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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.
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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
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Wang X, Feng S, Deng Q, Wu C, Duan R, Yang L. The role of estrogen in Alzheimer's disease pathogenesis and therapeutic potential in women. Mol Cell Biochem 2024:10.1007/s11010-024-05071-4. [PMID: 39088186 DOI: 10.1007/s11010-024-05071-4] [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: 04/11/2024] [Accepted: 07/11/2024] [Indexed: 08/02/2024]
Abstract
Estrogens are pivotal regulators of brain function throughout the lifespan, exerting profound effects from early embryonic development to aging. Extensive experimental evidence underscores the multifaceted protective roles of estrogens on neurons and neurotransmitter systems, particularly in the context of Alzheimer's disease (AD) pathogenesis. Studies have consistently revealed a greater risk of AD development in women compared to men, with postmenopausal women exhibiting heightened susceptibility. This connection between sex factors and long-term estrogen deprivation highlights the significance of estrogen signaling in AD progression. Estrogen's influence extends to key processes implicated in AD, including amyloid precursor protein (APP) processing and neuronal health maintenance mediated by brain-derived neurotrophic factor (BDNF). Reduced BDNF expression, often observed in AD, underscores estrogen's role in preserving neuronal integrity. Notably, hormone replacement therapy (HRT) has emerged as a sex-specific and time-dependent strategy for primary cardiovascular disease (CVD) prevention, offering an excellent risk profile against aging-related disorders like AD. Evidence suggests that HRT may mitigate AD onset and progression in postmenopausal women, further emphasizing the importance of estrogen signaling in AD pathophysiology. This review comprehensively examines the physiological and pathological changes associated with estrogen in AD, elucidating the therapeutic potential of estrogen-based interventions such as HRT. By synthesizing current knowledge, it aims to provide insights into the intricate interplay between estrogen signaling and AD pathogenesis, thereby informing future research directions and therapeutic strategies for this debilitating neurodegenerative disorder.
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Affiliation(s)
- Xinyi Wang
- Laboratory of Exercise and Neurobiology, School of Physical Education and Sports Science, South China Normal University, Guangzhou, 510006, China
| | - Shu Feng
- Laboratory of Exercise and Neurobiology, School of Physical Education and Sports Science, South China Normal University, Guangzhou, 510006, China
| | - Qianting Deng
- Laboratory of Exercise and Neurobiology, School of Physical Education and Sports Science, South China Normal University, Guangzhou, 510006, China
| | - Chongyun Wu
- Laboratory of Exercise and Neurobiology, School of Physical Education and Sports Science, South China Normal University, Guangzhou, 510006, China.
- Laboratory of Regenerative Medicine in Sports Science, School of Physical Education and Sports Science, South China Normal University, Guangzhou, China.
| | - Rui Duan
- Laboratory of Regenerative Medicine in Sports Science, School of Physical Education and Sports Science, South China Normal University, Guangzhou, China
| | - Luodan Yang
- Laboratory of Exercise and Neurobiology, School of Physical Education and Sports Science, South China Normal University, Guangzhou, 510006, China.
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Jarek DJ, Mizerka H, Nuszkiewicz J, Szewczyk-Golec K. Evaluating p-tau217 and p-tau231 as Biomarkers for Early Diagnosis and Differentiation of Alzheimer's Disease: A Narrative Review. Biomedicines 2024; 12:786. [PMID: 38672142 PMCID: PMC11048667 DOI: 10.3390/biomedicines12040786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/26/2024] [Accepted: 03/30/2024] [Indexed: 04/28/2024] Open
Abstract
The escalating prevalence of Alzheimer's disease (AD) highlights the urgent need to develop reliable biomarkers for early diagnosis and intervention. AD is characterized by the pathological accumulation of amyloid-beta plaques and tau neurofibrillary tangles. Phosphorylated tau (p-tau) proteins, particularly p-tau217 and p-tau231, have been identified as promising biomarker candidates to differentiate the disease progression from preclinical stages. This narrative review is devoted to a critical evaluation of the diagnostic accuracy, sensitivity, and specificity of p-tau217 and p-tau231 levels in the detection of AD, measured in plasma, serum, and cerebrospinal fluid, compared to established biomarkers. Additionally, the efficacy of these markers in distinguishing AD from other neurodegenerative disorders is examined. The significant advances offered by p-tau217 and p-tau231 in AD diagnostics are highlighted, demonstrating their unique utility in early detection and differential diagnosis. This comprehensive analysis not only confirms the excellent diagnostic capabilities of these markers, but also deepens the understanding of the molecular dynamics of AD, contributing to the broader scientific discourse on neurodegenerative diseases. This review is aimed to provide key information for researchers and clinicians across disciplines, filling interdisciplinary gaps and highlighting the role of p-tau proteins in revolutionizing AD research and clinical practice.
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Affiliation(s)
- Dorian Julian Jarek
- Student Research Club of Medical Biology and Biochemistry, Department of Medical Biology and Biochemistry, Faculty of Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland;
| | - Hubert Mizerka
- Student Research Club of Medical Biology and Biochemistry, Department of Medical Biology and Biochemistry, Faculty of Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland;
| | - Jarosław Nuszkiewicz
- Department of Medical Biology and Biochemistry, Faculty of Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland;
| | - Karolina Szewczyk-Golec
- Department of Medical Biology and Biochemistry, Faculty of Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland;
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Yaqing X, Yang G, Linlin Y, Youqing R, Henghui Y, Ping Y, Hongying Y, Shaojia W. Identification of different subtypes of ovarian cancer and construction of prognostic models based on glutamine-metabolism associated genes. Heliyon 2024; 10:e27358. [PMID: 38509907 PMCID: PMC10950510 DOI: 10.1016/j.heliyon.2024.e27358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Ovarian cancer (OC) is common malignant tumor of female reproductive system. Glutamine metabolism-related genes (GMRGs) play a key role in ovarian cancer. Here, available database-- The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Gene Expression Omnibus (GEO) databases were applied in our research. OC samples from TCGA were divided into different clusters based on Cox analysis, which filtering GMRGs with survival information. Then, differentially expressed genes (DEGs) between these clusters were intersected with DEGs between normal ovary samples and OC samples, and GMRGs in order to obtain GMRGs-related DEGs. Next, a risk model of OC was constructed and enrichment analysis of risk model was performed based on hallmark gene set. Besides, the immune cells ratio in OC samples were detected via Cell type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT). Finally, we explored a series of potential biomarkers of OC. In this research, 9 GMRGs-related DEGs were obtained. GMRGs-related DEGs were enriched to canonical Wnt signaling pathway.NKD2, C2orf88, and KLHDC8A, which were significantly associated with prognosis, were retained for risk model construction. Based on the risk model, 18 hallmark pathways with significant difference were enriched. Fifteen types of immune cells (such as iDC, NK CD56dim cells, and neutrophils) enjoying significant difference between these 2 risk groups (high risk group vs. low risk group) were detected, which indicates possible disparate TME in different metabolic subtypes of ovarian cancer.
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Affiliation(s)
| | | | - Yang Linlin
- Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming 650118, China
| | - Ruan Youqing
- Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming 650118, China
| | - Yang Henghui
- Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming 650118, China
| | - Yang Ping
- Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming 650118, China
| | - Yang Hongying
- Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming 650118, China
| | - Wang Shaojia
- Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming 650118, China
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Schwarz KG, Vicencio SC, Inestrosa NC, Villaseca P, Del Rio R. Autonomic nervous system dysfunction throughout menopausal transition: A potential mechanism underpinning cardiovascular and cognitive alterations during female ageing. J Physiol 2024; 602:263-280. [PMID: 38064358 DOI: 10.1113/jp285126] [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: 08/02/2023] [Accepted: 11/24/2023] [Indexed: 01/16/2024] Open
Abstract
Cardiovascular diseases (CVD) and neurodegenerative disorders, such as Alzheimer's disease (AD), are highly prevalent conditions in middle-aged women that severely impair quality of life. Recent evidence suggests the existence of an intimate cross-talk between the heart and the brain, resulting from a complex network of neurohumoral circuits. From a pathophysiological perspective, the higher prevalence of AD in women may be explained, at least in part, by sex-related differences in the incidence/prevalence of CVD. Notably, the autonomic nervous system, the main heart-brain axis physiological orchestrator, has been suggested to play a role in the incidence of adverse cardiovascular events in middle-aged women because of decreases in oestrogen-related signalling during transition into menopause. Despite its overt relevance for public health, this hypothesis has not been thoroughly tested. Accordingly, in this review, we aim to provide up to date evidence supporting how changes in circulating oestrogen levels during transition to menopause may trigger autonomic dysfunction, thus promoting cardiovascular and cognitive decline in women. A main focus on the effects of oestrogen-mediated signalling at CNS structures related to autonomic regulation is provided, particularly on the role of oestrogens in sympathoexcitation. Improving the understanding of the contribution of the autonomic nervous system on the development, maintenance and/or progression of both cardiovascular and cognitive dysfunction during the transition to menopause should help improve the clinical management of elderly women, with the outcome being an improved life quality during the natural ageing process.
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Affiliation(s)
- Karla G Schwarz
- Laboratory of Cardiorespiratory Control, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sinay C Vicencio
- Laboratory of Cardiorespiratory Control, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nibaldo C Inestrosa
- Centro de Excelencia en Biomedicina de Magallanes (CEBIMA), Universidad de Magallanes, Punta Arenas, Chile
| | - Paulina Villaseca
- Centro de Excelencia en Biomedicina de Magallanes (CEBIMA), Universidad de Magallanes, Punta Arenas, Chile
| | - Rodrigo Del Rio
- Laboratory of Cardiorespiratory Control, Pontificia Universidad Católica de Chile, Santiago, Chile
- Centro de Excelencia en Biomedicina de Magallanes (CEBIMA), Universidad de Magallanes, Punta Arenas, Chile
- Department of Cell Biology and Physiology, School of Medicine, University of Kansas Medical Center, Kansas City, KS, USA
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Zhang X, Huangfu Z, Wang S. Review of mendelian randomization studies on age at natural menopause. Front Endocrinol (Lausanne) 2023; 14:1234324. [PMID: 37766689 PMCID: PMC10520463 DOI: 10.3389/fendo.2023.1234324] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Menopause marks the end of the reproductive phase of life. Based on epidemiological studies, abnormal age at natural menopause (ANM) is thought to contribute to a number of adverse outcomes, such as osteoporosis, cardiovascular disease, and cancer. However, the causality of these associations remains unclear. A powerful epidemiological method known as Mendelian randomization (MR) can be used to clarify the causality between ANM and other diseases or traits. The present review describes MR studies that included ANM as an exposure, outcome and mediator. The findings of MR analyses on ANM have revealed that higher body mass index, poor educational level, early age at menarche, early age at first live birth, early age at first sexual intercourse, and autoimmune thyroid disease appear to be involved in early ANM etiology. The etiology of late ANM appears to be influenced by higher free thyroxine 4 and methylene tetrahydrofolate reductase gene mutations. Furthermore, early ANM has been found to be causally associated with an increased risk of osteoporosis, fracture, type 2 diabetes mellitus, glycosylated hemoglobin, and the homeostasis model of insulin resistance level. In addition, late ANM has been found to be causally associated with an increased systolic blood pressure, higher risk of breast cancer, endometrial cancer, endometrioid ovarian carcinoma, lung cancer, longevity, airflow obstruction, and lower risk of Parkinson's disease. ANM is also a mediator for breast cancer caused by birth weight and childhood body size. However, due to the different instrumental variables used, some results of studies are inconsistent. Future studies with more valid genetic variants are needed for traits with discrepancies between MRs or between MR and other types of epidemiological studies.
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Affiliation(s)
- Xiao Zhang
- Department of Obstetrics and Gynecology, Beijing Hospital, National Center of Gerontology, Beijing, China
- Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, China
- Graduate School of Peking Union Medical College, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhao Huangfu
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Shaowei Wang
- Department of Obstetrics and Gynecology, Beijing Hospital, National Center of Gerontology, Beijing, China
- Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, China
- Graduate School of Peking Union Medical College, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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