Biology subjects

Morozyuk, M.

Publications and source records attributed to Morozyuk, M..

3 recordsLinked to original sources

bioRxiv2026

Systematic evaluation of integration methods and parameters on single-cell RNA-sequencing biological insights: a case study on cattle embryos.

BackgroundSingle-cell RNA sequencing (scRNA-seq) integration methods remove technical variation while preserving biological signal, yet systematic frameworks for evaluating how parameter choices influence biological interpretation remain limited. Traditional benchmarking approaches evaluate single-parameter configurations per method, potentially missing systematic patterns in functional outcomes and method convergence. A framework for systematic integration parameter evaluation was developed and applied to bovine embryo development. ResultsSix integration methods (FastMNN, CCA, RPCA, scVI, Harmony, STACAS) combined with multiple parameters, including those for neighbor identification and clustering, yielded 8232 combinations. The main outputs evaluated were specific cell counts and marker identification. After filtering for extremely poor cell and marker identification, 4,287 integration parameter combinations were retained for analysis. There were three major patterns (clusters) with integration methods distributed non-randomly across clusters and distinct biological outcomes. One pattern emerged, composed of scVI and STACAS integration, dominated by the lack of identification of epiblast cells. Cluster 2 (n=29), also composed of scVI and STACAS integration, identified the most epiblast markers (n=7, 8, or 9) but had a limited number of epiblast cells (median=10). Cluster 1 (n=4,120 combinations) had the highest method diversity. Across clusters, trophoblast and mesoderm showed high functional distinctness, while epiblast and hypoblast showed moderate overlap in gene ontology classes. ConclusionsThe approach reveals that parameter choices influence cell type classification, functional interpretation, and the degree of method convergence, with implications for identifying specific biological inferences for further orthogonal validation. A systematic approach to evaluating integration methods, along with other parameters, is advisable for accurate biological inference.

genomics↗

bioRxiv2024

Genome-wide association analyses in dairy heifers highlight genes overlapping with mouse and human fertility and human health traits

Heifer Infertility and disease are important challenges in dairy cattle production. We investigated genetic differences between Holstein heifers with varying fertility potential and health. We carried out a genome-wide association analysis comparing heifers that conceived at first insemination against those requiring multiple attempts or failing to become pregnant, as well as heifers culled due to health issues. There were 12 significant SNPs (P<5x10-5) associated with fertility and 35 SNPs associated with health traits. There were 166 significant SNPs when infertile, sub-fertile and animals culled due to health issues were grouped. Two SNPs identified in the analysis of infertility were found near NUFIP1 and within TENM4 genes, both genes are linked to embryonic lethality in mouse knockouts. Follow-up CRISPR-Cas9 mediated disruption of NUFIP1 significantly (P<0.05) reduced in vitro blastocyst development in cattle embryos, while TENM4 editing did not alter in vitro blastocyst development. Additionally, SNPs overlapped with previously identified reproduction-related QTL (CNTN4, DLG2, PARP10, PRICKLE, TMEM150B) or health-related QTL (FAM162A, PARP10). We also identified genes within or near genes previously associated with age at menarche (CADM2, DLG2, FHIT, LSAMP and TENM4) or lung function or pulmonary diseases (ASCC2, BCAS3, BTBD9, CADM2, CNTN4, CPEB4, CTNNA2, DEUP1, DGKH, DLG2, ENOX1, EPHB1, ERC2, ERGIC1, EYA2, FAM162A, FGF18, FHIT, GRID1, KCNIP4, LINGO2, LRMDA, MALRD1, NEBL, PLA2G6, PLXDC2, PRPF18, SLC8A1, TEAD4, TSPAN9) in humans. These results further support genetic components of fertility and health in cattle. The findings also show overlapping genetic architecture between fertility and health traits, with a degree of conservation across mammals. Summary sentenceSeveral genetic variants that influence female fertility and health in cattle were identified, and many genes harboring or near significant polymorphisms are common to equivalent phenotypes in mice and humans.

genomics↗

bioRxiv2024

Identification of novel genes in cattle (Bos taurus) and biological insights into their function in embryo development

Appropriate regulation of genes expressed in oocytes and embryos is essential for acquisition of developmental competence in mammals. Here, we hypothesized that several genes expressed in oocytes and pre-implantation embryos remain unknown. Our goal was to reconstruct the transcriptome of oocytes (germinal vesicle and metaphase II) and pre-implantation cattle embryos (blastocysts) using short-read and long-read sequences to identify putative new genes. We identified 274,342 transcript sequences, and 3,033 of those transcripts do not match a gene present in an annotation, thus are potential new genes. Notably, 63.67% (1,931/3,033) of potential novel genes exhibited coding potential. Also noteworthy, 97.92% of the putative novel genes overlapped annotation with transposable elements. Comparative analysis of transcript abundance identified that 1,840 novel genes (recently added to the annotation) or potential new genes were differentially expressed between developmental stages (FDR<0.01). We also determined that 522 novel or potential new genes (448 and 34 respectively) were upregulated at eight-cell embryos compared to oocytes (FDR<0.01). In eight-cell embryos, 102 novel or putative new genes were co-expressed (|r|>0.85, P<1x10-8) with several genes annotated with gene ontology processes related to pluripotency maintenance and embryo development. CRISPR-Cas9 genome editing confirmed that the disruption of one of the novel genes highly expressed in eight-cell embryos reduced blastocyst development (ENSBTAG00000068261, P=1.55x10-7). In conclusion, our results revealed several putative new genes that need careful annotation. Many of the putative new genes have dynamic regulation during pre-implantation development and are important components of gene regulatory networks involved in pluripotency and blastocyst formation.

genomics↗