Integrin alpha 6 homozygous splice-site mutation causes a new form of junctional epidermolysis bullosa in Charolais cattle

Functional impact of splicing variants in the elaboration of complex traits in cattle

GWAS conducted directly on imputed whole genome sequence have led to the identification of numerous genetic variants associated with agronomic traits in cattle. However, such variants are often simply markers in linkage disequilibrium with the actual causal variants, which is a limiting factor for the development of accurate genomic predictions. It is possible to identify causal variants by integrating information on how variants impact gene expression into GWAS output. RNA splicing plays a major role in regulating gene expression. Thus, assessing the effect of variants on RNA splicing may explain their function. Here, we use a high-throughput strategy to functionally analyse putative splice-disrupting variants in the bovine genome. Using GWAS, massively parallel reporter assay and deep learning algorithms designed to predict splice-disrupting variants, we identify 38 splice-disrupting variants associated with complex traits in cattle, three of which could be classified as causal. Our results indicate that splice-disrupting variants are widely found in the quantitative trait loci related to these phenotypes. Using our combined approach, we also assess the validity of splicing predictors originally developed to analyse human variants in the context of the bovine genome.

Subpopulation commensalism promotes Rac1-dependent invasion of single cells via laminin-332

Phenotypic heterogeneity poses a significant hurdle for cancer treatment but is under-characterized in the context of tumor invasion. Amidst the range of phenotypic heterogeneity across solid tumor types, collectively invading cells and single cells have been extensively characterized as independent modes of invasion, but their intercellular interactions have rarely been explored. Here, we isolated collectively invading cells and single cells from the heterogeneous 4T1 cell line and observed extensive transcriptional and epigenetic diversity across these subpopulations. By integrating these datasets, we identified laminin-332 as a protein complex exclusively secreted by collectively invading cells. Live-cell imaging revealed that laminin-332 derived from collectively invading cells increased the velocity and directionality of single cells. Despite collectively invading and single cells having similar expression of the integrin α6β4 dimer, single cells demonstrated higher Rac1 activation upon laminin-332 binding to integrin α6β4. This mechanism suggests a novel commensal relationship between collectively invading and single cells, wherein collectively invading cells promote the invasive potential of single cells through a laminin-332/Rac1 axis.