson disease (WD) with dilated cardiomyopathy in which whole-genome sequencing (WGS) revealed the rare co-occurrence of two novel compound heterozygous ATP7B pathogenic variants (NM_001005918.3:c.2250del/p.N751Tfs*9 and c.3496C>T/p.L1166F) and a known FLNC pathogenic variant. Our results highlight the usefulness of WGS, even in the diagnosis of well-characterized genetic diseases such as WD.
Missense BICD2 variants in fetuses with congenital arthrogryposis and pterygia
Type 2 spinal muscular atrophy with lower extremity dominance (SMALED2) is caused by bicaudal D cargo adaptor 2 (BICD2) variants. However, the SMALED2 genotype and phenotype correlation have not been thoroughly characterized. We identified de novo heterozygous BICD2 missense variants in two fetuses with severe, prenatally diagnosed multiple arthrogryposis congenita. This report provides further insights into the genetics of this rare disease.
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