1
|
Oh E, Lee H. DeepPIG: deep neural network architecture with pairwise connected layers and stochastic gates using knockoff frameworks for feature selection. Sci Rep 2024; 14:15582. [PMID: 38971807 PMCID: PMC11227546 DOI: 10.1038/s41598-024-66061-6] [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: 03/28/2024] [Accepted: 06/26/2024] [Indexed: 07/08/2024] Open
Abstract
Selecting relevant feature subsets is essential for machine learning applications. Among the feature selection techniques, the knockoff filter procedure proposes a unique framework that minimizes false discovery rates (FDR). However, employing a deep neural network architecture for a knockoff filter framework requires higher detection power. Using the knockoff filter framework, we present a Deep neural network with PaIrwise connected layers integrated with stochastic Gates (DeepPIG) for the feature selection model. DeepPIG exhibited better detection power in synthetic data than the baseline and recent models such as Deep feature selection using Paired-Input Nonlinear Knockoffs (DeepPINK), Stochastic Gates (STG), and SHapley Additive exPlanations (SHAP) while not violating the preselected FDR level, especially when the signal of the features were weak. The selected features determined by DeepPIG demonstrated superior classification performance compared with the baseline model in real-world data analyses, including the prediction of certain cancer prognosis and classification tasks using microbiome and single-cell datasets. In conclusion, DeepPIG is a robust feature selection approach even when the signals of features are weak. Source code is available at https://github.com/DMCB-GIST/DeepPIG .
Collapse
Affiliation(s)
- Euiyoung Oh
- Gwangju Institute of Science and Technology, School of Electrical Engineering and Computer Science, Gwangju, 61005, South Korea
| | - Hyunju Lee
- Gwangju Institute of Science and Technology, School of Electrical Engineering and Computer Science, Gwangju, 61005, South Korea.
- Gwangju Institute of Science and Technology, Artificial Intelligence Graduate School, Gwangju, 61005, South Korea.
| |
Collapse
|
2
|
Łaszczych D, Czernicka A, Gostomczyk K, Szylberg Ł, Borowczak J. The role of IL-17 in the pathogenesis and treatment of glioblastoma-an update on the state of the art and future perspectives. Med Oncol 2024; 41:187. [PMID: 38918274 PMCID: PMC11199243 DOI: 10.1007/s12032-024-02434-1] [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: 05/06/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024]
Abstract
Glioblastoma (GBM) is the most common malignant brain tumor, which, despite significant progress made in the last years in the field of neuro-oncology, remains an incurable disease. GBM has a poor prognosis with a median survival of 12-15 months, and its aggressive clinical course is related to rapid growth, extensive infiltration of adjacent tissues, resistance to chemotherapy, radiotherapy and immunotherapy, and frequent relapse. Currently, several molecular biomarkers are used in clinical practice to predict patient prognosis and response to treatment. However, due to the overall unsatisfactory efficacy of standard multimodal treatment and the remaining poor prognosis, there is an urgent need for new biomarkers and therapeutic strategies for GBM. Recent evidence suggests that GBM tumorigenesis is associated with crosstalk between cancer, immune and stromal cells mediated by various cytokines. One of the key factors involved in this process appears to be interleukin-17 (IL-17), a pro-inflammatory cytokine that is significantly upregulated in the serum and tissue of GBM patients. IL-17 plays a key role in tumorigenesis, angiogenesis, and recurrence of GBM by activating pro-oncogenic signaling pathways and promoting cell survival, proliferation, and invasion. IL-17 facilitates the immunomodulation of the tumor microenvironment by promoting immune cells infiltration and cytokine secretion. In this article we review the latest scientific reports to provide an update on the role of IL-17 role in tumorigenesis, tumor microenvironment, diagnosis, prognosis, and treatment of GBM.
Collapse
Affiliation(s)
- Dariusz Łaszczych
- Department of Obstetrics, Gynaecology and Oncology, Collegium Medicum, Nicolaus Copernicus University in Bydgoszcz, Ujejskiego 75 street, 85-168, Bydgoszcz, Poland.
| | - Aleksandra Czernicka
- Department of Obstetrics, Gynaecology and Oncology, Collegium Medicum, Nicolaus Copernicus University in Bydgoszcz, Ujejskiego 75 street, 85-168, Bydgoszcz, Poland
| | - Karol Gostomczyk
- Department of Obstetrics, Gynaecology and Oncology, Collegium Medicum, Nicolaus Copernicus University in Bydgoszcz, Ujejskiego 75 street, 85-168, Bydgoszcz, Poland
| | - Łukasz Szylberg
- Department of Obstetrics, Gynaecology and Oncology, Collegium Medicum, Nicolaus Copernicus University in Bydgoszcz, Ujejskiego 75 street, 85-168, Bydgoszcz, Poland
- Department of Tumor Pathology and Pathomorphology, Oncology Centre - Prof. Franciszek Łukaszczyk Memorial Hospital, dr Izabeli Romanowskiej 2 street, 85-796, Bydgoszcz, Poland
| | - Jędrzej Borowczak
- Department of Clinical Oncology, Oncology Centre - Prof. Franciszek Łukaszczyk Memorial Hospital, dr Izabeli Romanowskiej 2 street, 85-796, Bydgoszcz, Poland
| |
Collapse
|
3
|
Liu ZY, Tang F, Wang J, Yang JZ, Chen X, Wang ZF, Li ZQ. Serum beta2-microglobulin acts as a biomarker for severity and prognosis in glioma patients: a preliminary clinical study. BMC Cancer 2024; 24:692. [PMID: 38844902 PMCID: PMC11155066 DOI: 10.1186/s12885-024-12441-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/28/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Gliomas are the deadliest malignant tumors of the adult central nervous system. We previously discovered that beta2-microglobulin (B2M) is abnormally upregulated in glioma tissues and that it exerts a range of oncogenic effects. Besides its tissue presence, serum B2M levels serve as biomarkers for various diseases. This study aimed to explore whether serum B2M levels can be used in the diagnosis and prognosis of gliomas. METHODS Medical records from 246 glioma patients were retrospectively analyzed. The relationship between preoperative serum B2M levels and clinicopathological features was examined. Kaplan-Meier analysis, alongside uni- and multivariate Cox regression, assessed the association between B2M levels, systemic inflammatory markers, and glioma patient prognosis. Receiver operating characteristic (ROC) curve analysis evaluated the diagnostic significance of these biomarkers specifically for glioblastoma (GBM). RESULTS Patients with malignant gliomas exhibited elevated preoperative serum B2M levels. Glioma patients with high serum B2M levels experienced shorter survival times. Multivariate Cox analysis determined the relationship between B2M levels (hazard ratio = 1.92, 95% confidence interval: 1.05-3.50, P = 0.034) and the overall survival of glioma patients. B2M demonstrated superior discriminatory power in distinguishing between GBM and non-GBM compared to inflammation indicators. Moreover, postoperative serum B2M levels were lower than preoperative levels in the majority of glioma patients. CONCLUSIONS High preoperative serum B2M levels correlated with malignant glioma and a poor prognosis. Serum B2M shows promise as a novel biomarker for predicting patient prognosis and reflecting the therapeutic response.
Collapse
Affiliation(s)
- Zhen-Yuan Liu
- Brain Glioma Center, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Feng Tang
- Brain Glioma Center, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jing Wang
- Department of Clinical Laboratory, Nanjing Jiangning Hospital, Nanjing, Jiangsu, China
| | - Jin-Zhou Yang
- Brain Glioma Center, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xi Chen
- Brain Glioma Center, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ze-Fen Wang
- Department of Physiology, Wuhan University School of Basic Medical Sciences, Wuhan, Hubei, China.
| | - Zhi-Qiang Li
- Brain Glioma Center, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.
- Hubei International Science and Technology Cooperation Base for Research and Clinical techniques for Brain Glioma Diagnosis and Treatment, Wuhan, Hubei, China.
| |
Collapse
|
4
|
Liu ZY, Tang F, Yang JZ, Chen X, Wang ZF, Li ZQ. The Role of Beta2-Microglobulin in Central Nervous System Disease. Cell Mol Neurobiol 2024; 44:46. [PMID: 38743119 PMCID: PMC11093819 DOI: 10.1007/s10571-024-01481-6] [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: 01/06/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
Central nervous system (CNS) disorders represent the leading cause of disability and the second leading cause of death worldwide, and impose a substantial economic burden on society. In recent years, emerging evidence has found that beta2 -microglobulin (B2M), a subunit of major histocompatibility complex class I (MHC-I) molecules, plays a crucial role in the development and progression in certain CNS diseases. On the one hand, intracellular B2M was abnormally upregulated in brain tumors and regulated tumor microenvironments and progression. On the other hand, soluble B2M was also elevated and involved in pathological stages in CNS diseases. Targeted B2M therapy has shown promising outcomes in specific CNS diseases. In this review, we provide a comprehensive summary and discussion of recent advances in understanding the pathological processes involving B2M in CNS diseases (e.g., Alzheimer's disease, aging, stroke, HIV-related dementia, glioma, and primary central nervous system lymphoma).
Collapse
Affiliation(s)
- Zhen-Yuan Liu
- Brain Glioma Center & Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Feng Tang
- Brain Glioma Center & Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jin-Zhou Yang
- Brain Glioma Center & Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xi Chen
- Brain Glioma Center & Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ze-Fen Wang
- Department of Physiology, Wuhan University School of Basic Medical Sciences, Wuhan, Hubei, China.
| | - Zhi-Qiang Li
- Brain Glioma Center & Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.
| |
Collapse
|
5
|
Mohammadi E, Dashti S, Shafizade N, Jin H, Zhang C, Lam S, Tahmoorespur M, Mardinoglu A, Sekhavati MH. Drug repositioning for immunotherapy in breast cancer using single-cell analysis. NPJ Syst Biol Appl 2024; 10:37. [PMID: 38589404 PMCID: PMC11001976 DOI: 10.1038/s41540-024-00359-z] [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: 01/13/2023] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Immunomodulatory peptides, while exhibiting potential antimicrobial, antifungal, and/or antiviral properties, can play a role in stimulating or suppressing the immune system, especially in pathological conditions like breast cancer (BC). Thus, deregulation of these peptides may serve as an immunotherapeutic strategy to enhance the immune response. In this meta-analysis, we utilized single-cell RNA sequencing data and known therapeutic peptides to investigate the deregulation of these peptides in malignant versus normal human breast epithelial cells. We corroborated our findings at the chromatin level using ATAC-seq. Additionally, we assessed the protein levels in various BC cell lines. Moreover, our in-house drug repositioning approach was employed to identify potential drugs that could positively impact the relapse-free survival of BC patients. Considering significantly deregulated therapeutic peptides and their role in BC pathology, our approach aims to downregulate B2M and SLPI, while upregulating PIGR, DEFB1, LTF, CLU, S100A7, and SCGB2A1 in BC epithelial cells through our drug repositioning pipeline. Leveraging the LINCS L1000 database, we propose BRD-A06641369 for B2M downregulation and ST-4070043 and BRD-K97926541 for SLPI downregulation without negatively affecting the MHC complex as a significantly correlated pathway with these two genes. Furthermore, we have compiled a comprehensive list of drugs for the upregulation of other selected immunomodulatory peptides. Employing an immunotherapeutic approach by integrating our drug repositioning pipeline with single-cell analysis, we proposed potential drugs and drug targets to fortify the immune system against BC.
Collapse
Affiliation(s)
- Elyas Mohammadi
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden.
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Samira Dashti
- Department of Internal Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | - Neda Shafizade
- Department of Internal Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | - Han Jin
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | | |
Collapse
|
6
|
Rudd CE. CD8 + T cell killing of MHC class I-deficient tumors. NATURE CANCER 2023; 4:1214-1216. [PMID: 37537302 DOI: 10.1038/s43018-023-00606-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Affiliation(s)
- Christopher E Rudd
- Department of Medicine, Université de Montréal, Montreal, Quebec, Canada.
- Division of Endocrinology and Metabolism, Department of Medicine & Health Sciences, McGill University, Montreal, Quebec, Canada.
- Division of Immunology Oncology, Centre de Recherche-Hôpital Maisonneuve-Rosemont (CR-HMR), Montreal, Quebec, Canada.
| |
Collapse
|
7
|
Lerner EC, Woroniecka KI, D'Anniballe VM, Wilkinson DS, Mohan AA, Lorrey SJ, Waibl-Polania J, Wachsmuth LP, Miggelbrink AM, Jackson JD, Cui X, Raj JA, Tomaszewski WH, Cook SL, Sampson JH, Patel AP, Khasraw M, Gunn MD, Fecci PE. CD8 + T cells maintain killing of MHC-I-negative tumor cells through the NKG2D-NKG2DL axis. NATURE CANCER 2023; 4:1258-1272. [PMID: 37537301 PMCID: PMC10518253 DOI: 10.1038/s43018-023-00600-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/20/2023] [Indexed: 08/05/2023]
Abstract
The accepted paradigm for both cellular and anti-tumor immunity relies upon tumor cell killing by CD8+ T cells recognizing cognate antigens presented in the context of target cell major histocompatibility complex (MHC) class I (MHC-I) molecules. Likewise, a classically described mechanism of tumor immune escape is tumor MHC-I downregulation. Here, we report that CD8+ T cells maintain the capacity to kill tumor cells that are entirely devoid of MHC-I expression. This capacity proves to be dependent instead on interactions between T cell natural killer group 2D (NKG2D) and tumor NKG2D ligands (NKG2DLs), the latter of which are highly expressed on MHC-loss variants. Necessarily, tumor cell killing in these instances is antigen independent, although prior T cell antigen-specific activation is required and can be furnished by myeloid cells or even neighboring MHC-replete tumor cells. In this manner, adaptive priming can beget innate killing. These mechanisms are active in vivo in mice as well as in vitro in human tumor systems and are obviated by NKG2D knockout or blockade. These studies challenge the long-advanced notion that downregulation of MHC-I is a viable means of tumor immune escape and instead identify the NKG2D-NKG2DL axis as a therapeutic target for enhancing T cell-dependent anti-tumor immunity against MHC-loss variants.
Collapse
Affiliation(s)
- Emily C Lerner
- Duke University School of Medicine, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | | | - Daniel S Wilkinson
- Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Aditya A Mohan
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Selena J Lorrey
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
| | | | - Lucas P Wachsmuth
- Duke University School of Medicine, Durham, NC, USA
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | | | - Joshua D Jackson
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Xiuyu Cui
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Jude A Raj
- Duke University School of Medicine, Durham, NC, USA
| | | | - Sarah L Cook
- Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - John H Sampson
- Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Anoop P Patel
- Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Mustafa Khasraw
- Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
| | - Michael D Gunn
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Peter E Fecci
- Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA.
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA.
| |
Collapse
|
8
|
Ren J, Xu B, Ren J, Liu Z, Cai L, Zhang X, Wang W, Li S, Jin L, Ding L. The Importance of M1-and M2-Polarized Macrophages in Glioma and as Potential Treatment Targets. Brain Sci 2023; 13:1269. [PMID: 37759870 PMCID: PMC10526262 DOI: 10.3390/brainsci13091269] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Glioma is the most common and malignant tumor of the central nervous system. Glioblastoma (GBM) is the most aggressive glioma, with a poor prognosis and no effective treatment because of its high invasiveness, metabolic rate, and heterogeneity. The tumor microenvironment (TME) contains many tumor-associated macrophages (TAMs), which play a critical role in tumor proliferation, invasion, metastasis, and angiogenesis and indirectly promote an immunosuppressive microenvironment. TAM is divided into tumor-suppressive M1-like (classic activation of macrophages) and tumor-supportive M2-like (alternatively activated macrophages) polarized cells. TAMs exhibit an M1-like phenotype in the initial stages of tumor progression, and along with the promotion of lysing tumors and the functions of T cells and NK cells, tumor growth is suppressed, and they rapidly transform into M2-like polarized macrophages, which promote tumor progression. In this review, we discuss the mechanism by which M1- and M2-polarized macrophages promote or inhibit the growth of glioblastoma and indicate the future directions for treatment.
Collapse
Affiliation(s)
- Jiangbin Ren
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Bangjie Xu
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Jianghao Ren
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China;
| | - Zhichao Liu
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Lingyu Cai
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Xiaotian Zhang
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Weijie Wang
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Shaoxun Li
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Luhao Jin
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Lianshu Ding
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| |
Collapse
|
9
|
Chunder R, Heider T, Kuerten S. The prevalence of IgG antibodies against milk and milk antigens in patients with multiple sclerosis. Front Immunol 2023; 14:1202006. [PMID: 37492579 PMCID: PMC10364054 DOI: 10.3389/fimmu.2023.1202006] [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: 04/07/2023] [Accepted: 06/21/2023] [Indexed: 07/27/2023] Open
Abstract
Introduction Multiple sclerosis (MS) is a chronic demyelinating disease of the central nervous system (CNS). The pathophysiology of MS is complex and is said to be influenced by multiple environmental determinants, including diet. We and others have previously demonstrated how consumption of bovine milk can aggravate disease severity in MS patients, which can be explained by molecular mimicry between milk antigens and those expressed within the CNS. In this study we set out to identify alternatives to drinking cow milk which might be less detrimental to MS patients who have a genetic predisposition towards developing antibody titers against bovine milk antigens that cross-react with CNS antigens. Methods To this end, we screened 35 patients with MS and 20 healthy controls for their IgG reactivity against an array of animal-sourced milk, plant-based alternatives as well as individual antigens from bovine milk. Results We demonstrate that MS patients have a significantly higher IgG response to animal-sourced milk, especially cow milk, in comparison to healthy donors. We also show that the reactivity to cow milk in MS patients can be attributed to reactivity against different bovine milk antigens. Finally, our correlation data indicate the co-existence of antibodies to individual bovine milk antigens and their corresponding cross-reactive CNS antigens. Discussion Taken together, we suggest screening of blood from MS patients for antibodies against different types of milk and milk antigens in order to establish a personalized diet regimen.
Collapse
Affiliation(s)
- Rittika Chunder
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, Bonn, Germany
| | - Thorsten Heider
- Clinic for Neurology, Klinikum St. Marien Amberg, Amberg, Germany
| | - Stefanie Kuerten
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, Bonn, Germany
| |
Collapse
|
10
|
Huang G, Wu Y, Du Y, Gan H, Hao S. Methyl-CpG Binding Protein 2 as a Potential Diagnostic and Prognostic Marker Facilitates Glioma Progression Through Activation of Wnt/β-Catenin Pathway. World Neurosurg 2023; 171:e560-e571. [PMID: 36529430 DOI: 10.1016/j.wneu.2022.12.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Glioma is the primary malignant tumor in the central nervous system and has high malignancy, mortality, and recurrence rates. Because of its heterogeneity and drug resistance, the blood-brain barrier, and other factors, the treatment of glioma has mainly been surgical resection combined with traditional radiotherapy and chemotherapy. However, the therapeutic effect has not been satisfactory. Methyl-CpG binding protein 2 (MeCP2) is an epigenetic regulator that has been reported to regulate the initiation and progression of glioma. However, the underlying mechanism in glioma has remained unclear. METHODS The gene expression of MeCp2, miR-138-5p, the epithelial-mesenchymal transition, the apoptosis-related gene, and the Wnt/β-Catenin pathway-related gene and proliferation were detected by reverse transcription-quantitative polymerase chain reaction or Western blot. The cell proliferation and apoptosis of the glioma cell was assessed using the CCK-8 assay and flow cytometry assay. The relationship between miR-138-5p and MeCp2 was measured using the dual luciferase reporter assay. The effect of MeCp2 in U87 cells was examined in a xenograft tumorigenesis model in vivo. RESULTS In our study, we found that MeCP2 was upregulated in glioma tissues and cell lines and that MeCP2 knockdown repressed cell proliferation and epithelial-mesenchymal transition but boosted cell apoptosis in glioma. Furthermore, MeCP2 knockdown attenuated in vivo glioma growth in a mice model. Mechanistically, miR-138-5p hindered the expression of MeCP2 by target MeCP2 and then inactivated the Wnt/β-catenin signaling pathway. In addition, subsequent rescue assays disclosed that miR-138-5p repressed the glioma malignant phenotype and MeCP2 overexpression reversed the inhibitory effect of miR-138-5p upregulation. Consistently, overexpression of MeCP2 elevated glioma development. However, inhibition of the Wnt/β-catenin signaling pathway with XAV-939 rescued the facilitation effect by overexpressing miR-138-5p. CONCLUSIONS Our results have revealed that miR-138-5p/MeCP2/Wnt/β-catenin signaling might be a new target axis for glioma treatment strategies.
Collapse
Affiliation(s)
- Guanyou Huang
- Department of Neurosurgery, The Second People's Hospital of Guiyang (Jingyang Hospital), Guiyang, China.
| | - Yujuan Wu
- Department of Neurology, The Second People's Hospital of Guiyang (Jingyang Hospital), Guiyang, China
| | - Yonggui Du
- Department of Neurosurgery, The Second People's Hospital of Guiyang (Jingyang Hospital), Guiyang, China
| | - Hongchuan Gan
- Department of Neurosurgery, The Second People's Hospital of Guiyang (Jingyang Hospital), Guiyang, China
| | - Shuyu Hao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
11
|
β 2 -Microglobulin Participates in the Development of Vestibular Schwannoma by Regulating Nuclear Factor-κB. Otol Neurotol 2022; 43:e1049-e1055. [PMID: 36006779 DOI: 10.1097/mao.0000000000003647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND OBJECTIVES Vestibular schwannoma (VS), the most common intercranial schwannoma, originates from the sheath of the vestibular nerve. The growth rate of VS varies greatly, with the tumor enlarging gradually, which can compress the peripheral nerve tissue and reveal corresponding symptoms. This study was aimed to elucidate the growth mechanism of VS by analyzing cellular changes at protein, messenger ribonucleic acid (mRNA), and other molecular levels. METHODS We determined mRNA and protein levels of β 2 -microglobulin (β 2 -M) and nuclear factor κB (NF-κB) in tumors of different sizes using the real-time polymerase chain reaction and Western blotting, respectively. The relationship between these factors was verified in VS primary cells cultured in vitro, and the potential role of β 2 -M and NF-κB in VS growth was elucidated. RESULTS In the secretions of freshly isolated tumor tissue cultured for 72 h, the concentration of β 2 -M was positively correlated with the tumor diameter. Furthermore, tumors with larger diameter showed higher expressions of β 2 -M and NF-κB at protein and mRNA level. β 2 -M treatment resulted in elevated protein expression of NF-κB and also its phosphorylated form in vitro. CONCLUSION β 2 -M may participate in VS growth by regulating NF-κB and act as a key regulatory molecule in VS tumor growth.
Collapse
|
12
|
Fan W, Wang D, Li G, Xu J, Ren C, Sun Z, Wang Z, Ma W, Zhao Z, Bao Z, Jiang T, Zhang Y. A novel chemokine-based signature for prediction of prognosis and therapeutic response in glioma. CNS Neurosci Ther 2022; 28:2090-2103. [PMID: 35985661 PMCID: PMC9627384 DOI: 10.1111/cns.13944] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 02/06/2023] Open
Abstract
AIMS Gliomas are the primary malignant brain tumor and characterized as the striking cellular heterogeneity and intricate tumor microenvironment (TME), where chemokines regulate immune cell trafficking by shaping local networks. This study aimed to construct a chemokine-based gene signature to evaluate the prognosis and therapeutic response in glioma. METHODS In this study, 1024 patients (699 from TCGA and 325 from CGGA database) with clinicopathological information and mRNA sequencing data were enrolled. A chemokine gene signature was constructed by combining LASSO and SVM-RFE algorithm. GO, KEGG, and GSVA analyses were performed for function annotations of the chemokine signature. Candidate mRNAs were subsequently verified through qRT-PCR in an independent cohort including 28 glioma samples. Then, through immunohistochemical staining (IHC), we detected the expression of immunosuppressive markers and explore the role of this gene signature in immunotherapy for glioma. Lastly, the Genomics of Drug Sensitivity in Cancer (GDSC) were leveraged to predict the potential drug related to the gene signature in glioma. RESULTS A constructed chemokine gene signature was significantly associated with poorer survival, especially in glioblastoma, IDH wildtype. It also played an independent prognostic factor in both datasets. Moreover, biological function annotations of the predictive signature indicated the gene signature was positively associated with immune-relevant pathways, and the immunosuppressive protein expressions (PD-L1, IBA1, TMEM119, CD68, CSF1R, and TGFB1) were enriched in the high-risk group. In an immunotherapy of glioblastoma cohort, we confirmed the chemokine signature showed a good predictor for patients' response. Lastly, we predicted twelve potential agents for glioma patients with higher riskscore. CONCLUSION In all, our results highlighted a potential 4-chemokine signature for predicting prognosis in glioma and reflected the intricate immune landscape in glioma. It also threw light on integrating tailored risk stratification with precision therapy for glioblastoma.
Collapse
Affiliation(s)
- Wenhua Fan
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina,Department Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA)BeijingChina
| | - Di Wang
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Guanzhang Li
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina,Department Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA)BeijingChina
| | - Jianbao Xu
- The Second Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Changyuan Ren
- Sanbo Brain HospitalCapital Medical UniversityBeijingChina
| | - Zhiyan Sun
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina,Department Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA)BeijingChina
| | - Zhiliang Wang
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA)BeijingChina
| | - Wenping Ma
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina,Department Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA)BeijingChina
| | - Zheng Zhao
- Department Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA)BeijingChina
| | - Zhaoshi Bao
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina,Department Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA)BeijingChina
| | - Tao Jiang
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina,Department Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA)BeijingChina
| | - Ying Zhang
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina,Department Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA)BeijingChina
| |
Collapse
|
13
|
Hu W, Liu H, Li Z, Liu J, Chen L. Impact of molecular and clinical variables on survival outcome with immunotherapy for glioblastoma patients: A systematic review and meta-analysis. CNS Neurosci Ther 2022; 28:1476-1491. [PMID: 35822692 PMCID: PMC9437230 DOI: 10.1111/cns.13915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Given that only a subset of patients with glioblastoma multiforme (GBM) responds to immuno-oncology, this study aimed to assess the impact of multiple factors on GBM immunotherapy prognosis and investigate the potential predictors. METHODS A quantitative meta-analysis was conducted using the random-effects model. Several potential factors were also reviewed qualitatively. RESULTS A total of 39 clinical trials were included after screening 1317 papers. Patients with O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation [hazard ratio (HR) for overall survival (OS) = 2.30, p < 0.0001; HR for progression-free survival (PFS) = 2.10, p < 0.0001], gross total resection (HR for OS = 0.70, p = 0.02; HR for PFS = 0.56, p = 0.004), and no baseline steroid use (HR for OS = 0.52, p = 0.0002; HR for PFS = 0.61, p = 0.02) had a relatively significant favorable OS and PFS following immunotherapy. Patients with a Karnofsky Performance Status score < 80 (HR = 1.73, p = 0.0007) and undergoing two prior relapses (HR = 2.08, p = 0.003) were associated with worse OS. Age, gender, tumor programmed death-ligand 1 expression, and history of chemotherapy were not associated with survival outcomes. Notably, immunotherapy significantly improved the OS among patients undergoing two prior recurrences (HR = 0.40, p = 0.008) but not among patients in any other subgroups, as opposed to non-immunotherapy. CONCLUSION Several factors were associated with prognostic outcomes of GBM patients receiving immunotherapy; multiple recurrences might be a candidate predictor. More marker-driven prospective studies are warranted.
Collapse
Affiliation(s)
- Wentao Hu
- School of Medicine, Nankai University, Tianjin, China.,Department of Neurosurgery, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Hongyu Liu
- Department of Neurosurgery, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Ze Li
- Department of Neurosurgery, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jialin Liu
- Department of Neurosurgery, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Ling Chen
- Department of Neurosurgery, First Medical Center of Chinese PLA General Hospital, Beijing, China
| |
Collapse
|
14
|
Palmitoyl transferases act as potential regulators of tumor-infiltrating immune cells and glioma progression. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:716-731. [PMID: 35664705 PMCID: PMC9126852 DOI: 10.1016/j.omtn.2022.04.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 04/29/2022] [Indexed: 12/20/2022]
Abstract
High immune-cell infiltration in glioblastomas (GBMs) leads to immunotherapy resistance. Emerging evidence has shown that zinc finger Asp-His-His-Cyc-type (ZDHHC) palmitoyl transferases participate in regulating tumor progression and the immune microenvironment. In the present study, a large cohort of patients with gliomas from The Cancer Genome Atlas (TCGA) and Rembrandt databases was included to perform omics analysis of ZDHHCs in gliomas. CCK-8, flow cytometry, quantitative real-time PCR, western blotting, and transwell assays were performed to determine the effects of ZDHHC inhibition on glioma cells and microglia. We found that five (ZDHHC11, ZDHHC12, ZDHHC15, ZDHHC22, and ZDHHC23) out of 23 ZDHHCs were aberrantly expressed in gliomas and might play their roles through the phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) signaling pathway. Further results indicated that inhibition of ZDHHCs with 2-bromopalmitate (2-BP) suppressed glioma-cell viability and autophagy, as well as promoted apoptosis. Targeting ZDHHCs also promoted the sensitivity of glioma cells to temozolomide (TMZ) chemotherapy. In addition, the inhibition of ZDHHCs weakened the migratory ability of microglia induced by glioma cells in vitro and in vivo. Taken together, our findings suggest that the inhibition of ZDHHCs suppresses glioma-cell viability and microglial infiltration. Targeting ZDHHCs may be promising for glioma treatments.
Collapse
|