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Du Y, Li R, Fu D, Zhang B, Cui A, Shao Y, Lai Z, Chen R, Chen B, Wang Z, Zhang W, Chu L. Multi-omics technologies and molecular biomarkers in brain tumor-related epilepsy. CNS Neurosci Ther 2024; 30:e14717. [PMID: 38641945 PMCID: PMC11031674 DOI: 10.1111/cns.14717] [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: 11/17/2023] [Revised: 03/04/2024] [Accepted: 03/29/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Brain tumors are one of the leading causes of epilepsy, and brain tumor-related epilepsy (BTRE) is recognized as the major cause of intractable epilepsy, resulting in huge treatment cost and burden to patients, their families, and society. Although optimal treatment regimens are available, the majority of patients with BTRE show poor resolution of symptoms. BTRE has a very complex and multifactorial etiology, which includes several influencing factors such as genetic and molecular biomarkers. Advances in multi-omics technologies have enabled to elucidate the pathophysiological mechanisms and related biomarkers of BTRE. Here, we reviewed multi-omics technology-based research studies on BTRE published in the last few decades and discussed the present status, development, opportunities, challenges, and prospects in treating BTRE. METHODS First, we provided a general review of epilepsy, BTRE, and multi-omics techniques. Next, we described the specific multi-omics (including genomics, transcriptomics, epigenomics, proteomics, and metabolomics) techniques and related molecular biomarkers for BTRE. We then presented the associated pathogenetic mechanisms of BTRE. Finally, we discussed the development and application of novel omics techniques for diagnosing and treating BTRE. RESULTS Genomics studies have shown that the BRAF gene plays a role in BTRE development. Furthermore, the BRAF V600E variant was found to induce epileptogenesis in the neuronal cell lineage and tumorigenesis in the glial cell lineage. Several genomics studies have linked IDH variants with glioma-related epilepsy, and the overproduction of D2HG is considered to play a role in neuronal excitation that leads to seizure occurrence. The high expression level of Forkhead Box O4 (FOXO4) was associated with a reduced risk of epilepsy occurrence. In transcriptomics studies, VLGR1 was noted as a biomarker of epileptic onset in patients. Several miRNAs such as miR-128 and miRNA-196b participate in BTRE development. miR-128 might be negatively associated with the possibility of tumor-related epilepsy development. The lncRNA UBE2R2-AS1 inhibits the growth and invasion of glioma cells and promotes apoptosis. Quantitative proteomics has been used to determine dynamic changes of protein acetylation in epileptic and non-epileptic gliomas. In another proteomics study, a high expression of AQP-4 was detected in the brain of GBM patients with seizures. By using quantitative RT-PCR and immunohistochemistry assay, a study revealed that patients with astrocytomas and oligoastrocytomas showed high BCL2A1 expression and poor seizure control. By performing immunohistochemistry, several studies have reported the relationship between D2HG overproduction and seizure occurrence. Ki-67 overexpression in WHO grade II gliomas was found to be associated with poor postoperative seizure control. According to metabolomics research, the PI3K/AKT/mTOR pathway is associated with the development of glioma-related epileptogenesis. Another metabolomics study found that SV2A, P-gb, and CAD65/67 have the potential to function as biomarkers for BTRE. CONCLUSIONS Based on the synthesized information, this review provided new research perspectives and insights into the early diagnosis, etiological factors, and personalized treatment of BTRE.
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Affiliation(s)
- Yaoqiang Du
- Laboratory Medicine Center, Department of Transfusion MedicineZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouChina
- School of Basic Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
| | - Rusong Li
- The Second School of Clinical MedicineZhejiang Chinese Medical UniversityHangzhouChina
| | - Danqing Fu
- School of Basic Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
| | - Biqin Zhang
- Cancer Center, Department of HematologyZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouChina
| | - Ailin Cui
- Cancer Center, Department of Ultrasound MedicineZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouChina
| | - Yutian Shao
- Zhejiang BioAsia Life Science InstitutePinghuChina
| | - Zeyu Lai
- The Second School of Clinical MedicineZhejiang Chinese Medical UniversityHangzhouChina
| | - Rongrong Chen
- School of Clinical MedicineHangzhou Normal UniversityHangzhouChina
| | - Bingyu Chen
- Laboratory Medicine Center, Department of Transfusion MedicineZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouChina
| | - Zhen Wang
- Laboratory Medicine Center, Department of Transfusion MedicineZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouChina
| | - Wei Zhang
- The Second School of Clinical MedicineZhejiang Chinese Medical UniversityHangzhouChina
| | - Lisheng Chu
- School of Basic Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
- Department of PhysiologyZhejiang Chinese Medical UniversityHangzhouChina
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Lejeune S, Kaushik A, Parsons ES, Chinthrajah S, Snyder M, Desai M, Manohar M, Prunicki M, Contrepois K, Gosset P, Deschildre A, Nadeau K. Untargeted metabolomic profiling in children identifies novel pathways in asthma and atopy. J Allergy Clin Immunol 2024; 153:418-434. [PMID: 38344970 DOI: 10.1016/j.jaci.2023.09.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 02/15/2024]
Abstract
BACKGROUND Asthma and other atopic disorders can present with varying clinical phenotypes marked by differential metabolomic manifestations and enriched biological pathways. OBJECTIVE We sought to identify these unique metabolomic profiles in atopy and asthma. METHODS We analyzed baseline nonfasted plasma samples from a large multisite pediatric population of 470 children aged <13 years from 3 different sites in the United States and France. Atopy positivity (At+) was defined as skin prick test result of ≥3 mm and/or specific IgE ≥ 0.35 IU/mL and/or total IgE ≥ 173 IU/mL. Asthma positivity (As+) was based on physician diagnosis. The cohort was divided into 4 groups of varying combinations of asthma and atopy, and 6 pairwise analyses were conducted to best assess the differential metabolomic profiles between groups. RESULTS Two hundred ten children were classified as At-As-, 42 as At+As-, 74 as At-As+, and 144 as At+As+. Untargeted global metabolomic profiles were generated through ultra-high-performance liquid chromatography-tandem mass spectroscopy. We applied 2 independent machine learning classifiers and short-listed 362 metabolites as discriminant features. Our analysis showed the most diverse metabolomic profile in the At+As+/At-As- comparison, followed by the At-As+/At-As- comparison, indicating that asthma is the most discriminant condition associated with metabolomic changes. At+As+ metabolomic profiles were characterized by higher levels of bile acids, sphingolipids, and phospholipids, and lower levels of polyamine, tryptophan, and gamma-glutamyl amino acids. CONCLUSION The At+As+ phenotype displays a distinct metabolomic profile suggesting underlying mechanisms such as modulation of host-pathogen and gut microbiota interactions, epigenetic changes in T-cell differentiation, and lower antioxidant properties of the airway epithelium.
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Affiliation(s)
- Stéphanie Lejeune
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; University of Lille, Pediatric Pulmonology and Allergy Department, Hôpital Jeanne de Flandre, CHU Lille, Lille, France; University of Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France.
| | - Abhinav Kaushik
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Environmental Health, T. H. Chan School of Public Health, Harvard University, Boston, Mass
| | - Ella S Parsons
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif
| | - Sharon Chinthrajah
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, Calif
| | - Manisha Desai
- Quantitative Science Unit, Department of Medicine, Stanford University School of Medicine, Stanford, Calif
| | - Monali Manohar
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif
| | - Mary Prunicki
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Environmental Health, T. H. Chan School of Public Health, Harvard University, Boston, Mass
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, Calif
| | - Philippe Gosset
- University of Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Antoine Deschildre
- University of Lille, Pediatric Pulmonology and Allergy Department, Hôpital Jeanne de Flandre, CHU Lille, Lille, France; University of Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Kari Nadeau
- Department of Environmental Health, T. H. Chan School of Public Health, Harvard University, Boston, Mass
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Han X, Krempski JW, Nadeau K. Advances and novel developments in mechanisms of allergic inflammation. Allergy 2020; 75:3100-3111. [PMID: 33068299 DOI: 10.1111/all.14632] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023]
Abstract
In the past decade, research in the molecular and cellular underpinnings of basic and clinical immunology has significantly advanced our understanding of allergic disorders, allowing scientists and clinicians to diagnose and treat disorders such as asthma, allergic and nonallergic rhinitis, and food allergy. In this review, we discuss several significant recent developments in basic and clinical research as well as important future research directions in allergic inflammation. Certain key regulatory cytokines, genes and molecules have recently been shown to play key roles in allergic disorders. For example, interleukin-33 (IL-33) plays an important role in refractory disorders such as asthma, allergic rhinitis and food allergy, mainly by inducing T helper (Th) 2 immune responses and clinical trials with IL-33 inhibitors are underway in food allergy. We discuss interleukin 4 receptor pathways, which recently have been shown to play a critical role among the allergic inflammatory pathways that drive allergic disorders and pathogenesis. Further, the cytokine thymic stromal lymphopoietin (TSLP) has recently been shown as a factor in maintaining immune homeostasis and regulating type 2 inflammatory responses at mucosal barriers in allergic inflammation and targeting TSLP-mediated signalling is considered an attractive therapeutic strategy. In addition, new findings establish an important T cell-intrinsic role of mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) proteolytic activity in the suppression of autoimmune responses. We have seen how mutations in the filaggrin gene are a significant risk factor for allergic diseases such as atopic dermatitis, asthma, allergic rhinitis, food allergy, contact allergy, and hand eczema. We are only beginning to understand the mechanisms by which the human microbiota may be regulating the immune system, and how sudden changes in the composition of the microbiota may have profound effects, linked with an increased risk of developing chronic inflammatory disorders, including allergies. New research has shown the important but complex role monocytes play in disorders such as food allergies. Finally, we discuss some of the new directions of research in this area, particularly the important use of biologicals in oral immunotherapy, advances in gene therapy, multifood therapy, novel diagnostics in diagnosing allergic disorders and the central role that omics play in creating molecular signatures and biomarkers of allergic disorders such as food allergy. Such exciting new developments and advances have significantly moved forth our ability to understand the mechanisms underlying allergic diseases for improved patient care.
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Affiliation(s)
- Xiaorui Han
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University Stanford University Stanford CA USA
| | - James W. Krempski
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University Stanford University Stanford CA USA
| | - Kari Nadeau
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University Stanford University Stanford CA USA
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Duan M, Zhao WL, Zhou L, Novák P, Zhu X, Yin K. Omics research in vascular calcification. Clin Chim Acta 2020; 511:319-328. [PMID: 33096035 DOI: 10.1016/j.cca.2020.10.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023]
Abstract
Vascular calcification (VC), the pathological process of hydroxyapatite mineral deposition in the vascular system, is closely associated with aging, atherosclerotic plaque formation, cardiovascular disease (CVD) and diabetes mellitus (DM). Studies have shown that VC is related to cellular phenotypic changes, extracellular vesicles, disordered calcium and phosphate homeostasis, and an imbalance between inducers and inhibitors of VC. Unfortunately, there is currently no effective preventive or targeted treatment for pathologic condition. The rapid evolution of omics technology (genomics, epigenomics, transcriptomics, proteomics and metabolomics) has provided a novel approach for elucidation of pathophysiologic mechanisms in general and those associated with VC specifically. Here, we review articles published over the last twenty years and focus on the current state, challenges, limitations and future of omics in VC research and clinical practice. Highlighting potential targets based on omics technology will improve our understanding of this pathologic condition and assist in the development of potential treatment options for VC related disease.
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Affiliation(s)
- Meng Duan
- Research Lab of Translational Medicine, Hengyang Medical School, University of South China, Hengyang 421001, China; Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin 541100, China
| | - Wen-Li Zhao
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin 541100, China
| | - Le Zhou
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin 541100, China
| | - Petr Novák
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin 541100, China
| | - Xiao Zhu
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin 541100, China.
| | - Kai Yin
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin 541100, China.
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Duan M, Zhao WL, Zhou L, Novák P, Zhu X, Yin K. Omics research in vascular calcification. Clin Chim Acta 2020; 511:198-207. [PMID: 33096032 DOI: 10.1016/j.cca.2020.10.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 02/07/2023]
Abstract
Vascular calcification (VC), the pathological process of hydroxyapatite mineral deposition in the vascular system, is closely associated with aging, atherosclerotic plaque formation, cardiovascular disease (CVD) and diabetes mellitus (DM). Studies have shown that VC is related to cellular phenotypic changes, extracellular vesicles, disordered calcium phosphate homeostasis and an imbalance between inducers and inhibitors of VC. Unfortunately, there is currently no effective preventive or targeted treatment for this disorder. Recently, the evolution of omics technology (genomics, epigenomics, transcriptomics, proteomics and metabolomics) has paved the way for elucidation of complex biochemical processes and, as such, may provide new insight on VC. Accordingly, we conducted a review of articles published over the last twenty years and herein focus on current and future potential of omics technology in clarifying mechanisms of this disease process. Identification of new biomarkers will provide additional tools in characterizing this pathology and will further assist in the development of potential therapeutic targets.
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Affiliation(s)
- Meng Duan
- Research Lab of Translational Medicine, Hengyang Medical School, University of South China, Hengyang 421001, China; Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin 541100, China
| | - Wen-Li Zhao
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin 541100, China
| | - Le Zhou
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin 541100, China
| | - Petr Novák
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin 541100, China
| | - Xiao Zhu
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin 541100, China.
| | - Kai Yin
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin 541100, China.
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Grayson MH, Marshall GD. Here come the omics! Ann Allergy Asthma Immunol 2020; 123:531. [PMID: 31761011 DOI: 10.1016/j.anai.2019.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Mitchell H Grayson
- Division of Allergy and Immunology, Department of Pediatrics, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio.
| | - Gailen D Marshall
- Division of Allergy, Asthma, and Clinical Immunology, Department of Medicine, The University of Mississippi Medical Center, Jackson, Mississippi
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