The thymus is a primary lymphoid organ, essential for T cell maturation and selection. There has been long-standing interest in processes underpinning thymus generation and the potential to manipulate it clinically, because alterations of thymus development or function can result in severe immunodeficiency and autoimmunity. Here, we identify epithelial-mesenchymal hybrid cells, capable of long-term expansion in vitro, and able to reconstitute an anatomic phenocopy of the native thymus, when combined with thymic interstitial cells and a natural decellularised extracellular matrix (ECM) obtained by whole thymus perfusion. This anatomical human thymus reconstruction is functional, as judged by its capacity to support mature T cell development in vivo after transplantation into humanised immunodeficient mice. These findings establish a basis for dissecting the cellular and molecular crosstalk between stroma, ECM and thymocytes, and offer practical prospects for treating congenital and acquired immunological diseases.

Inherited cardiomyopathies are a prevalent cause of heart failure and sudden cardiac death. Both hypertrophic (HCM) and dilated cardiomyopathy (DCM) are genetically heterogeneous and typically present with an autosomal dominant mode of transmission. Whole exome sequencing and autozygosity mapping was carried out in eight un-related probands from consanguineous Middle Eastern families presenting with HCM/DCM followed by bioinformatic and co-segregation analysis to predict the potential pathogenicity of candidate variants. We identified homozygous missense variants in TNNI3K, DSP, and RBCK1 linked with a dilated phenotype, in NRAP linked with a mixed phenotype of dilated/hypertrophic, and in KLHL24 linked with a mixed phenotype of dilated/hypertrophic and non-compaction features. Co-segregation analysis in family members confirmed autosomal recessive inheritance presenting in early childhood/early adulthood. Our findings add to the mutational spectrum of recessive cardiomyopathies, supporting inclusion of KLHL24, NRAP and RBCK1 as disease-causing genes. We also provide evidence for novel (recessive) modes of inheritance of a well-established gene TNNI3K and expand our knowledge of the clinical heterogeneity of cardiomyopathies. A greater understanding of the genetic causes of recessive cardiomyopathies has major implications for diagnosis and screening, particularly in underrepresented populations, such as those of the Middle East.

Mutations in the SNX14 gene cause spinocerebellar ataxia, autosomal recessive 20 (SCAR20) in both humans and dogs. Studies implicating the phenotypic consequences of SNX14 mutations to be consequences of subcellular disruption to autophagy and lipid metabolism have been limited to in vitro investigation of patient-derived dermal fibroblasts, laboratory engineered cell lines and developmental analysis of zebrafish morphants. SNX14 homologues Snz (Drosophila) and Mdm1 (yeast) have also been conducted, demonstrated an important biochemical role during lipid biogenesis. In this study we report the effect of loss of SNX14 in mice, which resulted in embryonic lethality around mid-gestation due to placental pathology that involves severe disruption to syncytiotrophoblast cell differentiation. In contrast to other vertebrates, zebrafish carrying a homozygous, maternal zygotic snx14 genetic loss-of-function mutation were both viable and anatomically normal. Whilst no obvious behavioural effects were observed, elevated levels of neutral lipids and phospholipids resemble previously reported effects on lipid homeostasis in other species. The biochemical role of SNX14 therefore appears largely conserved through evolution while the consequences of loss of function varies between species. Mouse and zebrafish models therefore provide valuable insights into the functional importance of SNX14 with distinct opportunities for investigating its cellular and metabolic function in vivo.

The BAF (also known as mammalian SWI/SNF) chromatin remodelling complexes are essential regulators of nucleosome positioning and transcription factor binding ^1,2 . Loss-of-function (LOF) mutations in genes encoding components of the BAF complexes are among the most frequent across cancer types ³ . However, a unifying mechanism that explains their widespread disruption remains unclear. Here we disrupted BAF function through pharmacological inhibition and ARID1A deletion across various mammalian cell types and tissues and observed a conserved chromatin response: increased accessibility at CTCF-binding sites. ARID1A LOF alone was sufficient to drive these changes, which demonstrates that canonical BAF (cBAF) disruption is the key driver of CTCF gain. Genomic profiling showed increased CTCF and SMC3 occupancy, which reveals an antagonistic relationship between cBAF and CTCF–cohesin complexes. Furthermore, cBAF loss restructured 3D genome organization, which led to a strengthening of topologically associating domain boundaries and subdivision of large domains into smaller insulated structures. Long-range enhancer–promoter loops were replaced by shorter, promoter-proximal loops anchored at CTCF-enriched sites. To determine how CTCF function is enabled following cBAF loss, we profiled CTCF-interacting cofactors and found that CTCF binds directly to fully assembled PBAF. After cBAF depletion, PBAF was recruited to sites of increased CTCF occupancy, which demonstrates that there is an antagonistic switch between SWI/SNF subcomplexes. In vivo, conditional Arid1a deletion in primary mouse cells resulted in the expansion of a highly proliferative population marked by elevated accessibility at CTCF sites. This phenotype was fully reversed by either Ctcf or Pbrm1 deletion, which establishes that cBAF and the activity of CTCF and PBAF have contrasting roles.