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Fu T, Amoah K, Chan TW, Bahn JH, Lee JH, Terrazas S, Chong R, Kosuri S, Xiao X. Massively parallel screen uncovers many rare 3' UTR variants regulating mRNA abundance of cancer driver genes. Nat Commun 2024; 15:3335. [PMID: 38637555 PMCID: PMC11026479 DOI: 10.1038/s41467-024-46795-7] [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: 05/01/2023] [Accepted: 03/06/2024] [Indexed: 04/20/2024] Open
Abstract
Understanding the function of rare non-coding variants represents a significant challenge. Using MapUTR, a screening method, we studied the function of rare 3' UTR variants affecting mRNA abundance post-transcriptionally. Among 17,301 rare gnomAD variants, an average of 24.5% were functional, with 70% in cancer-related genes, many in critical cancer pathways. This observation motivated an interrogation of 11,929 somatic mutations, uncovering 3928 (33%) functional mutations in 155 cancer driver genes. Functional MapUTR variants were enriched in microRNA- or protein-binding sites and may underlie outlier gene expression in tumors. Further, we introduce untranslated tumor mutational burden (uTMB), a metric reflecting the amount of somatic functional MapUTR variants of a tumor and show its potential in predicting patient survival. Through prime editing, we characterized three variants in cancer-relevant genes (MFN2, FOSL2, and IRAK1), demonstrating their cancer-driving potential. Our study elucidates the function of tens of thousands of non-coding variants, nominates non-coding cancer driver mutations, and demonstrates their potential contributions to cancer.
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Affiliation(s)
- Ting Fu
- Molecular, Cellular and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Kofi Amoah
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Tracey W Chan
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jae Hoon Bahn
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jae-Hyung Lee
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Life and Nanopharmaceutical Sciences & Oral Microbiology, School of Dentistry, Kyung Hee University, Seoul, South Korea
| | - Sari Terrazas
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Rockie Chong
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Xinshu Xiao
- Molecular, Cellular and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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2
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Vergani-Junior CA, Moro RDP, Pinto S, De-Souza EA, Camara H, Braga DL, Tonon-da-Silva G, Knittel TL, Ruiz GP, Ludwig RG, Massirer KB, Mair WB, Mori MA. An Intricate Network Involving the Argonaute ALG-1 Modulates Organismal Resistance to Oxidative Stress. Nat Commun 2024; 15:3070. [PMID: 38594249 PMCID: PMC11003958 DOI: 10.1038/s41467-024-47306-4] [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: 08/01/2023] [Accepted: 03/24/2024] [Indexed: 04/11/2024] Open
Abstract
Cellular response to redox imbalance is crucial for organismal health. microRNAs are implicated in stress responses. ALG-1, the C. elegans ortholog of human AGO2, plays an essential role in microRNA processing and function. Here we investigated the mechanisms governing ALG-1 expression in C. elegans and the players controlling lifespan and stress resistance downstream of ALG-1. We show that upregulation of ALG-1 is a shared feature in conditions linked to increased longevity (e.g., germline-deficient glp-1 mutants). ALG-1 knockdown reduces lifespan and oxidative stress resistance, while overexpression enhances survival against pro-oxidant agents but not heat or reductive stress. R02D3.7 represses alg-1 expression, impacting oxidative stress resistance at least in part via ALG-1. microRNAs upregulated in glp-1 mutants (miR-87-3p, miR-230-3p, and miR-235-3p) can target genes in the protein disulfide isomerase pathway and protect against oxidative stress. This study unveils a tightly regulated network involving transcription factors and microRNAs which controls organisms' ability to withstand oxidative stress.
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Affiliation(s)
- Carlos A Vergani-Junior
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Raíssa De P Moro
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Silas Pinto
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Evandro A De-Souza
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Henrique Camara
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Section on Integrative Physiology & Metabolism, Joslin Diabetes Center, Boston, MA, USA
| | - Deisi L Braga
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Guilherme Tonon-da-Silva
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Thiago L Knittel
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Gabriel P Ruiz
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Raissa G Ludwig
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Katlin B Massirer
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Center of Medicinal Chemistry (CQMED), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - William B Mair
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Marcelo A Mori
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
- Obesity and Comorbidities Research Center (OCRC), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
- Experimental Medicine Research Cluster (EMRC), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
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3
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Rich AL, Lin P, Gamazon ER, Zinkel SS. The broad impact of cell death genes on the human disease phenome. Cell Death Dis 2024; 15:251. [PMID: 38589365 PMCID: PMC11002008 DOI: 10.1038/s41419-024-06632-7] [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: 09/13/2023] [Revised: 03/09/2024] [Accepted: 03/22/2024] [Indexed: 04/10/2024]
Abstract
Cell death mediated by genetically defined signaling pathways influences the health and dynamics of all tissues, however the tissue specificity of cell death pathways and the relationships between these pathways and human disease are not well understood. We analyzed the expression profiles of an array of 44 cell death genes involved in apoptosis, necroptosis, and pyroptosis cell death pathways across 49 human tissues from GTEx, to elucidate the landscape of cell death gene expression across human tissues, and the relationship between tissue-specific genetically determined expression and the human phenome. We uncovered unique cell death gene expression profiles across tissue types, suggesting there are physiologically distinct cell death programs in different tissues. Using summary statistics-based transcriptome wide association studies (TWAS) on human traits in the UK Biobank (n ~ 500,000), we evaluated 513 traits encompassing ICD-10 defined diagnoses and laboratory-derived traits. Our analysis revealed hundreds of significant (FDR < 0.05) associations between genetically regulated cell death gene expression and an array of human phenotypes encompassing both clinical diagnoses and hematologic parameters, which were independently validated in another large-scale DNA biobank (BioVU) at Vanderbilt University Medical Center (n = 94,474) with matching phenotypes. Cell death genes were highly enriched for significant associations with blood traits versus non-cell-death genes, with apoptosis-associated genes enriched for leukocyte and platelet traits. Our findings are also concordant with independently published studies (e.g. associations between BCL2L11/BIM expression and platelet & lymphocyte counts). Overall, these results suggest that cell death genes play distinct roles in their contribution to human phenotypes, and that cell death genes influence a diverse array of human traits.
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Affiliation(s)
- Abigail L Rich
- Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Phillip Lin
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Sandra S Zinkel
- Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, USA.
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4
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Koutakis P, Hernandez H, Miserlis D, Thompson JR, Papoutsi E, Mietus CJ, Haynatzki G, Kim JK, Casale GP, Pipinos II. Oxidative damage in the gastrocnemius predicts long-term survival in patients with peripheral artery disease. NPJ Aging 2024; 10:21. [PMID: 38580664 PMCID: PMC10997596 DOI: 10.1038/s41514-024-00147-3] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/20/2024] [Indexed: 04/07/2024]
Abstract
Patients with peripheral artery disease (PAD) have increased mortality rates and a myopathy in their affected legs which is characterized by increased oxidative damage, reduced antioxidant enzymatic activity and defective mitochondrial bioenergetics. This study evaluated the hypothesis that increased levels of oxidative damage in gastrocnemius biopsies from patients with PAD predict long-term mortality rates. Oxidative damage was quantified as carbonyl adducts in myofibers of the gastrocnemius of PAD patients. The oxidative stress data were grouped into tertiles and the 5-year, all-cause mortality for each tertile was determined by Kaplan-Meier curves and compared by the Modified Peto test. A Cox-regression model was used to control the effects of clinical characteristics. Results were adjusted for age, sex, race, body mass index, ankle-brachial index, smoking, physical activity, and comorbidities. Of the 240 study participants, 99 died during a mean follow up of 37.8 months. Patients in the highest tertile of oxidative damage demonstrated the highest 5-year mortality rate. The mortality hazard ratios (HR) from the Cox analysis were statistically significant for oxidative damage (lowest vs middle tertile; HR = 6.33; p = 0.0001 and lowest vs highest; HR = 8.37; p < 0.0001). Survival analysis of a contemporaneous population of PAD patients identifies abundance of carbonyl adducts in myofibers of their gastrocnemius as a predictor of mortality rate independently of ankle-brachial index, disease stage and other clinical and myopathy-related covariates.
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Affiliation(s)
- Panagiotis Koutakis
- Department of Biology, Baylor University, Waco, TX, USA.
- Department of Surgery, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Hernan Hernandez
- Department of Surgery, University of Nebraska Medical Center, Omaha, NE, USA
| | - Dimitrios Miserlis
- Department of Surgery, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Surgery and Perioperative Care, University of Texas at Austin, Austin, TX, USA
| | - Jonathan R Thompson
- Department of Surgery, University of Nebraska Medical Center, Omaha, NE, USA
| | - Evlampia Papoutsi
- Department of Biology, Baylor University, Waco, TX, USA
- Department of Surgery, University of Nebraska Medical Center, Omaha, NE, USA
| | - Constance J Mietus
- Department of Surgery, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Neurological Surgery, University of Massachusetts Medical School, Worcester, MA, USA
| | - Gleb Haynatzki
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE, USA
| | - Julian K Kim
- Department of Biology, Baylor University, Waco, TX, USA
| | - George P Casale
- Department of Surgery, University of Nebraska Medical Center, Omaha, NE, USA
| | - Iraklis I Pipinos
- Department of Surgery, University of Nebraska Medical Center, Omaha, NE, USA.
- Department of Surgery and VA Research Service, VA Nebraska-Western Iowa Health Care System, Omaha, NE, USA.
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Bueichekú E, Diez I, Gagliardi G, Kim CM, Mimmack K, Sepulcre J, Vannini P. Multi-modal Neuroimaging Phenotyping of Mnemonic Anosognosia in the Aging Brain. Commun Med (Lond) 2024; 4:65. [PMID: 38580832 PMCID: PMC10997795 DOI: 10.1038/s43856-024-00497-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 03/28/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND Unawareness is a behavioral condition characterized by a lack of self-awareness of objective memory decline. In the context of Alzheimer's Disease (AD), unawareness may develop in predementia stages and contributes to disease severity and progression. Here, we use in-vivo multi-modal neuroimaging to profile the brain phenotype of individuals presenting altered self-awareness of memory during aging. METHODS Amyloid- and tau-PET (N = 335) and resting-state functional MRI (N = 713) imaging data of individuals from the Anti-Amyloid Treatment in Asymptomatic Alzheimer's Disease (A4)/Longitudinal Evaluation of Amyloid Risk and Neurodegeneration (LEARN) Study were used in this research. We applied whole-brain voxel-wise and region-of-interest analyses to characterize the cortical intersections of tau, amyloid, and functional connectivity networks underlying unawareness in the aging brain compared to aware, complainer and control groups. RESULTS Individuals with unawareness present elevated amyloid and tau burden in midline core regions of the default mode network compared to aware, complainer or control individuals. Unawareness is characterized by an altered network connectivity pattern featuring hyperconnectivity in the medial anterior prefrontal cortex and posterior occipito-parietal regions co-locating with amyloid and tau deposition. CONCLUSIONS Unawareness is an early behavioral biomarker of AD pathology. Failure of the self-referential system in unawareness of memory decline can be linked to amyloid and tau burden, along with functional network connectivity disruptions, in several medial frontal and parieto-occipital areas of the human brain.
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Affiliation(s)
- Elisenda Bueichekú
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ibai Diez
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Geoffroy Gagliardi
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chan-Mi Kim
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kayden Mimmack
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jorge Sepulcre
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA.
- Department of Radiology, Yale PET Center, Yale Medical School, Yale University, New Haven, CT, USA.
| | - Patrizia Vannini
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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Patel K, Xie Z, Yuan H, Islam SMS, Xie Y, He W, Zhang W, Gottlieb A, Chen H, Giancardo L, Knaack A, Fletcher E, Fornage M, Ji S, Zhi D. Unsupervised deep representation learning enables phenotype discovery for genetic association studies of brain imaging. Commun Biol 2024; 7:414. [PMID: 38580839 PMCID: PMC10997628 DOI: 10.1038/s42003-024-06096-7] [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: 01/31/2024] [Accepted: 03/22/2024] [Indexed: 04/07/2024] Open
Abstract
Understanding the genetic architecture of brain structure is challenging, partly due to difficulties in designing robust, non-biased descriptors of brain morphology. Until recently, brain measures for genome-wide association studies (GWAS) consisted of traditionally expert-defined or software-derived image-derived phenotypes (IDPs) that are often based on theoretical preconceptions or computed from limited amounts of data. Here, we present an approach to derive brain imaging phenotypes using unsupervised deep representation learning. We train a 3-D convolutional autoencoder model with reconstruction loss on 6130 UK Biobank (UKBB) participants' T1 or T2-FLAIR (T2) brain MRIs to create a 128-dimensional representation known as Unsupervised Deep learning derived Imaging Phenotypes (UDIPs). GWAS of these UDIPs in held-out UKBB subjects (n = 22,880 discovery and n = 12,359/11,265 replication cohorts for T1/T2) identified 9457 significant SNPs organized into 97 independent genetic loci of which 60 loci were replicated. Twenty-six loci were not reported in earlier T1 and T2 IDP-based UK Biobank GWAS. We developed a perturbation-based decoder interpretation approach to show that these loci are associated with UDIPs mapped to multiple relevant brain regions. Our results established unsupervised deep learning can derive robust, unbiased, heritable, and interpretable brain imaging phenotypes.
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Affiliation(s)
- Khush Patel
- McWilliams School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Ziqian Xie
- McWilliams School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Hao Yuan
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, 77843, USA
| | | | - Yaochen Xie
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Wei He
- McWilliams School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Wanheng Zhang
- School of Public Health, University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Assaf Gottlieb
- McWilliams School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Han Chen
- McWilliams School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, 77030, USA
- School of Public Health, University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Luca Giancardo
- McWilliams School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Alexander Knaack
- Department of Neurology and Imaging of Dementia and Aging (IDeA) Laboratory, University of California at Davis, Davis, CA, 95618, USA
| | - Evan Fletcher
- Department of Neurology and Imaging of Dementia and Aging (IDeA) Laboratory, University of California at Davis, Davis, CA, 95618, USA
| | - Myriam Fornage
- School of Public Health, University of Texas Health Science Center, Houston, TX, 77030, USA
- McGovern Medical School, University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Shuiwang Ji
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Degui Zhi
- McWilliams School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, 77030, USA.
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Shin Y, Lowerison MR, Wang Y, Chen X, You Q, Dong Z, Anastasio MA, Song P. Context-aware deep learning enables high-efficacy localization of high concentration microbubbles for super-resolution ultrasound localization microscopy. Nat Commun 2024; 15:2932. [PMID: 38575577 PMCID: PMC10995206 DOI: 10.1038/s41467-024-47154-2] [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: 04/13/2023] [Accepted: 03/20/2024] [Indexed: 04/06/2024] Open
Abstract
Ultrasound localization microscopy (ULM) enables deep tissue microvascular imaging by localizing and tracking intravenously injected microbubbles circulating in the bloodstream. However, conventional localization techniques require spatially isolated microbubbles, resulting in prolonged imaging time to obtain detailed microvascular maps. Here, we introduce LOcalization with Context Awareness (LOCA)-ULM, a deep learning-based microbubble simulation and localization pipeline designed to enhance localization performance in high microbubble concentrations. In silico, LOCA-ULM enhanced microbubble detection accuracy to 97.8% and reduced the missing rate to 23.8%, outperforming conventional and deep learning-based localization methods up to 17.4% in accuracy and 37.6% in missing rate reduction. In in vivo rat brain imaging, LOCA-ULM revealed dense cerebrovascular networks and spatially adjacent microvessels undetected by conventional ULM. We further demonstrate the superior localization performance of LOCA-ULM in functional ULM (fULM) where LOCA-ULM significantly increased the functional imaging sensitivity of fULM to hemodynamic responses invoked by whisker stimulations in the rat brain.
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Affiliation(s)
- YiRang Shin
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Matthew R Lowerison
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Yike Wang
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Xi Chen
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Qi You
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Zhijie Dong
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Mark A Anastasio
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Pengfei Song
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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8
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Kumar P, Goettemoeller AM, Espinosa-Garcia C, Tobin BR, Tfaily A, Nelson RS, Natu A, Dammer EB, Santiago JV, Malepati S, Cheng L, Xiao H, Duong DD, Seyfried NT, Wood LB, Rowan MJM, Rangaraju S. Native-state proteomics of Parvalbumin interneurons identifies unique molecular signatures and vulnerabilities to early Alzheimer's pathology. Nat Commun 2024; 15:2823. [PMID: 38561349 PMCID: PMC10985119 DOI: 10.1038/s41467-024-47028-7] [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: 08/09/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Dysfunction in fast-spiking parvalbumin interneurons (PV-INs) may represent an early pathophysiological perturbation in Alzheimer's Disease (AD). Defining early proteomic alterations in PV-INs can provide key biological and translationally-relevant insights. We used cell-type-specific in-vivo biotinylation of proteins (CIBOP) coupled with mass spectrometry to obtain native-state PV-IN proteomes. PV-IN proteomic signatures include high metabolic and translational activity, with over-representation of AD-risk and cognitive resilience-related proteins. In bulk proteomes, PV-IN proteins were associated with cognitive decline in humans, and with progressive neuropathology in humans and the 5xFAD mouse model of Aβ pathology. PV-IN CIBOP in early stages of Aβ pathology revealed signatures of increased mitochondria and metabolism, synaptic and cytoskeletal disruption and decreased mTOR signaling, not apparent in whole-brain proteomes. Furthermore, we demonstrated pre-synaptic defects in PV-to-excitatory neurotransmission, validating our proteomic findings. Overall, in this study we present native-state proteomes of PV-INs, revealing molecular insights into their unique roles in cognitive resiliency and AD pathogenesis.
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Affiliation(s)
- Prateek Kumar
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Annie M Goettemoeller
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Neuroscience Graduate Program, Laney Graduate School, Emory University, Atlanta, USA
| | - Claudia Espinosa-Garcia
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Brendan R Tobin
- Georgia W. Woodruff School of Mechanical Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, and Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Ali Tfaily
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Ruth S Nelson
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Aditya Natu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Eric B Dammer
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Juliet V Santiago
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Neuroscience Graduate Program, Laney Graduate School, Emory University, Atlanta, USA
| | - Sneha Malepati
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lihong Cheng
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
| | - Hailian Xiao
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
| | - Duc D Duong
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Levi B Wood
- Georgia W. Woodruff School of Mechanical Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, and Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30322, USA
- School of Chemical and Biological Engineering, GeoInsrgia titute of Technology, Atlanta, GA, 30322, USA
| | - Matthew J M Rowan
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA.
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Srikant Rangaraju
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA.
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA.
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9
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Dintica CS, Habes M, Schreiner PJ, Launer LJ, Yaffe K. Trajectories in depressive symptoms and midlife brain health. Transl Psychiatry 2024; 14:169. [PMID: 38553474 PMCID: PMC10980805 DOI: 10.1038/s41398-024-02883-2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 03/06/2024] [Accepted: 03/15/2024] [Indexed: 04/02/2024] Open
Abstract
Depressive symptoms may either be a risk factor or prodromal to dementia. Investigating this association in midlife may help clarify the role of depression in cognitive aging. We aimed to identify trajectories in depressive symptoms in early to mid-life and related cognitive and brain outcomes in midlife. This study includes 3944 Black and White participants (ages 26-45 years at baseline) from the Coronary Artery Risk Development in Young Adults (CARDIA) study with 20 years of follow-up. Depressive symptoms were assessed using the Center for Epidemiological Studies Depression scale at five time points over 20 years. Growth mixture modeling (GMM) was used to identify depressive symptom trajectories. Participants completed a neuropsychological battery 20 years after baseline, including the Digit Symbol Substitution Test (DSST), Rey-Auditory Verbal Learning Test (RAVLT), Stroop Test, Montreal Cognitive Assessment (MoCA), and category and letter fluency tests. A sub-sample of participants (n = 662) underwent brain magnetic resonance imaging (MRI) to characterize gray matter volumes and white matter hyperintensities (WMHs). We identified four classes of depressive symptom trajectories: a "declining" class (n = 286, 7.3%) with initially high symptoms and subsequent decline, a class with consistently high symptoms ("steady high"; n = 264, 6.7%), a class with late increases in symptoms ("increasing"; n = 277, 7%), and a class with consistently low symptoms ("steady low"; n = 3117, 79.0%). The steady high and the increasing classes had poorer performance on all cognitive tests, while the declining class had poorer performance on the DSST, verbal fluency, and MoCA. Compared to the steady low symptom class, the steady high class had lower volumes in the entorhinal cortex (β: -180.80, 95% CI: -336.69 to -24.91) and the amygdala (β: -40.97, 95% CI: -74.09 to -7.85), the increasing class had more WMHs (β: 0.55, 95% CI: 0.22 to 0.89), and the declining class was not significantly different in any brain measures. Trajectories in depressive symptoms in young to mid-adulthood show distinct cognitive and brain phenotypes in midlife. Steady high depressive symptoms may represent a group that is at risk for dementia, whereas increasing symptoms in midlife may be associated with white matter damage.
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Affiliation(s)
- Christina S Dintica
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, California, CA, USA.
| | - Mohamad Habes
- Neuroimage Analytics Laboratory (NAL) and the Biggs Institute Neuroimaging Core (BINC), Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center San Antonio (UTHSCSA), San Antonio, TX, USA
| | - Pamela J Schreiner
- Division of Epidemiology & Community Health, University of Minnesota, Minneapolis, MN, USA
| | | | - Kristine Yaffe
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, California, CA, USA
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10
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Cicardi ME, Kankate V, Sriramoji S, Krishnamurthy K, Markandaiah SS, Verdone BM, Girdhar A, Nelson A, Rivas LB, Boehringer A, Haeusler AR, Pasinelli P, Guo L, Trotti D. The nuclear import receptor Kapβ2 modifies neurotoxicity mediated by poly(GR) in C9orf72-linked ALS/FTD. Commun Biol 2024; 7:376. [PMID: 38548902 PMCID: PMC10978903 DOI: 10.1038/s42003-024-06071-2] [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: 07/19/2023] [Accepted: 03/19/2024] [Indexed: 04/01/2024] Open
Abstract
Expanded intronic G4C2 repeats in the C9ORF72 gene cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). These intronic repeats are translated through a non-AUG-dependent mechanism into five different dipeptide repeat proteins (DPRs), including poly-glycine-arginine (GR), which is aggregation-prone and neurotoxic. Here, we report that Kapβ2 and GR interact, co-aggregating, in cultured neurons in-vitro and CNS tissue in-vivo. Importantly, this interaction significantly decreased the risk of death of cultured GR-expressing neurons. Downregulation of Kapβ2 is detrimental to their survival, whereas increased Kapβ2 levels mitigated GR-mediated neurotoxicity. As expected, GR-expressing neurons displayed TDP-43 nuclear loss. Raising Kapβ2 levels did not restore TDP-43 into the nucleus, nor did alter the dynamic properties of GR aggregates. Overall, our findings support the design of therapeutic strategies aimed at up-regulating Kapβ2 expression levels as a potential new avenue for contrasting neurodegeneration in C9orf72-ALS/FTD.
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Affiliation(s)
- M E Cicardi
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - V Kankate
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - S Sriramoji
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - K Krishnamurthy
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - S S Markandaiah
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - B M Verdone
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - A Girdhar
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - A Nelson
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - L B Rivas
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - A Boehringer
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - A R Haeusler
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - P Pasinelli
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - L Guo
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
| | - D Trotti
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA.
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11
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Creekmore BC, Kixmoeller K, Black BE, Lee EB, Chang YW. Ultrastructure of human brain tissue vitrified from autopsy revealed by cryo-ET with cryo-plasma FIB milling. Nat Commun 2024; 15:2660. [PMID: 38531877 PMCID: PMC10965902 DOI: 10.1038/s41467-024-47066-1] [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: 09/27/2023] [Accepted: 03/19/2024] [Indexed: 03/28/2024] Open
Abstract
Ultrastructure of human brain tissue has traditionally been examined using electron microscopy (EM) following fixation, staining, and sectioning, which limit resolution and introduce artifacts. Alternatively, cryo-electron tomography (cryo-ET) allows higher resolution imaging of unfixed cellular samples while preserving architecture, but it requires samples to be vitreous and thin enough for transmission EM. Due to these requirements, cryo-ET has yet to be employed to investigate unfixed, never previously frozen human brain tissue. Here we present a method for generating lamellae in human brain tissue obtained at time of autopsy that can be imaged via cryo-ET. We vitrify the tissue via plunge-freezing and use xenon plasma focused ion beam (FIB) milling to generate lamellae directly on-grid at variable depth inside the tissue. Lamellae generated in Alzheimer's disease brain tissue reveal intact subcellular structures including components of autophagy and potential pathologic tau fibrils. Furthermore, we reveal intact compact myelin and functional cytoplasmic expansions. These images indicate that plasma FIB milling with cryo-ET may be used to elucidate nanoscale structures within the human brain.
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Affiliation(s)
- Benjamin C Creekmore
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn Kixmoeller
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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12
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Goralski TM, Meyerdirk L, Breton L, Brasseur L, Kurgat K, DeWeerd D, Turner L, Becker K, Adams M, Newhouse DJ, Henderson MX. Spatial transcriptomics reveals molecular dysfunction associated with cortical Lewy pathology. Nat Commun 2024; 15:2642. [PMID: 38531900 PMCID: PMC10966039 DOI: 10.1038/s41467-024-47027-8] [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: 01/30/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
A key hallmark of Parkinson's disease (PD) is Lewy pathology. Composed of α-synuclein, Lewy pathology is found both in dopaminergic neurons that modulate motor function, and cortical regions that control cognitive function. Recent work has established the molecular identity of dopaminergic neurons susceptible to death, but little is known about cortical neurons susceptible to Lewy pathology or molecular changes induced by aggregates. In the current study, we use spatial transcriptomics to capture whole transcriptome signatures from cortical neurons with α-synuclein pathology compared to neurons without pathology. We find, both in PD and related PD dementia, dementia with Lewy bodies and in the pre-formed fibril α-synucleinopathy mouse model, that specific classes of excitatory neurons are vulnerable to developing Lewy pathology. Further, we identify conserved gene expression changes in aggregate-bearing neurons that we designate the Lewy-associated molecular dysfunction from aggregates (LAMDA) signature. Neurons with aggregates downregulate synaptic, mitochondrial, ubiquitin-proteasome, endo-lysosomal, and cytoskeletal genes and upregulate DNA repair and complement/cytokine genes. Our results identify neurons vulnerable to Lewy pathology in the PD cortex and describe a conserved signature of molecular dysfunction in both mice and humans.
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Affiliation(s)
- Thomas M Goralski
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Lindsay Meyerdirk
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Libby Breton
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Laura Brasseur
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Kevin Kurgat
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Daniella DeWeerd
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Lisa Turner
- Van Andel Institute Pathology Core, Grand Rapids, MI, 49503, USA
| | - Katelyn Becker
- Van Andel Institute Genomics Core, Grand Rapids, MI, 49503, USA
| | - Marie Adams
- Van Andel Institute Genomics Core, Grand Rapids, MI, 49503, USA
| | | | - Michael X Henderson
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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13
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Wen J, Zhao B, Yang Z, Erus G, Skampardoni I, Mamourian E, Cui Y, Hwang G, Bao J, Boquet-Pujadas A, Zhou Z, Veturi Y, Ritchie MD, Shou H, Thompson PM, Shen L, Toga AW, Davatzikos C. The genetic architecture of multimodal human brain age. Nat Commun 2024; 15:2604. [PMID: 38521789 PMCID: PMC10960798 DOI: 10.1038/s41467-024-46796-6] [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: 05/13/2023] [Accepted: 03/06/2024] [Indexed: 03/25/2024] Open
Abstract
The complex biological mechanisms underlying human brain aging remain incompletely understood. This study investigated the genetic architecture of three brain age gaps (BAG) derived from gray matter volume (GM-BAG), white matter microstructure (WM-BAG), and functional connectivity (FC-BAG). We identified sixteen genomic loci that reached genome-wide significance (P-value < 5×10-8). A gene-drug-disease network highlighted genes linked to GM-BAG for treating neurodegenerative and neuropsychiatric disorders and WM-BAG genes for cancer therapy. GM-BAG displayed the most pronounced heritability enrichment in genetic variants within conserved regions. Oligodendrocytes and astrocytes, but not neurons, exhibited notable heritability enrichment in WM and FC-BAG, respectively. Mendelian randomization identified potential causal effects of several chronic diseases on brain aging, such as type 2 diabetes on GM-BAG and AD on WM-BAG. Our results provide insights into the genetics of human brain aging, with clinical implications for potential lifestyle and therapeutic interventions. All results are publicly available at https://labs.loni.usc.edu/medicine .
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Affiliation(s)
- Junhao Wen
- Laboratory of AI and Biomedical Science (LABS), Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
| | - Bingxin Zhao
- Department of Statistics and Data Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhijian Yang
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guray Erus
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ioanna Skampardoni
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth Mamourian
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuhan Cui
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gyujoon Hwang
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jingxuan Bao
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Zhen Zhou
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yogasudha Veturi
- Department of Biobehavioral Health and Statistics, Penn State University, University Park, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Haochang Shou
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Marina del Rey, CA, USA
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Arthur W Toga
- Laboratory of Neuro Imaging (LONI), Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Christos Davatzikos
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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14
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Hawks ZW, Beck ED, Jung L, Fonseca LM, Sliwinski MJ, Weinstock RS, Grinspoon E, Xu I, Strong RW, Singh S, Van Dongen HPA, Frumkin MR, Bulger J, Cleveland MJ, Janess K, Kudva YC, Pratley R, Rickels MR, Rizvi SR, Chaytor NS, Germine LT. Dynamic associations between glucose and ecological momentary cognition in Type 1 Diabetes. NPJ Digit Med 2024; 7:59. [PMID: 38499605 PMCID: PMC10948782 DOI: 10.1038/s41746-024-01036-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 02/14/2024] [Indexed: 03/20/2024] Open
Abstract
Type 1 diabetes (T1D) is a chronic condition characterized by glucose fluctuations. Laboratory studies suggest that cognition is reduced when glucose is very low (hypoglycemia) and very high (hyperglycemia). Until recently, technological limitations prevented researchers from understanding how naturally-occurring glucose fluctuations impact cognitive fluctuations. This study leveraged advances in continuous glucose monitoring (CGM) and cognitive ecological momentary assessment (EMA) to characterize dynamic, within-person associations between glucose and cognition in naturalistic environments. Using CGM and EMA, we obtained intensive longitudinal measurements of glucose and cognition (processing speed, sustained attention) in 200 adults with T1D. First, we used hierarchical Bayesian modeling to estimate dynamic, within-person associations between glucose and cognition. Consistent with laboratory studies, we hypothesized that cognitive performance would be reduced at low and high glucose, reflecting cognitive vulnerability to glucose fluctuations. Second, we used data-driven lasso regression to identify clinical characteristics that predicted individual differences in cognitive vulnerability to glucose fluctuations. Large glucose fluctuations were associated with slower and less accurate processing speed, although slight glucose elevations (relative to person-level means) were associated with faster processing speed. Glucose fluctuations were not related to sustained attention. Seven clinical characteristics predicted individual differences in cognitive vulnerability to glucose fluctuations: age, time in hypoglycemia, lifetime severe hypoglycemic events, microvascular complications, glucose variability, fatigue, and neck circumference. Results establish the impact of glucose on processing speed in naturalistic environments, suggest that minimizing glucose fluctuations is important for optimizing processing speed, and identify several clinical characteristics that may exacerbate cognitive vulnerability to glucose fluctuations.
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Affiliation(s)
- Z W Hawks
- Institute for Technology in Psychiatry, McLean Hospital, Belmont, MA, USA.
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA.
| | - E D Beck
- Department of Psychology, University of California Davis, Davis, CA, USA
| | - L Jung
- Institute for Technology in Psychiatry, McLean Hospital, Belmont, MA, USA
| | - L M Fonseca
- Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
- Programa Terceira Idade (PROTER, Old Age Research Group), Department and Institute of Psychiatry, University of São Paulo School of Medicine, São Paulo, Brazil
| | - M J Sliwinski
- Department of Human Development and Family Studies, Center for Healthy Aging, Pennsylvania State University, State College, PA, USA
| | | | - E Grinspoon
- Institute for Technology in Psychiatry, McLean Hospital, Belmont, MA, USA
| | - I Xu
- Department of Psychology, University of Notre Dame, Notre Dame, IN, USA
| | - R W Strong
- The Many Brains Project, Belmont, MA, USA
| | - S Singh
- Institute for Technology in Psychiatry, McLean Hospital, Belmont, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - H P A Van Dongen
- Sleep and Performance Research Center & Department of Translational Medicine and Physiology, Washington State University, Spokane, WA, USA
| | - M R Frumkin
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Department of Psychological & Brain Sciences, Washington University in St. Louis, St. Louis, MO, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - J Bulger
- SUNY Upstate Medical University, Syracuse, NY, USA
| | - M J Cleveland
- Department of Human Development, Washington State University, Pullman, WA, USA
| | - K Janess
- Jaeb Center for Health Research, Tampa, FL, USA
| | - Y C Kudva
- Division of Endocrinology, Diabetes and Nutrition, Mayo Clinic, Rochester, MN, USA
| | - R Pratley
- AdventHealth Translational Research Institute, Orlando, FL, USA
| | - M R Rickels
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - S R Rizvi
- Division of Endocrinology, Diabetes and Nutrition, Mayo Clinic, Rochester, MN, USA
| | - N S Chaytor
- Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - L T Germine
- Institute for Technology in Psychiatry, McLean Hospital, Belmont, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
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15
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Gidwani SV, Brahmbhatt D, Zomback A, Bassie M, Martinez J, Zhuang J, Schulze J, McLellan JS, Mariani R, Alff P, Frasca D, Blomberg BB, Marshall CP, Yondola MA. Engineered dityrosine-bonding of the RSV prefusion F protein imparts stability and potency advantages. Nat Commun 2024; 15:2202. [PMID: 38485927 PMCID: PMC10940300 DOI: 10.1038/s41467-024-46295-8] [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: 03/14/2023] [Accepted: 02/21/2024] [Indexed: 03/18/2024] Open
Abstract
Viral fusion proteins facilitate cellular infection by fusing viral and cellular membranes, which involves dramatic transitions from their pre- to postfusion conformations. These proteins are among the most protective viral immunogens, but they are metastable which often makes them intractable as subunit vaccine targets. Adapting a natural enzymatic reaction, we harness the structural rigidity that targeted dityrosine crosslinks impart to covalently stabilize fusion proteins in their native conformations. We show that the prefusion conformation of respiratory syncytial virus fusion protein can be stabilized with two engineered dityrosine crosslinks (DT-preF), markedly improving its stability and shelf-life. Furthermore, it has 11X greater potency as compared with the DS-Cav1 stabilized prefusion F protein in immunogenicity studies and overcomes immunosenescence in mice with simply a high-dose formulation on alum.
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Affiliation(s)
- Sonal V Gidwani
- Calder Biosciences Inc., Brooklyn Army Terminal, Brooklyn, NY, USA
| | | | - Aaron Zomback
- Calder Biosciences Inc., Brooklyn Army Terminal, Brooklyn, NY, USA
| | - Mamie Bassie
- Calder Biosciences Inc., Brooklyn Army Terminal, Brooklyn, NY, USA
| | | | - Jian Zhuang
- Calder Biosciences Inc., Brooklyn Army Terminal, Brooklyn, NY, USA
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - John Schulze
- Molecular Structure Facility, University of California, Davis, Davis, CA, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas at Austin, College of Natural Sciences, Austin, TX, USA
| | - Roberto Mariani
- Calder Biosciences Inc., Brooklyn Army Terminal, Brooklyn, NY, USA
- CUNY Kingsborough Community College, Brooklyn, NY, USA
| | - Peter Alff
- Calder Biosciences Inc., Brooklyn Army Terminal, Brooklyn, NY, USA
| | - Daniela Frasca
- Department of Microbiology and Immunology, University of Miami, Miami, FL, USA
| | - Bonnie B Blomberg
- Department of Microbiology and Immunology, University of Miami, Miami, FL, USA
| | | | - Mark A Yondola
- Calder Biosciences Inc., Brooklyn Army Terminal, Brooklyn, NY, USA.
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16
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Tays GD, Hupfeld KE, McGregor HR, Beltran NE, De Dios YE, Mulder E, Bloomberg JJ, Mulavara AP, Wood SJ, Seidler RD. Daily artificial gravity partially mitigates vestibular processing changes associated with head-down tilt bedrest. NPJ Microgravity 2024; 10:27. [PMID: 38472244 PMCID: PMC10933323 DOI: 10.1038/s41526-024-00367-7] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Microgravity alters vestibular signaling and reduces body loading, driving sensory reweighting. The unloading effects can be modelled using head-down tilt bedrest (HDT). Artificial gravity (AG) has been hypothesized to serve as an integrated countermeasure for the declines associated with HDT and spaceflight. Here, we examined the efficacy of 30 min of daily AG to counteract brain and behavior changes from 60 days of HDT. Two groups received 30 min of AG delivered via short-arm centrifuge daily (n = 8 per condition), either in one continuous bout, or in 6 bouts of 5 min. To improve statistical power, we combined these groups (AG; n = 16). Another group served as controls in HDT with no AG (CTRL; n = 8). We examined how HDT and AG affect vestibular processing by collecting fMRI scans during vestibular stimulation. We collected these data prior to, during, and post-HDT. We assessed brain activation initially in 12 regions of interest (ROIs) and then conducted an exploratory whole brain analysis. The AG group showed no changes in activation during vestibular stimulation in a cerebellar ROI, whereas the CTRL group showed decreased activation specific to HDT. Those that received AG and showed little pre- to post-HDT changes in left vestibular cortex activation had better post-HDT balance performance. Whole brain analyses identified increased pre- to during-HDT activation in CTRLs in the right precentral gyrus and right inferior frontal gyrus, whereas AG maintained pre-HDT activation levels. These results indicate that AG could mitigate activation changes in vestibular processing that is associated with better balance performance.
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Affiliation(s)
- G D Tays
- Department of Applied Physiology and Kinesiology, University of Florida, Gainesville, FL, USA
| | - K E Hupfeld
- Department of Applied Physiology and Kinesiology, University of Florida, Gainesville, FL, USA
| | - H R McGregor
- Department of Applied Physiology and Kinesiology, University of Florida, Gainesville, FL, USA
| | | | | | - E Mulder
- German Aerospace Center (DLR), Cologne, Germany
| | | | | | - S J Wood
- NASA Johnson Space Center, Houston, TX, USA
| | - R D Seidler
- Department of Applied Physiology and Kinesiology, University of Florida, Gainesville, FL, USA.
- Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, USA.
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17
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Mehdi SMA, Costa AP, Svob C, Pan L, Dartora WJ, Talati A, Gameroff MJ, Wickramaratne PJ, Weissman MM, McIntire LBJ. Depression and cognition are associated with lipid dysregulation in both a multigenerational study of depression and the National Health and Nutrition Examination Survey. Transl Psychiatry 2024; 14:142. [PMID: 38467624 PMCID: PMC10928164 DOI: 10.1038/s41398-024-02847-6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
Chronic dysregulation of peripheral lipids has been found to be associated with depression and cognition, but their interaction has not been investigated. Growing evidence has highlighted the association between peripheral lipoprotein levels with depression and cognition with inconsistent results. We assessed the association between peripheral lipids, depression, and cognition while evaluating their potential interactions using robust clinically relevant predictors such as lipoprotein levels and chronic medical disorders that dysregulate lipoproteins. We report an association between peripheral lipids, depression, and cognition, suggesting a common underlying biological mechanism driven by lipid dysregulation in two independent studies. Analysis of a longitudinal study of a cohort at high or low familial risk for major depressive disorder (MDD) (n = 526) found metabolic diseases, including diabetes, hypertension, and other cardiovascular diseases, were associated with MDD and cognitive outcomes. Investigating a cross-sectional population survey of adults in the National Health and Nutrition Examination Survey 2011-2014 (NHANES) (n = 2377), depression was found to be associated with high density lipoprotein (HDL) and cognitive assessments. In the familial risk study, medical conditions were found to be associated with chronic lipid dysregulation and were significantly associated with MDD using the structural equation model. A positive association between chronic lipid dysregulation and cognitive scores was found in an exploratory analysis of the familial risk study. In a complementary study, analysis of NHANES revealed a positive association of HDL levels with cognition. Further analysis of the NHANES cohort indicated that depression status mediated the interaction between HDL levels and cognitive tests. Importantly, the protective effect of HDL on cognition was absent in those with depressive symptoms, which may ultimately result in worse outcomes leading to cognitive decline. These findings highlight the potential for the early predictive value of medical conditions with chronic lipid dyshomeostasis for the risk of depression and cognitive decline.
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Affiliation(s)
- S M A Mehdi
- Mailman School of Public Health, Columbia University, New York, NY, USA
| | - A P Costa
- Department of Radiology, Weill Cornell Medicine, New York, NY, USA
- Brain Health Imaging Institute, New York, NY, USA
| | - C Svob
- Division of Translational Epidemiology and Mental Health Equity, New York State Psychiatric Institute, New York, NY, USA
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - L Pan
- Division of Translational Epidemiology and Mental Health Equity, New York State Psychiatric Institute, New York, NY, USA
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - W J Dartora
- Department of Radiology, Weill Cornell Medicine, New York, NY, USA
- Brain Health Imaging Institute, New York, NY, USA
| | - A Talati
- Division of Translational Epidemiology and Mental Health Equity, New York State Psychiatric Institute, New York, NY, USA
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - M J Gameroff
- Division of Translational Epidemiology and Mental Health Equity, New York State Psychiatric Institute, New York, NY, USA
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - P J Wickramaratne
- Division of Translational Epidemiology and Mental Health Equity, New York State Psychiatric Institute, New York, NY, USA
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - M M Weissman
- Mailman School of Public Health, Columbia University, New York, NY, USA.
- Division of Translational Epidemiology and Mental Health Equity, New York State Psychiatric Institute, New York, NY, USA.
- Department of Psychiatry, Columbia University, New York, NY, USA.
| | - L B J McIntire
- Department of Radiology, Weill Cornell Medicine, New York, NY, USA.
- Brain Health Imaging Institute, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
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18
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Virga DM, Hamilton S, Osei B, Morgan A, Kneis P, Zamponi E, Park NJ, Hewitt VL, Zhang D, Gonzalez KC, Russell FM, Grahame Hardie D, Prudent J, Bloss E, Losonczy A, Polleux F, Lewis TL. Activity-dependent compartmentalization of dendritic mitochondria morphology through local regulation of fusion-fission balance in neurons in vivo. Nat Commun 2024; 15:2142. [PMID: 38459070 PMCID: PMC10923867 DOI: 10.1038/s41467-024-46463-w] [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: 04/29/2023] [Accepted: 02/27/2024] [Indexed: 03/10/2024] Open
Abstract
Neuronal mitochondria play important roles beyond ATP generation, including Ca2+ uptake, and therefore have instructive roles in synaptic function and neuronal response properties. Mitochondrial morphology differs significantly between the axon and dendrites of a given neuronal subtype, but in CA1 pyramidal neurons (PNs) of the hippocampus, mitochondria within the dendritic arbor also display a remarkable degree of subcellular, layer-specific compartmentalization. In the dendrites of these neurons, mitochondria morphology ranges from highly fused and elongated in the apical tuft, to more fragmented in the apical oblique and basal dendritic compartments, and thus occupy a smaller fraction of dendritic volume than in the apical tuft. However, the molecular mechanisms underlying this striking degree of subcellular compartmentalization of mitochondria morphology are unknown, precluding the assessment of its impact on neuronal function. Here, we demonstrate that this compartment-specific morphology of dendritic mitochondria requires activity-dependent, Ca2+ and Camkk2-dependent activation of AMPK and its ability to phosphorylate two direct effectors: the pro-fission Drp1 receptor Mff and the recently identified anti-fusion, Opa1-inhibiting protein, Mtfr1l. Our study uncovers a signaling pathway underlying the subcellular compartmentalization of mitochondrial morphology in dendrites of neurons in vivo through spatially precise and activity-dependent regulation of mitochondria fission/fusion balance.
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Affiliation(s)
- Daniel M Virga
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Stevie Hamilton
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Bertha Osei
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Abigail Morgan
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Neuroscience, Biochemistry & Molecular Biology, Oklahoma University Health Science Campus, Oklahoma City, OK, USA
| | - Parker Kneis
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Neuroscience, Biochemistry & Molecular Biology, Oklahoma University Health Science Campus, Oklahoma City, OK, USA
| | - Emiliano Zamponi
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Natalie J Park
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Victoria L Hewitt
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - David Zhang
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Kevin C Gonzalez
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Fiona M Russell
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
| | - D Grahame Hardie
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
| | - Julien Prudent
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, CB2 0XY, Cambridge, UK
| | - Erik Bloss
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Attila Losonczy
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Franck Polleux
- Department of Neuroscience, Columbia University, New York, NY, USA.
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
| | - Tommy L Lewis
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.
- Neuroscience, Biochemistry & Molecular Biology, Oklahoma University Health Science Campus, Oklahoma City, OK, USA.
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19
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Gao F, Hu Q, Chen W, Li J, Qi C, Yan Y, Qian C, Wan M, Ficke J, Zheng J, Cao X. Brain regulates weight bearing bone through PGE2 skeletal interoception: implication of ankle osteoarthritis and pain. Bone Res 2024; 12:16. [PMID: 38443372 PMCID: PMC10914853 DOI: 10.1038/s41413-024-00316-w] [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: 09/04/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 03/07/2024] Open
Abstract
Bone is a mechanosensitive tissue and undergoes constant remodeling to adapt to the mechanical loading environment. However, it is unclear whether the signals of bone cells in response to mechanical stress are processed and interpreted in the brain. In this study, we found that the hypothalamus of the brain regulates bone remodeling and structure by perceiving bone prostaglandin E2 (PGE2) concentration in response to mechanical loading. Bone PGE2 levels are in proportion to their weight bearing. When weight bearing changes in the tail-suspension mice, the PGE2 concentrations in bones change in line with their weight bearing changes. Deletion of cyclooxygenase-2 (COX2) in the osteoblast lineage cells or knockout of receptor 4 (EP4) in sensory nerve blunts bone formation in response to mechanical loading. Moreover, knockout of TrkA in sensory nerve also significantly reduces mechanical load-induced bone formation. Moreover, mechanical loading induces cAMP-response element binding protein (CREB) phosphorylation in the hypothalamic arcuate nucleus (ARC) to inhibit sympathetic tyrosine hydroxylase (TH) expression in the paraventricular nucleus (PVN) for osteogenesis. Finally, we show that elevated PGE2 is associated with ankle osteoarthritis (AOA) and pain. Together, our data demonstrate that in response to mechanical loading, skeletal interoception occurs in the form of hypothalamic processing of PGE2-driven peripheral signaling to maintain physiologic bone homeostasis, while chronically elevated PGE2 can be sensed as pain during AOA and implication of potential treatment.
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Affiliation(s)
- Feng Gao
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - Qimiao Hu
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - Wenwei Chen
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - Jilong Li
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - Cheng Qi
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - Yiwen Yan
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - Cheng Qian
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - Mei Wan
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - James Ficke
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - Junying Zheng
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - Xu Cao
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA.
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA.
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20
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Yücel AD, Gladyshev VN. The long and winding road of reprogramming-induced rejuvenation. Nat Commun 2024; 15:1941. [PMID: 38431638 PMCID: PMC10908844 DOI: 10.1038/s41467-024-46020-5] [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: 07/22/2023] [Accepted: 02/12/2024] [Indexed: 03/05/2024] Open
Abstract
Organismal aging is inherently connected to the aging of its constituent cells and systems. Reducing the biological age of the organism may be assisted by reducing the age of its cells - an approach exemplified by partial cell reprogramming through the expression of Yamanaka factors or exposure to chemical cocktails. It is crucial to protect cell type identity during partial reprogramming, as cells need to retain or rapidly regain their functions following the treatment. Another critical issue is the ability to quantify biological age as reprogrammed older cells acquire younger states. We discuss recent advances in reprogramming-induced rejuvenation and offer a critical review of this procedure and its relationship to the fundamental nature of aging. We further comparatively analyze partial reprogramming, full reprogramming and transdifferentiation approaches, assess safety concerns and emphasize the importance of distinguishing rejuvenation from dedifferentiation. Finally, we highlight translational opportunities that the reprogramming-induced rejuvenation approach offers.
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Affiliation(s)
- Ali Doğa Yücel
- Department of Molecular Biology and Genetics, Koc University, Istanbul, 34450, Turkey
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Vadim N Gladyshev
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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21
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Elliott A, Walters RK, Pirinen M, Kurki M, Junna N, Goldstein JI, Reeve MP, Siirtola H, Lemmelä SM, Turley P, Lahtela E, Mehtonen J, Reis K, Elnahas AG, Reigo A, Palta P, Esko T, Mägi R, Palotie A, Daly MJ, Widén E. Distinct and shared genetic architectures of gestational diabetes mellitus and type 2 diabetes. Nat Genet 2024; 56:377-382. [PMID: 38182742 PMCID: PMC10937370 DOI: 10.1038/s41588-023-01607-4] [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: 03/04/2023] [Accepted: 11/07/2023] [Indexed: 01/07/2024]
Abstract
Gestational diabetes mellitus (GDM) is a common metabolic disorder affecting more than 16 million pregnancies annually worldwide1,2. GDM is related to an increased lifetime risk of type 2 diabetes (T2D)1-3, with over a third of women developing T2D within 15 years of their GDM diagnosis. The diseases are hypothesized to share a genetic predisposition1-7, but few studies have sought to uncover the genetic underpinnings of GDM. Most studies have evaluated the impact of T2D loci only8-10, and the three prior genome-wide association studies of GDM11-13 have identified only five loci, limiting the power to assess to what extent variants or biological pathways are specific to GDM. We conducted the largest genome-wide association study of GDM to date in 12,332 cases and 131,109 parous female controls in the FinnGen study and identified 13 GDM-associated loci, including nine new loci. Genetic features distinct from T2D were identified both at the locus and genomic scale. Our results suggest that the genetics of GDM risk falls into the following two distinct categories: one part conventional T2D polygenic risk and one part predominantly influencing mechanisms disrupted in pregnancy. Loci with GDM-predominant effects map to genes related to islet cells, central glucose homeostasis, steroidogenesis and placental expression.
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Grants
- R00 AG062787 NIA NIH HHS
- R01 MH101244 NIMH NIH HHS
- A.E. was a research Scholar supported by Sarnoff Cardiovascular Research Foundation
- U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- Academy of Finland (Suomen Akatemia)
- U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)
- The FinnGen project is funded by two grants from Business Finland (HUS 4685/31/2016 and UH 4386/31/2016) and by eleven industry partners (AbbVie Inc, AstraZeneca UK Ltd, Biogen MA Inc, Celgene Corporation, Celgene International II Sàrl, Genentech Inc, Merck Sharp & Dohme Corp, Pfizer Inc., GlaxoSmithKline, Sanofi, Maze Therapeutics Inc., Janssen Biotech Inc).
- EstBB GWAS analysis is supported by research funding from the Estonian Research Council: Team grant PRG1291 and PRG1911.
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Affiliation(s)
- Amanda Elliott
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Raymond K Walters
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Matti Pirinen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Mitja Kurki
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nella Junna
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Jacqueline I Goldstein
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mary Pat Reeve
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Harri Siirtola
- TAUCHI Research Center, Faculty of Information Technology and Communication Sciences (ITC), Tampere University, Tampere, Finland
| | - Susanna M Lemmelä
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Patrick Turley
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA
- Department of Economics, University of Southern California, Los Angeles, CA, USA
| | - Elisa Lahtela
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Juha Mehtonen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Kadri Reis
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Anu Reigo
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Priit Palta
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.
| | - Elisabeth Widén
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.
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22
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Noppert GA, Clarke P, Hoover A, Kubale J, Melendez R, Duchowny K, Hegde ST. State variation in neighborhood COVID-19 burden across the United States. Commun Med (Lond) 2024; 4:36. [PMID: 38429552 PMCID: PMC10907669 DOI: 10.1038/s43856-024-00459-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/12/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND A lack of fine, spatially-resolute case data for the U.S. has prevented the examination of how COVID-19 infection burden has been distributed across neighborhoods, a key determinant of both risk and resilience. Without more spatially resolute data, efforts to identify and mitigate the long-term fallout from COVID-19 in vulnerable communities will remain difficult to quantify and intervene on. METHODS We leveraged spatially-referenced data from 21 states collated through the COVID Neighborhood Project to examine the distribution of COVID-19 cases across neighborhoods and states in the U.S. We also linked the COVID-19 case data with data on the neighborhood social environment from the National Neighborhood Data Archive. We then estimated correlations between neighborhood COVID-19 burden and features of the neighborhood social environment. RESULTS We find that the distribution of COVID-19 at the neighborhood-level varies within and between states. The median case count per neighborhood (coefficient of variation (CV)) in Wisconsin is 3078.52 (0.17) per 10,000 population, indicating a more homogenous distribution of COVID-19 burden, whereas in Vermont the median case count per neighborhood (CV) is 810.98 (0.84) per 10,000 population. We also find that correlations between features of the neighborhood social environment and burden vary in magnitude and direction by state. CONCLUSIONS Our findings underscore the importance that local contexts may play when addressing the long-term social and economic fallout communities will face from COVID-19.
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Affiliation(s)
- Grace A Noppert
- Institute for Social Research, University of Michigan, Ann Arbor, USA.
| | - Philippa Clarke
- Institute for Social Research, University of Michigan, Ann Arbor, USA
| | - Andrew Hoover
- Institute for Social Research, University of Michigan, Ann Arbor, USA
| | - John Kubale
- Institute for Social Research, University of Michigan, Ann Arbor, USA
| | - Robert Melendez
- Institute for Social Research, University of Michigan, Ann Arbor, USA
| | - Kate Duchowny
- Institute for Social Research, University of Michigan, Ann Arbor, USA
| | - Sonia T Hegde
- Department of Epidemiology, Johns Hopkins University, Baltimore, USA
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23
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Choi J, Augenlicht LH. Intestinal stem cells: guardians of homeostasis in health and aging amid environmental challenges. Exp Mol Med 2024; 56:495-500. [PMID: 38424189 PMCID: PMC10985084 DOI: 10.1038/s12276-024-01179-1] [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: 11/14/2023] [Accepted: 12/11/2023] [Indexed: 03/02/2024] Open
Abstract
The intestinal epithelium is the first line of defense and acts as an interface between the vast microbial world within the gastrointestinal tract and the body's internal milieu. The intestinal epithelium not only facilitates nutrient absorption but also plays a key role in defending against pathogens and regulating the immune system. Central to maintaining a healthy epithelium are intestinal stem cells (ISCs), which are essential for replenishing the intestinal epithelium throughout an individual's lifespan. Recent research has unveiled the intricate interplay between ISCs and their niche, which includes various cell types, extracellular components, and signaling molecules. In this review, we delve into the most recent advances in ISC research, with a focus on the roles of ISCs in maintaining mucosal homeostasis and how ISC functionality is influenced by the niche environment. In this review, we explored the regulatory mechanisms that govern ISC behavior, emphasizing the dynamic adaptability of the intestinal epithelium in the face of various challenges. Understanding the intricate regulation of ISCs and the impact of aging and environmental factors is crucial for advancing our knowledge and developing translational approaches. Future studies should investigate the interactive effects of different risk factors on intestinal function and develop strategies for improving the regenerative capacity of the gut.
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Affiliation(s)
- Jiahn Choi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Leonard H Augenlicht
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
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24
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Mize TJ, Evans LM. Examination of a novel expression-based gene-SNP annotation strategy to identify tissue-specific contributions to heritability in multiple traits. Eur J Hum Genet 2024; 32:263-269. [PMID: 36446896 PMCID: PMC10924090 DOI: 10.1038/s41431-022-01244-1] [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: 06/17/2022] [Revised: 10/20/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Complex traits show clear patterns of tissue-specific expression influenced by single nucleotide polymorphisms (SNPs), yet current strategies aggregate SNP effects to genes by employing simple physical proximity-based windows. Here, we examined whether incorporating SNPs with effects on tissue-specific cis-expression would improve our ability to detect trait-relevant tissues across 31 complex traits using stratified linkage disequilibrium score regression (S-LDSC). We found that a physical proximity annotation produced more significant tissue enrichments and larger S-LDSC regression coefficients, as compared to an expression-based annotation. Furthermore, we showed that our expression-based annotation did not outperform an annotation strategy in which an equal number of randomly chosen SNPs were annotated to genes within the same genomic window, suggesting extensive redundancy among SNP effect estimates due to linkage disequilibrium. That said, current sample sizes limit estimation of cis-genetic SNP effects; therefore, we recommend reexamination of the expression-based annotation when larger tissue-specific expression datasets become available. To examine the influence of sample size, we used a large whole blood eQTL reference panel (N = 31,684) applying a similar expression-based annotation strategy. We found that significant cis-expression QTLs in whole blood did not outperform the physical proximity annotation when estimating tissue-specific SNP heritability enrichment for either high- or low-density lipoprotein phenotypes but performed similarly for inflammatory bowel disease. Finally, we report new and updated tissue enrichment estimates across 31 complex traits, such as significant heritability enrichment of the frontal cortex for cognitive performance, educational attainment, and intelligence, providing further evidence of this structure's importance in higher cognitive function.
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Affiliation(s)
- Travis J Mize
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA.
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
| | - Luke M Evans
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA.
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
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25
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Xie YR, Castro DC, Rubakhin SS, Trinklein TJ, Sweedler JV, Lam F. Multiscale biochemical mapping of the brain through deep-learning-enhanced high-throughput mass spectrometry. Nat Methods 2024; 21:521-530. [PMID: 38366241 PMCID: PMC10927565 DOI: 10.1038/s41592-024-02171-3] [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: 06/05/2023] [Accepted: 01/08/2024] [Indexed: 02/18/2024]
Abstract
Spatial omics technologies can reveal the molecular intricacy of the brain. While mass spectrometry imaging (MSI) provides spatial localization of compounds, comprehensive biochemical profiling at a brain-wide scale in three dimensions by MSI with single-cell resolution has not been achieved. We demonstrate complementary brain-wide and single-cell biochemical mapping using MEISTER, an integrative experimental and computational mass spectrometry (MS) framework. Our framework integrates a deep-learning-based reconstruction that accelerates high-mass-resolving MS by 15-fold, multimodal registration creating three-dimensional (3D) molecular distributions and a data integration method fitting cell-specific mass spectra to 3D datasets. We imaged detailed lipid profiles in tissues with millions of pixels and in large single-cell populations acquired from the rat brain. We identified region-specific lipid contents and cell-specific localizations of lipids depending on both cell subpopulations and anatomical origins of the cells. Our workflow establishes a blueprint for future development of multiscale technologies for biochemical characterization of the brain.
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Affiliation(s)
- Yuxuan Richard Xie
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Daniel C Castro
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Stanislav S Rubakhin
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Timothy J Trinklein
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jonathan V Sweedler
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carle-Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| | - Fan Lam
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carle-Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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26
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Tamman AJF, Koller D, Nagamatsu S, Cabrera-Mendoza B, Abdallah C, Krystal JH, Gelernter J, Montalvo-Ortiz JL, Polimanti R, Pietrzak RH. Psychosocial moderators of polygenic risk scores of inflammatory biomarkers in relation to GrimAge. Neuropsychopharmacology 2024; 49:699-708. [PMID: 37848731 PMCID: PMC10876568 DOI: 10.1038/s41386-023-01747-5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/25/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023]
Abstract
GrimAge acceleration has previously predicted age-related morbidities and mortality. In the current study, we sought to examine how GrimAge is associated with genetic predisposition for systemic inflammation and whether psychosocial factors moderate this association. Military veterans from the National Health and Resilience in Veterans study, which surveyed a nationally representative sample of European American male veterans, provided saliva samples for genotyping (N = 1135). We derived polygenic risk scores (PRS) from the UK Biobank as markers of genetic predisposition to inflammation. Results revealed that PRS for three inflammatory PRS markers-HDL (lower), apolipoprotein B (lower), and gamma-glutamyl transferase (higher)-were associated with accelerated GrimAge. Additionally, these PRS interacted with a range of potentially modifiable psychosocial variables, such as exercise and gratitude, previously identified as associated with accelerated GrimAge. Using gene enrichment, we identified anti-inflammatory and antihistamine drugs that perturbate pathways of genes highly represented in the inflammatory PRS, laying the groundwork for future work to evaluate the potential of these drugs in mitigating epigenetic aging.
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Affiliation(s)
- Amanda J F Tamman
- Department of Psychiatry, Baylor College of Medicine, Houston, TX, USA.
| | - Dora Koller
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Sheila Nagamatsu
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Brenda Cabrera-Mendoza
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Chadi Abdallah
- Department of Psychiatry, Baylor College of Medicine, Houston, TX, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - John H Krystal
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, Clinical Neurosciences Division, VA Connecticut Healthcare System, West Haven, CT, USA
| | - Joel Gelernter
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, Clinical Neurosciences Division, VA Connecticut Healthcare System, West Haven, CT, USA
| | - Janitza L Montalvo-Ortiz
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, Clinical Neurosciences Division, VA Connecticut Healthcare System, West Haven, CT, USA
| | - Renato Polimanti
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Robert H Pietrzak
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, Clinical Neurosciences Division, VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Social and Behavioral Sciences, Yale School of Public Health, New Haven, CT, USA
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27
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Panitch R, Sahelijo N, Hu J, Nho K, Bennett DA, Lunetta KL, Au R, Stein TD, Farrer LA, Jun GR. APOE genotype-specific methylation patterns are linked to Alzheimer disease pathology and estrogen response. Transl Psychiatry 2024; 14:129. [PMID: 38424036 PMCID: PMC10904829 DOI: 10.1038/s41398-024-02834-x] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
The joint effects of APOE genotype and DNA methylation on Alzheimer disease (AD) risk is relatively unknown. We conducted genome-wide methylation analyses using 2,021 samples in blood (91 AD cases, 329 mild cognitive impairment, 1,391 controls) and 697 samples in brain (417 AD cases, 280 controls). We identified differentially methylated levels in AD compared to controls in an APOE genotype-specific manner at 25 cytosine-phosphate-guanine (CpG) sites in brain and 36 CpG sites in blood. Additionally, we identified seven CpG sites in the APOE region containing TOMM40, APOE, and APOC1 genes with P < 5 × 10-8 between APOE ε4 carriers and non-carriers in brain or blood. In brain, the most significant CpG site hypomethylated in ε4 carriers compared to non-carriers was from the TOMM40 in the total sample, while most of the evidence was derived from AD cases. However, the CpG site was not significantly modulating expression of these three genes in brain. Three CpG sites from the APOE were hypermethylated in APOE ε4 carriers in brain or blood compared in ε4 non-carriers and nominally significant with APOE expression in brain. Three CpG sites from the APOC1 were hypermethylated in blood, which one of the 3 CpG sites significantly lowered APOC1 expression in blood using all subjects or ε4 non-carriers. Co-methylation network analysis in blood and brain detected eight methylation networks associated with AD and APOE ε4 status. Five of the eight networks included genes containing network CpGs that were significantly enriched for estradiol perturbation, where four of the five networks were enriched for the estrogen response pathway. Our findings provide further evidence of the role of APOE genotype on methylation levels associated with AD, especially linked to estrogen response pathway.
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Affiliation(s)
- Rebecca Panitch
- Biomedical Genetics Section, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
| | - Nathan Sahelijo
- Biomedical Genetics Section, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
| | - Junming Hu
- Biomedical Genetics Section, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences and Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W. Harrison Street, Suite 1000, Chicago, IL, 60612, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, 715 Albany Street, Boston, MA, 02118, USA
| | - Rhoda Au
- Department of Anatomy & Neurobiology, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
- Department of Neurology, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
- Department of Epidemiology, Boston University School of Public Health, 715 Albany Street, Boston, MA, 02118, USA
| | - Thor D Stein
- Department of Pathology & Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
- VA Bedford Healthcare System, Bedford, MA, 01730, USA
- VA Boston Healthcare Center, Boston, MA, 02130, USA
| | - Lindsay A Farrer
- Biomedical Genetics Section, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
- Department of Biostatistics, Boston University School of Public Health, 715 Albany Street, Boston, MA, 02118, USA.
- Department of Neurology, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
- Department of Epidemiology, Boston University School of Public Health, 715 Albany Street, Boston, MA, 02118, USA.
- Department of Ophthalmology, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
| | - Gyungah R Jun
- Biomedical Genetics Section, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
- Department of Biostatistics, Boston University School of Public Health, 715 Albany Street, Boston, MA, 02118, USA.
- Department of Ophthalmology, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
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28
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Pitrez PR, Monteiro LM, Borgogno O, Nissan X, Mertens J, Ferreira L. Cellular reprogramming as a tool to model human aging in a dish. Nat Commun 2024; 15:1816. [PMID: 38418829 PMCID: PMC10902382 DOI: 10.1038/s41467-024-46004-5] [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: 09/29/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
The design of human model systems is highly relevant to unveil the underlying mechanisms of aging and to provide insights on potential interventions to extend human health and life span. In this perspective, we explore the potential of 2D or 3D culture models comprising human induced pluripotent stem cells and transdifferentiated cells obtained from aged or age-related disorder-affected donors to enhance our understanding of human aging and to catalyze the discovery of anti-aging interventions.
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Affiliation(s)
- Patricia R Pitrez
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, 3000-548, Coimbra, Portugal
| | - Luis M Monteiro
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, 3000-548, Coimbra, Portugal
- IIIUC-institute of Interdisciplinary Research, University of Coimbra, Casa Costa Alemão, Coimbra, 3030-789, Portugal
| | - Oliver Borgogno
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Xavier Nissan
- CECS, I-STEM, AFM, Institute for Stem Cell Therapy and Exploration of Monogenic diseases, Evry cedex, France
| | - Jerome Mertens
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Lino Ferreira
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.
- Faculty of Medicine, University of Coimbra, 3000-548, Coimbra, Portugal.
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29
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Yan C, Grabowska ME, Dickson AL, Li B, Wen Z, Roden DM, Michael Stein C, Embí PJ, Peterson JF, Feng Q, Malin BA, Wei WQ. Leveraging generative AI to prioritize drug repurposing candidates for Alzheimer's disease with real-world clinical validation. NPJ Digit Med 2024; 7:46. [PMID: 38409350 PMCID: PMC10897392 DOI: 10.1038/s41746-024-01038-3] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Drug repurposing represents an attractive alternative to the costly and time-consuming process of new drug development, particularly for serious, widespread conditions with limited effective treatments, such as Alzheimer's disease (AD). Emerging generative artificial intelligence (GAI) technologies like ChatGPT offer the promise of expediting the review and summary of scientific knowledge. To examine the feasibility of using GAI for identifying drug repurposing candidates, we iteratively tasked ChatGPT with proposing the twenty most promising drugs for repurposing in AD, and tested the top ten for risk of incident AD in exposed and unexposed individuals over age 65 in two large clinical datasets: (1) Vanderbilt University Medical Center and (2) the All of Us Research Program. Among the candidates suggested by ChatGPT, metformin, simvastatin, and losartan were associated with lower AD risk in meta-analysis. These findings suggest GAI technologies can assimilate scientific insights from an extensive Internet-based search space, helping to prioritize drug repurposing candidates and facilitate the treatment of diseases.
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Affiliation(s)
- Chao Yan
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Monika E Grabowska
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alyson L Dickson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - C Michael Stein
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Peter J Embí
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - QiPing Feng
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bradley A Malin
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA.
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30
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Bayram E, Reho P, Litvan I, Ding J, Gibbs JR, Dalgard CL, Traynor BJ, Scholz SW, Chia R. Genetic analysis of the X chromosome in people with Lewy body dementia nominates new risk loci. NPJ Parkinsons Dis 2024; 10:39. [PMID: 38378815 PMCID: PMC10879525 DOI: 10.1038/s41531-024-00649-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Sex influences the prevalence and symptoms of Lewy body dementia (LBD). However, genome-wide association studies typically focus on autosomal variants and exclude sex-specific risk factors. We addressed this gap by performing an X chromosome-wide association study using whole-genome sequence data from 2591 LBD cases and 4391 controls. We identified a significant risk locus within intron 1 of MAP3K15 (rs141773145, odds ratio = 2.42, 95% confidence interval = 1.65-3.56, p-value = 7.0 × 10-6) in female LBD cases conditioned for APOE ε4 dosage. The locus includes an enhancer region that regulates MAP3K15 expression in ganglionic eminence cells derived from primary cultured neurospheres. Rare variant burden testing showed differential enrichment of missense mutations in TEX13A in female LBD cases, that did not reach significance (p-value = 1.34 × 10-4). These findings support the sex-specific effects of genetic factors and a potential role of Alzheimer's-related risk for females with LBD.
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Affiliation(s)
- Ece Bayram
- Department of Neurosciences, Parkinson and Other Movement Disorders Center, University of California San Diego, La Jolla, CA, USA
| | - Paolo Reho
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Irene Litvan
- Department of Neurosciences, Parkinson and Other Movement Disorders Center, University of California San Diego, La Jolla, CA, USA
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - J Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Bryan J Traynor
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA
- Therapeutics Development Laboratory, National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Ruth Chia
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA.
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31
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Brandhorst S, Levine ME, Wei M, Shelehchi M, Morgan TE, Nayak KS, Dorff T, Hong K, Crimmins EM, Cohen P, Longo VD. Fasting-mimicking diet causes hepatic and blood markers changes indicating reduced biological age and disease risk. Nat Commun 2024; 15:1309. [PMID: 38378685 PMCID: PMC10879164 DOI: 10.1038/s41467-024-45260-9] [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: 03/17/2021] [Accepted: 01/18/2024] [Indexed: 02/22/2024] Open
Abstract
In mice, periodic cycles of a fasting mimicking diet (FMD) protect normal cells while killing damaged cells including cancer and autoimmune cells, reduce inflammation, promote multi-system regeneration, and extend longevity. Here, we performed secondary and exploratory analysis of blood samples from a randomized clinical trial (NCT02158897) and show that 3 FMD cycles in adult study participants are associated with reduced insulin resistance and other pre-diabetes markers, lower hepatic fat (as determined by magnetic resonance imaging) and increased lymphoid to myeloid ratio: an indicator of immune system age. Based on a validated measure of biological age predictive of morbidity and mortality, 3 FMD cycles were associated with a decrease of 2.5 years in median biological age, independent of weight loss. Nearly identical findings resulted from a second clinical study (NCT04150159). Together these results provide initial support for beneficial effects of the FMD on multiple cardiometabolic risk factors and biomarkers of biological age.
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Affiliation(s)
- Sebastian Brandhorst
- Longevity Institute, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Morgan E Levine
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Min Wei
- Longevity Institute, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Mahshid Shelehchi
- Longevity Institute, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Todd E Morgan
- Longevity Institute, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Krishna S Nayak
- Ming Hsieh Department of Electrical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Tanya Dorff
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Kurt Hong
- Center of Clinical Nutrition and Applied Health Research, Keck School of Medicine of USC, Los Angeles, CA, 90033, USA
| | - Eileen M Crimmins
- Longevity Institute, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Center on Biodemography and Population Health, University of California Los Angeles and University of Southern California, Los Angeles, CA, 90089, USA
| | - Pinchas Cohen
- Longevity Institute, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Valter D Longo
- Longevity Institute, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
- AIRC Institute of Molecular Oncology, Italian Foundation for Cancer Research Institute of Molecular Oncology, 20139, Milan, Italy.
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32
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Lauffenburger JC, Yom-Tov E, Keller PA, McDonnell ME, Crum KL, Bhatkhande G, Sears ES, Hanken K, Bessette LG, Fontanet CP, Haff N, Vine S, Choudhry NK. The impact of using reinforcement learning to personalize communication on medication adherence: findings from the REINFORCE trial. NPJ Digit Med 2024; 7:39. [PMID: 38374424 PMCID: PMC10876539 DOI: 10.1038/s41746-024-01028-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/05/2024] [Indexed: 02/21/2024] Open
Abstract
Text messaging can promote healthy behaviors, like adherence to medication, yet its effectiveness remains modest, in part because message content is rarely personalized. Reinforcement learning has been used in consumer technology to personalize content but with limited application in healthcare. We tested a reinforcement learning program that identifies individual responsiveness ("adherence") to text message content and personalizes messaging accordingly. We randomized 60 individuals with diabetes and glycated hemoglobin A1c [HbA1c] ≥ 7.5% to reinforcement learning intervention or control (no messages). Both arms received electronic pill bottles to measure adherence. The intervention improved absolute adjusted adherence by 13.6% (95%CI: 1.7%-27.1%) versus control and was more effective in patients with HbA1c 7.5- < 9.0% (36.6%, 95%CI: 25.1%-48.2%, interaction p < 0.001). We also explored whether individual patient characteristics were associated with differential response to tested behavioral factors and unique clusters of responsiveness. Reinforcement learning may be a promising approach to improve adherence and personalize communication at scale.
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Affiliation(s)
- Julie C Lauffenburger
- Center for Healthcare Delivery Sciences, Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | | | - Punam A Keller
- Tuck School of Business, Dartmouth College, Hanover, NH, USA
| | - Marie E McDonnell
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Katherine L Crum
- Center for Healthcare Delivery Sciences, Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gauri Bhatkhande
- Center for Healthcare Delivery Sciences, Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ellen S Sears
- Center for Healthcare Delivery Sciences, Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kaitlin Hanken
- Center for Healthcare Delivery Sciences, Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lily G Bessette
- Center for Healthcare Delivery Sciences, Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Constance P Fontanet
- Center for Healthcare Delivery Sciences, Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Nancy Haff
- Center for Healthcare Delivery Sciences, Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Seanna Vine
- Center for Healthcare Delivery Sciences, Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Niteesh K Choudhry
- Center for Healthcare Delivery Sciences, Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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33
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Kim IJ, Gonzalez O, Tighe MP, Lanthier PA, Clark MJ, Travis KL, Low-Beer TC, Lanzer KG, Bernacki DT, Szaba FM, De La Barrera RA, Dussupt V, Mendez-Rivera L, Krebs SJ, Ross CN, Mdaki SD, Brasky KM, Layne-Colon D, Tardif SD, Thomas SJ, Modjarrad K, Blackman MA, Patterson JL. Protective efficacy of a Zika purified inactivated virus vaccine candidate during pregnancy in marmosets. NPJ Vaccines 2024; 9:35. [PMID: 38368443 PMCID: PMC10874403 DOI: 10.1038/s41541-024-00824-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 01/30/2024] [Indexed: 02/19/2024] Open
Abstract
Zika virus (ZIKV) infection during pregnancy poses significant threats to maternal and fetal health, leading to intrauterine fetal demise and severe developmental malformations that constitute congenital Zika syndrome (CZS). As such, the development of a safe and effective ZIKV vaccine is a critical public health priority. However, the safety and efficacy of such a vaccine during pregnancy remain uncertain. Historically, the conduct of clinical trials in pregnant women has been challenging. Therefore, clinically relevant animal pregnancy models are in high demand for testing vaccine efficacy. We previously reported that a marmoset pregnancy model of ZIKV infection consistently demonstrated vertical transmission from mother to fetus during pregnancy. Using this marmoset model, we also showed that vertical transmission could be prevented by pre-pregnancy vaccination with Zika purified inactivated virus (ZPIV) vaccine. Here, we further examined the efficacy of ZPIV vaccination during pregnancy. Vaccination during pregnancy elicited virus neutralizing antibody responses that were comparable to those elicited by pre-pregnancy vaccination. Vaccination also reduced placental pathology, viral burden and vertical transmission of ZIKV during pregnancy, without causing adverse effects. These results provide key insights into the safety and efficacy of ZPIV vaccination during pregnancy and demonstrate positive effects of vaccination on the reduction of ZIKV infection, an important advance in preparedness for future ZIKV outbreaks.
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Affiliation(s)
- In-Jeong Kim
- Trudeau Institute, Inc., Saranac Lake, NY, 12983, USA.
| | - Olga Gonzalez
- Southwest National Primate Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | | | | | | | | | | | | | | | - Frank M Szaba
- Trudeau Institute, Inc., Saranac Lake, NY, 12983, USA
| | - Rafael A De La Barrera
- Pilot Bioproduction Facility, Center for Enabling Capabilities, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Vincent Dussupt
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Letzibeth Mendez-Rivera
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Shelly J Krebs
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Corinna N Ross
- Southwest National Primate Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Stephanie D Mdaki
- Southwest National Primate Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
- Science and Technology, Joint Base San Antonio-Fort Sam AFB, San Antonio, TX, 78236, USA
| | - Kathleen M Brasky
- Southwest National Primate Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Donna Layne-Colon
- Southwest National Primate Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Suzette D Tardif
- Southwest National Primate Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Stephen J Thomas
- Institute for Global Health and Translational Sciences, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Pfizer Inc. Vaccine Research and Development, Pearl River, NY, 10965, USA
| | | | - Jean L Patterson
- Southwest National Primate Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA.
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Takahashi H, Bhagwagar S, Nies SH, Ye H, Han X, Chiasseu MT, Wang G, Mackenzie IR, Strittmatter SM. Reduced progranulin increases tau and α-synuclein inclusions and alters mouse tauopathy phenotypes via glucocerebrosidase. Nat Commun 2024; 15:1434. [PMID: 38365772 PMCID: PMC10873339 DOI: 10.1038/s41467-024-45692-3] [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: 05/16/2022] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
Comorbid proteinopathies are observed in many neurodegenerative disorders including Alzheimer's disease (AD), increase with age, and influence clinical outcomes, yet the mechanisms remain ill-defined. Here, we show that reduction of progranulin (PGRN), a lysosomal protein associated with TDP-43 proteinopathy, also increases tau inclusions, causes concomitant accumulation of α-synuclein and worsens mortality and disinhibited behaviors in tauopathy mice. The increased inclusions paradoxically protect against spatial memory deficit and hippocampal neurodegeneration. PGRN reduction in male tauopathy attenuates activity of β-glucocerebrosidase (GCase), a protein previously associated with synucleinopathy, while increasing glucosylceramide (GlcCer)-positive tau inclusions. In neuronal culture, GCase inhibition enhances tau aggregation induced by AD-tau. Furthermore, purified GlcCer directly promotes tau aggregation in vitro. Neurofibrillary tangles in human tauopathies are also GlcCer-immunoreactive. Thus, in addition to TDP-43, PGRN regulates tau- and synucleinopathies via GCase and GlcCer. A lysosomal PGRN-GCase pathway may be a common therapeutic target for age-related comorbid proteinopathies.
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Affiliation(s)
- Hideyuki Takahashi
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT, 06536, USA
| | - Sanaea Bhagwagar
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT, 06536, USA
- College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah H Nies
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT, 06536, USA
- Graduate School of Cellular and Molecular Neuroscience, University of Tübingen, D-72074, Tübingen, Germany
| | - Hongping Ye
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center At San Antonio, San Antonio, TX, 78229, USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center At San Antonio, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center At San Antonio, San Antonio, TX, 78229, USA
| | - Marius T Chiasseu
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT, 06536, USA
| | - Guilin Wang
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, CT, 06520, USA
| | - Ian R Mackenzie
- Department of Pathology, University of British Columbia and Vancouver General Hospital, Vancouver, BC, Canada
| | - Stephen M Strittmatter
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT, 06536, USA.
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35
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Di Lucente J, Persico G, Zhou Z, Jin LW, Ramsey JJ, Rutkowsky JM, Montgomery CM, Tomilov A, Kim K, Giorgio M, Maezawa I, Cortopassi GA. Ketogenic diet and BHB rescue the fall of long-term potentiation in an Alzheimer's mouse model and stimulates synaptic plasticity pathway enzymes. Commun Biol 2024; 7:195. [PMID: 38366025 PMCID: PMC10873348 DOI: 10.1038/s42003-024-05860-z] [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: 05/31/2023] [Accepted: 01/26/2024] [Indexed: 02/18/2024] Open
Abstract
The Ketogenic Diet (KD) improves memory and longevity in aged C57BL/6 mice. We tested 7 months KD vs. control diet (CD) in the mouse Alzheimer's Disease (AD) model APP/PS1. KD significantly rescued Long-Term-Potentiation (LTP) to wild-type levels, not by changing Amyloid-β (Aβ) levels. KD's 'main actor' is thought to be Beta-Hydroxy-butyrate (BHB) whose levels rose significantly in KD vs. CD mice, and BHB itself significantly rescued LTP in APP/PS1 hippocampi. KD's 6 most significant pathways induced in brains by RNAseq all related to Synaptic Plasticity. KD induced significant increases in synaptic plasticity enzymes p-ERK and p-CREB in both sexes, and of brain-derived neurotrophic factor (BDNF) in APP/PS1 females. We suggest KD rescues LTP through BHB's enhancement of synaptic plasticity. LTP falls in Mild-Cognitive Impairment (MCI) of human AD. KD and BHB, because they are an approved diet and supplement respectively, may be most therapeutically and translationally relevant to the MCI phase of Alzheimer's Disease.
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Affiliation(s)
- Jacopo Di Lucente
- Department of Pathology and MIND Institute, University of California Davis Medical Center, Sacramento, CA, 95817, USA
| | - Giuseppe Persico
- Department of Experimental Oncology, European Institute of Oncology, IRCCS, 21041, Milan, Italy
| | - Zeyu Zhou
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Lee-Way Jin
- Department of Pathology and MIND Institute, University of California Davis Medical Center, Sacramento, CA, 95817, USA
- Alzheimer's Disease Research Center, University of California Davis Medical Center, Sacramento, CA, 95817, USA
| | - Jon J Ramsey
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Jennifer M Rutkowsky
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Claire M Montgomery
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Alexey Tomilov
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Kyoungmi Kim
- Department of Public Health Sciences, School of Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Marco Giorgio
- Department of Biomedical Sciences, University of Padova, 35131, Padova, Italy
| | - Izumi Maezawa
- Department of Pathology and MIND Institute, University of California Davis Medical Center, Sacramento, CA, 95817, USA.
- Alzheimer's Disease Research Center, University of California Davis Medical Center, Sacramento, CA, 95817, USA.
| | - Gino A Cortopassi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, 95616, USA.
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36
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Yang L, Tu L, Bisht S, Mao Y, Petkovich D, Thursby SJ, Liang J, Patel N, Yen RWC, Largent T, Zahnow C, Brock M, Gabrielson K, Salimian KJ, Baylin SB, Easwaran H. Tissue-location-specific transcription programs drive tumor dependencies in colon cancer. Nat Commun 2024; 15:1384. [PMID: 38360902 PMCID: PMC10869357 DOI: 10.1038/s41467-024-45605-4] [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: 05/16/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Cancers of the same tissue-type but in anatomically distinct locations exhibit different molecular dependencies for tumorigenesis. Proximal and distal colon cancers exemplify such characteristics, with BRAFV600E predominantly occurring in proximal colon cancers along with increased DNA methylation phenotype. Using mouse colon organoids, here we show that proximal and distal colon stem cells have distinct transcriptional programs that regulate stemness and differentiation. We identify that the homeobox transcription factor, CDX2, which is silenced by DNA methylation in proximal colon cancers, is a key mediator of the differential transcriptional programs. Cdx2-mediated proximal colon-specific transcriptional program concurrently is tumor suppressive, and Cdx2 loss sufficiently creates permissive state for BRAFV600E-driven transformation. Human proximal colon cancers with CDX2 downregulation showed similar transcriptional program as in mouse proximal organoids with Cdx2 loss. Developmental transcription factors, such as CDX2, are thus critical in maintaining tissue-location specific transcriptional programs that create tissue-type origin specific dependencies for tumor development.
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Affiliation(s)
- Lijing Yang
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, PR China
| | - Lei Tu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Shilpa Bisht
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Yiqing Mao
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Daniel Petkovich
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Sara-Jayne Thursby
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Jinxiao Liang
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Nibedita Patel
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Ray-Whay Chiu Yen
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Tina Largent
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Cynthia Zahnow
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Malcolm Brock
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Kathy Gabrielson
- Department of Comparative Medicine, Johns Hopkins Medical Institutions, 863 Broadway Research Building, 733 N. Broadway, Baltimore, MD, 21205-2196, USA
| | - Kevan J Salimian
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Stephen B Baylin
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Hariharan Easwaran
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA.
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37
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Chen G, Zhou G, Zhai L, Bao X, Tiwari N, Li J, Mottillo E, Wang J. SHMT2 reduces fatty liver but is necessary for liver inflammation and fibrosis in mice. Commun Biol 2024; 7:173. [PMID: 38347107 PMCID: PMC10861579 DOI: 10.1038/s42003-024-05861-y] [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: 09/25/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
Non-alcoholic fatty liver disease is associated with an irregular serine metabolism. Serine hydroxymethyltransferase 2 (SHMT2) is a liver enzyme that breaks down serine into glycine and one-carbon (1C) units critical for liver methylation reactions and overall health. However, the contribution of SHMT2 to hepatic 1C homeostasis and biological functions has yet to be defined in genetically modified animal models. We created a mouse strain with targeted SHMT2 knockout in hepatocytes to investigate this. The absence of SHMT2 increased serine and glycine levels in circulation, decreased liver methylation potential, and increased susceptibility to fatty liver disease. Interestingly, SHMT2-deficient mice developed simultaneous fatty liver, but when fed a diet high in fat, fructose, and cholesterol, they had significantly less inflammation and fibrosis. This study highlights the critical role of SHMT2 in maintaining hepatic 1C homeostasis and its stage-specific functions in the pathogenesis of NAFLD.
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Affiliation(s)
- Guohua Chen
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, 48202, USA
| | - Guoli Zhou
- Biomedical Research Informatics Core, Clinical and Translational Sciences Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - Lidong Zhai
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xun Bao
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, 48202, USA
| | - Nivedita Tiwari
- Hypertension and Vascular Research Division, Henry Ford Hospital, Detroit, MI, 48202, USA
| | - Jing Li
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, 48202, USA
| | - Emilio Mottillo
- Hypertension and Vascular Research Division, Henry Ford Hospital, Detroit, MI, 48202, USA
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, 48202, USA
| | - Jian Wang
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, 48202, USA.
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38
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Rybnicek J, Chen Y, Milic M, Tio ES, McLaurin J, Hohman TJ, De Jager PL, Schneider JA, Wang Y, Bennett DA, Tripathy S, Felsky D, Lambe EK. CHRNA5 links chandelier cells to severity of amyloid pathology in aging and Alzheimer's disease. Transl Psychiatry 2024; 14:83. [PMID: 38331937 PMCID: PMC10853183 DOI: 10.1038/s41398-024-02785-3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
Changes in high-affinity nicotinic acetylcholine receptors are intricately connected to neuropathology in Alzheimer's Disease (AD). Protective and cognitive-enhancing roles for the nicotinic α5 subunit have been identified, but this gene has not been closely examined in the context of human aging and dementia. Therefore, we investigate the nicotinic α5 gene CHRNA5 and the impact of relevant single nucleotide polymorphisms (SNPs) in prefrontal cortex from 922 individuals with matched genotypic and post-mortem RNA sequencing in the Religious Orders Study and Memory and Aging Project (ROS/MAP). We find that a genotype robustly linked to increased expression of CHRNA5 (rs1979905A2) predicts significantly reduced cortical β-amyloid load. Intriguingly, co-expression analysis suggests CHRNA5 has a distinct cellular expression profile compared to other nicotinic receptor genes. Consistent with this prediction, single nucleus RNA sequencing from 22 individuals reveals CHRNA5 expression is disproportionately elevated in chandelier neurons, a distinct subtype of inhibitory neuron known for its role in excitatory/inhibitory (E/I) balance. We show that chandelier neurons are enriched in amyloid-binding proteins compared to basket cells, the other major subtype of PVALB-positive interneurons. Consistent with the hypothesis that nicotinic receptors in chandelier cells normally protect against β-amyloid, cell-type proportion analysis from 549 individuals reveals these neurons show amyloid-associated vulnerability only in individuals with impaired function/trafficking of nicotinic α5-containing receptors due to homozygosity of the missense CHRNA5 SNP (rs16969968A2). Taken together, these findings suggest that CHRNA5 and its nicotinic α5 subunit exert a neuroprotective role in aging and Alzheimer's disease centered on chandelier interneurons.
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Affiliation(s)
- Jonas Rybnicek
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Yuxiao Chen
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Milos Milic
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Earvin S Tio
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - JoAnne McLaurin
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Timothy J Hohman
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Julie A Schneider
- Department of Pathology, Rush University, Chicago, IL, USA
- Department of Neurological Sciences, Rush University, Chicago, IL, USA
| | - Yanling Wang
- Department of Neurological Sciences, Rush University, Chicago, IL, USA
| | - David A Bennett
- Department of Neurological Sciences, Rush University, Chicago, IL, USA
| | - Shreejoy Tripathy
- Department of Physiology, University of Toronto, Toronto, ON, Canada.
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
| | - Evelyn K Lambe
- Department of Physiology, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
- Department of OBGYN, University of Toronto, Toronto, ON, Canada.
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39
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Tilden EI, Maduskar A, Oldenborg A, Sabatini BL, Chen Y. A Cre-dependent reporter mouse for quantitative real-time imaging of protein kinase A activity dynamics. Sci Rep 2024; 14:3054. [PMID: 38321128 PMCID: PMC10847463 DOI: 10.1038/s41598-024-53313-8] [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: 11/17/2023] [Accepted: 01/30/2024] [Indexed: 02/08/2024] Open
Abstract
Intracellular signaling dynamics play a crucial role in cell function. Protein kinase A (PKA) is a key signaling molecule that has diverse functions, from regulating metabolism and brain activity to guiding development and cancer progression. We previously developed an optical reporter, FLIM-AKAR, that allows for quantitative imaging of PKA activity via fluorescence lifetime imaging microscopy and photometry. However, using viral infection or electroporation for the delivery of FLIM-AKAR is invasive and results in variable expression. Here, we developed a reporter mouse, FL-AK, which expresses FLIM-AKAR in a Cre-dependent manner from the ROSA26 locus. FL-AK provides robust and consistent expression of FLIM-AKAR over time. Functionally, the mouse line reports an increase in PKA activity in response to activation of both Gαs and Gαq-coupled receptors in brain slices. In vivo, FL-AK reports PKA phosphorylation in response to neuromodulator receptor activation. Thus, FL-AK provides a quantitative, robust, and flexible method to reveal the dynamics of PKA activity in diverse cell types.
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Affiliation(s)
- Elizabeth I Tilden
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA
- Ph.D. Program in Neuroscience, Washington University in St. Louis, St. Louis, MO, USA
| | - Aditi Maduskar
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA
| | - Anna Oldenborg
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA
| | - Bernardo L Sabatini
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Yao Chen
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA.
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40
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Yanai H, Park B, Koh H, Jang HJ, Vaughan KL, Tanaka-Yano M, Aon M, Blanton M, Messaoudi I, Diaz-Ruiz A, Mattison JA, Beerman I. Short-term periodic restricted feeding elicits metabolome-microbiome signatures with sex dimorphic persistence in primate intervention. Nat Commun 2024; 15:1088. [PMID: 38316796 PMCID: PMC10844192 DOI: 10.1038/s41467-024-45359-z] [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: 08/02/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024] Open
Abstract
Dietary restriction has shown benefits in physiological, metabolic, and molecular signatures associated with aging but is a difficult lifestyle to maintain for most individuals. In mice, a less restrictive diet that allows for cyclical periods of reduced calories mitigates aging phenotypes, yet the effects of such an intervention in a genetically heterogenous, higher-order mammal has not been examined. Here, using middle-aged rhesus macaques matched for age and sex, we show that a regimen of 4 days of low-calorie intake followed by 10 days of ad libitum feeding (4:10 diet) performed in repeating cycles over 12 weeks led to significant loss of weight and fat percentage, despite the free access to food for most of the study duration. We show the 4-day restriction period is sufficient to drive alterations to the serum metabolome characterized by substantial differences in lipid classes. These phenotypes were paralleled by changes in the gut microbiome of restricted monkeys that highlight the involvement of a microbiome-metabolome axis. This regimen shows promising phenotypes, with some sex-dimorphic responses, including residual memory of the diet. As many calorie restriction interventions are difficult to sustain, we propose that this short-term diet may be easier to adhere to and have benefits directly relevant to human aging.
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Affiliation(s)
- Hagai Yanai
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Bongsoo Park
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Hyunwook Koh
- Department of Applied Mathematics & Statistics, The State University of New York, Korea (SUNY Korea), Incheon, South Korea
| | - Hyo Jung Jang
- Department of Applied Mathematics & Statistics, The State University of New York, Korea (SUNY Korea), Incheon, South Korea
| | - Kelli L Vaughan
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Mayuri Tanaka-Yano
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Miguel Aon
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Madison Blanton
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Alberto Diaz-Ruiz
- Laboratory of Cellular and Molecular Gerontology, Precision Nutrition and Aging Program, Institute IMDEA Food (CEI UAM+CSIC), Madrid, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Madrid, Spain
| | - Julie A Mattison
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Isabel Beerman
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA.
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41
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Wu M, Wu S, Chen W, Li YP. The roles and regulatory mechanisms of TGF-β and BMP signaling in bone and cartilage development, homeostasis and disease. Cell Res 2024; 34:101-123. [PMID: 38267638 PMCID: PMC10837209 DOI: 10.1038/s41422-023-00918-9] [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: 02/26/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024] Open
Abstract
Transforming growth factor-βs (TGF-βs) and bone morphometric proteins (BMPs) belong to the TGF-β superfamily and perform essential functions during osteoblast and chondrocyte lineage commitment and differentiation, skeletal development, and homeostasis. TGF-βs and BMPs transduce signals through SMAD-dependent and -independent pathways; specifically, they recruit different receptor heterotetramers and R-Smad complexes, resulting in unique biological readouts. BMPs promote osteogenesis, osteoclastogenesis, and chondrogenesis at all differentiation stages, while TGF-βs play different roles in a stage-dependent manner. BMPs and TGF-β have opposite functions in articular cartilage homeostasis. Moreover, TGF-β has a specific role in maintaining the osteocyte network. The precise activation of BMP and TGF-β signaling requires regulatory machinery at multiple levels, including latency control in the matrix, extracellular antagonists, ubiquitination and phosphorylation in the cytoplasm, nucleus-cytoplasm transportation, and transcriptional co-regulation in the nuclei. This review weaves the background information with the latest advances in the signaling facilitated by TGF-βs and BMPs, and the advanced understanding of their diverse physiological functions and regulations. This review also summarizes the human diseases and mouse models associated with disordered TGF-β and BMP signaling. A more precise understanding of the BMP and TGF-β signaling could facilitate the development of bona fide clinical applications in treating bone and cartilage disorders.
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Affiliation(s)
- Mengrui Wu
- Department of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Shali Wu
- Department of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wei Chen
- Division in Cellular and Molecular Medicine, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA, USA
| | - Yi-Ping Li
- Division in Cellular and Molecular Medicine, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA, USA.
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42
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Kee TR, Khan SA, Neidhart MB, Masters BM, Zhao VK, Kim YK, McGill Percy KC, Woo JAA. The multifaceted functions of β-arrestins and their therapeutic potential in neurodegenerative diseases. Exp Mol Med 2024; 56:129-141. [PMID: 38212557 PMCID: PMC10834518 DOI: 10.1038/s12276-023-01144-4] [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: 04/20/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 01/13/2024] Open
Abstract
Arrestins are multifunctional proteins that regulate G-protein-coupled receptor (GPCR) desensitization, signaling, and internalization. The arrestin family consists of four subtypes: visual arrestin1, β-arrestin1, β-arrestin2, and visual arrestin-4. Recent studies have revealed the multifunctional roles of β-arrestins beyond GPCR signaling, including scaffolding and adapter functions, and physically interacting with non-GPCR receptors. Increasing evidence suggests that β-arrestins are involved in the pathogenesis of a variety of neurodegenerative diseases, including Alzheimer's disease (AD), frontotemporal dementia (FTD), and Parkinson's disease (PD). β-arrestins physically interact with γ-secretase, leading to increased production and accumulation of amyloid-beta in AD. Furthermore, β-arrestin oligomers inhibit the autophagy cargo receptor p62/SQSTM1, resulting in tau accumulation and aggregation in FTD. In PD, β-arrestins are upregulated in postmortem brain tissue and an MPTP model, and the β2AR regulates SNCA gene expression. In this review, we aim to provide an overview of β-arrestin1 and β-arrestin2, and describe their physiological functions and roles in neurodegenerative diseases. The multifaceted roles of β-arrestins and their involvement in neurodegenerative diseases suggest that they may serve as promising therapeutic targets.
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Affiliation(s)
- Teresa R Kee
- Department of Pathology, CWRU School of Medicine, Cleveland, OH, 44106, USA
- Department of Molecular Medicine, USF Health College of Medicine, Tampa, FL, 33613, USA
| | - Sophia A Khan
- Department of Pathology, CWRU School of Medicine, Cleveland, OH, 44106, USA
| | - Maya B Neidhart
- Department of Pathology, CWRU School of Medicine, Cleveland, OH, 44106, USA
| | - Brianna M Masters
- Department of Pathology, CWRU School of Medicine, Cleveland, OH, 44106, USA
| | - Victoria K Zhao
- Department of Pathology, CWRU School of Medicine, Cleveland, OH, 44106, USA
| | - Yenna K Kim
- Department of Pathology, CWRU School of Medicine, Cleveland, OH, 44106, USA
| | | | - Jung-A A Woo
- Department of Pathology, CWRU School of Medicine, Cleveland, OH, 44106, USA.
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43
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Irwin KE, Jasin P, Braunstein KE, Sinha IR, Garret MA, Bowden KD, Chang K, Troncoso JC, Moghekar A, Oh ES, Raitcheva D, Bartlett D, Miller T, Berry JD, Traynor BJ, Ling JP, Wong PC. A fluid biomarker reveals loss of TDP-43 splicing repression in presymptomatic ALS-FTD. Nat Med 2024; 30:382-393. [PMID: 38278991 PMCID: PMC10878965 DOI: 10.1038/s41591-023-02788-5] [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: 01/24/2023] [Accepted: 12/21/2023] [Indexed: 01/28/2024]
Abstract
Although loss of TAR DNA-binding protein 43 kDa (TDP-43) splicing repression is well documented in postmortem tissues of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), whether this abnormality occurs during early-stage disease remains unresolved. Cryptic exon inclusion reflects loss of function of TDP-43, and thus detection of proteins containing cryptic exon-encoded neoepitopes in cerebrospinal fluid (CSF) or blood could reveal the earliest stages of TDP-43 dysregulation in patients. Here we use a newly characterized monoclonal antibody specific to a TDP-43-dependent cryptic epitope (encoded by the cryptic exon found in HDGFL2) to show that loss of TDP-43 splicing repression occurs in ALS-FTD, including in presymptomatic C9orf72 mutation carriers. Cryptic hepatoma-derived growth factor-like protein 2 (HDGFL2) accumulates in CSF at significantly higher levels in familial ALS-FTD and sporadic ALS compared with controls and is elevated earlier than neurofilament light and phosphorylated neurofilament heavy chain protein levels in familial disease. Cryptic HDGFL2 can also be detected in blood of individuals with ALS-FTD, including in presymptomatic C9orf72 mutation carriers, and accumulates at levels highly correlated with those in CSF. Our findings indicate that loss of TDP-43 cryptic splicing repression occurs early in disease progression, even presymptomatically, and that detection of the HDGFL2 cryptic neoepitope serves as a potential diagnostic biomarker for ALS, which should facilitate patient recruitment and measurement of target engagement in clinical trials.
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Affiliation(s)
- Katherine E Irwin
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Pei Jasin
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
| | | | - Irika R Sinha
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Mark A Garret
- Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Kyra D Bowden
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Koping Chang
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department and Graduate Institute of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Esther S Oh
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medicine, Baltimore, MD, USA
| | | | | | - Timothy Miller
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - James D Berry
- Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Bryan J Traynor
- Department of Neurology, Johns Hopkins Medicine, Baltimore, MD, USA
- Neuromuscular Diseases Research Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- National Institute of Neurological Disorders, National Institutes of Health, Bethesda, MD, USA
- RNA Therapeutics Laboratory, Therapeutics Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Jonathan P Ling
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Philip C Wong
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA.
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA.
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44
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Zuffa S, Schmid R, Bauermeister A, P Gomes PW, Caraballo-Rodriguez AM, El Abiead Y, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, Pessotti RDC, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Silva Dos Santos M, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, Vera Ponce de León A, Pope PB, La Rosa SL, La Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nat Microbiol 2024; 9:336-345. [PMID: 38316926 PMCID: PMC10847041 DOI: 10.1038/s41564-023-01575-9] [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: 07/20/2023] [Accepted: 11/29/2023] [Indexed: 02/07/2024]
Abstract
microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.
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Affiliation(s)
- Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Anelize Bauermeister
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paulo Wender P Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Andres M Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Allegra T Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
| | - Emily C Gentry
- Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA
| | - Michael J Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Nicole E Avalon
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, Norman, OK, USA
| | - Ekaterina Buzun
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Marvic Carrillo Terrazas
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Chia-Yun Hsu
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Renee Oles
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Adriana Vasquez Ayala
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Jiaqi Zhao
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Hiutung Chu
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
- Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, San Diego, CA, USA
| | - Mirte C M Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Sara L Jackrel
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Fidele Tugizimana
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
- International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, Johannesburg, South Africa
| | - Lerato Pertunia Nephali
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Ian A Dubery
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Ntakadzeni Edwin Madala
- Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Thohoyandou, South Africa
| | - Eduarda Antunes Moreira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Norberto Peporine Lopes
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Paula Rezende-Teixeira
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula C Jimenez
- Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Santos, Brazil
| | - Bipin Rimal
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Matthew F Traxler
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA
| | - Rita de Cassia Pessotti
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA
| | - Daniel Alvarado-Villalobos
- Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Giselle Tamayo-Castillo
- Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
| | - Priscila Chaverri
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, MD, USA
| | - Efrain Escudero-Leyva
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Luis-Manuel Quiros-Guerrero
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Alexandre Jean Bory
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Juliette Joubert
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Adriano Rutz
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Andreas Sichert
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Benjamin S Pullman
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Katia Gindro
- Plant Protection, Mycology group, Agroscope, Nyon, Switzerland
| | | | - Berenike C Wagner
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Karl Forchhammer
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Daniel Petras
- Cluster of Excellence 'Controlling Microbes to Fight Infections' (CMFI), University of Tuebingen, Tuebingen, Germany
| | - Nicole Aiosa
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Manuel Liebeke
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Department for Metabolomics, Kiel University, Kiel, Germany
| | - Patric Bourceau
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Henna Gadhavi
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
- King's College London, London, UK
| | - Luiz Pedro Sorio de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
- Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
| | | | - Alicia Isabel Pérez-Lorente
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Carlos Molina-Santiago
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Diego Romero
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany
| | - Arturo Vera Ponce de León
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip Byron Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Giorgia La Barbera
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | | | - Fabian Hammerle
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Bianka Siewert
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Ursula Peintner
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Cuauhtemoc Licona-Cassani
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico
| | - Lorena Rodriguez-Orduña
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Felina Hildebrand
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Katharina Hohenwallner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Lisa Panzenboeck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Jane Odoi
- Faculty of Engineering, University of Nottingham, Nottingham, UK
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Su Ding
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Xue Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jerry J Cui
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
| | - Kou-San Ju
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
| | - Denise Brentan Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Fernanda Motta Ribeiro Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Hector H F Koolen
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Carlismari Grundmann
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kirk Broders
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Sidnee E Ober-Singleton
- Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, Eugene, OR, USA
| | | | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
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Xia M, Anderson TL, Prantzalos ER, Hawkinson TR, Clarke HA, Keohane SB, Sun RC, Turner JR, Ortinski PI. Voltage-gated potassium channels control extended access cocaine seeking: a role for nucleus accumbens astrocytes. Neuropsychopharmacology 2024; 49:551-560. [PMID: 37660129 PMCID: PMC10789875 DOI: 10.1038/s41386-023-01718-w] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/03/2023] [Accepted: 08/21/2023] [Indexed: 09/04/2023]
Abstract
Dopaminergic signaling in the nucleus accumbens shell (NAc) regulates neuronal activity relevant to reward-related learning, including cocaine-associated behaviors. Although astrocytes respond to dopamine and cocaine with structural changes, the impact of dopamine and cocaine on astrocyte functional plasticity has not been widely studied. Specifically, behavioral implications of voltage-gated channel activity in the canonically non-excitable astrocytes are not known. We characterized potassium channel function in NAc astrocytes following exposure to exogenous dopamine or cocaine self-administration training under short (2 h/day) and extended (6 h/day) access schedules. Electrophysiological, Ca2+ imaging, mRNA, and mass spectrometry tools were used for molecular characterization. Behavioral effects were examined after NAc-targeted microinjections of channel antagonists and astroglial toxins. Exogenous dopamine increased activity of currents mediated by voltage-gated (Kv7) channels in NAc astrocytes. This was associated with a ~5-fold increase in expression of Kcnq2 transcript level in homogenized NAc micropunches. Matrix-assisted laser desorption/ionization mass spectrometry revealed increased NAc dopamine levels in extended access, relative to short access, rats. Kv7 inhibition selectively increased frequency and amplitude of astrocyte intracellular Ca2+ transients in NAc of extended access rats. Inhibition of Kv7 channels in the NAc attenuated cocaine-seeking in extended access rats only, an effect that was occluded by microinjection of the astrocyte metabolic poison, fluorocitrate. These results suggest that voltage-gated K+ channel signaling in NAc astrocytes is behaviorally relevant, support Kv7-mediated regulation of astrocyte Ca2+ signals, and propose novel mechanisms of neuroglial interactions relevant to drug use.
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Affiliation(s)
- Mengfan Xia
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY, USA
| | - Tanner L Anderson
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA
| | - Emily R Prantzalos
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Tara R Hawkinson
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Harrison A Clarke
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Shannon B Keohane
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Ramon C Sun
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
- Center for Advanced Spatial Biomolecule Research, University of Florida, Gainesville, FL, USA
| | - Jill R Turner
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Pavel I Ortinski
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA.
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46
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Bernabe CS, Caliman IF, de Abreu ARR, Molosh AI, Truitt WA, Shekhar A, Johnson PL. Identification of a novel perifornical-hypothalamic-area-projecting serotonergic system that inhibits innate panic and conditioned fear responses. Transl Psychiatry 2024; 14:60. [PMID: 38272876 PMCID: PMC10811332 DOI: 10.1038/s41398-024-02769-3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
The serotonin (5-HT) system is heavily implicated in the regulation of anxiety and trauma-related disorders such as panic disorder and post-traumatic stress disorder, respectively. However, the neural mechanisms of how serotonergic neurotransmission regulates innate panic and fear brain networks are poorly understood. Our earlier studies have identified that orexin (OX)/glutamate neurons within the perifornical hypothalamic area (PFA) play a critical role in adaptive and pathological panic and fear. While site-specific and electrophysiological studies have shown that intracranial injection and bath application of 5-HT inhibits PFA neurons via 5-HT1a receptors, they largely ignore circuit-specific neurotransmission and its physiological properties that occur in vivo. Here, we investigate the role of raphe nuclei 5-HT inputs into the PFA in panic and fear behaviors. We initially confirmed that photostimulation of glutamatergic neurons in the PFA of rats produces robust cardioexcitation and flight/aversive behaviors resembling panic-like responses. Using the retrograde tracer cholera toxin B, we determined that the PFA receives discrete innervation of serotonergic neurons clustered in the lateral wings of the dorsal (lwDRN) and in the median (MRN) raphe nuclei. Selective lesions of these serotonergic projections with saporin toxin resulted in similar panic-like responses during the suffocation-related CO2 challenge and increased freezing to fear-conditioning paradigm. Conversely, selective stimulation of serotonergic fibers in the PFA attenuated both flight/escape behaviors and cardioexcitation responses elicited by the CO2 challenge and induced conditioned place preference. The data here support the hypothesis that PFA projecting 5-HT neurons in the lwDRN/MRN represents a panic/fear-off circuit and may also play a role in reward behavior.
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Affiliation(s)
- Cristian S Bernabe
- Department of Anatomy, Cellular Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Izabela F Caliman
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Aline R R de Abreu
- Departamento de Alimentos, Escola de Nutrição da Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Andrei I Molosh
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - William A Truitt
- Department of Anatomy, Cellular Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Anantha Shekhar
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Philip L Johnson
- Department of Biology, University of South Dakota, Vermillion, SD, USA
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47
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Leung YY, Naj AC, Chou YF, Valladares O, Schmidt M, Hamilton-Nelson K, Wheeler N, Lin H, Gangadharan P, Qu L, Clark K, Kuzma AB, Lee WP, Cantwell L, Nicaretta H, Haines J, Farrer L, Seshadri S, Brkanac Z, Cruchaga C, Pericak-Vance M, Mayeux RP, Bush WS, Destefano A, Martin E, Schellenberg GD, Wang LS. Human whole-exome genotype data for Alzheimer's disease. Nat Commun 2024; 15:684. [PMID: 38263370 PMCID: PMC10805795 DOI: 10.1038/s41467-024-44781-7] [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: 12/19/2022] [Accepted: 01/02/2024] [Indexed: 01/25/2024] Open
Abstract
The heterogeneity of the whole-exome sequencing (WES) data generation methods present a challenge to a joint analysis. Here we present a bioinformatics strategy for joint-calling 20,504 WES samples collected across nine studies and sequenced using ten capture kits in fourteen sequencing centers in the Alzheimer's Disease Sequencing Project. The joint-genotype called variant-called format (VCF) file contains only positions within the union of capture kits. The VCF was then processed specifically to account for the batch effects arising from the use of different capture kits from different studies. We identified 8.2 million autosomal variants. 96.82% of the variants are high-quality, and are located in 28,579 Ensembl transcripts. 41% of the variants are intronic and 1.8% of the variants are with CADD > 30, indicating they are of high predicted pathogenicity. Here we show our new strategy can generate high-quality data from processing these diversely generated WES samples. The improved ability to combine data sequenced in different batches benefits the whole genomics research community.
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Affiliation(s)
- Yuk Yee Leung
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Adam C Naj
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yi-Fan Chou
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Otto Valladares
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Schmidt
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Kara Hamilton-Nelson
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Nicholas Wheeler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Honghuang Lin
- Department of Medicine, UMass Chan Medical School, Boston, MA, USA
| | - Prabhakaran Gangadharan
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Liming Qu
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kaylyn Clark
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda B Kuzma
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wan-Ping Lee
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Cantwell
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Heather Nicaretta
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Lindsay Farrer
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Sudha Seshadri
- Boston University School of Medicine, Boston, MA, USA
- The Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Zoran Brkanac
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Carlos Cruchaga
- Washington University School of Medicine, St. Louis, MO, USA
| | - Margaret Pericak-Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Richard P Mayeux
- Department of Neurology, Taub Institute for Research on Alzheimer's Disease and the Aging Brain and the Gertrude H. Sergievsky Center, Columbia University and the New York Presbyterian Hospital, New York, NY, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Anita Destefano
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Eden Martin
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Gerard D Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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48
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Novais EJ, Narayanan R, Canseco JA, van de Wetering K, Kepler CK, Hilibrand AS, Vaccaro AR, Risbud MV. A new perspective on intervertebral disc calcification-from bench to bedside. Bone Res 2024; 12:3. [PMID: 38253615 PMCID: PMC10803356 DOI: 10.1038/s41413-023-00307-3] [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: 10/15/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/24/2024] Open
Abstract
Disc degeneration primarily contributes to chronic low back and neck pain. Consequently, there is an urgent need to understand the spectrum of disc degeneration phenotypes such as fibrosis, ectopic calcification, herniation, or mixed phenotypes. Amongst these phenotypes, disc calcification is the least studied. Ectopic calcification, by definition, is the pathological mineralization of soft tissues, widely studied in the context of conditions that afflict vasculature, skin, and cartilage. Clinically, disc calcification is associated with poor surgical outcomes and back pain refractory to conservative treatment. It is frequently seen as a consequence of disc aging and progressive degeneration but exhibits unique molecular and morphological characteristics: hypertrophic chondrocyte-like cell differentiation; TNAP, ENPP1, and ANK upregulation; cell death; altered Pi and PPi homeostasis; and local inflammation. Recent studies in mouse models have provided a better understanding of the mechanisms underlying this phenotype. It is essential to recognize that the presentation and nature of mineralization differ between AF, NP, and EP compartments. Moreover, the combination of anatomic location, genetics, and environmental stressors, such as aging or trauma, govern the predisposition to calcification. Lastly, the systemic regulation of calcium and Pi metabolism is less important than the local activity of PPi modulated by the ANK-ENPP1 axis, along with disc cell death and differentiation status. While there is limited understanding of this phenotype, understanding the molecular pathways governing local intervertebral disc calcification may lead to developing disease-modifying drugs and better clinical management of degeneration-related pathologies.
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Affiliation(s)
- Emanuel J Novais
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Unidade Local de Saúde do Litoral Alentejano, Orthopedic Department, Santiago do Cacém, Portugal
| | - Rajkishen Narayanan
- Rothman Orthopedic Institute at Thomas Jefferson University, Philadelphia, PA, USA
| | - Jose A Canseco
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Rothman Orthopedic Institute at Thomas Jefferson University, Philadelphia, PA, USA
| | - Koen van de Wetering
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Christopher K Kepler
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Rothman Orthopedic Institute at Thomas Jefferson University, Philadelphia, PA, USA
| | - Alan S Hilibrand
- Rothman Orthopedic Institute at Thomas Jefferson University, Philadelphia, PA, USA
| | - Alexander R Vaccaro
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Rothman Orthopedic Institute at Thomas Jefferson University, Philadelphia, PA, USA
| | - Makarand V Risbud
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA.
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49
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Yu Q, Du F, Belli I, Gomes PA, Sotiropoulos I, Waites CL. Glucocorticoid stress hormones stimulate vesicle-free Tau secretion and spreading in the brain. Cell Death Dis 2024; 15:73. [PMID: 38238309 PMCID: PMC10796385 DOI: 10.1038/s41419-024-06458-3] [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: 06/22/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/22/2024]
Abstract
Chronic stress and elevated levels of glucocorticoids (GCs), the main stress hormones, accelerate Alzheimer's disease (AD) onset and progression. A major driver of AD progression is the spreading of pathogenic Tau protein between brain regions, precipitated by neuronal Tau secretion. While stress and high GC levels are known to induce intraneuronal Tau pathology (i.e. hyperphosphorylation, oligomerization) in animal models, their role in trans-neuronal Tau spreading is unexplored. Here, we find that GCs promote secretion of full-length, primarily vesicle-free, phosphorylated Tau from murine hippocampal neurons and ex vivo brain slices. This process requires neuronal activity and the kinase GSK3β. GCs also dramatically enhance trans-neuronal Tau spreading in vivo, and this effect is blocked by an inhibitor of Tau oligomerization and type 1 unconventional protein secretion. These findings uncover a potential mechanism by which stress/GCs stimulate Tau propagation in AD.
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Affiliation(s)
- Qing Yu
- Department of Pathology and Cell Biology, Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Fang Du
- Department of Pathology and Cell Biology, Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Irla Belli
- Department of Pathology and Cell Biology, Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Patricia A Gomes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Ioannis Sotiropoulos
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
- Institute of Biosciences and Applications, National Centre for Scientific Research (NCSR) Demokritos, Agia Paraskevi, Greece
| | - Clarissa L Waites
- Department of Pathology and Cell Biology, Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Neuroscience, Columbia University, New York, NY, USA.
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50
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Lindenboim L, Zohar H, Gundersen GG, Worman HJ, Stein R. LINC complex protein nesprin-2 has pro-apoptotic activity via Bcl-2 family proteins. Cell Death Discov 2024; 10:29. [PMID: 38225256 PMCID: PMC10789774 DOI: 10.1038/s41420-023-01763-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/13/2023] [Accepted: 12/06/2023] [Indexed: 01/17/2024] Open
Abstract
The apoptotic intrinsic pathway is initiated by perforation of the mitochondrial outer membrane by the effector pro-apoptotic proteins of the Bcl-2 family, Bax and Bak. Bax and Bak need to be activated, a process facilitated by the action of BH3-only pro-apoptotic members of the Bcl-2 family. The latter either directly activates the effector proteins or antagonizes the action of pro-survival Bcl-2 family members such as Bcl-xL. The nuclear envelope is a known target of the apoptotic machinery; however, it may also act as mediator of apoptosis. We showed previously that the nuclear envelope protein nesprin-2, a component of the linker of nucleoskeleton and cytoskeleton (LINC) complex, can bind to Bax in close proximity to the mitochondria and that the binding increases in apoptotic cells. We now show that depleting nesprin-2 inhibits the apoptotic mitochondrial pathway as measured by Bax and Bak activation and cytochrome c release. This survival effect was Bcl-xL-dependent. Nesprin-2 depletion also inhibited spontaneous exposure of the N-terminus of Bak in cells lacking Bcl-xL and increased the presence of Bcl-xL and Bax in the mitochondria. These results indicate that nesprin-2 promotes Bak activation and regulates mitochondrial translocation/retrotranslocation of Bcl-2 family proteins. Our findings demonstrate a new apoptotic pathway whereby the nuclear envelope, via nesprin-2, regulates apoptosis.
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Affiliation(s)
- Liora Lindenboim
- Department of Neurobiology, School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Hila Zohar
- Department of Neurobiology, School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Gregg G Gundersen
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Howard J Worman
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Reuven Stein
- Department of Neurobiology, School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel.
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