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Toward understanding the role of genomic repeat elements in neurodegenerative diseases

Neural Regeneration Research 2025年第3期20卷 646-659页

作者： Zhengyu An Aidi Jiang Jingqi Chen Institute of Science and Technology for brain-inspired intelligence Fudan UniversityShanghaiChina MOE Frontiers Center for brain Science Fudan UniversityShanghaiChina MOE key laboratory of computational neuroscience and brain-inspired intelligence Fudan UniversityShanghaiChina Zhangjiang Fudan International Innovation Center ShanghaiChina

Neurodegenerative diseases cause great medical and economic burdens for both patients and society;however, the complex molecular mechanisms thereof are not yet well understood. With the development of high-coverage sequencing technology, researchers have started to notice that genomic repeat regions, previously neglected in search of disease culprits, are active contributors to multiple neurodegenerative diseases. In this review, we describe the association between repeat element variants and multiple degenerative diseases through genome-wide association studies and targeted sequencing. We discuss the identification of disease-relevant repeat element variants, further powered by the advancement of long-read sequencing technologies and their related tools, and summarize recent findings in the molecular mechanisms of repeat element variants in brain degeneration, such as those causing transcriptional silencing or RNA-mediated gain of toxic function. Furthermore, we describe how in silico predictions using innovative computational models, such as deep learning language models, could enhance and accelerate our understanding of the functional impact of repeat element variants. Finally, we discuss future directions to advance current findings for a better understanding of neurodegenerative diseases and the clinical applications of genomic repeat elements.

关键词： Alzheimer's disease ataxia deep learning long-read sequencing neurodegeneration neurodegenerative diseases Parkinson's disease repeat element structural variant

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Novel heterozygous USH1C mutation impacts hair cell mechanotransduction and causes progressive hearing loss

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Science Bulletin 2024年第2期69卷 167-172页

作者： Yanyan Jia Gaogan Jia Luo Guo Nan Song Yu-Meng Wang Luoying Jiang Yilai Shu Yan Chen Shujia Zhu Huawei Li Wenyan Li ENT Institute and Otorhinolaryngology Department of Eye&ENT Hospital State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceFudan UniversityShanghai 200031China Institutes of Biomedical Sciences Fudan UniversityShanghai 200032China NHC key laboratory of Hearing Medicine(Fudan University) Shanghai 200031China The Institutes of brain Science and the Collaborative Innovation Center for brain Science Fudan UniversityShanghai 200032China Shanghai Center for brain Science and brain-inspired intelligence Technology Shanghai 201210China Institute of neuroscience State Key Laboratory of NeuroscienceCAS Center for Excellence in Brain Science and Intelligence TechnologyChinese Academy of SciencesShanghai 200031China Department of Cardiology and Institute for Developmental and Regenerative Cardiovascular MedicineXinhua Hospital Affiliated to Shanghai Jiaotong University School of MedicineShanghai 200092China

Hearing loss is one of the most common sensory disorders worldwide,affecting approximately 466 million people,including 34 million children[1].Genetic mutations accounts for approximately 60%of inherited hearing loss cases[2,3].These genetic changes result in a wide variety of clinical manifestations,ranging from nonsyndromic hearing loss(NSHL)to over 400 syndromes involving hearing loss and from mild adult-onset hearing loss to profound congenital deafness,covering the entire spectrum of Mendelian inheritance.

关键词： mec hearing approximate

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Neural Stem Cell Competition

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neuroscience Bulletin 2024年第2期40卷 277-279页

作者： Yanan Li Jie He State key laboratory of neuroscience Institute of NeuroscienceCenter for Excellence in Brain Science and Intelligence TechnologyChinese Academy of SciencesShanghai 200031China University of Chinese Academy of Sciences Beijing 100049China

Cell competition is an adaptive surveillance mechanism to ensure the robustness of developmental outputs,maintain tissue integrity,and regulate tumor progression in multicellular organisms,which is highly conserved from invertebrates to vertebrates[1].At the cellular level,cell competition represents a non-cell-autonomous process in that cells can sense the fitness of their neighbors through cellular interactions,thereby eliminating low-fitness cells and expanding high-fitness counterparts,however,cells develop normally in homogenous populations.

关键词： thereby maintain eliminating

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Generation of mitochondrial replacement monkeys by female pronucleus transfer

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Zoological Research 2024年第2期45卷 292-298页

作者： Chun-Yang Li Xing-Chen Liu Yu-Zhuo Li Yan Wang Yan-Hong Nie Yu-Ting Xu Xiao-Tong Zhang Yong Lu Qiang Sun Institute of neuroscience Center for Excellence in Brain Science and Intelligence TechnologyState Key Laboratory of NeuroscienceChinese Academy of SciencesShanghai 200031China key laboratory of Genetic Evolution and Animal Models Chinese Academy of SciencesKunming 650201China University of Chinese Academy of Sciences Beijing 100049China

Mutations in mitochondrial DNA(mtDNA)are maternally inherited and have the potential to cause severe disorders.Mitochondrial replacement therapies,including spindle,polar body,and pronuclear transfers,are promising strategies for preventing the hereditary transmission of mtDNA diseases.While pronuclear transfer has been used to generate mitochondrial replacement mouse models and human embryos,its application in non-human primates has not been previously reported.In this study,we successfully generated four healthy cynomolgus monkeys(Macaca fascicularis)via female pronuclear transfer.These individuals all survived for more than two years and exhibited minimal mtDNA carryover(3.8%–6.7%),as well as relatively stable mtDNA heteroplasmy dynamics during development.The successful establishment of this nonhuman primate model highlights the considerable potential of pronuclear transfer in reducing the risk of inherited mtDNA diseases and provides a valuable preclinical research model for advancing mitochondrial replacement therapies in humans.

关键词： Non-human primates Mitochondrial replacement Female pronuclear transfer

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Distributions of Visual Receptive Fields from Retinotopic to Craniotopic Coordinates in the Lateral Intraparietal Area and Frontal Eye Fields of the Macaque

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neuroscience Bulletin 2024年第2期40卷 171-181页

作者： Lin Yang Min Jin Cong Zhang Ning Qian Mingsha Zhang key laboratory of Cognitive neuroscience and Learning Division of PsychologyBeijing Normal UniversityBeijing 100875China Institute of neuroscience Key Laboratory of Primate NeurobiologyCAS Center for Excellence in Brain Science and Intelligence TechnologyChinese Academy of SciencesShanghai 200031China Department of neuroscience and Zuckerman Institute Columbia UniversityNew York 10027USA

Even though retinal images of objects change their locations following each eye movement,we perceive a stable and continuous world.One possible mechanism by which the brain achieves such visual stability is to construct a craniotopic coordinate by integrating retinal and extraretinal information.There have been several proposals on how this may be done,including eye-position modulation(gain fields)of retinotopic receptive fields(RFs)and craniotopic RFs.In the present study,we investigated coordinate systems used by RFs in the lateral intraparietal(LIP)cortex and frontal eye fields(FEF)and compared the two areas.We mapped the two-dimensional RFs of neurons in detail under two eye fixations and analyzed how the RF of a given neuron changes with eye position to determine its coordinate representation.The same recording and analysis procedures were applied to the two brain areas.We found that,in both areas,RFs were distributed from retinotopic to craniotopic representations.There was no significant difference between the distributions in the LIP and FEF.Only a small fraction of neurons was fully craniotopic,whereas most neurons were between the retinotopic and craniotopic representations.The distributions were strongly biased toward the retinotopic side but with significant craniotopic shifts.These results suggest that there is only weak evidence for craniotopic RFs in the LIP and FEF,and that transformation from retinotopic to craniotopic coordinates in these areas must rely on other factors such as gain fields.

关键词： Reference frames Eye-centered Headcentered Visual stability

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Comparative transcriptome analysis between rhesus macaques(Macaca mulatta) and crab-eating macaques(M. fascicularis)

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Zoological Research 2024年第2期45卷 299-310页

作者： Yu-Xiang Mao Yamei Li Zikun Yang Ning Xu Shilong Zhang Xuankai Wang Xiangyu Yang Qiang Sun Yafei Mao Institute of neuroscience State Key Laboratory of NeuroscienceCenter for Excellence in Brain Science&Intelligence TechnologyChinese Academy of SciencesShanghai 200031China Shanghai Center for brain Science and brain-inspired intelligence Technology Shanghai 201210China University of Chinese Academy of Sciences Beijing 100049China key laboratory of Genetic Evolution&Animal Models Chinese Academy of SciencesKunmingYunnan 650201China Bio-X Institutes Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersMinistry of EducationShanghai Jiao Tong UniversityShanghai 200030China Zhiyuan College Shanghai Jiao Tong UniversityShanghai 200240China Center for Genomic Research International Institutes of MedicineFourth Affiliated HospitalZhejiang UniversityYiwuZhejiang 322000China

Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques(Macaca mulatta, MMU)and crab-eating macaques(M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from84 samples(41 MFA samples and 43 MMU samples)encompassing 14 common tissues. Our findings revealed a small fraction of genes(3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover,19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary,this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.

关键词： Crab-eating macaques Rhesus macaques Comparative transcriptomics Biomedical models Nonhuman primates RNA-seq Duplicated genes

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Enhanced Beta2-band Oscillations Denote Auditory Hallucination in Schizophrenia Patients and a Monkey Model of Psychosis

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neuroscience Bulletin 2024年第3期40卷 325-338页

作者： Shuo Ma Tianzhen Chen Wenjun Jia Jie Liu Shihan Ding Puzhe Li Hong Gan Dapeng Zhang Shuxin Shao Mu-Ming Poo Min Zhao Bomin Sun Jian Jiang Department of Neurosurgery Ruijin HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200020China Shanghai Mental Health Center Shanghai Jiao Tong University School of MedicineShanghai200030China Shanghai Center for brain Science and brain-inspired Technology Lingang LaboratoryShanghai201602China University of California at Berkeley BerkeleyCA94720USA School of Life Science and Technology ShanghaiTech UniversityShanghai201210China Institute of neuroscience CAS Center for Excellence in Brain Science and Intelligence TechnologyCAS Key Laboratory of Primate NeurobiologyState Key Laboratory of NeuroscienceChinese Academy of SciencesShanghai200031China Shanghai Center for brain Science and brain-inspired intelligence Technology Lingang LaboratoryShanghai201210China Fuyang Third People’s Hospital Fuyang Mental Health CenterFuyang236052China Shanghai key laboratory of Psychotic Disorders Shanghai200030China Institute of Psychological and Behavioral Science Shanghai Jiao Tong UniversityShanghai200030China Shanghai Quanlan Technology Co. LtdShanghai201602China

An electroencephalographic(EEG)signature of auditory hallucinations(AHs)is important for facilitating the diagnosis and treatment of AHs in schizophrenia.We recorded EEG from 25 schizophrenia patients with recurrent AHs.During the period of AHs,EEG recordings exhibited significantly elevated beta2-band power in the temporal region,as compared to those recorded in the absence of AHs or during stimulation with verbal sounds.We further generated methamphetamine-treated rhesus monkeys exhibiting psychosis-like behaviors,including repetitive sudden searching actions in the absence of external intrusion,suggesting the occurrence of AHs.Epidural EEG beta2-band power in the temporal region of these monkeys was enhanced immediately after methamphetamine treatment and positively correlated with the frequency of sudden searching actions.Thus,the enhancement of temporal beta2-band oscillations represents a signature for AHs in both patients and a monkey model of psychosis,and this monkey model can be used for developing closed-loop neuromodulation approaches for the treatment of refractory AHs in schizophrenia.

关键词： Schizophrenia Auditory hallucinations Non-human primate Methamphetamine Electroencephalography

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The Neural Mechanism of Knowledge Assembly in the Human brain Inspires Artificial intelligence Algorithm

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neuroscience Bulletin 2024年第2期40卷 280-282页

作者： Xiang Ji Wentao Jiang Xiaoru Zhang Ming Song Shan Yu Tianzi Jiang University of the Chinese Academy of Sciences Beijing 100049China brainnetome Center Institute of AutomationThe Chinese Academy of SciencesBeijing 100190China laboratory of brain Atlas and brain-inspired intelligence Institute of AutomationThe Chinese Academy of SciencesBeijing 100190China CAS Center for Excellence in brain Science and intelligence Technology The Chinese Academy of SciencesBeijing 100190China Research Center for Augmented intelligence Zhejiang LabHangzhou 311100China

When new information enters the brain,a human's prior knowledge of the world can change rapidly through a process referred to as"knowledge assembly".Recently,Nelli et al.investigated the neural correlates of knowledge assembly in the human brain using functional MRI.Further,inspired by the neural mechanism,the authors developed an artificial neural network algorithm to permit rapid knowledge assembly,improving the flexibility of the system[1].Once again,this research demonstrates that studying how the brain works can lead to better computational algorithms.

关键词： neural knowledge artificial

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A Comprehensive Overview of CFN From a Commonsense Perspective

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Machine intelligence Research 2024年第2期21卷 239-256页

作者： Ru Li Yunxiao Zhao Zhiqiang Wang Xuefeng Su Shaoru Guo Yong Guan Xiaoqi Han Hongyan Zhao key laboratory of computational intelligence and Chinese Information Processing of Ministry of Education School of Computer and Information TechnologyShanxi UniversityTaiyuan 030006China

Chinese FrameNet(CFN)is a scenario commonsense knowledge base(CKB)that plays an important role in research on Chinese language understanding.It is based on the theory of frame semantics and English FrameNet(FN).The CFN knowledge base contains a wealth of scenario commonsense knowledge,including frames,frame elements,and frame relations,as well as annotated instances with rich scenario-related labels on Chinese sentences and discourses.In this paper,we conduct a comprehensive overview of CFN from a commonsense perspective,covering topics such as scenario commonsense representation,CFN resources,and its applications.We also summarize recent breakthroughs and identify future research directions.First,we introduce the concept of scenario commonsense,including its definitions,examples,and representation methods,with a focus on the relationship between scenario commonsense and the frame concept in CFN.In addition,we provide a comprehensive overview of CFN resources and their applications,highlighting the newly proposed frame-based discourse representation and a human-machine collaboration framework for expanding the CFN corpus.Furthermore,we explore emerging topics such as expanding the CFN resource,improving the interpretability of machine reading comprehension,and using scenario CKBs for text generation.

关键词： Chinese FrameNet(CFN) commonsense scenario commonsense frame knowledge

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Adaptation of Ocular Opponency Neurons Mediates Attention-Induced Ocular Dominance Plasticity

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neuroscience Bulletin 2024年第3期40卷 339-349页

作者： Fangxing Song Lili Lyu Min Bao CAS key laboratory of Behavioral Science Institute of PsychologyChinese Academy of SciencesBeijing100101China Department of Psychology University of Chinese Academy of SciencesBeijing100049China Institute of neuroscience Key Laboratory of Primate NeurobiologyCAS Center for Excellence in Brain Science and Intelligence TechnologyChinese Academy of SciencesShanghai200031China

Previous research has shown that ocular dominance can be biased by prolonged attention to one eye.The ocular-opponency-neuron model of binocular rivalry has been proposed as a candidate account for this phenomenon.Yet direct neural evidence is still lacking.By manipulating the contrast of dichoptic testing gratings,here we measured the steady-state visually evoked potentials(SSVEPs)at the intermodulation frequencies to selectively track the activities of ocular-opponency-neurons before and after the“dichoptic-backward-movie”adaptation.One hour of adaptation caused a shift of perceptual and neural ocular dominance towards the unattended eye.More importantly,we found a decrease in the intermodulation SSVEP response after adaptation,which was significantly greater when high-contrast gratings were presented to the attended eye than when they were presented to the unattended eye.These results strongly support the view that the adaptation of ocular-opponency-neurons contributes to the ocular dominance plasticity induced by prolonged eye-based attention.

关键词： Attention Ocular dominance Opponency neuron Adaptation Steady-state visually evoked potential

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