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Page ML, Aguzzoli Heberle B, Brandon JA, Wadsworth ME, Gordon LA, Nations KA, Ebbert MTW. Surveying the landscape of RNA isoform diversity and expression across 9 GTEx tissues using long-read sequencing data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.579945. [PMID: 38405825 PMCID: PMC10888753 DOI: 10.1101/2024.02.13.579945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Even though alternative RNA splicing was discovered nearly 50 years ago (1977), we still understand very little about most isoforms arising from a single gene, including in which tissues they are expressed and if their functions differ. Human gene annotations suggest remarkable transcriptional complexity, with approximately 252,798 distinct RNA isoform annotations from 62,710 gene bodies (Ensembl v109; 2023), emphasizing the need to understand their biological effects. For example, 256 gene bodies have ≥50 annotated isoforms and 30 have ≥100, where one protein-coding gene (MAPK10) even has 192 distinct RNA isoform annotations. Whether such isoform diversity results from biological redundancy or spurious alternative splicing (i.e., noise), or whether individual isoforms have specialized functions (even if subtle) remains a mystery for most genes. Recent studies by Aguzzoli-Heberle et al., Leung et al., and Glinos et al. demonstrated long-read RNAseq enables improved RNA isoform quantification for essentially any tissue, cell type, or biological condition (e.g., disease, development, aging, etc.), making it possible to better assess individual isoform expression and function. While each study provided important discoveries related to RNA isoform diversity, deeper exploration is needed. We sought to quantify and characterize real isoform usage across tissues (compared to annotations). We used long-read RNAseq data from 58 GTEx samples across nine tissues (three brain, two heart, muscle, lung, liver, and cultured fibroblasts) generated by Glinos et al. and found considerable isoform diversity within and across tissues. Cerebellar hemisphere was the most transcriptionally complex tissue (22,522 distinct isoforms; 3,726 unique); liver was least diverse (12,435 distinct isoforms; 1,039 unique). We highlight gene clusters exhibiting high tissue-specific isoform diversity per tissue (e.g., TPM1 expresses 19 in heart's atrial appendage). We also validated 447 of the 700 new isoforms discovered by Aguzzoli-Heberle et al. and found that 88 were expressed in all nine tissues, while 58 were specific to a single tissue. This study represents a broad survey of the RNA isoform landscape, demonstrating isoform diversity across nine tissues and emphasizes the need to better understand how individual isoforms from a single gene body contribute to human health and disease.
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Affiliation(s)
- Madeline L. Page
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Division of Biomedical Informatics, Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
| | - Bernardo Aguzzoli Heberle
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Division of Biomedical Informatics, Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
| | - J. Anthony Brandon
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Division of Biomedical Informatics, Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
| | - Mark E. Wadsworth
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Division of Biomedical Informatics, Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
| | - Lacey A. Gordon
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Division of Biomedical Informatics, Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
| | - Kayla A. Nations
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Division of Biomedical Informatics, Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
| | - Mark T. W. Ebbert
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Division of Biomedical Informatics, Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
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2
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Chen S, Xing L, Xie Z, Zhao M, Yu H, Gan J, Zhao H, Ma Z, Li H. Single-cell transcriptomic reveals a cell atlas and diversity of chicken amygdala responded to social hierarchy. iScience 2024; 27:109880. [PMID: 38952686 PMCID: PMC11215297 DOI: 10.1016/j.isci.2024.109880] [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: 12/05/2023] [Revised: 02/29/2024] [Accepted: 04/29/2024] [Indexed: 07/03/2024] Open
Abstract
Amygdala serves as a highly cellular, heterogeneous brain region containing excitatory and inhibitory neurons and is involved in the dopamine and serotoninergic neuron systems. An increasing number of studies have revealed the underpinned mechanism mediating social hierarchy in mammal and vertebrate, however, there are rare studies conducted on how amygdala on social hierarchy in poultry. In this study, we conducted food competition tests and determined the social hierarchy of the rooster. We performed cross-species analysis with mammalian amygdala, and found that cell types of human and rhesus monkeys were more closely related and that of chickens were more distant. We identified 26 clusters and divided them into 10 main clusters, of which GABAergic and glutamatergic neurons were associated with social behaviors. In conclusion, our results provide to serve the developmental studies of the amygdala neuron system and new insights into the underpinned mechanism of social hierarchy in roosters.
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Affiliation(s)
- Siyu Chen
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Limin Xing
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Zhijiang Xie
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Mengqiao Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Hui Yu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Jiankang Gan
- Guangdong Tinoo’s FOODS Group Co., Ltd, Qingyuan 511500, China
| | - Haiquan Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Zheng Ma
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
- Guangdong Tinoo’s FOODS Group Co., Ltd, Qingyuan 511500, China
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3
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Leitch B. Parvalbumin Interneuron Dysfunction in Neurological Disorders: Focus on Epilepsy and Alzheimer's Disease. Int J Mol Sci 2024; 25:5549. [PMID: 38791587 PMCID: PMC11122153 DOI: 10.3390/ijms25105549] [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: 04/29/2024] [Revised: 05/11/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Parvalbumin expressing (PV+) GABAergic interneurons are fast spiking neurons that provide powerful but relatively short-lived inhibition to principal excitatory cells in the brain. They play a vital role in feedforward and feedback synaptic inhibition, preventing run away excitation in neural networks. Hence, their dysfunction can lead to hyperexcitability and increased susceptibility to seizures. PV+ interneurons are also key players in generating gamma oscillations, which are synchronized neural oscillations associated with various cognitive functions. PV+ interneuron are particularly vulnerable to aging and their degeneration has been associated with cognitive decline and memory impairment in dementia and Alzheimer's disease (AD). Overall, dysfunction of PV+ interneurons disrupts the normal excitatory/inhibitory balance within specific neurocircuits in the brain and thus has been linked to a wide range of neurodevelopmental and neuropsychiatric disorders. This review focuses on the role of dysfunctional PV+ inhibitory interneurons in the generation of epileptic seizures and cognitive impairment and their potential as targets in the design of future therapeutic strategies to treat these disorders. Recent research using cutting-edge optogenetic and chemogenetic technologies has demonstrated that they can be selectively manipulated to control seizures and restore the balance of neural activity in the brains of animal models. This suggests that PV+ interneurons could be important targets in developing future treatments for patients with epilepsy and comorbid disorders, such as AD, where seizures and cognitive decline are directly linked to specific PV+ interneuron deficits.
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Affiliation(s)
- Beulah Leitch
- Department of Anatomy, School of Biomedical Sciences, Brain Health Research Centre, University of Otago, Dunedin 9016, New Zealand
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4
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Zhong J, Wang C, Zhang D, Yao X, Zhao Q, Huang X, Lin F, Xue C, Wang Y, He R, Li XY, Li Q, Wang M, Zhao S, Afridi SK, Zhou W, Wang Z, Xu Y, Xu Z. PCDHA9 as a candidate gene for amyotrophic lateral sclerosis. Nat Commun 2024; 15:2189. [PMID: 38467605 PMCID: PMC10928119 DOI: 10.1038/s41467-024-46333-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 02/23/2024] [Indexed: 03/13/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease. To identify additional genetic factors, we analyzed exome sequences in a large cohort of Chinese ALS patients and found a homozygous variant (p.L700P) in PCDHA9 in three unrelated patients. We generated Pcdhα9 mutant mice harboring either orthologous point mutation or deletion mutation. These mice develop progressive spinal motor loss, muscle atrophy, and structural/functional abnormalities of the neuromuscular junction, leading to paralysis and early lethality. TDP-43 pathology is detected in the spinal motor neurons of aged mutant mice. Mechanistically, we demonstrate that Pcdha9 mutation causes aberrant activation of FAK and PYK2 in aging spinal cord, and dramatically reduced NKA-α1 expression in motor neurons. Our single nucleus multi-omics analysis reveals disturbed signaling involved in cell adhesion, ion transport, synapse organization, and neuronal survival in aged mutant mice. Together, our results present PCDHA9 as a potential ALS gene and provide insights into its pathogenesis.
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Affiliation(s)
- Jie Zhong
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Chaodong Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Disease, Beijing, 100053, China.
| | - Dan Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoli Yao
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Quanzhen Zhao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xusheng Huang
- Department of Neurology, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Feng Lin
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Chun Xue
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yaqing Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruojie He
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xu-Ying Li
- Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Disease, Beijing, 100053, China
| | - Qibin Li
- Shenzhen Clabee Biotechnology Incorporation, Shenzhen, 518057, China
| | - Mingbang Wang
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, 201102, China
| | - Shaoli Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Shabbir Khan Afridi
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenhao Zhou
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, 201102, China
| | - Zhanjun Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Disease, Beijing, 100053, China
| | - Yanming Xu
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
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5
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Yuan Z, Yang X, Hu Z, Gao Y, Yan P, Zheng F, Hong K, Cen K, Mai Y, Bai Y, Guo Y, Zhou J. Investigating the impact of inflammatory response-related genes on renal fibrosis diagnosis: a machine learning-based study with experimental validation. J Biomol Struct Dyn 2024:1-13. [PMID: 38381715 DOI: 10.1080/07391102.2024.2317992] [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: 08/16/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
Renal fibrosis plays a crucial role in the progression of renal diseases, yet the lack of effective diagnostic markers poses challenges in scientific and clinical practices. In this study, we employed machine learning techniques to identify potential biomarkers for renal fibrosis. Utilizing two datasets from the GEO database, we applied LASSO, SVM-RFE and RF algorithms to screen for differentially expressed genes related to inflammatory responses between the renal fibrosis group and the control group. As a result, we identified four genes (CCL5, IFITM1, RIPK2, and TNFAIP6) as promising diagnostic indicators for renal fibrosis. These genes were further validated through in vivo experiments and immunohistochemistry, demonstrating their utility as reliable markers for assessing renal fibrosis. Additionally, we conducted a comprehensive analysis to explore the relationship between these candidate biomarkers, immunity, and drug sensitivity. Integrating these findings, we developed a nomogram with a high discriminative ability, achieving a concordance index of 0.933, enabling the prediction of disease risk in patients with renal fibrosis. Overall, our study presents a predictive model for renal fibrosis and highlights the significance of four potential biomarkers, facilitating clinical diagnosis and personalized treatment. This finding presents valuable insights for advancing precision medicine approaches in the management of renal fibrosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ziwei Yuan
- Department of Endocrinology, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Xuejia Yang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zujian Hu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuanyuan Gao
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Penghua Yan
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fan Zheng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kai Hong
- Department of General Surgery, Ningbo First Hospital, Ningbo, China
| | - Kenan Cen
- Department of General Surgery, Ningbo First Hospital, Ningbo, China
| | - Yifeng Mai
- Department of General Surgery, Ningbo First Hospital, Ningbo, China
| | - Yongheng Bai
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yangyang Guo
- Department of General Surgery, Ningbo First Hospital, Ningbo, China
| | - Jingzong Zhou
- Department of Endocrinology, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou, Zhejiang, China
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6
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Fisher J, Verhagen M, Long Z, Moissidis M, Yan Y, He C, Wang J, Micoli E, Alastruey CM, Moors R, Marín O, Mi D, Lim L. Cortical somatostatin long-range projection neurons and interneurons exhibit divergent developmental trajectories. Neuron 2024; 112:558-573.e8. [PMID: 38086373 DOI: 10.1016/j.neuron.2023.11.013] [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: 11/07/2022] [Revised: 08/22/2023] [Accepted: 11/10/2023] [Indexed: 02/24/2024]
Abstract
The mammalian cerebral cortex contains an extraordinary diversity of cell types that emerge by implementing different developmental programs. Delineating when and how cellular diversification occurs is particularly challenging for cortical inhibitory neurons because they represent a small proportion of all cortical cells and have a protracted development. Here, we combine single-cell RNA sequencing and spatial transcriptomics to characterize the emergence of neuronal diversity among somatostatin-expressing (SST+) cells in mice. We found that SST+ inhibitory neurons segregate during embryonic stages into long-range projection (LRP) neurons and two types of interneurons, Martinotti cells and non-Martinotti cells, following distinct developmental trajectories. Two main subtypes of LRP neurons and several subtypes of interneurons are readily distinguishable in the embryo, although interneuron diversity is likely refined during early postnatal life. Our results suggest that the timing for cellular diversification is unique for different subtypes of SST+ neurons and particularly divergent for LRP neurons and interneurons.
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Affiliation(s)
- Josephine Fisher
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE1 1UL London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL, London, UK
| | - Marieke Verhagen
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Zhen Long
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Monika Moissidis
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE1 1UL London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL, London, UK
| | - Yiming Yan
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chenyi He
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingyu Wang
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Elia Micoli
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Clara Milían Alastruey
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Rani Moors
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE1 1UL London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL, London, UK.
| | - Da Mi
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Lynette Lim
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium.
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7
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Liao K, Xiang Y, Huang F, Huang M, Xu W, Lin Y, Liao P, Wang Z, Yang L, Tian X, Chen D, Wang Z, Liu S, Zhuang Z. Spatial and single-nucleus transcriptomics decoding the molecular landscape and cellular organization of avian optic tectum. iScience 2024; 27:109009. [PMID: 38333704 PMCID: PMC10850779 DOI: 10.1016/j.isci.2024.109009] [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: 09/30/2023] [Revised: 12/19/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
The avian optic tectum (OT) has been studied for its diverse functions, yet a comprehensive molecular landscape at the cellular level has been lacking. In this study, we applied spatial transcriptome sequencing and single-nucleus RNA sequencing (snRNA-seq) to explore the cellular organization and molecular characteristics of the avian OT from two species: Columba livia and Taeniopygia guttata. We identified precise layer structures and provided comprehensive layer-specific signatures of avian OT. Furthermore, we elucidated diverse functions in different layers, with the stratum griseum periventriculare (SGP) potentially playing a key role in advanced functions of OT, like fear response and associative learning. We characterized detailed neuronal subtypes and identified a population of FOXG1+ excitatory neurons, resembling those found in the mouse neocortex, potentially involved in neocortex-related functions and expansion of avian OT. These findings could contribute to our understanding of the architecture of OT, shedding light on visual perception and multifunctional association.
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Affiliation(s)
- Kuo Liao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- BGI Research, Hangzhou 310030, China
| | - Ya Xiang
- BGI Research, Hangzhou 310030, China
- College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Fubaoqian Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- BGI Research, Hangzhou 310030, China
| | - Maolin Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Wenbo Xu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Youning Lin
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Pingfang Liao
- BGI Research, Hangzhou 310030, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zishi Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Lin Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xinmao Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Duoyuan Chen
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shiping Liu
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Zhenkun Zhuang
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
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8
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Rhodes CT, Asokumar D, Sohn M, Naskar S, Elisha L, Stevenson P, Lee DR, Zhang Y, Rocha PP, Dale RK, Lee S, Petros TJ. Loss of Ezh2 in the medial ganglionic eminence alters interneuron fate, cell morphology and gene expression profiles. Front Cell Neurosci 2024; 18:1334244. [PMID: 38419656 PMCID: PMC10899338 DOI: 10.3389/fncel.2024.1334244] [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: 11/06/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Introduction Enhancer of zeste homolog 2 (Ezh2) is responsible for trimethylation of histone 3 at lysine 27 (H3K27me3), resulting in repression of gene expression. Here, we explore the role of Ezh2 in forebrain GABAergic interneuron development. Methods We removed Ezh2 in the MGE by generating Nkx2-1Cre;Ezh2 conditional knockout mice. We then characterized changes in MGE-derived interneuron fate and electrophysiological properties in juvenile mice, as well as alterations in gene expression, chromatin accessibility and histone modifications in the MGE. Results Loss of Ezh2 increases somatostatin-expressing (SST+) and decreases parvalbumin-expressing (PV+) interneurons in the forebrain. We observe fewer MGE-derived interneurons in the first postnatal week, indicating reduced interneuron production. Intrinsic electrophysiological properties in SST+ and PV+ interneurons are normal, but PV+ interneurons display increased axonal complexity in Ezh2 mutant mice. Single nuclei multiome analysis revealed differential gene expression patterns in the embryonic MGE that are predictive of these cell fate changes. Lastly, CUT&Tag analysis revealed that some genomic loci are particularly resistant or susceptible to shifts in H3K27me3 levels in the absence of Ezh2, indicating differential selectivity to epigenetic perturbation. Discussion Thus, loss of Ezh2 in the MGE alters interneuron fate, morphology, and gene expression and regulation. These findings have important implications for both normal development and potentially in disease etiologies.
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Affiliation(s)
- Christopher T Rhodes
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
| | - Dhanya Asokumar
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
- Unit on Genome Structure and Regulation, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
| | - Mira Sohn
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
| | - Shovan Naskar
- Unit on Functional Neural Circuits, National Institute of Mental Health (NIMH), NIH, Bethesda, MD, United States
| | - Lielle Elisha
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
| | - Parker Stevenson
- Unit on Functional Neural Circuits, National Institute of Mental Health (NIMH), NIH, Bethesda, MD, United States
| | - Dongjin R Lee
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
| | - Yajun Zhang
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
| | - Pedro P Rocha
- Unit on Genome Structure and Regulation, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
- National Cancer Institute (NCI), NIH, Bethesda, MD, United States
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
| | - Soohyun Lee
- Unit on Functional Neural Circuits, National Institute of Mental Health (NIMH), NIH, Bethesda, MD, United States
| | - Timothy J Petros
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
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Pavon N, Diep K, Yang F, Sebastian R, Martinez-Martin B, Ranjan R, Sun Y, Pak C. Patterning ganglionic eminences in developing human brain organoids using a morphogen-gradient-inducing device. CELL REPORTS METHODS 2024; 4:100689. [PMID: 38228151 PMCID: PMC10831957 DOI: 10.1016/j.crmeth.2023.100689] [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: 06/19/2023] [Revised: 10/21/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024]
Abstract
In early neurodevelopment, the central nervous system is established through the coordination of various neural organizers directing tissue patterning and cell differentiation. Better recapitulation of morphogen gradient production and signaling will be crucial for establishing improved developmental models of the brain in vitro. Here, we developed a method by assembling polydimethylsiloxane devices capable of generating a sustained chemical gradient to produce patterned brain organoids, which we termed morphogen-gradient-induced brain organoids (MIBOs). At 3.5 weeks, MIBOs replicated dorsal-ventral patterning observed in the ganglionic eminences (GE). Analysis of mature MIBOs through single-cell RNA sequencing revealed distinct dorsal GE-derived CALB2+ interneurons, medium spiny neurons, and medial GE-derived cell types. Finally, we demonstrate long-term culturing capabilities with MIBOs maintaining stable neural activity in cultures grown up to 5.5 months. MIBOs demonstrate a versatile approach for generating spatially patterned brain organoids for embryonic development and disease modeling.
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Affiliation(s)
- Narciso Pavon
- Graduate Program in Neuroscience and Behavior, UMass Amherst, Amherst, MA 01003, USA; Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Karmen Diep
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Feiyu Yang
- Department of Mechanical and Industrial Engineering, UMass Amherst, Amherst, MA 01003, USA
| | - Rebecca Sebastian
- Graduate Program in Neuroscience and Behavior, UMass Amherst, Amherst, MA 01003, USA; Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Beatriz Martinez-Martin
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA; Graduate Program in Molecular and Cellular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Ravi Ranjan
- Genomics Core, Institute of Applied Life Sciences, UMass Amherst, Amherst, MA 01003, USA
| | - Yubing Sun
- Department of Mechanical and Industrial Engineering, UMass Amherst, Amherst, MA 01003, USA.
| | - ChangHui Pak
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA.
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10
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Noort RJ, Zhu H, Flemmer RT, Moore CS, Belbin TJ, Esseltine JL. Apically localized PANX1 impacts neuroepithelial expansion in human cerebral organoids. Cell Death Discov 2024; 10:22. [PMID: 38212304 PMCID: PMC10784521 DOI: 10.1038/s41420-023-01774-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 01/13/2024] Open
Abstract
Dysfunctional paracrine signaling through Pannexin 1 (PANX1) channels is linked to several adult neurological pathologies and emerging evidence suggests that PANX1 plays an important role in human brain development. It remains unclear how early PANX1 influences brain development, or how loss of PANX1 alters the developing human brain. Using a cerebral organoid model of early human brain development, we find that PANX1 is expressed at all stages of organoid development from neural induction through to neuroepithelial expansion and maturation. Interestingly, PANX1 cellular distribution and subcellular localization changes dramatically throughout cerebral organoid development. During neural induction, PANX1 becomes concentrated at the apical membrane domain of neural rosettes where it co-localizes with several apical membrane adhesion molecules. During neuroepithelial expansion, PANX1-/- organoids are significantly smaller than control and exhibit significant gene expression changes related to cell adhesion, WNT signaling and non-coding RNAs. As cerebral organoids mature, PANX1 expression is significantly upregulated and is primarily localized to neuronal populations outside of the ventricular-like zones. Ultimately, PANX1 protein can be detected in all layers of a 21-22 post conception week human fetal cerebral cortex. Together, these results show that PANX1 is dynamically expressed by numerous cell types throughout embryonic and early fetal stages of human corticogenesis and loss of PANX1 compromises neuroepithelial expansion due to dysregulation of cell-cell and cell-matrix adhesion, perturbed intracellular signaling, and changes to gene regulation.
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Affiliation(s)
- Rebecca J Noort
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, A1B 3V6, NL, Canada
| | - Hanrui Zhu
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, A1B 3V6, NL, Canada
| | - Robert T Flemmer
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, A1B 3V6, NL, Canada
| | - Craig S Moore
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, A1B 3V6, NL, Canada
| | - Thomas J Belbin
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, A1B 3V6, NL, Canada
- Discipline of Oncology, Faculty of sp. Medicine, Memorial University of Newfoundland, St. John's, A1B 3V6, NL, Canada
| | - Jessica L Esseltine
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, A1B 3V6, NL, Canada.
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11
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Spildrejorde M, Samara A, Sharma A, Leithaug M, Falck M, Modafferi S, Sundaram AY, Acharya G, Nordeng H, Eskeland R, Gervin K, Lyle R. Multi-omics approach reveals dysregulated genes during hESCs neuronal differentiation exposure to paracetamol. iScience 2023; 26:107755. [PMID: 37731623 PMCID: PMC10507163 DOI: 10.1016/j.isci.2023.107755] [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: 03/27/2023] [Revised: 06/30/2023] [Accepted: 08/24/2023] [Indexed: 09/22/2023] Open
Abstract
Prenatal paracetamol exposure has been associated with neurodevelopmental outcomes in childhood. Pharmacoepigenetic studies show differences in cord blood DNA methylation between unexposed and paracetamol-exposed neonates, however, causality and impact of long-term prenatal paracetamol exposure on brain development remain unclear. Using a multi-omics approach, we investigated the effects of paracetamol on an in vitro model of early human neurodevelopment. We exposed human embryonic stem cells undergoing neuronal differentiation with paracetamol concentrations corresponding to maternal therapeutic doses. Single-cell RNA-seq and ATAC-seq integration identified paracetamol-induced chromatin opening changes linked to gene expression. Differentially methylated and/or expressed genes were involved in neurotransmission and cell fate determination trajectories. Some genes involved in neuronal injury and development-specific pathways, such as KCNE3, overlapped with differentially methylated genes previously identified in cord blood associated with prenatal paracetamol exposure. Our data suggest that paracetamol may play a causal role in impaired neurodevelopment.
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Affiliation(s)
- Mari Spildrejorde
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Athina Samara
- Division of Clinical Paediatrics, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
- Astrid Lindgren Children′s Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Ankush Sharma
- Department of Informatics, University of Oslo, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Magnus Leithaug
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Martin Falck
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Stefania Modafferi
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Arvind Y.M. Sundaram
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ganesh Acharya
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Alfred Nobels Allé 8, SE-14152 Stockholm, Sweden
- Center for Fetal Medicine, Karolinska University Hospital, SE-14186 Stockholm, Sweden
| | - Hedvig Nordeng
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Ragnhild Eskeland
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kristina Gervin
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, University of Oslo, Oslo, Norway
- Division of Clinical Neuroscience, Department of Research and Innovation, Oslo University Hospital, Oslo, Norway
| | - Robert Lyle
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
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12
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Zhao Z, Ding Y, Tran LJ, Chai G, Lin L. Innovative breakthroughs facilitated by single-cell multi-omics: manipulating natural killer cell functionality correlates with a novel subcategory of melanoma cells. Front Immunol 2023; 14:1196892. [PMID: 37435067 PMCID: PMC10332463 DOI: 10.3389/fimmu.2023.1196892] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/12/2023] [Indexed: 07/13/2023] Open
Abstract
Background Melanoma is typically regarded as the most dangerous form of skin cancer. Although surgical removal of in situ lesions can be used to effectively treat metastatic disease, this condition is still difficult to cure. Melanoma cells are removed in great part due to the action of natural killer (NK) and T cells on the immune system. Still, not much is known about how the activity of NK cell-related pathways changes in melanoma tissue. Thus, we performed a single-cell multi-omics analysis on human melanoma cells in this study to explore the modulation of NK cell activity. Materials and methods Cells in which mitochondrial genes comprised > 20% of the total number of expressed genes were removed. Gene ontology (GO), gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), and AUCcell analysis of differentially expressed genes (DEGs) in melanoma subtypes were performed. The CellChat package was used to predict cell-cell contact between NK cell and melanoma cell subtypes. Monocle program analyzed the pseudotime trajectories of melanoma cells. In addition, CytoTRACE was used to determine the recommended time order of melanoma cells. InferCNV was utilized to calculate the CNV level of melanoma cell subtypes. Python package pySCENIC was used to assess the enrichment of transcription factors and the activity of regulons in melanoma cell subtypes. Furthermore, the cell function experiment was used to confirm the function of TBX21 in both A375 and WM-115 melanoma cell lines. Results Following batch effect correction, 26,161 cells were separated into 28 clusters and designated as melanoma cells, neural cells, fibroblasts, endothelial cells, NK cells, CD4+ T cells, CD8+ T cells, B cells, plasma cells, monocytes and macrophages, and dendritic cells. A total of 10137 melanoma cells were further grouped into seven subtypes, i.e., C0 Melanoma BIRC7, C1 Melanoma CDH19, C2 Melanoma EDNRB, C3 Melanoma BIRC5, C4 Melanoma CORO1A, C5 Melanoma MAGEA4, and C6 Melanoma GJB2. The results of AUCell, GSEA, and GSVA suggested that C4 Melanoma CORO1A may be more sensitive to NK and T cells through positive regulation of NK and T cell-mediated immunity, while other subtypes of melanoma may be more resistant to NK cells. This suggests that the intratumor heterogeneity (ITH) of melanoma-induced activity and the difference in NK cell-mediated cytotoxicity may have caused NK cell defects. Transcription factor enrichment analysis indicated that TBX21 was the most important TF in C4 Melanoma CORO1A and was also associated with M1 modules. In vitro experiments further showed that TBX21 knockdown dramatically decreases melanoma cells' proliferation, invasion, and migration. Conclusion The differences in NK and T cell-mediated immunity and cytotoxicity between C4 Melanoma CORO1A and other melanoma cell subtypes may offer a new perspective on the ITH of melanoma-induced metastatic activity. In addition, the protective factors of skin melanoma, STAT1, IRF1, and FLI1, may modulate melanoma cell responses to NK or T cells.
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Affiliation(s)
- Zhijie Zhao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yantao Ding
- Department of Dermatology, The First Affiliated Hospital, Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- China Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Lisa Jia Tran
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gang Chai
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Lin
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
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13
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Xie Q, Liu T, Zhang X, Ding Y, Fan X. Construction of a telomere-related gene signature to predict prognosis and immune landscape for glioma. Front Endocrinol (Lausanne) 2023; 14:1145722. [PMID: 37351101 PMCID: PMC10284135 DOI: 10.3389/fendo.2023.1145722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023] Open
Abstract
Background Glioma is one of the commonest malignant tumors of the brain. However, glioma present with a poor clinical prognosis. Therefore, specific detection markers and therapeutic targets need to be explored as a way to promote the survival rate of BC patients. Therefore, we need to search for quality immune checkpoints to support the efficacy of immunotherapy for glioma. Methods We first recognized differentially expressed telomere-related genes (TRGs) and accordingly developed a risk model by univariate and multivariate Cox analysis. The accuracy of the model is then verified. We evaluated the variations in immune function and looked at the expression levels of immune checkpoint genes. Finally, to assess the anti-tumor medications often used in the clinical treatment of glioma, we computed the half inhibitory concentration of pharmaceuticals. Results We finally identified nine TRGs and built a risk model. Through the validation of the model, we found good agreement between the predicted and observed values. Then, we found 633 differentially expressed genes between various risk groups to identify the various molecular pathways between different groups. The enrichment of CD4+ T cells, CD8+ T cells, fibroblasts, endothelial cells, macrophages M0, M1, and M2, mast cells, myeloid dendritic cells, and neutrophils was favorably correlated with the risk score, but the enrichment of B cells and NK cells was negatively correlated with the risk score. The expression of several immune checkpoint-related genes differed significantly across the risk groups. Finally, in order to create individualized treatment plans for diverse individuals, we searched for numerous chemotherapeutic medications for patients in various groups. Conclusion The findings of this research provide evidence that TRGs may predict a patient's prognosis for glioma, assist in identifying efficient targets for glioma immunotherapy, and provide a foundation for an efficient, customized approach to treating glioma patients.
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Affiliation(s)
- Qin Xie
- Department of Neurosurgery, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang, China
| | - Tingting Liu
- Department of Endocrinology, Affiliated Haikou Hospital of Xiangya School of Central South University, Haikou, Hainan, China
| | - Xiaole Zhang
- Department of Neurosurgery, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang, China
| | - Yanli Ding
- Department of Neurosurgery, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang, China
| | - Xiaoyan Fan
- Intensive Care Unit, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang, China
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14
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Ren Q, Zhang P, Lin H, Feng Y, Chi H, Zhang X, Xia Z, Cai H, Yu Y. A novel signature predicts prognosis and immunotherapy in lung adenocarcinoma based on cancer-associated fibroblasts. Front Immunol 2023; 14:1201573. [PMID: 37325647 PMCID: PMC10264584 DOI: 10.3389/fimmu.2023.1201573] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
Background Extensive research has established the significant correlations between cancer-associated fibroblasts (CAFs) and various stages of cancer development, including initiation, angiogenesis, progression, and resistance to therapy. In this study, we aimed to investigate the characteristics of CAFs in lung adenocarcinoma (LUAD) and develop a risk signature to predict the prognosis of patients with LUAD. Methods We obtained single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data from the public database. The Seurat R package was used to process the scRNA-seq data and identify CAF clusters based on several biomarkers. CAF-related prognostic genes were further identified using univariate Cox regression analysis. To reduce the number of genes, Lasso regression was performed, and a risk signature was established. A novel nomogram that incorporated the risk signature and clinicopathological features was developed to predict the clinical applicability of the model. Additionally, we conducted immune landscape and immunotherapy responsiveness analyses. Finally, we performed in vitro experiments to verify the functions of EXO1 in LUAD. Results We identified 5 CAF clusters in LUAD using scRNA-seq data, of which 3 clusters were significantly associated with prognosis in LUAD. A total of 492 genes were found to be significantly linked to CAF clusters from 1731 DEGs and were used to construct a risk signature. Moreover, our immune landscape exploration revealed that the risk signature was significantly related to immune scores, and its ability to predict responsiveness to immunotherapy was confirmed. Furthermore, a novel nomogram incorporating the risk signature and clinicopathological features showed excellent clinical applicability. Finally, we verified the functions of EXP1 in LUAD through in vitro experiments. Conclusions The risk signature has proven to be an excellent predictor of LUAD prognosis, stratifying patients more appropriately and precisely predicting immunotherapy responsiveness. The comprehensive characterization of LUAD based on the CAF signature can predict the response of LUAD to immunotherapy, thus offering fresh perspectives into the management of LUAD patients. Our study ultimately confirms the role of EXP1 in facilitating the invasion and growth of tumor cells in LUAD. Nevertheless, further validation can be achieved by conducting in vivo experiments.
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Affiliation(s)
- Qianhe Ren
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pengpeng Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haoran Lin
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yanlong Feng
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Xiao Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhijia Xia
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University, Munich, Germany
| | - Huabao Cai
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yue Yu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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15
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Keefe F, Monzón-Sandoval J, Rosser AE, Webber C, Li M. Single-Cell Transcriptomics Reveals Conserved Regulatory Networks in Human and Mouse Interneuron Development. Int J Mol Sci 2023; 24:8122. [PMID: 37175835 PMCID: PMC10179417 DOI: 10.3390/ijms24098122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Inhibitory GABAergic interneurons originate in the embryonic medial ganglionic eminence (MGE) and control network activity in the neocortex. Dysfunction of these cells is believed to lead to runaway excitation underlying seizure-based neurological disorders such as epilepsy, autism, and schizophrenia. Despite their importance in heath and disease, our knowledge about the development of this diverse neuronal population remains incomplete. Here we conducted single-cell RNA sequencing (scRNA-seq) of human foetal MGE from 10 to 15 weeks post conception. These MGE tissues are composed of largely cycling progenitors and immature post-mitotic interneurons with characteristic regional marker expression. Analysis of integrated human and mouse MGE data revealed species-conserved transcriptomic profiles and regulatory programs. Moreover, we identified novel candidate transcription regulators for human interneuron differentiation. These findings provide a framework for in vitro modelling of interneuron development and a strategy for potentially enhancing interneuron production from human pluripotent stem cells.
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Affiliation(s)
- Francesca Keefe
- Neuroscience and Mental Health Research Institute, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | | | - Anne E. Rosser
- Neuroscience and Mental Health Research Institute, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
- Division of Neuroscience, School of Bioscience, Cardiff University, Cardiff CF10 3AX, UK
| | - Caleb Webber
- UK Dementia Research Institute Cardiff, Cardiff University, Cardiff CF24 4HQ, UK
| | - Meng Li
- Neuroscience and Mental Health Research Institute, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
- Division of Neuroscience, School of Bioscience, Cardiff University, Cardiff CF10 3AX, UK
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16
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Bandler RC, Mayer C. Deciphering inhibitory neuron development: The paths to diversity. Curr Opin Neurobiol 2023; 79:102691. [PMID: 36805715 DOI: 10.1016/j.conb.2023.102691] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/29/2022] [Accepted: 01/10/2023] [Indexed: 02/19/2023]
Abstract
The regulation of fate decisions in progenitor cells lays the foundation for the generation of neuronal diversity and the formation of specialized circuits with remarkable processing capacity. Since the discovery more than 20 years ago that inhibitory (GABAergic) neurons originate from progenitors in the ventral part of the embryonic brain, numerous details about their development and function have been unveiled. GABAergic neurons are an extremely heterogeneous group, comprising many specialized subtypes of local interneurons and long-range projection neurons. Clearly distinguishable types emerge during postmitotic maturation, at a time when precursors migrate, morphologically mature, and establish synaptic connections. Yet, differentiation begins at an earlier stage within their progenitor domains, where a combination of birthdate and place of origin are key drivers. This review explains how new insights from single-cell sequencing inform our current understanding of how GABAergic neuron diversity emerges.
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Affiliation(s)
- Rachel C Bandler
- Yale University, Department of Psychiatry, New Haven, CT 06510, USA; Max Planck Institute for Biological Intelligence, Martinsried, 82152, Germany. https://twitter.com/Rachel_Bandler
| | - Christian Mayer
- Max Planck Institute for Biological Intelligence, Martinsried, 82152, Germany.
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17
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Cortical interneuron specification and diversification in the era of big data. Curr Opin Neurobiol 2023; 80:102703. [PMID: 36933450 DOI: 10.1016/j.conb.2023.102703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 02/02/2023] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Inhibition in the mammalian cerebral cortex is mediated by a small population of highly diverse GABAergic interneurons. These largely local neurons are interspersed among excitatory projection neurons and exert pivotal regulation on the formation and function of cortical circuits. We are beginning to understand the extent of GABAergic neuron diversity and how this is generated and shaped during brain development in mice and humans. In this review, we summarise recent findings and discuss how new technologies are being used to further advance our knowledge. Understanding how inhibitory neurons are generated in the embryo is an essential pre-requisite of stem cell therapy, an evolving area of research, aimed at correcting human disorders that result in inhibitory dysfunction.
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18
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Cao Y. The uses of 3D human brain organoids for neurotoxicity evaluations: A review. Neurotoxicology 2022; 91:84-93. [PMID: 35561940 DOI: 10.1016/j.neuro.2022.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/26/2022] [Accepted: 05/05/2022] [Indexed: 12/22/2022]
Abstract
Neurotoxicity studies aim at understanding the toxic effects and mechanisms of toxicants to human central nervous systems (CNS). However, human brains are the most complex organs, whereas the most commonly used models, such as 2D cell cultures and animal brains, are probably too simple to predict the responses of human brains. Embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs)-based 3D human brain organoids hold unprecedented promise for the understanding of neurodevelopment and brain disease development. This review summarizes recent advances of using 3D human brain organoids for neurotoxicity studies. Comparative studies showed that 3D human brain organoids could support the findings obtained by animal or cohort studies, indicating that 3D human brain organoids are reliable models to evaluate the developmental neurotoxicity. 3D human brain organoids have been used to understand the toxicological mechanisms by using both conventional toxicological methods to investigate the signaling pathway changes as well as single cell RNA-sequencing to understand the neuron diversity. Some studies also used brain organoids carrying gene mutations or with virus infections to understand the toxicological responses of brains under diseased conditions. Although there are still limitations associated, 3D human brain organoids are promising tools for future neurotoxicity studies.
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Affiliation(s)
- Yi Cao
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China.
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19
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Zhang B, Yuan Q, Zhang B, Li S, Wang Z, Liu H, Meng F, Chen X, Shang D. Characterization of neuroendocrine regulation- and metabolism-associated molecular features and prognostic indicators with aid to clinical chemotherapy and immunotherapy of patients with pancreatic cancer. Front Endocrinol (Lausanne) 2022; 13:1078424. [PMID: 36743929 PMCID: PMC9895410 DOI: 10.3389/fendo.2022.1078424] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/23/2022] [Indexed: 01/21/2023] Open
Abstract
The worldwide prevalence of pancreatic cancer has been rising in recent decades, and its prognosis has not improved much. The imbalance of substance and energy metabolism in tumour cells is among the primary causes of tumour formation and occurrence, which is often controlled by the neuroendocrine system. We applied Cox and LASSO regression analysis to develop a neuroendocrine regulation- and metabolism-related prognostic risk score model with three genes (GSK3B, IL18 and VEGFA) for pancreatic cancer. TCGA dataset served as the training and internal validation sets, and GSE28735, GSE62452 and GSE57495 were designated as external validation sets. Patients classified as the low-risk population (category, group) exhibited considerably improved survival duration in contrast with those classified as the high-risk population, as determined by the Kaplan-Meier curve. Then, we combined all the samples, and divided them into three clusters using unsupervised clustering analysis. Unsupervised clustering, t-distributed stochastic neighbor embedding (t-SNE), and principal component analysis (PCA) were further utilized to demonstrate the reliability of the prognostic model. Moreover, the risk score was shown to independently function as a predictor of pancreatic cancer in both univariate and multivariate Cox regression analyses. The results of gene set enrichment analysis (GSEA) illustrated that the low-risk population was predominantly enriched in immune-associated pathways. "ESTIMATE" algorithm, single-sample GSEA (ssGSEA) and the Tumor Immune Estimation Resource (TIMER) database showed immune infiltration ratings were enhanced in the low-risk category in contrast with the high-risk group. Tumour immune dysfunction and exclusion (TIDE) database predicted that immunotherapy for pancreatic cancer may be more successful in the high-risk than in the low-risk population. Mutation analysis illustrated a positive link between the tumour mutation burden and risk score. Drug sensitivity analysis identified 44 sensitive drugs in the high- and low-risk population. GSK3B expression was negatively correlated with Oxaliplatin, and IL18 expression was negatively correlated with Paclitaxel. Lastly, we analyzed and verified gene expression at RNA and protein levels based on GENPIA platform, HPA database and quantitative real-time PCR. In short, we developed a neuroendocrine regulation- and metabolism-associated prognostic model for pancreatic cancer that takes into account the immunological microenvironment and drug sensitivity.
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Affiliation(s)
- Biao Zhang
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Qihang Yuan
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Bolin Zhang
- Department of Visceral, Vascular and Endocrine Surgery, Martin-Luther-University Halle-Wittenberg, University Medical Center Halle, Halle, Germany
| | - Shuang Li
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Zhizhou Wang
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Hangyu Liu
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Fanyue Meng
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Xu Chen
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- *Correspondence: Xu Chen, ; Dong Shang,
| | - Dong Shang
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- *Correspondence: Xu Chen, ; Dong Shang,
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