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Sziraki A, Lu Z, Lee J, Banyai G, Anderson S, Abdulraouf A, Metzner E, Liao A, Banfelder J, Epstein A, Schaefer C, Xu Z, Zhang Z, Gan L, Nelson PT, Zhou W, Cao J. A global view of aging and Alzheimer's pathogenesis-associated cell population dynamics and molecular signatures in human and mouse brains. Nat Genet 2023; 55:2104-2116. [PMID: 38036784 PMCID: PMC10703679 DOI: 10.1038/s41588-023-01572-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
Conventional methods fall short in unraveling the dynamics of rare cell types related to aging and diseases. Here we introduce EasySci, an advanced single-cell combinatorial indexing strategy for exploring age-dependent cellular dynamics in the mammalian brain. Profiling approximately 1.5 million single-cell transcriptomes and 400,000 chromatin accessibility profiles across diverse mouse brains, we identified over 300 cell subtypes, uncovering their molecular characteristics and spatial locations. This comprehensive view elucidates rare cell types expanded or depleted upon aging. We also investigated cell-type-specific responses to genetic alterations linked to Alzheimer's disease, identifying associated rare cell types. Additionally, by profiling 118,240 human brain single-cell transcriptomes, we discerned cell- and region-specific transcriptomic changes tied to Alzheimer's pathogenesis. In conclusion, this research offers a valuable resource for probing cell-type-specific dynamics in both normal and pathological aging.
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Affiliation(s)
- Andras Sziraki
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Ziyu Lu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Jasper Lee
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Gabor Banyai
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Sonya Anderson
- Department of Pathology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Abdulraouf Abdulraouf
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Eli Metzner
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The Tri-Institutional PhD Program in Computational Biology and Medicine, New York, NY, USA
| | - Andrew Liao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Jason Banfelder
- High Performance Computing Resource Center, The Rockefeller University, New York, NY, USA
| | - Alexander Epstein
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Chloe Schaefer
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Zihan Xu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Zehao Zhang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Li Gan
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Peter T Nelson
- Department of Pathology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Wei Zhou
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
| | - Junyue Cao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
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Bandyopadhyay S, Gurjar D, Saha B, Bodhale N. Decoding the contextual duality of CD40 functions. Hum Immunol 2023; 84:590-599. [PMID: 37596136 DOI: 10.1016/j.humimm.2023.08.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/13/2023] [Accepted: 08/11/2023] [Indexed: 08/20/2023]
Abstract
Previously, we established that as a function of its mode of interaction with its ligand or cellular conditions such as membrane lipids, preexisting signaling intermediates activation status, a transmembrane receptor, as represented here with CD40, can induce counteractive cellular responses. Using CD40-binding peptides, recombinant mutated CD40-ligands, and an agonistic antibody, we have established the functional duality of CD40. CD40 builds up two constitutionally different signalosomes on lipid raft and non-raft membrane domains initiating two different signaling pathways. Although this initial signaling may be modified by the pre-existing signaling conditions downstream and may be subjected to feed-forward or negative signaling effects, the initial CD40-CD40L interaction plays a crucial role in the functional outcome of CD40. Herein, we have reviewed the influence of interaction between the CD40-CD40L evoking the functional duality of CD40 contingent upon different physiological states of the cells.
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Affiliation(s)
| | - Dhiraj Gurjar
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Bhaskar Saha
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Neelam Bodhale
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
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Halim NFAA, Ali MSM, Leow ATC, Rahman RNZRA. Membrane fatty acid desaturase: biosynthesis, mechanism, and architecture. Appl Microbiol Biotechnol 2022; 106:5957-5972. [PMID: 36063178 DOI: 10.1007/s00253-022-12142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/25/2022]
Abstract
Fatty acid desaturase catalyzes the desaturation reactions by inserting double bonds into the fatty acyl chain, producing unsaturated fatty acids, which play a vital part in the synthesis of polyunsaturated fatty acids. Though soluble fatty acid desaturases have been described extensively in advanced organisms, there are very limited studies of membrane fatty acid desaturases due to their difficulties in producing a sufficient amount of recombinant desaturases. However, the advancement of technology has shown substantial progress towards the development of elucidating crystal structures of membrane fatty acid desaturase, thus, allowing modification of structure to be manipulated. Understanding the structure, mechanism, and biosynthesis of fatty acid desaturase lay a foundation for the potential production of various strategies associated with alteration and modifications of polyunsaturated fatty acids. This manuscript presents the current state of knowledge and understanding about the structure, mechanisms, and biosynthesis of fatty acid desaturase. In addition, the role of unsaturated fatty acid desaturases in health and diseases is also encompassed. This will be useful in understanding the molecular basis and structural protein of fatty acid desaturase that are significant for the advancement of therapeutic strategies associated with the improvement of health status. KEY POINTS: • Current state of knowledge and understanding about the biosynthesis, mechanisms, and structure of fatty acid desaturase. • The role of unsaturated fatty acid desaturase. • The molecular basis and structural protein elucidated the crystal structure of fatty acid desaturase.
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Affiliation(s)
- Nur Farah Anis Abd Halim
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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Qian N, Li S, Tan X. The curious case of TMEM120A: Mechanosensor, fat regulator, or antiviral defender? Bioessays 2022; 44:e2200045. [PMID: 35419854 DOI: 10.1002/bies.202200045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 11/06/2022]
Abstract
Mechanical pain sensing, adipogenesis, and STING-dependent innate immunity seem three distinct biological processes without substantial relationships. Intriguingly, TMEM120A, a transmembrane protein, has been shown to detect mechanical pain stimuli as a mechanosensitive channel, contribute to adipocyte differentiation/function by regulating genome organization and promote STING trafficking to active cellular innate immune response. However, the role of TMEM120A as a mechanosensitive channel was challenged by recent studies which cannot reproduce data supporting its role in mechanosensing. Furthermore, the molecular mechanism by which TMEM120A contributes to adipocyte differentiation/function and promotes STING trafficking remains elusive. In this review, we discuss these multiple proposed functions of TMEM120A and hypothesize the molecular mechanism underlying TMEM120A's role in fatty acid metabolism and STING signaling.
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Affiliation(s)
- Nianchao Qian
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Shuo Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Xu Tan
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China.,Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
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