1
|
Zhang H, Huang D, Chen E, Cao D, Xu T, Dizdar B, Li G, Chen Y, Payne P, Province M, Li F. mosGraphGPT: a foundation model for multi-omic signaling graphs using generative AI. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.01.606222. [PMID: 39149314 PMCID: PMC11326168 DOI: 10.1101/2024.08.01.606222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Generative pretrained models represent a significant advancement in natural language processing and computer vision, which can generate coherent and contextually relevant content based on the pre-training on large general datasets and fine-tune for specific tasks. Building foundation models using large scale omic data is promising to decode and understand the complex signaling language patterns within cells. Different from existing foundation models of omic data, we build a foundation model, mosGraphGPT, for multi-omic signaling (mos) graphs, in which the multi-omic data was integrated and interpreted using a multi-level signaling graph. The model was pretrained using multi-omic data of cancers in The Cancer Genome Atlas (TCGA), and fine-turned for multi-omic data of Alzheimer's Disease (AD). The experimental evaluation results showed that the model can not only improve the disease classification accuracy, but also is interpretable by uncovering disease targets and signaling interactions. And the model code are uploaded via GitHub with link: https://github.com/mosGraph/mosGraphGPT.
Collapse
Affiliation(s)
- Heming Zhang
- Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine
| | - Di Huang
- Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine
| | - Emily Chen
- Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine
- Department of Pediatrics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- School of Arts and Sciences, University of Rochester, Rochester, NY, 14627, USA
| | - Dekang Cao
- Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine
- Department of Computer Science and Engineering
| | - Tim Xu
- Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine
- Department of Computer Science and Engineering
| | - Ben Dizdar
- Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine
- Department of Computer Science and Engineering
| | - Guangfu Li
- Department of Surgery, School of Medicine, University of Connecticut, CT, 06032, USA
| | - Yixin Chen
- Department of Computer Science and Engineering
| | - Philip Payne
- Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine
| | | | - Fuhai Li
- Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine
- Department of Pediatrics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| |
Collapse
|
2
|
Chen Z, Balachandran YL, Chong WP, Chan KWY. Roles of Cytokines in Alzheimer's Disease. Int J Mol Sci 2024; 25:5803. [PMID: 38891990 PMCID: PMC11171747 DOI: 10.3390/ijms25115803] [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: 04/16/2024] [Revised: 05/18/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
The neuroimmune system is a collection of immune cells, cytokines, and the glymphatic system that plays a pivotal role in the pathogenesis and progression of Alzheimer's disease (AD). Of particular focus are cytokines, a group of immune signaling molecules that facilitate communication among immune cells and contribute to inflammation in AD. Extensive research has shown that the dysregulated secretion of certain cytokines (IL-1β, IL-17, IL-12, IL-23, IL-6, and TNF-α) promotes neuroinflammation and exacerbates neuronal damage in AD. However, anti-inflammatory cytokines (IL-2, IL-3, IL-33, and IL-35) are also secreted during AD onset and progression, thereby preventing neuroinflammation. This review summarizes the involvement of pro- and anti-inflammatory cytokines in AD pathology and discusses their therapeutic potential.
Collapse
Affiliation(s)
- Zilin Chen
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China; (Z.C.); (Y.L.B.)
| | - Yekkuni L. Balachandran
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China; (Z.C.); (Y.L.B.)
| | - Wai Po Chong
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen 518057, China
| | - Kannie W. Y. Chan
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China; (Z.C.); (Y.L.B.)
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering (COCHE), Hong Kong, China
- Shenzhen Research Institute, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
| |
Collapse
|
3
|
Bachstetter AD, Lutshumba J, Winford E, Abner EL, Martin BJ, Harp JP, Van Eldik LJ, Schmitt FA, Wilcock DM, Stowe AM, Jicha GA, Nikolajczyk BS. A blunted T H17 cytokine signature in women with mild cognitive impairment: insights from inflammatory profiling of a community-based cohort of older adults. Brain Commun 2023; 5:fcad259. [PMID: 37901041 PMCID: PMC10612408 DOI: 10.1093/braincomms/fcad259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 06/23/2023] [Accepted: 10/06/2023] [Indexed: 10/31/2023] Open
Abstract
People with dementia have an increase in brain inflammation, caused in part by innate and adaptive immune cells. However, it remains unknown whether dementia-associated diseases alter neuro-immune reflex arcs to impact the systemic immune system. We examined peripheral immune cells from a community-based cohort of older adults to test if systemic inflammatory cytokine signatures associated with early stages of cognitive impairment. Human peripheral blood mononuclear cells were cultured with monocyte or T-cell-targeted stimuli, and multiplex assays quantitated cytokines in the conditioned media. Following T-cell-targeted stimulation, cells from women with cognitive impairment produced lower amounts of TH17 cytokines compared with cells from cognitively healthy women, while myeloid-targeted stimuli elicited similar amounts of cytokines from cells of both groups. This TH17 signature correlated with the proportion of circulating CD4+ and CD8+ T cells and plasma glial fibrillary acidic protein and neurofilament light concentrations. These results suggest that decreases in TH17 cytokines could be an early systemic change in women at risk for developing dementia. Amelioration of TH17s cytokines in early cognitive impairment could, in part, explain the compromised ability of older adults to respond to vaccines or defend against infection.
Collapse
Affiliation(s)
- Adam D Bachstetter
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40536, USA
- Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
| | - Jenny Lutshumba
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40536, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
| | - Edric Winford
- Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA
| | - Erin L Abner
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
- Department of Epidemiology, University of Kentucky, Lexington, KY 40536, USA
| | - Barbra J Martin
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
| | - Jordan P Harp
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
- Department of Neurology, University of Kentucky, Lexington, KY 40536, USA
| | - Linda J Van Eldik
- Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
| | - Frederick A Schmitt
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40536, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
- Department of Neurology, University of Kentucky, Lexington, KY 40536, USA
- Department of Behavioral Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Donna M Wilcock
- Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
- Department of Physiology, University of Kentucky, Lexington, KY 40536, USA
| | - Ann M Stowe
- Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA
- Department of Neurology, University of Kentucky, Lexington, KY 40536, USA
| | - Gregory A Jicha
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
- Department of Neurology, University of Kentucky, Lexington, KY 40536, USA
| | - Barbara S Nikolajczyk
- Department of Pharmacology and Nutritional Science, and Barnstable Brown Diabetes and Obesity Center, University of Kentucky, Lexington, KY 40536, USA
| |
Collapse
|
4
|
Fu J, Huang Y, Bao T, Liu C, Liu X, Chen X. The role of Th17 cells/IL-17A in AD, PD, ALS and the strategic therapy targeting on IL-17A. J Neuroinflammation 2022; 19:98. [PMID: 35459141 PMCID: PMC9034482 DOI: 10.1186/s12974-022-02446-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 03/29/2022] [Indexed: 02/08/2023] Open
Abstract
Neurodegenerative diseases are a group of disorders characterized by progressive loss of certain populations of neurons, which eventually lead to dysfunction. These diseases include Alzheimer’s disease (AD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS). Immune pathway dysregulation is one of the common features of neurodegeneration. Recently, there is growing interest in the specific role of T helper Th 17 cells and Interleukin-17A (IL-17A), the most important cytokine of Th 17 cells, in the pathogenesis of the central nervous system (CNS) of neurodegenerative diseases. In the present study, we summarized current knowledge about the function of Th17/IL-17A, the physiology of Th17/IL-17A in diseases, and the contribution of Th17/IL-17A in AD, PD, and ALS. We also update the findings on IL-17A-targeting drugs as potentially immunomodulatory therapeutic agents for neurodegenerative diseases. Although the specific mechanism of Th17/IL-17A in this group of diseases is still controversial, uncovering the molecular pathways of Th17/IL-17A in neurodegeneration allows the identification of suitable targets to modulate these cellular processes. Therapeutics targeting IL-17A might represent potentially novel anti-neurodegeneration drugs.
Collapse
Affiliation(s)
- Jiajia Fu
- Department of Neurology, West China Hospital, Sichuan University, Wai Nan Guo Xue Xiang 37#, Chengdu, Sichuan, China
| | - Yan Huang
- Management Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ting Bao
- Management Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chengcheng Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xi Liu
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xueping Chen
- Department of Neurology, West China Hospital, Sichuan University, Wai Nan Guo Xue Xiang 37#, Chengdu, Sichuan, China.
| |
Collapse
|
5
|
Bogár F, Fülöp L, Penke B. Novel Therapeutic Target for Prevention of Neurodegenerative Diseases: Modulation of Neuroinflammation with Sig-1R Ligands. Biomolecules 2022; 12:363. [PMID: 35327555 PMCID: PMC8945408 DOI: 10.3390/biom12030363] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/20/2022] [Accepted: 02/23/2022] [Indexed: 12/13/2022] Open
Abstract
Neurodegenerative diseases (NDDs) are characterized by progressive deterioration of the structure and function of cells and their networks in the nervous system. There are currently no drugs or other treatments that can stop the progression of NDDs. NDDs have many similarities and common pathways, e.g., formation of misfolded amyloid proteins, intra- and extracellular amyloid deposits, and chronic inflammation. Initially, the inflammation process has a cytoprotective function; however, an elevated and prolonged immune response has damaging effects and causes cell death. Neuroinflammation has been a target of drug development for treating and curing NDDs. Treatment of different NDDs with non-steroid anti-inflammatory drugs (NSAIDs) has failed or has given inconsistent results. The use of NSAIDs in diagnosed Alzheimer's disease is currently not recommended. Sigma-1 receptor (Sig-1R) is a novel target for NDD drug development. Sig-1R plays a key role in cellular stress signaling, and it regulates endoplasmic reticulum stress and unfolded protein response. Activation of Sig-1R provides neuroprotection in cell cultures and animal studies. Clinical trials demonstrated that several Sig-1R agonists (pridopidine, ANAVEX3-71, fluvoxamine, dextrometorphan) and their combinations have a neuroprotective effect and slow down the progression of distinct NDDs.
Collapse
Affiliation(s)
- Ferenc Bogár
- MTA-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), Dóm Square 8, H-6720 Szeged, Hungary;
- Department of Medical Chemistry, University of Szeged, Dóm Square 8, H-6720 Szeged, Hungary;
| | - Lívia Fülöp
- Department of Medical Chemistry, University of Szeged, Dóm Square 8, H-6720 Szeged, Hungary;
| | - Botond Penke
- Department of Medical Chemistry, University of Szeged, Dóm Square 8, H-6720 Szeged, Hungary;
| |
Collapse
|