1
|
Liu Y, Lu S, Yang J, Yang Y, Jiao L, Hu J, Li Y, Yang F, Pang Y, Zhao Y, Gao Y, Liu W, Shu P, Ge W, He Z, Peng X. Analysis of the aging-related biomarker in a nonhuman primate model using multilayer omics. BMC Genomics 2024; 25:639. [PMID: 38926642 PMCID: PMC11209966 DOI: 10.1186/s12864-024-10556-z] [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: 02/09/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Aging is a prominent risk factor for diverse diseases; therefore, an in-depth understanding of its physiological mechanisms is required. Nonhuman primates, which share the closest genetic relationship with humans, serve as an ideal model for exploring the complex aging process. However, the potential of the nonhuman primate animal model in the screening of human aging markers is still not fully exploited. Multiomics analysis of nonhuman primate peripheral blood offers a promising approach to evaluate new therapies and biomarkers. This study explores aging-related biomarker through multilayer omics, including transcriptomics (mRNA, lncRNA, and circRNA) and proteomics (serum and serum-derived exosomes) in rhesus monkeys (Macaca mulatta). RESULTS Our findings reveal that, unlike mRNAs and circRNAs, highly expressed lncRNAs are abundant during the key aging period and are associated with cancer pathways. Comparative analysis highlighted exosomal proteins contain more types of proteins than serum proteins, indicating that serum-derived exosomes primarily regulate aging through metabolic pathways. Finally, eight candidate aging biomarkers were identified, which may serve as blood-based indicators for detecting age-related brain changes. CONCLUSIONS Our results provide a comprehensive understanding of nonhuman primate blood transcriptomes and proteomes, offering novel insights into the aging mechanisms for preventing or treating age-related diseases.
Collapse
Affiliation(s)
- Yunpeng Liu
- State Key Laboratory of Respiratory Health and Multimorbidity, National Center of Technology Innovation for Animal Model, National Human Diseases Animal Model Resource Center, NHC Key Laboratory of Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Sciences, CAMS & PUMC, Beijing, 100021, China
| | - Shuaiyao Lu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Jing Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Yun Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Li Jiao
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Jingwen Hu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Yanyan Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Fengmei Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Yunli Pang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Yuan Zhao
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Yanpan Gao
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMC, Beijing, 100005, China
| | - Wei Liu
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMC, Beijing, 100005, China
| | - Pengcheng Shu
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMC, Beijing, 100005, China
| | - Wei Ge
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMC, Beijing, 100005, China
| | - Zhanlong He
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China.
| | - Xiaozhong Peng
- State Key Laboratory of Respiratory Health and Multimorbidity, National Center of Technology Innovation for Animal Model, National Human Diseases Animal Model Resource Center, NHC Key Laboratory of Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Sciences, CAMS & PUMC, Beijing, 100021, China.
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China.
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMC, Beijing, 100005, China.
| |
Collapse
|
2
|
Alberti G, Amico MD, Caruso Bavisotto C, Rappa F, Marino Gammazza A, Bucchieri F, Cappello F, Scalia F, Szychlinska MA. Speeding up Glioblastoma Cancer Research: Highlighting the Zebrafish Xenograft Model. Int J Mol Sci 2024; 25:5394. [PMID: 38791432 PMCID: PMC11121320 DOI: 10.3390/ijms25105394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Glioblastoma multiforme (GBM) is a very aggressive and lethal primary brain cancer in adults. The multifaceted nature of GBM pathogenesis, rising from complex interactions between cells and the tumor microenvironment (TME), has posed great treatment challenges. Despite significant scientific efforts, the prognosis for GBM remains very poor, even after intensive treatment with surgery, radiation, and chemotherapy. Efficient GBM management still requires the invention of innovative treatment strategies. There is a strong necessity to complete cancer in vitro studies and in vivo studies to properly evaluate the mechanisms of tumor progression within the complex TME. In recent years, the animal models used to study GBM tumors have evolved, achieving highly invasive GBM models able to provide key information on the molecular mechanisms of GBM onset. At present, the most commonly used animal models in GBM research are represented by mammalian models, such as mouse and canine ones. However, the latter present several limitations, such as high cost and time-consuming management, making them inappropriate for large-scale anticancer drug evaluation. In recent years, the zebrafish (Danio rerio) model has emerged as a valuable tool for studying GBM. It has shown great promise in preclinical studies due to numerous advantages, such as its small size, its ability to generate a large cohort of genetically identical offspring, and its rapid development, permitting more time- and cost-effective management and high-throughput drug screening when compared to mammalian models. Moreover, due to its transparent nature in early developmental stages and genetic and anatomical similarities with humans, it allows for translatable brain cancer research and related genetic screening and drug discovery. For this reason, the aim of the present review is to highlight the potential of relevant transgenic and xenograft zebrafish models and to compare them to the traditionally used animal models in GBM research.
Collapse
Affiliation(s)
- Giusi Alberti
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BiND), University of Palermo, 90127 Palermo, Italy; (G.A.); (M.D.A.); (C.C.B.); (F.R.); (A.M.G.); (F.B.); (F.C.); (F.S.)
| | - Maria Denise Amico
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BiND), University of Palermo, 90127 Palermo, Italy; (G.A.); (M.D.A.); (C.C.B.); (F.R.); (A.M.G.); (F.B.); (F.C.); (F.S.)
| | - Celeste Caruso Bavisotto
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BiND), University of Palermo, 90127 Palermo, Italy; (G.A.); (M.D.A.); (C.C.B.); (F.R.); (A.M.G.); (F.B.); (F.C.); (F.S.)
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | - Francesca Rappa
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BiND), University of Palermo, 90127 Palermo, Italy; (G.A.); (M.D.A.); (C.C.B.); (F.R.); (A.M.G.); (F.B.); (F.C.); (F.S.)
- The Institute of Translational Pharmacology, National Research Council of Italy (CNR), 90146 Palermo, Italy
| | - Antonella Marino Gammazza
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BiND), University of Palermo, 90127 Palermo, Italy; (G.A.); (M.D.A.); (C.C.B.); (F.R.); (A.M.G.); (F.B.); (F.C.); (F.S.)
| | - Fabio Bucchieri
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BiND), University of Palermo, 90127 Palermo, Italy; (G.A.); (M.D.A.); (C.C.B.); (F.R.); (A.M.G.); (F.B.); (F.C.); (F.S.)
| | - Francesco Cappello
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BiND), University of Palermo, 90127 Palermo, Italy; (G.A.); (M.D.A.); (C.C.B.); (F.R.); (A.M.G.); (F.B.); (F.C.); (F.S.)
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | - Federica Scalia
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BiND), University of Palermo, 90127 Palermo, Italy; (G.A.); (M.D.A.); (C.C.B.); (F.R.); (A.M.G.); (F.B.); (F.C.); (F.S.)
| | - Marta Anna Szychlinska
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), University of Palermo, 90127 Palermo, Italy
| |
Collapse
|
3
|
Zhang S, Xu N, Fu L, Yang X, Li Y, Yang Z, Feng Y, Ma K, Jiang X, Han J, Hu R, Zhang L, de Gennaro L, Ryabov F, Meng D, He Y, Wu D, Yang C, Paparella A, Mao Y, Bian X, Lu Y, Antonacci F, Ventura M, Shepelev VA, Miga KH, Alexandrov IA, Logsdon GA, Phillippy AM, Su B, Zhang G, Eichler EE, Lu Q, Shi Y, Sun Q, Mao Y. Comparative genomics of macaques and integrated insights into genetic variation and population history. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.07.588379. [PMID: 38645259 PMCID: PMC11030432 DOI: 10.1101/2024.04.07.588379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The crab-eating macaques ( Macaca fascicularis ) and rhesus macaques ( M. mulatta ) are widely studied nonhuman primates in biomedical and evolutionary research. Despite their significance, the current understanding of the complex genomic structure in macaques and the differences between species requires substantial improvement. Here, we present a complete genome assembly of a crab-eating macaque and 20 haplotype-resolved macaque assemblies to investigate the complex regions and major genomic differences between species. Segmental duplication in macaques is ∼42% lower, while centromeres are ∼3.7 times longer than those in humans. The characterization of ∼2 Mbp fixed genetic variants and ∼240 Mbp complex loci highlights potential associations with metabolic differences between the two macaque species (e.g., CYP2C76 and EHBP1L1 ). Additionally, hundreds of alternative splicing differences show post-transcriptional regulation divergence between these two species (e.g., PNPO ). We also characterize 91 large-scale genomic differences between macaques and humans at a single-base-pair resolution and highlight their impact on gene regulation in primate evolution (e.g., FOLH1 and PIEZO2 ). Finally, population genetics recapitulates macaque speciation and selective sweeps, highlighting potential genetic basis of reproduction and tail phenotype differences (e.g., STAB1 , SEMA3F , and HOXD13 ). In summary, the integrated analysis of genetic variation and population genetics in macaques greatly enhances our comprehension of lineage-specific phenotypes, adaptation, and primate evolution, thereby improving their biomedical applications in human diseases.
Collapse
|
4
|
Ding W, Li X, Zhang J, Ji M, Zhang M, Zhong X, Cao Y, Liu X, Li C, Xiao C, Wang J, Li T, Yu Q, Mo F, Zhang B, Qi J, Yang JC, Qi J, Tian L, Xu X, Peng Q, Zhou WZ, Liu Z, Fu A, Zhang X, Zhang JJ, Sun Y, Hu B, An NA, Zhang L, Li CY. Adaptive functions of structural variants in human brain development. SCIENCE ADVANCES 2024; 10:eadl4600. [PMID: 38579006 DOI: 10.1126/sciadv.adl4600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/01/2024] [Indexed: 04/07/2024]
Abstract
Quantifying the structural variants (SVs) in nonhuman primates could provide a niche to clarify the genetic backgrounds underlying human-specific traits, but such resource is largely lacking. Here, we report an accurate SV map in a population of 562 rhesus macaques, verified by in-house benchmarks of eight macaque genomes with long-read sequencing and another one with genome assembly. This map indicates stronger selective constrains on inversions at regulatory regions, suggesting a strategy for prioritizing them with the most important functions. Accordingly, we identified 75 human-specific inversions and prioritized them. The top-ranked inversions have substantially shaped the human transcriptome, through their dual effects of reconfiguring the ancestral genomic architecture and introducing regional mutation hotspots at the inverted regions. As a proof of concept, we linked APCDD1, located on one of these inversions and down-regulated specifically in humans, to neuronal maturation and cognitive ability. We thus highlight inversions in shaping the human uniqueness in brain development.
Collapse
Affiliation(s)
- Wanqiu Ding
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xiangshang Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Mingjun Ji
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Mengling Zhang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Xiaoming Zhong
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yong Cao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119S Fourth Ring Rd W, Fengtai District, Beijing, China
| | - Xiaoge Liu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Chunqiong Li
- Chinese Institute for Brain Research, Beijing, China
| | - Chunfu Xiao
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jiaxin Wang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Ting Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Qing Yu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Fan Mo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Boya Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jianhuan Qi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jie-Chun Yang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Juntian Qi
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Lu Tian
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xinwei Xu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Qi Peng
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Wei-Zhen Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Aisi Fu
- Wuhan Dgensee Clinical Laboratory, Wuhan, China
| | - Xiuqin Zhang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jian-Jun Zhang
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, National International Joint Research Center for Molecular Chinese Medicine, Shanxi University of Chinese Medicine, Jinzhong, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Baoyang Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ni A An
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- National Biomedical Imaging Center, College of Future Technology, Peking University, Beijing, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | - Chuan-Yun Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- National Biomedical Imaging Center, College of Future Technology, Peking University, Beijing, China
- Southwest United Graduate School, Kunming 650092, China
| |
Collapse
|
5
|
Wu M, Tang W, Chen Y, Xue L, Dai J, Li Y, Zhu X, Wu C, Xiong J, Zhang J, Wu T, Zhou S, Chen D, Sun C, Yu J, Li H, Guo Y, Huang Y, Zhu Q, Wei S, Zhou Z, Wu M, Li Y, Xiang T, Qiao H, Wang S. Spatiotemporal transcriptomic changes of human ovarian aging and the regulatory role of FOXP1. NATURE AGING 2024; 4:527-545. [PMID: 38594460 PMCID: PMC11031396 DOI: 10.1038/s43587-024-00607-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 03/05/2024] [Indexed: 04/11/2024]
Abstract
Limited understanding exists regarding how aging impacts the cellular and molecular aspects of the human ovary. This study combines single-cell RNA sequencing and spatial transcriptomics to systematically characterize human ovarian aging. Spatiotemporal molecular signatures of the eight types of ovarian cells during aging are observed. An analysis of age-associated changes in gene expression reveals that DNA damage response may be a key biological pathway in oocyte aging. Three granulosa cells subtypes and five theca and stromal cells subtypes, as well as their spatiotemporal transcriptomics changes during aging, are identified. FOXP1 emerges as a regulator of ovarian aging, declining with age and inhibiting CDKN1A transcription. Silencing FOXP1 results in premature ovarian insufficiency in mice. These findings offer a comprehensive understanding of spatiotemporal variability in human ovarian aging, aiding the prioritization of potential diagnostic biomarkers and therapeutic strategies.
Collapse
Affiliation(s)
- Meng Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Weicheng Tang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Ying Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Liru Xue
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Jun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China.
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China.
| | - Yan Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China.
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China.
| | - Xiaoran Zhu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Chuqing Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Jiaqiang Xiong
- Department of Obstetrics and Gynecology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Jinjin Zhang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Tong Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Su Zhou
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Dan Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Jing Yu
- Shanghai Health Commission Key Lab of Artificial Intelligence (AI)-Based Management of Inflammation and Chronic Diseases, Sino-French Cooperative Central Lab, Shanghai Pudong Gongli Hospital, Secondary Military Medical University, Shanghai, China
| | - Hongyi Li
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yican Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Yibao Huang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Qingqing Zhu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Simin Wei
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Ziliang Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mingfu Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Ya Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | - Tao Xiang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China
| | | | - Shixuan Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China.
- Key Laboratory of Cancer Invasion and Metastasis, Ministry of Education, Wuhan, China.
| |
Collapse
|
6
|
Deycmar S, Johnson BJ, Ray K, Schaaf GW, Ryan DP, Cullin C, Dozier BL, Ferguson B, Bimber BN, Olson JD, Caudell DL, Whitlow CT, Solingapuram Sai KK, Romero EC, Villinger FJ, Burgos AG, Ainsworth HC, Miller LD, Hawkins GA, Chou JW, Gomes B, Hettich M, Ceppi M, Charo J, Cline JM. Epigenetic MLH1 silencing concurs with mismatch repair deficiency in sporadic, naturally occurring colorectal cancer in rhesus macaques. J Transl Med 2024; 22:292. [PMID: 38504345 PMCID: PMC10953092 DOI: 10.1186/s12967-024-04869-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/08/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Naturally occurring colorectal cancers (CRC) in rhesus macaques share many features with their human counterparts and are useful models for cancer immunotherapy; but mechanistic data are lacking regarding the comparative molecular pathogenesis of these cancers. METHODS We conducted state-of-the-art imaging including CT and PET, clinical assessments, and pathological review of 24 rhesus macaques with naturally occurring CRC. Additionally, we molecularly characterized these tumors utilizing immunohistochemistry (IHC), microsatellite instability assays, DNAseq, transcriptomics, and developed a DNA methylation-specific qPCR assay for MLH1, CACNA1G, CDKN2A, CRABP1, and NEUROG1, human markers for CpG island methylator phenotype (CIMP). We furthermore employed Monte-Carlo simulations to in-silico model alterations in DNA topology in transcription-factor binding site-rich promoter regions upon experimentally demonstrated DNA methylation. RESULTS Similar cancer histology, progression patterns, and co-morbidities could be observed in rhesus as reported for human CRC patients. IHC identified loss of MLH1 and PMS2 in all cases, with functional microsatellite instability. DNA sequencing revealed the close genetic relatedness to human CRCs, including a similar mutational signature, chromosomal instability, and functionally-relevant mutations affecting KRAS (G12D), TP53 (R175H, R273*), APC, AMER1, ALK, and ARID1A. Interestingly, MLH1 mutations were rarely identified on a somatic or germline level. Transcriptomics not only corroborated the similarities of rhesus and human CRCs, but also demonstrated the significant downregulation of MLH1 but not MSH2, MSH6, or PMS2 in rhesus CRCs. Methylation-specific qPCR suggested CIMP-positivity in 9/16 rhesus CRCs, but all 16/16 exhibited significant MLH1 promoter hypermethylation. DNA hypermethylation was modelled to affect DNA topology, particularly propeller twist and roll profiles. Modelling the DNA topology of a transcription factor binding motif (TFAP2A) in the MLH1 promoter that overlapped with a methylation-specific probe, we observed significant differences in DNA topology upon experimentally shown DNA methylation. This suggests a role of transcription factor binding interference in epigenetic silencing of MLH1 in rhesus CRCs. CONCLUSIONS These data indicate that epigenetic silencing suppresses MLH1 transcription, induces the loss of MLH1 protein, abrogates mismatch repair, and drives genomic instability in naturally occurring CRC in rhesus macaques. We consider this spontaneous, uninduced CRC in immunocompetent, treatment-naïve rhesus macaques to be a uniquely informative model for human CRC.
Collapse
Affiliation(s)
- Simon Deycmar
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Roche Postdoctoral Fellowship (RPF) Program, Basel, Switzerland
| | - Brendan J Johnson
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Karina Ray
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - George W Schaaf
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Declan Patrick Ryan
- School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Cassandra Cullin
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Brandy L Dozier
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Betsy Ferguson
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Benjamin N Bimber
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - John D Olson
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - David L Caudell
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Christopher T Whitlow
- Department of Radiology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | | | - Emily C Romero
- New Iberia Research Center, University of Louisiana-Lafayette, New Iberia, LA, USA
| | - Francois J Villinger
- New Iberia Research Center, University of Louisiana-Lafayette, New Iberia, LA, USA
| | - Armando G Burgos
- Caribbean Primate Research Center, University of Puerto Rico, Toa Baja, PR, USA
| | - Hannah C Ainsworth
- Department of Biostatistics and Data Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Center for Cancer Genomics and Precision Oncology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Gregory A Hawkins
- Center for Cancer Genomics and Precision Oncology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jeff W Chou
- Center for Cancer Genomics and Precision Oncology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Bruno Gomes
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Michael Hettich
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Maurizio Ceppi
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
- iTeos Therapeutics, Translational Medicine, Gosselies, Belgium
| | - Jehad Charo
- Roche Pharma Research and Early Development, Roche Innovation Center Zurich, Zurich, Switzerland
| | - J Mark Cline
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
| |
Collapse
|
7
|
Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Yoo D, Gordon DS, Fair T, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Mao Y, Shi Y, Sun Q, Lu Q, Paten B, Bakken TE, Pollen AA, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE. Structurally divergent and recurrently mutated regions of primate genomes. Cell 2024; 187:1547-1562.e13. [PMID: 38428424 PMCID: PMC10947866 DOI: 10.1016/j.cell.2024.01.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 11/26/2023] [Accepted: 01/31/2024] [Indexed: 03/03/2024]
Abstract
We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.
Collapse
Affiliation(s)
- Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Allison Rozanski
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Xiangyu Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David S Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Tyler Fair
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaoxi Wei
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ricardo Del Rosario
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vanessa L Bauer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA
| | - Will T Fattor
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA
| | - Gregory K Wilkerson
- Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX, USA; Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Yuxiang Mao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China; Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Qiang Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Qing Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - 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
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA
| | - Wesley C Warren
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA; Institute of Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA; Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| |
Collapse
|
8
|
Pozo G, Albuja-Quintana M, Larreátegui L, Gutiérrez B, Fuentes N, Alfonso-Cortés F, Torres MDL. First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies. G3 (BETHESDA, MD.) 2024; 14:jkae014. [PMID: 38244218 PMCID: PMC10917520 DOI: 10.1093/g3journal/jkae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/11/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024]
Abstract
The Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is currently considered one of the most endangered primates in the world and is classified as critically endangered [International union for conservation of nature (IUCN)]. It faces multiple threats, the most significant one being habitat loss due to deforestation in western Ecuador. Genomic tools are keys for the management of endangered species, but this requires a reference genome, which until now was unavailable for A. f. fusciceps. The present study reports the first whole-genome sequence and assembly of A. f. fusciceps generated using Oxford Nanopore long reads. DNA was extracted from a subadult male, and libraries were prepared for sequencing following the Ligation Sequencing Kit SQK-LSK112 workflow. Sequencing was performed using a MinION Mk1C sequencer. The sequencing reads were processed to generate a genome assembly. Two different assemblers were used to obtain draft genomes using raw reads, of which the Flye assembly was found to be superior. The final assembly has a total length of 2.63 Gb and contains 3,861 contigs, with an N50 of 7,560,531 bp. The assembly was analyzed for annotation completeness based on primate ortholog prediction using a high-resolution database, and was found to be 84.3% complete, with a low number of duplicated genes indicating a precise assembly. The annotation of the assembly predicted 31,417 protein-coding genes, comparable with other mammal assemblies. A reference genome for this critically endangered species will allow researchers to gain insight into the genetics of its populations and thus aid conservation and management efforts of this vulnerable species.
Collapse
Affiliation(s)
- Gabriela Pozo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Instituto Nacional de Biodiversidad (INABIO), Quito 170135, Ecuador
| | - Martina Albuja-Quintana
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
| | - Lizbeth Larreátegui
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
| | - Bernardo Gutiérrez
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Nathalia Fuentes
- Proyecto Washu/Fundación Naturaleza y Arte, Quito 170521, Ecuador
| | | | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Instituto Nacional de Biodiversidad (INABIO), Quito 170135, Ecuador
| |
Collapse
|
9
|
Xia B, Zhang W, Zhao G, Zhang X, Bai J, Brosh R, Wudzinska A, Huang E, Ashe H, Ellis G, Pour M, Zhao Y, Coelho C, Zhu Y, Miller A, Dasen JS, Maurano MT, Kim SY, Boeke JD, Yanai I. On the genetic basis of tail-loss evolution in humans and apes. Nature 2024; 626:1042-1048. [PMID: 38418917 PMCID: PMC10901737 DOI: 10.1038/s41586-024-07095-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/19/2024] [Indexed: 03/02/2024]
Abstract
The loss of the tail is among the most notable anatomical changes to have occurred along the evolutionary lineage leading to humans and to the 'anthropomorphous apes'1-3, with a proposed role in contributing to human bipedalism4-6. Yet, the genetic mechanism that facilitated tail-loss evolution in hominoids remains unknown. Here we present evidence that an individual insertion of an Alu element in the genome of the hominoid ancestor may have contributed to tail-loss evolution. We demonstrate that this Alu element-inserted into an intron of the TBXT gene7-9-pairs with a neighbouring ancestral Alu element encoded in the reverse genomic orientation and leads to a hominoid-specific alternative splicing event. To study the effect of this splicing event, we generated multiple mouse models that express both full-length and exon-skipped isoforms of Tbxt, mimicking the expression pattern of its hominoid orthologue TBXT. Mice expressing both Tbxt isoforms exhibit a complete absence of the tail or a shortened tail depending on the relative abundance of Tbxt isoforms expressed at the embryonic tail bud. These results support the notion that the exon-skipped transcript is sufficient to induce a tail-loss phenotype. Moreover, mice expressing the exon-skipped Tbxt isoform develop neural tube defects, a condition that affects approximately 1 in 1,000 neonates in humans10. Thus, tail-loss evolution may have been associated with an adaptive cost of the potential for neural tube defects, which continue to affect human health today.
Collapse
Affiliation(s)
- Bo Xia
- Institute for Computational Medicine, NYU Langone Health, New York, NY, USA.
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Society of Fellows, Harvard University, Cambridge, MA, USA.
| | - Weimin Zhang
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Guisheng Zhao
- Institute for Computational Medicine, NYU Langone Health, New York, NY, USA
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Xinru Zhang
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Jiangshan Bai
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | | | - Emily Huang
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Hannah Ashe
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Gwen Ellis
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Maayan Pour
- Institute for Computational Medicine, NYU Langone Health, New York, NY, USA
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Yu Zhao
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Camila Coelho
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Yinan Zhu
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Alexander Miller
- Department of Neuroscience and Physiology, NYU Langone Health, New York, NY, USA
| | - Jeremy S Dasen
- Department of Neuroscience and Physiology, NYU Langone Health, New York, NY, USA
| | - Matthew T Maurano
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - Sang Y Kim
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA.
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA.
| | - Itai Yanai
- Institute for Computational Medicine, NYU Langone Health, New York, NY, USA.
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA.
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
| |
Collapse
|
10
|
Berry N, Mee ET, Almond N, Rose NJ. The Impact and Effects of Host Immunogenetics on Infectious Disease Studies Using Non-Human Primates in Biomedical Research. Microorganisms 2024; 12:155. [PMID: 38257982 PMCID: PMC10818626 DOI: 10.3390/microorganisms12010155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Understanding infectious disease pathogenesis and evaluating novel candidate treatment interventions for human use frequently requires prior or parallel analysis in animal model systems. While rodent species are frequently applied in such studies, there are situations where non-human primate (NHP) species are advantageous or required. These include studies of animals that are anatomically more akin to humans, where there is a need to interrogate the complexity of more advanced biological systems or simply reflect susceptibility to a specific infectious agent. The contribution of different arms of the immune response may be addressed in a variety of NHP species or subspecies in specific physiological compartments. Such studies provide insights into immune repertoires not always possible from human studies. However, genetic variation in outbred NHP models may confound, or significantly impact the outcome of a particular study. Thus, host factors need to be considered when undertaking such studies. Considerable knowledge of the impact of host immunogenetics on infection dynamics was elucidated from HIV/SIV research. NHP models are now important for studies of emerging infections. They have contributed to delineating the pathogenesis of SARS-CoV-2/COVID-19, which identified differences in outcomes attributable to the selected NHP host. Moreover, their use was crucial in evaluating the immunogenicity and efficacy of vaccines against COVID-19 and establishing putative correlates of vaccine protection. More broadly, neglected or highly pathogenic emerging or re-emergent viruses may be studied in selected NHPs. These studies characterise protective immune responses following infection or the administration of candidate immunogens which may be central to the accelerated licensing of new vaccines. Here, we review selected aspects of host immunogenetics, specifically MHC background and TRIM5 polymorphism as exemplars of adaptive and innate immunity, in commonly used Old and New World host species. Understanding this variation within and between NHP species will ensure that this valuable laboratory source is used most effectively to combat established and emerging virus infections and improve human health worldwide.
Collapse
Affiliation(s)
- Neil Berry
- Research & Development—Science, Research and Innovation, Medicines and Healthcare products Regulatory Agency, South Mimms, Hertfordshire EN6 3QG, UK; (E.T.M.); (N.A.); (N.J.R.)
| | | | | | | |
Collapse
|
11
|
Schaaf GW, Justice JN, Quillen EE, Cline JM. Resilience, aging, and response to radiation exposure (RARRE) in nonhuman primates: a resource review. GeroScience 2023; 45:3371-3379. [PMID: 37188889 PMCID: PMC10643677 DOI: 10.1007/s11357-023-00812-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
The Wake Forest nonhuman primate (NHP) Radiation Late Effects Cohort (RLEC) is a unique and irreplaceable population of aging NHP radiation survivors which serves the nation's need to understand the late effects of radiation exposure. Over the past 16 years, Wake Forest has evaluated > 250 previously irradiated rhesus macaques (Macaca mulatta) that were exposed to single total body irradiation (IR) doses of 1.14-8.5 Gy or to partial body exposures of up to 10 Gy (5% bone marrow sparing) or 10.75 Gy (whole thorax). Though primarily used to examine IR effects on disease-specific processes or to develop radiation countermeasures, this resource provides insights on resilience across physiologic systems and its relationship with biological aging. Exposure to IR has well documented deleterious effects on health, but the late effects of IR are highly variable. Some animals exhibit multimorbidity and accumulated health deficits, whereas others remain relatively resilient years after exposure to total body IR. This provides an opportunity to evaluate biological aging at the nexus of resilient/vulnerable responses to a stressor. Consideration of inter-individual differences in response to this stressor can inform individualized strategies to manage late effects of radiation exposure, and provide insight into mechanisms underlying systemic resilience and aging. The utility of this cohort for age-related research questions was summarized at the 2022 Trans-NIH Geroscience Interest Group's Workshop on Animal Models for Geroscience. We present a brief review of radiation injury and its relationship to aging and resilience in NHPs with a focus on the RLEC.
Collapse
Affiliation(s)
- George W Schaaf
- Department of Pathology, Section On Comparative Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
| | - Jamie N Justice
- Department of Internal Medicine, Section On Gerontology and Geriatric Medicine, and Stich Center for Health Aging and Alzheimer's Prevention, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Ellen E Quillen
- Department of Internal Medicine, Section On Molecular Medicine, and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - J Mark Cline
- Department of Pathology, Section On Comparative Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| |
Collapse
|
12
|
Zhao S, Chi L, Chen H. CEGA: a method for inferring natural selection by comparative population genomic analysis across species. Genome Biol 2023; 24:219. [PMID: 37789379 PMCID: PMC10548728 DOI: 10.1186/s13059-023-03068-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/20/2023] [Indexed: 10/05/2023] Open
Abstract
We developed maximum likelihood method for detecting positive selection or balancing selection using multilocus or genomic polymorphism and divergence data from two species. The method is especially useful for investigating natural selection in noncoding regions. Simulations demonstrate that the method outperforms existing methods in detecting both positive and balancing selection. We apply the method to population genomic data from human and chimpanzee. The list of genes identified under selection in the noncoding regions is prominently enriched in pathways related to the brain and nervous system. Therefore, our method will serve as a useful tool for comparative population genomic analysis.
Collapse
Affiliation(s)
- Shilei Zhao
- CAS Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
- School of Future Technology, College of Life Sciences and Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lianjiang Chi
- CAS Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
| | - Hua Chen
- CAS Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- China National Center for Bioinformation, Beijing, 100101, China.
- School of Future Technology, College of Life Sciences and Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China.
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Chiu KP, Stuart L, Ooi HS, Yu J, Smith DG, Pei KJC. Genome sequencing and application of Taiwanese macaque Macaca cyclopis. Sci Rep 2023; 13:11545. [PMID: 37460589 DOI: 10.1038/s41598-023-38402-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
Formosan macaque (Macaca cyclopis) is the only non-human primate in Taiwan Island. We performed de novo hybrid assembly for M. cyclopis using Illumina paired-end short reads, mate-pair reads and Nanopore long reads and obtained 5065 contigs with a N50 of 2.66 megabases. M. cyclopis contigs > = 10 kb were assigned to chromosomes using Indian rhesus macaque (Macaca mulatta mulatta) genome assembly Mmul_10 as reference, resulting in a draft of M. cyclopis genome of 2,846,042,475 bases, distributed in 21 chromosomes. The draft genome contains 23,462 transcriptional origins (genes), capable of expressing 716,231 exons in 59,484 transcripts. Genome-based phylogenetic study using the assembled M. cyclopis genome together with genomes of four other macaque species, human, orangutan and chimpanzee showed similar result as previously reported. However, the M. cyclopis species was found to diverge from Chinese M. mulatta lasiota about 1.8 million years ago. Fossil gene analysis detected the presence of gap and pol endogenous viral elements of simian retrovirus in all macaques tested, including M. fascicularis, M. m. mulatta and M. cyclopis. However, M. cyclopis showed ~ 2 times less in number and more uniform in chromosomal locations. The constrain in foreign genome disturbance, presumably due to geographical isolation, should be able to simplify genomics-related investigations, making M. cyclopis an ideal primate species for medical research.
Collapse
Affiliation(s)
- Kuo-Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
- Top Science Biotechnologies, Inc., 4F, 50-2 Dingping Rd., Sec. 1, Shiding District, New Taipei City, 223002, Taiwan.
| | - Lutimba Stuart
- Top Science Biotechnologies, Inc., 4F, 50-2 Dingping Rd., Sec. 1, Shiding District, New Taipei City, 223002, Taiwan
| | - Hong Sain Ooi
- Top Science Biotechnologies, Inc., 4F, 50-2 Dingping Rd., Sec. 1, Shiding District, New Taipei City, 223002, Taiwan
| | - John Yu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, No.5, Fu-Shin St., Kuei Shang, Taoyuan, 333, Taiwan
| | - David Glenn Smith
- Department of Anthropology, University of California Davis, Davis, CA, USA
| | - Kurtis Jai-Chyi Pei
- Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| |
Collapse
|
15
|
Shao Y, Zhou L, Li F, Zhao L, Zhang BL, Shao F, Chen JW, Chen CY, Bi X, Zhuang XL, Zhu HL, Hu J, Sun Z, Li X, Wang D, Rivas-González I, Wang S, Wang YM, Chen W, Li G, Lu HM, Liu Y, Kuderna LFK, Farh KKH, Fan PF, Yu L, Li M, Liu ZJ, Tiley GP, Yoder AD, Roos C, Hayakawa T, Marques-Bonet T, Rogers J, Stenson PD, Cooper DN, Schierup MH, Yao YG, Zhang YP, Wang W, Qi XG, Zhang G, Wu DD. Phylogenomic analyses provide insights into primate evolution. Science 2023; 380:913-924. [PMID: 37262173 DOI: 10.1126/science.abn6919] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/26/2023] [Indexed: 06/03/2023]
Abstract
Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.
Collapse
Affiliation(s)
- Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Long Zhou
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fang Li
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Institute of Animal Sex and Development, ZhejiangWanli University, Ningbo 315100, China
| | - Lan Zhao
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China
| | | | - Chun-Yan Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xupeng Bi
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiao-Lin Zhuang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China
| | | | - Jiang Hu
- Grandomics Biosciences, Beijing 102206, China
| | - Zongyi Sun
- Grandomics Biosciences, Beijing 102206, China
| | - Xin Li
- Grandomics Biosciences, Beijing 102206, China
| | - Depeng Wang
- Grandomics Biosciences, Beijing 102206, China
| | | | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Yun-Mei Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou 510070, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Hui-Meng Lu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA 92122, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA 92122, USA
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-Jin Liu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - George P Tiley
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | | | - Yong-Gang Yao
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Guang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650204, China
| |
Collapse
|
16
|
Amiez C, Sallet J, Giacometti C, Verstraete C, Gandaux C, Morel-Latour V, Meguerditchian A, Hadj-Bouziane F, Ben Hamed S, Hopkins WD, Procyk E, Wilson CRE, Petrides M. A revised perspective on the evolution of the lateral frontal cortex in primates. SCIENCE ADVANCES 2023; 9:eadf9445. [PMID: 37205762 DOI: 10.1126/sciadv.adf9445] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/14/2023] [Indexed: 05/21/2023]
Abstract
Detailed neuroscientific data from macaque monkeys have been essential in advancing understanding of human frontal cortex function, particularly for regions of frontal cortex without homologs in other model species. However, precise transfer of this knowledge for direct use in human applications requires an understanding of monkey to hominid homologies, particularly whether and how sulci and cytoarchitectonic regions in the frontal cortex of macaques relate to those in hominids. We combine sulcal pattern analysis with resting-state functional magnetic resonance imaging and cytoarchitectonic analysis to show that old-world monkey brains have the same principles of organization as hominid brains, with the notable exception of sulci in the frontopolar cortex. This essential comparative framework provides insights into primate brain evolution and a key tool to drive translation from invasive research in monkeys to human applications.
Collapse
Affiliation(s)
- Céline Amiez
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Jérôme Sallet
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
- Wellcome Integrative Neuroimaging Centre, Department of Experimental Psychology, University of Oxford, Oxford OX1 3SR, UK
| | - Camille Giacometti
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Charles Verstraete
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Clémence Gandaux
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Valentine Morel-Latour
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Adrien Meguerditchian
- Laboratoire de Psychologie Cognitive, UMR7290, Université Aix-Marseille, CNRS, 13331 Marseille, France
- Station de Primatologie CNRS, UPS846, 13790 Rousset, France
- Brain and Language Research Institute, Université Aix-Marseille, CNRS, 13604 Aix-en-Provence, France
| | - Fadila Hadj-Bouziane
- Integrative Multisensory Perception Action and Cognition Team (ImpAct), INSERM U1028, CNRS UMR5292, Lyon Neuroscience Research Center (CRNL), Lyon, France; University of Lyon 1, Lyon, France
| | - Suliann Ben Hamed
- Institut des Sciences Cognitives Marc Jeannerod, UMR5229, CNRS-Université Claude Bernard Lyon I, Bron, France
| | - William D Hopkins
- Department of Comparative Medicine, University of Texas MD Anderson Cancer Center, Bastrop, TX, 78602, USA
| | - Emmanuel Procyk
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Charles R E Wilson
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Michael Petrides
- Department of Neurology and Neurosurgery and Department of Psychology, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| |
Collapse
|
17
|
Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Gordon DS, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Lu Q, Paten B, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE. Structurally divergent and recurrently mutated regions of primate genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531415. [PMID: 36945442 PMCID: PMC10028934 DOI: 10.1101/2023.03.07.531415] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
To better understand the pattern of primate genome structural variation, we sequenced and assembled using multiple long-read sequencing technologies the genomes of eight nonhuman primate species, including New World monkeys (owl monkey and marmoset), Old World monkey (macaque), Asian apes (orangutan and gibbon), and African ape lineages (gorilla, bonobo, and chimpanzee). Compared to the human genome, we identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. Across 50 million years of primate evolution, we estimate that 819.47 Mbp or ~27% of the genome has been affected by SVs based on analysis of these primate lineages. We identify 1,607 structurally divergent regions (SDRs) wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (CARDs, ABCD7, OLAH) and new lineage-specific genes are generated (e.g., CKAP2, NEK5) and have become targets of rapid chromosomal diversification and positive selection (e.g., RGPDs). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species for the first time.
Collapse
Affiliation(s)
- Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Allison Rozanski
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Xiangyu Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - David S Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Xiaoxi Wei
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ricardo Del Rosario
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vanessa L Bauer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Will T Fattor
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Gregory K Wilkerson
- Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX, USA
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Qing Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Wesley C Warren
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA
- Institute of Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| |
Collapse
|
18
|
King SB, Singh M. Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. PLoS Comput Biol 2023; 19:e1010966. [PMID: 36952575 PMCID: PMC10035887 DOI: 10.1371/journal.pcbi.1010966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/22/2023] [Indexed: 03/25/2023] Open
Abstract
Despite the vast phenotypic differences observed across primates, their protein products are largely similar to each other at the sequence level. We hypothesized that, since proteins accomplish all their functions via interactions with other molecules, alterations in the sites that participate in these interactions may be of critical importance. To uncover the extent to which these sites evolve across primates, we built a structurally-derived dataset of ~4,200 one-to-one orthologous sequence groups across 18 primate species, consisting of ~68,000 ligand-binding sites that interact with DNA, RNA, small molecules, ions, or peptides. Using this dataset, we identify functionally important patterns of conservation and variation within the amino acid residues that facilitate protein-ligand interactions across the primate phylogeny. We uncover that interaction sites are significantly more conserved than other sites, and that sites binding DNA and RNA further exhibit the lowest levels of variation. We also show that the subset of ligand-binding sites that do vary are enriched in components of gene regulatory pathways and uncover several instances of human-specific ligand-binding site changes within transcription factors. Altogether, our results suggest that ligand-binding sites have experienced selective pressure in primates and propose that variation in these sites may have an outsized effect on phenotypic variation in primates through pleiotropic effects on gene regulation.
Collapse
Affiliation(s)
- Sean B King
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Mona Singh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
| |
Collapse
|
19
|
Soto DC, Uribe-Salazar JM, Shew CJ, Sekar A, McGinty SP, Dennis MY. Genomic structural variation: A complex but important driver of human evolution. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023. [PMID: 36794631 DOI: 10.1002/ajpa.24713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 01/21/2023] [Accepted: 02/05/2023] [Indexed: 02/17/2023]
Abstract
Structural variants (SVs)-including duplications, deletions, and inversions of DNA-can have significant genomic and functional impacts but are technically difficult to identify and assay compared with single-nucleotide variants. With the aid of new genomic technologies, it has become clear that SVs account for significant differences across and within species. This phenomenon is particularly well-documented for humans and other primates due to the wealth of sequence data available. In great apes, SVs affect a larger number of nucleotides than single-nucleotide variants, with many identified SVs exhibiting population and species specificity. In this review, we highlight the importance of SVs in human evolution by (1) how they have shaped great ape genomes resulting in sensitized regions associated with traits and diseases, (2) their impact on gene functions and regulation, which subsequently has played a role in natural selection, and (3) the role of gene duplications in human brain evolution. We further discuss how to incorporate SVs in research, including the strengths and limitations of various genomic approaches. Finally, we propose future considerations in integrating existing data and biospecimens with the ever-expanding SV compendium propelled by biotechnology advancements.
Collapse
Affiliation(s)
- Daniela C Soto
- Genome Center, MIND Institute, Department of Biochemstry & Molecular Medicine, University of California, Davis, California, USA.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, California, USA
| | - José M Uribe-Salazar
- Genome Center, MIND Institute, Department of Biochemstry & Molecular Medicine, University of California, Davis, California, USA.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, California, USA
| | - Colin J Shew
- Genome Center, MIND Institute, Department of Biochemstry & Molecular Medicine, University of California, Davis, California, USA.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, California, USA
| | - Aarthi Sekar
- Genome Center, MIND Institute, Department of Biochemstry & Molecular Medicine, University of California, Davis, California, USA.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, California, USA
| | - Sean P McGinty
- Genome Center, MIND Institute, Department of Biochemstry & Molecular Medicine, University of California, Davis, California, USA.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, California, USA
| | - Megan Y Dennis
- Genome Center, MIND Institute, Department of Biochemstry & Molecular Medicine, University of California, Davis, California, USA.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, California, USA
| |
Collapse
|
20
|
Vallender EJ, Hotchkiss CE, Lewis AD, Rogers J, Stern JA, Peterson SM, Ferguson B, Sayers K. Nonhuman primate genetic models for the study of rare diseases. Orphanet J Rare Dis 2023; 18:20. [PMID: 36721163 PMCID: PMC9887761 DOI: 10.1186/s13023-023-02619-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
Pre-clinical research and development relies heavily upon translationally valid models of disease. A major difficulty in understanding the biology of, and developing treatments for, rare disease is the lack of animal models. It is important that these models not only recapitulate the presentation of the disease in humans, but also that they share functionally equivalent underlying genetic causes. Nonhuman primates share physiological, anatomical, and behavioral similarities with humans resulting from close evolutionary relationships and high genetic homology. As the post-genomic era develops and next generation sequencing allows for the resequencing and screening of large populations of research animals, naturally occurring genetic variation in nonhuman primates with clinically relevant phenotypes is regularly emerging. Here we review nonhuman primate models of multiple rare genetic diseases with a focus on the similarities and differences in manifestation and etiologies across species. We discuss how these models are being developed and how they can offer new tools and opportunities for researchers interested in exploring novel therapeutics for these and other genetic diseases. Modeling human genetic diseases in translationally relevant nonhuman primates presents new prospects for development of therapeutics and a better understanding of rare diseases. The post-genomic era offers the opportunity for the discovery and further development of more models like those discussed here.
Collapse
Affiliation(s)
- Eric J. Vallender
- University of Mississippi Medical Center, Jackson, MS USA
- Tulane National Primate Research Center, Covington, LA USA
| | - Charlotte E. Hotchkiss
- University of Washington, Seattle, WA USA
- Washington National Primate Research Center, Seattle, WA USA
| | - Anne D. Lewis
- Oregon Health and Sciences University, Beaverton, OR USA
- Oregon National Primate Research Center, Beaverton, OR USA
| | - Jeffrey Rogers
- Baylor College of Medicine, Houston, TX USA
- Wisconsin National Primate Research Center, Madison, WI USA
| | - Joshua A. Stern
- University of California-Davis, Davis, CA USA
- California National Primate Research Center, Davis, CA USA
| | - Samuel M. Peterson
- Oregon Health and Sciences University, Beaverton, OR USA
- Oregon National Primate Research Center, Beaverton, OR USA
| | - Betsy Ferguson
- Oregon Health and Sciences University, Beaverton, OR USA
- Oregon National Primate Research Center, Beaverton, OR USA
| | - Ken Sayers
- Texas Biomedical Research Institute, San Antonio, TX USA
- Southwest National Primate Research Center, San Antonio, TX USA
| |
Collapse
|
21
|
Current advances in primate genomics: novel approaches for understanding evolution and disease. Nat Rev Genet 2023; 24:314-331. [PMID: 36599936 DOI: 10.1038/s41576-022-00554-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2022] [Indexed: 01/05/2023]
Abstract
Primate genomics holds the key to understanding fundamental aspects of human evolution and disease. However, genetic diversity and functional genomics data sets are currently available for only a few of the more than 500 extant primate species. Concerted efforts are under way to characterize primate genomes, genetic polymorphism and divergence, and functional landscapes across the primate phylogeny. The resulting data sets will enable the connection of genotypes to phenotypes and provide new insight into aspects of the genetics of primate traits, including human diseases. In this Review, we describe the existing genome assemblies as well as genetic variation and functional genomic data sets. We highlight some of the challenges with sample acquisition. Finally, we explore how technological advances in single-cell functional genomics and induced pluripotent stem cell-derived organoids will facilitate our understanding of the molecular foundations of primate biology.
Collapse
|
22
|
Silva L, Antunes A. Omics and Remote Homology Integration to Decipher Protein Functionality. Methods Mol Biol 2023; 2627:61-81. [PMID: 36959442 DOI: 10.1007/978-1-0716-2974-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
In the recent years, several "omics" technologies based on specific biomolecules (from DNA, RNA, proteins, or metabolites) have won growing importance in the scientific field. Despite each omics possess their own laboratorial protocols, they share a background of bioinformatic tools for data integration and analysis. A recent subset of bioinformatic tools, based on available templates or remote homology protocols, allow computational fast and high-accuracy prediction of protein structures. The quickly predict of actually unsolved protein structures, together with late omics findings allow a boost of scientific advances in multiple fields such as cancer, longevity, immunity, mitochondrial function, toxicology, drug design, biosensors, and recombinant protein engineering. In this chapter, we assessed methodological approaches for the integration of omics and remote homology inferences to decipher protein functionality, opening the door to the next era of biological knowledge.
Collapse
Affiliation(s)
- Liliana Silva
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.
| |
Collapse
|
23
|
Kress A, Poch O, Lecompte O, Thompson JD. Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events. FRONTIERS IN BIOINFORMATICS 2023; 3:1178926. [PMID: 37151482 PMCID: PMC10158824 DOI: 10.3389/fbinf.2023.1178926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/05/2023] [Indexed: 05/09/2023] Open
Abstract
Protein annotation errors can have significant consequences in a wide range of fields, ranging from protein structure and function prediction to biomedical research, drug discovery, and biotechnology. By comparing the domains of different proteins, scientists can identify common domains, classify proteins based on their domain architecture, and highlight proteins that have evolved differently in one or more species or clades. However, genome-wide identification of different protein domain architectures involves a complex error-prone pipeline that includes genome sequencing, prediction of gene exon/intron structures, and inference of protein sequences and domain annotations. Here we developed an automated fact-checking approach to distinguish true domain loss/gain events from false events caused by errors that occur during the annotation process. Using genome-wide ortholog sets and taking advantage of the high-quality human and Saccharomyces cerevisiae genome annotations, we analyzed the domain gain and loss events in the predicted proteomes of 9 non-human primates (NHP) and 20 non-S. cerevisiae fungi (NSF) as annotated in the Uniprot and Interpro databases. Our approach allowed us to quantify the impact of errors on estimates of protein domain gains and losses, and we show that domain losses are over-estimated ten-fold and three-fold in the NHP and NSF proteins respectively. This is in line with previous studies of gene-level losses, where issues with genome sequencing or gene annotation led to genes being falsely inferred as absent. In addition, we show that insistent protein domain annotations are a major factor contributing to the false events. For the first time, to our knowledge, we show that domain gains are also over-estimated by three-fold and two-fold respectively in NHP and NSF proteins. Based on our more accurate estimates, we infer that true domain losses and gains in NHP with respect to humans are observed at similar rates, while domain gains in the more divergent NSF are observed twice as frequently as domain losses with respect to S. cerevisiae. This study highlights the need to critically examine the scientific validity of protein annotations, and represents a significant step toward scalable computational fact-checking methods that may 1 day mitigate the propagation of wrong information in protein databases.
Collapse
|
24
|
Iriki A, Tramacere A. “Natural Laboratory Complex” for novel primate neuroscience. Front Integr Neurosci 2022; 16:927605. [PMID: 36274659 PMCID: PMC9581230 DOI: 10.3389/fnint.2022.927605] [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: 04/24/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022] Open
Abstract
We propose novel strategies for primate experimentation that are ethically valuable and pragmatically useful for cognitive neuroscience and neuropsychiatric research. Specifically, we propose Natural Laboratory Complex or Natural Labs, which are a combination of indoor-outdoor structures for studying free moving and socially housed primates in natural or naturalistic environment. We contend that Natural Labs are pivotal to improve primate welfare, and at the same time to implement longitudinal and socio-ecological studies of primate brain and behavior. Currently emerging advanced technologies and social systems (including recent COVID-19 induced “remote” infrastructures) can speed-up cognitive neuroscience approaches in freely behaving animals. Experimental approaches in natural(istic) settings are not in competition with conventional approaches of laboratory investigations, and could establish several benefits at the ethical, experimental, and economic levels.
Collapse
Affiliation(s)
- Atsushi Iriki
- Laboratory for Symbolic Cognitive Development, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- *Correspondence: Atsushi Iriki,
| | - Antonella Tramacere
- Department of Philosophy and Communication Studies, University of Bologna, Bologna, Italy
- Department of Cultural and Linguistic Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
| |
Collapse
|
25
|
Zhang X. Effects of Anesthesia on Cerebral Blood Flow and Functional Connectivity of Nonhuman Primates. Vet Sci 2022; 9:vetsci9100516. [PMID: 36288129 PMCID: PMC9609818 DOI: 10.3390/vetsci9100516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 02/07/2023] Open
Abstract
Nonhuman primates (NHPs) are the closest living relatives of humans and play a critical and unique role in neuroscience research and pharmaceutical development. General anesthesia is usually required in neuroimaging studies of NHPs to keep the animal from stress and motion. However, the adverse effects of anesthesia on cerebral physiology and neural activity are pronounced and can compromise the data collection and interpretation. Functional connectivity is frequently examined using resting-state functional MRI (rsfMRI) to assess the functional abnormality in the animal brain under anesthesia. The fMRI signal can be dramatically suppressed by most anesthetics in a dose-dependent manner. In addition, rsfMRI studies may be further compromised by inter-subject variations when the sample size is small (as seen in most neuroscience studies of NHPs). Therefore, proper use of anesthesia is strongly demanded to ensure steady and consistent physiology maintained during rsfMRI data collection of each subject. The aim of this review is to summarize typical anesthesia used in rsfMRI scans of NHPs and the effects of anesthetics on cerebral physiology and functional connectivity. Moreover, the protocols with optimal rsfMRI data acquisition and anesthesia procedures for functional connectivity study of macaque monkeys are introduced.
Collapse
Affiliation(s)
- Xiaodong Zhang
- EPC Imaging Center and Division of Neuropharmacology and Neurologic Diseases, Emory National Primate Research Center, Emory University, 954 Gatewood RD, Atlanta, GA 30329, USA
| |
Collapse
|
26
|
Total-Body Irradiation Is Associated With Increased Incidence of Mesenchymal Neoplasia in a Radiation Late Effects Cohort of Rhesus Macaques (Macaca mulatta). Int J Radiat Oncol Biol Phys 2022; 113:661-674. [PMID: 35361520 PMCID: PMC9250621 DOI: 10.1016/j.ijrobp.2022.02.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/04/2022] [Accepted: 02/13/2022] [Indexed: 11/21/2022]
Abstract
PURPOSE Cancer is a severe delayed effect of acute radiation exposure. Total-body irradiation has been associated with an increased risk of solid cancer and leukemia in Japanese atomic bomb survivors, and secondary malignancies, such as sarcoma, are a serious consequence of cancer radiation therapy. The radiation late effects cohort (RLEC) of rhesus macaques (Macaca mulatta) is a unique resource of more than 200 animals for studying the long-term consequences of total-body irradiation in an animal model that closely resembles humans at the genetic and physiologic levels. METHODS AND MATERIALS Using clinical records, clinical imaging, histopathology, and immunohistochemistry, this retrospective study characterized the incidence of neoplasia in the RLEC. RESULTS Since 2007, 61 neoplasms in 44 of 239 irradiated animals were documented (18.4% of the irradiated population). Only 1 neoplasm was diagnosed among the 51 nonirradiated controls of the RLEC (2.0%). The most common malignancies in the RLEC were sarcomas (38.3% of diagnoses), which are rare neoplasms in nonirradiated macaques. The most common sarcomas included malignant nerve sheath tumors and malignant glomus tumors. Carcinomas were less common (19.7% of diagnoses), and consisted primarily of renal cell and hepatocellular carcinomas. Neoplasia occurred in most major body systems, with the skin and subcutis being the most common site (40%). RNA analysis showed similarities in transcriptional profiles between RLEC and human malignant nerve sheath tumors. CONCLUSIONS This study indicates that total-body irradiation is associated with an increased incidence of neoplasia years following irradiation, at more than double the incidence described in aging, nonirradiated animals, and promotes tumor histotypes that are rarely observed in nonirradiated, aging rhesus macaques.
Collapse
|
27
|
Bangari DS, Lanigan LG, Goulet F, Siso S, Bolon B. Society of Toxicologic Pathology Neuropathology Interest Group Article: Neuropathologic Findings in Nonhuman Primates Associated With Administration of Biomolecule-Based Test Articles. Toxicol Pathol 2022; 50:693-711. [PMID: 35695393 DOI: 10.1177/01926233221101314] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The increasing specificity of novel druggable targets coupled with the complexity of emerging therapeutic modalities for treating human diseases has created a growing need for nonhuman primates (NHPs) as models for translational drug discovery and nonclinical safety assessment. In particular, NHPs are critical for investigating potential unexpected/undesired on-target and off-target liabilities associated with administration of candidate biotherapeutics (nucleic acids, proteins, viral gene therapy vectors, etc.) to treat nervous system disorders. Nervous system findings unique to or overrepresented in NHPs administered biomolecule-based ("biologic") test articles include mononuclear cell infiltration in most neural tissues for all biomolecule classes as well as neuronal necrosis with glial cell proliferation in sensory ganglia for certain viral vectors. Such test article-related findings in NHPs often must be differentiated from procedural effects (e.g., local parenchymal or meningeal reactions associated with an injection site or implanted catheter to administer a test article directly into the central nervous system) or spontaneous background findings (e.g., neuronal autophagy in sensory ganglia).
Collapse
Affiliation(s)
- Dinesh S Bangari
- Global Discovery Pathology, Translational In-Vivo Models Platform, Sanofi, Cambridge, Massachusetts, USA
| | | | - Felix Goulet
- Charles River Laboratories, Senneville, Quebec, Canada
| | - Silvia Siso
- Translational Imaging and Pathology, Codiak BioSciences, Cambridge, Massachusetts, USA
| | | |
Collapse
|
28
|
Karimzadeh M, Hoffman MM. Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome. Genome Biol 2022; 23:126. [PMID: 35681170 PMCID: PMC9185870 DOI: 10.1186/s13059-022-02690-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/16/2022] [Indexed: 11/29/2022] Open
Abstract
Existing methods for computational prediction of transcription factor (TF) binding sites evaluate genomic regions with similarity to known TF sequence preferences. Most TF binding sites, however, do not resemble known TF sequence motifs, and many TFs are not sequence-specific. We developed Virtual ChIP-seq, which predicts binding of individual TFs in new cell types, integrating learned associations with gene expression and binding, TF binding sites from other cell types, and chromatin accessibility data in the new cell type. This approach outperforms methods that predict TF binding solely based on sequence preference, predicting binding for 36 TFs (MCC>0.3).
Collapse
Affiliation(s)
- Mehran Karimzadeh
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Princess Margaret Cancer Centre, Toronto, ON, Canada.,Vector Institute, Toronto, ON, Canada
| | - Michael M Hoffman
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. .,Princess Margaret Cancer Centre, Toronto, ON, Canada. .,Vector Institute, Toronto, ON, Canada. .,Department of Computer Science, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
29
|
Singh NP, Krumlauf R. Diversification and Functional Evolution of HOX Proteins. Front Cell Dev Biol 2022; 10:798812. [PMID: 35646905 PMCID: PMC9136108 DOI: 10.3389/fcell.2022.798812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 01/07/2023] Open
Abstract
Gene duplication and divergence is a major contributor to the generation of morphological diversity and the emergence of novel features in vertebrates during evolution. The availability of sequenced genomes has facilitated our understanding of the evolution of genes and regulatory elements. However, progress in understanding conservation and divergence in the function of proteins has been slow and mainly assessed by comparing protein sequences in combination with in vitro analyses. These approaches help to classify proteins into different families and sub-families, such as distinct types of transcription factors, but how protein function varies within a gene family is less well understood. Some studies have explored the functional evolution of closely related proteins and important insights have begun to emerge. In this review, we will provide a general overview of gene duplication and functional divergence and then focus on the functional evolution of HOX proteins to illustrate evolutionary changes underlying diversification and their role in animal evolution.
Collapse
Affiliation(s)
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, United States
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, United States
- *Correspondence: Robb Krumlauf,
| |
Collapse
|
30
|
Pozzi L, Penna A. Rocks and clocks revised: New promises and challenges in dating the primate tree of life. Evol Anthropol 2022; 31:138-153. [PMID: 35102633 DOI: 10.1002/evan.21940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 10/04/2021] [Accepted: 01/12/2022] [Indexed: 01/14/2023]
Abstract
In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.
Collapse
Affiliation(s)
- Luca Pozzi
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Anna Penna
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
| |
Collapse
|
31
|
Tello JA, Williams HE, Eppler RM, Steinhilb ML, Khanna M. Animal Models of Neurodegenerative Disease: Recent Advances in Fly Highlight Innovative Approaches to Drug Discovery. Front Mol Neurosci 2022; 15:883358. [PMID: 35514431 PMCID: PMC9063566 DOI: 10.3389/fnmol.2022.883358] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 12/22/2022] Open
Abstract
Neurodegenerative diseases represent a formidable challenge to global health. As advances in other areas of medicine grant healthy living into later decades of life, aging diseases such as Alzheimer's disease (AD) and other neurodegenerative disorders can diminish the quality of these additional years, owed largely to the lack of efficacious treatments and the absence of durable cures. Alzheimer's disease prevalence is predicted to more than double in the next 30 years, affecting nearly 15 million Americans, with AD-associated costs exceeding $1 billion by 2050. Delaying onset of AD and other neurodegenerative diseases is critical to improving the quality of life for patients and reducing the burden of disease on caregivers and healthcare systems. Significant progress has been made to model disease pathogenesis and identify points of therapeutic intervention. While some researchers have contributed to our understanding of the proteins and pathways that drive biological dysfunction in disease using in vitro and in vivo models, others have provided mathematical, biophysical, and computational technologies to identify potential therapeutic compounds using in silico modeling. The most exciting phase of the drug discovery process is now: by applying a target-directed approach that leverages the strengths of multiple techniques and validates lead hits using Drosophila as an animal model of disease, we are on the fast-track to identifying novel therapeutics to restore health to those impacted by neurodegenerative disease.
Collapse
Affiliation(s)
- Judith A. Tello
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States
- Center of Innovation in Brain Science, Tucson, AZ, United States
| | - Haley E. Williams
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States
- Center of Innovation in Brain Science, Tucson, AZ, United States
| | - Robert M. Eppler
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States
| | - Michelle L. Steinhilb
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States
| | - May Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States
- Center of Innovation in Brain Science, Tucson, AZ, United States
- Department of Molecular Pathobiology, New York University, New York, NY, United States
| |
Collapse
|
32
|
Ozirmak Lermi N, Gray SB, Bowen CM, Reyes-Uribe L, Dray BK, Deng N, Harris RA, Raveendran M, Benavides F, Hodo CL, Taggart MW, Colbert Maresso K, Sinha KM, Rogers J, Vilar E. Comparative molecular genomic analyses of a spontaneous rhesus macaque model of mismatch repair-deficient colorectal cancer. PLoS Genet 2022; 18:e1010163. [PMID: 35446842 PMCID: PMC9064097 DOI: 10.1371/journal.pgen.1010163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 05/03/2022] [Accepted: 03/23/2022] [Indexed: 12/02/2022] Open
Abstract
Colorectal cancer (CRC) remains the third most common cancer in the US with 15% of cases displaying Microsatellite Instability (MSI) secondary to Lynch Syndrome (LS) or somatic hypermethylation of the MLH1 promoter. A cohort of rhesus macaques from our institution developed spontaneous mismatch repair deficient (MMRd) CRC with a notable fraction harboring a pathogenic germline mutation in MLH1 (c.1029C
Collapse
Affiliation(s)
- Nejla Ozirmak Lermi
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Stanton B. Gray
- Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Charles M. Bowen
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Laura Reyes-Uribe
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Beth K. Dray
- Charles River Laboratories, Ashland, Ohio, United States of America
| | - Nan Deng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fernando Benavides
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Carolyn L. Hodo
- Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Melissa W. Taggart
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Karen Colbert Maresso
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Krishna M. Sinha
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| |
Collapse
|
33
|
Calapai A, Cabrera-Moreno J, Moser T, Jeschke M. Flexible auditory training, psychophysics, and enrichment of common marmosets with an automated, touchscreen-based system. Nat Commun 2022; 13:1648. [PMID: 35347139 PMCID: PMC8960775 DOI: 10.1038/s41467-022-29185-9] [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: 02/05/2021] [Accepted: 02/28/2022] [Indexed: 11/09/2022] Open
Abstract
Devising new and more efficient protocols to analyze the phenotypes of non-human primates, as well as their complex nervous systems, is rapidly becoming of paramount importance. This is because with genome-editing techniques, recently adopted to non-human primates, new animal models for fundamental and translational research have been established. One aspect in particular, namely cognitive hearing, has been difficult to assess compared to visual cognition. To address this, we devised autonomous, standardized, and unsupervised training and testing of auditory capabilities of common marmosets with a cage-based standalone, wireless system. All marmosets tested voluntarily operated the device on a daily basis and went from naïve to experienced at their own pace and with ease. Through a series of experiments, here we show, that animals autonomously learn to associate sounds with images; to flexibly discriminate sounds, and to detect sounds of varying loudness. The developed platform and training principles combine in-cage training of common marmosets for cognitive and psychoacoustic assessment with an enriched environment that does not rely on dietary restriction or social separation, in compliance with the 3Rs principle. The authors present a cage-based stand-alone platform for autonomous, standardized, and unsupervised training and testing of visuo-auditory-cued behaviours of common marmosets. The experiments do not require dietary restriction or social separation.
Collapse
Affiliation(s)
- A Calapai
- Cognitive Neuroscience Laboratory, German Primate Center - Leibniz-Institute for Primate Research, Göttingen, Germany.,Cognitive Hearing in Primates (CHiP) Group, Auditory Neuroscience and Optogenetics Laboratory, German Primate Center - Leibniz-Institute for Primate Research, Göttingen, Germany.,Auditory Neuroscience and Optogenetics Laboratory, German Primate Center - Leibniz-Institute for Primate Research, Göttingen, Germany.,Leibniz ScienceCampus "Primate Cognition", Göttingen, Germany
| | - J Cabrera-Moreno
- Cognitive Hearing in Primates (CHiP) Group, Auditory Neuroscience and Optogenetics Laboratory, German Primate Center - Leibniz-Institute for Primate Research, Göttingen, Germany.,Auditory Neuroscience and Optogenetics Laboratory, German Primate Center - Leibniz-Institute for Primate Research, Göttingen, Germany.,Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075, Göttingen, Germany.,Göttingen Graduate School for Neurosciences, Biophysics and Molecular Biosciences, University of Göttingen, 37075, Göttingen, Germany
| | - T Moser
- Auditory Neuroscience and Optogenetics Laboratory, German Primate Center - Leibniz-Institute for Primate Research, Göttingen, Germany.,Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075, Göttingen, Germany.,Göttingen Graduate School for Neurosciences, Biophysics and Molecular Biosciences, University of Göttingen, 37075, Göttingen, Germany.,Auditory Neuroscience Group and Synaptic Nanophysiology Group, Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075, Göttingen, Germany
| | - M Jeschke
- Cognitive Hearing in Primates (CHiP) Group, Auditory Neuroscience and Optogenetics Laboratory, German Primate Center - Leibniz-Institute for Primate Research, Göttingen, Germany. .,Auditory Neuroscience and Optogenetics Laboratory, German Primate Center - Leibniz-Institute for Primate Research, Göttingen, Germany. .,Leibniz ScienceCampus "Primate Cognition", Göttingen, Germany. .,Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075, Göttingen, Germany.
| |
Collapse
|
34
|
Wu Y, Wu H, Lu X, Chen Y, Zhang X, Ju J, Zhang D, Zhu B, Huang S. Development and Evaluation of Targeted Optical Imaging Probes for Image‐Guided Surgery in Head and Neck Cancer. ADVANCED THERAPEUTICS 2022. [DOI: 10.1002/adtp.202100196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yue Wu
- Department of Oral and Maxillofacial Surgery Shandong Provincial Hospital Cheeloo College of Medicine Shandong University Jinan Shandong 250021 China
| | - Haiwei Wu
- Department of Oral and Maxillofacial Surgery Shandong Provincial Hospital Cheeloo College of Medicine Shandong University Jinan Shandong 250021 China
| | - Xiaoya Lu
- Department of Oral and Maxillofacial Surgery Shandong Provincial Hospital Cheeloo College of Medicine Shandong University Jinan Shandong 250021 China
| | - Yi Chen
- Department of Oral and Maxillofacial Surgery Shandong Provincial Hospital Cheeloo College of Medicine Shandong University Jinan Shandong 250021 China
| | - Xue Zhang
- University of Jinan Jinan Shandong 250021 China
| | - Jiandong Ju
- Department of Oral and Maxillofacial Surgery Shandong Provincial Hospital Cheeloo College of Medicine Shandong University Jinan Shandong 250021 China
| | - Dongsheng Zhang
- Department of Oral and Maxillofacial Surgery Shandong Provincial Hospital Cheeloo College of Medicine Shandong University Jinan Shandong 250021 China
| | - Baocun Zhu
- University of Jinan Jinan Shandong 250021 China
| | - Shengyun Huang
- Department of Oral and Maxillofacial Surgery Shandong Provincial Hospital Cheeloo College of Medicine Shandong University Jinan Shandong 250021 China
| |
Collapse
|
35
|
Schmidt JK, Jones KM, Van Vleck T, Emborg ME. Modeling genetic diseases in nonhuman primates through embryonic and germline modification: Considerations and challenges. Sci Transl Med 2022; 14:eabf4879. [PMID: 35235338 PMCID: PMC9373237 DOI: 10.1126/scitranslmed.abf4879] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Genetic modification of the embryo or germ line of nonhuman primates is envisioned as a method to develop improved models of human disease, yet the promise of such animal models remains unfulfilled. Here, we discuss current methods and their limitations for producing nonhuman primate genetic models that faithfully genocopy and phenocopy human disease. We reflect on how to ethically maximize the translational relevance of such models in the search for new therapeutic strategies to treat human disease.
Collapse
Affiliation(s)
- Jenna K Schmidt
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Kathryn M Jones
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Trevor Van Vleck
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Marina E Emborg
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
36
|
Wozar F, Seitz I, Reichel F, Fischer MD. Importance of Nonhuman Primates as a Model System for Gene Therapy Development in Ophthalmology. Klin Monbl Augenheilkd 2022; 239:270-274. [PMID: 35189657 DOI: 10.1055/a-1777-5033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Gene therapy is a treatment concept that uses, in most cases, viral vectors to deliver a therapeutic transgene to target cells. Although the idea of gene therapy dates back over 50 years ago, due to the complexity of the treatment concept, it took until the last decade for the responsible agencies like FDA and EMA to recommend the first gene therapy products for clinical use. The development of these therapies relies on molecular engineering of specifically designed vectors and models to test the effectiveness and safety of the treatment. Despite an increasing effort to find effective surrogates, animal models are still irreplaceable in gene therapy development. Rodents are important for exploring pathways and disease mechanisms and identifying potential treatment targets. However, only the primate eye resembles the human eye to a degree where most structures are nearly identical. Some research questions can therefore only be answered using a nonhuman primate (NHP) model. In this review, we want to summarize these key features and highlight the importance of the NHP model for gene therapy development in ophthalmology.
Collapse
Affiliation(s)
- Fabian Wozar
- University Eye Hospital, University Hospital Tübingen Centre of Ophthalmology, Tübingen, Germany
| | - Immanuel Seitz
- University Eye Hospital, University Hospital Tübingen Centre of Ophthalmology, Tübingen, Germany
| | - Felix Reichel
- University Eye Hospital, University Hospital Tübingen Centre of Ophthalmology, Tübingen, Germany
| | - M Dominik Fischer
- University Eye Hospital, University Hospital Tübingen Centre of Ophthalmology, Tübingen, Germany.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom of Great Britain and Northern Ireland.,Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom of Great Britain and Northern Ireland
| |
Collapse
|
37
|
Pougnault L, Levréro F, Leroux M, Paulet J, Bombani P, Dentressangle F, Deruti L, Mulot B, Lemasson A. Social pressure drives "conversational rules" in great apes. Biol Rev Camb Philos Soc 2021; 97:749-765. [PMID: 34873806 DOI: 10.1111/brv.12821] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 01/07/2023]
Abstract
In the last decade, two hypotheses, one on the evolution of animal vocal communication in general and the other on the origins of human language, have gained ground. The first hypothesis argues that the complexity of communication co-evolved with the complexity of sociality. Species forming larger groups with complex social networks have more elaborate vocal repertoires. The second hypothesis posits that the core of communication is represented not only by what can be expressed by an isolated caller, but also by the way that vocal interactions are structured, language being above all a social act. Primitive forms of conversational rules based on a vocal turn-taking principle are thought to exist in primates. To support and bring together these hypotheses, more comparative studies of socially diverse species at different levels of the primate phylogeny are needed. However, the majority of available studies focus on monkeys, primates that are distant from the human lineage. Great apes represent excellent candidates for such comparative studies because of their phylogenetic proximity to humans and their varied social lives. We propose that studying vocal turn-taking in apes could address several major gaps regarding the social relevance of vocal turn-taking and the evolutionary trajectory of this behaviour among anthropoids. Indeed, how the social structure of a species may influence the vocal interaction patterns observed among group members remains an open question. We gathered data from the literature as well as original unpublished data (where absent in the literature) on four great ape species: chimpanzees Pan troglodytes, bonobos Pan paniscus, western lowland gorillas Gorilla gorilla gorilla and Bornean orang-utans Pongo pygmaeus. We found no clear-cut relationship between classical social complexity metrics (e.g. number of group members, interaction rates) and vocal complexity parameters (e.g. repertoire size, call rates). Nevertheless, the nature of the society (i.e. group composition, diversity and valence of social bonds) and the type of vocal interaction patterns (isolated calling, call overlap, turn-taking-based vocal exchanges) do appear to be related. Isolated calling is the main vocal pattern found in the species with the smallest social networks (orang-utan), while the other species show vocal interactions that are structured according to temporal rules. A high proportion of overlapping vocalisations is found in the most competitive species (chimpanzee), while vocal turn-taking predominates in more tolerant bonobos and gorillas. Also, preferentially interacting individuals and call types used to interact are not randomly distributed. Vocal overlap ('chorusing') and vocal exchange ('conversing') appear as possible social strategies used to advertise/strengthen social bonds. Our analyses highlight that: (i) vocal turn-taking is also observed in non-human great apes, revealing universal rules for conversing that may be deeply rooted in the primate lineage; (ii) vocal interaction patterns match the species' social lifestyle; (iii) although limited to four species here, adopting a targeted comparative approach could help to identify the multiple and subtle factors underlying social and vocal complexity. We believe that vocal interaction patterns form the basis of a promising field of investigation that may ultimately improve our understanding of the socially driven evolution of communication.
Collapse
Affiliation(s)
- Loïc Pougnault
- Univ Rennes, Normandie Univ, CNRS, EthoS (Éthologie animale et humaine) - UMR 6552, 263 avenue du Général Leclerc, Rennes, 35042, France.,Université de Lyon/Saint-Etienne, CNRS, Equipe Neuro-Ethologie Sensorielle, ENES/CRNL, UMR5292, INSERM UMR_S 1028, 23 rue Paul Michelon, Saint-Etienne, 42023, France.,ZooParc de Beauval & Beauval Nature, Avenue du Blanc, Saint Aignan, 41110, France
| | - Florence Levréro
- Université de Lyon/Saint-Etienne, CNRS, Equipe Neuro-Ethologie Sensorielle, ENES/CRNL, UMR5292, INSERM UMR_S 1028, 23 rue Paul Michelon, Saint-Etienne, 42023, France
| | - Maël Leroux
- Department of Comparative Linguistics, University of Zürich, Thurgauerstrasse 30, Zürich-Oerlikon, 8050, Switzerland.,Budongo Conservation Field Station, Masindi, Uganda.,Center for the Interdisciplinary Study of Language Evolution (ISLE), University of Zürich, Plattenstrasse 54, Zürich, 8032, Switzerland
| | - Julien Paulet
- Univ Rennes, Normandie Univ, CNRS, EthoS (Éthologie animale et humaine) - UMR 6552, 263 avenue du Général Leclerc, Rennes, 35042, France
| | - Pablo Bombani
- NGO Mbou-Mon-Tour, Nkala, Territoire de Bolodo, Maï-Ndombe, Democratic Republic of the Congo
| | - Fabrice Dentressangle
- Université de Lyon/Saint-Etienne, CNRS, Equipe Neuro-Ethologie Sensorielle, ENES/CRNL, UMR5292, INSERM UMR_S 1028, 23 rue Paul Michelon, Saint-Etienne, 42023, France
| | - Laure Deruti
- Université de Lyon/Saint-Etienne, CNRS, Equipe Neuro-Ethologie Sensorielle, ENES/CRNL, UMR5292, INSERM UMR_S 1028, 23 rue Paul Michelon, Saint-Etienne, 42023, France
| | - Baptiste Mulot
- ZooParc de Beauval & Beauval Nature, Avenue du Blanc, Saint Aignan, 41110, France
| | - Alban Lemasson
- Univ Rennes, Normandie Univ, CNRS, EthoS (Éthologie animale et humaine) - UMR 6552, 263 avenue du Général Leclerc, Rennes, 35042, France.,Institut Universitaire de France, 1 rue Descartes, Paris, 75231, France
| |
Collapse
|
38
|
Oggenfuss U, Badet T, Wicker T, Hartmann FE, Singh NK, Abraham L, Karisto P, Vonlanthen T, Mundt C, McDonald BA, Croll D. A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen. eLife 2021; 10:e69249. [PMID: 34528512 PMCID: PMC8445621 DOI: 10.7554/elife.69249] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/28/2021] [Indexed: 12/16/2022] Open
Abstract
Genome evolution is driven by the activity of transposable elements (TEs). The spread of TEs can have deleterious effects including the destabilization of genome integrity and expansions. However, the precise triggers of genome expansions remain poorly understood because genome size evolution is typically investigated only among deeply divergent lineages. Here, we use a large population genomics dataset of 284 individuals from populations across the globe of Zymoseptoria tritici, a major fungal wheat pathogen. We built a robust map of genome-wide TE insertions and deletions to track a total of 2456 polymorphic loci within the species. We show that purifying selection substantially depressed TE frequencies in most populations, but some rare TEs have recently risen in frequency and likely confer benefits. We found that specific TE families have undergone a substantial genome-wide expansion from the pathogen's center of origin to more recently founded populations. The most dramatic increase in TE insertions occurred between a pair of North American populations collected in the same field at an interval of 25 years. We find that both genome-wide counts of TE insertions and genome size have increased with colonization bottlenecks. Hence, the demographic history likely played a major role in shaping genome evolution within the species. We show that both the activation of specific TEs and relaxed purifying selection underpin this incipient expansion of the genome. Our study establishes a model to recapitulate TE-driven genome evolution over deeper evolutionary timescales.
Collapse
Affiliation(s)
- Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Thomas Wicker
- Institute for Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Fanny E Hartmann
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-SaclayOrsayFrance
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Nikhil Kumar Singh
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Leen Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Petteri Karisto
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Tiziana Vonlanthen
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Christopher Mundt
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallisUnited States
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| |
Collapse
|
39
|
Fredrick M, Danson M, John K, Stanislaus K, David N, Maina N, Michael G, Suleiman M, Mercy A. Schistosoma mansoni and soil transmtted helminths in olive baboons and potential zoonosis. Vet Med Sci 2021; 7:2026-2031. [PMID: 33942545 PMCID: PMC8464276 DOI: 10.1002/vms3.495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/25/2021] [Accepted: 04/01/2021] [Indexed: 11/30/2022] Open
Abstract
Zoonotic pathogens are among the most important causes of ill health all over the world. The presence of these pathogens in free ranging baboons may have significant implications for humans. In Kenya, the encroachment of wildlife habitats has led to increased interaction between humans and wildlife especially non-human primates. The current study therefore aimed at investigating any possible zoonotic gastrointestinal helminths of olive baboons (Papio anubis) at the human-wildlife interface in two park borders and a ranch in Kenya, namely, Tsavo West National Park, Tana River Primate Reserve and Mutara Ranch, Laikipia, Kenya. One hundred and forty-seven baboons were used in the study. They were trapped in the wild, sampled for stool marked and then released back to the wild. Gastrointestinal (GIT) helminths identified were Strongyloides, Oesophagostomum, Enterobius spp and Trichuris Trichiura from all the three sites while Schistosoma mansoni was only detected from Tsavo baboons and with very low incidence (2.1%). The prevalence of these parasites varied among the sites but significant difference in prevalence was only noted in Strongyloides and Oesophagostomum (p < 0.05) among the three sites. This therefore implies that even with control measures instituted on the human population, baboons will always be a source of zoonotic GIT helminths especially S. mansoni even if the incidence are low. There is need to put in place measures aiming to reduce their interactions with humans and also try to control these infections in the baboons.
Collapse
Affiliation(s)
- Maloba Fredrick
- Department of Zoological SciencesKenyatta UniversityNairobiKenya
| | - Mwangi Danson
- Department of Conservation BiologyInstitute of Primate ResearchNairobiKenya
| | - Kagira John
- Jommo Kenyatta University of Agriculture and TechnologyNairobiKenya
| | - Kivai Stanislaus
- Department of Conservation BiologyInstitute of Primate ResearchNairobiKenya
| | | | | | - Gicheru Michael
- Department of Zoological SciencesKenyatta UniversityNairobiKenya
| | | | - Akinyi Mercy
- Department of Conservation BiologyInstitute of Primate ResearchNairobiKenya
- Department of BiologyDuke UniversityDurhamNCUSA
| |
Collapse
|
40
|
Shauli T, Brandes N, Linial M. Evolutionary and functional lessons from human-specific amino acid substitution matrices. NAR Genom Bioinform 2021; 3:lqab079. [PMID: 34541526 PMCID: PMC8445205 DOI: 10.1093/nargab/lqab079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 08/02/2021] [Accepted: 09/14/2021] [Indexed: 12/26/2022] Open
Abstract
Human genetic variation in coding regions is fundamental to the study of protein structure and function. Most methods for interpreting missense variants consider substitution measures derived from homologous proteins across different species. In this study, we introduce human-specific amino acid (AA) substitution matrices that are based on genetic variations in the modern human population. We analyzed the frequencies of >4.8M single nucleotide variants (SNVs) at codon and AA resolution and compiled human-centric substitution matrices that are fundamentally different from classic cross-species matrices (e.g. BLOSUM, PAM). Our matrices are asymmetric, with some AA replacements showing significant directional preference. Moreover, these AA matrices are only partly predicted by nucleotide substitution rates. We further test the utility of our matrices in exposing functional signals of experimentally-validated protein annotations. A significant reduction in AA transition frequencies was observed across nine post-translational modification (PTM) types and four ion-binding sites. Our results propose a purifying selection signal in the human proteome across a diverse set of functional protein annotations and provide an empirical baseline for interpreting human genetic variation in coding regions.
Collapse
Affiliation(s)
- Tair Shauli
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Nadav Brandes
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| |
Collapse
|
41
|
Liu X, Ogilvie HA, Nakhleh L. Variational inference using approximate likelihood under the coalescent with recombination. Genome Res 2021; 31:2107-2119. [PMID: 34426513 PMCID: PMC8559707 DOI: 10.1101/gr.273631.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 08/17/2021] [Indexed: 11/30/2022]
Abstract
Coalescent methods are proven and powerful tools for population genetics, phylogenetics, epidemiology, and other fields. A promising avenue for the analysis of large genomic alignments, which are increasingly common, is coalescent hidden Markov model (coalHMM) methods, but these methods have lacked general usability and flexibility. We introduce a novel method for automatically learning a coalHMM and inferring the posterior distributions of evolutionary parameters using black-box variational inference, with the transition rates between local genealogies derived empirically by simulation. This derivation enables our method to work directly with three or four taxa and through a divide-and-conquer approach with more taxa. Using a simulated data set resembling a human–chimp–gorilla scenario, we show that our method has comparable or better accuracy to previous coalHMM methods. Both species divergence times and population sizes were accurately inferred. The method also infers local genealogies, and we report on their accuracy. Furthermore, we discuss a potential direction for scaling the method to larger data sets through a divide-and-conquer approach. This accuracy means our method is useful now, and by deriving transition rates by simulation, it is flexible enough to enable future implementations of various population models.
Collapse
Affiliation(s)
- Xinhao Liu
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Huw A Ogilvie
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Luay Nakhleh
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| |
Collapse
|
42
|
Jeon S, Kim S, Oh MH, Liang P, Tang W, Han K. A comprehensive analysis of gorilla-specific LINE-1 retrotransposons. Genes Genomics 2021; 43:1133-1141. [PMID: 34406591 DOI: 10.1007/s13258-021-01146-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/29/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Long interspersed element-1 (LINE-1 or L1) is the most abundant retrotransposons in the primate genome. They have approximately 520,000 copies and make up ~ 17% of the primate genome. Full-length L1s can mobilize to a new genomic location using their enzymatic machinery. Gorilla is the second closest species to humans after the chimpanzee, and human-gorilla split 7-12 million years ago. The gorilla genome provides an opportunity to explore primate origins and evolution. OBJECTIVE L1s have contributed to genome diversity and variations during primate evolution. This study aimed to identify gorilla-specific L1s using a more recent version of the gorilla reference genome (Mar. 2016 GSMRT3/gorGor5). METHODS We collected gorilla-specific L1 candidates through computational analysis and manual inspection. L1Xplorer was used to identify whether full-length gorilla-specific L1s were intact. In addition, to determine the level of sequence conservation between intact fulllength gorilla-specific L1s, two ORFs of intact L1s were aligned with the L1PA2 consensus sequence. RESULTS 2002 gorilla-specific L1 candidates were identified through computational analysis. Among them, we manually inspected 1,883 gorilla-specific L1s, among which most of them belong to the L1PA2 subfamily and 12 were intact L1s that could influence genomic variations in the gorilla genome. Interestingly, the 12 intact full-length gorilla-specific L1s have 14 highly conserved nonsynonymous mutations, including 6 mutations and 8 mutations in ORF1 and ORF2, respectively. In comparison to the intact full-length chimpanzee-specific L1s and human-specific hot-L1s, two of these in ORF1 (L256F and E293G) were shown as gorilla-specific nonsynonymous mutations. CONCLUSION The gorilla-specific L1s may have had significantly affected the gorilla genome to compose a genome different form that of other primates during primate evolution.
Collapse
Affiliation(s)
- Soyeon Jeon
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Songmi Kim
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Man Hwan Oh
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Ping Liang
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada.,Centre of Biotechnologies, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Wanxiangfu Tang
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Kyudong Han
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea. .,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.
| |
Collapse
|
43
|
Marceca GP, Distefano R, Tomasello L, Lagana A, Russo F, Calore F, Romano G, Bagnoli M, Gasparini P, Ferro A, Acunzo M, Ma Q, Croce CM, Nigita G. MiREDiBase, a manually curated database of validated and putative editing events in microRNAs. Sci Data 2021; 8:199. [PMID: 34349127 PMCID: PMC8338996 DOI: 10.1038/s41597-021-00979-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/10/2021] [Indexed: 11/08/2022] Open
Abstract
MicroRNAs (miRNAs) are regulatory small non-coding RNAs that function as translational repressors. MiRNAs are involved in most cellular processes, and their expression and function are presided by several factors. Amongst, miRNA editing is an epitranscriptional modification that alters the original nucleotide sequence of selected miRNAs, possibly influencing their biogenesis and target-binding ability. A-to-I and C-to-U RNA editing are recognized as the canonical types, with the A-to-I type being the predominant one. Albeit some bioinformatics resources have been implemented to collect RNA editing data, it still lacks a comprehensive resource explicitly dedicated to miRNA editing. Here, we present MiREDiBase, a manually curated catalog of editing events in miRNAs. The current version includes 3,059 unique validated and putative editing sites from 626 pre-miRNAs in humans and three primates. Editing events in mature human miRNAs are supplied with miRNA-target predictions and enrichment analysis, while minimum free energy structures are inferred for edited pre-miRNAs. MiREDiBase represents a valuable tool for cell biology and biomedical research and will be continuously updated and expanded at https://ncrnaome.osumc.edu/miredibase .
Collapse
Affiliation(s)
- Gioacchino P Marceca
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Rosario Distefano
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Luisa Tomasello
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alessandro Lagana
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesco Russo
- Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Federica Calore
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Giulia Romano
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Marina Bagnoli
- Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Pierluigi Gasparini
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Carlo M Croce
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
44
|
Yang H, Shao N, Holmström A, Zhao X, Chour T, Chen H, Itzhaki I, Wu H, Ameen M, Cunningham NJ, Tu C, Zhao MT, Tarantal AF, Abilez OJ, Wu JC. Transcriptome analysis of non human primate-induced pluripotent stem cell-derived cardiomyocytes in 2D monolayer culture vs. 3D engineered heart tissue. Cardiovasc Res 2021; 117:2125-2136. [PMID: 33002105 PMCID: PMC8318103 DOI: 10.1093/cvr/cvaa281] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/27/2020] [Accepted: 09/17/2020] [Indexed: 12/22/2022] Open
Abstract
AIMS Stem cell therapy has shown promise for treating myocardial infarction via re-muscularization and paracrine signalling in both small and large animals. Non-human primates (NHPs), such as rhesus macaques (Macaca mulatta), are primarily utilized in preclinical trials due to their similarity to humans, both genetically and physiologically. Currently, induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) are delivered into the infarcted myocardium by either direct cell injection or an engineered tissue patch. Although both approaches have advantages in terms of sample preparation, cell-host interaction, and engraftment, how the iPSC-CMs respond to ischaemic conditions in the infarcted heart under these two different delivery approaches remains unclear. Here, we aim to gain a better understanding of the effects of hypoxia on iPSC-CMs at the transcriptome level. METHODS AND RESULTS NHP iPSC-CMs in both monolayer culture (2D) and engineered heart tissue (EHT) (3D) format were exposed to hypoxic conditions to serve as surrogates of direct cell injection and tissue implantation in vivo, respectively. Outcomes were compared at the transcriptome level. We found the 3D EHT model was more sensitive to ischaemic conditions and similar to the native in vivo myocardium in terms of cell-extracellular matrix/cell-cell interactions, energy metabolism, and paracrine signalling. CONCLUSION By exposing NHP iPSC-CMs to different culture conditions, transcriptome profiling improves our understanding of the mechanism of ischaemic injury.
Collapse
Affiliation(s)
- Huaxiao Yang
- Stanford Cardiovascular Institute, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Division of Cardiology, Department of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Department of Biomedical Engineering, University of North Texas, 390 N. Elm Street K240B, Denton, TX 76207-7102, USA
| | - Ningyi Shao
- Stanford Cardiovascular Institute, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Division of Cardiology, Department of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
| | - Alexandra Holmström
- Stanford Cardiovascular Institute, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Division of Cardiology, Department of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
| | - Xin Zhao
- Stanford Cardiovascular Institute, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Division of Cardiology, Department of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
| | - Tony Chour
- Stanford Cardiovascular Institute, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Division of Cardiology, Department of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
| | - Haodong Chen
- Stanford Cardiovascular Institute, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Division of Cardiology, Department of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
| | - Ilanit Itzhaki
- Stanford Cardiovascular Institute, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Division of Cardiology, Department of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
| | - Haodi Wu
- Stanford Cardiovascular Institute, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Division of Cardiology, Department of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
| | - Mohamed Ameen
- Stanford Cardiovascular Institute, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Division of Cardiology, Department of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
| | - Nathan J Cunningham
- Stanford Cardiovascular Institute, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Division of Cardiology, Department of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
| | - Chengyi Tu
- Stanford Cardiovascular Institute, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Division of Cardiology, Department of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
| | - Ming-Tao Zhao
- Stanford Cardiovascular Institute, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Division of Cardiology, Department of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
| | - Alice F Tarantal
- Department of Pediatrics, School of Medicine, One Shields Avenue, Davis, CA 95616-8542, USA
- Department Cell Biology and Human Anatomy, School of Medicine, One Shields Avenue, Davis, CA 95616-8542, USA
- California National Primate Research Center, UC Davis, One Shields Avenue, Davis, CA 95616-8542, USA
| | - Oscar J Abilez
- Stanford Cardiovascular Institute, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Division of Cardiology, Department of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Division of Cardiology, Department of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive G1120B, Stanford, CA 94305-5454, USA
| |
Collapse
|
45
|
Rosenkrantz JL, Gaffney JE, Roberts VHJ, Carbone L, Chavez SL. Transcriptomic analysis of primate placentas and novel rhesus trophoblast cell lines informs investigations of human placentation. BMC Biol 2021; 19:127. [PMID: 34154587 PMCID: PMC8218487 DOI: 10.1186/s12915-021-01056-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Proper placentation, including trophoblast differentiation and function, is essential for the health and well-being of both the mother and baby throughout pregnancy. Placental abnormalities that occur during the early stages of development are thought to contribute to preeclampsia and other placenta-related pregnancy complications. However, relatively little is known about these stages in humans due to obvious ethical and technical limitations. Rhesus macaques are considered an ideal surrogate for studying human placentation, but the unclear translatability of known human placental markers and lack of accessible rhesus trophoblast cell lines can impede the use of this animal model. RESULTS Here, we performed a cross-species transcriptomic comparison of human and rhesus placenta and determined that while the majority of human placental marker genes (HPGs) were similarly expressed, 952 differentially expressed genes (DEGs) were identified between the two species. Functional enrichment analysis of the 447 human-upregulated DEGs, including ADAM12, ERVW-1, KISS1, LGALS13, PAPPA2, PGF, and SIGLEC6, revealed over-representation of genes implicated in preeclampsia and other pregnancy disorders. Additionally, to enable in vitro functional studies of early placentation, we generated and thoroughly characterized two highly pure first trimester telomerase (TERT) immortalized rhesus trophoblast cell lines (iRP-D26 and iRP-D28A) that retained crucial features of isolated primary trophoblasts. CONCLUSIONS Overall, our findings help elucidate the molecular translatability between human and rhesus placenta and reveal notable expression differences in several HPGs and genes implicated in pregnancy complications that should be considered when using the rhesus animal model to study normal and pathological human placentation.
Collapse
Affiliation(s)
- Jimi L. Rosenkrantz
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239 USA
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006 USA
| | - Jessica E. Gaffney
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006 USA
| | - Victoria H. J. Roberts
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006 USA
| | - Lucia Carbone
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239 USA
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR 97006 USA
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239 USA
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239 USA
| | - Shawn L. Chavez
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239 USA
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006 USA
- Department of Obstetrics and Gynecology, Oregon Health and Science University School of Medicine, Portland, OR 97239 USA
- Department of Biomedical Engineering, Oregon Health and Science University School of Medicine, Portland, OR 97239 USA
| |
Collapse
|
46
|
Delfi M, Sartorius R, Ashrafizadeh M, Sharifi E, Zhang Y, De Berardinis P, Zarrabi A, Varma RS, Tay FR, Smith BR, Makvandi P. Self-assembled peptide and protein nanostructures for anti-cancer therapy: Targeted delivery, stimuli-responsive devices and immunotherapy. NANO TODAY 2021; 38:101119. [PMID: 34267794 PMCID: PMC8276870 DOI: 10.1016/j.nantod.2021.101119] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Self-assembled peptides and proteins possess tremendous potential as targeted drug delivery systems and key applications of these well-defined nanostructures reside in anti-cancer therapy. Peptides and proteins can self-assemble into nanostructures of diverse sizes and shapes in response to changing environmental conditions such as pH, temperature, ionic strength, as well as host and guest molecular interactions; their countless benefits include good biocompatibility and high loading capacity for hydrophobic and hydrophilic drugs. These self-assembled nanomaterials can be adorned with functional moieties to specifically target tumor cells. Stimuli-responsive features can also be incorporated with respect to the tumor microenvironment. This review sheds light on the growing interest in self-assembled peptides and proteins and their burgeoning applications in cancer treatment and immunotherapy.
Collapse
Affiliation(s)
- Masoud Delfi
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cintia, Naples 80126, Italy
| | - Rossella Sartorius
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Naples 80131, Italy
| | - Milad Ashrafizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Orhanlı, Tuzla, 34956 Istanbul, Turkey
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956, Istanbul, Turkey
| | - Esmaeel Sharifi
- Department of Tissue Engineering and Biomaterials, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, 6517838736, Hamadan, Iran
- Institute for Polymers, Composites and Biomaterials, National Research Council, IPCB-CNR, Naples 80125, Italy
| | - Yapei Zhang
- Department of Biomedical Engineering, Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI 48824, USA
| | | | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956, Istanbul, Turkey
| | - Rajender S. Varma
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Franklin R Tay
- The Graduate School, Augusta University, Augusta, GA 30912, USA
| | - Bryan Ronain Smith
- Department of Biomedical Engineering, Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Radiology and the Molecular Imaging Program, Stanford University, Stanford, CA, 94305, USA
| | - Pooyan Makvandi
- Istituto Italiano di Tecnologia, Centre for Micro-BioRobotics, Viale Rinaldo Piaggio 34, 56025 Pontedera, Pisa, Italy
| |
Collapse
|
47
|
Brown JG. Ticks, Hair Loss, and Non-Clinging Babies: A Novel Tick-Based Hypothesis for the Evolutionary Divergence of Humans and Chimpanzees. Life (Basel) 2021; 11:435. [PMID: 34066043 PMCID: PMC8150933 DOI: 10.3390/life11050435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/12/2021] [Accepted: 04/30/2021] [Indexed: 02/06/2023] Open
Abstract
Human straight-legged bipedalism represents one of the earliest events in the evolutionary split between humans (Homo spp.) and chimpanzees (Pan spp.), although its selective basis is a mystery. A carrying-related hypothesis has recently been proposed in which hair loss within the hominin lineage resulted in the inability of babies to cling to their mothers, requiring mothers to walk upright to carry their babies. However, a question remains for this model: what drove the hair loss that resulted in upright walking? Observers since Darwin have suggested that hair loss in humans may represent an evolutionary strategy for defence against ticks. The aim of this review is to propose and evaluate a novel tick-based evolutionary hypothesis wherein forest fragmentation in hominin paleoenvironments created conditions that were favourable for tick proliferation, selecting for hair loss in hominins and grooming behaviour in chimpanzees as divergent anti-tick strategies. It is argued that these divergent anti-tick strategies resulted in different methods for carrying babies, driving the locomotor divergence of humans and chimpanzees.
Collapse
|
48
|
Mitogenomic phylogeny of Callithrix with special focus on human transferred taxa. BMC Genomics 2021; 22:239. [PMID: 33823806 PMCID: PMC8025498 DOI: 10.1186/s12864-021-07533-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/15/2021] [Indexed: 12/04/2022] Open
Abstract
Background Callithrix marmosets are a relatively young primate radiation, whose phylogeny is not yet fully resolved. These primates are naturally para- and allopatric, but three species with highly invasive potential have been introduced into the southeastern Brazilian Atlantic Forest by the pet trade. There, these species hybridize with each other and endangered, native congeners. We aimed here to reconstruct a robust Callithrix phylogeny and divergence time estimates, and identify the biogeographic origins of autochthonous and allochthonous Callithrix mitogenome lineages. We sequenced 49 mitogenomes from four species (C. aurita, C. geoffroyi, C. jacchus, C. penicillata) and anthropogenic hybrids (C. aurita x Callithrix sp., C. penicillata x C. jacchus, Callithrix sp. x Callithrix sp., C. penicillata x C. geoffroyi) via Sanger and whole genome sequencing. We combined these data with previously published Callithrix mitogenomes to analyze five Callithrix species in total. Results We report the complete sequence and organization of the C. aurita mitogenome. Phylogenetic analyses showed that C. aurita was the first to diverge within Callithrix 3.54 million years ago (Ma), while C. jacchus and C. penicillata lineages diverged most recently 0.5 Ma as sister clades. MtDNA clades of C. aurita, C. geoffroyi, and C. penicillata show intraspecific geographic structure, but C. penicillata clades appear polyphyletic. Hybrids, which were identified by phenotype, possessed mainly C. penicillata or C. jacchus mtDNA haplotypes. The biogeographic origins of mtDNA haplotypes from hybrid and allochthonous Callithrix were broadly distributed across natural Callithrix ranges. Our phylogenetic results also evidence introgression of C. jacchus mtDNA into C. aurita. Conclusion Our robust Callithrix mitogenome phylogeny shows C. aurita lineages as basal and C. jacchus lineages among the most recent within Callithrix. We provide the first evidence that parental mtDNA lineages of anthropogenic hybrid and allochthonous marmosets are broadly distributed inside and outside of the Atlantic Forest. We also show evidence of cryptic hybridization between allochthonous Callithrix and autochthonous C. aurita. Our results encouragingly show that further development of genomic resources will allow to more clearly elucidate Callithrix evolutionary relationships and understand the dynamics of Callithrix anthropogenic introductions into the Brazilian Atlantic Forest. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07533-1.
Collapse
|
49
|
Ayoola AO, Zhang BL, Meisel RP, Nneji LM, Shao Y, Morenikeji OB, Adeola AC, Ng’ang’a SI, Ogunjemite BG, Okeyoyin AO, Roos C, Wu DD. Population Genomics Reveals Incipient Speciation, Introgression, and Adaptation in the African Mona Monkey (Cercopithecus mona). Mol Biol Evol 2021; 38:876-890. [PMID: 32986826 PMCID: PMC7947840 DOI: 10.1093/molbev/msaa248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Guenons (tribe Cercopithecini) are the most widely distributed nonhuman primate in the tropical forest belt of Africa and show considerable phenotypic, taxonomic, and ecological diversity. However, genomic information for most species within this group is still lacking. Here, we present a high-quality de novo genome (total 2.90 Gb, contig N50 equal to 22.7 Mb) of the mona monkey (Cercopithecus mona), together with genome resequencing data of 13 individuals sampled across Nigeria. Our results showed differentiation between populations from East and West of the Niger River ∼84 ka and potential ancient introgression in the East population from other mona group species. The PTPRK, FRAS1, BNC2, and EDN3 genes related to pigmentation displayed signals of introgression in the East population. Genomic scans suggest that immunity genes such as AKT3 and IL13 (possibly involved in simian immunodeficiency virus defense), and G6PD, a gene involved in malaria resistance, are under positive natural selection. Our study gives insights into differentiation, natural selection, and introgression in guenons.
Collapse
Affiliation(s)
- Adeola Oluwakemi Ayoola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Olanrewaju B Morenikeji
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY
- Department of Biology, Hamilton College, Clinton, NY
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Said I Ng’ang’a
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Babafemi G Ogunjemite
- Department of Ecotourism and Wildlife Management, Federal University of Technology, Akure, Nigeria
| | - Agboola O Okeyoyin
- National Park Service Headquarters, Federal Capital Territory, Abuja, Nigeria
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| |
Collapse
|
50
|
Murphy MK, Moon JT, Skolaris AT, Mikulin JA, Wilson TJ. Evidence for the loss and recovery of SLAMF9 during human evolution: implications on Dollo's law. Immunogenetics 2021; 73:243-251. [PMID: 33616677 PMCID: PMC7898023 DOI: 10.1007/s00251-021-01208-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/05/2021] [Indexed: 11/04/2022]
Abstract
Signaling lymphocyte activation molecule family member 9 (SLAMF9) is a cell surface protein of the CD2/SLAM family of leukocyte surface receptors. It is conserved throughout mammals and has roles in the initiation of inflammatory responses and regulation of plasmacytoid dendritic cell function. Through comparison of reference sequences encoding SLAMF9 in human, mouse, and primate sequences, we have determined that the SLAMF9 gene underwent successive mutation events, resulting in the loss of the protein and subsequent recovery of a less stable version. The mutations included a single base pair deletion in the second exon and a change in the splice acceptor site of that same exon. These changes would have had the effect of creating and later repairing a frameshift in the coding sequence. These events took place since the divergence of the human lineage from the chimpanzee-human last common ancestor and represent the first known case of the functional loss and recovery of a gene within the human lineage.
Collapse
Affiliation(s)
- Maegan K Murphy
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH, 45056, USA
| | - Justin T Moon
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH, 45056, USA
| | - Alexis T Skolaris
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH, 45056, USA
| | - Joseph A Mikulin
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH, 45056, USA
| | - Timothy J Wilson
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH, 45056, USA.
| |
Collapse
|