Biology subjects

Stefanovic, S.

Publications and source records attributed to Stefanovic, S..

8 recordsLinked to original sources

bioRxiv2026

Single-Cell Multimodal Profiling Reveals Maternal Diabetes-Nkx2-5 Interaction in Congenital Heart Disease in a Genetic Model Recapitulating Human Embryopathies

The etiological complexity of congenital heart disease (CHD) arises from the interaction between genetic and environmental factors. We hypothesized that environmental exposure could potentiate a genetic susceptibility, leading to an increased incidence of specific cardiac defects. To test this hypothesis, we used betaV59M+ female mice exhibiting severe hyperglycemia (>28 mmol/L) without dyslipidemia, a model we characterized that faithfully recapitulates human diabetic embryopathy. These females were crossed with males haploinsufficient for Nkx2-5, a transcription factor essential for cardiac development and implicated in human CHD. Our results show that the combination of genetic susceptibility and a hyperglycemic maternal environment (GxE) leads to a higher frequency and severity of cardiac malformations, including ventricular septal defects specifically involving the muscular septum, univentricular morphologies, and dilation with thinning of the myocardium. These structural abnormalities were associated with transcriptional changes affecting the contractile identity of the chamber myocardium. Single-nucleus multiomic profiling (snRNA-seq and snATAC-seq) of the E9.5 cardiac region revealed that the interaction between maternal diabetes and Nkx2-5 haploinsufficiency profoundly reshapes transcriptional and chromatin accessibility landscapes. These changes affect not only metabolic pathways, but also cell cycle progression in second heart field (SHF) progenitors, likely contributing to the observed structural cardiac defects. Multiomic integration further identifies a disrupted indirect Nkx2-5-Aldh1a2 regulatory axis in posterior SHF progenitors, while demonstrating that maternal diabetes selectively affects a restricted subset of Nkx2-5-dependent regulatory elements associated with cardiomyocyte maturation. Our findings establish a comprehensive single-cell multiomic resource that will facilitate the integration of human GWAS and other genomic datasets, enabling the identification and functional interpretation of disease-associated loci.

developmental biology↗

bioRxiv2026

Ancient whole genomes reveal regional selection during adaptation to Neolithic lifestyle in Western Eurasia

The introduction of agriculture in Western Eurasia during the Mesolithic-Neolithic transition reshaped human lifestyle, demography and pathogen exposure. Yet, the associated selective pressures remain incompletely resolved because previous ancient DNA studies relied on targeted SNP panels and yielded non-overlapping results. Here, using high-coverage whole-genome data from 152 ancient individuals, including 12 newly sequenced genomes from the Iron Gates, we show that adaptation during this transition was geographically structured and involved selection of both Early Farmer and Hunter-Gatherer alleles. By combining scans of population differentiation, extended haplotype homozygosity, and adaptive admixture, we identify candidate loci under selection in ancestral and admixed populations. Extending the analysis beyond SNPs, we also detect differential copy-number variants, ancestry-associated shifts in transposable-element abundance, and an early Neolithic hepatitis B infection. Functional analyses including effects on gene expression suggested selection on immune, metabolic, reproductive, sensory, and behavioural processes. Taken together, our results reveal a broader and more regionally variable adaptive landscape than previously appreciated.

evolutionary biology↗

bioRxiv2024

Cytogenetic comparison of Cuscuta psorothamnensis and C. veatchii (Convolvulaceae), two species originated from recurrent hybridization between the same diploid parents

Genus Cuscuta L. (Convolvulaceae) exhibits cases of hybridization and allopolyploidy. Section Denticulatae, subg. Grammica, includes four species: the allopolyploids, C. veatchii and C. psorothamnensis (2n = 60), which originated from two independent reticulation events between the diploids, C. denticulata and C. nevadensis (2n = 30). The allopolyploids are morphologically similar, but are differing in their geographical distribution and host specificity. While cytogenetic data have been reported for C. veatchii, this study aims to provide a comparative analysis with C. psorothamnensis. To characterize the chromosomal complement of C. psorothamnensis and compare it with C. veatchii, we used CMA/DAPI banding, FISH, and GISH. The karyotypes of both species displayed similarity in chromosome number, size, and symmetry, and interphase nucleus organization. Both species exhibited a pair of 5S and 35S rDNA sites adjacent on the same chromosome. The number of 5S rDNA sites in C. psorothamnensis is variable, with some individuals displaying four, five, and six sites. Our results show: 1) the chromosomal pair carrying adjacent 5S and 35S rDNA in C. denticulata is retained in the polyploids; 2) the loss of C. nevadensis rDNA sites occurred in both tetraploids; 3) C. psorothamnensis and C. veatchii are allopolyploids part of a species complex, originated from successive independent hybridization events between C. denticulata and C. nevadensis; and 4) C. psorothamnensis is probably more recent in origin than C. veatchii based on the degree of diploidization. This cytogenetic comparison allows us to understand the processes involved in the emergence of new polyploid species by hybridization. Main ConclusionCuscuta psorothamnensis and C. veatchii form a complex of allopolyploid species originating from independent, successive hybridization events between C. denticulata and C. nevadensis.

plant biology↗

bioRxiv2022

Between fishing and farming: palaeogenomic analyses reveal cross-cultural interactions triggered by the arrival of the Neolithic in the Danube Gorges

While early Neolithic populations in Europe were largely descended from early Aegean farmers, there is also evidence of episodic gene flow from local Mesolithic hunter-gatherers into early Neolithic communities. Exactly how and where this occurred is still unknown. Here we report direct evidence for admixture between the two groups at the Danube Gorges in Serbia. Analysis of palaeogenomes recovered from skeletons revealed that second-generation mixed individuals were buried amidst individuals whose ancestry was either exclusively Aegean Neolithic or exclusively local Mesolithic. The mixed ancestry is also reflected in a corresponding mosaic of grave goods. With its deep sequence of occupation and its unique dwellings that suggest at least semi-sedentary occupation since the late Mesolithic, the area of the Danube Gorges has been at the center of the debate about the contribution of Mesolithic societies to the Neolithisation of Europe. As suggested by our data, which were processed exclusively with uncertainty-aware bioinformatic tools, it may have been precisely in such contexts that close interactions between these societies were established, and Mesolithic ancestry and cultural elements were assimilated.

genomics↗

bioRxiv2021

Karyotype asymmetry in Cuscuta L. subgenus Pachystigma reflects its repeat DNA composition

Cuscuta is a cytogenetically diverse genus, with karyotypes varying 18-fold in chromosome number and 89-fold in genome size. Each of its four subgenera also presents particular chromosomal features, such as bimodal karyotypes in Pachystigma. We used low coverage sequencing of the Cuscuta nitida genome (subgenus Pachystigma), as well as chromosome banding and molecular cytogenetics of three subgenus representatives, to understand the origin of bimodal karyotypes. All three species, C. nitida, C. africana (2n = 28) and C. angulata (2n = 30), showed heterochromatic bands mainly in the largest chromosome pairs. Eighteen satellite DNAs were identified in C. nitida genome, two showing similarity to mobile elements. The most abundant were present at the largest pairs, as well as the highly abundant ribosomal DNAs. The most abundant Ty1/Copia and Ty3/Gypsy elements were also highly enriched in the largest pairs, except for the Ty3/Gypsy CRM, which also labelled the pericentromeric regions of the smallest chromosomes. This accumulation of repetitive DNA in the larger pairs indicates that these sequences are largely responsible for the formation of bimodal karyotypes in the subgenus Pachystigma. The repetitive DNA fraction is directly linked to karyotype evolution in Cuscuta. HighlightsCuscuta subgenus Pachystigma contains species with strikingly bimodal karyotypes. The emergence of these karyotypes is linked to the enrichment of varied repetitive sequences in the largest chromosomal pairs.

plant biology↗

bioRxiv2020

Kinship, acquired and inherited status, and population structure at the Early Bronze Age Mokrin necropolis in northern Serbia.

Twenty-four ancient genomes with an average sequencing coverage of 0.85{+/-}0.25 X were produced from the Mokrin necropolis, an Early Bronze Age (2,100-1,800 BC) Maros culture site in Serbia, to provide unambiguous identification of biological sex, population structure, and genetic kinship between individuals. Of the 24 investigated individuals, 15 were involved in kinship relationships of varying degrees, including 3 parent-offspring relationships. All observed parent-offspring pairs were mother and son. In addition to the absence of biological daughters, we observed a number of young women and girls with no biological relatives in our sample. These observations, together with the high mitochondrial diversity in our sample, are consistent with the practice of female exogamy in the population served by Mokrin. However, moderate-to-high Y-chromosomal diversity suggests a degree of male mobility greater than that expected under strict patrilocality. Individual status differences at Mokrin, as indicated by grave goods, support the inference that females could inherit status, but could not transmit status to all their sons. The case of a son whose grave good richness outstrips that of his biological mother suggests that sons had the possibility to acquire status during their lifetimes. The Mokrin sample resembles a genetically unstructured population, suggesting that the communitys social hierarchies were not accompanied by strict marriage barriers.

genomics↗

bioRxiv2020

Hox-dependent coordination of cardiac progenitor cell patterning and differentiation

Perturbation of addition of second heart field (SHF) cardiac progenitor cells to the poles of the heart tube results in congenital heart defects (CHD). The transcriptional programs and upstream regulatory events operating in different subpopulations of the SHF remain unclear. Here, we profile the transcriptome and chromatin accessibility of anterior and posterior SHF sub-populations at genome-wide levels and demonstrate that Hoxb1 negatively regulates differentiation in the posterior SHF. Spatial mis-expression of Hoxb1 in the anterior SHF results in hypoplastic right ventricle. Activation of Hoxb1 in embryonic stem cells arrests cardiac differentiation, whereas Hoxb1-deficient embryos display premature cardiac differentiation. Moreover, ectopic differentiation in the posterior SHF of embryos lacking both Hoxb1 and its paralog Hoxa1 results in atrioventricular septal defects. Our results show that Hoxb1 plays a key role in patterning cardiac progenitor cells that contribute to both cardiac poles and provide new insights into the pathogenesis of CHD.

developmental biology↗

bioRxiv2018

Ectopic expression of Hoxb1 induces cardiac and craniofacial malformations

Members of the large family of Hox transcription factors are encoded by genes whose tightly regulated expression in development and in space within different embryonic tissues confer positional identity from the neck to the tips of the limbs. Many structures of the face, head and heart develop from cell populations expressing few or no Hox genes. Hoxb1 is the member of its chromosomal cluster expressed in the most rostral domain during vertebrate development, but never by the multipotent neural crest cell population anterior to the cerebellum. We have developed a novel floxed transgenic mouse line, CAG-Hoxb1,-EGFP (CAG-Hoxb1), which upon recombination by Cre recombinase conditionally induces robust Hoxb1 and eGFP over-expression. When induced within the neural crest lineage, pups die at birth. A variable phenotype develops from E11.5 on, associating frontonasal hypoplasia/aplasia, micrognathia/agnathia, major ocular and forebrain anomalies, and cardiovascular malformations. Neural crest derivatives in the body appear unaffected. Transcription of effectors of developmental signaling pathways (Bmp, Shh, Vegfa) and transcription factors (Pax3, Sox9) is altered in mutants. These outcomes emphasize that repression of Hoxb1, along with other paralog group 1 and 2 Hox genes, is strictly necessary in anterior cephalic NC for craniofacial, visual, auditory and cardiovascular development.

developmental biology↗