1
|
Hou W, Hou W, Zhao X. Exploring transcriptomic databases: unraveling circadian gene disruptions in lower grade glioma. Sci Rep 2024; 14:16960. [PMID: 39043735 PMCID: PMC11266536 DOI: 10.1038/s41598-024-67559-9] [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: 01/31/2024] [Accepted: 07/12/2024] [Indexed: 07/25/2024] Open
Abstract
The study explored the role of circadian rhythm genes (CRGs) in lower grade glioma (LGG) development and found that certain genes, such as CRY1, NPAS2, and RORB, were associated with increased or decreased risk of LGG. The study also investigated the correlation between CRGs and immune cell infiltration, revealing a negative association with macrophage infiltration and a positive correlation with B cell and CD8 + T cell infiltration. Additionally, the study identified major mutated CRGs, including PER2, BMAL1, CLOCK, and BMAL2, and their potential interaction with other CNS-associated genes. The study suggests that CRGs play a crucial role in immune response and tumorigenesis in LGG patients and warrants further investigation.
Collapse
Affiliation(s)
- Weiyu Hou
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, 030012, China
| | - Weiming Hou
- Department of Medical Engineering, Air Force Medical Center, PLA, Beijing, 100142, China
| | - Xueming Zhao
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, 030012, China.
| |
Collapse
|
2
|
Nayak L, Bettegowda C, Scherer F, Galldiks N, Ahluwalia M, Baraniskin A, von Baumgarten L, Bromberg JEC, Ferreri AJM, Grommes C, Hoang-Xuan K, Kühn J, Rubenstein JL, Rudà R, Weller M, Chang SM, van den Bent MJ, Wen PY, Soffietti R. Liquid biopsy for improving diagnosis and monitoring of CNS lymphomas: A RANO review. Neuro Oncol 2024; 26:993-1011. [PMID: 38598668 PMCID: PMC11145457 DOI: 10.1093/neuonc/noae032] [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: 12/01/2023] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND The utility of liquid biopsies is well documented in several extracranial and intracranial (brain/leptomeningeal metastases, gliomas) tumors. METHODS The RANO (Response Assessment in Neuro-Oncology) group has set up a multidisciplinary Task Force to critically review the role of blood and cerebrospinal fluid (CSF)-liquid biopsy in CNS lymphomas, with a main focus on primary central nervous system lymphomas (PCNSL). RESULTS Several clinical applications are suggested: diagnosis of PCNSL in critical settings (elderly or frail patients, deep locations, and steroid responsiveness), definition of minimal residual disease, early indication of tumor response or relapse following treatments, and prediction of outcome. CONCLUSIONS Thus far, no clinically validated circulating biomarkers for managing both primary and secondary CNS lymphomas exist. There is need of standardization of biofluid collection, choice of analytes, and type of technique to perform the molecular analysis. The various assays should be evaluated through well-organized central testing within clinical trials.
Collapse
Affiliation(s)
- Lakshmi Nayak
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Florian Scherer
- Department of Medicine I, Faculty of Medicine, Medical Center—University of Freiburg, University of Freiburg, Freiburg, Germany
| | - Norbert Galldiks
- Department of Neurology, University of Cologne, Medical Faculty and University Hospital Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), and Institute of Neuroscience and Medicine (INM-3), Research Center Juelich, Juelich, Germany
| | - Manmeet Ahluwalia
- Rose and Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland OH and Miami Cancer Institute, Baptist Health South Florida, International University, Miami, Florida, USA
| | - Alexander Baraniskin
- Department of Hematology, Oncology and Palliative Care, Evangelisches Krankenhaus Hamm, Hamm, Germany
| | - Louisa von Baumgarten
- Department of Neurosurgery, Ludwig-Maximilians—University of Munich, Munich, Germany
- German Cancer Consortium, Partner Site Munich, Munich, Germany
| | | | - Andrés J M Ferreri
- Università Vita-Salute San Raffaele and IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Christian Grommes
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Neurology, Weill Cornell Medical College, New York, New York, USA
| | - Khê Hoang-Xuan
- APHP, Department of Neuro-oncology, Groupe Hospitalier Pitié-Salpêtrière; Sorbonne Université, Paris Brain Institute ICM, Paris, France
| | - Julia Kühn
- Department of Medicine I, Faculty of Medicine, Medical Center University of Freiburg, University of Freiburg, Freiburg, Germany
| | - James L Rubenstein
- UCSF Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | - Roberta Rudà
- Division of Neuro-Oncology, Department of Neuroscience “Rita Levi Montalcini,” University of Turin, Turin, Italy
| | - Michael Weller
- Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Susan M Chang
- Department of Neurosurgery and Division of Neuro-Oncology, University of California, San Francisco, California, USA
| | | | - Patrick Y Wen
- Department of Neuroscience “Rita Levi Montalcini,” University of Turin, Turin, Italy
| | - Riccardo Soffietti
- Department of Neuroscience “Rita Levi Montalcini,” University of Turin, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| |
Collapse
|
3
|
Bin Masroni MS, Ling Eng GW, Jeon AJ, Gao Y, Cheng H, Leong SM, Cheong JK, Hue SSS, Tan SY. MicroRNA expression signature as a biomarker in the diagnosis of nodal T-cell lymphomas. Cancer Cell Int 2024; 24:48. [PMID: 38291429 PMCID: PMC10826179 DOI: 10.1186/s12935-024-03226-3] [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: 10/27/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND The diagnosis of T-cell lymphomas is typically established through a multiparameter approach that combines clinical, morphologic, immunophenotypic, and genetic features, utilizing a variety of histopathologic and molecular techniques. However, accurate diagnosis of such lymphomas and distinguishing them from reactive lymph nodes remains challenging due to their low prevalence and heterogeneous features, hence limiting the confidence of pathologists. We investigated the use of microRNA (miRNA) expression signatures as an adjunctive tool in the diagnosis and classification of T-cell lymphomas that involve lymph nodes. This study seeks to distinguish reactive lymph nodes (RLN) from two types of frequently occurring nodal T-cell lymphomas: nodal T-follicular helper (TFH) cell lymphomas (nTFHL) and peripheral T-cell lymphomas, not otherwise specified (nPTCL). METHODS From the formalin-fixed paraffin-embedded (FFPE) samples from a cohort of 88 subjects, 246 miRNAs were quantified and analyzed by differential expression. Two-class logistic regression and random forest plot models were built to distinguish RLN from the nodal T-cell lymphomas. Gene set enrichment analysis was performed on the target genes of the miRNA to identify pathways and transcription factors that may be regulated by the differentially expressed miRNAs in each subtype. RESULTS Using logistic regression analysis, we identified miRNA signatures that can distinguish RLN from nodal T-cell lymphomas (AUC of 0.92 ± 0.05), from nTFHL (AUC of 0.94 ± 0.05) and from nPTCL (AUC of 0.94 ± 0.08). Random forest plot modelling was also capable of distinguishing between RLN and nodal T-cell lymphomas, but performed worse than logistic regression. However, the miRNA signatures are not able to discriminate between nTFHL and nPTCL, owing to large similarity in miRNA expression patterns. Bioinformatic analysis of the gene targets of unique miRNA expression revealed the enrichment of both known and potentially understudied signalling pathways and genes in such lymphomas. CONCLUSION This study suggests that miRNA biomarkers may serve as a promising, cost-effective tool to aid the diagnosis of nodal T-cell lymphomas, which can be challenging. Bioinformatic analysis of differentially expressed miRNAs revealed both relevant or understudied signalling pathways that may contribute to the progression and development of each T-cell lymphoma entity. This may help us gain further insight into the biology of T-cell lymphomagenesis.
Collapse
Affiliation(s)
- Muhammad Sufyan Bin Masroni
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117596, Singapore
| | | | - Ah-Jung Jeon
- MiRXES Lab Pte Ltd, Singapore, 138667, Singapore
| | - Yuan Gao
- MiRXES Lab Pte Ltd, Singapore, 138667, Singapore
| | - He Cheng
- MiRXES Lab Pte Ltd, Singapore, 138667, Singapore
| | - Sai Mun Leong
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117596, Singapore
- NUS Centre for Cancer Research, Singapore, 117599, Singapore
| | - Jit Kong Cheong
- NUS Centre for Cancer Research, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117596, Singapore
| | - Susan Swee-Shan Hue
- Department of Pathology, National University Hospital, Singapore, 119077, Singapore.
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117596, Singapore.
- NUS Centre for Cancer Research, Singapore, 117599, Singapore.
| | - Soo Yong Tan
- Department of Pathology, National University Hospital, Singapore, 119077, Singapore.
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117596, Singapore.
- Advanced Molecular Pathology Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore, 138673, Singapore.
| |
Collapse
|
4
|
Hu Y, Zhang Q, Wu Z, Chen K, Xu X, Ma W, Chen B, Jin L, Guan M. Exosomal miR-200c and miR-141 as cerebrospinal fluid biopsy biomarkers for the response to chemotherapy in primary central nervous system lymphoma. Discov Oncol 2023; 14:205. [PMID: 37971595 PMCID: PMC10654293 DOI: 10.1007/s12672-023-00812-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND To improve early diagnosis and chemotherapy efficacy monitoring in primary central nervous system lymphoma (PCNSL), cerebrospinal fluid (CSF) exosomal microRNA (miRNA) studies were performed. METHOD Small RNA sequencing was performed to identify candidate exosomal miRNAs as CSF biopsy biomarkers from two patients with de novo PCNSL and two patients in remission after chemotherapy. miR-200c and miR-141 expression in CSF exosomes was further validated using relative quantitative real-time polymerase chain reaction in patients with PCNSL (n = 20), patients with other neurological diseases (n = 10), and normal subjects (n = 10). Receiver operating characteristic (ROC) curve analyses of miR-200c and miR-141 in the diagnosis and prediction of chemotherapy efficacy in PCNSL were performed in patients treated with methotrexate. Additionally, bioinformatics tools were utilized to predict the potential targets of miR-200c and miR-141. RESULTS Exosomal miR-200c and miR-141 levels in CSF from patients with PCNSL were significantly lower than those in control subjects. Importantly, miR-200c and miR-141 were upregulated in patients with PCNSL after chemotherapy (P = 0.002). There was a significant correlation between the levels of miR-141 and IL-10 in CSF (P = 0.04). The combination of miR-200c and miR-141 yielded an area under the ROC curve of 0.761 for distinguishing PCNSL with sensitivity and specificity of 60.0% and 96.7%, respectively. The potential target genes of miR-200c and miR-141 in PCNSL included ATP1B3, DYNC1H1, MATR3, NUCKS1, ZNF638, NUDT4, RCN2, GNPDA1, ZBTB38, and DOLK. CONCLUSION Collectively, miR-200c and miR-141 are likely to be upregulated in CSF exosomes after chemotherapy in patients with PCNSL, highlighting their potential as reliable liquid biopsy biomarkers for PCNSL diagnosis and chemotherapy efficacy monitoring.
Collapse
Affiliation(s)
- Yao Hu
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Qingyun Zhang
- Department of Central Laboratory, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Zhiyuan Wu
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Kun Chen
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Xiao Xu
- Department of Central Laboratory, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Weizhe Ma
- Department of Central Laboratory, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Bobin Chen
- Department of Hematology, Huashan Hospital, Shanghai Medical College, Fudan University, 200040, Shanghai, China
| | - Limin Jin
- Department of Laboratory Medicine, Jiaxing Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Jiaxing, 314001, Zhejiang, China.
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China.
| |
Collapse
|
5
|
Yang H, Xun Y, Ke C, Tateishi K, You H. Extranodal lymphoma: pathogenesis, diagnosis and treatment. MOLECULAR BIOMEDICINE 2023; 4:29. [PMID: 37718386 PMCID: PMC10505605 DOI: 10.1186/s43556-023-00141-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023] Open
Abstract
Approximately 30% of lymphomas occur outside the lymph nodes, spleen, or bone marrow, and the incidence of extranodal lymphoma has been rising in the past decade. While traditional chemotherapy and radiation therapy can improve survival outcomes for certain patients, the prognosis for extranodal lymphoma patients remains unsatisfactory. Extranodal lymphomas in different anatomical sites often have distinct cellular origins, pathogenic mechanisms, and clinical manifestations, significantly influencing their diagnosis and treatment. Therefore, it is necessary to provide a comprehensive summary of the pathogenesis, diagnosis, and treatment progress of extranodal lymphoma overall and specifically for different anatomical sites. This review summarizes the current progress in the common key signaling pathways in the development of extranodal lymphomas and intervention therapy. Furthermore, it provides insights into the pathogenesis, diagnosis, and treatment strategies of common extranodal lymphomas, including gastric mucosa-associated lymphoid tissue (MALT) lymphoma, mycosis fungoides (MF), natural killer/T-cell lymphoma (nasal type, NKTCL-NT), and primary central nervous system lymphoma (PCNSL). Additionally, as PCNSL is one of the extranodal lymphomas with the worst prognosis, this review specifically summarizes prognostic indicators and discusses the challenges and opportunities related to its clinical applications. The aim of this review is to assist clinical physicians and researchers in understanding the current status of extranodal lymphomas, enabling them to make informed clinical decisions that contribute to improving patient prognosis.
Collapse
Affiliation(s)
- Hua Yang
- Department of Basic Medicine and Biomedical Engineering, School of Medicine, Foshan University, Foshan, 528000, China
| | - Yang Xun
- Department of Basic Medicine and Biomedical Engineering, School of Medicine, Foshan University, Foshan, 528000, China
| | - Chao Ke
- Department of Neurosurgery and Neuro-Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Kensuke Tateishi
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Yokohama, 2360004, Japan
| | - Hua You
- Laboratory for Excellence in Systems Biomedicine of Pediatric Oncology, Department of Pediatric Hematology and Oncology, Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation base of Child development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 401122, China.
| |
Collapse
|
6
|
Ma Y, Xu X, Wang H, Liu Y, Piao H. Non-coding RNA in tumor-infiltrating regulatory T cells formation and associated immunotherapy. Front Immunol 2023; 14:1228331. [PMID: 37671150 PMCID: PMC10475737 DOI: 10.3389/fimmu.2023.1228331] [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: 05/24/2023] [Accepted: 07/28/2023] [Indexed: 09/07/2023] Open
Abstract
Cancer immunotherapy has exhibited promising antitumor effects in various tumors. Infiltrated regulatory T cells (Tregs) in the tumor microenvironment (TME) restrict protective immune surveillance, impede effective antitumor immune responses, and contribute to the formation of an immunosuppressive microenvironment. Selective depletion or functional attenuation of tumor-infiltrating Tregs, while eliciting effective T-cell responses, represents a potential approach for anti-tumor immunity. Furthermore, it does not disrupt the Treg-dependent immune homeostasis in healthy organs and does not induce autoimmunity. Yet, the shared cell surface molecules and signaling pathways between Tregs and multiple immune cell types pose challenges in this process. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), regulate both cancer and immune cells and thus can potentially improve antitumor responses. Here, we review recent advances in research of tumor-infiltrating Tregs, with a focus on the functional roles of immune checkpoint and inhibitory Tregs receptors and the regulatory mechanisms of ncRNAs in Treg plasticity and functionality.
Collapse
Affiliation(s)
- Yue Ma
- Department of Gynecology, Cancer Hospital of Dalian University of Technology (Liaoning Cancer Hospital & Institute), Shenyang, Liaoning, China
| | - Xin Xu
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Huaitao Wang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yang Liu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Haiyan Piao
- Medical Oncology Department of Gastrointestinal Cancer, Cancer Hospital of Dalian University of Technology (Liaoning Cancer Hospital & Institute), Shenyang, Liaoning, China
| |
Collapse
|
7
|
Qiao XR, Zheng T, Xie Y, Yao X, Yuan Z, Wu Y, Zhou D, Chen T. MiR-146a rs2910164 (G/C) polymorphism is associated with the development and prognosis of acute coronary syndromes: an observational study including case control and validation cohort. J Transl Med 2023; 21:325. [PMID: 37189131 DOI: 10.1186/s12967-023-04140-4] [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: 02/01/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Polymorphisms in microRNAs (miRNAs) play an important role in acute coronary syndromes (ACS). The purpose of this study was to assess the association of miR-146a rs2910164 and miR-34b rs4938723 polymorphisms with the development and prognosis of ACS and to explore the underlying mechanisms. METHODS A case-control study of 1171 subjects was included to determine the association of miR-146a rs2910164 and miR-34b rs4938723 polymorphisms with ACS risk. An additional 612 patients with different miR-146a rs2910164 genotypes, who underwent percutaneous coronary intervention (PCI) were included in the validation cohort and followed for 14 to 60 months. The endpoint was major adverse cardiovascular events (MACE). A luciferase reporter gene assay was used to validate the interaction of oxi-miR-146a(G) with the IKBA 3'UTR. Potential mechanisms were validated using immunoblotting and immunostaining. RESULTS The miR-146a rs2910164 polymorphism was significantly associated with the risk of ACS (Dominant model: CG + GG vs. CC, OR = 1.270, 95% CI (1.000-1.613), P = 0.049; Recessive model: GG vs. CC + CG, OR = 1.402, 95% CI (1.017-1.934), P = 0.039). Serum inflammatory factor levels were higher in patients with the miR-146a rs2910164 G allele than in those with the C allele. MiR-146a rs2910164 polymorphism in dominant model was associated with the incidence of MACE in post-PCI patients (CG + GG vs. CC, HR = 1.405, 95% CI (1.018-1.939), P = 0.038). However, the miR-34b rs4938723 polymorphism was not associated with the prevalence and prognosis of ACS. The G allele of miR-146a rs2910164 tends to be oxidized in ACS patients. The miRNA fractions purified from monocytes isolated from ACS patients were recognized by the 8OHG antibody. Mispairing of Oxi-miR-146a(G) with the 3'UTR of IKBA results in decreased IκBα protein expression and activation of the NF-κB inflammatory pathway. P65 expression was higher in atherosclerotic plaques from patients carrying the miR-146a rs2910164 G allele. CONCLUSION The variant of miR-146a rs2910164 is closely associated with the risk of ACS in Chinese Han population. Patients carrying miR-146a rs2910164 G allele may have worse pathological change and poorer post-PCI prognosis, partly due to the oxidatively modified miR-146a mispairing with 3'UTR of IKBA and activating NF-κB inflammatory pathways.
Collapse
Affiliation(s)
- Xiang-Rui Qiao
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Molecular Cardiology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
| | - Tao Zheng
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Molecular Cardiology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
| | - Yifei Xie
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Molecular Cardiology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
| | - Xinyi Yao
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Molecular Cardiology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
| | - Zuyi Yuan
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Molecular Cardiology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
| | - Yue Wu
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Molecular Cardiology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
| | - Dong Zhou
- Department of Cardiovascular Medicine, Yongchuan Hospital of Chongqing Medical University, 439 XuanHua Road, Chongqing, 402160, China.
| | - Tao Chen
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China.
- Key Laboratory of Molecular Cardiology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China.
| |
Collapse
|
8
|
Yan A, Song X, Liu B, Zhu K. IGF2BP3 Worsens Lung Cancer through Modifying Long Non-coding RNA CERS6-AS1/microRNA-1202 Axis. Curr Med Chem 2023; 30:878-891. [PMID: 35702784 DOI: 10.2174/0929867329666220614091445] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/07/2022] [Accepted: 04/15/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND Insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) can epigenetically regulate lung cancer progression, but its regulatory mechanism in the disease lacks sufficient exploration. OBJECTIVE The study was conducted to probe the regulatory function of IGF2BP3 in lung cancer via modulating the long non-coding RNA CERS6-AS1/microRNA-1202 (CERS6- AS1/miR-1202) axis. METHODS Clinical samples were collected to evaluate IGF2BP3, CERS6-AS1, miR-1202 and glycerophosphodiester phosphodiesterase domain containing 5 (GDPD5) levels. The interactions among IGF2BP3, CERS6-AS1, miR-1202 and GDPD5 were assessed. IGF2BP3-, CERS6-AS1-, and miR-1202-related constructs were transfected into lung cancer cells to determine cell biological functions. Cell tumor formation ability was further detected in vivo. RESULTS High expression of IGF2BP3, CERS6-AS1 and GDPD5, and low expression of miR-1202 levels were witnessed in lung cancer tissues. Suppression of IGF2BP3 restrained lung cancer progression. IGF2BP3 positively modulated CERS6-AS1 to regulate miR-1202-targeted GDPD5. Inhibition of CERS6-AS1 or promotion of miR-1202 depressed lung cancer aggravation. CERS6-AS1 silencing or miR-1202 overexpression reversed the impacts induced by IGF2BP3 on lung cancer. CONCLUSION IGF2BP3 facilitates the development of lung cancer cells via binding to the CERS6-AS1 promoter and down-regulating miR-1202, which may be related to GDPD5 upregulation.
Collapse
Affiliation(s)
- An Yan
- Department of Thoracic Oncology, Harbin Medical University Cancer Hospital, Harbin 150000, Heilongjiang, China
| | - Xiaowei Song
- Department of Medical Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150000, Heilongjiang, China
| | - Bao Liu
- Department of Thoracic Oncology, Harbin Medical University Cancer Hospital, Harbin 150000, Heilongjiang, China
| | - Kaibin Zhu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin 150000, Heilongjiang, China
| |
Collapse
|
9
|
Liu N, Yang C, Gao A, Sun M, Lv D. MiR-101: An Important Regulator of Gene Expression and Tumor Ecosystem. Cancers (Basel) 2022; 14:cancers14235861. [PMID: 36497343 PMCID: PMC9739992 DOI: 10.3390/cancers14235861] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
MiRNAs are small single-stranded non-coding RNAs. MiRNA contributes to the transcriptional and post-transcriptional regulation of mRNA in different cell types, including mRNA transcription inhibition and mRNA decay and phenotypes via the effect of several essential oncogenic processes and tumor microenvironment. MiR-101 is a highly conserved miRNA that was found to alter the expression in various human cancers. MiR-101 has been reported to have tumor oncogenic and suppressive effects to regulate tumorigenesis and tumor progression. In this review, we summarize the new findings about the roles of miR-101 in cancers and the underlying mechanisms of targeting genes degradation and microenvironment regulation, which will improve biological understanding and design of novel therapeutics.
Collapse
Affiliation(s)
- Ning Liu
- Department of Oncology, Central Hospital Affiliated to Shandong First Medical University, Jinan 250013, China
| | - Chunsheng Yang
- Department of Oncology, Central Hospital Affiliated to Shandong First Medical University, Jinan 250013, China
| | - Ang Gao
- Department of Oncology, Central Hospital Affiliated to Shandong First Medical University, Jinan 250013, China
| | - Meili Sun
- Department of Oncology, Central Hospital Affiliated to Shandong First Medical University, Jinan 250013, China
- Correspondence: (M.S.); (D.L.)
| | - Deguan Lv
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Correspondence: (M.S.); (D.L.)
| |
Collapse
|
10
|
Zhang L, Sun F, Lu X, Wang X, Wang J, Li J, Xu Y, Kou D, Lv H, Don B. Molecular characteristics of immunocytes infiltration in primary central nervous system lymphoma. Front Genet 2022; 13:921823. [PMID: 36061189 PMCID: PMC9428130 DOI: 10.3389/fgene.2022.921823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Primary central nervous system lymphoma (PCNSL) is a rare B-cell lymphoma of central nervous system, which is often found in immunocompromised patients. The common clinical treatment of PCNSL is methotrexate (MTX) and whole brain radiation therapy. With the development of tumour immunology research, the tumour microenvironment of PCNSL is characterised by abnormal expression of different immune signature molecules and patients with PCNSL may benefit from tumour immunotherapy.Methods: In our research, RNA-seq data from 82 PCNSL patients were collated by mining the microarray data from the GEO database. All samples were classified into three types related to tumour immune response by the Cibersort algorithm and consistent clustering. Differential analysis of genes was used to uncover 2 sets of differential genes associated with tumour immunity. The ICI scores of each sample were obtained by PCA algorithm, and the relationship between ICI scores and immune checkpoint expression, immunotherapy and drug sensitivity was investigated. Genes associated with ICI scores and their functional characteristics were investigated by WGCNA analysis and PPI analysis, based on the ICI scores of each sample.Results: The tumour microenvironment in PCNSL has a greater relationship with the tumour immune response. ICI scores obtained from 375 differential genes were associated with multiple immune responses in PCNSL. PCNSL patients with higher ICI scores had a better tumour microenvironment and were sensitive to immunotherapy and some small molecule drug. This study also identified 64 genes associated with ICI scores, which may serve as important therapeutic and prognostic targets for PCNSL.Conclusion: The presence of multiple immunosuppressive responses in the tumour microenvironment of PCNSL which suggested that improving the immune function of PCNSL patients through immunotherapy and targeted therapies can be an effective treatment for PCNSL. And the ICI score and associated genes may also provide a better predictor of the clinical use of immunotherapy.
Collapse
Affiliation(s)
- Linyun Zhang
- Department of Neurosurgery, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Fei Sun
- Department of Neurosurgery, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xiaona Lu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Xiaotong Wang
- Department of Neurosurgery, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jie Wang
- Department of Neurosurgery, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jun Li
- Department of Neurosurgery, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yingsong Xu
- Department of Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Daqing Kou
- Department of Clinical Laboratory, First Affiliated Hospital of Dalian Medical University, Dalian, China
- *Correspondence: Daqing Kou, ; Hongtao Lv, ; Bin Dong,
| | - Hongtao Lv
- Department of Neurosurgery, First Affiliated Hospital of Dalian Medical University, Dalian, China
- *Correspondence: Daqing Kou, ; Hongtao Lv, ; Bin Dong,
| | - Bin Don
- Department of Neurosurgery, First Affiliated Hospital of Dalian Medical University, Dalian, China
- *Correspondence: Daqing Kou, ; Hongtao Lv, ; Bin Dong,
| |
Collapse
|
11
|
Ting CY, Tan SY, Gan GG, Zain SM, Pung YF, Ong DBL, Bee PC. Downregulation of hsa-miR-548d-3p and overexpression of HOXA9 in diffuse large B-cell lymphoma patients and the risk of R-CHOP chemotherapy resistance and disease progression. Int J Lab Hematol 2022; 44:907-917. [PMID: 35830966 DOI: 10.1111/ijlh.13928] [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: 01/31/2022] [Accepted: 06/12/2022] [Indexed: 10/17/2022]
Abstract
INTRODUCTION Routine categorization of DLBCL patients into GCB and non-GCB groups by Hans' criteria could not accurately predict chemotherapy resistance and disease progression in patients treated with standard R-CHOP therapy. There is a need to identify better biomarker predictors to enhance assisted selection of chemotherapy regimens for DLBCL patients. AIM OF THE STUDY To identify dysregulated miRNAs and mRNAs that are predictive of resistance to R-CHOP chemotherapy or disease progression in patients with DLBCL. METHODS miRNA and mRNA profiling were performed on archival FFPE samples of the DLBCL patients. miRabel and miRNet bioinformatic tools were applied to determine experimental validated miRNA-mRNA target interaction. The significance of the genomic predictive values was assessed using adjusted odds ratios (AOR) and 95% confidence intervals (CI). RESULTS 19/36 were R-CHOP therapy-resistant whilst 17/36 were R-CHOP therapy-sensitive. Ten dysregulated miRNAs and 12 dysregulated mRNAs were identified in therapy-resistant DLBCL patients. These dysregulated miRNAs and mRNA cause therapy resistance and disease progression in DLBCL patients, most likely via upregulation of the anti-apoptotic protein bcl2, activation of the JAK/STAT signalling pathway and dysregulation of p53 pathway. Downregulation of hsa-miR-548d-3p and overexpression of HOXA9 mRNA were significantly associated with therapy resistance and disease progression in DLBCL patients [hsa-miR-548d-3p AOR: 0.258, 95%CI: 0.097-0.684, p = 0.006]. CONCLUSION DLBCL patients with downregulation of hsa-miR-548d-3p and overexpression of HOXA9 mRNA are more likely to experience R-CHOP therapy resistance and disease progression.
Collapse
Affiliation(s)
- Choo-Yuen Ting
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Soo-Yong Tan
- Department of Pathology, National University of Singapore, Singapore, Singapore
| | - Gin-Gin Gan
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Shamsul-Mohd Zain
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yuh-Fen Pung
- Division of Biomedical Science, University of Nottingham Malaysia, Semenyih, selangor, Malaysia
| | - Diana Bee-Lan Ong
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Ping-Chong Bee
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
12
|
Tian Y, Huang B, Li J, Tian X, Zeng X. Identification of the Association Between Toll-Like Receptors and T-Cell Activation in Takayasu’s Arteritis. Front Immunol 2022; 12:792901. [PMID: 35126357 PMCID: PMC8812403 DOI: 10.3389/fimmu.2021.792901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/22/2021] [Indexed: 12/26/2022] Open
Abstract
To explore the relationships between Toll-like receptors (TLRs) and the activation and differentiation of T-cells in Takayasu’s arteritis (TAK), using real-time fluorescence quantitative polymerase chain reaction, mRNA abundance of 29 target genes in peripheral blood mononuclear cells (PBMCs) were detected from 27 TAK patients and 10 healthy controls. Compared with the healthy control group, the untreated TAK group and the treated TAK group had an increased mRNA level of TLR2 and TLR4. A sample-to-sample matrix revealed that 80% of healthy controls could be separated from the TAK patients. Correlation analysis showed that the inactive-treated TAK group exhibited a unique pattern of inverse correlations between the TLRs gene clusters (including TLR1/2/4/6/8, BCL6, TIGIT, NR4A1, etc) and the gene cluster associated with T-cell activation and differentiation (including TCR, CD28, T-bet, GATA3, FOXP3, CCL5, etc). The dynamic gene co-expression network indicated the TAK groups had more active communication between TLRs and T-cell activation than healthy controls. BCL6, CCL5, FOXP3, GATA3, CD28, T-bet, TIGIT, IκBα, and NR4A1 were likely to have a close functional relation with TLRs at the inactive stage. The co-expression of TLR4 and TLR6 could serve as a biomarker of disease activity in treated TAK (the area under curve/sensitivity/specificity, 0.919/100%/90.9%). The largest gene co-expression cluster of the inactive-treated TAK group was associated with TLR signaling pathways, while the largest gene co-expression cluster of the active-treated TAK group was associated with the activation and differentiation of T-cells. The miRNA sequencing of the plasma exosomes combining miRDB, DIANA-TarBase, and miRTarBase databases suggested that the miR-548 family miR-584, miR-3613, and miR-335 might play an important role in the cross-talk between TLRs and T-cells at the inactive stage. This study found a novel relation between TLRs and T-cell in the pathogenesis of autoimmune diseases, proposed a new concept of TLR-co-expression signature which might distinguish different disease activity of TAK, and highlighted the miRNA of exosomes in TLR signaling pathway in TAK.
Collapse
Affiliation(s)
- Yixiao Tian
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, Peking Union Medical College Hospital (PUMCH), Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Beijing, China
- Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Biqing Huang
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, Peking Union Medical College Hospital (PUMCH), Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Beijing, China
- Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Jing Li
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, Peking Union Medical College Hospital (PUMCH), Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Beijing, China
- Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
- *Correspondence: Jing Li, ; Xiaofeng Zeng,
| | - Xinping Tian
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, Peking Union Medical College Hospital (PUMCH), Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Beijing, China
- Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Xiaofeng Zeng
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, Peking Union Medical College Hospital (PUMCH), Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Beijing, China
- Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
- *Correspondence: Jing Li, ; Xiaofeng Zeng,
| |
Collapse
|
13
|
A novel regQTL-SNP and the risk of lung cancer: a multi-dimensional study. Arch Toxicol 2021; 95:3815-3827. [PMID: 34596730 DOI: 10.1007/s00204-021-03170-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/23/2021] [Indexed: 01/15/2023]
Abstract
RegQTL, a novel concept, indicates that different genotypes of some SNPs have differential effects on the expression patterns of miRNAs and their target mRNAs. We aimed to identify the association between regQTL-SNPs and lung cancer risk and to explore the underlying mechanisms. The two-stage case-control study included the first stage in a Chinese population (626 lung cancer cases and 667 healthy controls) and the second stage in a European population (18,082 lung cancer cases and 13,780 healthy controls). Functional annotations were conducted based on the GTEx and the TCGA databases. Functional experiments were performed to explore the underlying biological mechanisms in vitro and vivo. After strict screening, five candidate regQTL-SNPs (rs7110737, rs273957, rs6593210, rs3768617, and rs6836432) were selected. Among them, the variant T allele of rs3768617 in LAMC1 was found to significantly increase the risk of lung cancer (first stage: P = 0.044; second stage: P = 0.007). The eQTL analysis showed that LAMC1 expression level was significantly higher in subjects with the variant T allele of rs3768617 (P = 1.10 × 10-14). In TCGA paired database, the regQTL annotation indicated the different expression patterns between LAMC1 and miRNA-548b-3p for the distinct genotypes of rs3768617. Additionally, LAMC1 knockdown significantly inhibited malignant phenotypes in lung cancer cell lines and suppressed tumor growth. A novel regQTL-SNP, rs3768617, might affect lung cancer risk by modulating the expression patterns of miRNA-548b-3p and LAMC1. RegQTL-SNPs could provide a new perspective for evaluating the regulatory function of SNPs in lung cancer development.
Collapse
|
14
|
Alsaadi M, Khan MY, Dalhat MH, Bahashwan S, Khan MU, Albar A, Almehdar H, Qadri I. Dysregulation of miRNAs in DLBCL: Causative Factor for Pathogenesis, Diagnosis and Prognosis. Diagnostics (Basel) 2021; 11:1739. [PMID: 34679437 PMCID: PMC8535125 DOI: 10.3390/diagnostics11101739] [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: 07/25/2021] [Revised: 09/10/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022] Open
Abstract
MicroRNA is a small non-coding RNA (sncRNA) involved in gene silencing and regulating post-transcriptional gene expression. miRNAs play an essential role in the pathogenesis of numerous diseases, including diabetes, cardiovascular diseases, viral diseases and cancer. Diffuse large B-cell lymphoma (DLBCL) is an aggressive non-Hodgkin's lymphoma (NHL), arising from different stages of B-cell differentiation whose pathogenesis involves miRNAs. Various viral and non-viral vectors are used as a delivery vehicle for introducing specific miRNA inside the cell. Adenoviruses are linear, double-stranded DNA viruses with 35 kb genome size and are extensively used in gene therapy. Meanwhile, Adeno-associated viruses accommodate up to 4.8 kb foreign genetic material and are favorable for transferring miRNA due to small size of miRNA. The genetic material is integrated into the DNA of the host cell by retroviruses so that only dividing cells are infected and stable expression of miRNA is achieved. Over the years, remarkable progress was made to understand DLBCL biology using advanced genomics and epigenomics technologies enabling oncologists to uncover multiple genetic mutations in DLBCL patients. These genetic mutations are involved in epigenetic modification, ability to escape immunosurveillance, impaired BCL6 and NF-κβ signaling pathways and blocking terminal differentiation. These pathways have since been identified and used as therapeutic targets for the treatment of DLBCL. Recently miRNAs were also identified to act either as oncogenes or tumor suppressors in DLBCL pathology by altering the expression levels of some of the known DLBCL related oncogenes. i.e., miR-155, miR-17-92 and miR-21 act as oncogenes by altering the expression levels of MYC, SHIP and FOXO1, respectively, conversely; miR-34a, mir-144 and miR-181a act as tumor suppressors by altering the expression levels of SIRT1, BCL6 and CARD11, respectively. Hundreds of miRNAs have already been identified as biomarkers in the prognosis and diagnosis of DLBCL because of their significant roles in DLBCL pathogenesis. In conclusion, miRNAs in addition to their role as biomarkers of prognosis and diagnosis could also serve as potential therapeutic targets for treating DLBCL.
Collapse
Affiliation(s)
- Mohammed Alsaadi
- Department of Biological Science, Faculty of Science, King AbdulAziz University, Jeddah 21589, Saudi Arabia; (M.A.); (M.Y.K.); (A.A.); (H.A.)
- Hematology Research Unit, King Fahad Medical Research Center, King AbdulAziz University, Jeddah 21589, Saudi Arabia;
| | - Muhammad Yasir Khan
- Department of Biological Science, Faculty of Science, King AbdulAziz University, Jeddah 21589, Saudi Arabia; (M.A.); (M.Y.K.); (A.A.); (H.A.)
- Vaccine and Immunotherapy Unit, King Fahad Medical Research Center, King AbdulAziz University, Jeddah 21589, Saudi Arabia
| | - Mahmood Hassan Dalhat
- Department of Biochemistry, Faculty of Science, King AbdulAziz University, Jeddah 21589, Saudi Arabia;
| | - Salem Bahashwan
- Hematology Research Unit, King Fahad Medical Research Center, King AbdulAziz University, Jeddah 21589, Saudi Arabia;
- Department of Hematology, Faculty of Medicine, King AbdulAziz University, Jeddah 21589, Saudi Arabia
- King AbdulAziz University Hospital, King AbdulAziz University, Jeddah 21589, Saudi Arabia
| | - Muhammad Uzair Khan
- Department of Health Sciences, City University of Science and Information Technology, Peshawar 25000, Pakistan;
| | - Abdulgader Albar
- Department of Biological Science, Faculty of Science, King AbdulAziz University, Jeddah 21589, Saudi Arabia; (M.A.); (M.Y.K.); (A.A.); (H.A.)
- Department of Microbiology, Faculty of Medicine, Jeddah University, Jeddah 23218, Saudi Arabia
| | - Hussein Almehdar
- Department of Biological Science, Faculty of Science, King AbdulAziz University, Jeddah 21589, Saudi Arabia; (M.A.); (M.Y.K.); (A.A.); (H.A.)
| | - Ishtiaq Qadri
- Department of Biological Science, Faculty of Science, King AbdulAziz University, Jeddah 21589, Saudi Arabia; (M.A.); (M.Y.K.); (A.A.); (H.A.)
| |
Collapse
|
15
|
Takashima Y, Kawaguchi A, Fukai J, Iwadate Y, Kajiwara K, Hondoh H, Yamanaka R. Survival prediction based on the gene expression associated with cancer morphology and microenvironment in primary central nervous system lymphoma. PLoS One 2021; 16:e0251272. [PMID: 34166375 PMCID: PMC8224980 DOI: 10.1371/journal.pone.0251272] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/23/2021] [Indexed: 11/18/2022] Open
Abstract
Dysregulation of cell morphology and cell-cell interaction results in cancer cell growth, migration, invasion, and metastasis. Besides, a balance between the extracellular matrix (ECM) and matrix metalloprotease (MMP) is required for cancer cell morphology and angiogenesis. Here, we determined gene signatures associated with the morphology and microenvironment of primary central nervous system lymphoma (PCNSL) to enable prognosis prediction. Next-generation sequencing (NGS) on 31 PCNSL samples revealed gene signatures as follows: ACTA2, ACTR10, CAPG, CORO1C, KRT17, and PALLD in cytoskeleton, CDH5, CLSTN1, ITGA10, ITGAX, ITGB7, ITGA8, FAT4, ITGAE, CDH10, ITGAM, ITGB6, and CDH18 in adhesion, COL8A2, FBN1, LAMB3, and LAMA2 in ECM, ADAM22, ADAM28, MMP11, and MMP24 in MMP. Prognosis prediction formulas with the gene expression values and the Cox regression model clearly divided survival curves of the subgroups in each status. Furthermore, collagen genes contributed to gene network formation in glasso, suggesting that the ECM balance controls the PCNSL microenvironment. Finally, the comprehensive balance of morphology and microenvironment enabled prognosis prediction by a combinatorial expression of 8 representative genes, including KRT17, CDH10, CDH18, COL8A2, ADAM22, ADAM28, MMP11, and MMP24. Besides, these genes could also diagnose PCNSL cell types with MTX resistances in vitro. These results would not only facilitate the understanding of biology of PCNSL but also consider targeting pathways for anti-cancer treatment in personalized precision medicine in PCNSL.
Collapse
Affiliation(s)
- Yasuo Takashima
- Osaka Iseikai Clinic for Cancer Therapy, Iseikai Holonics Group, Osaka, Japan
- Laboratory of Molecular Target Therapy for Cancer, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Atsushi Kawaguchi
- Faculty of Medicine, Center for Comprehensive Community Medicine, Saga University, Saga, Japan
| | - Junya Fukai
- Department of Neurological Surgery, Wakayama Medical University School of Medicine, Wakayama, Japan
| | - Yasuo Iwadate
- Department of Neurosurgery, Graduate School of Medical Sciences, Chiba University, Chiba, Japan
| | - Koji Kajiwara
- Department of Neurosurgery, Graduate School of Medical Sciences, Yamaguchi University, Ube, Yamaguchi, Japan
| | - Hiroaki Hondoh
- Department of Neurosurgery, Toyama Prefectural Central Hospital, Toyama, Japan
| | - Ryuya Yamanaka
- Osaka Iseikai Clinic for Cancer Therapy, Iseikai Holonics Group, Osaka, Japan
- Laboratory of Molecular Target Therapy for Cancer, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- * E-mail:
| |
Collapse
|
16
|
Zhao H, Chang A, Ling J, Zhou W, Ye H, Zhuo X. Construction and analysis of miRNA-mRNA regulatory networks in the radioresistance of nasopharyngeal carcinoma. 3 Biotech 2020; 10:511. [PMID: 33184596 DOI: 10.1007/s13205-020-02504-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 10/24/2020] [Indexed: 12/12/2022] Open
Abstract
Radiotherapy has been the major treatment strategy for nasopharyngeal carcinoma (NPC), while the occurrence of radioresistance may lead to cancer recurrence or progression. This study aimed to identify the key microRNAs (miRNAs) and their target genes in the development of NPC radioresistance. Public microarray data were searched and analyzed to screen the differentially expressed miRNAs (DEMs) and genes (DEGs) between radioresistant and radiosensitive NPC samples. MiRNA-mRNA networks were constructed. As a result, 5 DEMs and 195 DEGs were screened out. The DEGs were enriched in various signaling pathways, such as Cytokine-cytokine receptor interaction, Jak-STAT signaling pathway, and Toll-like receptor signaling pathway. Several hub genes, such as IGF2, OLA1, BBS10, MMP9, and BBS7 were identified. A regulatory miRNA-mRNA network containing 87 miRNA-mRNA pairs was constructed. Then, 14 key miRNA-mRNA pairs that contained the hub genes were further filtered out. In the networks, miR-203a-3p had the largest number of target genes. Afterwards, the candidate pairs (miR-203a-3p/BTK and miR-484/OLA1) have been verified by a qRT-PCR assay. In summary, we identified several miRNAs and hub genes via big data screening. A total of 87 miRNA-mRNA pairs (including 14 key pairs) were predicted to play a crucial role in the development of NPC radioresistance. These data provide a bioinformatics basis for further exploring the molecular mechanism of radiotherapy resistance in NPC. Future studies are needed to validate the results.
Collapse
|
17
|
GSEA-assisted gene signatures valid for combinations of prognostic markers in PCNSL. Sci Rep 2020; 10:8435. [PMID: 32439996 PMCID: PMC7242340 DOI: 10.1038/s41598-020-65463-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 05/05/2020] [Indexed: 02/07/2023] Open
Abstract
Primary central nervous system lymphoma (PCNSL) is a brain malignant non-Hodgkin’s B-cell lymphoma. The standard treatments are high-dose methotrexate (MTX)-based chemotherapies and deferred whole brain radiotherapy. However, MTX resistance-dependent global expression and signaling pathway changes and their relationship with prognoses have not yet been elucidated. Here, we conducted a global expression analysis with next-generation sequencing and gene set enrichment analysis (GSEA) in MTX-resistant PCNSL cell lines (HKBML-MTX and TK-MTX) and PCNSL tissues. In rank scores, genes listed in HKBML-MTX and TK-MTX were enriched in PCNSL with poor prognoses. In fold changes, a part of differentially-expressed genes in PCNSL tissues were also detected in HKBML-MTX and TK-MTX cells; FOXD2-AS1 and MMP19 were commonly expressed in both HKBML-MTX and TK-MTX, FABP5 and CD70 were HKBML-MTX-specifically expressed, and CLCN2, HOXB9, INE1, and LRP5L were TK-MTX-specifically expressed, which may provide a combination of prognostic markers on MTX-sensitivities in PCNSL. Additionally, PCNSL subgroups, divided with hierarchical clustering and Kaplan-Meier methods, included twenty commonly expressed genes in both HKBML-MTX and TK-MTX, ten HKBML-MTX-specifically expressed genes, and two TK-MTX-specifically expressed genes. These results suggest that the GSEA-assisted gene signatures can provide a combination for prognostic markers in recurrent PCNSL with MTX resistances.
Collapse
|