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Zhang L, Cavallini M, Wang J, Xin R, Zhang Q, Feng G, Sanes JR, Peng YR. Evolutionary and developmental specialization of foveal cell types in the marmoset. Proc Natl Acad Sci U S A 2024; 121:e2313820121. [PMID: 38598343 PMCID: PMC11032471 DOI: 10.1073/pnas.2313820121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 03/13/2024] [Indexed: 04/12/2024] Open
Abstract
In primates, high-acuity vision is mediated by the fovea, a small specialized central region of the retina. The fovea, unique to the anthropoid lineage among mammals, undergoes notable neuronal morphological changes during postnatal maturation. However, the extent of cellular similarity across anthropoid foveas and the molecular underpinnings of foveal maturation remain unclear. Here, we used high-throughput single-cell RNA sequencing to profile retinal cells of the common marmoset (Callithrix jacchus), an early divergent in anthropoid evolution from humans, apes, and macaques. We generated atlases of the marmoset fovea and peripheral retina for both neonates and adults. Our comparative analysis revealed that marmosets share almost all their foveal types with both humans and macaques, highlighting a conserved cellular structure among primate foveas. Furthermore, by tracing the developmental trajectory of cell types in the foveal and peripheral retina, we found distinct maturation paths for each. In-depth analysis of gene expression differences demonstrated that cone photoreceptors and Müller glia (MG), among others, show the greatest molecular divergence between these two regions. Utilizing single-cell ATAC-seq and gene-regulatory network inference, we uncovered distinct transcriptional regulations differentiating foveal cones from their peripheral counterparts. Further analysis of predicted ligand-receptor interactions suggested a potential role for MG in supporting the maturation of foveal cones. Together, these results provide valuable insights into foveal development, structure, and evolution.
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Affiliation(s)
- Lin Zhang
- Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA90095
| | - Martina Cavallini
- Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA90095
| | - Junqiang Wang
- Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA90095
| | - Ruiqi Xin
- Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA90095
| | - Qiangge Zhang
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
| | - Yi-Rong Peng
- Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA90095
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2
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Kim B, Ding W, Yang L, Chen Q, Mao J, Feng G, Choi JH, Shen S. Simultaneous two-photon imaging and wireless EEG recording in mice. Heliyon 2024; 10:e25910. [PMID: 38449613 PMCID: PMC10915345 DOI: 10.1016/j.heliyon.2024.e25910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/05/2024] [Accepted: 02/05/2024] [Indexed: 03/08/2024] Open
Abstract
Background In vivo two-photon imaging is a reliable method with high spatial resolution that allows observation of individual neuron and dendritic activity longitudinally. Neurons in local brain regions can be influenced by global brain states such as levels of arousal and attention that change over relatively short time scales, such as minutes. As such, the scientific rigor of investigating regional neuronal activities could be enhanced by considering the global brain state. New method In order to assess the global brain state during in vivo two-photon imaging, CBRAIN (collective brain research platform aided by illuminating neural activity), a wireless EEG collecting and labeling device, was controlled by the same computer of two-photon microscope. In an experiment to explore neuronal responses to isoflurane anesthesia through two-photon imaging, we investigated whether the response of individual cells correlated with concurrent EEG changes induced by anesthesia. Results In two-photon imaging, calcium activities of the excitatory neurons in the primary somatosensory cortex disappeared in about 30s after to the initiation of isoflurane anesthesia. The simultaneously recorded EEG showed various transitional activity for about 7 min from the initiation of anesthesia and continued with burst and suppression alternating pattern thereafter. As such, there was a dissociation between excitatory neuron activity of the primary somatosensory cortex and the global brain activity under anesthesia. Comparison with existing methods Existing methods to combine two-photon and EEG recording used wired EEG recording. In this study, wireless EEG was used in conjunction with two-photon imaging, facilitated by CBRAIN. More importantly, built-in algorithms of the CBRAIN can automatically detect brain state such as sleep. The codes used for EEG classification are easy to use, with no prior experience required. Conclusion Simultaneous recording of wireless EEG and two-photon imaging provides a practical way to capture individual neuronal activities with respect to global brain state in an experimental set-up.
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Affiliation(s)
- Bowon Kim
- Center for Translational Pain Research, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
- Center for Neuroscience, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Weihua Ding
- Center for Translational Pain Research, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Liuyue Yang
- Center for Translational Pain Research, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Qian Chen
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge MA, USA
- Current address: Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jianren Mao
- Center for Translational Pain Research, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge MA, USA
| | - Jee Hyun Choi
- Center for Neuroscience, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Shiqian Shen
- Center for Translational Pain Research, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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4
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Zhou T, Ho YY, Lee RX, Fath AB, He K, Scott J, Bajwa N, Hartley ND, Wilde J, Gao X, Li C, Hong E, Nassar MR, Wimmer RD, Singh T, Halassa MM, Feng G. Enhancement of mediodorsal thalamus rescues aberrant belief dynamics in a mouse model with schizophrenia-associated mutation. bioRxiv 2024:2024.01.08.574745. [PMID: 38260581 PMCID: PMC10802391 DOI: 10.1101/2024.01.08.574745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Optimizing behavioral strategy requires belief updating based on new evidence, a process that engages higher cognition. In schizophrenia, aberrant belief dynamics may lead to psychosis, but the mechanisms underlying this process are unknown, in part, due to lack of appropriate animal models and behavior readouts. Here, we address this challenge by taking two synergistic approaches. First, we generate a mouse model bearing patient-derived point mutation in Grin2a (Grin2aY700X+/-), a gene that confers high-risk for schizophrenia and recently identified by large-scale exome sequencing. Second, we develop a computationally trackable foraging task, in which mice form and update belief-driven strategies in a dynamic environment. We found that Grin2aY700X+/- mice perform less optimally than their wild-type (WT) littermates, showing unstable behavioral states and a slower belief update rate. Using functional ultrasound imaging, we identified the mediodorsal (MD) thalamus as hypofunctional in Grin2aY700X+/- mice, and in vivo task recordings showed that MD neurons encoded dynamic values and behavioral states in WT mice. Optogenetic inhibition of MD neurons in WT mice phenocopied Grin2aY700X+/- mice, and enhancing MD activity rescued task deficits in Grin2aY700X+/- mice. Together, our study identifies the MD thalamus as a key node for schizophrenia-relevant cognitive dysfunction, and a potential target for future therapeutics.
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Affiliation(s)
- Tingting Zhou
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Yi-Yun Ho
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Ray X Lee
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Amanda B Fath
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Kathleen He
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Jonathan Scott
- Department of Neuroscience, Tufts University School of Medicine
| | - Navdeep Bajwa
- Department of Neuroscience, Tufts University School of Medicine
| | - Nolan D Hartley
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard
| | - Jonathan Wilde
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Xian Gao
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Cui Li
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Evan Hong
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | | | - Ralf D Wimmer
- Department of Neuroscience, Tufts University School of Medicine
| | - Tarjinder Singh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard
| | | | - Guoping Feng
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard
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5
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Jin L, Sullivan HA, Zhu M, Lavin TK, Matsuyama M, Fu X, Lea NE, Xu R, Hou Y, Rutigliani L, Pruner M, Babcock KR, Ip JPK, Hu M, Daigle TL, Zeng H, Sur M, Feng G, Wickersham IR. Publisher Correction: Long-term labeling and imaging of synaptically connected neuronal networks in vivo using double-deletion-mutant rabies viruses. Nat Neurosci 2024; 27:385. [PMID: 38267526 PMCID: PMC10849943 DOI: 10.1038/s41593-024-01584-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Affiliation(s)
- Lei Jin
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Lingang Laboratory, Shanghai, China
| | - Heather A Sullivan
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mulangma Zhu
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas K Lavin
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Makoto Matsuyama
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xin Fu
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas E Lea
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ran Xu
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - YuanYuan Hou
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luca Rutigliani
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Maxwell Pruner
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kelsey R Babcock
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jacque Pak Kan Ip
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ming Hu
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Mriganka Sur
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- 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
| | - Ian R Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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6
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Jin L, Sullivan HA, Zhu M, Lavin TK, Matsuyama M, Fu X, Lea NE, Xu R, Hou Y, Rutigliani L, Pruner M, Babcock KR, Ip JPK, Hu M, Daigle TL, Zeng H, Sur M, Feng G, Wickersham IR. Long-term labeling and imaging of synaptically connected neuronal networks in vivo using double-deletion-mutant rabies viruses. Nat Neurosci 2024; 27:373-383. [PMID: 38212587 PMCID: PMC10849964 DOI: 10.1038/s41593-023-01545-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 12/05/2023] [Indexed: 01/13/2024]
Abstract
Rabies-virus-based monosynaptic tracing is a widely used technique for mapping neural circuitry, but its cytotoxicity has confined it primarily to anatomical applications. Here we present a second-generation system for labeling direct inputs to targeted neuronal populations with minimal toxicity, using double-deletion-mutant rabies viruses. Viral spread requires expression of both deleted viral genes in trans in postsynaptic source cells. Suppressing this expression with doxycycline following an initial period of viral replication reduces toxicity to postsynaptic cells. Longitudinal two-photon imaging in vivo indicated that over 90% of both presynaptic and source cells survived for the full 12-week course of imaging. Ex vivo whole-cell recordings at 5 weeks postinfection showed that the second-generation system perturbs input and source cells much less than the first-generation system. Finally, two-photon calcium imaging of labeled networks of visual cortex neurons showed that their visual response properties appeared normal for 10 weeks, the longest we followed them.
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Affiliation(s)
- Lei Jin
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Lingang Laboratory, Shanghai, China
| | - Heather A Sullivan
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mulangma Zhu
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas K Lavin
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Makoto Matsuyama
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xin Fu
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas E Lea
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ran Xu
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - YuanYuan Hou
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luca Rutigliani
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Maxwell Pruner
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kelsey R Babcock
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jacque Pak Kan Ip
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ming Hu
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Mriganka Sur
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- 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
| | - Ian R Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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7
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Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, Chang L, Dong K, Indralingam HS, Rink JA, Xie Y, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Lein ES, Behrens MM, Ecker JR, Ren B. Author Correction: Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature 2024; 625:E26. [PMID: 38200319 PMCID: PMC10808050 DOI: 10.1038/s41586-023-07013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Affiliation(s)
- Nathan R Zemke
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Ethan J Armand
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Wenliang Wang
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Seoyeon Lee
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jingtian Zhou
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Eric Li
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Wei Tian
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rosa G Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Julia K Osteen
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Daofeng Li
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Xiaoyu Zhuo
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Vincent Xu
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Lei Chang
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Keyi Dong
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hannah S Indralingam
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jonathan A Rink
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Xie
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Miller
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Fenna M Krienen
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Qiangge Zhang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Naz Taskin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edward M Callaway
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Ting Wang
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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8
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Zhang W, Zhang Y, Xia Y, Feng G, Wang Y, Wei C, Tang A, Song K, Qiu R, Wu Y, Jin S. Choline induced cardiac dysfunction by inhibiting the production of endogenous hydrogen sulfide in spontaneously hypertensive rats. Physiol Res 2023; 72:719-730. [PMID: 38215059 PMCID: PMC10805251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 09/07/2023] [Indexed: 01/14/2024] Open
Abstract
To investigate the exact effects of dietary choline on hypertensive heart disease (HHD) and explore the potential mechanisms, male spontaneously hypertensive rats (SHR) and Wistar Kyoto rats (WKY) were randomly divided into five groups as follows: WKY group, WKY + Choline group, SHR group, SHR + Choline group, and SHR + Choline + NaHS group. In choline treatment groups, rats were fed with 1.3% (w/v) choline in the drinking water for 3 months. The rats in the SHR + Choline + NaHS group were intraperitoneally injected with NaHS (100 micromol/kg/day, a hydrogen sulfide (H2S) donor) for 3 months. After 3 months, left ventricular ejection fraction (LVEF) and fractional shortening (LVFS), the indicators of cardiac function measured by echocardiography, were increased significantly in SHR as compared to WKY, although there was no significant difference in collagen volumes and Bax/Bcl-2 ratio between the two groups, indicating the early stage of cardiac hypertrophy. There was a significant decrease in LVEF and LVFS and an increase in collagen volumes and Bax/Bcl-2 ratio in SHR fed with choline, meanwhile, plasma H2S levels were significantly decreased significantly in SHR fed with choline accompanying by the decrease of cystathionine-gamma-lyase (CSE) activity. Three months of NaHS significantly increased plasma H2S levels, ameliorated cardiac dysfunction and inhibited cardiac fibrosis and apoptosis in SHR fed with choline. In conclusion, choline aggravated cardiac dysfunction in HHD through inhibiting the production of endogenous H2S, which was reversed by supplementation of exogenous H2S donor.
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Affiliation(s)
- W Zhang
- Department of Physiology, Hebei Medical University, Hebei, China
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9
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Zhang L, Cavallini M, Wang J, Xin R, Zhang Q, Feng G, Sanes JR, Peng YR. Evolutionary and Developmental Specialization of Foveal Cell Types in the Marmoset. bioRxiv 2023:2023.12.10.570996. [PMID: 38106142 PMCID: PMC10723441 DOI: 10.1101/2023.12.10.570996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
In primates, high-acuity vision is mediated by the fovea, a small specialized central region of the retina. The fovea, unique to the anthropoid lineage among mammals, undergoes notable neuronal morphological changes during postnatal maturation. However, the extent of cellular similarity across anthropoid foveas and the molecular underpinnings of foveal maturation remain unclear. Here, we used high throughput single cell RNA sequencing to profile retinal cells of the common marmoset ( Callithrix jacchus ), an early divergent in anthropoid evolution from humans, apes, and macaques. We generated atlases of the marmoset fovea and peripheral retina for both neonates and adults. Our comparative analysis revealed that marmosets share almost all its foveal types with both humans and macaques, highlighting a conserved cellular structure among primate foveas. Furthermore, by tracing the developmental trajectory of cell types in the foveal and peripheral retina, we found distinct maturation paths for each. In-depth analysis of gene expression differences demonstrated that cone photoreceptors and Müller glia, among others, show the greatest molecular divergence between these two regions. Utilizing single-cell ATAC-seq and gene-regulatory network inference, we uncovered distinct transcriptional regulations differentiating foveal cones from their peripheral counterparts. Further analysis of predicted ligand-receptor interactions suggested a potential role for Müller glia in supporting the maturation of foveal cones. Together, these results provide valuable insights into foveal development, structure, and evolution. Significance statement The sharpness of our eyesight hinges on a tiny retinal region known as the fovea. The fovea is pivotal for primate vision and is susceptible to diseases like age-related macular degeneration. We studied the fovea in the marmoset-a primate with ancient evolutionary ties. Our data illustrated the cellular and molecular composition of its fovea across different developmental ages. Our findings highlighted a profound cellular consistency among marmosets, humans, and macaques, emphasizing the value of marmosets in visual research and the study of visual diseases.
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10
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Winter CC, Jacobi A, Su J, Chung L, van Velthoven CTJ, Yao Z, Lee C, Zhang Z, Yu S, Gao K, Duque Salazar G, Kegeles E, Zhang Y, Tomihiro MC, Zhang Y, Yang Z, Zhu J, Tang J, Song X, Donahue RJ, Wang Q, McMillen D, Kunst M, Wang N, Smith KA, Romero GE, Frank MM, Krol A, Kawaguchi R, Geschwind DH, Feng G, Goodrich LV, Liu Y, Tasic B, Zeng H, He Z. A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons. Nature 2023; 624:403-414. [PMID: 38092914 PMCID: PMC10719099 DOI: 10.1038/s41586-023-06817-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
The brain controls nearly all bodily functions via spinal projecting neurons (SPNs) that carry command signals from the brain to the spinal cord. However, a comprehensive molecular characterization of brain-wide SPNs is still lacking. Here we transcriptionally profiled a total of 65,002 SPNs, identified 76 region-specific SPN types, and mapped these types into a companion atlas of the whole mouse brain1. This taxonomy reveals a three-component organization of SPNs: (1) molecularly homogeneous excitatory SPNs from the cortex, red nucleus and cerebellum with somatotopic spinal terminations suitable for point-to-point communication; (2) heterogeneous populations in the reticular formation with broad spinal termination patterns, suitable for relaying commands related to the activities of the entire spinal cord; and (3) modulatory neurons expressing slow-acting neurotransmitters and/or neuropeptides in the hypothalamus, midbrain and reticular formation for 'gain setting' of brain-spinal signals. In addition, this atlas revealed a LIM homeobox transcription factor code that parcellates the reticulospinal neurons into five molecularly distinct and spatially segregated populations. Finally, we found transcriptional signatures of a subset of SPNs with large soma size and correlated these with fast-firing electrophysiological properties. Together, this study establishes a comprehensive taxonomy of brain-wide SPNs and provides insight into the functional organization of SPNs in mediating brain control of bodily functions.
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Affiliation(s)
- Carla C Winter
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- PhD Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
- Harvard-MIT MD-PhD Program, Harvard Medical School, Boston, MA, USA
| | - Anne Jacobi
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.
- Department of Neurology, Harvard Medical School, Boston, MA, USA.
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
- F. Hoffman-La Roche, pRED, Basel, Switzerland.
| | - Junfeng Su
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Leeyup Chung
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zicong Zhang
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Shuguang Yu
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Kun Gao
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Geraldine Duque Salazar
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Evgenii Kegeles
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- PhD Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Yu Zhang
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Makenzie C Tomihiro
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Yiming Zhang
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Zhiyun Yang
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Junjie Zhu
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Jing Tang
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Xuan Song
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Ryan J Donahue
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Qing Wang
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | | | - Ning Wang
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Gabriel E Romero
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Michelle M Frank
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Alexandra Krol
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Riki Kawaguchi
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lisa V Goodrich
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Yuanyuan Liu
- Somatosensation and Pain Unit, National Institute of Dental and Craniofacial Research, National Center for Complementary and Integrative Health, National Institutes of Health, Bethesda, MD, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA.
| | - Zhigang He
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.
- Department of Neurology, Harvard Medical School, Boston, MA, USA.
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
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11
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Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, Chang L, Dong K, Indralingam HS, Rink JA, Xie Y, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Lein ES, Behrens MM, Ecker JR, Ren B. Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature 2023; 624:390-402. [PMID: 38092918 PMCID: PMC10719095 DOI: 10.1038/s41586-023-06819-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
Divergence of cis-regulatory elements drives species-specific traits1, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains unclear. Here we investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset and mouse using single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 200,000 cells. From these data, we show evidence that divergence of transcription factor expression corresponds to species-specific epigenome landscapes. We find that conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome. Transposable elements contribute to nearly 80% of the human-specific candidate cis-regulatory elements in cortical cells. Through machine learning, we develop sequence-based predictors of candidate cis-regulatory elements in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Finally, we show that epigenetic conservation combined with sequence similarity helps to uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.
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Affiliation(s)
- Nathan R Zemke
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Ethan J Armand
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Wenliang Wang
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Seoyeon Lee
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jingtian Zhou
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Eric Li
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Wei Tian
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rosa G Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Julia K Osteen
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Daofeng Li
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Xiaoyu Zhuo
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Vincent Xu
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Lei Chang
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Keyi Dong
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hannah S Indralingam
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jonathan A Rink
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Xie
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Miller
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Fenna M Krienen
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Qiangge Zhang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Naz Taskin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edward M Callaway
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Ting Wang
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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12
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Malgady JM, Baez A, Hobel ZB, Jimenez K, Goldfried J, Prager EM, Wilking JA, Zhang Q, Feng G, Plotkin JL. Pathway-specific alterations in striatal excitability and cholinergic modulation in a SAPAP3 mouse model of compulsive motor behavior. Cell Rep 2023; 42:113384. [PMID: 37934666 PMCID: PMC10872927 DOI: 10.1016/j.celrep.2023.113384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 09/06/2023] [Accepted: 10/22/2023] [Indexed: 11/09/2023] Open
Abstract
Deletion of the obsessive-compulsive disorder (OCD)-associated gene SAP90/PSD-95-associated protein 3 (Sapap3), which encodes a postsynaptic anchoring protein at corticostriatal synapses, causes OCD-like motor behaviors in mice. While corticostriatal synaptic dysfunction is central to this phenotype, the striatum efficiently adapts to pathological changes, often in ways that expand upon the original circuit impairment. Here, we show that SAPAP3 deletion causes non-synaptic and pathway-specific alterations in dorsolateral striatum circuit function. While somatic excitability was elevated in striatal projection neurons (SPNs), dendritic excitability was exclusively enhanced in direct pathway SPNs. Layered on top of this, cholinergic modulation was altered in opposing ways: striatal cholinergic interneuron density and evoked acetylcholine release were elevated, while basal muscarinic modulation of SPNs was reduced. These data describe how SAPAP3 deletion alters the striatal landscape upon which impaired corticostriatal inputs will act, offering a basis for how pathological synaptic integration and unbalanced striatal output underlying OCD-like behaviors may be shaped.
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Affiliation(s)
- Jeffrey M Malgady
- Department of Neurobiology & Behavior, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794, USA; Graduate Program in Neuroscience, College of Arts & Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Alexander Baez
- Department of Neurobiology & Behavior, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794, USA; Medical Scientist Training Program, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Zachary B Hobel
- Department of Neurobiology & Behavior, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794, USA; Graduate Program in Neuroscience, College of Arts & Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kimberly Jimenez
- Department of Neurobiology & Behavior, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794, USA
| | - Jack Goldfried
- Department of Neurobiology & Behavior, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794, USA
| | - Eric M Prager
- Department of Neurobiology & Behavior, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794, USA
| | - Jennifer A Wilking
- Department of Neurobiology & Behavior, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794, USA
| | - Qiangge Zhang
- Yang Tan Collective and McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guoping Feng
- Yang Tan Collective and McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joshua L Plotkin
- Department of Neurobiology & Behavior, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794, USA; Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY 11794, USA.
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13
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Jin L, Sullivan HA, Zhu M, Lea NE, Lavin TK, Fu X, Matsuyama M, Hou Y, Feng G, Wickersham IR. Third-generation rabies viral vectors allow nontoxic retrograde targeting of projection neurons with greatly increased efficiency. Cell Rep Methods 2023; 3:100644. [PMID: 37989085 PMCID: PMC10694603 DOI: 10.1016/j.crmeth.2023.100644] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/16/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
Rabies viral vectors have become important components of the systems neuroscience toolkit, allowing both direct retrograde targeting of projection neurons and monosynaptic tracing of inputs to defined postsynaptic populations, but the rapid cytotoxicity of first-generation (ΔG) vectors limits their use to short-term experiments. We recently introduced second-generation, double-deletion-mutant (ΔGL) rabies viral vectors, showing that they efficiently retrogradely infect projection neurons and express recombinases effectively but with little to no detectable toxicity; more recently, we have shown that ΔGL viruses can be used for monosynaptic tracing with far lower cytotoxicity than the first-generation system. Here, we introduce third-generation (ΔL) rabies viral vectors, which appear to be as nontoxic as second-generation ones but have the major advantage of growing to much higher titers, resulting in significantly increased numbers of retrogradely labeled neurons in vivo.
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Affiliation(s)
- Lei Jin
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Heather A Sullivan
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mulangma Zhu
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas E Lea
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas K Lavin
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xin Fu
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Makoto Matsuyama
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - YuanYuan Hou
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA; 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
| | - Ian R Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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14
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Ding W, Yang L, Shi E, Kim B, Low S, Hu K, Gao L, Chen P, Ding W, Borsook D, Luo A, Choi JH, Wang C, Akeju O, Yang J, Ran C, Schreiber KL, Mao J, Chen Q, Feng G, Shen S. Author Correction: The endocannabinoid N-arachidonoyl dopamine is critical for hyperalgesia induced by chronic sleep disruption. Nat Commun 2023; 14:7342. [PMID: 37957140 PMCID: PMC10643668 DOI: 10.1038/s41467-023-43155-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023] Open
Affiliation(s)
- Weihua Ding
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Liuyue Yang
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eleanor Shi
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bowon Kim
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sarah Low
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kun Hu
- Department of Pathology, Tuft University School of Medicine, Boston, MA, USA
| | - Lei Gao
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ping Chen
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA
| | - Wei Ding
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA
| | - David Borsook
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew Luo
- Summer Intern Program of the Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, currently at Brandeis University, Boston, MA, USA
| | - Jee Hyun Choi
- Center for Neuroscience, Korea Institute of Science and Technology, Seoul, South Korea
| | - Changning Wang
- Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Oluwaseun Akeju
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jun Yang
- Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chongzhao Ran
- Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kristin L Schreiber
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jianren Mao
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Qian Chen
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Guoping Feng
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Shiqian Shen
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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15
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Uzunparmak B, Haymaker C, Raso G, Masciari S, Wang L, Lin H, Gorur A, Kirby B, Cimo AM, Kennon A, Ding Q, Urschel G, Yuan Y, Feng G, Rizvi Y, Hussain A, Zhu C, Kim P, Abbadessa G, Subbiah V, Yap TA, Rodon J, Piha-Paul SA, Meric-Bernstam F, Dumbrava EE. HER2-low expression in patients with advanced or metastatic solid tumors. Ann Oncol 2023; 34:1035-1046. [PMID: 37619847 DOI: 10.1016/j.annonc.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Human epidermal growth factor receptor 2 (HER2)-low is a newly defined category with HER2 1+ or 2+ expression by immunohistochemistry (IHC) and lack of HER2 gene amplification measured by in situ hybridization (ISH). Much remains unknown about the HER2-low status across tumor types and changes in HER2 status between primary and metastatic samples. PATIENTS AND METHODS HER2 expression by IHC was evaluated in 4701 patients with solid tumors. We have evaluated the HER2 expression by IHC and amplification by ISH in paired breast and gastric/gastroesophageal (GEJ) primary and metastatic samples. HER2 expression was correlated with ERBB2 genomic alterations evaluated by next-generation sequencing (NGS) in non-breast, non-gastric/GEJ samples. RESULTS HER2 expression (HER2 IHC 1-3+) was found in half (49.8%) of the cancers, with HER2-low (1 or 2+) found in many tumor types: 47.1% in breast, 34.6% in gastric/GEJ, 50.0% in salivary gland, 46.9% in lung, 46.5% in endometrial, 46% in urothelial, and 45.5% of gallbladder cancers. The concordance evaluation of HER2 expression between primary and metastatic breast cancer samples showed that HER2 3+ remained unchanged in 87.1% with a strong agreement between primary and metastatic samples, with a weighted kappa (Κ) of 0.85 (95% confidence interval 0.79-0.91). ERBB2 alterations were identified in 117 (7.5%) patients with non-breast, non-gastric/GEJ solid tumors who had NGS testing. Of 1436 patients without ERBB2 alterations, 512 (35.7%) showed any level HER2 expression by IHC. CONCLUSION Our results show that HER2-low expression is frequently found across tumor types. These findings suggest that many patients with HER2-low solid tumors might benefit from HER2-targeted therapies.
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Affiliation(s)
- B Uzunparmak
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - C Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - G Raso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Masciari
- Department of Sanofi, The University of Texas MD Anderson Cancer Center, Cambridge, USA
| | - L Wang
- Department of Sanofi, The University of Texas MD Anderson Cancer Center, Cambridge, USA
| | - H Lin
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Gorur
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - B Kirby
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A-M Cimo
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Kennon
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Q Ding
- Department of Anatomical Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - G Urschel
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Y Yuan
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - G Feng
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Y Rizvi
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Hussain
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - C Zhu
- Department of Sanofi, The University of Texas MD Anderson Cancer Center, Cambridge, USA
| | - P Kim
- Department of Sanofi, The University of Texas MD Anderson Cancer Center, Cambridge, USA
| | - G Abbadessa
- Department of Sanofi, The University of Texas MD Anderson Cancer Center, Cambridge, USA
| | - V Subbiah
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - T A Yap
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA; Department of The Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, USA; Department of Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Rodon
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA; Department of Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S A Piha-Paul
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - F Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA; Department of Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, USA; Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - E E Dumbrava
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA.
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16
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Ding W, Yang L, Shi E, Kim B, Low S, Hu K, Gao L, Chen P, Ding W, Borsook D, Luo A, Choi JH, Wang C, Akeju O, Yang J, Ran C, Schreiber KL, Mao J, Chen Q, Feng G, Shen S. The endocannabinoid N-arachidonoyl dopamine is critical for hyperalgesia induced by chronic sleep disruption. Nat Commun 2023; 14:6696. [PMID: 37880241 PMCID: PMC10600211 DOI: 10.1038/s41467-023-42283-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 10/05/2023] [Indexed: 10/27/2023] Open
Abstract
Chronic pain is highly prevalent and is linked to a broad range of comorbidities, including sleep disorders. Epidemiological and clinical evidence suggests that chronic sleep disruption (CSD) leads to heightened pain sensitivity, referred to as CSD-induced hyperalgesia. However, the underlying mechanisms are unclear. The thalamic reticular nucleus (TRN) has unique integrative functions in sensory processing, attention/arousal and sleep spindle generation. We report that the TRN played an important role in CSD-induced hyperalgesia in mice, through its projections to the ventroposterior region of the thalamus. Metabolomics revealed that the level of N-arachidonoyl dopamine (NADA), an endocannabinoid, was decreased in the TRN after CSD. Using a recently developed CB1 receptor (cannabinoid receptor 1) activity sensor with spatiotemporal resolution, CB1 receptor activity in the TRN was found to be decreased after CSD. Moreover, CSD-induced hyperalgesia was attenuated by local NADA administration to the TRN. Taken together, these results suggest that TRN NADA signaling is critical for CSD-induced hyperalgesia.
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Affiliation(s)
- Weihua Ding
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Liuyue Yang
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eleanor Shi
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bowon Kim
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sarah Low
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kun Hu
- Department of Pathology, Tuft University School of Medicine, Boston, MA, USA
| | - Lei Gao
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ping Chen
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA
| | - Wei Ding
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA
| | - David Borsook
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew Luo
- Summer Intern Program of the Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, currently at Brandeis University, Boston, MA, USA
| | - Jee Hyun Choi
- Center for Neuroscience, Korea Institute of Science and Technology, Seoul, South Korea
| | - Changning Wang
- Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Oluwaseun Akeju
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jun Yang
- Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chongzhao Ran
- Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kristin L Schreiber
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jianren Mao
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Qian Chen
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Guoping Feng
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Shiqian Shen
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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17
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del Rosario RC, Krienen FM, Zhang Q, Goldman M, Mello C, Lutservitz A, Ichihara K, Wysoker A, Nemesh J, Feng G, McCarroll SA. Sibling chimerism among microglia in marmosets. bioRxiv 2023:2023.10.16.562516. [PMID: 37904944 PMCID: PMC10614798 DOI: 10.1101/2023.10.16.562516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Chimerism happens rarely among most mammals but is common in marmosets and tamarins, a result of fraternal twin or triplet birth patterns in which in utero connected circulatory systems (through which stem cells transit) lead to persistent blood chimerism (12-80%) throughout life. The presence of Y-chromosome DNA sequences in other organs of female marmosets has long suggested that chimerism might also affect these organs. However, a longstanding question is whether this chimerism is driven by blood-derived cells or involves contributions from other cell types. To address this question, we analyzed single-cell RNA-seq data from blood, liver, kidney and multiple brain regions across a number of marmosets, using transcribed single nucleotide polymorphisms (SNPs) to identify cells with the sibling's genome in various cell types within these tissues. Sibling-derived chimerism in all tissues arose entirely from cells of hematopoietic origin (i.e., myeloid and lymphoid lineages). In brain tissue this was reflected as sibling-derived chimerism among microglia (20-52%) and macrophages (18-64%) but not among other resident cell types (i.e., neurons, glia or ependymal cells). The percentage of microglia that were sibling-derived showed significant variation across brain regions, even within individual animals, likely reflecting distinct responses by siblings' microglia to local recruitment or proliferation cues or, potentially, distinct clonal expansion histories in different brain areas. In the animals and tissues we analyzed, microglial gene expression profiles bore a much stronger relationship to local/host context than to sibling genetic differences. Naturally occurring marmoset chimerism will provide new ways to understand the effects of genes, mutations and brain contexts on microglial biology and to distinguish between effects of microglia and other cell types on brain phenotypes.
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Affiliation(s)
- Ricardo C.H. del Rosario
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Fenna M. Krienen
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- current address: Princeton Neuroscience Institute
| | - Qiangge Zhang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Melissa Goldman
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Curtis Mello
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alyssa Lutservitz
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kiku Ichihara
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alec Wysoker
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - James Nemesh
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- current address: Princeton Neuroscience Institute
| | - Steven A. McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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18
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Jorstad NL, Song JH, Exposito-Alonso D, Suresh H, Castro-Pacheco N, Krienen FM, Yanny AM, Close J, Gelfand E, Long B, Seeman SC, Travaglini KJ, Basu S, Beaudin M, Bertagnolli D, Crow M, Ding SL, Eggermont J, Glandon A, Goldy J, Kiick K, Kroes T, McMillen D, Pham T, Rimorin C, Siletti K, Somasundaram S, Tieu M, Torkelson A, Feng G, Hopkins WD, Höllt T, Keene CD, Linnarsson S, McCarroll SA, Lelieveldt BP, Sherwood CC, Smith K, Walsh CA, Dobin A, Gillis J, Lein ES, Hodge RD, Bakken TE. Comparative transcriptomics reveals human-specific cortical features. Science 2023; 382:eade9516. [PMID: 37824638 PMCID: PMC10659116 DOI: 10.1126/science.ade9516] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 09/13/2023] [Indexed: 10/14/2023]
Abstract
The cognitive abilities of humans are distinctive among primates, but their molecular and cellular substrates are poorly understood. We used comparative single-nucleus transcriptomics to analyze samples of the middle temporal gyrus (MTG) from adult humans, chimpanzees, gorillas, rhesus macaques, and common marmosets to understand human-specific features of the neocortex. Human, chimpanzee, and gorilla MTG showed highly similar cell-type composition and laminar organization as well as a large shift in proportions of deep-layer intratelencephalic-projecting neurons compared with macaque and marmoset MTG. Microglia, astrocytes, and oligodendrocytes had more-divergent expression across species compared with neurons or oligodendrocyte precursor cells, and neuronal expression diverged more rapidly on the human lineage. Only a few hundred genes showed human-specific patterning, suggesting that relatively few cellular and molecular changes distinctively define adult human cortical structure.
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Affiliation(s)
| | - Janet H.T. Song
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | - David Exposito-Alonso
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Hamsini Suresh
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Fenna M. Krienen
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Jennie Close
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Emily Gelfand
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Brian Long
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | | | | | - Soumyadeep Basu
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
- Computer Graphics and Visualization Group, Delft University of Technology, Delft, Netherlands
| | - Marc Beaudin
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | | | - Megan Crow
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Song-Lin Ding
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Jeroen Eggermont
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
| | | | - Jeff Goldy
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Katelyn Kiick
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Thomas Kroes
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
| | | | | | | | - Kimberly Siletti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Michael Tieu
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Amy Torkelson
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William D. Hopkins
- Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, Houston, TX 78602, USA
| | - Thomas Höllt
- Computer Graphics and Visualization Group, Delft University of Technology, Delft, Netherlands
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 981915, USA
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Steven A. McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Boudewijn P. Lelieveldt
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
- Pattern Recognition and Bioinformatics group, Delft University of Technology, Delft, Netherlands
| | - Chet C. Sherwood
- Department of Anthropology, The George Washington University, Washington, DC 20037, USA
| | - Kimberly Smith
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Christopher A. Walsh
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Alexander Dobin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jesse Gillis
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Ed S. Lein
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
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19
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Krienen FM, Levandowski KM, Zaniewski H, del Rosario RC, Schroeder ME, Goldman M, Wienisch M, Lutservitz A, Beja-Glasser VF, Chen C, Zhang Q, Chan KY, Li KX, Sharma J, McCormack D, Shin TW, Harrahill A, Nyase E, Mudhar G, Mauermann A, Wysoker A, Nemesh J, Kashin S, Vergara J, Chelini G, Dimidschstein J, Berretta S, Deverman BE, Boyden E, McCarroll SA, Feng G. A marmoset brain cell census reveals regional specialization of cellular identities. Sci Adv 2023; 9:eadk3986. [PMID: 37824615 PMCID: PMC10569717 DOI: 10.1126/sciadv.adk3986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023]
Abstract
The mammalian brain is composed of many brain structures, each with its own ontogenetic and developmental history. We used single-nucleus RNA sequencing to sample over 2.4 million brain cells across 18 locations in the common marmoset, a New World monkey primed for genetic engineering, and examined gene expression patterns of cell types within and across brain structures. The adult transcriptomic identity of most neuronal types is shaped more by developmental origin than by neurotransmitter signaling repertoire. Quantitative mapping of GABAergic types with single-molecule FISH (smFISH) reveals that interneurons in the striatum and neocortex follow distinct spatial principles, and that lateral prefrontal and other higher-order cortical association areas are distinguished by high proportions of VIP+ neurons. We use cell type-specific enhancers to drive AAV-GFP and reconstruct the morphologies of molecularly resolved interneuron types in neocortex and striatum. Our analyses highlight how lineage, local context, and functional class contribute to the transcriptional identity and biodistribution of primate brain cell types.
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Affiliation(s)
- Fenna M. Krienen
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kirsten M. Levandowski
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heather Zaniewski
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ricardo C.H. del Rosario
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Margaret E. Schroeder
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Melissa Goldman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Martin Wienisch
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alyssa Lutservitz
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Victoria F. Beja-Glasser
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Cindy Chen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Qiangge Zhang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ken Y. Chan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Katelyn X. Li
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jitendra Sharma
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dana McCormack
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tay Won Shin
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Andrew Harrahill
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eric Nyase
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gagandeep Mudhar
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA
| | - Abigail Mauermann
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Alec Wysoker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - James Nemesh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Seva Kashin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Josselyn Vergara
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gabriele Chelini
- Center for Mind/Brain Sciences, University of Trento, Piazza della Manifattura n.1, Rovereto (TN) 38068, Italy
| | - Jordane Dimidschstein
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sabina Berretta
- Basic Neuroscience Division, McLean Hospital, Belmont, MA 02478, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin E. Deverman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ed Boyden
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Steven A. McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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Xue J, Shi R, Ma J, Liu Z, Feng G, Chen QQ, Li Y, He Y, Ji S, Shi J, Zhu X, Zhou J. Concurrent Chemoradiotherapy plus Programmed Death-1 (PD-1) Blockade for Locally Advanced Cervical Cancer: Preliminary Results of a Single-Arm, Open-Label, Phase II Trial. Int J Radiat Oncol Biol Phys 2023; 117:e542-e543. [PMID: 37785675 DOI: 10.1016/j.ijrobp.2023.06.1838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) This study aims to assess the anti-tumor activity and safety of concurrent chemoradiotherapy plus PD-1 blockade in patients with locally advanced cervical cancer. MATERIALS/METHODS This is a single-arm, open-label, prospective phase II study. The key inclusion criteria were treatment-naive patients aged 18-75 years with stage II A2-IVA (FIGO 2018) locally advanced cervical cancer. All patients were treated with concurrent chemoradiotherapy including 2 cycle cisplatin (75mg/m2, for three days, every 3 weeks[Q3W]), nedaplatin or carboplatin can be selected for patients who can't tolerate cisplatin. After CCRT, patients achieving complete response (CR), partial responses(PR), stable disease(SD) received adjuvant chemotherapy (docetaxel 75 mg/m2 day 1+ cisplatin DDP 25 mg/m2 day 1-3, Q3W) for 2 cycle. PD-1 blockade Sintilimab and Tislelizumab was administered intravenously at 200 mg every 3 weeks up to 1 year or until disease progression, unacceptable toxicity, or withdrawal of consent. The primary endpoint was objective response rate (ORR) assessed by investigators per Response Evaluation Criteria In Solid Tumours (RECIST) version 1.1. Secondary endpoints were the 12, 24-month overall survival (OS) rates, the 12, 24-month disease free survival (DFS) rates and safety. RESULTS From February 2020 to June 2022, a total of 15 patients was enrolled. Median age was 57 years (range, 36-74 years). Stage IIA1 was documented in 2 patients, stage IIA2 in two patients, stage IIIA in one patient, stage IIIC1 in eight patients, and stage IVA in two patients. And 66.7% (10/15) of patients had Metastatic lymph node. Four patients received adjuvant chemotherapy. The ORR was 100%, with 4 patients achieving CR and 11 PR. The 12 and 24-month OS rates are 93.3% and 84%, the 12 and 24-month DFS rates are 86% and 75.4%, respectively. Treatment-related adverse events (TRAEs) occurred in 86.7% (13/15) of patients. Grade 3 TRAEs are leukocyte (n = 1), thrombocytopenia (n = 1), hepatitis (n = 1), skin reaction (n = 1). No treatment-related deaths occurred. And IFN-γ was significantly elevated after radiotherapy (p = 0.0073). CONCLUSION Concurrent chemoradiotherapy plus PD-1 blockade showed promising antitumor activity and manageable toxicities in patients with locally advanced cervical cancer. Long-term outcomes are still pending to further evaluate their therapeutic effects. (ChiCTR2000032856).
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Affiliation(s)
- J Xue
- Department of Radiation Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215001, China., Suzhou, China
| | - R Shi
- Department of Radiation Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215001, China., Suzhou, China
| | - J Ma
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Z Liu
- Department of Radiation Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215001, China., Suzhou, China
| | - G Feng
- Department of Gynecology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215001, China., Suzhou, China
| | - Q Q Chen
- Department of Radiation Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Y Li
- Department of Radiation Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215001, China., Suzhou, China
| | - Y He
- Department of Radiation Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215001, China., Suzhou, China
| | - S Ji
- Department of Radiation Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - J Shi
- Department of Radiation Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215001, China., Suzhou, China
| | - X Zhu
- Department of Radiation Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215001, China., Suzhou, China
| | - J Zhou
- Department of Radiotherapy Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
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21
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Yu N, Li J, Chen X, Wang Z, Kang X, Zhang R, Qin J, Zheng Q, Feng G, Deng L, Zhang T, Wang W, Liu W, Wang J, Feng Q, Lv J, Chen D, Zhou Z, Xiao Z, Li Y, Bi N, Li Y, Wang X. Chemoradiotherapy Combined with Nab-Paclitaxel plus Cisplatin in Patients with Locally Advanced Borderline Resectable or Unresectable Esophageal Squamous Cell Carcinoma: A Phase I/II Study. Int J Radiat Oncol Biol Phys 2023; 117:e354. [PMID: 37785224 DOI: 10.1016/j.ijrobp.2023.06.2433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) To evaluate the efficacy and safety of nanoparticle albumin-bound paclitaxel (nab-PTX) plus cisplatin as the regimen of conversional chemoradiotherapy (cCRT) in locally advanced borderline resectable or unresectable esophageal squamous cell carcinoma (ESCC). MATERIALS/METHODS Patients with locally advanced ESCC (cT3-4, Nany, M0-1, M1 was limited to lymph node metastasis in the supraclavicular area) were enrolled. All the patients received the cCRT of nab-PTX plus cisplatin. After the cCRT, those resectable patients received esophagectomy; those unresectable patients continued to receive the definitive chemoradiotherapy (dCRT). The locoregional control (LRC), overall survival (OS), progression-free survival (PFS), distant metastasis free survival (DMFS), pathological complete response (pCR), R0 resection rate and adverse events (AEs) were calculated. RESULTS A total of 45 patients with ESCC treated from October 2019 to May 2021 were finally included. The median follow-up time was 30.3 months. The LRC, OS, EFS, DMFS at 1and 2 years were 81.5%, 86.6%, 64.3%, 73.2% and 72.4%, 68.8%, 44.8%, 52.7% respectively. 21 patients (46.7%) received conversional chemoradiotherapy plus surgery (cCRT+S). The pCR rate and R0 resection rate were 47.6% and 84.0%. The LRC rate at 1 and 2 years were 95.0%, 87.1% in cCRT+S patients and 69.3%, 58.7% in dCRT patients respectively (HR, 5.14; 95% CI, 1.10-23.94; P = 0.021). The OS rate at 1 and 2 years were 95.2% and 84.2% in resectable patients compared to 78.8% and 54.4% in unresectable patients (HR, 3.41; 95% CI, 1.10-10.61; P = 0.024). The toxicities during chemoradiotherapy were tolerated, the most common grade 3-4 toxicities were radiation esophagitis (15.6%). CONCLUSION Nab-PTX plus cisplatin were effective and safe as the regimen of conversional chemoradiotherapy of ESCC. The patients receiving conversional chemoradiotherapy plus surgery (cCRT+S) were prone to have a better survival.
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Affiliation(s)
- N Yu
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - J Li
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - X Chen
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Z Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - X Kang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - R Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - J Qin
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Q Zheng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - G Feng
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - L Deng
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - T Zhang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing, China
| | - W Wang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - W Liu
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - J Wang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing, China
| | - Q Feng
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - J Lv
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - D Chen
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Z Zhou
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing, China
| | - Z Xiao
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Y Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - N Bi
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Y Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - X Wang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Behrens MM, Lein ES, Ecker JR, Ren B. Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex. bioRxiv 2023:2023.04.08.536119. [PMID: 37066152 PMCID: PMC10104177 DOI: 10.1101/2023.04.08.536119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Sequence divergence of cis- regulatory elements drives species-specific traits, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains to be elucidated. We investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset, and mouse with single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome, and chromosomal conformation profiles from a total of over 180,000 cells. For each modality, we determined species-specific, divergent, and conserved gene expression and epigenetic features at multiple levels. We find that cell type-specific gene expression evolves more rapidly than broadly expressed genes and that epigenetic status at distal candidate cis -regulatory elements (cCREs) evolves faster than promoters. Strikingly, transposable elements (TEs) contribute to nearly 80% of the human-specific cCREs in cortical cells. Through machine learning, we develop sequence-based predictors of cCREs in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Lastly, we show that epigenetic conservation combined with sequence similarity helps uncover functional cis -regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.
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23
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Zhang X, Feng G, Han H, Dong B, Yang Y, Zhu H, Fan S, Tang H. 39P Preliminary clinical investigations and mechanism exploration of furmonertinib in NSCLC with EGFR exon 20 insertion. J Thorac Oncol 2023. [DOI: 10.1016/s1556-0864(23)00293-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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24
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Fischer KB, Collins HK, Pang Y, Roy DS, Zhang Y, Feng G, Li SJ, Kepecs A, Callaway EM. Monosynaptic restriction of the anterograde herpes simplex virus strain H129 for neural circuit tracing. J Comp Neurol 2023; 531:584-595. [PMID: 36606699 PMCID: PMC10040246 DOI: 10.1002/cne.25451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 11/09/2022] [Accepted: 12/13/2022] [Indexed: 01/07/2023]
Abstract
Identification of synaptic partners is a fundamental task for systems neuroscience. To date, few reliable techniques exist for whole brain labeling of downstream synaptic partners in a cell-type-dependent and monosynaptic manner. Herein, we describe a novel monosynaptic anterograde tracing system based on the deletion of the gene UL6 from the genome of a cre-dependent version of the anterograde Herpes Simplex Virus 1 strain H129. Given that this knockout blocks viral genome packaging and thus viral spread, we reasoned that co-infection of a HSV H129 ΔUL6 virus with a recombinant adeno-associated virus expressing UL6 in a cre-dependent manner would result in monosynaptic spread from target cre-expressing neuronal populations. Application of this system to five nonreciprocal neural circuits resulted in labeling of neurons in expected projection areas. While some caveats may preclude certain applications, this system provides a reliable method to label postsynaptic partners in a brain-wide fashion.
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Affiliation(s)
- Kyle B Fischer
- Systems Neurobiology Laboratories, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Hannah K Collins
- Systems Neurobiology Laboratories, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Yan Pang
- Systems Neurobiology Laboratories, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Dheeraj S Roy
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ying Zhang
- Department of Brain and Cognitive Sciences, McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA
| | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Sciences, McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA
| | - Shu-Jing Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Adam Kepecs
- Departments of Neuroscience and Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Edward M Callaway
- Systems Neurobiology Laboratories, Salk Institute for Biological Studies, La Jolla, California, USA
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25
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He N, Feng G, Zhang FN, Hao S, Li R, Zhao ZQ, Tian YW, Yan HL. [Expression and clinical significance of plasma methylated SEPT 9 gene in patients with primary liver cancer]. Zhonghua Gan Zang Bing Za Zhi 2023; 31:265-270. [PMID: 37137852 DOI: 10.3760/cma.j.cn501113-20211114-00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Objective: To investigate the expression and clinical significance of plasma methylated SEPT9 (mSEPT9) gene in patients with primary liver cancer. Methods: 393 cases who visited our hospital from May 2016 to October 2018 were selected. Among them, 75 cases were in the primary liver cancer (PLC) group, 50 cases were in the liver cirrhosis (LC) group, and 268 cases were in the healthy control group (HC). The three groups' positive rates of mSEPT9 expression in the peripheral plasma were detected by the polymerase chain reaction (PCR) fluorescent probe method. The correlational clinical features of liver cancer were analyzed. At the same time, the electrochemiluminescence detection method was used to compare the AFP positive rate. Statistical analysis was conducted using chi-square tests or continuity-corrected chi-square tests. Results: 367 cases actually had valid samples. There were 64, 42, and 64 cases in the liver cancer group, cirrhosis group, and healthy control group, respectively. Among them, 34 cases of liver cancer were verified from pathological tissues. The positive rate of plasma mSEPT9 was significantly higher in the liver cancer group than that in the liver cirrhosis and healthy control groups [76.6% (49/64), 35.7% (15/42), and 3.8% (10/261), respectively], and the differences were statistically significant (χ (2) = 176.017, P < 0.001). The sensitivity of plasma mSEPT9 detection (76.6%) was significantly better in liver cancer (76.6%) than that of AFP patients (54.7%), and the difference was statistically significant (χ (2) = 6.788, P < 0.01). Compared with the single detection, the sensitivity and specificity of plasma mSEPT9 combined with AFP were significantly improved (89.7% vs. 96.3%, respectively). Patients with liver cancer aged≥50 years, with clinical stage II or above, and those with pathological signs of moderate to low differentiation had higher levels of plasma mSEPT9 positive expression, and the differences were statistically significant (χ (2) = 6.41, 9.279, 6.332, P < 0.05). During the follow-up period, the survival time of liver cancer patients with positive plasma mSEPT9 expression was significantly shorter than that of those with negative expression (310 ± 26 days vs. 487 ± 59 days, respectively), with statistically significant differences (Log Rank P = 0.039). Conclusion: In China, the positive rate of plasma mSEPT9 detection in liver cancer patients is higher than that of AFP in relation to age, clinical stage, and degree of tissue differentiation; additionally, it has certain survival predictive values. As a result, detecting this gene has important clinical significance and potential clinical application value in the non-invasive diagnosis and prognosis assessment of patients with primary liver cancer.
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Affiliation(s)
- N He
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Medical University, Xi 'an 710006, China
| | - G Feng
- Institute of General Medicine, Xi 'an Medical University, Xi'an 710077, China
| | - F N Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Medical University, Xi 'an 710006, China
| | - S Hao
- Xi 'an Medical College, Xi 'an 710077, China
| | - R Li
- Xi 'an Medical College, Xi 'an 710077, China
| | - Z Q Zhao
- Xi 'an Medical College, Xi 'an 710077, China
| | - Y W Tian
- Xi 'an Medical College, Xi 'an 710077, China
| | - H L Yan
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Medical University, Xi 'an 710006, China
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26
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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 2023:2023.03.07.531415. [PMID: 36945442 PMCID: PMC10028934 DOI: 10.1101/2023.03.07.531415] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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27
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Ding W, Fischer L, Chen Q, Li Z, Yang L, You Z, Hu K, Wu X, Zhou X, Chao W, Hu P, Dagnew TM, Dubreuil DM, Wang S, Xia S, Bao C, Zhu S, Chen L, Wang C, Wainger B, Jin P, Mao J, Feng G, Harnett MT, Shen S. Highly synchronized cortical circuit dynamics mediate spontaneous pain in mice. J Clin Invest 2023; 133:166408. [PMID: 36602876 PMCID: PMC9974100 DOI: 10.1172/jci166408] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
Cortical neural dynamics mediate information processing for the cerebral cortex, which is implicated in fundamental biological processes such as vision and olfaction, in addition to neurological and psychiatric diseases. Spontaneous pain is a key feature of human neuropathic pain. Whether spontaneous pain pushes the cortical network into an aberrant state and, if so, whether it can be brought back to a "normal" operating range to ameliorate pain are unknown. Using a clinically relevant mouse model of neuropathic pain with spontaneous pain-like behavior, we report that orofacial spontaneous pain activated a specific area within the primary somatosensory cortex (S1), displaying synchronized neural dynamics revealed by intravital two-photon calcium imaging. This synchronization was underpinned by local GABAergic interneuron hypoactivity. Pain-induced cortical synchronization could be attenuated by manipulating local S1 networks or clinically effective pain therapies. Specifically, both chemogenetic inhibition of pain-related c-Fos-expressing neurons and selective activation of GABAergic interneurons significantly attenuated S1 synchronization. Clinically effective pain therapies including carbamazepine and nerve root decompression could also dampen S1 synchronization. More important, restoring a "normal" range of neural dynamics through attenuation of pain-induced S1 synchronization alleviated pain-like behavior. These results suggest that spontaneous pain pushed the S1 regional network into a synchronized state, whereas reversal of this synchronization alleviated pain.
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Affiliation(s)
- Weihua Ding
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital (MGH), Harvard Medical School, Boston, Massachusetts, USA
| | - Lukas Fischer
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Qian Chen
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Liuyue Yang
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital (MGH), Harvard Medical School, Boston, Massachusetts, USA
| | - Zerong You
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital (MGH), Harvard Medical School, Boston, Massachusetts, USA
| | - Kun Hu
- Department of Pathology, Tufts University School of Medicine, Medford, Massachusetts, USA
| | - Xinbo Wu
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital (MGH), Harvard Medical School, Boston, Massachusetts, USA
| | - Xue Zhou
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital (MGH), Harvard Medical School, Boston, Massachusetts, USA
| | - Wei Chao
- Department of Anesthesiology, Center for Shock, Trauma and Anesthesiology Research, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Peter Hu
- Department of Anesthesiology, Center for Shock, Trauma and Anesthesiology Research, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Tewodros Mulugeta Dagnew
- MGH/HST Martinos Center for Biomedical Imaging, Department of Radiology, MGH, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel M. Dubreuil
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital (MGH), Harvard Medical School, Boston, Massachusetts, USA
| | - Shiyu Wang
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital (MGH), Harvard Medical School, Boston, Massachusetts, USA
| | - Suyun Xia
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital (MGH), Harvard Medical School, Boston, Massachusetts, USA
| | - Caroline Bao
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Shengmei Zhu
- Department of Anesthesiology, the First Affiliate Hospital of Zhejiang University, Hangzhou, China
| | - Lucy Chen
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital (MGH), Harvard Medical School, Boston, Massachusetts, USA
| | - Changning Wang
- MGH/HST Martinos Center for Biomedical Imaging, Department of Radiology, MGH, Harvard Medical School, Boston, Massachusetts, USA
| | - Brian Wainger
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital (MGH), Harvard Medical School, Boston, Massachusetts, USA
| | - Peng Jin
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Jianren Mao
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital (MGH), Harvard Medical School, Boston, Massachusetts, USA
| | - Guoping Feng
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mark T. Harnett
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Shiqian Shen
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital (MGH), Harvard Medical School, Boston, Massachusetts, USA
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28
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Wang T, Bai Y, Zheng X, Liu X, Xing S, Wang L, Wang H, Feng G, Li C. Sapap4 deficiency leads to postsynaptic defects and abnormal behaviors relevant to hyperkinetic neuropsychiatric disorder in mice. Cereb Cortex 2023; 33:1104-1118. [PMID: 35368073 DOI: 10.1093/cercor/bhac123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Postsynaptic proteins play critical roles in synaptic development, function, and plasticity. Dysfunction of postsynaptic proteins is strongly linked to neurodevelopmental and psychiatric disorders. SAP90/PSD95-associated protein 4 (SAPAP4; also known as DLGAP4) is a key component of the PSD95-SAPAP-SHANK excitatory postsynaptic scaffolding complex, which plays important roles at synapses. However, the exact function of the SAPAP4 protein in the brain is poorly understood. Here, we report that Sapap4 knockout (KO) mice have reduced spine density in the prefrontal cortex and abnormal compositions of key postsynaptic proteins in the postsynaptic density (PSD) including reduced PSD95, GluR1, and GluR2 as well as increased SHANK3. These synaptic defects are accompanied by a cluster of abnormal behaviors including hyperactivity, impulsivity, reduced despair/depression-like behavior, hypersensitivity to low dose of amphetamine, memory deficits, and decreased prepulse inhibition, which are reminiscent of mania. Furthermore, the hyperactivity of Sapap4 KO mice could be partially rescued by valproate, a mood stabilizer used for mania treatment in humans. Together, our findings provide evidence that SAPAP4 plays an important role at synapses and reinforce the view that dysfunction of the postsynaptic scaffolding protein SAPAP4 may contribute to the pathogenesis of hyperkinetic neuropsychiatric disorder.
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Affiliation(s)
- Tianhua Wang
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Yunxia Bai
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Xianjie Zheng
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Xinxia Liu
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Shuang Xing
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Linbin Wang
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Huimin Wang
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China.,NYU-ECNU Institute of Brain and Cognitive Science at NYU Shanghai, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 43 Vassar Street, Cambridge, Massachusetts, 02139, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, Massachusetts, 02142, USA
| | - Chunxia Li
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
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29
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Zhang X, Feng G, Han H, Dong B, Yang Y, Zhu H, Fan S, Tang H. 48P Efficacy analysis and mechanism exploration of furmonertinib for advanced NSCLC with EGFR exon 20 insertion mutation. ESMO Open 2023. [DOI: 10.1016/j.esmoop.2023.100906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
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30
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Zhang Y, Roy DS, Feng G. Finding pleasure in repetitive behaviors. Neuron 2022; 110:3225-3227. [DOI: 10.1016/j.neuron.2022.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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31
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Vormstein-Schneider D, Lin JD, Pelkey KA, Chittajallu R, Guo B, Arias-Garcia MA, Allaway K, Sakopoulos S, Schneider G, Stevenson O, Vergara J, Sharma J, Zhang Q, Franken TP, Smith J, Ibrahim LA, Mastro KJ, Sabri E, Huang S, Favuzzi E, Burbridge T, Xu Q, Guo L, Vogel I, Sanchez V, Saldi GA, Gorissen BL, Yuan X, Zaghloul KA, Devinsky O, Sabatini BL, Batista-Brito R, Reynolds J, Feng G, Fu Z, McBain CJ, Fishell G, Dimidschstein J. Publisher Correction: Viral manipulation of functionally distinct interneurons in mice, non-human primates and humans. Nat Neurosci 2022; 25:1247. [PMID: 35945454 DOI: 10.1038/s41593-022-01155-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Jessica D Lin
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kenneth A Pelkey
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Ramesh Chittajallu
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Baolin Guo
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mario A Arias-Garcia
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kathryn Allaway
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- NYU Langone Medical Center, New York University, New York, NY, USA
| | - Sofia Sakopoulos
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Gates Schneider
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Olivia Stevenson
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Josselyn Vergara
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jitendra Sharma
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Qiangge Zhang
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tom P Franken
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jared Smith
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Leena A Ibrahim
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Kevin J Mastro
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Ehsan Sabri
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Shuhan Huang
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Emilia Favuzzi
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Timothy Burbridge
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Qing Xu
- Center for Genomics & Systems Biology, New York University, Abu Dhabi, UAE
| | - Lihua Guo
- Center for Genomics & Systems Biology, New York University, Abu Dhabi, UAE
| | - Ian Vogel
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Vanessa Sanchez
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Giuseppe A Saldi
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Bram L Gorissen
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Xiaoqing Yuan
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Kareem A Zaghloul
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, New York University School of Medicine, New York, NY, USA
| | - Bernardo L Sabatini
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | | | - John Reynolds
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhanyan Fu
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Chris J McBain
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Gord Fishell
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Jordane Dimidschstein
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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32
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Zhang Y, Roy DS, Zhu Y, Chen Y, Aida T, Hou Y, Shen C, Lea NE, Schroeder ME, Skaggs KM, Sullivan HA, Fischer KB, Callaway EM, Wickersham IR, Dai J, Li XM, Lu Z, Feng G. Targeting thalamic circuits rescues motor and mood deficits in PD mice. Nature 2022; 607:321-329. [PMID: 35676479 PMCID: PMC9403858 DOI: 10.1038/s41586-022-04806-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/26/2022] [Indexed: 01/03/2023]
Abstract
Although bradykinesia, tremor and rigidity are the hallmark motor defects in patients with Parkinson's disease (PD), patients also experience motor learning impairments and non-motor symptoms such as depression1. The neural circuit basis for these different symptoms of PD are not well understood. Although current treatments are effective for locomotion deficits in PD2,3, therapeutic strategies targeting motor learning deficits and non-motor symptoms are lacking4-6. Here we found that distinct parafascicular (PF) thalamic subpopulations project to caudate putamen (CPu), subthalamic nucleus (STN) and nucleus accumbens (NAc). Whereas PF→CPu and PF→STN circuits are critical for locomotion and motor learning, respectively, inhibition of the PF→NAc circuit induced a depression-like state. Whereas chemogenetically manipulating CPu-projecting PF neurons led to a long-term restoration of locomotion, optogenetic long-term potentiation (LTP) at PF→STN synapses restored motor learning behaviour in an acute mouse model of PD. Furthermore, activation of NAc-projecting PF neurons rescued depression-like phenotypes. Further, we identified nicotinic acetylcholine receptors capable of modulating PF circuits to rescue different PD phenotypes. Thus, targeting PF thalamic circuits may be an effective strategy for treating motor and non-motor deficits in PD.
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Affiliation(s)
- Ying Zhang
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Dheeraj S. Roy
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,These authors contributed equally to this work
| | - Yi Zhu
- Center for Neuroscience and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yefei Chen
- Shenzhen Key Laboratory for Molecular Biology of Neural Development, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, China
| | - Tomomi Aida
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yuanyuan Hou
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chenjie Shen
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas E. Lea
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Margaret E. Schroeder
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Keith M. Skaggs
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Heather A. Sullivan
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kyle B. Fischer
- Systems Neurobiology Laboratories, Salk Institute for Biological Studies, La Jolla, CA, USA.,Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Edward M. Callaway
- Systems Neurobiology Laboratories, Salk Institute for Biological Studies, La Jolla, CA, USA.,Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Ian R. Wickersham
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ji Dai
- Shenzhen Key Laboratory for Molecular Biology of Neural Development, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, China
| | - Xiao-Ming Li
- Center for Neuroscience and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,NHC and CAMS Key Laboratory of Medical Neurobiology, Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong-Macao Greater Bay Area, Zhejiang University, Hangzhou, China.,Joint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou, China
| | - Zhonghua Lu
- Shenzhen Key Laboratory for Molecular Biology of Neural Development, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, China
| | - 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.
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33
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Zhao JF, Hao DF, Li T, Feng G. [Analysis of clinical features and treatment of pyoderma gangrenosum]. Zhonghua Shao Shang Yu Chuang Mian Xiu Fu Za Zhi 2022; 38:506-511. [PMID: 35764575 DOI: 10.3760/cma.j.cn501225-20220317-00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Objective: To explore the clinical features and treatment of pyoderma gangrenosum (PG). Methods: A retrospective observational study was conducted. From January 2012 to July 2021, 25 patients with PG who met the inclusion criteria were admitted to Beijing Fucheng Hospital, including 16 males and 9 females, with the age of onset of disease being 14 to 75 years. Among them, the classification of PG identified 17 cases of ulcerative type, 6 cases of pustular type, 1 case of proliferative type, and 1 case of bullous type. Six patients were accompanied with systemic diseases, while 19 patients were not accompanied with systemic diseases. At the same time of systemic treatment with glucocorticoids, dressing changes or surgical skin grafting was performed on the wounds. The results of laboratory and histopathological examinations, the overall curative effects and follow-up of patients, the wound healing time of patients with negative and positive microbial culture results of wound secretion specimens, and the curative effects of patients with and without systemic diseases were analyzed. Results: The results of blood routine examination of 19 patients were abnormal, and all the immunological indexes were normal in all the patients; the microbial culture results of wound secretion specimens were positive in 14 patients; and the histopathological examination results of ulcer boundary tissue in 15 patients with rapid wound progress were mainly local tissue inflammatory changes. The wounds were cured in 17 patients, mostly healed in 7 patients, and not healed in 1 patient. After one-year's follow-up, the PG in 3 patients relapsed due to self-discontinuation of medication after discharge, and the wounds were healed gradually after adjustment of medication, while the remaining patients had no relapse. The days of wound healing in 14 patients with positive microbial culture results of wound secretion specimens were 21-55 days, and the days of wound healing in 11 patients with negative microbial culture results in wound secretion specimens were 20-54 days. In the 6 patients with systemic diseases, the wounds of 3 patients were cured, and the wounds of the other 3 patients were mostly healed. In the 19 patients without systemic diseases, the wounds of 14 patients were cured, the wounds of 4 patients were mostly healed, and the wound of 1 patient was not healed. Conclusions: The laboratory examination and pathological manifestations of patients with PG lacks characteristics, and their clinical manifestations are rich and diverse, thus PG can be easily misdiagnosed. The glucocorticoids combined with immunosuppressive therapy have good effects on PG. Surgical intervention can be performed on the wounds. Specifically, excessive debridement is not recommended in the acute phase, but skin grafting can be performed in the contraction phase.
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Affiliation(s)
- J F Zhao
- Wound Repair and Reconstruction Center, Beijing Fucheng Hospital, Beijing 100143, China
| | - D F Hao
- Wound Repair and Reconstruction Center, Beijing Fucheng Hospital, Beijing 100143, China
| | - T Li
- Wound Repair and Reconstruction Center, Beijing Fucheng Hospital, Beijing 100143, China
| | - G Feng
- Wound Repair and Reconstruction Center, Beijing Fucheng Hospital, Beijing 100143, China
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34
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Yuan Y, Feng G, Yang J, Yang C, Tu YH. Polydatin alleviates osteoporosis by enhancing the osteogenic differentiation of osteoblasts. Eur Rev Med Pharmacol Sci 2022; 26:4392-4402. [PMID: 35776040 DOI: 10.26355/eurrev_202206_29078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE: Osteoporosis is a severe degenerative chronic metabolic bone disease associated with high fracture risk. Polydatin (PD), a major bioactive component of Polygonum cuspidatum, has antioxidant and anti-inflammatory effects. This study investigated the anti-osteoporotic activity of PD in ovariectomized (OVX) mice and elucidated its underlying molecular mechanisms. SUBJECTS AND METHODS: An osteoporosis mouse model was established using OVX mice. OVX mice were then administered 10 or 40 mg/kg of PD for 60 days. Micro-CT and three-point bending tests were used to determine the therapeutic activities of PD in OVX mice. H&E staining was used to determine whether PD induced hepatorenal toxicity. In addition, the cellular and molecular mechanisms underlying the functionality of PD were elucidated. RESULTS: Micro-CT results showed that compared to control mice, the bone mass of OVX mice was significantly reduced due to estrogen deficiency; however, PD administration significantly elevated bone mass. Furthermore, PD substantially improved the trabecular microstructure parameters of the femur and enhanced bone strength compared with OVX mice. Hepatorenal toxicity was not observed in liver and kidney samples stained with H&E. PD significantly increased the proliferation of pre-osteoblast MC3T3-E1 cells and upregulated the expression of osteogenic differentiation markers compared to those in controls, as determined by qRT-PCR and western blotting. CONCLUSIONS: PD exerted a significant anti-osteoporotic effect in OVX mice by promoting osteogenesis. PD has great potential as a therapeutic option for osteoporosis.
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Affiliation(s)
- Y Yuan
- School of Medicine, Tongji University, Shanghai, China.
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Yu X, Wang J, Hu Y, Sun Y, Zhao J, Yu Y, Hu C, Yang K, Feng G, Leaw S, Yuan Y, Lin X, Bai F, Lu S. 18P RATIONALE-307: Safety analysis of patients (pts) receiving tislelizumab (TIS) plus chemotherapy (chemo) vs chemo alone in advanced squamous (sq) NSCLC. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Lauer J, Zhou M, Ye S, Menegas W, Schneider S, Nath T, Rahman MM, Di Santo V, Soberanes D, Feng G, Murthy VN, Lauder G, Dulac C, Mathis MW, Mathis A. Multi-animal pose estimation, identification and tracking with DeepLabCut. Nat Methods 2022; 19:496-504. [PMID: 35414125 PMCID: PMC9007739 DOI: 10.1038/s41592-022-01443-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/04/2022] [Indexed: 11/23/2022]
Abstract
Estimating the pose of multiple animals is a challenging computer vision problem: frequent interactions cause occlusions and complicate the association of detected keypoints to the correct individuals, as well as having highly similar looking animals that interact more closely than in typical multi-human scenarios. To take up this challenge, we build on DeepLabCut, an open-source pose estimation toolbox, and provide high-performance animal assembly and tracking-features required for multi-animal scenarios. Furthermore, we integrate the ability to predict an animal's identity to assist tracking (in case of occlusions). We illustrate the power of this framework with four datasets varying in complexity, which we release to serve as a benchmark for future algorithm development.
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Affiliation(s)
- Jessy Lauer
- Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA
| | - Mu Zhou
- Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Shaokai Ye
- Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - William Menegas
- Department of Brain and Cognitive Sciences and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steffen Schneider
- Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Tanmay Nath
- Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA
| | - Mohammed Mostafizur Rahman
- Department for Molecular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute (HHMI), Chevy Chase, MD, USA
| | - Valentina Di Santo
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Daniel Soberanes
- Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA
| | - Guoping Feng
- Department of Brain and Cognitive Sciences and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Venkatesh N Murthy
- Department for Molecular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - George Lauder
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Catherine Dulac
- Department for Molecular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute (HHMI), Chevy Chase, MD, USA
| | - Mackenzie Weygandt Mathis
- Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA.
| | - Alexander Mathis
- Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA.
- Department for Molecular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA.
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Shama MBD, Yu B, Yang SJ, Wuniumo AR, Luo XX, Sun ZT, Feng ZH, Wang GAJ, Nengge TL, Li ZG, Wang J, Wang XY, Feng G, Yu KCN, Jike C. [Analysis on migration of HIV/AIDS cases and related factors in Liangshan Yi Autonomous Prefecture in Sichuan province, 2020]. Zhonghua Liu Xing Bing Xue Za Zhi 2022; 43:44-49. [PMID: 35130651 DOI: 10.3760/cma.j.cn112338-20210827-00686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Objective: To analyze the migration of the HIV/AIDS cases and related factors in Liangshan Yi autonomous prefecture (Liangshan). Methods: According to HIV/AIDS Comprehensive Response Information Management System of China Information System for Disease Control and Prevention, a total of 28 772 HIV/AIDS cases who had follow-up records in Liangshan in 2020 were included in the survey. The migration of the HIV/AIDS cases was described and the related factors were analyzed using multiple logistic regression models, and the migration destinations of the HIV/AIDS cases were mapped. Results: Among the 28 772 HIV/AIDS cases, 20.89% (6 010/28 772) had migration in 2020. Multivariate logistic regression analysis showed that among the HIV/AIDS cases, the migration related factors included being aged 15-24 years (compared with being aged 0-14 years, OR=2.74, 95%CI:2.04-3.69) and ethnic group (compared with Han ethnic group, OR=2.44, 95%CI:2.19-2.72), having education level of junior high school (compared with having education level of primary school or below, OR=1.25, 95%CI:1.14-1.38), being unmarried (compared with being married, OR=1.29, 95%CI:1.20-1.39), being engaged in business services (compared with being engaged in farming, OR=1.96, 95%CI:1.31-2.92), receiving antiviral treatment <1 year (compared with receiving antiviral treatment >3 years, OR=1.42, 95%CI:1.26-1.61), having recent CD4+T lymphocytes (CD4) counts >500 cells/μl (compared with having recent CD4 counts <200 cells/μl, OR=1.15, 95%CI:1.03-1.29). The geographical distribution maps showed that among all cities in Sichuan, Xichang (13.26%, 797/6 010) and Chengdu (10.12%,608/6 010) were the main migration destinations of the HIV/AIDS cases, and the provinces outside Sichuan where the HIV/AIDS cases would like to migrate to were mainly Guangdong (18.19%, 1 093/6 010) and Zhejiang provinces (7.67%, 461/6 010) in 2020. The HIV/AIDS cases who migrated where Liangshan, within Sichuan province, and to other provinces accounted for 27.67% (1 663/6 010), 15.34% (922/6 010) and 56.99% (3 425/6 010), respectively. Conclusions: More attention should be paid to the mobility characteristics and the classification management of HIV/AIDS cases according to their characteristics in Liangshan. Timely access to information on changes in the place of work and residence of HIV/AIDS cases should be warranted when they have migration. Good referrals and management for mobility of HIV/AIDS cases in different places should be made to reduce loss to follow-up and improving interventions.
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Affiliation(s)
- M B D Shama
- Department of HIV/AIDS Control and Prevention, Liangshan Yi Autonomous Prefecture Center for Disease Control and Prevention, Xichang 615000, China
| | - B Yu
- West China Second University Hospital/Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Sichuan University , Chengdu 610041, China
| | - S J Yang
- West China School of Public Health /West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - A R Wuniumo
- Department of HIV/AIDS Control and Prevention, Liangshan Yi Autonomous Prefecture Center for Disease Control and Prevention, Xichang 615000, China
| | - X X Luo
- Department of HIV/AIDS Control and Prevention, Liangshan Yi Autonomous Prefecture Center for Disease Control and Prevention, Xichang 615000, China
| | - Z T Sun
- Department of HIV/AIDS Control and Prevention, Liangshan Yi Autonomous Prefecture Center for Disease Control and Prevention, Xichang 615000, China
| | - Z H Feng
- West China School of Public Health /West China Fourth Hospital, Sichuan University, Chengdu 610041, China Institute for Disaster Management and Reconstruction, Sichuan University, Chengdu 610207, China
| | - G A J Wang
- West China School of Public Health /West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - T L Nengge
- Department of HIV/AIDS Control and Prevention, Liangshan Yi Autonomous Prefecture Center for Disease Control and Prevention, Xichang 615000, China
| | - Z G Li
- Department of HIV/AIDS Control and Prevention, Liangshan Yi Autonomous Prefecture Center for Disease Control and Prevention, Xichang 615000, China
| | - J Wang
- Department of HIV/AIDS Control and Prevention, Liangshan Yi Autonomous Prefecture Center for Disease Control and Prevention, Xichang 615000, China
| | - X Y Wang
- Department of HIV/AIDS Control and Prevention, Liangshan Yi Autonomous Prefecture Center for Disease Control and Prevention, Xichang 615000, China
| | - G Feng
- Department of HIV/AIDS Control and Prevention, Liangshan Yi Autonomous Prefecture Center for Disease Control and Prevention, Xichang 615000, China
| | - K C N Yu
- Department of HIV/AIDS Control and Prevention, Liangshan Yi Autonomous Prefecture Center for Disease Control and Prevention, Xichang 615000, China
| | - Chunnong Jike
- Department of HIV/AIDS Control and Prevention, Liangshan Yi Autonomous Prefecture Center for Disease Control and Prevention, Xichang 615000, China
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Song DJ, Li Z, Zhang YX, Zhou B, Lyu CL, Tang YY, Yi L, Luo ZH, Wang ZY, Hua ZZ, Feng G. [Clinical effects of transplantation of turbocharged bipedicle deep inferior epigastric perforator flap in breast reconstruction]. Zhonghua Shao Shang Za Zhi 2021; 37:1143-1148. [PMID: 34937154 DOI: 10.3760/cma.j.cn501120-20200824-00390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To explore the clinical effects of transplantation of turbocharged bipedicle deep inferior epigastric perforator (DIEP) flap in breast reconstruction. Methods: A retrospective observational study was used. From December 2008 to December 2016, 24 patients who met the inclusion criteria were treated in the Department of Plastic Surgery of Hunan Cancer Hospital, all patients were female, aged 28-51 (36.5±1.6) years. All cases received turbocharged bipedicle DIEP flap for two-staged breast reconstruction. According to the patterns of turbocharged vessels anastomosis, the turbocharged bipedicle DIEP flaps with length of (27.5±0.3) cm and width of (12.8±1.4) cm, were divided into three types: distal end of pedicle anastomosis type, main branch of pedicle anastomosis type, and muscular branch of pedicle anastomosis type. After complete hemostasis in the donor region, the anterior sheath was repaired with intermittent suture, and umbilical reconstruction was completed. Two negative pressure drainage tubes were indwelled, and subcutaneous tissue and skin were sutured layer by layer. The specific ways of vascular anastomosis of the flap pedicle with the internal thoracic vessels of recipient site included anastomosing the proximal end of one artery and one vein, anastomosing the proximal and distal end of one artery and one vein, and anastomosing the proximal end of one artery and two veins. Postoperatively, the survival and blood supply of flaps were observed. The patients were followed up to observe the reconstructed breast shape satisfaction, donor site complications, abdominal wall function, and scar hyperplasia. Results: All turbocharged bipedicle DIEP flaps for two-staged breast reconstruction survived well, with good blood supply. During follow-up for 14 to 56 (20±6) months, the shape of reconstructed breasts was satisfied. Only linear scar was left in the donor sites of abdomen with no complications, and the function of abdominal wall was not affected. Conclusions: For patients with clear indications, transplantation of free turbocharged bipedicle DIEP flap is a safe, reliable, and satisfactory choice for breast reconstruction with autologous tissue.
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Affiliation(s)
- D J Song
- Department of Plastic Surgery, Hunan Cancer Hospital, Changsha 410008, China
| | - Z Li
- Department of Plastic Surgery, Hunan Cancer Hospital, Changsha 410008, China
| | - Y X Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - B Zhou
- Department of Plastic Surgery, Hunan Cancer Hospital, Changsha 410008, China
| | - C L Lyu
- Department of Plastic Surgery, Hunan Cancer Hospital, Changsha 410008, China
| | - Y Y Tang
- Department of Plastic Surgery, Hunan Cancer Hospital, Changsha 410008, China
| | - L Yi
- Department of Plastic Surgery, Hunan Cancer Hospital, Changsha 410008, China
| | - Z H Luo
- Department of Plastic Surgery, Hunan Cancer Hospital, Changsha 410008, China
| | - Z Y Wang
- Ultrasonic Diagnosis Center, Hunan Cancer Hospital, Changsha 410008, China
| | - Z Z Hua
- Department of Plastic and Reconstructive Surgery, Shanghai Electric Power Hospital, Shanghai 200050, China
| | - G Feng
- Rehabilitation and Reconstruction Center, Beijing Fucheng Hospital, Beijing 100048, China
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Yang H, Puts M, Breunis H, Feng G, Parthipan M, Fleshner N, Cameron J, Alibhai S. Family Caregivers Of Older Adults With Metastatic Prostate Cancer: A Qualitative Exploration Of The Caregiving Experience. J Geriatr Oncol 2021. [DOI: 10.1016/s1879-4068(21)00387-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Donison V, Feng G, Parthipan M, Toledano N, Breunis H, Emmenegger U, Soto-Perez-de-Celis E, Matthew A, Alibhai S, Puts M. Symptom experiences of older men undergoing hormonal treatment for metastatic castrate resistant prostate cancer (mCRPC). J Geriatr Oncol 2021. [DOI: 10.1016/s1879-4068(21)00389-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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41
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Zhou T, Yang Y, Ma S, Lin L, Zhou T, Zhang C, Ding X, Wang R, Feng G, Chen Y, Xu R, Huang Y, Zhang L. Bevacizumab versus placebo in combination with paclitaxel and carboplatin as first-line treatment for recurrent or metastatic nasopharyngeal carcinoma: a multicentre, randomised, open-label, phase II trial. ESMO Open 2021; 6:100313. [PMID: 34837744 PMCID: PMC8637468 DOI: 10.1016/j.esmoop.2021.100313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The value of anti-angiogenesis antibody therapy in recurrent or metastatic nasopharyngeal carcinoma (R/M NPC) remains unknown. We carried out a phase II study to evaluate the addition of bevacizumab to paclitaxel plus carboplatin in R/M NPC. MATERIALS AND METHODS A total of 80 patients with previously untreated R/M NPC were randomly assigned (1 : 1) to CPB or CP groups to receive carboplatin (area under the curve 6) and paclitaxel (175 mg/m2) intravenously every 3 weeks for a maximum of six cycles in combination with or without bevacizumab (7.5 mg/kg), respectively. The primary endpoint was progression-free survival (PFS) as per investigators, and the secondary endpoints were PFS as per independent review committee (IRC), overall survival (OS), objective response rate (ORR), and safety. This study was registered with ClinicalTrials.gov (NCT02250599). RESULTS The median PFS as per investigators was 7.5 months [95% confidence interval (CI), 6.53-8.45 months] in the CPB group and 6.5 months (95% CI, 5.53-7.52 months) in the CP group (P = 0.148), which were similar to IRC-assessed PFS. The median OS was also alike between CPB and CP arms (21.0 versus 24.7 months; P = 0.326). ORRs were 87.2% and 72.5%, respectively (P = 0.105). However, the tumor-shrinking rate was higher in the CPB arm than in the CP arm (P = 0.035). No differences in grade 3 or higher adverse events between the groups were observed. CONCLUSIONS Addition of bevacizumab to paclitaxel plus carboplatin as first-line treatment did not prolong PFS and OS in patients with R/M NPC but improved tumor-shrinking rate. These results indicated that bevacizumab plus chemotherapy might be an optional choice for NPC with heavy tumor load or those pursuing short-term efficacy in neoadjuvant and concurrent chemotherapy.
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Affiliation(s)
- T Zhou
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China; State Key Laboratory of Oncology in South China, Guangzhou, China; Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Y Yang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China; State Key Laboratory of Oncology in South China, Guangzhou, China; Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - S Ma
- Department of Internal Medicine, Henan Cancer Hospital, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - L Lin
- Department of Medical Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - T Zhou
- Department of Radiotherapy, Cancer Center of Guangzhou Medical University, Guangzhou, China
| | - C Zhang
- Department of Radiotherapy, Dongguan People's Hospital, Dongguan, Guangdong, China
| | - X Ding
- Department of Medical Oncology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, Guangdong, China
| | - R Wang
- Department of Radiotherapy, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - G Feng
- Department of Medical Oncology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Y Chen
- Department of Medical Oncology, Hainan General Hospital, Hainan, China
| | - R Xu
- Department of Medical Oncology, Shenzhen People's Hospital, Shenzhen, China
| | - Y Huang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China; State Key Laboratory of Oncology in South China, Guangzhou, China; Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
| | - L Zhang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China; State Key Laboratory of Oncology in South China, Guangzhou, China; Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
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He N, Hao S, Feng G, Gao J, Kong FJ, Ren ZX, Xu MQ, Yang YQ. [Analysis of the factors influencing the elimination strategies with the current status of diagnosis and treatment of hepatitis C in hospital]. Zhonghua Gan Zang Bing Za Zhi 2021; 29:1053-1058. [PMID: 34933422 DOI: 10.3760/cma.j.cn501113-20210119-00034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Objective: To understand the current status of screening, diagnosis, and treatment and analyze the factors influencing micro-elimination strategy, so as to achieve hepatitis C elimination in hospital. Methods: Anti-HCV and HCV RNA test results of patients from October 2017 to September 2020 were retrospectively analyzed. Anti-HCV positive rates and factors influencing different genders, ages, places of residence and departments were analyzed. After comparing anti-HCV-positive patients with HCV RNA-positive patients with duplicate entries in "Name" and "Date of birth", the data were divided into three categories: anti-HCV positive without HCV RNA test, HCV RNA positive in single test, and HCV RNA positive many times in multiple tests. The above three types of patients were followed-up by telephone. According to the hospital follow-up results, current status of diagnosis and treatment and the factors influencing the micro-elimination strategy of hepatitis C were studied and analyzed. The comparison of data between groups were performed using χ(2) or χ(2) continuity-correction test. Results: Anti-HCV positive detection rate was 1.34% (899/66 866). The positive rate of male patients aged 40 and over residing in cities was significantly higher than female patients under 40 years old residing in rural areas, and the difference was statistically significant (χ(2) = 55.178, 264.11, 36, 351, P < 0.05). There were 90 (10.02%) and 809 cases (89.98%) in outpatient and inpatient departments, respectively, with no statistically significant difference between the two (χ(2) = 0.002, P > 0.05). The total number of anti-HCV positive cases were 196 in Gastroenterology (22.0%), 75 in Respiratory and Critical Care Medicine (8.3%), 74 in Neurology (8.2%), 63 in Orthopedics (7.0%) and 55 in Endocrinology departments (6.1%), and the difference in the positive rate among different departments were also statistically significant (χ(2) = 271.585, P < 0.05). Among the 480 cases who were followed-up, 215 (44.79%) were lost to follow-up, 84 cases (39.07%) were unregistered, 77 cases (16.04%) were untreated, 15 cases (19.48%) were unaware of their state of illness, 46 cases (59.74%) were diagnosed without concern, 16 cases (20.78%) were diagnosed but did not take medicine, 60 cases were under treatment, and 29 cases were mostly on counterfeit drugs (48.33%). Conclusion: Comprehensive diagnosis and treatment education to non-specialist clinicians and timely manner regular follow-up of patients is a key factor and an important link to formulate a simple, easy and sustainable model to improve the efficiency of screening, diagnosis, and treatment of hepatitis C micro-elimination strategy in hospital. In addition, it will also play an important role in achieving the strategic goal of "eliminating hepatitis C as a public health threat by 2030".
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Affiliation(s)
- N He
- Department of Gastroenteology, The First Affiliated Hospital of Xi 'an Medical University, Xi 'an 710006, China
| | - S Hao
- Xi 'an Medical University, Xi 'an 710077, China
| | - G Feng
- Institute of General Practice, Xi 'an Medical University, Xi 'an 710077, China
| | - J Gao
- Clinical Laboratory, The First Affiliated Hospital of Xi 'an Medical University, Xi 'an 710006, China
| | - F J Kong
- Xi 'an Medical University, Xi 'an 710077, China
| | - Z X Ren
- Xi 'an Medical University, Xi 'an 710077, China
| | - M Q Xu
- Xi 'an Medical University, Xi 'an 710077, China
| | - Y Q Yang
- Department of Gastroenteology, The First Affiliated Hospital of Xi 'an Medical University, Xi 'an 710006, China
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Park J, Khan S, Yun DH, Ku T, Villa KL, Lee JE, Zhang Q, Park J, Feng G, Nedivi E, Chung K. Epitope-preserving magnified analysis of proteome (eMAP). Sci Adv 2021; 7:eabf6589. [PMID: 34767453 PMCID: PMC8589305 DOI: 10.1126/sciadv.abf6589] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 09/24/2021] [Indexed: 05/28/2023]
Abstract
Synthetic tissue-hydrogel methods have enabled superresolution investigation of biological systems using diffraction-limited microscopy. However, chemical modification by fixatives can cause loss of antigenicity, limiting molecular interrogation of the tissue gel. Here, we present epitope-preserving magnified analysis of proteome (eMAP) that uses purely physical tissue-gel hybridization to minimize the loss of antigenicity while allowing permanent anchoring of biomolecules. We achieved success rates of 96% and 94% with synaptic antibodies for mouse and marmoset brains, respectively. Maximal preservation of antigenicity allows imaging of nanoscopic architectures in 1000-fold expanded tissues without additional signal amplification. eMAP-processed tissue gel can endure repeated staining and destaining without epitope loss or structural damage, enabling highly multiplexed proteomic analysis. We demonstrated the utility of eMAP as a nanoscopic proteomic interrogation tool by investigating molecular heterogeneity in inhibitory synapses in the mouse brain neocortex and characterizing the spatial distributions of synaptic proteins within synapses in mouse and marmoset brains.
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Affiliation(s)
- Joha Park
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
| | - Sarim Khan
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Department of Chemical Engineering, Indian Institute of Technology (IIT), Roorkee, Uttarakhand 247667, India
| | - Dae Hee Yun
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Taeyun Ku
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
| | - Katherine L. Villa
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Jiachen E. Lee
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Qiangge Zhang
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Juhyuk Park
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
- Department of Chemical Engineering, MIT, Cambridge, MA 02142, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
| | - Guoping Feng
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Elly Nedivi
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
- Department of Chemical Engineering, MIT, Cambridge, MA 02142, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
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Gao F, Yang Y, Zhu H, Wang J, Xiao D, Zhou Z, Dai T, Zhang Y, Feng G, Li J, Lin B, Xie G, Ke Q, Zhou K, Li P, Sheng X, Wang H, Yan L, Lao C, Shan L, Li M, Lu Y, Chen M, Feng S, Zhao J, Wu D, Du X. First Demonstration of the FLASH Effect With Ultrahigh Dose-Rate High-Energy X-Rays. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Yanny AM, Zhang R, Ament SA, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preissl S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, Zeng H, Zhang K, Feng G, Ecker JR, Linnarsson S, Lein ES. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature 2021; 598:111-119. [PMID: 34616062 PMCID: PMC8494640 DOI: 10.1038/s41586-021-03465-8] [Citation(s) in RCA: 258] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 03/17/2021] [Indexed: 12/11/2022]
Abstract
The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch-seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.
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Affiliation(s)
| | | | - Qiwen Hu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Blue B Lake
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Wei Tian
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Brian E Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Megan Crow
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Fenna M Krienen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Jeroen Eggermont
- LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Andrew I Aldridge
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | - Rosa G Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nikolai Dembrow
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
- Epilepsy Center of Excellence, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Dinh Diep
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | | | - Weixiu Dong
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Rongxin Fang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Stephan Fischer
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Melissa Goldman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Brian R Herb
- Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Xiaomeng Hou
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jayaram Kancherla
- Department of Computer Science, University of Maryland College Park, College Park, MD, USA
| | | | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Baldur van Lew
- LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Yang Eric Li
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Christine S Liu
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Biomedical Sciences Program, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Anup Mahurkar
- Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | | | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Sheng-Yong Niu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Computer Science and Engineering Program, University of California, San Diego, La Jolla, CA, USA
| | - Joshua Orvis
- Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Julia K Osteen
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Scott Owen
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Carter R Palmer
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Biomedical Sciences Program, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Thanh Pham
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nongluk Plongthongkum
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivier Poirion
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nora M Reed
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Angeline Rivkin
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - William J Romanow
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Kimberly Siletti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Xinxin Wang
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Fangming Xie
- Department of Physics, University of California, San Diego, La Jolla, CA, USA
| | | | - Renee Zhang
- J. Craig Venter Institute, La Jolla, CA, USA
| | - Seth A Ament
- Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Hector Corrada Bravo
- Department of Computer Science, University of Maryland College Park, College Park, MD, USA
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Ronna Hertzano
- Departments of Otorhinolaryngology, Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Höllt
- Computer Graphics and Visualization Group, Delt University of Technology, Delft, The Netherlands
| | - Gregory D Horwitz
- Department of Physiology and Biophysics, Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA
- Regional Epilepsy Center, Harborview Medical Center, Seattle, WA, USA
| | - Boudewijn P Lelieveldt
- LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Pattern Recognition and Bioinformatics group, Delft University of Technology, Delft, The Netherlands
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA
| | | | - Sebastian Preissl
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bing Ren
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pathology, University of California, San Diego, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - William J Spain
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
- Epilepsy Center of Excellence, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Owen R White
- Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | | | | | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
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Callaway EM, Dong HW, Ecker JR, Hawrylycz MJ, Huang ZJ, Lein ES, Ngai J, Osten P, Ren B, Tolias AS, White O, Zeng H, Zhuang X, Ascoli GA, Behrens MM, Chun J, Feng G, Gee JC, Ghosh SS, Halchenko YO, Hertzano R, Lim BK, Martone ME, Ng L, Pachter L, Ropelewski AJ, Tickle TL, Yang XW, Zhang K, Bakken TE, Berens P, Daigle TL, Harris JA, Jorstad NL, Kalmbach BE, Kobak D, Li YE, Liu H, Matho KS, Mukamel EA, Naeemi M, Scala F, Tan P, Ting JT, Xie F, Zhang M, Zhang Z, Zhou J, Zingg B, Armand E, Yao Z, Bertagnolli D, Casper T, Crichton K, Dee N, Diep D, Ding SL, Dong W, Dougherty EL, Fong O, Goldman M, Goldy J, Hodge RD, Hu L, Keene CD, Krienen FM, Kroll M, Lake BB, Lathia K, Linnarsson S, Liu CS, Macosko EZ, McCarroll SA, McMillen D, Nadaf NM, Nguyen TN, Palmer CR, Pham T, Plongthongkum N, Reed NM, Regev A, Rimorin C, Romanow WJ, Savoia S, Siletti K, Smith K, Sulc J, Tasic B, Tieu M, Torkelson A, Tung H, van Velthoven CTJ, Vanderburg CR, Yanny AM, Fang R, Hou X, Lucero JD, Osteen JK, Pinto-Duarte A, Poirion O, Preissl S, Wang X, Aldridge AI, Bartlett A, Boggeman L, O’Connor C, Castanon RG, Chen H, Fitzpatrick C, Luo C, Nery JR, Nunn M, Rivkin AC, Tian W, Dominguez B, Ito-Cole T, Jacobs M, Jin X, Lee CT, Lee KF, Miyazaki PA, Pang Y, Rashid M, Smith JB, Vu M, Williams E, Biancalani T, Booeshaghi AS, Crow M, Dudoit S, Fischer S, Gillis J, Hu Q, Kharchenko PV, Niu SY, Ntranos V, Purdom E, Risso D, de Bézieux HR, Somasundaram S, Street K, Svensson V, Vaishnav ED, Van den Berge K, Welch JD, An X, Bateup HS, Bowman I, Chance RK, Foster NN, Galbavy W, Gong H, Gou L, Hatfield JT, Hintiryan H, Hirokawa KE, Kim G, Kramer DJ, Li A, Li X, Luo Q, Muñoz-Castañeda R, Stafford DA, Feng Z, Jia X, Jiang S, Jiang T, Kuang X, Larsen R, Lesnar P, Li Y, Li Y, Liu L, Peng H, Qu L, Ren M, Ruan Z, Shen E, Song Y, Wakeman W, Wang P, Wang Y, Wang Y, Yin L, Yuan J, Zhao S, Zhao X, Narasimhan A, Palaniswamy R, Banerjee S, Ding L, Huilgol D, Huo B, Kuo HC, Laturnus S, Li X, Mitra PP, Mizrachi J, Wang Q, Xie P, Xiong F, Yu Y, Eichhorn SW, Berg J, Bernabucci M, Bernaerts Y, Cadwell CR, Castro JR, Dalley R, Hartmanis L, Horwitz GD, Jiang X, Ko AL, Miranda E, Mulherkar S, Nicovich PR, Owen SF, Sandberg R, Sorensen SA, Tan ZH, Allen S, Hockemeyer D, Lee AY, Veldman MB, Adkins RS, Ament SA, Bravo HC, Carter R, Chatterjee A, Colantuoni C, Crabtree J, Creasy H, Felix V, Giglio M, Herb BR, Kancherla J, Mahurkar A, McCracken C, Nickel L, Olley D, Orvis J, Schor M, Hood G, Dichter B, Grauer M, Helba B, Bandrowski A, Barkas N, Carlin B, D’Orazi FD, Degatano K, Gillespie TH, Khajouei F, Konwar K, Thompson C, Kelly K, Mok S, Sunkin S. A multimodal cell census and atlas of the mammalian primary motor cortex. Nature 2021; 598:86-102. [PMID: 34616075 PMCID: PMC8494634 DOI: 10.1038/s41586-021-03950-0] [Citation(s) in RCA: 205] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 08/25/2021] [Indexed: 12/14/2022]
Abstract
Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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Lu S, Yu X, Wang J, Zhao J, Yu Y, Hu C, Feng G, Ying K, Zhuang W, Zhou J, Wu J, Leaw S, Bai F, Lin X. P17.02 RATIONALE 307: A Subgroup Analysis of Tislelizumab Plus Chemo vs Chemo Alone As 1L Treatment for Stage IIIB Advanced Sq NSCLC. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Yu X, Wang J, Lu S, Zhao J, Yu Y, Hu C, Feng G, Ying K, Zhuang W, Zhou J, Wu J, Leaw S, Lin X, Zhang J. 1297P RATIONALE 307: Tislelizumab (TIS) plus chemotherapy (chemo) vs chemo alone as first-line (1L) treatment for advanced squamous non-small cell lung cancer (sq NSCLC) in patients (pts) who were smokers vs non-smokers. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Wilde JJ, Aida T, Del Rosario RCH, Kaiser T, Qi P, Wienisch M, Zhang Q, Colvin S, Feng G. Efficient embryonic homozygous gene conversion via RAD51-enhanced interhomolog repair. Cell 2021; 184:3267-3280.e18. [PMID: 34043941 PMCID: PMC8240950 DOI: 10.1016/j.cell.2021.04.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 03/03/2021] [Accepted: 04/19/2021] [Indexed: 12/20/2022]
Abstract
Searching for factors to improve knockin efficiency for therapeutic applications, biotechnology, and generation of non-human primate models of disease, we found that the strand exchange protein RAD51 can significantly increase Cas9-mediated homozygous knockin in mouse embryos through an interhomolog repair (IHR) mechanism. IHR is a hallmark of meiosis but only occurs at low frequencies in somatic cells, and its occurrence in zygotes is controversial. Using multiple approaches, we provide evidence for an endogenous IHR mechanism in the early embryo that can be enhanced by RAD51. This process can be harnessed to generate homozygotes from wild-type zygotes using exogenous donors and to convert heterozygous alleles into homozygous alleles without exogenous templates. Furthermore, we identify additional IHR-promoting factors and describe features of IHR events. Together, our findings show conclusive evidence for IHR in mouse embryos and describe an efficient method for enhanced gene conversion.
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Affiliation(s)
- Jonathan J Wilde
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
| | - Tomomi Aida
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Ricardo C H Del Rosario
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tobias Kaiser
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Peimin Qi
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Martin Wienisch
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Qiangge Zhang
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Steven Colvin
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Guoping Feng
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Liang YJ, Feng G, Zhang X, Li JX, Jiang Y. Erratum to: BIS(PYRIDYL) ANCILLARY LIGANDS AND PYRAZINE SULFONIC ACID IN THE SYNTHESIS OF TWO Ag(I) SUPRAMOLECULAR STRUCTURES AND FLUORESCENT PROPERTIES OF THE LATTER. J STRUCT CHEM+ 2021. [DOI: 10.1134/s0022476621040193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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