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Riego ML, Meher PK, Brzozowska B, Akuwudike P, Bucher M, Oestreicher U, Lundholm L, Wojcik A. Chromosomal damage, gene expression and alternative transcription in human lymphocytes exposed to mixed ionizing radiation as encountered in space. Sci Rep 2024; 14:11502. [PMID: 38769353 PMCID: PMC11106305 DOI: 10.1038/s41598-024-62313-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 05/15/2024] [Indexed: 05/22/2024] Open
Abstract
Astronauts travelling in space will be exposed to mixed beams of particle radiation and photons. Exposure limits that correspond to defined cancer risk are calculated by multiplying absorbed doses by a radiation-type specific quality factor that reflects the biological effectiveness of the particle without considering possible interaction with photons. We have shown previously that alpha radiation and X-rays may interact resulting in synergistic DNA damage responses in human peripheral blood lymphocytes but the level of intra-individual variability was high. In order to assess the variability and validate the synergism, blood from two male donors was drawn at 9 time points during 3 seasons of the year and exposed to 0-2 Gy of X-rays, alpha particles or 1:1 mixture of both (half the dose each). DNA damage response was quantified by chromosomal aberrations and by mRNA levels of 3 radiation-responsive genes FDXR, CDKN1A and MDM2 measured 24 h post exposure. The quality of response in terms of differential expression of alternative transcripts was assessed by using two primer pairs per gene. A consistently higher than expected effect of mixed beams was found in both donors for chromosomal aberrations and gene expression with some seasonal variability for the latter. No synergy was detected for alternative transcription.
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Affiliation(s)
- Milagrosa López Riego
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
| | - Prabodha Kumar Meher
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
| | - Beata Brzozowska
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Pamela Akuwudike
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
| | - Martin Bucher
- Federal Office for Radiation Protection, Oberschleissheim, Germany
| | | | - Lovisa Lundholm
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
| | - Andrzej Wojcik
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden.
- Institute of Biology, Jan Kochanowski University, Kielce, Poland.
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Jose A, Sukumaran S, Roul SK, Azeez PA, Kizhakudan SJ, Raj N, Nisha K, Gopalakrishnan A. Genetic analyses reveal panmixia in Indian waters and population subdivision across Indian Ocean and Indo-Malay Archipelago for Decapterus russelli. Sci Rep 2023; 13:22860. [PMID: 38129501 PMCID: PMC10739887 DOI: 10.1038/s41598-023-49805-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
The Indian Scad, Decapterus russelli is an important pelagic carangid widely distributed throughout the Indian Ocean and the Indo-West Pacific. Despite being widely distributed in the Indian Ocean, the information regarding genetic structuring and diversity has been lacking compared to its Indo Malay Archipelago counterparts. The present study was conducted to investigate the genetic stock structure of D. russelli based on mitochondrial (Cyt b) and nuclear (DrAldoB1) markers along Indian waters. The results indicated the presence of a single panmictic stock across the Indian Ocean region. High haplotype diversity associated with low nucleotide diversity suggested a population bottleneck followed by rapid population growth. Phylogenetic analysis revealed the absence of geographical clustering of lineages with the most common haplotype distributed globally. The pelagic life style, migratory capabilities, and larval dispersal may be the contributing factors to the observed spatial homogeneity of D. russelli. However, significant genetic differentiation was observed between the populations from Indian Ocean and Indo-Malay Archipelago. Hierarchical molecular variance analysis (AMOVA), pairwise FST comparisons and SAMOVA showed existence of two distinct genetic stocks of D. russelli in the Indian Ocean and IMA. The observed interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the Indo-Malay Archipelago and the Indian Ocean regions suggest the influence of historic isolation, ocean surface currents and biotic and abiotic features of the ocean. Also, there was a significant relationship between genetic distance and geographical distance between population pairs in a manner consistent with isolation-by-distance. These resulted in the evolution of a phylogeographic break for this species between these regions. The findings of these results suggest that D. russelli from the Indian Ocean shall be managed in its entire area of distribution as a single stock. Further, the Indian Ocean and Indo-Malayan stocks can be managed separately.
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Affiliation(s)
- Anjaly Jose
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India.
- Mangalore University, Mangalagangotri, Mangalore, Karnataka, 574199, India.
| | - Sandhya Sukumaran
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - Subal Kumar Roul
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - P Abdul Azeez
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - Shoba Joe Kizhakudan
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - Neenu Raj
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - K Nisha
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - A Gopalakrishnan
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
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Liu P, Li J, Tang L, Cong W, Jin H, Zhang H, Cui B, Yang S, Xiao J, Liu C, Saiyin W. Mutations of family with sequence similarity 20-member C gene causing lethal and nonlethal Raine syndrome causes hypophosphatemia rickets. J Cell Physiol 2023; 238:2556-2569. [PMID: 37698039 DOI: 10.1002/jcp.31105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 09/13/2023]
Abstract
Family with sequence similarity 20-member C (FAM20C) is a kinase specific to most of the secreted phosphoproteome. FAM20C has been identified as the causative gene of Raine syndrome, initially characterized by lethal osteosclerosis bone dysplasia. However, since the identification of the cases of nonlethal Raine syndrome characterized by hypophosphatemia rickets, the previous definition of Raine syndrome has become debatable and raised a question about the role of mutations of FAM20C in controversial skeletal manifestation in the two forms of the disease. In this study, we aimed to investigate the influence of FAM20C mutations on skeletogenesis. We developed transgenic mice expressing Fam20c mutations mimicking those associated with human lethal and nonlethal Raine syndrome. The results revealed that transgenic mice expressing the mutant Fam20c found in the lethal (KO;G374R) and nonlethal (KO;D446N) Raine syndrome exhibited osteomalacia without osteosclerotic features. Additionally, both mutants significantly increased the expression of the Fgf23, indicating that Fam20c deficiency in skeletal compartments causes hypophosphatemia rickets. Furthermore, as FAM20C kinase activity catalyzes the phosphorylation of secreted proteomes other than those in the skeletal system, global FAM20C deficiency may trigger alterations in other systems resulting in osteosclerosis secondary to hypophosphatemia rickets. Together, the findings of this study suggest that FAM20C deficiency primarily causes hypophosphatemia rickets or osteomalacia; however, the heterogeneous skeletal manifestation in Raine syndrome was not determined solely by specific mutations of FAM20C. The findings also implicated that rickets or osteomalacia caused by FAM20C deficiency would deteriorate into osteosclerosis by the defects from other systems or environmental impacts.
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Affiliation(s)
- Peihong Liu
- Department of Stomatology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Laboratory of Longjiang Scholar, The First Affifiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiaxuan Li
- Department of Stomatology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Linghao Tang
- Department of Otorhinolaryngology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Wei Cong
- Department of Oral Pathology, School of Stomatology, Dalian Medical University, Dalian, China
| | - Han Jin
- Heilongjiang Provincial Key Laboratory of Hard Tissue Development and Regeneration, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hong Zhang
- Department of Stomatology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bing Cui
- Department of Stomatology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shan Yang
- Department of Stomatology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jing Xiao
- Department of Oral Pathology, School of Stomatology, Dalian Medical University, Dalian, China
| | - Chao Liu
- Department of Oral Pathology, School of Stomatology, Dalian Medical University, Dalian, China
| | - Wuliji Saiyin
- Department of Stomatology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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Metabolic Phenotyping of Marine Heterotrophs on Refactored Media Reveals Diverse Metabolic Adaptations and Lifestyle Strategies. mSystems 2022; 7:e0007022. [PMID: 35856685 PMCID: PMC9426600 DOI: 10.1128/msystems.00070-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial communities, through their metabolism, drive carbon cycling in marine environments. These complex communities are composed of many different microorganisms including heterotrophic bacteria, each with its own nutritional needs and metabolic capabilities. Yet, models of ecosystem processes typically treat heterotrophic bacteria as a “black box,” which does not resolve metabolic heterogeneity nor address ecologically important processes such as the successive modification of different types of organic matter. Here we directly address the heterogeneity of metabolism by characterizing the carbon source utilization preferences of 63 heterotrophic bacteria representative of several major marine clades. By systematically growing these bacteria on 10 media containing specific subsets of carbon sources found in marine biomass, we obtained a phenotypic fingerprint that we used to explore the relationship between metabolic preferences and phylogenetic or genomic features. At the class level, these bacteria display broadly conserved patterns of preference for different carbon sources. Despite these broad taxonomic trends, growth profiles correlate poorly with phylogenetic distance or genome-wide gene content. However, metabolic preferences are strongly predicted by a handful of key enzymes that preferentially belong to a few enriched metabolic pathways, such as those involved in glyoxylate metabolism and biofilm formation. We find that enriched pathways point to enzymes directly involved in the metabolism of the corresponding carbon source and suggest potential associations between metabolic preferences and other ecologically relevant traits. The availability of systematic phenotypes across multiple synthetic media constitutes a valuable resource for future quantitative modeling efforts and systematic studies of interspecies interactions. IMPORTANCE Half of the Earth’s annual primary production is carried out by phytoplankton in the surface ocean. However, this metabolic activity is heavily impacted by heterotrophic bacteria, which dominate the transformation of organic matter released from phytoplankton. Here, we characterize the diversity of metabolic preferences across many representative heterotrophs by systematically growing them on different fractions of dissolved organic carbon. Our analysis suggests that different clades of bacteria have substantially distinct preferences for specific carbon sources, in a way that cannot be simply mapped onto phylogeny. These preferences are associated with the presence of specific genes and pathways, reflecting an association between metabolic capabilities and ecological lifestyles. In addition to helping understand the importance of heterotrophs under different conditions, the phenotypic fingerprint we obtained can help build higher resolution quantitative models of global microbial activity and biogeochemical cycles in the oceans.
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Mukherjee K, LaConte LEW, Srivastava S. The Non-Linear Path from Gene Dysfunction to Genetic Disease: Lessons from the MICPCH Mouse Model. Cells 2022; 11:1131. [PMID: 35406695 PMCID: PMC8997851 DOI: 10.3390/cells11071131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/09/2022] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
Most human disease manifests as a result of tissue pathology, due to an underlying disease process (pathogenesis), rather than the acute loss of specific molecular function(s). Successful therapeutic strategies thus may either target the correction of a specific molecular function or halt the disease process. For the vast majority of brain diseases, clear etiologic and pathogenic mechanisms are still elusive, impeding the discovery or design of effective disease-modifying drugs. The development of valid animal models and their proper characterization is thus critical for uncovering the molecular basis of the underlying pathobiological processes of brain disorders. MICPCH (microcephaly and pontocerebellar hypoplasia) is a monogenic condition that results from variants of an X-linked gene, CASK (calcium/calmodulin-dependent serine protein kinase). CASK variants are associated with a wide range of clinical presentations, from lethality and epileptic encephalopathies to intellectual disabilities, microcephaly, and autistic traits. We have examined CASK loss-of-function mutations in model organisms to simultaneously understand the pathogenesis of MICPCH and the molecular function/s of CASK. Our studies point to a highly complex relationship between the potential molecular function/s of CASK and the phenotypes observed in model organisms and humans. Here we discuss the implications of our observations from the pathogenesis of MICPCH as a cautionary narrative against oversimplifying molecular interpretations of data obtained from genetically modified animal models of human diseases.
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Affiliation(s)
- Konark Mukherjee
- Fralin Biomedical Research Institute at VTC, Roanoke, VA 24016, USA; (L.E.W.L.); (S.S.)
- Department of Psychiatry, Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA
| | - Leslie E. W. LaConte
- Fralin Biomedical Research Institute at VTC, Roanoke, VA 24016, USA; (L.E.W.L.); (S.S.)
- Department of Basic Science Education, Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA
| | - Sarika Srivastava
- Fralin Biomedical Research Institute at VTC, Roanoke, VA 24016, USA; (L.E.W.L.); (S.S.)
- Department of Internal Medicine, Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA
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Ali A, Almesmari FSA, Dhahouri NA, Saleh Ali AM, Aldhanhani MAAMA, Vijayan R, Al Tenaiji A, Al Shamsi A, Hertecant J, Al Jasmi F. Clinical, Biochemical, and Genetic Heterogeneity in Glutaric Aciduria Type II Patients. Genes (Basel) 2021; 12:1334. [PMID: 34573316 PMCID: PMC8466204 DOI: 10.3390/genes12091334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/19/2021] [Accepted: 08/25/2021] [Indexed: 12/03/2022] Open
Abstract
The variants of electron transfer flavoprotein (ETFA, ETFB) and ETF dehydrogenase (ETFDH) are the leading cause of glutaric aciduria type II (GA-II). In this study, we identified 13 patients harboring six variants of two genes associated with GA-II. Out of the six variants, four were missense, and two were frameshift mutations. A missense variant (ETFDH:p.Gln269His) was observed in a homozygous state in nine patients. Among nine patients, three had experienced metabolic crises with recurrent vomiting, abdominal pain, and nausea. In one patient with persistent metabolic acidosis, hypoglycemia, and a high anion gap, the ETFDH:p.Gly472Arg, and ETFB:p.Pro94Thrfs*8 variants were identified in a homozygous, and heterozygous state, respectively. A missense variant ETFDH:p.Ser442Leu was detected in a homozygous state in one patient with metabolic acidosis, hypoglycemia, hyperammonemia and liver dysfunction. The ETFDH:p.Arg41Leu, and ETFB:p.Ile346Phefs*19 variants were observed in a homozygous state in one patient each. Both these variants have not been reported so far. In silico approaches were used to evaluate the pathogenicity and structural changes linked with these six variants. Overall, the results indicate the importance of a newborn screening program and genetic investigations for patients with GA-II. Moreover, careful interpretation and correlation of variants of uncertain significance with clinical and biochemical findings are needed to confirm the pathogenicity of such variants.
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Affiliation(s)
- Amanat Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (A.A.); (F.S.A.A.); (N.A.D.); (A.M.S.A.); (M.A.A.M.A.A.)
| | - Fatmah Saeed Ali Almesmari
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (A.A.); (F.S.A.A.); (N.A.D.); (A.M.S.A.); (M.A.A.M.A.A.)
| | - Nahid Al Dhahouri
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (A.A.); (F.S.A.A.); (N.A.D.); (A.M.S.A.); (M.A.A.M.A.A.)
| | - Arwa Mohammad Saleh Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (A.A.); (F.S.A.A.); (N.A.D.); (A.M.S.A.); (M.A.A.M.A.A.)
| | - Mohammed Ahmed Ali Mohamed Ahmed Aldhanhani
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (A.A.); (F.S.A.A.); (N.A.D.); (A.M.S.A.); (M.A.A.M.A.A.)
| | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates;
| | - Amal Al Tenaiji
- Department of Pediatrics, Sheikh Khalifa Medical City, Abu Dhabi P.O. Box 51900, United Arab Emirates;
| | - Aisha Al Shamsi
- Department of Pediatrics, Tawam Hospital, Al Ain P.O. Box 15551, United Arab Emirates; (A.A.S.); (J.H.)
| | - Jozef Hertecant
- Department of Pediatrics, Tawam Hospital, Al Ain P.O. Box 15551, United Arab Emirates; (A.A.S.); (J.H.)
| | - Fatma Al Jasmi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (A.A.); (F.S.A.A.); (N.A.D.); (A.M.S.A.); (M.A.A.M.A.A.)
- Department of Pediatrics, Tawam Hospital, Al Ain P.O. Box 15551, United Arab Emirates; (A.A.S.); (J.H.)
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Developmental Dyslexia: Environment Matters. Brain Sci 2021; 11:brainsci11060782. [PMID: 34199166 PMCID: PMC8231524 DOI: 10.3390/brainsci11060782] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/15/2022] Open
Abstract
Developmental dyslexia (DD) is a multifactorial, specific learning disorder. Susceptibility genes have been identified, but there is growing evidence that environmental factors, and especially stress, may act as triggering factors that determine an individual's risk of developing DD. In DD, as in most complex phenotypes, the presence of a genetic mutation fails to explain the broad phenotypic spectrum observed. Early life stress has been repeatedly associated with the risk of multifactorial disorders, due to its effects on chromatin regulation, gene expression, HPA axis function and its long-term effects on the systemic stress response. Based on recent evidence, we discuss the potential role of stress on DD occurrence, its putative epigenetic effects on the HPA axis of affected individuals, as well as the necessity of early and appropriate intervention, based on the individual stress-associated (endo)phenotype.
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Froehlich JJ, Uyar B, Herzog M, Theil K, Glažar P, Akalin A, Rajewsky N. Parallel genetics of regulatory sequences using scalable genome editing in vivo. Cell Rep 2021; 35:108988. [PMID: 33852857 DOI: 10.1016/j.celrep.2021.108988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/13/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022] Open
Abstract
How regulatory sequences control gene expression is fundamental for explaining phenotypes in health and disease. Regulatory elements must ultimately be understood within their genomic environment and development- or tissue-specific contexts. Because this is technically challenging, few regulatory elements have been characterized in vivo. Here, we use inducible Cas9 and multiplexed guide RNAs to create hundreds of mutations in enhancers/promoters and 3' UTRs of 16 genes in C. elegans. Our software crispr-DART analyzes indel mutations in targeted DNA sequencing. We quantify the impact of mutations on expression and fitness by targeted RNA sequencing and DNA sampling. When applying our approach to the lin-41 3' UTR, generating hundreds of mutants, we find that the two adjacent binding sites for the miRNA let-7 can regulate lin-41 expression independently of each other. Finally, we map regulatory genotypes to phenotypic traits for several genes. Our approach enables parallel analysis of regulatory sequences directly in animals.
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Affiliation(s)
- Jonathan J Froehlich
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Bora Uyar
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Margareta Herzog
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Kathrin Theil
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Petar Glažar
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany.
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Gualtieri CT. Genomic Variation, Evolvability, and the Paradox of Mental Illness. Front Psychiatry 2021; 11:593233. [PMID: 33551865 PMCID: PMC7859268 DOI: 10.3389/fpsyt.2020.593233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
Twentieth-century genetics was hard put to explain the irregular behavior of neuropsychiatric disorders. Autism and schizophrenia defy a principle of natural selection; they are highly heritable but associated with low reproductive success. Nevertheless, they persist. The genetic origins of such conditions are confounded by the problem of variable expression, that is, when a given genetic aberration can lead to any one of several distinct disorders. Also, autism and schizophrenia occur on a spectrum of severity, from mild and subclinical cases to the overt and disabling. Such irregularities reflect the problem of missing heritability; although hundreds of genes may be associated with autism or schizophrenia, together they account for only a small proportion of cases. Techniques for higher resolution, genomewide analysis have begun to illuminate the irregular and unpredictable behavior of the human genome. Thus, the origins of neuropsychiatric disorders in particular and complex disease in general have been illuminated. The human genome is characterized by a high degree of structural and behavioral variability: DNA content variation, epistasis, stochasticity in gene expression, and epigenetic changes. These elements have grown more complex as evolution scaled the phylogenetic tree. They are especially pertinent to brain development and function. Genomic variability is a window on the origins of complex disease, neuropsychiatric disorders, and neurodevelopmental disorders in particular. Genomic variability, as it happens, is also the fuel of evolvability. The genomic events that presided over the evolution of the primate and hominid lineages are over-represented in patients with autism and schizophrenia, as well as intellectual disability and epilepsy. That the special qualities of the human genome that drove evolution might, in some way, contribute to neuropsychiatric disorders is a matter of no little interest.
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Wu C, Sirard MA. Parental Effects on Epigenetic Programming in Gametes and Embryos of Dairy Cows. Front Genet 2020; 11:557846. [PMID: 33173533 PMCID: PMC7591718 DOI: 10.3389/fgene.2020.557846] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022] Open
Abstract
The bovine represents an important agriculture species and dairy breeds have experienced intense genetic selection over the last decades. The selection of breeders focused initially on milk production, but now includes feed efficiency, health, and fertility, although these traits show lower heritability. The non-genetic paternal and maternal effects on the next generation represent a new research topic that is part of epigenetics. The evidence for embryo programming from both parents is increasing. Both oocytes and spermatozoa carry methylation marks, histones modifications, small RNAs, and chromatin state variations. These epigenetic modifications may remain active in the early zygote and influence the embryonic period and beyond. In this paper, we review parental non-genetic effects retained in gametes on early embryo development of dairy cows, with emphasis on parental age (around puberty), the metabolism of the mother at the time of conception and in vitro culture (IVC) conditions. In our recent findings, transcriptomic signatures and DNA methylation patterns of blastocysts and gametes originating from various parental and IVC conditions revealed surprisingly similar results. Embryos from all these experiments displayed a metabolic signature that could be described as an "economy" mode where protein synthesis is reduced, mitochondria are considered less functional. In the absence of any significant phenotype, these results indicated a possible similar adaptation of the embryo to younger parental age, post-partum metabolic status and IVC conditions mediated by epigenetic factors.
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Affiliation(s)
| | - Marc-André Sirard
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Québec City, QC, Canada
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11
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Applegate KE, Rühm W, Wojcik A, Bourguignon M, Brenner A, Hamasaki K, Imai T, Imaizumi M, Imaoka T, Kakinuma S, Kamada T, Nishimura N, Okonogi N, Ozasa K, Rübe CE, Sadakane A, Sakata R, Shimada Y, Yoshida K, Bouffler S. Individual response of humans to ionising radiation: governing factors and importance for radiological protection. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2020; 59:185-209. [PMID: 32146555 DOI: 10.1007/s00411-020-00837-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/26/2020] [Indexed: 05/23/2023]
Abstract
Tissue reactions and stochastic effects after exposure to ionising radiation are variable between individuals but the factors and mechanisms governing individual responses are not well understood. Individual responses can be measured at different levels of biological organization and using different endpoints following varying doses of radiation, including: cancers, non-cancer diseases and mortality in the whole organism; normal tissue reactions after exposures; and, cellular endpoints such as chromosomal damage and molecular alterations. There is no doubt that many factors influence the responses of people to radiation to different degrees. In addition to the obvious general factors of radiation quality, dose, dose rate and the tissue (sub)volume irradiated, recognized and potential determining factors include age, sex, life style (e.g., smoking, diet, possibly body mass index), environmental factors, genetics and epigenetics, stochastic distribution of cellular events, and systemic comorbidities such as diabetes or viral infections. Genetic factors are commonly thought to be a substantial contributor to individual response to radiation. Apart from a small number of rare monogenic diseases such as ataxia telangiectasia, the inheritance of an abnormally responsive phenotype among a population of healthy individuals does not follow a classical Mendelian inheritance pattern. Rather it is considered to be a multi-factorial, complex trait.
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Affiliation(s)
| | - W Rühm
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Radiation Medicine, Neuherberg, Germany
| | - A Wojcik
- Centre for Radiation Protection Research, MBW Department, Stockholm University, Stockholm, Sweden
| | - M Bourguignon
- Department of Biophysics and Nuclear Medicine, University of Paris Saclay (UVSQ), Verseilles, France
| | - A Brenner
- Department of Epidemiology, Radiation Effects Research Foundation, Hiroshima, Japan
| | - K Hamasaki
- Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima, Japan
| | - T Imai
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Sciences and Technology, Chiba, Japan
| | - M Imaizumi
- Department of Nagasaki Clinical Studies, Radiation Effects Research Foundation, Nagasaki, Japan
| | - T Imaoka
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institute for Quantum and Radiological Science and Technology, Chiba, Japan
| | - S Kakinuma
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institute for Quantum and Radiological Science and Technology, Chiba, Japan
| | - T Kamada
- QST Hospital, National Institute of Radiological Sciences, National Institute for Quantum and Radiological Science and Technology, Chiba, Japan
| | - N Nishimura
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institute for Quantum and Radiological Science and Technology, Chiba, Japan
| | - N Okonogi
- QST Hospital, National Institute of Radiological Sciences, National Institute for Quantum and Radiological Science and Technology, Chiba, Japan
| | - K Ozasa
- Department of Epidemiology, Radiation Effects Research Foundation, Hiroshima, Japan
| | - C E Rübe
- Department of Radiation Oncology, Saarland University Medical Center, Homburg/Saar, Germany
| | - A Sadakane
- Department of Epidemiology, Radiation Effects Research Foundation, Hiroshima, Japan
| | - R Sakata
- Department of Epidemiology, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Y Shimada
- National Institute for Quantum and Radiological Science and Technology, Chiba, Japan
- Institute for Environmental Sciences, Aomori, Japan
| | - K Yoshida
- Immunology Laboratory, Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima, Japan
| | - S Bouffler
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilto, Didcot, UK
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12
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Averbeck D, Candéias S, Chandna S, Foray N, Friedl AA, Haghdoost S, Jeggo PA, Lumniczky K, Paris F, Quintens R, Sabatier L. Establishing mechanisms affecting the individual response to ionizing radiation. Int J Radiat Biol 2020; 96:297-323. [PMID: 31852363 DOI: 10.1080/09553002.2019.1704908] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Purpose: Humans are increasingly exposed to ionizing radiation (IR). Both low (<100 mGy) and high doses can cause stochastic effects, including cancer; whereas doses above 100 mGy are needed to promote tissue or cell damage. 10-15% of radiotherapy (RT) patients suffer adverse reactions, described as displaying radiosensitivity (RS). Sensitivity to IR's stochastic effects is termed radiosusceptibility (RSu). To optimize radiation protection we need to understand the range of individual variability and underlying mechanisms. We review the potential mechanisms contributing to RS/RSu focusing on RS following RT, the most tractable RS group.Conclusions: The IR-induced DNA damage response (DDR) has been well characterized. Patients with mutations in the DDR have been identified and display marked RS but they represent only a small percentage of the RT patients with adverse reactions. We review the impacting mechanisms and additional factors influencing RS/RSu. We discuss whether RS/RSu might be genetically determined. As a recommendation, we propose that a prospective study be established to assess RS following RT. The study should detail tumor site and encompass a well-defined grading system. Predictive assays should be independently validated. Detailed analysis of the inflammatory, stress and immune responses, mitochondrial function and life style factors should be included. Existing cohorts should also be optimally exploited.
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Affiliation(s)
| | - Serge Candéias
- CEA, CNRS, LCMB, University of Grenoble Alpes, Grenoble, France
| | - Sudhir Chandna
- Division of Radiation Biosciences, Institute of Nuclear Medicine & Allied Sciences, Delhi, India
| | - Nicolas Foray
- Inserm UA8 Unit Radiations: Defense, Health and Environment, Lyon, France
| | - Anna A Friedl
- Department of Radiation Oncology, University Hospital, LMU, Munich, Germany
| | - Siamak Haghdoost
- Cimap-Laria, Advanced Resource Center for HADrontherapy in Europe (ARCHADE,), University of Caen Normandy, France.,Centre for Radiation Protection Research, Department of Molecular Bioscience, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Penelope A Jeggo
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Katalin Lumniczky
- Department of Radiation Medicine, Division of Radiobiology and Radiohygiene, National Public Health Center, Budapest, Hungary
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13
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Impact of ATM and DNA-PK Inhibition on Gene Expression and Individual Response of Human Lymphocytes to Mixed Beams of Alpha Particles and X-Rays. Cancers (Basel) 2019; 11:cancers11122013. [PMID: 31847107 PMCID: PMC6966634 DOI: 10.3390/cancers11122013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 01/06/2023] Open
Abstract
Accumulating evidence suggests a synergistic effect in cells simultaneously exposed to different types of clustered and dispersed DNA damage. We aimed to analyse the effect of mixed beams of alpha particles and X-rays (1:1 dose of each) on DNA damage response genes in human peripheral blood lymphocytes isolated from four donors. Two donors were compared upon inhibition of ATM or DNA-PK and at different sampling times. qPCR was used to measure mRNA levels of FDXR, GADD45A, BBC3, MDM2, CDKN1A, and XPC 24 h following exposure. Generally, alpha particles and mixed beams were stronger inducers of gene expression compared to X-rays, displaying saturated versus linear dose–response curves, respectively. Three out of four donors responded synergistically to mixed beams. When two donors were sampled again one year later, the former additive effect in one donor was now synergistic and no significant difference in intrinsic radiosensitivity was displayed, as determined by gamma-radiation-induced micronuclei. ATM, but not DNA-PK inhibition, reduced the radiation-induced gene expression, but differently for alpha radiation between the two donors. In conclusion, synergy was present for all donors, but the results suggest individual variability in the response to mixed beams, most likely due to lifestyle changes.
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14
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Rand DM, Mossman JA. Mitonuclear conflict and cooperation govern the integration of genotypes, phenotypes and environments. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190188. [PMID: 31787039 PMCID: PMC6939372 DOI: 10.1098/rstb.2019.0188] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The mitonuclear genome is the most successful co-evolved mutualism in the history of life on Earth. The cross-talk between the mitochondrial and nuclear genomes has been shaped by conflict and cooperation for more than 1.5 billion years, yet this system has adapted to countless genomic reorganizations by each partner, and done so under changing environments that have placed dramatic biochemical and physiological pressures on evolving lineages. From putative anaerobic origins, mitochondria emerged as the defining aerobic organelle. During this transition, the two genomes resolved rules for sex determination and transmission that made uniparental inheritance the dominant, but not a universal pattern. Mitochondria are much more than energy-producing organelles and play crucial roles in nutrient and stress signalling that can alter how nuclear genes are expressed as phenotypes. All of these interactions are examples of genotype-by-environment (GxE) interactions, gene-by-gene (GxG) interactions (epistasis) or more generally context-dependent effects on the link between genotype and phenotype. We provide evidence from our own studies in Drosophila, and from those of other systems, that mitonuclear interactions—either conflicting or cooperative—are common features of GxE and GxG. We argue that mitonuclear interactions are an important model for how to better understand the pervasive context-dependent effects underlying the architecture of complex phenotypes. Future research in this area should focus on the quantitative genetic concept of effect size to place mitochondrial links to phenotype in a proper context. This article is part of the theme issue ‘Linking the mitochondrial genotype to phenotype: a complex endeavour’.
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Affiliation(s)
- David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI, USA
| | - Jim A Mossman
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI, USA
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15
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Domingo J, Baeza-Centurion P, Lehner B. The Causes and Consequences of Genetic Interactions (Epistasis). Annu Rev Genomics Hum Genet 2019; 20:433-460. [PMID: 31082279 DOI: 10.1146/annurev-genom-083118-014857] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The same mutation can have different effects in different individuals. One important reason for this is that the outcome of a mutation can depend on the genetic context in which it occurs. This dependency is known as epistasis. In recent years, there has been a concerted effort to quantify the extent of pairwise and higher-order genetic interactions between mutations through deep mutagenesis of proteins and RNAs. This research has revealed two major components of epistasis: nonspecific genetic interactions caused by nonlinearities in genotype-to-phenotype maps, and specific interactions between particular mutations. Here, we provide an overview of our current understanding of the mechanisms causing epistasis at the molecular level, the consequences of genetic interactions for evolution and genetic prediction, and the applications of epistasis for understanding biology and determining macromolecular structures.
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Affiliation(s)
- Júlia Domingo
- Systems Biology Program, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; , ,
| | - Pablo Baeza-Centurion
- Systems Biology Program, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; , ,
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; , , .,Universitat Pompeu Fabra, 08003 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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16
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Byrne JJ, Soh MS, Chandhok G, Vijayaraghavan T, Teoh JS, Crawford S, Cobham AE, Yapa NMB, Mirth CK, Neumann B. Disruption of mitochondrial dynamics affects behaviour and lifespan in Caenorhabditis elegans. Cell Mol Life Sci 2019; 76:1967-1985. [PMID: 30840087 PMCID: PMC6478650 DOI: 10.1007/s00018-019-03024-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 01/11/2019] [Accepted: 01/22/2019] [Indexed: 01/29/2023]
Abstract
Mitochondria are essential components of eukaryotic cells, carrying out critical physiological processes that include energy production and calcium buffering. Consequently, mitochondrial dysfunction is associated with a range of human diseases. Fundamental to their function is the ability to transition through fission and fusion states, which is regulated by several GTPases. Here, we have developed new methods for the non-subjective quantification of mitochondrial morphology in muscle and neuronal cells of Caenorhabditis elegans. Using these techniques, we uncover surprising tissue-specific differences in mitochondrial morphology when fusion or fission proteins are absent. From ultrastructural analysis, we reveal a novel role for the fusion protein FZO-1/mitofusin 2 in regulating the structure of the inner mitochondrial membrane. Moreover, we have determined the influence of the individual mitochondrial fission (DRP-1/DRP1) and fusion (FZO-1/mitofusin 1,2; EAT-3/OPA1) proteins on animal behaviour and lifespan. We show that loss of these mitochondrial fusion or fission regulators induced age-dependent and progressive deficits in animal movement, as well as in muscle and neuronal function. Our results reveal that disruption of fusion induces more profound defects than lack of fission on animal behaviour and tissue function, and imply that while fusion is required throughout life, fission is more important later in life likely to combat ageing-associated stressors. Furthermore, our data demonstrate that mitochondrial function is not strictly dependent on morphology, with no correlation found between morphological changes and behavioural defects. Surprisingly, we find that disruption of either mitochondrial fission or fusion significantly reduces median lifespan, but maximal lifespan is unchanged, demonstrating that mitochondrial dynamics play an important role in limiting variance in longevity across isogenic populations. Overall, our study provides important new insights into the central role of mitochondrial dynamics in maintaining organismal health.
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Affiliation(s)
- Joseph J Byrne
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Ming S Soh
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Gursimran Chandhok
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Tarika Vijayaraghavan
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Jean-Sébastien Teoh
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Simon Crawford
- Monash Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Melbourne, VIC, 3800, Australia
| | - Ansa E Cobham
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Nethmi M B Yapa
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Christen K Mirth
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Brent Neumann
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia.
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17
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Wojcik A, Bouffler S, Hauptmann M, Rajaraman P. Considerations on the use of the terms radiosensitivity and radiosusceptibility. JOURNAL OF RADIOLOGICAL PROTECTION : OFFICIAL JOURNAL OF THE SOCIETY FOR RADIOLOGICAL PROTECTION 2018; 38:N25-N29. [PMID: 29877193 DOI: 10.1088/1361-6498/aacb03] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The separate use of the terms 'radiosensitivity' and 'radiosusceptibility' has been suggested to describe variability in the risk of, respectively, adverse tissue reactions (deterministic effect) following radiotherapy and radiation-induced cancer (stochastic effect). The aim of this note is to present arguments against such distinction. We feel that it is premature to make a concrete final judgement on these definitions because of the limited understanding of the mechanisms underlying individual sensitivity to both radiation-related cancers and radiation-related tissue injury. Moreover, the exclusive application of 'radiosensitivity' in relation to deterministic effects and the term 'radiosusceptibility' in relation to cancer carries the risk of being wrongly interpreted as evidence for a high, genetically driven sensitivity to radiation in all patients who develop adverse tissue reactions and a high genetic susceptibility to cancer in those who develop radiation-induced malignancies. There is a need for further research to better define these phenomena and their interrelationships.
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Affiliation(s)
- Andrzej Wojcik
- Centre for Radiation Protection Research, MBW Department, Stockholm University, Sweden and Institute for Biology, Jan Kochanowski University, Kielce, Poland
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18
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Abstract
Intratumoral heterogeneity has been shown to play an important role in diagnostic accuracy, development of treatment resistance, and prognosis of cancer patients. Recent studies have proposed quantitative measurement of phenotypic intratumoral heterogeneity, but no study is yet available in endometrial carcinomas. In our study we evaluated the phenotypic intratumoral heterogeneity of a consecutive series of 10 endometrial carcinomas using measures of dispersion and diversity. Morphometric architectural (%tumor cells, %solid tumor, %differentiated tumor, and %lumens) and nuclear [volume-weighted mean nuclear volume ((Equation is included in full-text article.))] parameters, as well as estrogen receptor, progesterone receptor, p53, vimentin, and beta-catenin immunoexpression (H-score) were digitally analyzed in 20 microscopic fields per carcinoma. Quantitative measures of intratumoral heterogeneity included coefficient of variation (CV) and relative quadratic entropy (rQE). In each endometrial carcinoma there was slight variation of architecture from field to field, resulting in globally low levels of heterogeneity measures (mean CV %tumor cells: 0.10, %solid tumor: 0.73, %differentiated tumor: 0.19, %lumens: 0.61 and mean rQE %tumor cells: 18.5, %solid tumor: 20.3, %differentiated tumor: 25.6, %lumens: 21.8). Nuclear intratumoral heterogeneity was also globally low (mean (Equation is included in full-text article.)CV: 0.23 and rQE: 27.3), but significantly higher than the heterogeneity of architectural parameters within most carcinomas. In general, there was low to moderate variability of immunoexpression markers within each carcinoma, but estrogen receptor (mean CV: 0.56 and rQE: 46.2) and progesterone receptor (mean CV: 0.60 and rQE: 39.3) displayed the highest values of heterogeneity measures. Intratumoral heterogeneity of immunoexpression was significantly higher than that observed for morphometric parameters. In conclusion, our study indicates that endometrial carcinomas present a variable but predominantly low degree of phenotypic intratumoral heterogeneity.
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19
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Kammenga JE. The background puzzle: how identical mutations in the same gene lead to different disease symptoms. FEBS J 2017; 284:3362-3373. [PMID: 28390082 DOI: 10.1111/febs.14080] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 03/31/2017] [Accepted: 04/05/2017] [Indexed: 01/05/2023]
Abstract
Identical disease-causing mutations can lead to different symptoms in different people. The reason for this has been a puzzling problem for geneticists. Differential penetrance and expressivity of mutations has been observed within individuals with different and similar genetic backgrounds. Attempts have been made to uncover the underlying mechanisms that determine differential phenotypic effects of identical mutations through studies of model organisms. From these studies evidence is accumulating that to understand disease mechanism or predict disease prevalence, an understanding of the influence of genetic background is as important as the putative disease-causing mutations of relatively large effect. This review highlights current insights into phenotypic variation due to gene interactions, epigenetics and stochasticity in model organisms, and discusses their importance for understanding the mutational effect on disease symptoms.
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Affiliation(s)
- Jan E Kammenga
- Laboratory of Nematology, Wageningen University, The Netherlands
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20
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Putignani L, Dallapiccola B. Foodomics as part of the host-microbiota-exposome interplay. J Proteomics 2016; 147:3-20. [PMID: 27130534 DOI: 10.1016/j.jprot.2016.04.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 04/10/2016] [Accepted: 04/20/2016] [Indexed: 02/08/2023]
Abstract
UNLABELLED The functional complexity of human gut microbiota and its relationship with host physiology and environmental modulating factors, offers the opportunity to investigate (i) the host and microbiota role in organism-environment relationship; (ii) the individual functional diversity and response to environmental stimuli (exposome); (iii) the host genome and microbiota metagenomes' modifications by diet-mediated epigenomic controls (nutriepigenomics); and (iv) the genotype-phenotype "trajectories" under physiological and disease constraints. Systems biology-based approaches aim at integrating biological data at cellular, tissue and organ organization levels, using computational modeling to interpret diseases' physiopathological mechanisms (i.e., onset and progression). Proteomics improves the existing gene models by profiling molecular phenotypes at protein abundance level, by analyzing post-translational modifications and protein-protein interactions and providing specific pathway information, hence contributing to functional molecular networks. Transcriptomics and metabolomics may determine host ad microbiota changes induced by food ingredients at molecular level, complementing functional genomics and proteomics data. Since foodomics is an -omic wide methodology may feed back all integrative data to foster the omics-based systems medicine field. Hence, coupled to ecological genomics of gut microbial communities, foodomics may highlight health benefits from nutrients, dissecting diet-induced gut microbiota eubiosis mechanisms and significantly contributing to understand and prevent complex disease phenotypes. BIOLOGICAL SIGNIFICANCE Besides transcriptomics and proteomics there is a growing interest in applying metabolic profiling to food science for the development of functional foods. Indeed, one of the biggest challenges of modern nutrition is to propose a healthy diet to populations worldwide, intrinsically respecting the high inter-individual variability, driven by complex host/nutrients/microbiota/environment interactions. Therefore, metabolic profiling can assist at various levels for the development of functional foods, starting from screening for food composition to identification of new biomarkers to trace food intake. This current approach can support diet intervention strategies, epidemiological studies, and controlling of metabolic disorders worldwide spreading, hence ensuring healthy aging. With high-throughput molecular technologies driving foodomics, studying bidirectional interactions of host-microbial co-metabolism, innate immune development, dysfunctional nutrient absorption and processing, complex signaling pathways involved in nutritional metabolism, is now likely. In all cases, as microbiome pipeline efforts continue, it is possible that enhanced standardized protocols can be developed, which may lead to new testable biological and clinical hypotheses. This Review provides a comprehensive update on the current state-of-the-art of the integrated -omics route in food, microbiota and host co-metabolism studies, which may revolutionize the design of new dietary intervention strategies.
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Affiliation(s)
- Lorenza Putignani
- Units of Parasitology and Human Microbiome, Bambino Gesù Children's Hospital and Research Institute, Piazza Sant'Onofrio 4, 00165 Rome, Italy.
| | - Bruno Dallapiccola
- Scientific Directorate, Bambino Gesù Children's Hospital and Research Institute, Piazza Sant'Onofrio 4, 00165 Rome, Italy
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21
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Methodisch-statistische Herausforderungen an die genombasierte Vorhersage von Erkrankungen. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2015; 58:131-8. [DOI: 10.1007/s00103-014-2091-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Díaz-Castillo C. Evidence for a sexual dimorphism in gene expression noise in metazoan species. PeerJ 2015; 3:e750. [PMID: 25649874 PMCID: PMC4314086 DOI: 10.7717/peerj.750] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/15/2015] [Indexed: 11/20/2022] Open
Abstract
Many biological processes depend on very few copies of intervening elements, which makes such processes particularly susceptible to the stochastic fluctuations of these elements. The intrinsic stochasticity of certain processes is propagated across biological levels, causing genotype- and environment-independent biological variation which might permit populations to better cope with variable environments. Biological variations of stochastic nature might also allow the accumulation of variations at the genetic level that are hidden from natural selection, which might have a great potential for population diversification. The study of any mechanism that resulted in the modulation of stochastic variation is, therefore, of potentially wide interest. I propose that sex might be an important modulator of the stochastic variation in gene expression, i.e., gene expression noise. Based on known associations between different patterns of gene expression variation, I hypothesize that in metazoans the gene expression noise might be generally larger in heterogametic than in homogametic individuals. I directly tested this hypothesis by comparing putative genotype- and environment-independent variations in gene expression between females and males of Drosophila melanogaster strains. Also, considering the potential effect of the propagation of gene expression noise across biological levels, I indirectly tested the existence of a metazoan sexual dimorphism in gene expression noise by analyzing putative genotype- and environment-independent variation in phenotypes related to interaction with the environment in D. melanogaster strains and metazoan species. The results of these analyses are consistent with the hypothesis that gene expression is generally noisier in heterogametic than in homogametic individuals. Further analyses and discussion of existing literature permits the speculation that the sexual dimorphism in gene expression noise is ultimately based on the nuclear dynamics in gametogenesis and very early embryogenesis of sex-specific chromosomes, i.e., Y and W chromosomes.
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Affiliation(s)
- Carlos Díaz-Castillo
- Department of Developmental & Cell Biology, University of California, Irvine , CA , USA
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23
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Okser S, Pahikkala T, Airola A, Salakoski T, Ripatti S, Aittokallio T. Regularized machine learning in the genetic prediction of complex traits. PLoS Genet 2014; 10:e1004754. [PMID: 25393026 PMCID: PMC4230844 DOI: 10.1371/journal.pgen.1004754] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Sebastian Okser
- Department of Information Technology, University of Turku, Turku, Finland
- Turku Centre for Computer Science (TUCS), University of Turku and Åbo Akademi University, Turku, Finland
| | - Tapio Pahikkala
- Department of Information Technology, University of Turku, Turku, Finland
- Turku Centre for Computer Science (TUCS), University of Turku and Åbo Akademi University, Turku, Finland
| | - Antti Airola
- Department of Information Technology, University of Turku, Turku, Finland
- Turku Centre for Computer Science (TUCS), University of Turku and Åbo Akademi University, Turku, Finland
| | - Tapio Salakoski
- Department of Information Technology, University of Turku, Turku, Finland
- Turku Centre for Computer Science (TUCS), University of Turku and Åbo Akademi University, Turku, Finland
| | - Samuli Ripatti
- Hjelt Institute, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Tero Aittokallio
- Turku Centre for Computer Science (TUCS), University of Turku and Åbo Akademi University, Turku, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- * E-mail:
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24
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One gene, many neuropsychiatric disorders: lessons from Mendelian diseases. Nat Neurosci 2014; 17:773-81. [PMID: 24866043 DOI: 10.1038/nn.3713] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 03/31/2014] [Indexed: 12/14/2022]
Abstract
Recent human genetic studies have consistently shown that mutations in the same gene or same genomic region can increase the risk of a broad range of complex neuropsychiatric disorders. Despite the steadily increasing number of examples of such nonspecific effects on risk, the underlying biological causes remain mysterious. Here we investigate the phenomenon of such nonspecific risk by identifying Mendelian disease genes that are associated with multiple diseases and explore what is known about the underlying mechanisms in these more 'simple' examples. Our analyses make clear that there are a variety of mechanisms at work, emphasizing how challenging it will be to elucidate the causes of nonspecific risk in complex disease. Ultimately, we conclude that functional approaches will be critical for explaining the causes of nonspecific risk factors discovered by human genetic studies of neuropsychiatric disorders.
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Gallaher J, Anderson ARA. Evolution of intratumoral phenotypic heterogeneity: the role of trait inheritance. Interface Focus 2014; 3:20130016. [PMID: 24511380 DOI: 10.1098/rsfs.2013.0016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A tumour is a heterogeneous population of cells that competes for limited resources. In the clinic, we typically probe the tumour by biopsy, and then characterize it by the dominant genetic clone. But genotypes are only the first link in the chain of hierarchical events that leads to a specific cell phenotype. The relationship between genotype and phenotype is not simple, and the so-called genotype to phenotype map is poorly understood. Many genotypes can produce the same phenotype, so genetic heterogeneity may not translate directly to phenotypic heterogeneity. We therefore choose to focus on the functional endpoint, the phenotype as defined by a collection of cellular traits (e.g. proliferative and migratory ability). Here, we will examine how phenotypic heterogeneity evolves in space and time and how the way in which phenotypes are inherited will drive this evolution. A tumour can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a growing tumour with increased proliferation capacity must compete for space as a limited resource. Hypercellularity leads to a contact-inhibited core with a competitive proliferating rim. Evolution and selection occurs, and an individual cell's capacity to survive and propagate is determined by its combination of traits and interaction with the environment. With heterogeneity in phenotypes, the clone that will dominate is not always obvious as there are both local interactions and global pressures. Several combinations of phenotypes can coexist, changing the fitness of the whole. To understand some aspects of heterogeneity in a growing tumour, we build an off-lattice agent-based model consisting of individual cells with assigned trait values for proliferation and migration rates. We represent heterogeneity in these traits with frequency distributions and combinations of traits with density maps. How the distributions change over time is dependent on how traits are passed on to progeny cells, which is our main enquiry. We bypass the translation of genetics to behaviour by focusing on the functional end result of inheritance of the phenotype combined with the environmental influence of limited space.
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Affiliation(s)
- Jill Gallaher
- Department of Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612 , USA
| | - Alexander R A Anderson
- Department of Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612 , USA
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Etges WJ. No boundaries: genomes, organisms, and ecological interactions responsible for divergence and reproductive isolation. J Hered 2014; 105 Suppl 1:756-70. [PMID: 25149252 PMCID: PMC4170711 DOI: 10.1093/jhered/esu039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 05/31/2014] [Indexed: 12/23/2022] Open
Abstract
Revealing the genetic basis of traits that cause reproductive isolation, particularly premating or sexual isolation, usually involves the same challenges as most attempts at genotype-phenotype mapping and so requires knowledge of how these traits are expressed in different individuals, populations, and environments, particularly under natural conditions. Genetic dissection of speciation phenotypes thus requires understanding of the internal and external contexts in which underlying genetic elements are expressed. Gene expression is a product of complex interacting factors internal and external to the organism including developmental programs, the genetic background including nuclear-cytotype interactions, epistatic relationships, interactions among individuals or social effects, stochasticity, and prevailing variation in ecological conditions. Understanding of genomic divergence associated with reproductive isolation will be facilitated by functional expression analysis of annotated genomes in organisms with well-studied evolutionary histories, phylogenetic affinities, and known patterns of ecological variation throughout their life cycles. I review progress and prospects for understanding the pervasive role of host plant use on genetic and phenotypic expression of reproductive isolating mechanisms in cactophilic Drosophila mojavensis and suggest how this system can be used as a model for revealing the genetic basis for species formation in organisms where speciation phenotypes are under the joint influences of genetic and environmental factors.
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Affiliation(s)
- William J Etges
- From Program in Ecology and Evolutionary Biology, Department of Biological Sciences, 1 University of Arkansas, Fayetteville, AR.
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van Oosten-Hawle P, Porter RS, Morimoto RI. Regulation of organismal proteostasis by transcellular chaperone signaling. Cell 2013; 153:1366-78. [PMID: 23746847 DOI: 10.1016/j.cell.2013.05.015] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/16/2013] [Accepted: 05/06/2013] [Indexed: 10/26/2022]
Abstract
A major challenge for metazoans is to ensure that different tissues, each expressing distinctive proteomes, are nevertheless well protected at an organismal level from proteotoxic stress. We show that expression of endogenous metastable proteins in muscle cells, which rely on chaperones for proper folding, induces a systemic stress response throughout multiple tissues of C. elegans. Suppression of misfolding in muscle cells can be achieved not only by enhanced expression of HSP90 in muscle cells but as effectively by elevated expression of HSP90 in intestine or neuronal cells. This cell-nonautonomous control of HSP90 expression relies upon transcriptional feedback between somatic tissues that is regulated by the FoxA transcription factor PHA-4. This transcellular chaperone signaling response maintains organismal proteostasis when challenged by a local tissue imbalance in folding and provides the basis for organismal stress-sensing surveillance.
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Affiliation(s)
- Patricija van Oosten-Hawle
- Department Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208, USA
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28
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The genomic determinants of genotype × environment interactions in gene expression. Trends Genet 2013; 29:479-87. [DOI: 10.1016/j.tig.2013.05.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 05/02/2013] [Accepted: 05/14/2013] [Indexed: 11/17/2022]
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Stambolian D. Genetic susceptibility and mechanisms for refractive error. Clin Genet 2013; 84:102-8. [PMID: 23647423 DOI: 10.1111/cge.12180] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 04/29/2013] [Accepted: 04/29/2013] [Indexed: 12/19/2022]
Abstract
Refractive errors, myopia and hyperopia, are the most common causes of visual impairment worldwide. Recent advances in genetics have been utilized to identify a wealth of genetic loci believed to contain susceptibility genes for refractive error (RE). The current genetic evidence confirms that RE is influenced by both common and rare variants with a significant environmental component. These studies argue that only by combining genetic and environmental knowledge with in vivo measurements of biological states will it be possible to understand the underlying biology of RE that will lead to novel therapeutic targets and accurate genetic predictions.
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Affiliation(s)
- D Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Burga A, Lehner B. Predicting phenotypic variation from genotypes, phenotypes and a combination of the two. Curr Opin Biotechnol 2013; 24:803-9. [PMID: 23540420 DOI: 10.1016/j.copbio.2013.03.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 03/05/2013] [Accepted: 03/06/2013] [Indexed: 11/29/2022]
Abstract
A central challenge for medicine is to predict disease risk and treatment outcomes for individuals. But what kind of information should be used to make useful predictions in biology? One important cause of phenotypic variation is of course genetics. However genetic predictions have both practical and fundamental limitations: most genetic influences on a trait are usually unknown, and phenotypic variation is not just due to genetics. A pragmatic alternative is to use intermediate phenotypes such as gene expression and other molecular measurements to make predictions about later trait variation such as disease risk. Intermediate phenotypes are useful because they capture both genetic and non-genetic influences on a system, and can reflect both the current state of a system and its history. Here we discuss examples of both genetic and non-genetic approaches to predicting phenotypic variation. Moreover, we argue that it will be by combining these two sources of information-genetics and intermediate molecular phenotypes-that it will be possible to make accurate predictions about variation in many phenotypic traits, even if we will not always mechanistically understand why this is the case. In particular, we encourage the human genetics community to focus more on combining genetics with intermediate phenotypes when attempting to predict clinically relevant traits such as disease risk.
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Affiliation(s)
- Alejandro Burga
- Genetic Systems, EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader 88, 08003 Barcelona, Spain
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Abstract
To what extent can variation in phenotypic traits such as disease risk be accurately predicted in individuals? In this Review, I highlight recent studies in model organisms that are relevant both to the challenge of accurately predicting phenotypic variation from individual genome sequences ('whole-genome reverse genetics') and for understanding why, in many cases, this may be impossible. These studies argue that only by combining genetic knowledge with in vivo measurements of biological states will it be possible to make accurate genetic predictions for individual humans.
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