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Badia-Bringué G, Canive M, Fernandez-Jimenez N, Lavín JL, Casais R, Blanco-Vázquez C, Vázquez P, Fernández A, Bilbao JR, Garrido JM, Juste RA, González-Recio O, Alonso-Hearn M. Summary-data based Mendelian randomization identifies gene expression regulatory polymorphisms associated with bovine paratuberculosis by modulation of the nuclear factor Kappa β (NF-κß)-mediated inflammatory response. BMC Genomics 2023; 24:605. [PMID: 37821814 PMCID: PMC10568764 DOI: 10.1186/s12864-023-09710-w] [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: 01/12/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified host genetic variants associated with paratuberculosis (PTB) susceptibility. Most of the GWAS-identified SNPs are in non-coding regions. Connecting these non-coding variants and downstream affected genes is a challenge and, up to date, only a few functional mutations or expression quantitative loci (cis-eQTLs) associated with PTB susceptibility have been identified. In the current study, the associations between imputed whole-genome sequence genotypes and whole RNA-Sequencing data from peripheral blood (PB) and ileocecal valve (ICV) samples of Spanish Holstein cows (N = 16) were analyzed with TensorQTL. This approach allowed the identification of 88 and 37 cis-eQTLs regulating the expression levels of 90 and 37 genes in PB and ICV samples, respectively (False discorey rate, FDR ≤ 0.05). Next, we applied summary-based data Mendelian randomization (SMR) to integrate the cis-eQTL dataset with GWAS data obtained from a cohort of 813 culled cattle that were classified according to the presence or absence of PTB-associated histopathological lesions in gut tissues. After multiple testing corrections (FDR ≤ 0.05), we identified two novel cis-eQTLs affecting the expression of the early growth response factor 4 (EGR4) and the bovine neuroblastoma breakpoint family member 6-like protein isoform 2 (MGC134040) that showed pleiotropic associations with the presence of multifocal and diffuse lesions in gut tissues; P = 0.002 and P = 0.017, respectively. While EGR4 acts as a brake on T-cell proliferation and cytokine production through interaction with the nuclear factor Kappa β (NF-κß), MGC134040 is a target gene of NF-κß. Our findings provide a better understanding of the genetic factors influencing PTB outcomes, confirm that the multifocal lesions are localized/confined lesions that have different underlying host genetics than the diffuse lesions, and highlight regulatory SNPs and regulated-gene targets to design future functional studies.
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Affiliation(s)
- Gerard Badia-Bringué
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
- Doctoral Program in Molecular Biology and Biomedicine, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Bizkaia, Spain
| | - Maria Canive
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia HRI, Leioa, Bizkaia, Spain
| | - José Luis Lavín
- Department of Applied Mathematics, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Rosa Casais
- Center of Animal Biotechnology, SERIDA, Servicio Regional de Investigación y Desarrollo Agroalimentario, Deva, Asturias, Spain
| | - Cristina Blanco-Vázquez
- Center of Animal Biotechnology, SERIDA, Servicio Regional de Investigación y Desarrollo Agroalimentario, Deva, Asturias, Spain
| | - Patricia Vázquez
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC, Madrid, Spain
| | - Jose Ramón Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia HRI, Leioa, Bizkaia, Spain
| | - Joseba M Garrido
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Ramón A Juste
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC, Madrid, Spain
| | - Marta Alonso-Hearn
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain.
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2
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Pollen AA, Kilik U, Lowe CB, Camp JG. Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution. Nat Rev Genet 2023; 24:687-711. [PMID: 36737647 PMCID: PMC9897628 DOI: 10.1038/s41576-022-00568-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 02/05/2023]
Abstract
Our ancestors acquired morphological, cognitive and metabolic modifications that enabled humans to colonize diverse habitats, develop extraordinary technologies and reshape the biosphere. Understanding the genetic, developmental and molecular bases for these changes will provide insights into how we became human. Connecting human-specific genetic changes to species differences has been challenging owing to an abundance of low-effect size genetic changes, limited descriptions of phenotypic differences across development at the level of cell types and lack of experimental models. Emerging approaches for single-cell sequencing, genetic manipulation and stem cell culture now support descriptive and functional studies in defined cell types with a human or ape genetic background. In this Review, we describe how the sequencing of genomes from modern and archaic hominins, great apes and other primates is revealing human-specific genetic changes and how new molecular and cellular approaches - including cell atlases and organoids - are enabling exploration of the candidate causal factors that underlie human-specific traits.
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Affiliation(s)
- Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Umut Kilik
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
| | - J Gray Camp
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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3
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Glunčić M, Vlahović I, Rosandić M, Paar V. Tandem NBPF 3mer HORs (Olduvai triplets) in Neanderthal and two novel HOR tandem arrays in human chromosome 1 T2T-CHM13 assembly. Sci Rep 2023; 13:14420. [PMID: 37660151 PMCID: PMC10475015 DOI: 10.1038/s41598-023-41517-3] [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: 05/24/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023] Open
Abstract
It is known that the ~ 1.6 kb Neuroblastoma BreakPoint Family (NBPF) repeats are human specific and contributing to cognitive capabilities, with increasing frequency in higher order repeat 3mer HORs (Olduvai triplets). From chimpanzee to modern human there is a discontinuous jump from 0 to ~ 50 tandemly organized 3mer HORs. Here we investigate the structure of NBPF 3mer HORs in the Neanderthal genome assembly of Pääbo et al., comparing it to the results obtained for human hg38.p14 chromosome 1. Our findings reveal corresponding NBPF 3mer HOR arrays in Neanderthals with slightly different monomer structures and numbers of HOR copies compared to humans. Additionally, we compute the NBPF 3mer HOR pattern for the complete telomere-to-telomere human genome assembly (T2T-CHM13) by Miga et al., identifying two novel tandem arrays of NBPF 3mer HOR repeats with 5 and 9 NBPF 3mer HOR copies. We hypothesize that these arrays correspond to novel NBPF genes (here referred to as NBPFA1 and NBPFA2). Further improving the quality of the Neanderthal genome using T2T-CHM13 as a reference would be of great interest in determining the presence of such distant novel NBPF genes in the Neanderthal genome and enhancing our understanding of human evolution.
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Affiliation(s)
- Matko Glunčić
- Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia.
| | | | - Marija Rosandić
- University Hospital Centre Zagreb (Ret.), 10000, Zagreb, Croatia
- Croatian Academy of Sciences and Arts, 10000, Zagreb, Croatia
| | - Vladimir Paar
- Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
- Croatian Academy of Sciences and Arts, 10000, Zagreb, Croatia
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4
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Jin L, Wang D, Zhang J, Liu P, Wang Y, Lin Y, Liu C, Han Z, Long K, Li D, Jiang Y, Li G, Zhang Y, Bai J, Li X, Li J, Lu L, Kong F, Wang X, Li H, Huang Z, Ma J, Fan X, Shen L, Zhu L, Jiang Y, Tang G, Feng B, Zeng B, Ge L, Li X, Tang Q, Zhang Z, Li M. Dynamic chromatin architecture of the porcine adipose tissues with weight gain and loss. Nat Commun 2023; 14:3457. [PMID: 37308492 DOI: 10.1038/s41467-023-39191-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 06/02/2023] [Indexed: 06/14/2023] Open
Abstract
Using an adult female miniature pig model with diet-induced weight gain/weight loss, we investigated the regulatory mechanisms of three-dimensional (3D) genome architecture in adipose tissues (ATs) associated with obesity. We generated 249 high-resolution in situ Hi-C chromatin contact maps of subcutaneous AT and three visceral ATs, analyzing transcriptomic and chromatin architectural changes under different nutritional treatments. We find that chromatin architecture remodeling underpins transcriptomic divergence in ATs, potentially linked to metabolic risks in obesity development. Analysis of chromatin architecture among subcutaneous ATs of different mammals suggests the presence of transcriptional regulatory divergence that could explain phenotypic, physiological, and functional differences in ATs. Regulatory element conservation analysis in pigs and humans reveals similarities in the regulatory circuitry of genes responsible for the obesity phenotype and identified non-conserved elements in species-specific gene sets that underpin AT specialization. This work provides a data-rich tool for discovering obesity-related regulatory elements in humans and pigs.
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Affiliation(s)
- Long Jin
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China
| | - Danyang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101, Beijing, China
- School of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China
- Sars-Fang Centre and MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266100, China
| | - Jiaman Zhang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pengliang Liu
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yujie Wang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Lin
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Can Liu
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ziyin Han
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Animal Molecular Design and Precise Breeding Key Laboratory of Guangdong Province, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Keren Long
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Guisen Li
- Institute of Nephrology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Yu Zhang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jingyi Bai
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaokai Li
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Li
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lu Lu
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fanli Kong
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xun Wang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hua Li
- Animal Molecular Design and Precise Breeding Key Laboratory of Guangdong Province, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Zhiqing Huang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jideng Ma
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaolan Fan
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linyuan Shen
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China
| | - Li Zhu
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yanzhi Jiang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoqing Tang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bin Feng
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bo Zeng
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Ya'an Digital Economy Operation Company, Ya'an, 625014, China
| | - Liangpeng Ge
- Pig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing, 402460, China
| | - Xuewei Li
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qianzi Tang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhihua Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101, Beijing, China.
- School of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Mingzhou Li
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China.
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5
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Pacheco A, Issaian A, Davis J, Anderson N, Nemkov T, Paukovich N, Henen MA, Vögeli B, Sikela JM, Hansen K. Proteolytic activation of human-specific Olduvai domains by the furin protease. Int J Biol Macromol 2023; 234:123041. [PMID: 36581038 PMCID: PMC10038901 DOI: 10.1016/j.ijbiomac.2022.12.260] [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: 11/23/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Olduvai protein domains (formerly DUF1220) show the greatest human-specific increase in copy number of any coding region in the genome and are highly correlated with human brain evolution and cognitive disease. The majority of human copies are found within four NBPF genes organized in a variable number of a tandemly arranged three-domain blocks called Olduvai triplets. Here we show that these human-specific Olduvai domains are posttranslationally processed by the furin protease, with a cleavage site occurring once at each triplet. These findings suggest that all expanded human-specific NBPF genes encode proproteins consisting of many independent Olduvai triplet proteins which are activated by furin processing. The exceptional correlation of Olduvai copy number and brain size taken together with our new furin data, indicates the ultimate target of selection was a rapid increase in dosage of autonomously functioning Olduvai triplet proteins, and that these proteins are the primary active agent underlying Olduvai's role in human brain expansion.
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Affiliation(s)
- Ashley Pacheco
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, USA
| | - Aaron Issaian
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, USA
| | - Jonathan Davis
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, USA
| | - Nathan Anderson
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, USA
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, USA
| | - Natasia Paukovich
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, USA
| | - James M Sikela
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, USA.
| | - Kirk Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, USA.
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6
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Remnants of SIRE1 retrotransposons in human genome? J Genet 2022. [DOI: 10.1007/s12041-022-01398-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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7
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Glunčić M, Vlahović I, Rosandić M, Paar V. Tandemly repeated NBPF HOR copies (Olduvai triplets): Possible impact on human brain evolution. Life Sci Alliance 2022; 6:6/1/e202101306. [PMID: 36261226 PMCID: PMC9584774 DOI: 10.26508/lsa.202101306] [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: 11/19/2021] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/24/2022] Open
Abstract
Previously it was found that the neuroblastoma breakpoint family (NBPF) gene repeat units of ∼1.6 kb have an important role in human brain evolution and function. The higher order organization of these repeat units has been discovered by both methods, the higher order repeat (HOR)-searching method and the HLS searching method. Using the HOR searching method with global repeat map algorithm, here we identified the tandemly organized NBPF HORs in the human and nonhuman primate NCBI reference genomes. We identified 50 tandemly organized canonical 3mer NBPF HOR copies (Olduvai triplets), but none in nonhuman primates chimpanzee, gorilla, orangutan, and Rhesus macaque. This discontinuous jump in tandemly organized HOR copy number is in sharp contrast to the known gradual increase in the number of Olduvai domains (NBPF monomers) from nonhuman primates to human, especially from ∼138 in chimpanzee to ∼300 in human genome. Using the same global repeat map algorithm method we have also determined the 3mer tandems of canonical 3mer HOR copies in 20 randomly chosen human genomes (10 male and 10 female). In all cases, we found the same 3mer HOR copy numbers as in the case of the reference human genome, with no mutation. On the other hand, some point mutations with respect to reference genome are found for some NBPF monomers which are not tandemly organized in canonical HORs.
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Affiliation(s)
- Matko Glunčić
- Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Marija Rosandić
- University Hospital Centre Zagreb (ret), Zagreb, Croatia,Croatian Academy of Sciences and Arts, Zagreb, Croatia
| | - Vladimir Paar
- Faculty of Science, University of Zagreb, Zagreb, Croatia,Croatian Academy of Sciences and Arts, Zagreb, Croatia
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8
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Ben-Mahmoud A, Jun KR, Gupta V, Shastri P, de la Fuente A, Park Y, Shin KC, Kim CA, da Cruz AD, Pinto IP, Minasi LB, Silva da Cruz A, Faivre L, Callier P, Racine C, Layman LC, Kong IK, Kim CH, Kim WY, Kim HG. A rigorous in silico genomic interrogation at 1p13.3 reveals 16 autosomal dominant candidate genes in syndromic neurodevelopmental disorders. Front Mol Neurosci 2022; 15:979061. [PMID: 36277487 PMCID: PMC9582330 DOI: 10.3389/fnmol.2022.979061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Genome-wide chromosomal microarray is extensively used to detect copy number variations (CNVs), which can diagnose microdeletion and microduplication syndromes. These small unbalanced chromosomal structural rearrangements ranging from 1 kb to 10 Mb comprise up to 15% of human mutations leading to monogenic or contiguous genomic disorders. Albeit rare, CNVs at 1p13.3 cause a variety of neurodevelopmental disorders (NDDs) including development delay (DD), intellectual disability (ID), autism, epilepsy, and craniofacial anomalies (CFA). Most of the 1p13.3 CNV cases reported in the pre-microarray era encompassed a large number of genes and lacked the demarcating genomic coordinates, hampering the discovery of positional candidate genes within the boundaries. In this study, we present four subjects with 1p13.3 microdeletions displaying DD, ID, autism, epilepsy, and CFA. In silico comparative genomic mapping with three previously reported subjects with CNVs and 22 unreported DECIPHER CNV cases has resulted in the identification of four different sub-genomic loci harboring five positional candidate genes for DD, ID, and CFA at 1p13.3. Most of these genes have pathogenic variants reported, and their interacting genes are involved in NDDs. RT-qPCR in various human tissues revealed a high expression pattern in the brain and fetal brain, supporting their functional roles in NDDs. Interrogation of variant databases and interacting protein partners led to the identification of another set of 11 potential candidate genes, which might have been dysregulated by the position effect of these CNVs at 1p13.3. Our studies define 1p13.3 as a genomic region harboring 16 NDD candidate genes and underscore the critical roles of small CNVs in in silico comparative genomic mapping for disease gene discovery. Our candidate genes will help accelerate the isolation of pathogenic heterozygous variants from exome/genome sequencing (ES/GS) databases.
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Affiliation(s)
- Afif Ben-Mahmoud
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Kyung Ran Jun
- Department of Laboratory Medicine, Inje University Haeundae Paik Hospital, Busan, South Korea
| | - Vijay Gupta
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Pinang Shastri
- Department of Cardiovascular Medicine, Cape Fear Valley Medical Center, Fayetteville, NC, United States
| | - Alberto de la Fuente
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Yongsoo Park
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Kyung Chul Shin
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Chong Ae Kim
- Faculdade de Medicina, Unidade de Genética do Instituto da Criança – Hospital das Clínicas HCFMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Aparecido Divino da Cruz
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Irene Plaza Pinto
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Lysa Bernardes Minasi
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Alex Silva da Cruz
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Laurence Faivre
- Inserm UMR 1231 GAD, Genetics of Developmental Disorders, Université de Bourgogne-Franche Comté, Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d’Enfants, Dijon, France
| | - Patrick Callier
- UMR 1231 GAD, Inserm – Université Bourgogne-Franche Comté, Dijon, France
| | - Caroline Racine
- UMR 1231 GAD, Inserm – Université Bourgogne-Franche Comté, Dijon, France
| | - Lawrence C. Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, United States
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA, United States
| | - Il-Keun Kong
- Department of Animal Science, Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, South Korea
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Woo-Yang Kim
- Department of Biological Sciences, Kent State University, Kent, OH, United States
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- *Correspondence: Hyung-Goo Kim,
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9
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Vořechovský I. Selection of Olduvai Domains during Evolution: A Role for Primate-Specific Splicing Super-Enhancer and RNA Guanine Quadruplex in Bipartite NBPF Exons. Brain Sci 2022; 12:brainsci12070874. [PMID: 35884681 PMCID: PMC9313022 DOI: 10.3390/brainsci12070874] [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: 05/16/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023] Open
Abstract
Olduvai protein domains (also known as DUF1220 or NBPF) have undergone the greatest human-specific increase in the copy number of any coding region in the genome. Their repeat number was strongly associated with the evolutionary expansion of brain volumes, neuron counts and cognitive abilities, as well as with disorders of the autistic spectrum. Nevertheless, the domain function and cellular mechanisms underlying the positive selection of Olduvai DNA sequences in higher primates remain obscure. Here, I show that the inclusion of Olduvai exon doublets in mature transcripts is facilitated by a potent splicing enhancer that was created through duplication within the first exon. The enhancer is the strongest among the NBPF transcripts and further promotes the already high splicing activity of the unexpanded first exons of the two-exon domains, safeguarding the expanded Olduvai exon doublets in the mature transcriptome. The duplication also creates a predicted RNA guanine quadruplex that may regulate the access to spliceosomal components of the super-enhancer and influence the splicing of adjacent exons. Thus, positive Olduvai selection during primate evolution is likely to result from a combination of multiple targets in gene expression pathways, including RNA splicing.
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Affiliation(s)
- Igor Vořechovský
- Faculty of Medicine, University of Southampton, HDH, MP808, Southampton SO16 6YD, UK
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10
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Pengelly RJ, Bakhtiar D, Borovská I, Královičová J, Vořechovský I. Exonic splicing code and protein binding sites for calcium. Nucleic Acids Res 2022; 50:5493-5512. [PMID: 35474482 PMCID: PMC9177970 DOI: 10.1093/nar/gkac270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 11/12/2022] Open
Abstract
Auxilliary splicing sequences in exons, known as enhancers (ESEs) and silencers (ESSs), have been subject to strong selection pressures at the RNA and protein level. The protein component of this splicing code is substantial, recently estimated at ∼50% of the total information within ESEs, but remains poorly understood. The ESE/ESS profiles were previously associated with the Irving-Williams (I-W) stability series for divalent metals, suggesting that the ESE/ESS evolution was shaped by metal binding sites. Here, we have examined splicing activities of exonic sequences that encode protein binding sites for Ca2+, a weak binder in the I-W affinity order. We found that predicted exon inclusion levels for the EF-hand motifs and for Ca2+-binding residues in nonEF-hand proteins were higher than for average exons. For canonical EF-hands, the increase was centred on the EF-hand chelation loop and, in particular, on Ca2+-coordinating residues, with a 1>12>3∼5>9 hierarchy in the 12-codon loop consensus and usage bias at codons 1 and 12. The same hierarchy but a lower increase was observed for noncanonical EF-hands, except for S100 proteins. EF-hand loops preferentially accumulated exon splits in two clusters, one located in their N-terminal halves and the other around codon 12. Using splicing assays and published crosslinking and immunoprecipitation data, we identify candidate trans-acting factors that preferentially bind conserved GA-rich motifs encoding negatively charged amino acids in the loops. Together, these data provide evidence for the high capacity of codons for Ca2+-coordinating residues to be retained in mature transcripts, facilitating their exon-level expansion during eukaryotic evolution.
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Affiliation(s)
- Reuben J Pengelly
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Dara Bakhtiar
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Ivana Borovská
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Jana Královičová
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
- Slovak Academy of Sciences, Institute of Zoology, 845 06 Bratislava, Slovak Republic
| | - Igor Vořechovský
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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11
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Espinós A, Fernández‐Ortuño E, Negri E, Borrell V. Evolution of genetic mechanisms regulating cortical neurogenesis. Dev Neurobiol 2022; 82:428-453. [PMID: 35670518 PMCID: PMC9543202 DOI: 10.1002/dneu.22891] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/26/2022] [Accepted: 05/24/2022] [Indexed: 11/20/2022]
Abstract
The size of the cerebral cortex increases dramatically across amniotes, from reptiles to great apes. This is primarily due to different numbers of neurons and glial cells produced during embryonic development. The evolutionary expansion of cortical neurogenesis was linked to changes in neural stem and progenitor cells, which acquired increased capacity of self‐amplification and neuron production. Evolution works via changes in the genome, and recent studies have identified a small number of new genes that emerged in the recent human and primate lineages, promoting cortical progenitor proliferation and increased neurogenesis. However, most of the mammalian genome corresponds to noncoding DNA that contains gene‐regulatory elements, and recent evidence precisely points at changes in expression levels of conserved genes as key in the evolution of cortical neurogenesis. Here, we provide an overview of basic cellular mechanisms involved in cortical neurogenesis across amniotes, and discuss recent progress on genetic mechanisms that may have changed during evolution, including gene expression regulation, leading to the expansion of the cerebral cortex.
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Affiliation(s)
- Alexandre Espinós
- Instituto de Neurociencias CSIC ‐ UMH, 03550 Sant Joan d'Alacant Spain
| | | | - Enrico Negri
- Instituto de Neurociencias CSIC ‐ UMH, 03550 Sant Joan d'Alacant Spain
| | - Víctor Borrell
- Instituto de Neurociencias CSIC ‐ UMH, 03550 Sant Joan d'Alacant Spain
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12
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Hercules SM, Liu X, Bassey-Archibong BBI, Skeete DHA, Smith Connell S, Daramola A, Banjo AA, Ebughe G, Agan T, Ekanem IO, Udosen J, Obiorah C, Ojule AC, Misauno MA, Dauda AM, Egbujo EC, Hercules JC, Ansari A, Brain I, MacColl C, Xu Y, Jin Y, Chang S, Carpten JD, Bédard A, Pond GR, Blenman KRM, Manojlovic Z, Daniel JM. Analysis of the genomic landscapes of Barbadian and Nigerian women with triple negative breast cancer. Cancer Causes Control 2022; 33:831-841. [PMID: 35384527 PMCID: PMC9085672 DOI: 10.1007/s10552-022-01574-x] [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: 09/09/2021] [Accepted: 03/12/2022] [Indexed: 11/10/2022]
Abstract
PURPOSE Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype that disproportionately affects women of African ancestry (WAA) and is often associated with poor survival. Although there is a high prevalence of TNBC across West Africa and in women of the African diaspora, there has been no comprehensive genomics study to investigate the mutational profile of ancestrally related women across the Caribbean and West Africa. METHODS This multisite cross-sectional study used 31 formalin-fixed paraffin-embedded (FFPE) samples from Barbadian and Nigerian TNBC participants. High-resolution whole exome sequencing (WES) was performed on the Barbadian and Nigerian TNBC samples to identify their mutational profiles and comparisons were made to African American, European American and Asian American sequencing data obtained from The Cancer Genome Atlas (TCGA). Whole exome sequencing was conducted on tumors with an average of 382 × coverage and 4335 × coverage for pooled germline non-tumor samples. RESULTS Variants detected at high frequency in our WAA cohorts were found in the following genes NBPF12, PLIN4, TP53 and BRCA1. In the TCGA TNBC cases, these genes had a lower mutation rate, except for TP53 (32% in our cohort; 63% in TCGA-African American; 67% in TCGA-European American; 63% in TCGA-Asian). For all altered genes, there were no differences in frequency of mutations between WAA TNBC groups including the TCGA-African American cohort. For copy number variants, high frequency alterations were observed in PIK3CA, TP53, FGFR2 and HIF1AN genes. CONCLUSION This study provides novel insights into the underlying genomic alterations in WAA TNBC samples and shines light on the importance of inclusion of under-represented populations in cancer genomics and biomarker studies.
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Affiliation(s)
- Shawn M. Hercules
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
- African Caribbean Cancer Consortium, Philadelphia, PA USA
| | - Xiyu Liu
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | | | - Desiree H. A. Skeete
- African Caribbean Cancer Consortium, Philadelphia, PA USA
- grid.412886.10000 0004 0592 769XFaculty of Medical Sciences, University of the West Indies at Cave Hill, Bridgetown, Barbados
- grid.415521.60000 0004 0570 5165Department of Pathology, Queen Elizabeth Hospital, Bridgetown, Barbados
| | - Suzanne Smith Connell
- grid.412886.10000 0004 0592 769XFaculty of Medical Sciences, University of the West Indies at Cave Hill, Bridgetown, Barbados
- grid.415521.60000 0004 0570 5165Department of Radiation Oncology, Queen Elizabeth Hospital, Bridgetown, Barbados
- Present Address: Cancer Specialists Inc, Bridgetown, Barbados
| | - Adetola Daramola
- grid.411283.d0000 0000 8668 7085Department of Anatomic and Molecular Pathology, Lagos University Teaching Hospital, Lagos, Nigeria
| | - Adekunbiola A. Banjo
- grid.411283.d0000 0000 8668 7085Department of Anatomic and Molecular Pathology, Lagos University Teaching Hospital, Lagos, Nigeria
| | - Godwin Ebughe
- grid.413097.80000 0001 0291 6387Department of Pathology, University of Calabar Teaching Hospital, Calabar, Nigeria
| | - Thomas Agan
- grid.413097.80000 0001 0291 6387Department of Obstetrics & Gynaecology, College of Medical Sciences, University of Calabar Teaching Hospital, Calabar, Nigeria
| | - Ima-Obong Ekanem
- grid.413097.80000 0001 0291 6387Department of Pathology, College of Medical Sciences, University of Calabar Teaching Hospital, Calabar, Nigeria
| | - Joe Udosen
- grid.413097.80000 0001 0291 6387Division of General and Breast Surgery, University of Calabar Teaching Hospital, Calabar, Nigeria
| | - Christopher Obiorah
- grid.412738.bDepartment of Anatomical Pathology, University of Port Harcourt Teaching Hospital, Port Harcourt, Nigeria
| | - Aaron C. Ojule
- grid.412738.bDepartment of Chemical Pathology, University of Port Harcourt Teaching Hospital, Port Harcourt, Nigeria
| | - Michael A. Misauno
- grid.411946.f0000 0004 1783 4052Department of Surgery, Jos University Teaching Hospital, Jos, Nigeria
| | - Ayuba M. Dauda
- grid.411946.f0000 0004 1783 4052Department of Pathology, Jos University Teaching Hospital, Jos, Nigeria
| | | | - Jevon C. Hercules
- grid.12916.3d0000 0001 2322 4996Department of Mathematics, University of the West Indies at Mona, Kingston, Jamaica
- grid.12955.3a0000 0001 2264 7233Present Address: Wang Yanan Institute for Studies in Economics, Xiamen University, Xiamen, China
| | - Amna Ansari
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
| | - Ian Brain
- grid.25073.330000 0004 1936 8227Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada
| | - Christine MacColl
- grid.25073.330000 0004 1936 8227Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada
| | - Yili Xu
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Yuxin Jin
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Sharon Chang
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - John D. Carpten
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - André Bédard
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
| | - Greg R. Pond
- grid.25073.330000 0004 1936 8227Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON Canada
- grid.25073.330000 0004 1936 8227Department of Oncology, McMaster University, Hamilton, ON Canada
| | - Kim R. M. Blenman
- grid.433818.5Department of Internal Medicine, Section of Medical Oncology, Yale Cancer Center, School of Medicine, New Haven, CT USA
- grid.47100.320000000419368710Department of Computer Science, School of Engineering and Applied Science, Yale University, New Haven, CT USA
| | - Zarko Manojlovic
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Juliet M. Daniel
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
- African Caribbean Cancer Consortium, Philadelphia, PA USA
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13
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Mora-Bermúdez F, Huttner WB. What Are the Human-Specific Aspects of Neocortex Development? Front Neurosci 2022; 16:878950. [PMID: 35495057 PMCID: PMC9047014 DOI: 10.3389/fnins.2022.878950] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
When considering what makes us human, the development of the neocortex, the seat of our higher cognitive abilities, is of central importance. Throughout this complex developmental process, neocortical stem and progenitor cells (NSPCs) exert a priming role in determining neocortical tissue fate, through a series of cellular and molecular events. In this Perspective article, we address five questions of relevance for potentially human-specific aspects of NSPCs, (i) Are there human-specific NSPC subtypes? (ii) What is the functional significance of the known temporal differences in NSPC dynamics between human and other great apes? (iii) Are there functional interactions between the human-specific genes preferentially expressed in NSPCs? (iv) Do humans amplify certain metabolic pathways for NSPC proliferation? and finally (v) Have differences evolved during human evolution, notably between modern humans and Neandertals, that affect the performance of key genes operating in NSPCs? We discuss potential implications inherent to these questions, and suggest experimental approaches on how to answer them, hoping to provide incentives to further understand key issues of human cortical development.
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14
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Elling CL, Scholes MA, Streubel SO, Larson ED, Wine TM, Bootpetch TC, Yoon PJ, Kofonow JM, Gubbels SP, Cass SP, Robertson CE, Jenkins HA, Prager JD, Frank DN, Chan KH, Friedman NR, Ryan AF, Santos-Cortez RLP. The FUT2 Variant c.461G>A (p.Trp154*) Is Associated With Differentially Expressed Genes and Nasopharyngeal Microbiota Shifts in Patients With Otitis Media. Front Cell Infect Microbiol 2022; 11:798246. [PMID: 35096646 PMCID: PMC8798324 DOI: 10.3389/fcimb.2021.798246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/20/2021] [Indexed: 12/30/2022] Open
Abstract
Otitis media (OM) is a leading cause of childhood hearing loss. Variants in FUT2, which encodes alpha-(1,2)-fucosyltransferase, were identified to increase susceptibility to OM, potentially through shifts in the middle ear (ME) or nasopharyngeal (NP) microbiotas as mediated by transcriptional changes. Greater knowledge of differences in relative abundance of otopathogens in carriers of pathogenic variants can help determine risk for OM in patients. In order to determine the downstream effects of FUT2 variation, we examined gene expression in relation to carriage of a common pathogenic FUT2 c.461G>A (p.Trp154*) variant using RNA-sequence data from saliva samples from 28 patients with OM. Differential gene expression was also examined in bulk mRNA and single-cell RNA-sequence data from wildtype mouse ME mucosa after inoculation with non-typeable Haemophilus influenzae (NTHi). In addition, microbiotas were profiled from ME and NP samples of 65 OM patients using 16S rRNA gene sequencing. In human carriers of the FUT2 variant, FN1, KMT2D, MUC16 and NBPF20 were downregulated while MTAP was upregulated. Post-infectious expression in the mouse ME recapitulated these transcriptional differences, with the exception of Fn1 upregulation after NTHi-inoculation. In the NP, Candidate Division TM7 was associated with wildtype genotype (FDR-adj-p=0.009). Overall, the FUT2 c.461G>A variant was associated with transcriptional changes in processes related to response to infection and with increased load of potential otopathogens in the ME and decreased commensals in the NP. These findings provide increased understanding of how FUT2 variants influence gene transcription and the mucosal microbiota, and thus contribute to the pathology of OM.
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Affiliation(s)
- Christina L. Elling
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Melissa A. Scholes
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Sven-Olrik Streubel
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Eric D. Larson
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Todd M. Wine
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Tori C. Bootpetch
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Patricia J. Yoon
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Jennifer M. Kofonow
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Samuel P. Gubbels
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Stephen P. Cass
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Charles E. Robertson
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Herman A. Jenkins
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jeremy D. Prager
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Daniel N. Frank
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Kenny H. Chan
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Norman R. Friedman
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Allen F. Ryan
- Division of Otolaryngology, Department of Surgery, San Diego School of Medicine and Veterans Affairs Medical Center, University of California, La Jolla, CA, United States
| | - Regie Lyn P. Santos-Cortez
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Center for Children’s Surgery, Children’s Hospital Colorado, Aurora, CO, United States
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15
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Global gene expression analysis of systemic sclerosis myofibroblasts demonstrates a marked increase in the expression of multiple NBPF genes. Sci Rep 2021; 11:20435. [PMID: 34650102 PMCID: PMC8516909 DOI: 10.1038/s41598-021-99292-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 09/08/2021] [Indexed: 12/22/2022] Open
Abstract
Myofibroblasts are the key effector cells responsible for the exaggerated tissue fibrosis in Systemic Sclerosis (SSc). Despite their importance to SSc pathogenesis, the specific transcriptome of SSc myofibroblasts has not been described. The purpose of this study was to identify transcriptome differences between SSc myofibroblasts and non-myofibroblastic cells. Alpha smooth muscle actin (α-SMA) expressing myofibroblasts and α-SMA negative cells were isolated employing laser capture microdissection from dermal cell cultures from four patients with diffuse SSc of recent onset. Total mRNA was extracted from both cell populations, amplified and analyzed employing microarrays. Results for specific genes were validated by Western blots and by immunohistochemistry. Transcriptome analysis revealed 97 differentially expressed transcripts in SSc myofibroblasts compared with non-myofibroblasts. Annotation clustering of the SSc myofibroblast-specific transcripts failed to show a TGF-β signature. The most represented transcripts corresponded to several different genes from the Neuroblastoma Breakpoint Family (NBPF) of genes. NBPF genes are highly expanded in humans but are not present in murine or rat genomes. In vitro studies employing cultured SSc dermal fibroblasts and immunohistochemistry of affected SSc skin confirmed increased NBPF expression in SSc. These results indicate that SSc myofibroblasts represent a unique cell lineage expressing a specific transcriptome that includes very high levels of transcripts corresponding to numerous NBPF genes. Elevated expression of NBPF genes in SSc myofibroblasts suggests that NBPF gene products may play a role in SSc pathogenesis and may represent a novel therapeutic target.
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16
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Anuntakarun S, Larbcharoensub N, Payungporn S, Reamtong O. Identification of genes associated with Kikuchi-Fujimoto disease using RNA and exome sequencing. Mol Cell Probes 2021; 57:101728. [PMID: 33819568 DOI: 10.1016/j.mcp.2021.101728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/16/2021] [Accepted: 03/29/2021] [Indexed: 12/15/2022]
Abstract
Kikuchi-Fujimoto disease (KFD) is an extremely rare disease, and although it is reported to have a worldwide distribution, young Asian women are most likely to be affected. Although this disease is generally benign and self-limiting, distinguishing it from other diseases that cause lymphadenopathy (e.g., leukemia, lymphoma, and infectious diseases) is challenging. A lymph node biopsy is a definitive diagnostic technique for KFD and only requires skillful pathologists. There are no specific symptoms or laboratory tests for KFD, and more than 50% of KFD patients have suffered from being misdiagnosed with lymphoma, which leads to improper treatment. In this study, lymph node tissue samples from KFD patients were used to reveal their exomes and transcriptomes using a high-throughput nucleotide sequencer. Fourteen single nucleotide polymorphisms (SNPs) were identified as candidate KFD markers and were compared with a healthy lymph node exome dataset. The mutation of these genes caused disruptive impact in the proteins. Several SNPs associated with KFD involve genes related to human cancers, olfaction, and osteoblast differentiation. According to the transcriptome data, there were 238 up-regulated and 1,519 down-regulated genes. RANBP2-like and ribosomal protein L13 were the most up-regulated and down-regulated genes in KFD patients, respectively. The altered gene expression involved in the human immune system, chromatin remodeling, and gene transcription. A comparison of KFD and healthy datasets of exomes and transcriptomes may allow further insights into the KFD phenotype. The results may also facilitate future KFD diagnosis and treatment.
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Affiliation(s)
- Songtham Anuntakarun
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Noppadol Larbcharoensub
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand; Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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17
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Heide M, Huttner WB. Human-Specific Genes, Cortical Progenitor Cells, and Microcephaly. Cells 2021; 10:1209. [PMID: 34063381 PMCID: PMC8156310 DOI: 10.3390/cells10051209] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/13/2022] Open
Abstract
Over the past few years, human-specific genes have received increasing attention as potential major contributors responsible for the 3-fold difference in brain size between human and chimpanzee. Accordingly, mutations affecting these genes may lead to a reduction in human brain size and therefore, may cause or contribute to microcephaly. In this review, we will concentrate, within the brain, on the cerebral cortex, the seat of our higher cognitive abilities, and focus on the human-specific gene ARHGAP11B and on the gene family comprising the three human-specific genes NOTCH2NLA, -B, and -C. These genes are thought to have significantly contributed to the expansion of the cerebral cortex during human evolution. We will summarize the evolution of these genes, as well as their expression and functional role during human cortical development, and discuss their potential relevance for microcephaly. Furthermore, we will give an overview of other human-specific genes that are expressed during fetal human cortical development. We will discuss the potential involvement of these genes in microcephaly and how these genes could be studied functionally to identify a possible role in microcephaly.
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Affiliation(s)
- Michael Heide
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstr. 108, D-01307 Dresden, Germany
| | - Wieland B. Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstr. 108, D-01307 Dresden, Germany
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18
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Theut Riis P, Loft I, Yazdanyar S, Kjærsgaard Andersen R, Pedersen O, Ring H, Huber R, Sultan M, Loesche C, Saunte D, Jemec G. Full exome sequencing of 11 families with Hidradenitis suppurativa. J Eur Acad Dermatol Venereol 2021; 35:1203-1211. [DOI: 10.1111/jdv.17095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/01/2020] [Indexed: 12/25/2022]
Affiliation(s)
- P. Theut Riis
- Department of Dermatology Zealand University Hospital Roskilde Denmark
| | - I.C. Loft
- Department of Clinical Immunology Naestved Hospital Naestved Denmark
| | - S. Yazdanyar
- Department of Dermatology Zealand University Hospital Roskilde Denmark
| | | | - O.B. Pedersen
- Department of Clinical Immunology Naestved Hospital Naestved Denmark
| | - H.C. Ring
- Department of Dermatology Zealand University Hospital Roskilde Denmark
| | - R. Huber
- Novartis Institutes for BioMedical Research Basel Switzerland
| | - M. Sultan
- Novartis Institutes for BioMedical Research Basel Switzerland
| | - C. Loesche
- Novartis Institutes for BioMedical Research Basel Switzerland
| | - D.M.L. Saunte
- Department of Dermatology Zealand University Hospital Roskilde Denmark
- Department of Clinical Medicine Health Sciences Faculty University of Copenhagen Copenhagen Denmark
| | - G.B.E. Jemec
- Department of Dermatology Zealand University Hospital Roskilde Denmark
- Department of Clinical Medicine Health Sciences Faculty University of Copenhagen Copenhagen Denmark
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19
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Liu Q, Hu Y, Stucky A, Fang L, Zhong JF, Wang K. LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing. BMC Genomics 2020; 21:793. [PMID: 33372596 PMCID: PMC7771079 DOI: 10.1186/s12864-020-07207-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Long-read RNA-Seq techniques can generate reads that encompass a large proportion or the entire mRNA/cDNA molecules, so they are expected to address inherited limitations of short-read RNA-Seq techniques that typically generate < 150 bp reads. However, there is a general lack of software tools for gene fusion detection from long-read RNA-seq data, which takes into account the high basecalling error rates and the presence of alignment errors. RESULTS In this study, we developed a fast computational tool, LongGF, to efficiently detect candidate gene fusions from long-read RNA-seq data, including cDNA sequencing data and direct mRNA sequencing data. We evaluated LongGF on tens of simulated long-read RNA-seq datasets, and demonstrated its superior performance in gene fusion detection. We also tested LongGF on a Nanopore direct mRNA sequencing dataset and a PacBio sequencing dataset generated on a mixture of 10 cancer cell lines, and found that LongGF achieved better performance to detect known gene fusions over existing computational tools. Furthermore, we tested LongGF on a Nanopore cDNA sequencing dataset on acute myeloid leukemia, and pinpointed the exact location of a translocation (previously known in cytogenetic resolution) in base resolution, which was further validated by Sanger sequencing. CONCLUSIONS In summary, LongGF will greatly facilitate the discovery of candidate gene fusion events from long-read RNA-Seq data, especially in cancer samples. LongGF is implemented in C++ and is available at https://github.com/WGLab/LongGF .
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Affiliation(s)
- Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Yu Hu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Andres Stucky
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Jiang F Zhong
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Nait Saada J, Kalantzis G, Shyr D, Cooper F, Robinson M, Gusev A, Palamara PF. Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations. Nat Commun 2020; 11:6130. [PMID: 33257650 PMCID: PMC7704644 DOI: 10.1038/s41467-020-19588-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/02/2020] [Indexed: 12/14/2022] Open
Abstract
Detection of Identical-By-Descent (IBD) segments provides a fundamental measure of genetic relatedness and plays a key role in a wide range of analyses. We develop FastSMC, an IBD detection algorithm that combines a fast heuristic search with accurate coalescent-based likelihood calculations. FastSMC enables biobank-scale detection and dating of IBD segments within several thousands of years in the past. We apply FastSMC to 487,409 UK Biobank samples and detect ~214 billion IBD segments transmitted by shared ancestors within the past 1500 years, obtaining a fine-grained picture of genetic relatedness in the UK. Sharing of common ancestors strongly correlates with geographic distance, enabling the use of genomic data to localize a sample's birth coordinates with a median error of 45 km. We seek evidence of recent positive selection by identifying loci with unusually strong shared ancestry and detect 12 genome-wide significant signals. We devise an IBD-based test for association between phenotype and ultra-rare loss-of-function variation, identifying 29 association signals in 7 blood-related traits.
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Affiliation(s)
| | | | - Derek Shyr
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Fergus Cooper
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Martin Robinson
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Alexander Gusev
- Brigham & Women's Hospital, Division of Genetics, Boston, MA, 02215, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Pier Francesco Palamara
- Department of Statistics, University of Oxford, Oxford, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
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21
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An integrated Asian human SNV and indel benchmark established using multiple sequencing methods. Sci Rep 2020; 10:9821. [PMID: 32555294 PMCID: PMC7300012 DOI: 10.1038/s41598-020-66605-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 05/05/2020] [Indexed: 11/08/2022] Open
Abstract
Sequencing technologies have been rapidly developed recently, leading to the breakthrough of sequencing-based clinical diagnosis, but accurate and complete genome variation benchmark would be required for further assessment of precision medicine applications. Despite the human cell line of NA12878 has been successfully developed to be a variation benchmark, population-specific variation benchmark is still lacking. Here, we established an Asian human variation benchmark by constructing and sequencing a stabilized cell line of a Chinese Han volunteer. By using seven different sequencing strategies, we obtained ~3.88 Tb clean data from different laboratories, hoping to reach the point of high sequencing depth and accurate variation detection. Through the combination of variations identified from different sequencing strategies and different analysis pipelines, we identified 3.35 million SNVs and 348.65 thousand indels, which were well supported by our sequencing data and passed our strict quality control, thus should be high confidence variation benchmark. Besides, we also detected 5,913 high-quality SNVs which had 969 sites were novel and located in the high homologous regions supported by long-range information in both the co-barcoding single tube Long Fragment Read (stLFR) data and PacBio HiFi CCS data. Furthermore, by using the long reads data (stLFR and HiFi CCS), we were able to phase more than 99% heterozygous SNVs, which helps to improve the benchmark to be haplotype level. Our study provided comprehensive sequencing data as well as the integrated variation benchmark of an Asian derived cell line, which would be valuable for future sequencing-based clinical development.
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Bekpen C, Tautz D. Human core duplicon gene families: game changers or game players? Brief Funct Genomics 2020; 18:402-411. [PMID: 31529038 PMCID: PMC6920530 DOI: 10.1093/bfgp/elz016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/01/2019] [Accepted: 06/24/2019] [Indexed: 01/09/2023] Open
Abstract
Illuminating the role of specific gene duplications within the human lineage can provide insights into human-specific adaptations. The so-called human core duplicon gene families have received particular attention in this respect, due to special features, such as expansion along single chromosomes, newly acquired protein domains and signatures of positive selection. Here, we summarize the data available for 10 such families and include some new analyses. A picture emerges that suggests broad functions for these protein families, possibly through modification of core cellular pathways. Still, more dedicated studies are required to elucidate the function of core-duplicons gene families and how they have shaped adaptations and evolution of humans.
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Affiliation(s)
| | - Diethard Tautz
- Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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23
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Evolutionary Dynamics of the POTE Gene Family in Human and Nonhuman Primates. Genes (Basel) 2020; 11:genes11020213. [PMID: 32085667 PMCID: PMC7073761 DOI: 10.3390/genes11020213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/06/2020] [Accepted: 02/13/2020] [Indexed: 12/20/2022] Open
Abstract
POTE (prostate, ovary, testis, and placenta expressed) genes belong to a primate-specific gene family expressed in prostate, ovary, and testis as well as in several cancers including breast, prostate, and lung cancers. Due to their tumor-specific expression, POTEs are potential oncogenes, therapeutic targets, and biomarkers for these malignancies. This gene family maps within human and primate segmental duplications with a copy number ranging from two to 14 in different species. Due to the high sequence identity among the gene copies, specific efforts are needed to assemble these loci in order to correctly define the organization and evolution of the gene family. Using single-molecule, real-time (SMRT) sequencing, in silico analyses, and molecular cytogenetics, we characterized the structure, copy number, and chromosomal distribution of the POTE genes, as well as their expression in normal and disease tissues, and provided a comparative analysis of the POTE organization and gene structure in primate genomes. We were able, for the first time, to de novo sequence and assemble a POTE tandem duplication in marmoset that is misassembled and collapsed in the reference genome, thus revealing the presence of a second POTE copy. Taken together, our findings provide comprehensive insights into the evolutionary dynamics of the primate-specific POTE gene family, involving gene duplications, deletions, and long interspersed nuclear element (LINE) transpositions to explain the actual repertoire of these genes in human and primate genomes.
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24
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The N-terminal of NBPF15 causes multiple types of aggregates and mediates phase transition. Biochem J 2020; 477:445-458. [DOI: 10.1042/bcj20190566] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 12/26/2022]
Abstract
The neuroblastoma breakpoint family (NBPF) consists of 24 members that play an important role in neuroblastoma and other cancers. NBPF is an evolutionarily recent gene family that encodes several repeats of Olduvai domain and an abundant N-terminal region. The function and biochemical properties of both Olduvai domain and the N-terminal region remain enigmatic. Human NBPF15 encodes a 670 AA protein consisting of six clades of Olduvai domains. In this study, we synthesized and expressed full-length NBPF15, and purified a range of NBPF15 truncations which were analyzed using dynamic light scattering (DLS), superdex200 (S200), small-angle X-ray scattering (SAXS), far-UV circular dichroism (CD) spectroscopy, transmission electron microscope (TEM), and crystallography. We found that proteins containing both the N-terminal region and Olduvai domain are heterogeneous with multiple types of aggregates, and some of them underwent a liquid-to-solid phase transition, probably because of the entanglement within the N-terminal coiled-coil. Proteins that contain only the Olduvai domain are homogeneous extended monomers, and those with the conserved clade 1 (CON1) have manifested a tendency to crystallize. We suggest that the entanglements between the mosaic disorder-ordered segments in NBPF15 N terminus have triggered the multiple types of aggregates and phase transition of NBPF15 proteins, which could be associated with Olduvai-related cognitive dysfunction diseases.
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25
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Heft IE, Mostovoy Y, Levy-Sakin M, Ma W, Stevens AJ, Pastor S, McCaffrey J, Boffelli D, Martin DI, Xiao M, Kennedy MA, Kwok PY, Sikela JM. The Driver of Extreme Human-Specific Olduvai Repeat Expansion Remains Highly Active in the Human Genome. Genetics 2020; 214:179-191. [PMID: 31754017 PMCID: PMC6944415 DOI: 10.1534/genetics.119.302782] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/05/2019] [Indexed: 11/18/2022] Open
Abstract
Sequences encoding Olduvai protein domains (formerly DUF1220) show the greatest human lineage-specific increase in copy number of any coding region in the genome and have been associated, in a dosage-dependent manner, with brain size, cognitive aptitude, autism, and schizophrenia. Tandem intragenic duplications of a three-domain block, termed the Olduvai triplet, in four NBPF genes in the chromosomal 1q21.1-0.2 region, are primarily responsible for the striking human-specific copy number increase. Interestingly, most of the Olduvai triplets are adjacent to, and transcriptionally coregulated with, three human-specific NOTCH2NL genes that have been shown to promote cortical neurogenesis. Until now, the underlying genomic events that drove the Olduvai hyperamplification in humans have remained unexplained. Here, we show that the presence or absence of an alternative first exon of the Olduvai triplet perfectly discriminates between amplified (58/58) and unamplified (0/12) triplets. We provide sequence and breakpoint analyses that suggest the alternative exon was produced by an nonallelic homologous recombination-based mechanism involving the duplicative transposition of an existing Olduvai exon found in the CON3 domain, which typically occurs at the C-terminal end of NBPF genes. We also provide suggestive in vitro evidence that the alternative exon may promote instability through a putative G-quadraplex (pG4)-based mechanism. Lastly, we use single-molecule optical mapping to characterize the intragenic structural variation observed in NBPF genes in 154 unrelated individuals and 52 related individuals from 16 families and show that the presence of pG4-containing Olduvai triplets is strongly correlated with high levels of Olduvai copy number variation. These results suggest that the same driver of genomic instability that allowed the evolutionarily recent, rapid, and extreme human-specific Olduvai expansion remains highly active in the human genome.
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Affiliation(s)
- Ilea E Heft
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Yulia Mostovoy
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Michal Levy-Sakin
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Walfred Ma
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Aaron J Stevens
- Department of Pathology, University of Otago, Christchurch, New Zealand 8140
| | - Steven Pastor
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania 19104
| | - Jennifer McCaffrey
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania 19104
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, Oakland, California 94609
| | - David I Martin
- Children's Hospital Oakland Research Institute, Oakland, California 94609
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania 19104
| | - Martin A Kennedy
- Department of Pathology, University of Otago, Christchurch, New Zealand 8140
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California, San Francisco, California
- Department of Dermatology, University of California, San Francisco, California
- Institute for Human Genetics, University of California, San Francisco, California
| | - James M Sikela
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado 80045
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Issaian A, Schmitt L, Born A, Nichols PJ, Sikela J, Hansen K, Vögeli B, Henen MA. Solution NMR backbone assignment reveals interaction-free tumbling of human lineage-specific Olduvai protein domains. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:339-343. [PMID: 31264103 PMCID: PMC6715528 DOI: 10.1007/s12104-019-09902-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/26/2019] [Indexed: 06/09/2023]
Abstract
Olduvai protein domains, encoded primarily by NBPF genes, have been linked to both human brain evolution and cognitive diseases such as autism and schizophrenia. There are six primary domains that comprise the Olduvai family: three conserved domains (CON1-3) and three human lineage-specific domains (HLS1-3), which typically occur as a triplet (HLS1, HLS2 and HLS3). Herein, we present the solution NMR assignment of the backbone chemical shifts of the separate HLS1, 2 and 3 domains of NBPF15. Our data suggest that there is no change in the structure of the separate domains when compared to the full-length triplet (HLS1-HLS2-HLS3). We also demonstrate that there is no direct interaction between the three domains.
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Affiliation(s)
- Aaron Issaian
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Lauren Schmitt
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Alexandra Born
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Parker J Nichols
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA
| | - James Sikela
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Kirk Hansen
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Beat Vögeli
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA.
| | - Morkos A Henen
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
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Florou V, Rosenberg AE, Wieder E, Komanduri KV, Kolonias D, Uduman M, Castle JC, Buell JS, Trent JC, Wilky BA. Angiosarcoma patients treated with immune checkpoint inhibitors: a case series of seven patients from a single institution. J Immunother Cancer 2019; 7:213. [PMID: 31395100 PMCID: PMC6686562 DOI: 10.1186/s40425-019-0689-7] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/23/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Angiosarcoma is an uncommon endothelial malignancy and a highly aggressive soft tissue sarcoma. Due to its infiltrative nature, successful management of localized angiosarcoma is often challenging. Systemic chemotherapy is used in the metastatic setting and occasionally in patients with high-risk localized disease in neoadjuvant or adjuvant settings. However, responses tend to be short-lived and most patients succumb to metastatic disease. Novel therapies are needed for patients with angiosarcomas. METHODS We performed a retrospective analysis of patients with locally advanced or metastatic angiosarcoma, who were treated with checkpoint inhibitors at our institution. We collected their clinical information and outcome measurements. In one patient with achieved complete response, we analyzed circulating and infiltrating T cells within peripheral blood and tumor tissue. RESULTS We have treated seven angiosarcoma (AS) patients with checkpoint inhibitors either in the context of clinical trials or off label [Pembrolizumab + Axitinib (NCT02636725; n = 1), AGEN1884, a CTLA-4 inhibitor (NCT02694822; n = 2), Pembrolizumab (n = 4)]. Five patients had cutaneous angiosarcoma, one primary breast angiosarcoma and one radiation-associated breast angiosarcoma. At 12 weeks, 5/7 patients (71%) had partial response of their lesions either on imaging and/or clinical exam and two (29%) had progressive disease. 6/7 patients are alive to date and, thus far, 3/7 patients (43%) have progressed (median 3.4 months)- one achieved partial response after pembrolizumab was switched to ongoing Nivolumab/Ipilimumab, one died of progressive disease at 31 weeks (primary breast angiosarcoma) and one was placed on pazopanib. One patient had a complete response (CR) following extended treatment with monotherapy AGEN1884. No patient experienced any ≥ grade 2 toxicities. CONCLUSIONS This case series underscores the value of targeted immunotherapy in treating angiosarcoma. It also identifies genetic heterogeneity of cutaneous angiosarcomas and discusses specific genetic findings that may explain reported benefits from immunotherapy.
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Affiliation(s)
- Vaia Florou
- Department of Medicine, Division of Oncology, Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine, 1475 NW 12th Avenue, Miami, FL 33136 USA
| | - Andrew E. Rosenberg
- Department of Medicine, Division of Oncology, Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine, 1475 NW 12th Avenue, Miami, FL 33136 USA
| | - Eric Wieder
- Department of Medicine, Division of Oncology, Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine, 1475 NW 12th Avenue, Miami, FL 33136 USA
| | - Krishna V. Komanduri
- Department of Medicine, Division of Oncology, Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine, 1475 NW 12th Avenue, Miami, FL 33136 USA
| | - Despina Kolonias
- Department of Medicine, Division of Oncology, Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine, 1475 NW 12th Avenue, Miami, FL 33136 USA
| | | | | | | | - Jonathan C. Trent
- Department of Medicine, Division of Oncology, Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine, 1475 NW 12th Avenue, Miami, FL 33136 USA
| | - Breelyn A. Wilky
- Department of Medicine, Division of Oncology, Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine, 1475 NW 12th Avenue, Miami, FL 33136 USA
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Davis JM, Heft I, Scherer SW, Sikela JM. A Third Linear Association Between Olduvai (DUF1220) Copy Number and Severity of the Classic Symptoms of Inherited Autism. Am J Psychiatry 2019; 176:643-650. [PMID: 30764650 PMCID: PMC6675654 DOI: 10.1176/appi.ajp.2018.18080993] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE The authors previously reported that the copy number of sequences encoding an Olduvai protein domain subtype (CON1) shows a linear association with the severity of social deficits and communication impairment in individuals with autism. In this study, using an improved measurement method, the authors replicated this association in an independent population. METHOD The authors obtained whole genome sequence (WGS) data and phenotype data on 215 individuals from the Autism Speaks MSSNG project. They derived copy number from WGS data using a modified sequence read-depth technique. A linear mixed-effects model was used to test the association between Olduvai CON1 copy number and symptom severity as measured by the Autism Diagnostic Interview-Revised. The authors then combined data from previous studies (N=524) for final analyses. RESULTS A significant linear association was observed between CON1 copy number and social diagnostic score (SDS) (β=0.24) and communicative diagnostic score (CDS) (β=0.23). Using the combined data, the authors present strong significant associations of CON1 dosage with SDS (β=0.18) and CDS (β=0.13). The authors also implicate Olduvai subtypes found in two genes, NBPF1 and NBPF14 (R2=6.2%). Associations were preferentially found in multiplex versus simplex families. CONCLUSIONS The finding of a third dose-dependent association between Olduvai sequences and autism severity, preferentially in multiplex families, provides strong evidence that this highly duplicated and underexamined protein domain family plays an important role in inherited autism.
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Affiliation(s)
- Jonathan M. Davis
- Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Genomics Program and Neuroscience Program, University of Colorado School of Medicine
| | - Ilea Heft
- Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Genomics Program and Neuroscience Program, University of Colorado School of Medicine
| | - Stephen W. Scherer
- McLaughlin Centre and Department of Molecular Genetics, University of Toronto,The Centre for Applied Genomics and Program in Genetics and Genome Biology, Hospital for Sick Children
| | - James M. Sikela
- Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Genomics Program and Neuroscience Program, University of Colorado School of Medicine
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Ishiura H, Shibata S, Yoshimura J, Suzuki Y, Qu W, Doi K, Almansour MA, Kikuchi JK, Taira M, Mitsui J, Takahashi Y, Ichikawa Y, Mano T, Iwata A, Harigaya Y, Matsukawa MK, Matsukawa T, Tanaka M, Shirota Y, Ohtomo R, Kowa H, Date H, Mitsue A, Hatsuta H, Morimoto S, Murayama S, Shiio Y, Saito Y, Mitsutake A, Kawai M, Sasaki T, Sugiyama Y, Hamada M, Ohtomo G, Terao Y, Nakazato Y, Takeda A, Sakiyama Y, Umeda-Kameyama Y, Shinmi J, Ogata K, Kohno Y, Lim SY, Tan AH, Shimizu J, Goto J, Nishino I, Toda T, Morishita S, Tsuji S. Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease. Nat Genet 2019; 51:1222-1232. [DOI: 10.1038/s41588-019-0458-z] [Citation(s) in RCA: 178] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 05/29/2019] [Indexed: 11/09/2022]
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30
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Genno PG, Nemer GM, Zein Eddine SB, Macari AT, Ghafari JG. Three novel genes tied to mandibular prognathism in eastern Mediterranean families. Am J Orthod Dentofacial Orthop 2019; 156:104-112.e3. [PMID: 31256822 DOI: 10.1016/j.ajodo.2018.08.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 08/01/2018] [Accepted: 08/01/2018] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Mandibular prognathism (MP) is subject to major polygenic influence and segregates within families in autosomal dominance with variable expressivity and incomplete penetrance. We aimed to identify the inheritance pattern and genes and loci involved in the development of MP in Mediterranean families and to evaluate the dentoskeletal characteristics of affected individuals. METHODS Fifty-one eastern Mediterranean families with individuals affected by MP were identified. Data and biospecimens were collected from 14 of the families, including clinical examination, lateral cephalography (on subjects with Class III malocclusion), and 5 mL blood drawn from consenting affected and nonaffected relatives. Next-generation sequencing (NGS) was performed on 8 families (7 Lebanese, 1 Lebanese/Syrian), including large numbers of affected individuals over many generations and severe conditions, with the use of whole-exome sequencing. RESULTS Most pedigrees suggested autosomal-dominant inheritance with an equal number of affected male and female individuals. Affected individuals had macrognathic and prognathic mandibles with dentoalveolar compensation. Genetic screening did not correspond with previously reported MP-linked genes, but yielded 3 novel genes (C1orf167, NBPF8, NBPF9) on chromosome 1 potentially responsible for mandibular development and macrognathism. CONCLUSIONS In this first genetic study with the use of NGS on the largest reported number of families with MP, novel genes (C1orf167, NBPF8, NBPF9) were associated with familial MP in the eastern Mediterranean population.
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Affiliation(s)
- Pamela G Genno
- Division of Orthodontics and Dentofacial Orthopedics, Department of Otolaryngology and Head and Neck Surgery, American University of Beirut, Beirut, Lebanon
| | - Georges M Nemer
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Savo Bou Zein Eddine
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Anthony T Macari
- Division of Orthodontics and Dentofacial Orthopedics, Department of Otolaryngology and Head and Neck Surgery, American University of Beirut, Beirut, Lebanon.
| | - Joseph G Ghafari
- Division of Orthodontics and Dentofacial Orthopedics, Department of Otolaryngology and Head and Neck Surgery, American University of Beirut, Beirut, Lebanon
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31
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Fiddes IT, Pollen AA, Davis JM, Sikela JM. Paired involvement of human-specific Olduvai domains and NOTCH2NL genes in human brain evolution. Hum Genet 2019; 138:715-721. [PMID: 31087184 PMCID: PMC6611739 DOI: 10.1007/s00439-019-02018-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 04/16/2019] [Indexed: 02/07/2023]
Abstract
Sequences encoding Olduvai (DUF1220) protein domains show the largest human-specific increase in copy number of any coding region in the genome and have been linked to human brain evolution. Most human-specific copies of Olduvai (119/165) are encoded by three NBPF genes that are adjacent to three human-specific NOTCH2NL genes that have been shown to promote cortical neurogenesis. Here, employing genomic, phylogenetic, and transcriptomic evidence, we show that these NOTCH2NL/NBPF gene pairs evolved jointly, as two-gene units, very recently in human evolution, and are likely co-regulated. Remarkably, while three NOTCH2NL paralogs were added, adjacent Olduvai sequences hyper-amplified, adding 119 human-specific copies. The data suggest that human-specific Olduvai domains and adjacent NOTCH2NL genes may function in a coordinated, complementary fashion to promote neurogenesis and human brain expansion in a dosage-related manner.
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Affiliation(s)
| | - Alex A Pollen
- Department of Neurology and the Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan M Davis
- Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Genomics Program and Neuroscience Program, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - James M Sikela
- Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Genomics Program and Neuroscience Program, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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32
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Derpoorter C, Vandepoele K, Diez-Fraile A, Vandemeulebroecke K, De Wilde B, Speleman F, Van Roy N, Lammens T, Laureys G. Pinpointing a potential role for CLEC12B in cancer predisposition through familial exome sequencing. Pediatr Blood Cancer 2019; 66:e27513. [PMID: 30350915 DOI: 10.1002/pbc.27513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 09/24/2018] [Accepted: 09/24/2018] [Indexed: 11/06/2022]
Abstract
Predisposition to cancer is only partly understood, and thus, the contribution of still undiscovered cancer predisposing variants necessitates further research. In search of such variants, we performed exome sequencing on the germline DNA of a family with two children affected by ganglioneuroma and neuroblastoma. Applying stringent selection criteria, we identified a potential deleterious, missense mutation in CLEC12B, coding for a lectin C-type receptor that is predicted to regulate immune function. Although further screening in a larger population and functional characterization is needed, we propose CLEC12B as a candidate cancer predisposition gene.
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Affiliation(s)
- Charlotte Derpoorter
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Karl Vandepoele
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Araceli Diez-Fraile
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Katrien Vandemeulebroecke
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Bram De Wilde
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Frank Speleman
- Cancer Research Institute Ghent, Ghent, Belgium.,Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Nadine Van Roy
- Cancer Research Institute Ghent, Ghent, Belgium.,Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Tim Lammens
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Geneviève Laureys
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
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33
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Shi X, Cheng L, Jiao X, Chen B, Li Z, Liang Y, Liu W, Wang J, Liu G, Xu Y, Sun J, Fu Q, Lu Y, Chen S. Rare Copy Number Variants Identify Novel Genes in Sporadic Total Anomalous Pulmonary Vein Connection. Front Genet 2018; 9:559. [PMID: 30532766 PMCID: PMC6265481 DOI: 10.3389/fgene.2018.00559] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/02/2018] [Indexed: 12/12/2022] Open
Abstract
Total anomalous pulmonary venous connection (TAPVC) is a rare congenital heart anomaly. Several genes have been associated TAPVC but the mechanisms remain elusive. To search novel CNVs and candidate genes, we screened a cohort of 78 TAPVC cases and 100 healthy controls for rare copy number variants (CNVs) using whole exome sequencing (WES). Then we identified pathogenic CNVs by statistical comparisons between case and control groups. After that, we identified altogether eight pathogenic CNVs of seven candidate genes (PCSK7, RRP7A, SERHL, TARP, TTN, SERHL2, and NBPF3). All these seven genes have not been described previously to be related to TAPVC. After network analysis of these candidate genes and 27 known pathogenic genes derived from the literature and publicly database, PCSK7 and TTN were the most important genes for TAPVC than other genes. Our study provides novel candidate genes potentially related to this rare congenital birth defect (CHD) which should be further fundamentally researched and discloses the possible molecular pathogenesis of TAPVC.
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Affiliation(s)
- Xin Shi
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liangping Cheng
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - XianTing Jiao
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Chen
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zixiong Li
- Department of Medical Oncology, Bayi Hospital, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yulai Liang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wei Liu
- Department of Cardiothoracic Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Wang
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Gang Liu
- Medical Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuejuan Xu
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Sun
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qihua Fu
- Medical Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanan Lu
- Department of Cardiothoracic Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Sun Chen
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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34
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Rajendran BK, Deng CX. Characterization of potential driver mutations involved in human breast cancer by computational approaches. Oncotarget 2018; 8:50252-50272. [PMID: 28477017 PMCID: PMC5564847 DOI: 10.18632/oncotarget.17225] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/26/2017] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the second most frequently occurring form of cancer and is also the second most lethal cancer in women worldwide. A genetic mutation is one of the key factors that alter multiple cellular regulatory pathways and drive breast cancer initiation and progression yet nature of these cancer drivers remains elusive. In this article, we have reviewed various computational perspectives and algorithms for exploring breast cancer driver mutation genes. Using both frequency based and mutational exclusivity based approaches, we identified 195 driver genes and shortlisted 63 of them as candidate drivers for breast cancer using various computational approaches. Finally, we conducted network and pathway analysis to explore their functions in breast tumorigenesis including tumor initiation, progression, and metastasis.
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Affiliation(s)
- Barani Kumar Rajendran
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chu-Xia Deng
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
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35
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Dharanipragada P, Vogeti S, Parekh N. iCopyDAV: Integrated platform for copy number variations-Detection, annotation and visualization. PLoS One 2018; 13:e0195334. [PMID: 29621297 PMCID: PMC5886540 DOI: 10.1371/journal.pone.0195334] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/20/2018] [Indexed: 12/14/2022] Open
Abstract
Discovery of copy number variations (CNVs), a major category of structural variations, have dramatically changed our understanding of differences between individuals and provide an alternate paradigm for the genetic basis of human diseases. CNVs include both copy gain and copy loss events and their detection genome-wide is now possible using high-throughput, low-cost next generation sequencing (NGS) methods. However, accurate detection of CNVs from NGS data is not straightforward due to non-uniform coverage of reads resulting from various systemic biases. We have developed an integrated platform, iCopyDAV, to handle some of these issues in CNV detection in whole genome NGS data. It has a modular framework comprising five major modules: data pre-treatment, segmentation, variant calling, annotation and visualization. An important feature of iCopyDAV is the functional annotation module that enables the user to identify and prioritize CNVs encompassing various functional elements, genomic features and disease-associations. Parallelization of the segmentation algorithms makes the iCopyDAV platform even accessible on a desktop. Here we show the effect of sequencing coverage, read length, bin size, data pre-treatment and segmentation approaches on accurate detection of the complete spectrum of CNVs. Performance of iCopyDAV is evaluated on both simulated data and real data for different sequencing depths. It is an open-source integrated pipeline available at https://github.com/vogetihrsh/icopydav and as Docker’s image at http://bioinf.iiit.ac.in/icopydav/.
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Affiliation(s)
- Prashanthi Dharanipragada
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
| | - Sriharsha Vogeti
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
| | - Nita Parekh
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
- * E-mail:
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36
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Levchenko A, Kanapin A, Samsonova A, Gainetdinov RR. Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development. Genome Biol Evol 2018; 10:166-188. [PMID: 29149249 PMCID: PMC5767953 DOI: 10.1093/gbe/evx240] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2017] [Indexed: 12/24/2022] Open
Abstract
The review discusses, in a format of a timeline, the studies of different types of genetic variants, present in Homo sapiens, but absent in all other primate, mammalian, or vertebrate species, tested so far. The main characteristic of these variants is that they are found in regions of high evolutionary conservation. These sequence variations include single nucleotide substitutions (called human accelerated regions), deletions, and segmental duplications. The rationale for finding such variations in the human genome is that they could be responsible for traits, specific to our species, of which the human brain is the most remarkable. As became obvious, the vast majority of human-specific single nucleotide substitutions are found in noncoding, likely regulatory regions. A number of genes, associated with these human-specific alleles, often through novel enhancer activity, were in fact shown to be implicated in human-specific development of certain brain areas, including the prefrontal cortex. Human-specific deletions may remove regulatory sequences, such as enhancers. Segmental duplications, because of their large size, create new coding sequences, like new functional paralogs. Further functional study of these variants will shed light on evolution of our species, as well as on the etiology of neurodevelopmental disorders.
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Affiliation(s)
- Anastasia Levchenko
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
| | - Alexander Kanapin
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
- Department of Oncology, University of Oxford, United Kingdom
| | - Anastasia Samsonova
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
- Department of Oncology, University of Oxford, United Kingdom
| | - Raul R Gainetdinov
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia
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37
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Sikela JM, Searles Quick VB. Genomic trade-offs: are autism and schizophrenia the steep price of the human brain? Hum Genet 2018; 137:1-13. [PMID: 29335774 PMCID: PMC5898792 DOI: 10.1007/s00439-017-1865-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/29/2017] [Indexed: 01/29/2023]
Abstract
Evolution often deals in genomic trade-offs: changes in the genome that are beneficial overall persist even though they also produce disease in a subset of individuals. Here, we explore the possibility that such trade-offs have occurred as part of the evolution of the human brain. Specifically, we provide support for the possibility that the same key genes that have been major contributors to the rapid evolutionary expansion of the human brain and its exceptional cognitive capacity also, in different combinations, are significant contributors to autism and schizophrenia. Furthermore, the model proposes that one of the primary genes behind this trade-off may not technically be "a gene" or "genes" but rather are the highly duplicated sequences that encode the Olduvai protein domain family (formerly called DUF1220). This is not an entirely new idea. Others have proposed that the same genes involved in schizophrenia were also critical to the rapid expansion of the human brain, a view that has been expressed as "the same 'genes' that drive us mad have made us human". What is new is that a "gene", or more precisely a protein domain family, has been found that may satisfy these requirements.
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Affiliation(s)
- J M Sikela
- University of Colorado School of Medicine, Aurora, CO, USA.
| | - V B Searles Quick
- University of Colorado School of Medicine, Aurora, CO, USA
- Department of Psychiatry, University of California, San Francisco, California, USA
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38
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Abstract
We are jointly proposing a new name for a protein domain of approximately 65 amino acids that has been previously termed NBPF or DUF1220. Our two labs independently reported the initial studies of this domain, which is encoded almost entirely within a single gene family. The name Neuroblastoma Breakpoint Family (
NBPF) was applied to this gene family when the first identified member of the family was found to be interrupted in an individual with neuroblastoma. Prior to this discovery, the Pfam database had termed the domain DUF1220, denoting it as one of many protein
domains of
unknown
function. It has been Pfam’s intention to use “DUF” nomenclature to serve only as a temporary placeholder until more appropriate names are proposed based on research findings. We believe that additional studies of this domain, primarily from our laboratories over the past 10 years, have resulted in furthering our understanding of these sequences to the point where proposing a new name for this domain is warranted. Because of considerable data linking the domain to human-specific evolution, brain expansion and cognition, we believe a name reflecting these findings would be appropriate. With this in mind, we have chosen to name the domain (and the repeat that encodes it) Olduvai. The gene family will remain as
NBPF for now. The primary domain subtypes will retain their previously assigned names (e.g. CON1-3; HLS1-3), and the three-domain block that expanded dramatically in the human lineage will be termed the Olduvai triplet. The new name refers to Olduvai Gorge, which is a site in East Africa that has been the source of major anthropological discoveries in the early-mid 1900’s. We also chose the name as a tribute to the scientists who made important contributions to the early studies of human origins and our African genesis.
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Affiliation(s)
- James M Sikela
- Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Neuroscience Programs, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Frans van Roy
- Department of Biomedical Molecular Biology, Ghent University, Ghent, 9052, Belgium.,VIB-UGent Center for Inflammation Research, Ghent, 9052, Belgium
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39
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Regulation of Androgen Receptor Activity by Transient Interactions of Its Transactivation Domain with General Transcription Regulators. Structure 2017; 26:145-152.e3. [PMID: 29225078 DOI: 10.1016/j.str.2017.11.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/12/2017] [Accepted: 11/10/2017] [Indexed: 11/23/2022]
Abstract
The androgen receptor is a transcription factor that plays a key role in the development of prostate cancer, and its interactions with general transcription regulators are therefore of potential therapeutic interest. The mechanistic basis of these interactions is poorly understood due to the intrinsically disordered nature of the transactivation domain of the androgen receptor and the generally transient nature of the protein-protein interactions that trigger transcription. Here, we identify a motif of the transactivation domain that contributes to transcriptional activity by recruiting the C-terminal domain of subunit 1 of the general transcription regulator TFIIF. These findings provide molecular insights into the regulation of androgen receptor function and suggest strategies for treating castration-resistant prostate cancer.
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40
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Singh J, Minster RL, Schupf N, Kraja A, Liu Y, Christensen K, Newman AB, Kammerer CM. Genomewide Association Scan of a Mortality Associated Endophenotype for a Long and Healthy Life in the Long Life Family Study. J Gerontol A Biol Sci Med Sci 2017; 72:1411-1416. [PMID: 28329217 DOI: 10.1093/gerona/glx011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Indexed: 01/21/2023] Open
Abstract
Background Identification of genes or fundamental biological pathways that regulate aging phenotypes and longevity could lead to possible interventions to increase healthy longevity. Methods Using data from the Long Life Family Study, we performed genomewide association analyses on an endophenotype construct, LF1, comprising a linear combination of traits across health domains. LF1 primarily reflected traits from the pulmonary and physical activity domains. Results We detected a significant association between LF1 and a locus on chromosome 10p15 (p-value = 4.65 × 10-8) and suggestive evidence (p-value < 5 × 10-6) for association on chromosomes 1, 2, 8, 12, 15, 18, and 22. Using data from the Health, Aging and Body Composition Study, we subsequently replicated the association for the 1p13 region near the NBPF6 locus (p-value = 3.65 × 10-4). Conclusions Our analyses indicate that loci influencing a healthy aging endophenotype construct predominantly comprised of pulmonary and physical function domains may be located on chromosome 1p13 near the NBPF6 locus. Further investigation of this possible locus and other suggestive loci may reveal novel biological pathways that influence healthy aging.
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Affiliation(s)
- Jatinder Singh
- Department of Human Genetics, University of Pittsburgh, Pennsylvania
| | - Ryan L Minster
- Department of Human Genetics, University of Pittsburgh, Pennsylvania
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, New York
| | - Aldi Kraja
- Division of Statistical Genomics, School of Medicine, Washington University in St. Louis, Missouri
| | - YongMei Liu
- Department of Epidemiology & Prevention, Wake Forest University Health Sciences, Winston-Salem, North Carolina
| | - Kaare Christensen
- The Danish Aging Research Center, University of Southern Denmark; Department of Clinical Biochemistry and Pharmacology and Department of Clinical Genetics, Odense University Hospital, Denmark
| | - Anne B Newman
- Department of Epidemiology, University of Pittsburgh, Pennsylvania
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41
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Astling DP, Heft IE, Jones KL, Sikela JM. High resolution measurement of DUF1220 domain copy number from whole genome sequence data. BMC Genomics 2017; 18:614. [PMID: 28807002 PMCID: PMC5556342 DOI: 10.1186/s12864-017-3976-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 07/31/2017] [Indexed: 11/10/2022] Open
Abstract
Background DUF1220 protein domains found primarily in Neuroblastoma BreakPoint Family (NBPF) genes show the greatest human lineage-specific increase in copy number of any coding region in the genome. There are 302 haploid copies of DUF1220 in hg38 (~160 of which are human-specific) and the majority of these can be divided into 6 different subtypes (referred to as clades). Copy number changes of specific DUF1220 clades have been associated in a dose-dependent manner with brain size variation (both evolutionarily and within the human population), cognitive aptitude, autism severity, and schizophrenia severity. However, no published methods can directly measure copies of DUF1220 with high accuracy and no method can distinguish between domains within a clade. Results Here we describe a novel method for measuring copies of DUF1220 domains and the NBPF genes in which they are found from whole genome sequence data. We have characterized the effect that various sequencing and alignment parameters and strategies have on the accuracy and precision of the method and defined the parameters that lead to optimal DUF1220 copy number measurement and resolution. We show that copy number estimates obtained using our read depth approach are highly correlated with those generated by ddPCR for three representative DUF1220 clades. By simulation, we demonstrate that our method provides sufficient resolution to analyze DUF1220 copy number variation at three levels: (1) DUF1220 clade copy number within individual genes and groups of genes (gene-specific clade groups) (2) genome wide DUF1220 clade copies and (3) gene copy number for DUF1220-encoding genes. Conclusions To our knowledge, this is the first method to accurately measure copies of all six DUF1220 clades and the first method to provide gene specific resolution of these clades. This allows one to discriminate among the ~300 haploid human DUF1220 copies to an extent not possible with any other method. The result is a greatly enhanced capability to analyze the role that these sequences play in human variation and disease. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3976-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David P Astling
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ilea E Heft
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - James M Sikela
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA.
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42
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Davis LE, Jeng S, Svalina MN, Huang E, Pittsenbarger J, Cantor EL, Berlow N, Seguin B, Mansoor A, McWeeney SK, Keller C. Integration of genomic, transcriptomic and functional profiles of aggressive osteosarcomas across multiple species. Oncotarget 2017; 8:76241-76256. [PMID: 29100308 PMCID: PMC5652702 DOI: 10.18632/oncotarget.19532] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 07/11/2017] [Indexed: 01/14/2023] Open
Abstract
In complex, highly unstable genomes such as in osteosarcoma, targeting aberrant checkpoint processes (metabolic, cell cycle or immune) may prove more successful than targeting specific kinase or growth factor signaling pathways. Here, we establish a comparative oncology approach characterizing the most lethal osteosarcomas identified in a biorepository of tumors from three different species: human, mouse and canine. We describe the development of a genetically-engineered mouse model of osteosarcoma, establishment of primary cell cultures from fatal human tumors, and a biorepository of osteosarcoma surgical specimens from pet dogs. We analyzed the DNA mutations, differential RNA expression and in vitro drug sensitivity from two phenotypically-distinct cohorts: tumors with a highly aggressive biology resulting in death from rapidly progressive, refractory metastatic disease, and tumors with a non-aggressive, curable phenotype. We identified ARK5 (AMPK-Related Protein Kinase 5, also referred to as NUAK Family Kinase 1) as a novel metabolic target present in all species, and independent analyses confirmed glucose metabolism as the most significantly aberrant cellular signaling pathway in a model system for highly metastatic tumors. Pathway integration analysis identified Polo Like Kinase 1 (PLK1)-mediated checkpoint adaptation as critical to the survival of a distinctly aggressive osteosarcoma. The tumor-associated macrophage cytokine CCL18 (C-C Motif Chemokine Ligand 18) was significantly over-expressed in aggressive human osteosarcomas, and a clustering of mutations in the BAGE (B Melanoma Antigen) tumor antigen gene family was found. The theme of these features of high risk osteosarcoma is checkpoint adaptations, which may prove both prognostic and targetable.
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Affiliation(s)
- Lara E Davis
- Knight Cancer Institute, Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health and Sciences University, Portland, Oregon, USA.,Department of Pediatrics, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Sophia Jeng
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Matthew N Svalina
- Department of Pediatrics, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Elaine Huang
- Department of Pediatrics, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Janét Pittsenbarger
- Knight Cancer Institute, Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Emma L Cantor
- Department of Pediatrics, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Noah Berlow
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
| | - Bernard Seguin
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, USA
| | - Atiya Mansoor
- Department of Pathology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Shannon K McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
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NBPF7 promotes the proliferation of α-catenin-knockdown HaCaT cells via functional interaction with the NF-κB pathway. Oncotarget 2017; 8:65800-65808. [PMID: 29029473 PMCID: PMC5630373 DOI: 10.18632/oncotarget.19480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/29/2017] [Indexed: 12/24/2022] Open
Abstract
Loss of key components that form cell-cell adherens junctions, such as α-catenin, triggers severe epidermal hyperproliferation. However, the underlying molecular mechanisms remain largely unknown. We report here that neuroblastoma breakpoint family (NBPF) genes are upregulated and that NBPF7 specifically promotes cellular proliferation of α-catenin-silenced HaCaT cells through functional linkage with the NF-κB pathway. Genome-wide profiling of HaCaT cells shows that NBPF genes are upregulated following α-catenin knockdown. Data from western blot analyses are consistent with the activation of the NF-κB pathway as well as increased expression of NBPF7 by α-catenin knockdown. Co-immunoprecipitation assays indicate that NBPF7 could be detected in endogenous activated NF-κB immunoprecipitates. Immunoflurence analyses demonstrate that NBPF7 co-localizes with activated NF-κB in the nucleus after α-catenin silencing. Moreover, inhibition of NBPF7 decreases the proliferation of HaCaT cells and abolishes the enhanced proliferation associated with α-catenin knockdown in HaCaT cells. These results indicate that NBPF7 plays a key role in the α-catenin signaling pathway that regulates cell proliferation of keratinocytes. Our findings suggest that the classical NF-κB pathway plays a critical role in cellular proliferation and that NBPF7 is a functional mediator for α-catenin in the regulation of keratinocyte growth.
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Dougherty ML, Nuttle X, Penn O, Nelson BJ, Huddleston J, Baker C, Harshman L, Duyzend MH, Ventura M, Antonacci F, Sandstrom R, Dennis MY, Eichler EE. The birth of a human-specific neural gene by incomplete duplication and gene fusion. Genome Biol 2017; 18:49. [PMID: 28279197 PMCID: PMC5345166 DOI: 10.1186/s13059-017-1163-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/27/2017] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Gene innovation by duplication is a fundamental evolutionary process but is difficult to study in humans due to the large size, high sequence identity, and mosaic nature of segmental duplication blocks. The human-specific gene hydrocephalus-inducing 2, HYDIN2, was generated by a 364 kbp duplication of 79 internal exons of the large ciliary gene HYDIN from chromosome 16q22.2 to chromosome 1q21.1. Because the HYDIN2 locus lacks the ancestral promoter and seven terminal exons of the progenitor gene, we sought to characterize transcription at this locus by coupling reverse transcription polymerase chain reaction and long-read sequencing. RESULTS 5' RACE indicates a transcription start site for HYDIN2 outside of the duplication and we observe fusion transcripts spanning both the 5' and 3' breakpoints. We observe extensive splicing diversity leading to the formation of altered open reading frames (ORFs) that appear to be under relaxed selection. We show that HYDIN2 adopted a new promoter that drives an altered pattern of expression, with highest levels in neural tissues. We estimate that the HYDIN duplication occurred ~3.2 million years ago and find that it is nearly fixed (99.9%) for diploid copy number in contemporary humans. Examination of 73 chromosome 1q21 rearrangement patients reveals that HYDIN2 is deleted or duplicated in most cases. CONCLUSIONS Together, these data support a model of rapid gene innovation by fusion of incomplete segmental duplications, altered tissue expression, and potential subfunctionalization or neofunctionalization of HYDIN2 early in the evolution of the Homo lineage.
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Affiliation(s)
- Max L Dougherty
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Xander Nuttle
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Osnat Penn
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Lana Harshman
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Michael H Duyzend
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Mario Ventura
- Department of Biology, University of Bari, Bari, 70121, Italy
| | | | | | - Megan Y Dennis
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, 95616, CA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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Yuan J, Hu J, Li Z, Zhang F, Zhou D, Jin C. A replication study of schizophrenia-related rare copy number variations in a Han Southern Chinese population. Hereditas 2017; 154:2. [PMID: 28096781 PMCID: PMC5237532 DOI: 10.1186/s41065-016-0025-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/26/2016] [Indexed: 11/24/2022] Open
Abstract
Background Schizophrenia (SCZ) is a common, complex and severe psychiatric disorder associated with many different genetic and environmental risk factors. Evidence from genetic studies has revealed the role of genome structural variations, specifically copy number variants (CNVs), in the etiology of SCZ. Nevertheless, the occurrence of CNVs and their relation to SCZ has remained relatively unstudied in the diverse Han Chinese population. Results We used a case/control paradigm, including 476 cases and 1023 controls. All samples were genotyped using the Axiom® Exome Genotyping Arrays. Four CNVs, including two deletions and two duplications, were detected in this study. Notably, the 16p11.2 duplication from 29.3 Mb to 29.6 Mb was detected in four cases (0.84%) and one control (0.098%) (p = 0.0377). Conclusions The results highlight the potential role of these deletions and duplications in the development of SCZ. Clearly, larger sample sized studies are needed for a careful localization of these CNVs and to possibly detect more deletions and/or duplications, associated with the development of SCZ in the Han Chinese population. Electronic supplementary material The online version of this article (doi:10.1186/s41065-016-0025-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jianmin Yuan
- Wuxi Mental Health Center, Nanjing Medial University, 156 Qianrong Road, Wuxi, 214151 Jiangsu Province China
| | - Jianlin Hu
- Wuxi Second Traditional Chinese Medicine Hospital, Wuxi, 214151 Jiangsu Province China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Fuquan Zhang
- Wuxi Mental Health Center, Nanjing Medial University, 156 Qianrong Road, Wuxi, 214151 Jiangsu Province China
| | - Dexiang Zhou
- Wuxi Mental Health Center, Nanjing Medial University, 156 Qianrong Road, Wuxi, 214151 Jiangsu Province China
| | - Chunhui Jin
- Wuxi Mental Health Center, Nanjing Medial University, 156 Qianrong Road, Wuxi, 214151 Jiangsu Province China
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Dennis MY, Eichler EE. Human adaptation and evolution by segmental duplication. Curr Opin Genet Dev 2016; 41:44-52. [PMID: 27584858 PMCID: PMC5161654 DOI: 10.1016/j.gde.2016.08.001] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/02/2016] [Accepted: 08/02/2016] [Indexed: 12/29/2022]
Abstract
Duplications are the primary force by which new gene functions arise and provide a substrate for large-scale structural variation. Analysis of thousands of genomes shows that humans and great apes have more genetic differences in content and structure over recent segmental duplications than any other euchromatic region. Novel human-specific duplicated genes, ARHGAP11B and SRGAP2C, have recently been described with a potential role in neocortical expansion and increased neuronal spine density. Large segmental duplications and the structural variants they promote are also frequently stratified between human populations with a subset being subjected to positive selection. The impact of recent duplications on human evolution and adaptation is only beginning to be realized as new technologies enhance their discovery and accurate genotyping.
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Affiliation(s)
- Megan Y Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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47
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Keel BN, Lindholm-Perry AK, Snelling WM. Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome. Front Genet 2016; 7:207. [PMID: 27920798 PMCID: PMC5118444 DOI: 10.3389/fgene.2016.00207] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/08/2016] [Indexed: 01/18/2023] Open
Abstract
Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV. We identified and characterized CNV regions by utilizing exome sequence from 175 influential sires used in the Germplasm Evaluation project, representing 10 breeds. We examined various evolutionary and functional aspects of these CNVs, including selective constraint on CNV-overlapped genes, centrality of CNV genes in protein-protein interaction networks, and tissue-specific expression of CNV genes. Patterns of CNV in the Bos taurus genome reveal that reduced functional constraint and mutational bias may play a prominent role in shaping this type of structural variation.
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Affiliation(s)
- Brittney N Keel
- Agricultural Research Service (USDA), Meat Animal Research Center Clay Center, NE, USA
| | | | - Warren M Snelling
- Agricultural Research Service (USDA), Meat Animal Research Center Clay Center, NE, USA
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48
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Sapkota Y, Narasimhan A, Kumaran M, Sehrawat BS, Damaraju S. A Genome-Wide Association Study to Identify Potential Germline Copy Number Variants for Sporadic Breast Cancer Susceptibility. Cytogenet Genome Res 2016; 149:156-164. [PMID: 27668787 DOI: 10.1159/000448558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2016] [Indexed: 11/19/2022] Open
Abstract
Breast cancer (BC) predisposition in populations arises from both genetic and nongenetic risk factors. Structural variations such as copy number variations (CNVs) are heritable determinants for disease susceptibility. The primary objectives of this study are (1) to identify CNVs associated with sporadic BC using a genome-wide association study (GWAS) design; (2) to utilize 2 distinct CNV calling algorithms to identify concordant CNVs as a strategy to reduce false positive associations in the hypothesis-generating GWAS discovery phase, and (3) to identify potential candidate CNVs for follow-up replication studies. We used Affymetrix SNP Array 6.0 data profiled on Caucasian subjects (422 cases/348 controls) to call CNVs using algorithms implemented in Nexus Copy Number and Partek Genomics Suite software. Nexus algorithm identified CNVs associated with BC (731 autosomal CNVs with >5% frequency in the total sample and Q < 0.05). Thirteen CNVs were identified when Partek algorithm-called CNVs were overlapped with Nexus-identified CNVs; these CNVs showed concordances for frequency, effect size, and direction. Coding genes present within BC-associated CNVs were known to play a role in disease etiology and prognosis. Long noncoding RNAs identified within CNVs showed tissue-specific expression, indicating potential functional relevance of the findings. The identified candidate CNVs warrant independent replication.
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Affiliation(s)
- Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tenn., USA
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49
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Sanders AD, Hills M, Porubský D, Guryev V, Falconer E, Lansdorp PM. Characterizing polymorphic inversions in human genomes by single-cell sequencing. Genome Res 2016; 26:1575-1587. [PMID: 27472961 PMCID: PMC5088599 DOI: 10.1101/gr.201160.115] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 06/13/2016] [Indexed: 12/23/2022]
Abstract
Identifying genomic features that differ between individuals and cells can help uncover the functional variants that drive phenotypes and disease susceptibilities. For this, single-cell studies are paramount, as it becomes increasingly clear that the contribution of rare but functional cellular subpopulations is important for disease prognosis, management, and progression. Until now, studying these associations has been challenged by our inability to map structural rearrangements accurately and comprehensively. To overcome this, we coupled single-cell sequencing of DNA template strands (Strand-seq) with custom analysis software to rapidly discover, map, and genotype genomic rearrangements at high resolution. This allowed us to explore the distribution and frequency of inversions in a heterogeneous cell population, identify several polymorphic domains in complex regions of the genome, and locate rare alleles in the reference assembly. We then mapped the entire genomic complement of inversions within two unrelated individuals to characterize their distinct inversion profiles and built a nonredundant global reference of structural rearrangements in the human genome. The work described here provides a powerful new framework to study structural variation and genomic heterogeneity in single-cell samples, whether from individuals for population studies or tissue types for biomarker discovery.
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Affiliation(s)
- Ashley D Sanders
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Mark Hills
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - David Porubský
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, NL-9713 AV Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, NL-9713 AV Groningen, The Netherlands
| | - Ester Falconer
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Peter M Lansdorp
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada.,European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, NL-9713 AV Groningen, The Netherlands.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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50
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Searles Quick VB, Davis JM, Olincy A, Sikela JM. DUF1220 copy number is associated with schizophrenia risk and severity: implications for understanding autism and schizophrenia as related diseases. Transl Psychiatry 2015; 5:e697. [PMID: 26670282 PMCID: PMC5068589 DOI: 10.1038/tp.2015.192] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/29/2015] [Accepted: 10/21/2015] [Indexed: 11/30/2022] Open
Abstract
The copy number of DUF1220, a protein domain implicated in human brain evolution, has been linearly associated with autism severity. Given the possibility that autism and schizophrenia are related disorders, the present study examined DUF1220 copy number variation in schizophrenia severity. There are notable similarities between autism symptoms and schizophrenia negative symptoms, and divergence between autism symptoms and schizophrenia positive symptoms. We therefore also examined DUF1220 copy number in schizophrenia subgroups defined by negative and positive symptom features, versus autistic individuals and controls. In the schizophrenic population (N=609), decreased DUF1220 copy number was linearly associated with increasing positive symptom severity (CON1 P=0.013, HLS1 P=0.0227), an association greatest in adult-onset schizophrenia (CON1 P=0.00155, HLS1 P=0.00361). In schizophrenic males, DUF1220 CON1 subtype copy number increase was associated with increased negative symptom severity (P=0.0327), a finding similar to that seen in autistic populations. Subgroup analyses demonstrated that schizophrenic individuals with predominantly positive symptoms exhibited reduced CON1 copy number compared with both controls (P=0.0237) and schizophrenic individuals with predominantly negative symptoms (P=0.0068). These findings support the view that (1) autism and schizophrenia exhibit both opposing and partially overlapping phenotypes and may represent a disease continuum, (2) variation in DUF1220 copy number contributes to schizophrenia disease risk and to the severity of both disorders, and (3) schizophrenia and autism may be, in part, a harmful by-product of the rapid and extreme evolutionary increase in DUF1220 copy number in the human species.
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Affiliation(s)
- V B Searles Quick
- Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Genomics and Medical Scientist Training Programs, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J M Davis
- Department of Psychiatry, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - A Olincy
- Department of Psychiatry, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J M Sikela
- Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Genomics and Medical Scientist Training Programs, University of Colorado Anschutz Medical Campus, Aurora, CO, USA,Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Genomics and Medical Scientist Training Programs, University of Colorado Anschutz Medical Campus, 12801 E. 17th Avenue, Aurora, CO 80045, USA. E-mail:
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