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Gunasekaran TI, Reyes-Dumeyer D, Faber KM, Goate A, Boeve B, Cruchaga C, Pericak-Vance M, Haines JL, Rosenberg R, Tsuang D, Mejia DR, Medrano M, Lantigua RA, Sweet RA, Bennett DA, Wilson RS, Alba C, Dalgard C, Foroud T, Vardarajan BN, Mayeux R. Missense and loss-of-function variants at GWAS loci in familial Alzheimer's disease. Alzheimers Dement 2024. [PMID: 39233587 DOI: 10.1002/alz.14221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 07/10/2024] [Accepted: 08/06/2024] [Indexed: 09/06/2024]
Abstract
BACKGROUND Few rare variants have been identified in genetic loci from genome-wide association studies (GWAS) of Alzheimer's disease (AD), limiting understanding of mechanisms, risk assessment, and genetic counseling. METHODS Using genome sequencing data from 197 families in the National Institute on Aging Alzheimer's Disease Family Based Study and 214 Caribbean Hispanic families, we searched for rare coding variants within known GWAS loci from the largest published study. RESULTS Eighty-six rare missense or loss-of-function (LoF) variants completely segregated in 17.5% of families, but in 91 (22.1%) families Apolipoprotein E (APOE)-𝜀4 was the only variant segregating. However, in 60.3% of families, APOE 𝜀4, missense, and LoF variants were not found within the GWAS loci. DISCUSSION Although APOE 𝜀4and several rare variants were found to segregate in both family datasets, many families had no variant accounting for their disease. This suggests that familial AD may be the result of unidentified rare variants. HIGHLIGHTS Rare coding variants from GWAS loci segregate in familial Alzheimer's disease. Missense or loss of function variants were found segregating in nearly 7% of families. APOE-𝜀4 was the only segregating variant in 29.7% in familial Alzheimer's disease. In Hispanic and non-Hispanic families, different variants were found in segregating genes. No coding variants were found segregating in many Hispanic and non-Hispanic families.
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Affiliation(s)
- Tamil Iniyan Gunasekaran
- Department of Neurology, Taub Institute for Research on Alzheimer's Disease and the Aging Brain and the Gertrude H. Sergievsky Center, Columbia University, New York, New York, USA
| | - Dolly Reyes-Dumeyer
- Department of Neurology, Taub Institute for Research on Alzheimer's Disease and the Aging Brain and the Gertrude H. Sergievsky Center, Columbia University, New York, New York, USA
| | - Kelley M Faber
- Department of Medical and Molecular Genetics, National Centralized Repository for Alzheimer's Disease and Related Dementias (NCRAD), 410 W. 10th St., HS 4000. Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Alison Goate
- Department of Genetics & Genomic Sciences, Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, Icahn Bldg., One Gustave L. Levy Place, New York, New York, USA
| | - Brad Boeve
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in St. Louis, Rand Johnson Building, 600 S Euclid Ave., Wohl Hospital Building, St. Louis, Missouri, USA
| | - Margaret Pericak-Vance
- John P Hussman Institute for Human Genomics, Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Jonathan L Haines
- Department of Population & Quantitative Health Sciences and Cleveland Institute for Computational Biology. Case Western Reserve University, Cleveland, Ohio, USA
| | - Roger Rosenberg
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Debby Tsuang
- Department of Psychiatry and Behavioral Sciences, University of Washington, GRECC VA Puget Sound, 1660 South Columbian Way, Seattle, Washington, USA
| | - Diones Rivera Mejia
- Los Centros de Diagnóstico y Medicina Avanzada y de Conferencias Médicas y Telemedicina, CEDIMAT, Arturo Logroño, Plaza de la Salud, Dr. Juan Manuel Taveras Rodríguez, C. Pepillo Salcedo esq, Santo Domingo, Dominican Republic
- Universidad Pedro Henríquez Urena, Av. John F. Kennedy Km. 7-1/2 Santo Domingo 1423, Santo Domingo, Dominican Republic
| | - Martin Medrano
- Pontíficia Universidad Católica Madre y Maestra (PUCMM), Autopista Duarte Km 1 1/2, Santiago de los Caballeros, Dominican Republic
| | - Rafael A Lantigua
- Department of Neurology, Taub Institute for Research on Alzheimer's Disease and the Aging Brain and the Gertrude H. Sergievsky Center, Columbia University, New York, New York, USA
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, and the New York Presbyterian Hospital, New York, New York, USA
| | - Robert A Sweet
- Departments of Psychiatry and Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750, West Harrison St, Chicago, Illinois, USA
| | - Robert S Wilson
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750, West Harrison St, Chicago, Illinois, USA
| | - Camille Alba
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Clifton Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, National Centralized Repository for Alzheimer's Disease and Related Dementias (NCRAD), 410 W. 10th St., HS 4000. Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Badri N Vardarajan
- Department of Neurology, Taub Institute for Research on Alzheimer's Disease and the Aging Brain and the Gertrude H. Sergievsky Center, Columbia University, New York, New York, USA
| | - Richard Mayeux
- Department of Neurology, Taub Institute for Research on Alzheimer's Disease and the Aging Brain and the Gertrude H. Sergievsky Center, Columbia University, New York, New York, USA
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Gunasekaran TI, Reyes-Dumeyer D, Faber KM, Goate A, Boeve B, Cruchaga C, Pericak-Vance M, Haines JL, Rosenberg R, Tsuang D, Mejia DR, Medrano M, Lantigua RA, Sweet RA, Bennett DA, Wilson RS, Alba C, Dalgard C, Foroud T, Vardarajan BN, Mayeux R. Missense and Loss of Function Variants at GWAS Loci in Familial Alzheimer's Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.12.18.23300145. [PMID: 38196599 PMCID: PMC10775337 DOI: 10.1101/2023.12.18.23300145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
BACKGROUND Few rare variants have been identified in genetic loci from genome wide association studies of Alzheimer's disease (AD), limiting understanding of mechanisms and risk assessment, and genetic counseling. METHODS Using genome sequencing data from 197 families in The NIA Alzheimer's Disease Family Based Study, and 214 Caribbean Hispanic families, we searched for rare coding variants within known GWAS loci from the largest published study. RESULTS Eighty-six rare missense or loss of function (LoF) variants completely segregated in 17.5% of families, but in 91 (22.1%) of families APOE-e4 was the only variant segregating. However, in 60.3% of families neither APOE-e4 nor missense or LoF variants were found within the GWAS loci. DISCUSSION Although APOE-ε4 and several rare variants were found to segregate in both family datasets, many families had no variant accounting for their disease. This suggests that familial AD may be the result of unidentified rare variants.
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Mu X, Cui C, Liao J, Wu Z, Hu L. Regional changes in brain metabolism during the progression of mild cognitive impairment: a longitudinal study based on radiomics. EJNMMI REPORTS 2024; 8:19. [PMID: 38945980 PMCID: PMC11214937 DOI: 10.1186/s41824-024-00206-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/22/2024] [Indexed: 07/02/2024]
Abstract
BACKGROUND This study aimed to establish radiomics models based on positron emission tomography (PET) images to longitudinally predict transition from mild cognitive impairment (MCI) to Alzheimer's disease (AD). METHODS In our study, 278 MCI patients from the ADNI database were analyzed, where 60 transitioned to AD (pMCI) and 218 remained stable (sMCI) over 48 months. Patients were divided into a training set (n = 222) and a validation set (n = 56). We first employed voxel-based analysis of 18F-FDG PET images to identify brain regions that present significant SUV difference between pMCI and sMCI groups. Radiomic features were extracted from these regions, key features were selected, and predictive models were developed for individual and combined brain regions. The models' effectiveness was evaluated using metrics like AUC to determine the most accurate predictive model for MCI progression. RESULTS Voxel-based analysis revealed four brain regions implicated in the progression from MCI to AD. These include ROI1 within the Temporal lobe, ROI2 and ROI3 in the Thalamus, and ROI4 in the Limbic system. Among the predictive models developed for these individual regions, the model utilizing ROI4 demonstrated superior predictive accuracy. In the training set, the AUC for the ROI4 model was 0.803 (95% CI 0.736, 0.865), and in the validation set, it achieved an AUC of 0.733 (95% CI 0.559, 0.893). Conversely, the model based on ROI3 showed the lowest performance, with an AUC of 0.75 (95% CI 0.685, 0.809). Notably, the comprehensive model encompassing all identified regions (ROI total) outperformed the single-region models, achieving an AUC of 0.884 (95% CI 0.845, 0.921) in the training set and 0.816 (95% CI 0.705, 0.909) in the validation set, indicating significantly enhanced predictive capability for MCI progression to AD. CONCLUSION Our findings underscore the Limbic system as the brain region most closely associated with the progression from MCI to AD. Importantly, our study demonstrates that a PET brain radiomics model encompassing multiple brain regions (ROI total) significantly outperforms models based on single brain regions. This comprehensive approach more accurately identifies MCI patients at high risk of progressing to AD, offering valuable insights for non-invasive diagnostics and facilitating early and timely interventions in clinical settings.
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Affiliation(s)
- Xuxu Mu
- Shanxi Key Laboratory of Molecular Imaging, Shanxi Medical University, Taiyuan, 030001, Shanxi, People's Republic of China
- Department of Nuclear Medicine, First Hospital of Shanxi Medical University, Shanxi Medical University, Taiyuan, 030001, Shanxi, People's Republic of China
| | - Caozhe Cui
- Shanxi Key Laboratory of Molecular Imaging, Shanxi Medical University, Taiyuan, 030001, Shanxi, People's Republic of China
- Department of Nuclear Medicine, First Hospital of Shanxi Medical University, Shanxi Medical University, Taiyuan, 030001, Shanxi, People's Republic of China
| | - Jue Liao
- Shanxi Key Laboratory of Molecular Imaging, Shanxi Medical University, Taiyuan, 030001, Shanxi, People's Republic of China
- Collaborative Innovation Center for Molecular Imaging of Precision Medicine, Shanxi Medical University, Taiyuan, 030001, Shanxi, People's Republic of China
| | - Zhifang Wu
- Shanxi Key Laboratory of Molecular Imaging, Shanxi Medical University, Taiyuan, 030001, Shanxi, People's Republic of China
- Department of Nuclear Medicine, First Hospital of Shanxi Medical University, Shanxi Medical University, Taiyuan, 030001, Shanxi, People's Republic of China
- Collaborative Innovation Center for Molecular Imaging of Precision Medicine, Shanxi Medical University, Taiyuan, 030001, Shanxi, People's Republic of China
| | - Lingzhi Hu
- Collaborative Innovation Center for Molecular Imaging of Precision Medicine, Shanxi Medical University, Taiyuan, 030001, Shanxi, People's Republic of China.
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Soelter TM, Howton TC, Wilk EJ, Whitlock JH, Clark AD, Birnbaum A, Patterson DC, Cortes CJ, Lasseigne BN. Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595199. [PMID: 38826305 PMCID: PMC11142088 DOI: 10.1101/2024.05.21.595199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Alzheimer's disease (AD) is the most common form of dementia and is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-β plaque and intracellular neurofibrillary tangles of phosphorylated tau, along with neuronal loss. While neuronal loss is an AD hallmark, cell-cell communication between neuronal and non-neuronal cell populations maintains neuronal health and brain homeostasis. To study changes in cell-cell communication during disease progression, we performed snRNA-sequencing of the hippocampus from female 3xTg-AD and wild-type littermates at 6 and 12 months. We inferred differential cell-cell communication between 3xTg-AD and wild-type mice across time points and between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) of interest. We also assessed the downstream effects of altered glia-neuron communication using pseudobulk differential gene expression, functional enrichment, and gene regulatory analyses. We found that glia-neuron communication is increasingly dysregulated in 12-month 3xTg-AD mice. We also identified 23 AD-associated ligand-receptor pairs that are upregulated in the 12-month-old 3xTg-AD hippocampus. Our results suggest increased AD association of interactions originating from microglia. Signaling mediators were not significantly differentially expressed but showed altered gene regulation and TF activity. Our findings indicate that altered glia-neuron communication is increasingly dysregulated and affects the gene regulatory mechanisms in neurons of 12-month-old 3xTg-AD mice.
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Affiliation(s)
- Tabea M. Soelter
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Elizabeth J. Wilk
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jordan H. Whitlock
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Amanda D. Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Allison Birnbaum
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Dalton C. Patterson
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Constanza J. Cortes
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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Firdaus Z, Li X. Unraveling the Genetic Landscape of Neurological Disorders: Insights into Pathogenesis, Techniques for Variant Identification, and Therapeutic Approaches. Int J Mol Sci 2024; 25:2320. [PMID: 38396996 PMCID: PMC10889342 DOI: 10.3390/ijms25042320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Genetic abnormalities play a crucial role in the development of neurodegenerative disorders (NDDs). Genetic exploration has indeed contributed to unraveling the molecular complexities responsible for the etiology and progression of various NDDs. The intricate nature of rare and common variants in NDDs contributes to a limited understanding of the genetic risk factors associated with them. Advancements in next-generation sequencing have made whole-genome sequencing and whole-exome sequencing possible, allowing the identification of rare variants with substantial effects, and improving the understanding of both Mendelian and complex neurological conditions. The resurgence of gene therapy holds the promise of targeting the etiology of diseases and ensuring a sustained correction. This approach is particularly enticing for neurodegenerative diseases, where traditional pharmacological methods have fallen short. In the context of our exploration of the genetic epidemiology of the three most prevalent NDDs-amyotrophic lateral sclerosis, Alzheimer's disease, and Parkinson's disease, our primary goal is to underscore the progress made in the development of next-generation sequencing. This progress aims to enhance our understanding of the disease mechanisms and explore gene-based therapies for NDDs. Throughout this review, we focus on genetic variations, methodologies for their identification, the associated pathophysiology, and the promising potential of gene therapy. Ultimately, our objective is to provide a comprehensive and forward-looking perspective on the emerging research arena of NDDs.
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Affiliation(s)
- Zeba Firdaus
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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Chien MH, Yang YC, Ho KH, Ding YF, Chen LH, Chiu WK, Chen JQ, Tung MC, Hsiao M, Lee WJ. Cyclic increase in the ADAMTS1-L1CAM-EGFR axis promotes the EMT and cervical lymph node metastasis of oral squamous cell carcinoma. Cell Death Dis 2024; 15:82. [PMID: 38263290 PMCID: PMC10805752 DOI: 10.1038/s41419-024-06452-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/25/2024]
Abstract
The matrix metalloprotease A disintegrin and metalloprotease with thrombospondin motifs 1 (ADAMTS1) was reported to be involved in tumor progression in several cancer types, but its contributions appear discrepant. At present, the role of ADAMTS1 in oral squamous cell carcinoma (SCC; OSCC) remains unclear. Herein, The Cancer Genome Atlas (TCGA) database showed that ADAMTS1 transcripts were downregulated in head and neck SCC (HNSCC) tissues compared to normal tissues, but ADAMTS1 levels were correlated with poorer prognoses of HNSCC patients. In vitro, we observed that ADAMTS1 expression levels were correlated with the invasive abilities of four OSCC cell lines, HSC-3, SCC9, HSC-3M, and SAS. Knockdown of ADAMTS1 in OSCC cells led to a decrease and its overexpression led to an increase in cell-invasive abilities in vitro as well as tumor growth and lymph node (LN) metastasis in OSCC xenografts. Mechanistic investigations showed that the cyclic increase in ADAMTS1-L1 cell adhesion molecule (L1CAM) axis-mediated epidermal growth factor receptor (EGFR) activation led to exacerbation of the invasive abilities of OSCC cells via inducing epithelial-mesenchymal transition (EMT) progression. Clinical analyses revealed that ADAMTS1, L1CAM, and EGFR levels were all correlated with worse prognoses of HNSCC patients, and patients with ADAMTS1high/L1CAMhigh or EGFRhigh tumors had the shortest overall and disease-specific survival times. As to therapeutic aspects, we discovered that an edible plant-derived flavonoid, apigenin (API), drastically inhibited expression of the ADAMTS1-L1CAM-EGFR axis and reduced the ADAMTS1-triggered invasion and LN metastasis of OSCC cells in vitro and in vivo. Most importantly, API treatment significantly prolonged survival rates of xenograft mice with OSCC. In summary, ADAMTS1 may be a useful biomarker for predicting OSCC progression, and API potentially retarded OSCC progression by targeting the ADAMTS1-L1CAM-EGFR signaling pathway.
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Affiliation(s)
- Ming-Hsien Chien
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan
- Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- Traditional Herbal Medicine Research Center, Taipei Medical University Hospital Taipei, Taipei, Taiwan
| | - Yi-Chieh Yang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Medical Research, Tungs' Taichung MetroHarbor Hospital, Taichung, Taiwan
| | - Kuo-Hao Ho
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yi-Fang Ding
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Otolaryngology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Li-Hsin Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wen-Kuan Chiu
- Division of Plastic Surgery, Department of Surgery, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- Department of Surgery, School of Medicine, College of Surgery, Taipei Medical University, Taipei, Taiwan
| | - Ji-Qing Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Cancer Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Min-Che Tung
- Department of Surgery, Tungs' Taichung Metro Harbor Hospital, Taichung, Taiwan
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Wei-Jiunn Lee
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
- Department of Urology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
- Department of Medical Education and Research, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
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