Biology subjects

Arca, M.

Publications and source records attributed to Arca, M..

5 recordsLinked to original sources

bioRxiv2025

ANGPTL3 binds to PCSK9 to coordinately regulate intracellular lipid homeostasis.

ANGPTL3 and PCSK9 are core proteins involved in lipid metabolism. Literature evidence highlights a potential mutual regulation between them: patients harboring loss-of-function variants in ANGPTL3 show reduced levels of circulating PCSK9. After predicting their interaction using an in-silico model, we verified the direct interaction between ANGPTL3 and PCSK9 through co-immunoprecipitation. The ANGPTL3-PCSK9 complex persisted under fasting conditions and dissociated under feeding conditions. Treatment with human LDLs was sufficient to simulate the feeding response. Then, we observed that the overexpression of PCSK9 enhances the uptake of LDLs that are not further metabolized, while the overexpression of ANGPTL3 enhances LDL turnover. The overexpression of both proteins restored LDL uptake and degradation, which became comparable to those of control cells. In conclusion, our findings indicate the existence of an ANGPTL3-PCSK9 complex, which coordinately contributes to the regulation of intracellular lipid homeostasis, aiming to prevent cellular metabolic overload. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/631413v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1339998org.highwire.dtl.DTLVardef@a8d715org.highwire.dtl.DTLVardef@c0a92aorg.highwire.dtl.DTLVardef@a22ed7_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO Mechanistic model of ANGPTL3-PCSK9 complex function in the regulation of lipoprotein metabolism Increased uptake of extracellular nutrients determines the separation of the ANGPTL3-PCSK9 complex. The two free proteins have different functions (1). Increased levels of PCSK9 determine an increased intracellular entrapment of circulating LDLs (2) that are not catabolized unless there is a presence of high intracellular levels of ANGPTL3. Increased ANGPTL3 levels also favor ApoB lipidation and secretion (3), whereas an increase in intracellular PCSK9 increases intracellular ApoB degradation. The increase in intracellular PCSK9 also determines a block in lipogenesis and favors beta-oxidation, thus decreasing the intracellular lipid content (4). C_FIG

cell biology↗

bioRxiv2021

Genomic analyses of the extinct Sardinian dhole (Cynotherium sardous) reaveal its evolutionary history

The Sardinian dhole (Cynotherium sardous)1 was an iconic and unique canid species of canid that was endemic of Sardinia and Corsica until it became extinct at the end of the Late Pleistocene2-5. Given its peculiar dental morphology, small body size and high level of endemism, several canids have been proposed as possible ancestors of the Sardinian dhole, including the Asian dhole and African hunting dog ancestor 3,6-9. Morphometric analyses3,6,8-12 have failed to clarify the evolutionary relationship with other canids. We sequenced the genome of a ca 21,100 year old Sardinian dhole in order to understand its genomic history and clarify its phylogenetic position. We found it represents a separate taxon from all other living canids from Eurasia, Africa and North America, and that the Sardinian and Asian dhole lineages diverged ca 885 ka. We additionally detected historical gene flow between the Sardinian and Asian dhole lineages, that ended approximately 500-300 ka, when the landbridge between Sardinia and mainland Italy was broken, severing their population connectivity. Our sample showed low genome-wide diversity compared to other extant canids - probably a result of the long-term isolation - that could have contributed to the subsequent extinction of the Sardinian dhole.

genomics↗

bioRxiv2020

Genome-wide SNP genotyping of DNA pools identifies untapped landraces and genomic regions that could enrich the maize breeding pool

Maize landraces preserved in genebanks have a large genetic diversity that is still poorly characterized and underexploited in modern breeding programs. Here, we genotyped DNA pools from 156 American and European landraces with a 50K SNP Illumina array to study the effect of both human selection and environmental adaptation on the genome-wide diversity of maize landraces. Genomic diversity of landraces varied strongly in different parts of the genome and with geographic origin. We detected selective footprints between landraces of different geographic origin in genes involved in the starch pathway (Su1, Waxy1), flowering time (Zcn8, Vgt3, ZmCCT9) and tolerance to abiotic and biotic stress (ZmASR, NAC and dkg genes). Landrace diversity was compared to that of (i) 327 inbred lines representing American and European diversity ("CK lines) and (ii) 103 new lines derived directly from landraces ("DH-SSD lines"). We observed limited diversity loss or selective sweep between landraces and CK lines, except in peri-centromeric regions. However, analysis of modified Rogers distance between landraces and the CK lines showed that most landraces were not closely related to CK lines. Assignment of CK lines to landraces using supervised analysis showed that only a few landraces, such as Reids Yellow Dent, Lancaster Surecrop and Lacaune, strongly contributed to modern European and American breeding pools. Haplotype diversity of CK lines was more enriched by DH-SSD lines that derived from the landraces with no related lines and the lowest contribution to CK lines. Our approach opens an avenue for the identification of promising landraces for pre-breeding. SIGNIFICANCE STATEMENTSMaize landraces are a valuable source of genetic diversity for addressing the challenges of climate change and the requirements of low input agriculture as they have been long selected to be well adapted to local agro-climatic conditions and human uses. However, they are underutilized in modern breeding programs because they are poorly characterized, genetically heterogeneous and exhibit poor agronomic performance compared to elite hybrid material. In this study, we developed a high-throughput approach to identify landraces that could potentially enlarge the genetic diversity of modern breeding pools. We genotyped DNA pools from landraces using 50K array technology, which is widely used by breeders to characterize the genetic diversity of inbred lines. To identify landraces that could enrich the modern maize germplasm, we estimated their contribution to inbred lines using supervised analysis and a new measurement of genetic distance.

genetics↗

bioRxiv2020

Deciphering the genetic diversity of landraces with high-throughput SNP genotyping of DNA bulks: methodology and application to the maize 50k array

Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains however poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on SNP Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Rogers genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 SSRs using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species.

genetics↗

bioRxiv2018

Metabolomic signature of angiopoietin-like protein 3 deficiency in fasting and postprandial state

ObjectiveLoss-of-function variants in the angiopoietin-like 3 gene (ANGPTL3) have been associated with low levels of plasma lipoproteins and decreased coronary artery disease risk. We aimed to determine detailed metabolic effects of genetically-induced ANGPTL3 deficiency in fasting and postprandial state.\n\nApproach and ResultsWe studied individuals carrying S17X loss-of-function mutation in ANGPTL3 (6 homozygous and 32 heterozygous carriers) and 38 noncarriers. Nuclear magnetic resonance metabolomics was used to quantify 225 circulating metabolic measures. We compared metabolic differences between loss-of-function carriers and noncarriers in fasting state and after a high fat meal. In fasting, ANGPTL3 deficiency was characterized by similar extent of reductions in low-density lipoprotein cholesterol (0.74 SD-units lower concentration per loss-of-function allele [95%CI 0.42-1.06]) as observed for many triglyceride-rich lipoprotein measures, including very-low-density lipoprotein cholesterol (0.75 [0.45-1.05]). Within most lipoprotein subclasses, absolute levels of cholesterol were decreased more than triglycerides, resulting in the relative proportion of cholesterol being reduced within triglyceride-rich lipoproteins and their remnants. Further, beta-hydroxybutyrate was elevated (0.55 [0.21-0.89]). Homozygous ANGPTL3 loss-of-function carriers showed essentially no postprandial increase in triglyceride-rich lipoproteins and fatty acids, without evidence for adverse compensatory metabolic effects.\n\nConclusionsIn addition to overall triglyceride and low-density lipoprotein cholesterol lowering effects, ANGPTL3 deficiency results in reduction of cholesterol proportion within triglyceride-rich lipoproteins and their remnants. Further, ANGPTL3 loss-of-function carriers had elevated ketone body production, suggesting enhanced hepatic fatty acid beta-oxidation. The detailed metabolic profile in human knockouts of ANGPTL3 reinforces inactivation of ANGPTL3 as a promising therapeutic target for decreasing cardiovascular risk.\n\nHIGHLIGHTSO_LIANGPTL3 deficiency results in similar reductions in LDL cholesterol and many triglyceride-rich lipoprotein lipids measures, such as VLDL cholesterol, with no evidence of substantial adverse effects on the comprehensive panel of circulating metabolite biomarkers tested here.\nC_LIO_LIIn particular, ANGPTL3 deficiency results in reduction of cholesterol content in triglyceride-rich lipoproteins and their remnants, which have been highlighted as risk factor for cardiovascular disease independently of LDL levels.\nC_LIO_LIHomozygous ANGPTL3 loss-of-function carriers show essentially no postprandial increase in triglyceride-rich lipoproteins and fatty acids in response to a fat challenge, and display consistently elevated postprandial levels of ketone bodies and lactate when compared to noncarriers, suggesting enhanced hepatic fatty acid beta-oxidation.\nC_LI

genetics↗