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Baltazar-Soares M, Karell P, Wright D, Nilsson JÅ, Brommer JE. Genomic basis of melanin-associated phenotypes suggests colour-specific environmental adaptations in tawny owls. Mol Ecol 2024; 33:e17247. [PMID: 38173194 DOI: 10.1111/mec.17247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024]
Abstract
Feathers comprise a series of evolutionary innovations but also harbour colour, a key biological trait known to co-vary with life history or complex traits. Those relationships are particularly true in melanin-based pigmentation species due to known pleiotropic effects of the melanocortin pathway - originating from melanin-associated phenotypes. Here, we explore the molecular basis of melanin colouration and expected co-variation at the molecular level in the melanin-based, colour polymorphic system of the tawny owl (Strix aluco). An extensive body of literature has revealed that grey and brown tawny owl colour morphs differ in a series of life history and behavioural traits. Thus, it is plausible to expect co-variation also at molecular level between colour morphs. To investigate this possibility, we assembled the first draft genome of the species against which we mapped ddRADseq reads from 220 grey and 150 brown morphs - representing 10 years of pedigree data from a population in Southern Finland - and explored genome-wide associations with colour phenotype. Our results revealed putative molecular signatures of cold adaptation strongly associated with the grey phenotype, namely, a non-synonymous substitution in MCHR1, plus 2 substitutions in non-coding regions of FTCD and FAM135A whose genotype combinations obtained a predictive power of up to 100% (predicting grey colour). These suggest a molecular basis of cold environment adaptations predicted to be grey-morph specific. Our results potentially reveal part of the molecular machinery of melanin-associated phenotypes and provide novel insights towards understanding the functional genomics of colour polymorphism in melanin-based pigmented species.
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Affiliation(s)
| | - Patrik Karell
- Department of Biology, Section of Evolutionary Ecology, Lund University, Lund, Sweden
- Department of Ecology and Genetics, University of Uppsala, Uppsala, Sweden
- Department of Bioeconomy, Novia University of Applied Sciences, Ekenäs, Finland
| | | | - Jan-Åke Nilsson
- Department of Biology, Section of Evolutionary Ecology, Lund University, Lund, Sweden
| | - Jon E Brommer
- Department of Biology, University of Turku, Turku, Finland
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Leońska-Duniec A, Borczyk M, Korostyński M, Massidda M, Maculewicz E, Cięszczyk P. Genetic variants in myostatin and its receptors promote elite athlete status. BMC Genomics 2023; 24:761. [PMID: 38082252 PMCID: PMC10712039 DOI: 10.1186/s12864-023-09869-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND While product of the myostatin gene (MSTN) is an important factor influencing muscle growth, which is well confirmed in nonhuman species, it has not been clearly confirmed whether MSTN expression influences interindividual differences in skeletal muscle mass, affects posttraining changes, or plays a role in the age-related loss of muscle mass and function in humans. Although the inconclusive results are usually explained by ethnic differences and the low frequency of some alleles, it is possible that the role of receptors (ACVR2A and ACVR2B) that affect the biological activity of myostatin is crucial. Therefore, we investigated the sequences of the MSTN, ACVR2A, and ACVR2B genes and determined the interaction between allelic variants and athletic performance and competition level in the Caucasian population. One hundred-two athletes were recruited for the sequencing study, and whole-genome sequencing (WGS) was performed. Second, 330 athletes and 365 controls were included, and real-time PCR was performed. RESULTS The sequence analysis revealed two polymorphisms relatively common in the athlete cohort, and the alternate allele showed overrepresentation in athletes: MSTN rs11333758 and ACVR2A rs3764955. Regarding the polymorphic site MSTN rs11333758, there was a significant overrepresentation of the -/- genotype in all high-elite and mixed-sport high-elite athletes. Carriers of the ACVR2A rs3764955 CC and GG genotypes were more likely to be elite and high-elite athletes. In addition, carriers of the CC genotype were more likely to be in the mixed-sport subelite group. The gene‒gene interaction analysis revealed that mixed-sport high elite athletes showed significant underrepresentation of the ACVR2A rs3764955 GC - MSTN rs11333758 AA genotype combination. In the same group, we observed a significant overrepresentation of the ACVR2A rs3764955 GC - MSTN rs11333758 -/- and the ACVR2A rs3764955 CC - MSTN rs11333758 -/- genotype combinations. CONCLUSIONS We showed that the specific genotypes of the MSTN rs11333758 and ACVR2A rs3764955, either individually or in gene‒gene combination, are significantly associated with athletes' competition level in the Polish population, especially in the mixed-sports athlete group. Thus, although further research is required, these polymorphisms, alone or in combination with other polymorphisms, are among the numerous candidates that could explain individual variations in muscle phenotypes.
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Affiliation(s)
- Agata Leońska-Duniec
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, Gdansk, 80-336, Poland
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, 09124, Italy
| | - Małgorzata Borczyk
- Laboratory of Pharmacogenomics, Department of Molecular Neuropharmacology, Maj Institute of Pharmacology, Polish Academy of Sciences, Cracow, 31-343, Poland
| | - Michał Korostyński
- Laboratory of Pharmacogenomics, Department of Molecular Neuropharmacology, Maj Institute of Pharmacology, Polish Academy of Sciences, Cracow, 31-343, Poland
| | - Myosotis Massidda
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, 09124, Italy
| | - Ewelina Maculewicz
- Faculty of Physical Education, Jozef Pilsudski University of Physical Education in Warsaw, Warsaw, 00-809, Poland.
| | - Paweł Cięszczyk
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, Gdansk, 80-336, Poland
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Evaluating the detection ability of a range of epistasis detection methods on simulated data for pure and impure epistatic models. PLoS One 2022; 17:e0263390. [PMID: 35180244 PMCID: PMC8856572 DOI: 10.1371/journal.pone.0263390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/18/2022] [Indexed: 11/19/2022] Open
Abstract
Background Numerous approaches have been proposed for the detection of epistatic interactions within GWAS datasets in order to better understand the drivers of disease and genetics. Methods A selection of state-of-the-art approaches were assessed. These included the statistical tests, fast-epistasis, BOOST, logistic regression and wtest; swarm intelligence methods, namely AntEpiSeeker, epiACO and CINOEDV; and data mining approaches, including MDR, GSS, SNPRuler and MPI3SNP. Data were simulated to provide randomly generated models with no individual main effects at different heritabilities (pure epistasis) as well as models based on penetrance tables with some main effects (impure epistasis). Detection of both two and three locus interactions were assessed across a total of 1,560 simulated datasets. The different methods were also applied to a section of the UK biobank cohort for Atrial Fibrillation. Results For pure, two locus interactions, PLINK’s implementation of BOOST recovered the highest number of correct interactions, with 53.9% and significantly better performing than the other methods (p = 4.52e − 36). For impure two locus interactions, MDR exhibited the best performance, recovering 62.2% of the most significant impure epistatic interactions (p = 6.31e − 90 for all but one test). The assessment of three locus interaction prediction revealed that wtest recovered the highest number (17.2%) of pure epistatic interactions(p = 8.49e − 14). wtest also recovered the highest number of three locus impure epistatic interactions (p = 6.76e − 48) while AntEpiSeeker ranked as the most significant the highest number of such interactions (40.5%). Finally, when applied to a real dataset for Atrial Fibrillation, most notably finding an interaction between SYNE2 and DTNB.
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Strafella C, Caputo V, Termine A, Assogna F, Pellicano C, Pontieri FE, Macchiusi L, Minozzi G, Gambardella S, Centonze D, Bossù P, Spalletta G, Caltagirone C, Giardina E, Cascella R. Immune System and Neuroinflammation in Idiopathic Parkinson's Disease: Association Analysis of Genetic Variants and miRNAs Interactions. Front Genet 2021; 12:651971. [PMID: 34149802 PMCID: PMC8209518 DOI: 10.3389/fgene.2021.651971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
The present study investigated the association of SNPs involved in the regulation of immune response, cellular degenerative and neuroinflammatory pathways with the susceptibility and progression of idiopathic Parkinson's Disease (PD). In particular, 342 PD patients were subjected to a genotyping analysis of a panel of 120 SNPs by Open Array Technology. As control group, 503 samples representative of the European general population were utilized. The genetic analysis identified 26 SNPs associated with PD susceptibility. Of them, 12 SNPs were described as significant expression Quantitative Loci (eQTL) variants in different brain regions associated with motor and non-motor PD phenomenology. Moreover, the study highlighted 11 novel susceptibility genes for PD, which may alter multiple signaling pathways critically involved in peripheral immune response, neuroinflammation, neurodegeneration and dopaminergic neurons wiring. The study of miRNA-target genes highlighted a possible role of miR-499a, miR-196a2, and miR-29a in the modulation of multiple neuroinflammatory and neurodegenerative mechanisms underlying PD physiopathology. The study described a network of interconnected genes (APOE, CLU, IL6, IL7R, IL12B, INPP5D, MAPK1, MEF2C, MIF, and TNFSF14), which may act as upstream regulators in the modulation of biological pathways relevant to PD. Intriguingly, IL6 stands out as a master gene regulator since it may indirectly regulate the network of interconnected genes. The study highlighted different genes and miRNAs interactions potentially involved in PD physiopathology, which are worth to be further explored to improve the knowledge of disease and the research of novel treatments strategies.
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Affiliation(s)
- Claudia Strafella
- Genomic Medicine Laboratory, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Valerio Caputo
- Genomic Medicine Laboratory, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Andrea Termine
- Genomic Medicine Laboratory, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Francesca Assogna
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Clelia Pellicano
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Francesco E. Pontieri
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
- Department of Neuroscience, Mental Health and Sensory Organs, “Sapienza” Università di Roma, Rome, Italy
| | - Lucia Macchiusi
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Giulietta Minozzi
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Stefano Gambardella
- Neuromed Institute IRCCS, Pozzilli, Italy
- Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, Urbino, Italy
| | | | - Paola Bossù
- Laboratory of Experimental Neuropsychobiology, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Gianfranco Spalletta
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Carlo Caltagirone
- Department of Clinical and Behavioral Neurology, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Raffaella Cascella
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
- Department of Biomedical Sciences, Catholic University Our Lady of Good Counsel, Tirana, Albania
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Strafella C, Caputo V, Termine A, Fabrizio C, Ruffo P, Potenza S, Cusumano A, Ricci F, Caltagirone C, Giardina E, Cascella R. Genetic Determinants Highlight the Existence of Shared Etiopathogenetic Mechanisms Characterizing Age-Related Macular Degeneration and Neurodegenerative Disorders. Front Neurol 2021; 12:626066. [PMID: 34135841 PMCID: PMC8200556 DOI: 10.3389/fneur.2021.626066] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 04/20/2021] [Indexed: 01/03/2023] Open
Abstract
Age-related macular degeneration (AMD) showed several processes and risk factors in common with neurodegenerative disorders (NDDs). The present work explored the existence of genetic determinants associated with AMD, which may provide insightful clues concerning its relationship with NDDs and their possible application into the clinical practice. In this study, 400 AMD patients were subjected to the genotyping analysis of 120 genetic variants by OpenArray technology. As the reference group, 503 samples representative of the European general population were utilized. Statistical analysis revealed the association of 23 single-nucleotide polymorphisms (SNPs) with AMD risk. The analysis of epistatic effects revealed that ARMS2, IL6, APOE, and IL2RA could contribute to AMD and neurodegenerative processes by synergistic modulation of the expression of disease-relevant genes. In addition, the bioinformatic analysis of the associated miRNA variants highlighted miR-196a, miR-6796, miR-6499, miR-6810, miR-499, and miR-7854 as potential candidates for counteracting AMD and neurodegenerative processes. Finally, this work highlighted the existence of shared disease mechanisms (oxidative stress, immune-inflammatory response, mitochondrial dysfunction, axonal guidance pathway, and synaptogenesis) between AMD and NDDs and described the associated SNPs as candidate biomarkers for developing novel strategies for early diagnosis, monitoring, and treatment of such disorders in a progressive aging population.
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Affiliation(s)
- Claudia Strafella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy.,Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Valerio Caputo
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy.,Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Andrea Termine
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Carlo Fabrizio
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Paola Ruffo
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Saverio Potenza
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Andrea Cusumano
- UOSD of Ophthalmology PTV Foundation "Policlinico Tor Vergata", Rome, Italy
| | - Federico Ricci
- UNIT Retinal Diseases PTV Foundation "Policlinico Tor Vergata", Rome, Italy
| | - Carlo Caltagirone
- Department of Clinical and Behavioral Neurology, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy.,Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Raffaella Cascella
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy.,Department of Biomedical Sciences, Catholic University Our Lady of Good Counsel, Tirana, Albania
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Yashin AI, Wu D, Arbeev K, Yashkin AP, Akushevich I, Bagley O, Duan M, Ukraintseva S. Roles of interacting stress-related genes in lifespan regulation: insights for translating experimental findings to humans. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2021; 5:357-379. [PMID: 34825130 PMCID: PMC8612394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
AIM Experimental studies provided numerous evidence that caloric/dietary restriction may improve health and increase the lifespan of laboratory animals, and that the interplay among molecules that sense cellular stress signals and those regulating cell survival can play a crucial role in cell response to nutritional stressors. However, it is unclear whether the interplay among corresponding genes also plays a role in human health and lifespan. METHODS Literature about roles of cellular stressors have been reviewed, such as amino acid deprivation, and the integrated stress response (ISR) pathway in health and aging. Single nucleotide polymorphisms (SNPs) in two candidate genes (GCN2/EIF2AK4 and CHOP/DDIT3) that are closely involved in the cellular stress response to amino acid starvation, have been selected using information from experimental studies. Associations of these SNPs and their interactions with human survival in the Health and Retirement Study data have been estimated. The impact of collective associations of multiple interacting SNP pairs on survival has been evaluated, using a recently developed composite index: the SNP-specific Interaction Polygenic Risk Score (SIPRS). RESULTS Significant interactions have been found between SNPs from GCN2/EIF2AK4 and CHOP/DDI3T genes that were associated with survival 85+ compared to survival between ages 75 and 85 in the total sample (males and females combined) and in females only. This may reflect sex differences in genetic regulation of the human lifespan. Highly statistically significant associations of SIPRS [constructed for the rs16970024 (GCN2/EIF2AK4) and rs697221 (CHOP/DDIT3)] with survival in both sexes also been found in this study. CONCLUSION Identifying associations of the genetic interactions with human survival is an important step in translating the knowledge from experimental to human aging research. Significant associations of multiple SNPxSNP interactions in ISR genes with survival to the oldest old age that have been found in this study, can help uncover mechanisms of multifactorial regulation of human lifespan and its heterogeneity.
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