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IGFBP3 Enhances Treatment Outcome and Predicts Favorable Prognosis in ABC-DLBCL. JOURNAL OF ONCOLOGY 2023; 2023:1388041. [PMID: 36660244 PMCID: PMC9845052 DOI: 10.1155/2023/1388041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/25/2022] [Accepted: 12/26/2022] [Indexed: 01/11/2023]
Abstract
Chemoresistance is a key obstacle in the clinical treatment and management of activated B cell-like diffuse large B-cell lymphoma (ABC-DLBCL), which leads to the poor prognosis of patients. Exploring novel biomarkers to early warn drug resistance and ameliorate the patients' outcome in ABC-DLBCL is urgent and crucial. Previously, we found that insulin-like growth factor-binding protein 3 (IGFBP3) was remarkably associated with immunochemotherapy treatment response through microarray screening. Based on a retrospective cohort (n = 160) and a GEO cohort (n = 292), here we determined the positive expression rate of IGFBP3 and analyzed the role of IGFBP3 in treatment response and prognostics in ABC-DLBCL. The results demonstrated that the complete response (CR) rate of R-CHOP treatment was higher in ABC-DLBCL with IGFBP3 positive expression than those with IGFBP3 negative expression (42.0% vs 26.4%), and IGFBP3 positive expression in ABC-DLBCL was significantly correlated with enhanced therapeutic response (P = 0.037). High level of IGFBP3 was negatively correlated with tumorigenesis and development and predicted favorable survival time in ABC-DLBCL. In conclusion, IGFBP3 may be utilized as a promising biomarker for prognosis evaluation and a potential therapy target in ABC-DLBCL patients.
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Peng L, Tu Y, Huang L, Li Y, Fu X, Chen X. DAESTB: inferring associations of small molecule-miRNA via a scalable tree boosting model based on deep autoencoder. Brief Bioinform 2022; 23:6827720. [PMID: 36377749 DOI: 10.1093/bib/bbac478] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/28/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs (miRNAs) are closely related to a variety of human diseases, not only regulating gene expression, but also having an important role in human life activities and being viable targets of small molecule drugs for disease treatment. Current computational techniques to predict the potential associations between small molecule and miRNA are not that accurate. Here, we proposed a new computational method based on a deep autoencoder and a scalable tree boosting model (DAESTB), to predict associations between small molecule and miRNA. First, we constructed a high-dimensional feature matrix by integrating small molecule-small molecule similarity, miRNA-miRNA similarity and known small molecule-miRNA associations. Second, we reduced feature dimensionality on the integrated matrix using a deep autoencoder to obtain the potential feature representation of each small molecule-miRNA pair. Finally, a scalable tree boosting model is used to predict small molecule and miRNA potential associations. The experiments on two datasets demonstrated the superiority of DAESTB over various state-of-the-art methods. DAESTB achieved the best AUC value. Furthermore, in three case studies, a large number of predicted associations by DAESTB are confirmed with the public accessed literature. We envision that DAESTB could serve as a useful biological model for predicting potential small molecule-miRNA associations.
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Affiliation(s)
- Li Peng
- College of Computer Science and Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China.,Hunan Key Laboratory for Service computing and Novel Software Technology
| | - Yuan Tu
- College of Computer Science and Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Li Huang
- Academy of Arts and Design, Tsinghua University, Beijing, 10084, China.,The Future Laboratory, Tsinghua University, Beijing, 10084, China
| | - Yang Li
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan, 411105, China
| | - Xiangzheng Fu
- College of Information Science and Engineering, Hunan University, Changsha, 410082, Hunan, China
| | - Xiang Chen
- College of Computer Science and Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
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Ruhela V, Gupta A, Sriram K, Ahuja G, Kaur G, Gupta R. A Unified Computational Framework for a Robust, Reliable, and Reproducible Identification of Novel miRNAs From the RNA Sequencing Data. FRONTIERS IN BIOINFORMATICS 2022; 2:842051. [PMID: 36304305 PMCID: PMC9580950 DOI: 10.3389/fbinf.2022.842051] [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: 12/23/2021] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
In eukaryotic cells, miRNAs regulate a plethora of cellular functionalities ranging from cellular metabolisms, and development to the regulation of biological networks and pathways, both under homeostatic and pathological states like cancer.Despite their immense importance as key regulators of cellular processes, accurate and reliable estimation of miRNAs using Next Generation Sequencing is challenging, largely due to the limited availability of robust computational tools/methods/pipelines. Here, we introduce miRPipe, an end-to-end computational framework for the identification, characterization, and expression estimation of small RNAs, including the known and novel miRNAs and previously annotated pi-RNAs from small-RNA sequencing profiles. Our workflow detects unique novel miRNAs by incorporating the sequence information of seed and non-seed regions, concomitant with clustering analysis. This approach allows reliable and reproducible detection of unique novel miRNAs and functionally same miRNAs (paralogues). We validated the performance of miRPipe with the available state-of-the-art pipelines using both synthetic datasets generated using the newly developed miRSim tool and three cancer datasets (Chronic Lymphocytic Leukemia, Lung cancer, and breast cancer). In the experiment over the synthetic dataset, miRPipe is observed to outperform the existing state-of-the-art pipelines (accuracy: 95.23% and F1-score: 94.17%). Analysis on all the three cancer datasets shows that miRPipe is able to extract more number of known dysregulated miRNAs or piRNAs from the datasets as compared to the existing pipelines.
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Affiliation(s)
- Vivek Ruhela
- Department of Computational Biology & Centre for Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-D), New Delhi, India
- *Correspondence: Vivek Ruhela, ; Anubha Gupta, ; Ritu Gupta,
| | - Anubha Gupta
- SBILab, Department of ECE & Centre of Excellence in Healthcare, Indraprastha Institute of Information Technology-Delhi (IIIT-D), New Delhi, India
- *Correspondence: Vivek Ruhela, ; Anubha Gupta, ; Ritu Gupta,
| | - K. Sriram
- Department of Computational Biology & Centre for Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-D), New Delhi, India
| | - Gaurav Ahuja
- Department of Computational Biology & Centre for Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-D), New Delhi, India
| | - Gurvinder Kaur
- Laboratory Oncology Unit, IRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Ritu Gupta
- Laboratory Oncology Unit, IRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, India
- *Correspondence: Vivek Ruhela, ; Anubha Gupta, ; Ritu Gupta,
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4
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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Taheri M, Jamali E. The emerging role non-coding RNAs in B cell-related disorders. Cancer Cell Int 2022; 22:91. [PMID: 35193592 PMCID: PMC8862212 DOI: 10.1186/s12935-022-02521-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/10/2022] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs and microRNAs have recently attained much attention regarding their role in the development of B cell lineage as well as participation in the lymphomagenesis. These transcripts have a highly cell type specific signature which endows them the potential to be used as biomarkers for clinical situations. Aberrant expression of several non-coding RNAs has been linked with B cell malignancies and immune related disorders such as rheumatoid arthritis, systemic lupus erythematous, asthma and graft-versus-host disease. Moreover, these transcripts can alter response of immune system to infectious conditions. miR-7, miR-16-1, miR-15a, miR-150, miR-146a, miR-155, miR-212 and miR-132 are among microRNAs whose role in the development of B cell-associated disorders has been investigated. Similarly, SNHG14, MALAT1, CRNDE, AL133346.1, NEAT1, SMAD5-AS1, OR3A4 and some other long non-coding RNAs participate in this process. In the current review, we describe the role of non-coding RNAs in B cell malignancies.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq.,Center of Research and Strategic Studies, Lebanese French University, Erbil, Kurdistan Region, Iraq
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran. .,Institute of Human Genetics, Jena University Hospital, Jena, Germany.
| | - Elena Jamali
- Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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miRNA- and lncRNA-Based Therapeutics for Non-Hodgkin’s Lymphoma: Moving towards an RNA-Guided Precision Medicine. Cancers (Basel) 2021; 13:cancers13246324. [PMID: 34944942 PMCID: PMC8699447 DOI: 10.3390/cancers13246324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Non-Hodgkin’s lymphoma (NHL) is a very heterogenous class of hematological cancers, with variable patient outcomes. Therefore, there is an urgent need to develop new and more effective therapeutic approaches. MiRNAs and lncRNAs have emerged as the central gene expression regulators, and their deregulation has been reported to be involved in lymphomagenesis. Given their ability to simultaneously modulate multiple targets, they provide an attractive therapeutic approach to treat NHL patients. In this review, we discuss the scientific rationale behind miRNA/lncRNA-based therapies in NHL and the different targeting technologies, such as antisense oligonucleotides, CRISPR-Cas9, and nanomedicines. Abstract Increasing evidence has demonstrated the functional roles of miRNAs and lncRNAs in lymphoma onset and progression, either by acting as tumor-promoting ncRNAs or as tumor suppressors, emphasizing their appeal as lymphoma therapeutics. In fact, their intrinsic ability to modulate multiple dysregulated genes and/or signaling pathways makes them an attractive therapeutic approach for a multifactorial pathology like lymphoma. Currently, the clinical application of miRNA- and lncRNA-based therapies still faces obstacles regarding effective delivery systems, off-target effects, and safety, which can be minimized with the appropriate chemical modifications and the development of tumor site-specific delivery approaches. Moreover, miRNA- and lncRNA-based therapeutics are being studied not only as monotherapies but also as complements of standard treatment regimens to provide a synergic effect, improving the overall treatment efficacy and reducing the therapeutic resistance. In this review, we summarize the fundamentals of miRNA- and lncRNA-based therapeutics by discussing the different types of delivery systems, with a focus on those that have been investigated in lymphoma in vitro and in vivo. Moreover, we described the ongoing clinical trials of novel miRNA- and lncRNA-based therapeutics in lymphoma.
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6
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Zheng W, Lai G, Lin Q, Issah MA, Fu H, Shen J. A miR-129-5P/ARID3A Negative Feedback Loop Modulates Diffuse Large B Cell Lymphoma Progression and Immune Evasion Through Regulating the PD-1/PD-L1 Checkpoint. Front Cell Dev Biol 2021; 9:735855. [PMID: 34778251 PMCID: PMC8579866 DOI: 10.3389/fcell.2021.735855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 10/05/2021] [Indexed: 12/14/2022] Open
Abstract
The activated B cell (ABC) and germinal center B cell (GCB) subtypes of diffuse large B cell lymphoma (DLBCL) have different gene expression profiles and clinical outcomes, and miRNAs have been reported to play important roles in tumorigenesis, progression, and metastasis. This study aimed to explore the differentially expressed miRNAs and target genes in the two main subtypes of DLBCL. Hub miRNAs were identified by constructing a regulatory network, and in vitro experiments and peripheral blood samples of DLBCL were used to explore the functions and mechanisms of differential miRNAs and mRNAs. Differentially expressed miRNAs and genes associated with the two DLBCL subtypes were identified using GEO datasets. Weighted gene co-expression network analysis shows that one gene module was associated with a better prognosis of patients with the GCB subtype. Through the construction of a regulatory network and qPCR verification of clinical samples and cell lines, miR-129-5p was identified as an important differential miRNA between the ABC and GCB subtypes. The negative relationship between miR-129-5p and ARID3A in DLBCL was confirmed using luciferase reporter assays. Overexpression of miR-129-5p and knockdown of ARID3A inhibited the proliferation of SU-DHL-2 (ABC-type) cells and promoted their apoptosis through the JAK and STAT6 signaling pathways. In addition, inhibition of miR-129-5p and overexpression of ARID3A promoted the proliferation and reduced apoptosis of DB and SU-DHL-6 (GCB-type) cells. Inhibition of miR-129-5p and overexpression of ARID3A in DB and SU-DHL-6 promoted immune escape by increasing PD-L1 expression, which was transcriptionally activated by ARID3A. In conclusion, we showed for the first time that the mir-129-5P/ARID3A negative feedback loop modulates DLBCL progression and immune evasion by regulating PD-1/PD-L1.
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Affiliation(s)
- Weili Zheng
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical Center of Hematology, Fujian Institute of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fujian Medical University Union Hospital, Fuzhou, China
| | - Guilan Lai
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical Center of Hematology, Fujian Institute of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fujian Medical University Union Hospital, Fuzhou, China
| | - Qiaochu Lin
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical Center of Hematology, Fujian Institute of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fujian Medical University Union Hospital, Fuzhou, China
| | - Mohammed Awal Issah
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical Center of Hematology, Fujian Institute of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fujian Medical University Union Hospital, Fuzhou, China
| | - Haiying Fu
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical Center of Hematology, Fujian Institute of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fujian Medical University Union Hospital, Fuzhou, China
| | - Jianzhen Shen
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical Center of Hematology, Fujian Institute of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fujian Medical University Union Hospital, Fuzhou, China
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7
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Usuda D, Izumida T, Terada N, Sangen R, Higashikawa T, Sekiguchi S, Tanaka R, Suzuki M, Hotchi Y, Shimozawa S, Tokunaga S, Osugi I, Katou R, Ito S, Asako S, Takagi Y, Mishima K, Kondo A, Mizuno K, Takami H, Komatsu T, Oba J, Nomura T, Sugita M, Kasamaki Y. Diffuse large B cell lymphoma originating from the maxillary sinus with skin metastases: A case report and review of literature. World J Clin Cases 2021; 9:6886-6899. [PMID: 34447839 PMCID: PMC8362537 DOI: 10.12998/wjcc.v9.i23.6886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/12/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Diffuse large B-cell lymphoma (DLBCL) is the most common type of malignant lymphoma (ML), accounting for 30%-40% of cases of non-Hodgkin’s lymphoma (NHL) in adults. Primary paranasal sinus lymphoma is a rare presentation of extranodal NHL that accounts for only 0.17% of all lymphomas. ML from the maxillary sinus (MS) is a particularly rare presentation, and is thus often difficult to diagnose. We have reported the first known case of DLBCL originating from the MS with rapidly occurrent multiple skin metastasis.
CASE SUMMARY An 81-year-old Japanese man visited our hospital due to continuous pain for 12 d in the left maxillary nerve area. His medical history included splenectomy due to a traffic injury, an old right cerebral infarction from when he was 74-years-old, hypertension, and type 2 diabetes mellitus. A plain head computed tomography (CT) scan revealed a 3 cm × 3.1 cm × 3 cm sized left MS. On day 25, left diplopia and ptosis occurred, and a follow-up CT on day 31 revealed the growth of the left MS mass. Based on an MS biopsy on day 50, we established a definitive diagnosis of DLBCL, non-germinal center B-cell-like originating from the left MS. The patient was admitted on day 62 due to rapid deterioration of his condition, and a plain CT scan revealed the further growth of the left MS mass, as well as multiple systemic metastasis, including of the skin. A skin biopsy on day 70 was found to be the same as that of the left MS mass. We notified the patient and his family of the disease, and they opted for palliative care, considering on his condition and age. The patient died on day 80.
CONCLUSION This case suggests the need for careful, detailed examination, and for careful follow-up, when encountering patients presenting with a mass.
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Affiliation(s)
- Daisuke Usuda
- Department of General Medicine, Kanazawa Medical University Himi Municipal Hospital, Himi-shi 935-8531, Toyama-ken, Japan
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Toshihide Izumida
- Department of General Medicine, Kanazawa Medical University Himi Municipal Hospital, Himi-shi 935-8531, Toyama-ken, Japan
| | - Nao Terada
- Department of General Medicine, Kanazawa Medical University Himi Municipal Hospital, Himi-shi 935-8531, Toyama-ken, Japan
| | - Ryusho Sangen
- Department of General Medicine, Kanazawa Medical University Himi Municipal Hospital, Himi-shi 935-8531, Toyama-ken, Japan
| | - Toshihiro Higashikawa
- Department of Geriatric Medicine, Kanazawa Medical University Himi Municipal Hospital, Himi-shi 935-8531, Toyama-ken, Japan
| | - Sayumi Sekiguchi
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Risa Tanaka
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Makoto Suzuki
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Yuta Hotchi
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Shintaro Shimozawa
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Shungo Tokunaga
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Ippei Osugi
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Risa Katou
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Sakurako Ito
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Suguru Asako
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Yoshie Takagi
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Kentaro Mishima
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Akihiko Kondo
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Keiko Mizuno
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Hiroki Takami
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Takayuki Komatsu
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Jiro Oba
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Tomohisa Nomura
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Manabu Sugita
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Nerima-ku 177-0035, Tokyo-to, Japan
| | - Yuji Kasamaki
- Department of General Medicine, Kanazawa Medical University Himi Municipal Hospital, Himi-shi 935-8531, Toyama-ken, Japan
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Distinct Molecular Subtypes of Diffuse Large B Cell Lymphoma Patients Treated with Rituximab-CHOP Are Associated with Different Clinical Outcomes and Molecular Mechanisms. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5514726. [PMID: 34250086 PMCID: PMC8238567 DOI: 10.1155/2021/5514726] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/27/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023]
Abstract
Objective Our purpose was to characterize distinct molecular subtypes of diffuse large B cell lymphoma (DLBCL) patients treated with rituximab-CHOP (R-CHOP). Methods Two gene expression datasets of R-CHOP-treated DLBCL patients were downloaded from GSE10846 (n = 233, training set) and GSE31312 (n = 470, validation set) datasets. Cluster analysis was presented via the ConsensusClusterPlus package in R. Using the limma package, differential expression analysis was utilized to identify feature genes. Kaplan-Meier survival analysis was presented to compare the differences in the prognosis between distinct molecular subtypes. Correlation between molecular subtypes and clinical features was analyzed. Based on the sets of highly expressed genes, biological functions were explored by gene set enrichment analysis (GSEA). Several feature genes were validated in the molecular subtypes via qRT-PCR and western blot. Results DLBCL samples were clustered into two molecular subtypes. Samples in subtype I displayed poorer overall survival time in the training set (p < 0.0001). Consistently, patients in subtype I had shorter overall survival (p = 0.0041) and progression-free survival time (p < 0.0001) than those in subtype II. Older age, higher stage, and higher international prognostic index (IPI) were found in subtype I. In subtype I, T cell activation, lymphocyte activation, and immune response were distinctly enriched, while cell adhesion, migration, and motility were significantly enriched in subtype II. T cell exhaustion-related genes including TIM3 (p < 0.001), PD-L1 (p < 0.0001), LAG3 (p < 0.0001), CD160 (p < 0.001), and CD244 (p < 0.001) were significantly highly expressed in subtype I than subtype II. Conclusion Two molecular subtypes were constructed in DLBCL, which were characterized by different clinical outcomes and molecular mechanisms. Our findings may offer a novel insight into risk stratification and prognosis prediction for DLBCL patients.
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Differential expression of miRNAs as biomarkers for predicting the outcomes of diffuse large B-cell lymphoma patients. Biosci Rep 2021; 41:228975. [PMID: 34109978 PMCID: PMC8239963 DOI: 10.1042/bsr20201551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/17/2021] [Accepted: 06/08/2021] [Indexed: 11/26/2022] Open
Abstract
Background: Diffuse large B-cell lymphoma (DLBCL) used to be defined as germinal center B-like and non-germinal center B-like subtypes, associated with different prognoses, but the conventional classification does not meet the needs of clinical practice because of DLBCL heterogeneity, a problem that might be improved by selection of miRNAs as biomarkers. Methods: Twelve patients with DLBCLs were used to screen out the aberrant miRNA profile using miRNA microarray technology in two patient subtypes (six germinal center B-like and six non-germinal center B-like patients). The potential biomarkers were further analyzed using the quantitative reverse transcription-polymerase chain reaction method in 95 DLBCL patients to investigate relationships among expression levels of potent miRNA, clinicopathological features and survival rates of patients. Results: miR-208a-5p, miR-296-5p and miR-1304-5p were screened as potential biomarkers. miR-208a-5p and miR-296-5p were shown to be associated with better survival of patients after Kaplan–Meier analysis, whereas miR-1304-5p overexpression indicated a poor survival prognosis independent of the DLBCL subtype. In addition, changes of miR-296-5p and miR-1304-5p expression, the International Prognostic Index (IPI) status and the age of patients were all independent indicators for DLBCL prognosis. We also found that high miR-208a-5p expression led to better outcomes in DLBCL patients with similar IPI scores; however high miR-1304-5p expression tended to indicate the opposite. Conclusions: MiR-208a-5p, miR-296-5p and miR-1304-5p levels might be potential biomarkers for the prediction of the prognosis of DLBCL patients.
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10
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Shi Y, Ding D, Qu R, Tang Y, Hao S. Non-Coding RNAs in Diffuse Large B-Cell Lymphoma. Onco Targets Ther 2020; 13:12097-12112. [PMID: 33262609 PMCID: PMC7699984 DOI: 10.2147/ott.s281810] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma worldwide. The molecular mechanisms underlying DLBCL have not been fully elucidated, and approximately 40% of patients who undergo standard chemoimmunotherapy still present with primary refractory disease or relapse. Non-coding RNAs (ncRNAs), a group of biomolecules functioning at the RNA level, are increasingly recognized as vital components of molecular biology. With the development of RNA-sequencing (RNA-Seq) technology, accumulating evidence shows that ncRNAs are important mediators of diverse biological processes such as cell proliferation, differentiation, and apoptosis. They are also considered promising biomarkers and better candidates than proteins and genes for the early recognition of disease onset, as they are associated with relative stability, specificity, and reproducibility. In this review, we provide the first comprehensive description of the current knowledge regarding three groups of ncRNAs—microRNAs (miRNAs), circular RNAs (circRNAs), and long non-coding RNAs (lncRNAs)—focusing on their characteristics, molecular functions, as well as diagnostic and therapeutic potential in DLBCL. This review provides an exhaustive account for researchers to explore novel biomarkers for the diagnosis and prognosis of DLBCL and therapeutic targets.
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Affiliation(s)
- Yan Shi
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Daihong Ding
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Rongfeng Qu
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Yan Tang
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Shuhong Hao
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
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Fuertes T, Ramiro AR, de Yebenes VG. miRNA-Based Therapies in B Cell Non-Hodgkin Lymphoma. Trends Immunol 2020; 41:932-947. [PMID: 32888820 DOI: 10.1016/j.it.2020.08.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/06/2020] [Accepted: 08/06/2020] [Indexed: 12/17/2022]
Abstract
Non-Hodgkin lymphoma (NHL) is a diverse class of hematological cancers, many of which arise from germinal center (GC)-experienced B cells. Thus GCs, the sites of antibody affinity maturation triggered during immune responses, also provide an environment that facilitates B cell oncogenic transformation. miRNAs provide attractive and mechanistically different strategies to treat these malignancies based on their potential for simultaneous modulation of multiple targets. Here, we discuss the scientific rationale for miRNA-based therapeutics in B cell neoplasias and review recent advances that may help establish a basis for novel candidate miRNA-based therapies for B cell-NHL (B-NHL).
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Affiliation(s)
- Teresa Fuertes
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | | | - Virginia G de Yebenes
- Universidad Complutense de Madrid School of Medicine, Department of Immunology, Ophthalmology and ENT, 12 de Octubre Health Research Institute (imas12), Madrid, Spain.
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12
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Rashad S, Han X, Saqr K, Tupin S, Ohta M, Niizuma K, Tominaga T. Epigenetic response of endothelial cells to different wall shear stress magnitudes: A report of new mechano-miRNAs. J Cell Physiol 2020; 235:7827-7839. [PMID: 31912899 DOI: 10.1002/jcp.29436] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 12/23/2019] [Indexed: 12/12/2022]
Abstract
Endothelial cells (ECs) respond to flow stress via a variety of mechanisms, leading to various intracellular responses that can modulate the vessel wall and lead to diseases if the flow is disturbed. Mechano-microRNAs (miRNAs) are a subset of miRNAs in the ECs that are flow responsive. Mechano-miRNAs were shown to be related to atherosclerosis pathophysiology, and a number of them were identified as pathologic. Here, we exposed human carotid ECs to different wall shear stresses (WSS), high and low, and evaluated the response of miRNAs by microarray and quantitative polymerase chain reaction analysis. We discovered five new mechano-miRNAs that were not reported in that context previously to the best of our knowledge. Moreover, functional pathway analysis revealed that under low WSS conditions, several pathways regulating apoptosis are affected. In addition, KLF2 and KLF4, known atheroprotective genes, were downregulated under low WSS and upregulated under high WSS. KLF2 and VCAM1, both angiogenic, were upregulated under high WSS. NOS3, which is vascular protective, was also upregulated with higher WSS. On the contrary, ICAM-1 and E-selectin, both atherogenic and proinflammatory, were upregulated with high WSS. Collectively, the epigenetic landscape with the gene expression analysis reveals that low WSS is associated with a proapoptotic state, while high WSS is associated with a proliferative and proinflammatory state.
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Affiliation(s)
- Sherif Rashad
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Xiaobo Han
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Khalid Saqr
- Biomedical Flow Dynamics Laboratory, Institute of Fluid Science, Tohoku University, Sendai, Japan
| | - Simon Tupin
- Biomedical Flow Dynamics Laboratory, Institute of Fluid Science, Tohoku University, Sendai, Japan
| | - Makoto Ohta
- Biomedical Flow Dynamics Laboratory, Institute of Fluid Science, Tohoku University, Sendai, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
| | - Teiji Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
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Ting CY, Liew SM, Price A, Gan GG, Bee-Lan Ong D, Tan SY, Bee PC. Clinical significance of aberrant microRNAs expression in predicting disease relapse/refractoriness to treatment in diffuse large B-cell lymphoma: A meta-analysis. Crit Rev Oncol Hematol 2019; 144:102818. [PMID: 31733445 DOI: 10.1016/j.critrevonc.2019.102818] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 09/27/2019] [Accepted: 10/07/2019] [Indexed: 12/19/2022] Open
Abstract
The clinical significance of aberrantly expressed microRNAs in predicting treatment response to chemotherapy in diffuse large B-cell lymphoma patients (DLBCL) remains uncertain. Feasibility of microRNA testing to predict treatment outcome was evaluated. Twenty-two types of aberrantly expressed microRNAs were associated with poor treatment response; pooled hazard ratio (HR) was 2.14 [95%CI:1.78-2.57, P < 0.00001]. DLBCL patients with aberrant expression of miR-155, miR-17/92 clusters, miR-21, miR-224, or miR-146b-5p had a higher risk of treatment resistance or shorter period of disease relapse/progression free survival, with HR = 2.71 (95%CI:1.66-4.42, P < 0.0001), HR = 2.70 (95%CI:1.50-4.85, P = 0.0010), HR = 2.20 (95%CI:1.31-3.69, P = 0.003), HR = 2.07 (95%CI:1.50-2.86, P < 0.00001), HR = 2.26 (95%CI:1.40-3.65, P = 0.0009), respectively. The association between aberrant expression of microRNAs and treatment response appears to be stronger in formalin-fixed-paraffin-embedded tissue (HR = 2.41, 95%CI:1.79-3.25, P < 0.00001) than in fresh-frozen samples (HR = 1.94, 95%CI: 1.22-3.08, P = 0.005) and peripheral blood samples (HR = 1.94, 95%CI:1.53-2.46, P < 0.00001). Mir-155, miR-17/92 clusters, miR-21, miR-224, and mir-146b-5p have value in predicting treatment response to chemotherapy in DLBCL.
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Affiliation(s)
- Choo-Yuen Ting
- Department of Medicine, Faculty of Medicine, University of Malaya, Malaysia
| | - Su-May Liew
- Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Malaysia
| | - Amy Price
- University of Oxford, Centre for Evidence Based Medicine, England, United Kingdom
| | - Gin-Gin Gan
- Department of Medicine, Faculty of Medicine, University of Malaya, Malaysia
| | - Diana Bee-Lan Ong
- Department of Pathology, Faculty of Medicine, University of Malaya, Malaysia
| | - Soo-Yong Tan
- Department of Pathology, National University of Singapore, Singapore
| | - Ping-Chong Bee
- Department of Medicine, Faculty of Medicine, University of Malaya, Malaysia.
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Luo B, Huang L, Gu Y, Li C, Lu H, Chen G, Peng Z, Feng Z. Expression of exportin-1 in diffuse large B-cell lymphoma: immunohistochemistry and TCGA analyses. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:5547-5560. [PMID: 31949642 PMCID: PMC6963058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 10/22/2018] [Indexed: 06/10/2023]
Abstract
UNLABELLED Exportin-1 (XPO1) is an essential nuclear export receptor that is involved in the pathogenesis of multiple tumors. However, the role of XPO1 in diffuse large B-cell lymphoma (DLBCL) requires clarification. This study aims to detect XPO1 expression in DLBCL and to explore its relationships with clinicopathologic parameters and prognoses. METHODS A total of 131 cases of DLBCL and 30 cases of reactive lymphoid hyperplasia were selected for immunohistochemistry to examine XPO1 expression and analyze the relationships of XPO1 expression with clinicopathologic parameters and prognosis. DLBCL datasets downloaded from The Cancer Genome Atlas (TCGA) were used to analyze the mutations, expressions, and clinical values of XPO1 in DLBCL. RESULTS XPO1 expression was markedly upregulated in DLBCL compared to the reactive lymphoid hyperplasia group (χ2 = 10.734, P = 0.001). High XPO1 expression was associated with an advanced clinical stage (χ2 = 4.036, P = 0.045) and a risky International Prognostic Index (IPI) score (χ2 = 5.301, P = 0.025). Moreover, high XPO1 expression was associated with a lower overall survival rate compared with low expression (P = 0.043). XPO1 was an independent prognostic factor for DLBCL (risk ratio, RR = 3.772, P = 0.006). Furthermore, XPO1 overexpression in DLBCL was correlated with a high IPI score (P = 0.024) in TCGA datasets. CONCLUSION High XPO1 expression in DLBCL was related to an advanced clinical stage, poor IPI score, and poor prognosis. Thus, XPO1 may be useful for condition identification and prognostic assessment.
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Affiliation(s)
- Bin Luo
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Lanshan Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Yongyao Gu
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Chunyao Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Huiping Lu
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Zhigang Peng
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Zhenbo Feng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
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