Iwata, H. | bioRxiv Science

bioRxiv2019

Tuning intercellular cohesion with membrane-anchored oligonucleotides

Cohesive interactions between cells play an integral role in development, differentiation, and regeneration. Existing methods for controlling cell-cell cohesion by manipulating protein expression are constrained by biological interdependencies, e.g. coupling of cadherins to actomyosin force-feedback mechanisms. We use oligonucleotides conjugated to PEGylated lipid anchors (ssDNAPEGDPPE) to introduce artificial cell-cell cohesion that is largely decoupled from the internal cytoskeleton. We describe cell-cell doublets with a mechanical model based on isotropic, elastic deformation of spheres to estimate the cohesion at the cell-cell interface. Physical manipulation of cohesion by modulating PEG-lipid to ssDNAPEGDPPE ratio, and conversely treatment with actin-depolymerizing cytochalsin-D, resulted respectively in decreases and increases in doublet contact area. Our data are relevant to the ongoing discussion over mechanisms of tissue surface tension and in agreement with models based on opposing cortical and cohesive forces. PEG-lipid modulation of doublet geometries resulted in a well-defined curve indicating continuity, enabling prescriptive calibration for controlling doublet geometry. Our study demonstrates tuning of basic doublet cohesion, laying the foundation for more complex multicellular cohesion control independent of protein expression.

biophysics↗

bioRxiv2019

Haplotype-based genome wide association study using a novel SNP-set method : RAINBOW

BackgroundDiffculty in detecting rare variants is one of the problems in conventional genome wide association studies (GWAS). The problem is closely related to the complex gene compositions comprising multiple alleles, such as haplotypes. Several single nucleotide polymorphism (SNP) set approaches have been proposed to solve this problem. These methods, however, have been rarely discussed in connection with haplotypes. In this study, we developed a novel SNP-set GWAS method named \"RAINBOW\" and applied the method to haplotype-based GWAS by regarding a haplotype block as a SNP-set. Combining haplotype block estimation and SNP-set GWAS, haplotype-based GWAS can be conducted without prior information of haplotypes.\n\nResultsWe prepared 100 datasets of simulated phenotypic data and real marker genotype data of Oryza sativa subsp. indica, and performed GWAS of the datasets. We compared the power of our method, the conventional single-SNP GWAS, the conventional haplotype-based GWAS, and the conventional SNP-set GWAS. The results of the comparison indicated that the proposed method was able to better control false positives than the others. The proposed method was also excellent at detecting causal variants without relying on the linkage disequilibrium if causal variants were genotyped in the dataset. Moreover, the proposed method showed greater power than the other methods, i.e., it was able to detect causal variants that were not detected by the others, especially when the causal variants were located very close to each other and the directions of their effects were opposite.\n\nConclusionThe proposed method, RAINBOW, is especially superior in controlling false positives, detecting causal variants, and detecting nearby causal variants with opposite effects. By using the SNP-set approach as the proposed method, we expect that detecting not only rare variants but also genes with complex mechanisms, such as genes with multiple causal variants, can be realized. RAINBOW was implemented as the R package and is available at https://github.com/KosukeHamazaki/RAINBOW.

genetics↗