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Abedi Kichi Z, Dini N, Rojhannezhad M, Shirvani Farsani Z. Noncoding RNAs in B cell non-Hodgkins lymphoma. Gene 2024; 917:148480. [PMID: 38636814 DOI: 10.1016/j.gene.2024.148480] [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: 01/05/2024] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
B-cell non-Hodgkins lymphomas (BCNHLs) are a category of B-cell cancers that show heterogeneity. These blood disorders are derived from different levels of B-cell maturity. Among NHL cases, ∼80-90 % are derived from B-cells. Recent studies have demonstrated that noncoding RNAs (ncRNAs) contribute to almost all parts of mechanisms and are essential in tumorigenesis, including B-cell non-Hodgkins lymphomas. The study of ncRNA dysregulations in B-cell lymphoma unravels important mysteries in lymphoma's molecular etiology. It seems also necessary for discovering novel trials as well as investigating the potential of ncRNAs as markers for their diagnosis and prognosis. In the current study, we summarize the role of ncRNAs involving miRNAs, long noncoding RNAs, as well as circular RNAs in the development or progression of BCNHLs.
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Affiliation(s)
- Zahra Abedi Kichi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IR Iran; Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians University Munich, Germany
| | - Niloofar Dini
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Mahbubeh Rojhannezhad
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IR Iran
| | - Zeinab Shirvani Farsani
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
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2
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Feng H, Zhang X, Kang J. Analyzing the involvement of diverse cell death-related genes in diffuse large B-cell lymphoma using bioinformatics techniques. Heliyon 2024; 10:e30831. [PMID: 38779021 PMCID: PMC11108851 DOI: 10.1016/j.heliyon.2024.e30831] [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: 12/28/2023] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) stands as the most prevalent subtype of non-Hodgkin's lymphoma and exhibits significant heterogeneity. Various forms of programmed cell death (PCD) have been established to have close associations with tumor onset and progression. To this end, this study has compiled 16 PCD-related genes. The investigation delved into genes linked with prognosis, constructing risk models through consecutive application of univariate Cox regression analysis and Lasso-Cox regression analysis. Furthermore, we employed RT-qPCR to validate the mRNA expression levels of certain diagnosis-related genes. Subsequently, the models underwent validation through KM survival curves and ROC curves, respectively. Additionally, nomogram models were formulated employing prognosis-related genes and risk scores. Lastly, disparities in immune cell infiltration abundance and the expression of immune checkpoint-associated genes between high- and low-risk groups, as classified by risk models, were explored. These findings contribute to a more comprehensive understanding of the role played by the 16 PCD-associated genes in DLBCL, shedding light on potential novel therapeutic strategies for the condition.
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Affiliation(s)
- Heyuan Feng
- Flow Cytometry Room, Beijing Gaobo Boren Hospital, Beijing, China
| | - Xiyuan Zhang
- Department of Blood Transfusion, No.970 Hospital of PLA Joint Logistics Support Force, Shandong, China
| | - Jian Kang
- Flow Cytometry Room, Beijing Gaobo Boren Hospital, Beijing, China
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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.
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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.
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Fader KA, Gosink MM, Xia S, Lanz TA, Halsey C, Vaidya VS, Radi ZA. Thymic lymphoma detection in RORγ knockout mice using 5-hydroxymethylcytosine profiling of circulating cell-free DNA. Toxicol Appl Pharmacol 2023; 473:116582. [PMID: 37295732 DOI: 10.1016/j.taap.2023.116582] [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: 06/04/2023] [Indexed: 06/12/2023]
Abstract
A high incidence of thymic lymphoma has been noted in mice deficient of retinoid-related orphan receptor γ2 (RORγ2), which is required for differentiation of naïve CD4+ T cells into TH17 cells. Using a RORγ homozygous knockout (KO) mouse model of thymic lymphoma, we characterized this tumor progression and investigated the utility of 5-hydroxymethylcytosine (5hmC) signatures as a non-invasive circulating biomarker for early prediction of malignancy. No evidence for malignancy was noted in the wild-type mice, while primary thymic lymphoma with multi-organ metastasis was observed microscopically in 97% of the homozygous RORγ KO mice. The severity of thymic lymphoma was not age-dependent in the KO mice of 2 to 4 months old. Differential enrichment of 5hmC in thymic DNA and plasma cell-free DNA (cfDNA) was compared across different stages of tumor progression. Random forest modeling of plasma cfDNA achieved good predictivity (AUC = 0.74) in distinguishing early non-metastatic thymic lymphoma compared to cancer-free controls, while perfect predictivity was achieved with advanced multi-organ metastatic disease (AUC = 1.00). Lymphoid-specific genes involved in thymocyte selection during T cell development (Themis, Tox) were differentially enriched in both plasma and thymic tissue. This could help in differentiating thymic lymphoma from other tumors commonly detected in rodent carcinogenicity studies used in pharmaceutical drug development to inform human malignancy risk. Overall, these results provide a proof-of-concept for using circulating cfDNA profiles in rodent carcinogenicity studies for early risk assessment of novel pharmaceutical targets.
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Affiliation(s)
- Kelly A Fader
- Pfizer Worldwide Research, Development and Medical; Early Clinical Development; Groton, CT, USA.
| | - Mark M Gosink
- Boehringer Ingelheim Pharmaceuticals, Inc.; Ridgefield, CT, USA
| | - Shuhua Xia
- Pfizer Worldwide Research, Development and Medical; Drug Safety Research and Development; Groton, CT, USA
| | - Thomas A Lanz
- Pfizer Worldwide Research, Development and Medical; Drug Safety Research and Development; Groton, CT, USA
| | - Charles Halsey
- Pfizer Worldwide Research, Development and Medical; Drug Safety Research and Development; Groton, CT, USA
| | - Vishal S Vaidya
- Pfizer Worldwide Research, Development and Medical; Drug Safety Research and Development; Cambridge, MA, USA
| | - Zaher A Radi
- Pfizer Worldwide Research, Development and Medical; Drug Safety Research and Development; Cambridge, MA, USA
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Zhu Z, Hu E, Shen H, Tan J, Zeng S. The functional and clinical roles of liquid biopsy in patient-derived models. J Hematol Oncol 2023; 16:36. [PMID: 37031172 PMCID: PMC10082989 DOI: 10.1186/s13045-023-01433-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/28/2023] [Indexed: 04/10/2023] Open
Abstract
The liquid biopsy includes the detection of circulating tumor cells (CTCs) and CTC clusters in blood, as well as the detection of, cell-free DNA (cfDNA)/circulating tumor DNA (ctDNA) and extracellular vesicles (EVs) in the patient's body fluid. Liquid biopsy has important roles in translational research. But its clinical utility is still under investigation. Newly emerged patient-derived xenograft (PDX) and CTC-derived xenograft (CDX) faithfully recapitulate the genetic and morphological features of the donor patients' tumor and patient-derived organoid (PDO) can mostly mimic tumor growth, tumor microenvironment and its response to drugs. In this review, we describe how the development of these patient-derived models has assisted the studies of CTCs and CTC clusters in terms of tumor biological behavior exploration, genomic analysis, and drug testing, with the help of the latest technology. We then summarize the studies of EVs and cfDNA/ctDNA in PDX and PDO models in early cancer diagnosis, tumor burden monitoring, drug test and response monitoring, and molecular profiling. The challenges faced and future perspectives of research related to liquid biopsy using patient-derived models are also discussed.
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Affiliation(s)
- Ziqing Zhu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Erya Hu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Jun Tan
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
| | - Shan Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
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Li M, Huang F, Xie Z, Hong H, Xu Q, Peng Z. Identification of three small nucleolar RNAs (snoRNAs) as potential prognostic markers in diffuse large B-cell lymphoma. Cancer Med 2022; 12:3812-3829. [PMID: 36812125 PMCID: PMC9939161 DOI: 10.1002/cam4.5115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 07/13/2022] [Accepted: 07/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Diffuse large B-cell lymphoma (DLBCL) is a non-Hodgkin lymphoma with high mortality rates. Small nucleolar RNAs (snoRNAs) are tumor-specific biological markers, but there are few studies on the role of snoRNAs in DLBCL. MATERIALS AND METHODS Survival-related snoRNAs were selected to construct a specific snoRNA-based signature via computational analyses (Cox regression and independent prognostic analyses) to predict the prognosis of DLBCL patients. To assist in clinical applications, a nomogram was built by combining the risk model and other independent prognostic factors. Pathway analysis, gene ontology analysis, transcription factor enrichment, protein-protein interactions, and single nucleotide variant analysis were used to explore the potential biological mechanisms of co-expressed genes. RESULTS Twelve prognosis-correlated snoRNAs were selected from the DLBCL patient cohort of microarray profiles, and a three-snoRNA signature consisting of SNORD1A, SNORA60, and SNORA66 was constructed. DLBCL patients could be divided into high-risk and low-risk cohorts using the risk model, and the high-risk group and activated B cell-like (ABC) type DLBCL were linked with disappointing survival. In addition, SNORD1A co-expressed genes were inseparably linked to the biological functions of the ribosome and mitochondria. Potential transcriptional regulatory networks have also been identified. MYC and RPL10A were the most mutated SNORD1A co-expressed genes in DLBCL. CONCLUSION Put together, our findings explored the potential biological effects of snoRNAs in DLBCL, and provided a new predictor for DLBCL prediction.
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Affiliation(s)
- Mei‐wei Li
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
| | - Feng‐xiang Huang
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
| | - Zu‐cheng Xie
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
| | - Hao‐yuan Hong
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
| | - Qing‐yuan Xu
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
| | - Zhi‐gang Peng
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
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Pathway importance by graph convolutional network and Shapley additive explanations in gene expression phenotype of diffuse large B-cell lymphoma. PLoS One 2022; 17:e0269570. [PMID: 35749395 PMCID: PMC9231717 DOI: 10.1371/journal.pone.0269570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 05/09/2022] [Indexed: 11/30/2022] Open
Abstract
Deep learning techniques have recently been applied to analyze associations between gene expression data and disease phenotypes. However, there are concerns regarding the black box problem: it is difficult to interpret why the prediction results are obtained using deep learning models from model parameters. New methods have been proposed for interpreting deep learning model predictions but have not been applied to genetics. In this study, we demonstrated that applying SHapley Additive exPlanations (SHAP) to a deep learning model using graph convolutions of genetic pathways can provide pathway-level feature importance for classification prediction of diffuse large B-cell lymphoma (DLBCL) gene expression subtypes. Using Kyoto Encyclopedia of Genes and Genomes pathways, a graph convolutional network (GCN) model was implemented to construct graphs with nodes and edges. DLBCL datasets, including microarray gene expression data and clinical information on subtypes (germinal center B-cell-like type and activated B-cell-like type), were retrieved from the Gene Expression Omnibus to evaluate the model. The GCN model showed an accuracy of 0.914, precision of 0.948, recall of 0.868, and F1 score of 0.906 in analysis of the classification performance for the test datasets. The pathways with high feature importance by SHAP included highly enriched pathways in the gene set enrichment analysis. Moreover, a logistic regression model with explanatory variables of genes in pathways with high feature importance showed good performance in predicting DLBCL subtypes. In conclusion, our GCN model for classifying DLBCL subtypes is useful for interpreting important regulatory pathways that contribute to the prediction.
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miRNA Expression Profiling in Subcutaneous Adipose Tissue of Monozygotic Twins Discordant for HIV Infection: Validation of Differentially Expressed miRNA and Bioinformatic Analysis. Int J Mol Sci 2022; 23:ijms23073486. [PMID: 35408847 PMCID: PMC8998861 DOI: 10.3390/ijms23073486] [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: 02/21/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 02/04/2023] Open
Abstract
Combined AntiRetroviral Treatments (cARTs) used for HIV infection may result in varied metabolic complications, which in some cases, may be related to patient genetic factors, particularly microRNAs. The use of monozygotic twins, differing only for HIV infection, presents a unique and powerful model for the controlled analysis of potential alterations of miRNAs regulation consequent to cART treatment. Profiling of 2578 mature miRNA in the subcutaneous (SC) adipose tissue and plasma of monozygotic twins was investigated by the GeneChip® miRNA 4.1 array. Real-time PCR and ddPCR experiments were performed in order to validate differentially expressed miRNAs. Target genes of deregulated miRNAs were predicted by the miRDB database (prediction score > 70) and enrichment analysis was carried out with g:Profiler. Processes in SC adipose tissue most greatly affected by miRNA up-regulation included (i) macromolecular metabolic processes, (ii) regulation of neurogenesis, and (iii) protein phosphorylation. Furthermore, KEGG analysis revealed miRNA up-regulation involvement in (i) insulin signaling pathways, (ii) neurotrophin signaling pathways, and (iii) pancreatic cancer. By contrast, miRNA up-regulation in plasma was involved in (i) melanoma, (ii) p53 signaling pathways, and (iii) focal adhesion. Our findings suggest a mechanism that may increase the predisposition of HIV+ patients to insulin resistance and cancer.
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Mukherjee S, Shelar B, Krishna S. Versatile role of miR-24/24-1*/24-2* expression in cancer and other human diseases. Am J Transl Res 2022; 14:20-54. [PMID: 35173828 PMCID: PMC8829624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/08/2021] [Indexed: 06/14/2023]
Abstract
MiRNAs (miRs) have been proven to be well-validated therapeutic targets. Emerging evidence has demonstrated that intricate, intrinsic and paradoxical functions of miRs are context-dependent because of their multiple upstream regulators, broad spectrum of downstream molecular targets and distinct expression in various tissues, organs and disease states. Targeted therapy has become an emerging field of research. One key for the development of successful miR-based/targeted therapy is to acquire integrated knowledge of its regulatory network and its association with disease phenotypes to identify critical nodes of the underlying pathogenesis. Herein, we systematically summarized the comprehensive role of miR-24-3p (miR-24), along with its passenger strands miR-24-1-5p* (miR-24-1) and miR-24-2-5p* (miR-24-2), emphasizing their microenvironment, intracellular targets, and associated gene networks and regulatory phenotypes in 18 different cancer types and 13 types of other disorders. MiR-24 targets and regulates numerous genes in various cancer types and enhances the expression of several oncogenes (e.g., cMyc, BCL2 and HIF1), which are challenging in terms of druggability. In contrast, several tumor suppressor proteins (p21 and p53) have been reported to be downregulated by miR-24. MiR-24 also regulates the cell cycle and is associated with numerous cancer hallmarks such as apoptosis, proliferation, metastasis, invasion, angiogenesis, autophagy, drug resistance and other diseases pathogenesis. Overall, miR-24 plays an emerging role in the diagnosis, prognosis and pathobiology of various diseases. MiR-24 is a potential target for targeted therapy in the era of precision medicine, which expands the landscape of targetable macromolecules, including undruggable proteins.
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Fernandes M, Marques H, Teixeira AL, Medeiros R. Competitive Endogenous RNA Network Involving miRNA and lncRNA in Non-Hodgkin Lymphoma: Current Advances and Clinical Perspectives. Biomedicines 2021; 9:1934. [PMID: 34944752 PMCID: PMC8698845 DOI: 10.3390/biomedicines9121934] [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: 11/15/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/18/2022] Open
Abstract
Non-Hodgkin lymphoma (NHL) is a heterogeneous malignancy with variable patient outcomes. There is still a lack of understanding about the different players involved in lymphomagenesis, and the identification of new diagnostic and prognostic biomarkers is urgent. MicroRNAs and long non-coding RNAs emerged as master regulators of B-cell development, and their deregulation has been associated with the initiation and progression of lymphomagenesis. They can function by acting alone or, as recently proposed, by creating competing endogenous RNA (ceRNA) networks. Most studies have focused on individual miRNAs/lncRNAs function in lymphoma, and there is still limited data regarding their interactions in lymphoma progression. The study of miRNAs' and lncRNAs' deregulation in NHL, either alone or as ceRNAs networks, offers new insights into the molecular mechanisms underlying lymphoma pathogenesis and opens a window of opportunity to identify potential diagnostic and prognostic biomarkers. In this review, we summarized the current knowledge regarding the role of miRNAs and lncRNAs in B-cell lymphoma, including their interactions and regulatory networks. Finally, we summarized the studies investigating the potential of miRNAs and lncRNAs as clinical biomarkers, with a special focus on the circulating profiles, to be applied as a non-invasive, easy-to-obtain, and reproducible liquid biopsy for dynamic management of NHL patients.
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Affiliation(s)
- Mara Fernandes
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal; (M.F.); (A.L.T.)
- Research Department of the Portuguese League against Cancer Regional Nucleus of the North (LPCC-NRN), 4200-177 Porto, Portugal
- Faculty of Medicine, University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Herlander Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal;
- ICVS/3B’s–PT Government Associate Laboratory, 4805-017 Braga/Guimarães, Portugal
- Department of Oncology, Hospital de Braga, 4710-243 Braga, Portugal
- CINTESIS, Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, 4200-450 Porto, Portugal
| | - Ana Luísa Teixeira
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal; (M.F.); (A.L.T.)
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-513 Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal; (M.F.); (A.L.T.)
- Research Department of the Portuguese League against Cancer Regional Nucleus of the North (LPCC-NRN), 4200-177 Porto, Portugal
- Faculty of Medicine, University of Porto (FMUP), 4200-319 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-513 Porto, Portugal
- Biomedical Research Center (CEBIMED), Faculty of Health Sciences of Fernando Pessoa University (UFP), 4249-004 Porto, Portugal
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Olmedillas-López S, Olivera-Salazar R, García-Arranz M, García-Olmo D. Current and Emerging Applications of Droplet Digital PCR in Oncology: An Updated Review. Mol Diagn Ther 2021; 26:61-87. [PMID: 34773243 DOI: 10.1007/s40291-021-00562-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2021] [Indexed: 12/14/2022]
Abstract
In the era of personalized medicine and targeted therapies for the management of patients with cancer, ultrasensitive detection methods for tumor genotyping, such as next-generation sequencing or droplet digital polymerase chain reaction (ddPCR), play a significant role. In the search for less invasive strategies for diagnosis, prognosis and disease monitoring, the number of publications regarding liquid biopsy approaches using ddPCR has increased substantially in recent years. There is a long list of malignancies in which ddPCR provides a reliable and accurate tool for detection of nucleic acid-based markers derived from cell-free DNA, cell-free RNA, circulating tumor cells, extracellular vesicles or exosomes when isolated from whole blood, plasma and serum, helping to anticipate tumor relapse or unveil intratumor heterogeneity and clonal evolution in response to treatment. This updated review describes recent developments in ddPCR platforms and provides a general overview about the major applications of liquid biopsy in blood, including its utility for molecular response and minimal residual disease monitoring in hematological malignancies or the therapeutic management of patients with colorectal or lung cancer, particularly for the selection and monitoring of treatment with tyrosine kinase inhibitors. Although plasma is the main source of genetic material for tumor genomic profiling, liquid biopsy by ddPCR is being investigated in a wide variety of biologic fluids, such as cerebrospinal fluid, urine, stool, ocular fluids, sputum, saliva, bronchoalveolar lavage, pleural effusion, mucin, peritoneal fluid, fine needle aspirate, bile or pancreatic juice. The present review focuses on these "alternative" sources of genetic material and their analysis by ddPCR in different kinds of cancers.
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Affiliation(s)
- Susana Olmedillas-López
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.
| | - Rocío Olivera-Salazar
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain
| | - Mariano García-Arranz
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain
| | - Damián García-Olmo
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain.,Department of Surgery, Fundación Jiménez Díaz University Hospital (FJD), 28040, Madrid, Spain
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12
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Gao HX, Li SJ, Wang MB, Yan SF, Cui WL, Ma ZP, Xue J, Sang W, Zhang W, Li XX. Screening and identification of differentially expressed microRNAs in diffuse large B-cell lymphoma based on microRNA microarray. Oncol Lett 2021; 22:753. [PMID: 34539857 PMCID: PMC8436336 DOI: 10.3892/ol.2021.13014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 05/18/2021] [Indexed: 02/07/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common type of B-cell non-Hodgkin lymphoma in adults and the pathogenesis of DLBCL is multifactorial and complex. Understanding the molecular mechanisms involved in DLBCL is important to identify new therapeutic targets. The present study aimed to screen and identify differentially expressed microRNAs (miRNAs/miRs) between diffuse large B-cell lymphoma (DLBCL) and control [lymph node reactive hyperplasia (LRH)] groups, and to investigate whether miRNAs associated with DLBCL could serve as potential therapeutic targets. In total, 5 DLBCL experimental samples and 5 control samples were obtained from fresh patient tissues. Firstly, the fresh samples were analyzed using miRNA microarray to identify differentially expressed miRNAs. Next, three databases (TargetScan, microRNA.org and PITA) were used to predict by intersection the potential target genes of the 204 differential miRNAs identified, and a Venn diagram of the results was performed. Subsequently, the target genes of differential miRNAs were analyzed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. Finally, to validate the miRNA microarray data, reverse transcription-quantitative PCR (RT-qPCR) was performed for 8 differentially expressed miRNAs (miR-193a-3p, miR-19a-3p, miR-19b-3p, miR-370-3p, miR-1275, miR-490-5p, miR-630 and miR-665) using DLBCL and LRH fresh samples. In total, 204 miRNAs exhibited differential expression, including 105 downregulated and 54 upregulated miRNAs. The cut-off criteria were set as P≤0.05 and fold-change ≥2. A total of 7,522 potential target genes for the 204 miRNAs were predicted. Potential target genes were enriched in the following pathways: ‘Cancer’, ‘MAPK signaling pathway’, ‘regulation of actin cytoskeleton’, ‘focal adhesion’, ‘endocytosis’, ‘Wnt signaling pathway’, ‘axon guidance’, ‘calcium signaling pathway’ and ‘PI3K/AKT signaling pathway’. A total of 8 miRNAs were validated by RT-qPCR, and 4 miRNAs (miR-19b-3p, miR-193a-3p, miR-370-3p and miR-490-5p) exhibited low expression levels in DLBCL (P<0.05), while miR-630 was highly expressed in DLBCL (P<0.05). Overall, the present study screened 204 differentially expressed miRNAs and analyzed the expression levels of 8 differentially expressed miRNAs in DLBCL. These differentially expressed miRNAs may serve as therapeutic targets for improvement of therapeutic efficacy in DLBCL in the future.
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Affiliation(s)
- Hai-Xia Gao
- Department of Pathology and NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region 832002, P.R. China.,Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Si-Jing Li
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Meng-Bo Wang
- Department of Ultrasound, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region 832002, P.R. China
| | - Shu-Fang Yan
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Wen-Li Cui
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Zhi-Ping Ma
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Jing Xue
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Wei Sang
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Wei Zhang
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Xin-Xia Li
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
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A Set of 17 microRNAs Common for Brain and Cerebrospinal Fluid Differentiates Primary Central Nervous System Lymphoma from Non-Malignant Brain Tumors. Biomolecules 2021; 11:biom11091395. [PMID: 34572608 PMCID: PMC8466839 DOI: 10.3390/biom11091395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/07/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
The diagnosis of primary central nervous system (CNS) lymphoma, which is predominantly of the diffuse large B-cell lymphoma type (CNS DLBCL), is challenging. MicroRNAs (miRs) are gene expression-regulating non-coding RNAs that are potential biomarkers. We aimed to distinguish miR expression patterns differentiating CNS DLBCL and non-malignant CNS diseases with tumor presentation (n-ML). Next generation sequencing-based miR profiling of cerebrospinal fluids (CSFs) and brain tumors was performed. Sample source-specific (CSF vs. brain tumor) miR patterns were revealed. Even so, a set of 17 miRs differentiating CNS DLBCL from n-ML, no matter if assessed in CSF or in a tumor, was identified. Along with the results of pathway analyses, this suggests their pathogenic role in CNS DLBCL. A combination of just four of those miRs (miR-16-5p, miR-21-5p, miR-92a-3p, and miR-423-5p), assessed in CSFs, discriminated CNS DLBCL from n-ML samples with 100% specificity and 67.0% sensitivity. Analyses of paired CSF-tumor samples from patients with CNS DLBCL showed significantly lower CSF levels of miR-26a, and higher CSF levels of miR-15a-5p, miR-15b-5p, miR-19a-3p, miR-106b-3p, miR-221-3p, and miR-423-5p. Noteworthy, the same miRs belonged to the abovementioned set differentiating CNS DLBCL from non-malignant CNS diseases. Our results not only add to the basic knowledge, but also hold significant translational potential.
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14
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MicroRNA and Other Non-Coding RNAs in Epstein-Barr Virus-Associated Cancers. Cancers (Basel) 2021; 13:cancers13153909. [PMID: 34359809 PMCID: PMC8345394 DOI: 10.3390/cancers13153909] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/27/2021] [Accepted: 08/01/2021] [Indexed: 12/12/2022] Open
Abstract
EBV is a direct causative agent in around 1.5% of all cancers. The oncogenic properties of EBV are related to its ability to activate processes needed for cellular proliferation, survival, migration, and immune evasion. The EBV latency program is required for the immortalization of infected B cells and involves the expression of non-coding RNAs (ncRNAs), including viral microRNAs. These ncRNAs have different functions that contribute to virus persistence in the asymptomatic host and to the development of EBV-associated cancers. In this review, we discuss the function and potential clinical utility of EBV microRNAs and other ncRNAs in EBV-associated malignancies. This review is not intended to be comprehensive, but rather to provide examples of the importance of ncRNAs.
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15
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Caner V, Cetin GO, Hacioglu S, Baris IC, Tepeli E, Turk NS, Bagci G, Yararbas K, Cagliyan G. The miRNA content of circulating exosomes in DLBCL patients and in vitro influence of DLBCL-derived exosomes on miRNA expression of healthy B cells from peripheral blood. Cancer Biomark 2021; 32:519-529. [PMID: 34275894 DOI: 10.3233/cbm-210110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Due to the heterogeneous nature of Diffuse Large B-cell Lymphoma (DLBCL), the mechanisms underlying tumor development and progression have not yet been fully elucidated. OBJECTIVE This study aimed to compare the characteristics of plasma exosomes of DLBCL patients and healthy individuals and to evaluate the exosomal interactions between DLBCL cell lines and normal B-cells. METHODS Exosome isolation was performed using an ultracentrifugation-based protocol from plasma of 20 patients with DLBCL and 20 controls. The expression of miRNAs from exosome samples was analyzed using a miRNA expression microarray. The presence of exosome-mediated communication between the lymphoma cells and normal B-cells was determined by the co-culture model. RESULTS A significant increase in plasma exosome concentrations of DLBCL patients was observed. There was also a significant decrease in the expression of 33 miRNAs in plasma exosomes of DLBCL patients. It was determined that normal B-cells internalize DLBCL-derived exosomes and then miRNA expression differences observed in normal B-cells are specific to lymphoma-subtypes. CONCLUSIONS MiR-3960, miR-6089 and miR-939-5p can be used as the miRNA signature in DLBCL diagnosis. We suppose that the exosomes changed the molecular signature of the target cells depending on the genomic characterization of the lymphoma cells they have originated.
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Affiliation(s)
- Vildan Caner
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Gokhan Ozan Cetin
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Sibel Hacioglu
- Department of Hematology, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Ikbal Cansu Baris
- Department of Medical Biology, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Emre Tepeli
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Nilay Sen Turk
- Department of Medical Pathology, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Gulseren Bagci
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Kanay Yararbas
- Department of Medical Genetics, School of Medicine, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - Gulsum Cagliyan
- Department of Hematology, School of Medicine, Pamukkale University, Denizli, Turkey
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16
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Lv L, Liu Y. Clinical Application of Liquid Biopsy in Non-Hodgkin Lymphoma. Front Oncol 2021; 11:658234. [PMID: 33816315 PMCID: PMC8013700 DOI: 10.3389/fonc.2021.658234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/02/2021] [Indexed: 12/14/2022] Open
Abstract
Non-Hodgkin lymphoma (NHL) is a common type of hematological malignant tumor, composed of multiple subtypes that originate from B lymphocytes, T lymphocytes, and natural killer cells. A diagnosis of NHL depends on the results of a pathology examination, which requires an invasive tissue biopsy. However, due to their invasive nature, tissue biopsies have many limitations in clinical applications, especially in terms of evaluating the therapeutic response and monitoring tumor progression. To overcome these limitations of traditional tissue biopsies, a technique known as "liquid biopsies" (LBs) was proposed. LBs refer to noninvasive examinations that can provide biological tumor data for analysis. Many studies have shown that LBs can be broadly applied to the diagnosis, treatment, prognosis, and monitoring of NHL. This article will briefly review various LB methods that aim to improve NHL management, including the evaluation of cell-free DNA/circulating tumor DNA, microRNA, and tumor-derived exosomes extracted from peripheral blood in NHL.
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Affiliation(s)
- Liwei Lv
- Department of Hematology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuanbo Liu
- Department of Hematology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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17
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Decruyenaere P, Offner F, Vandesompele J. Circulating RNA biomarkers in diffuse large B-cell lymphoma: a systematic review. Exp Hematol Oncol 2021; 10:13. [PMID: 33593440 PMCID: PMC7885416 DOI: 10.1186/s40164-021-00208-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/06/2021] [Indexed: 12/31/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common histological subtype of non-Hodgkin's lymphomas (NHL). DLBCL is an aggressive malignancy that displays a great heterogeneity in terms of morphology, genetics and biological behavior. While a sustained complete remission is obtained in the majority of patients with standard immunochemotherapy, patients with refractory of relapsed disease after first-line treatment have a poor prognosis. This patient group represents an important unmet need in lymphoma treatment. In recent years, improved understanding of the underlying molecular pathogenesis had led to new classification and prognostication tools, including the development of cell-free biomarkers in liquid biopsies. Although the majority of studies have focused on the use of cell-free fragments of DNA (cfDNA), there has been an increased interest in circulating-free coding and non-coding RNA, including messenger RNA (mRNA), microRNA (miRNA), long non-coding RNA (lncRNA) and circular RNA (circRNA), as well as RNA encapsulated in extracellular vesicles or tumor-educated platelets (TEPs). We performed a systematic search in PubMed to identify articles that evaluated circulating RNA as diagnostic, subtype, treatment response or prognostic biomarkers in a human DLBCL population. A total of 35 articles met the inclusion criteria. The aim of this systematic review is to present the current understanding of circulating RNA molecules as biomarker in DLBCL and to discuss their future potential.
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Affiliation(s)
- Philippe Decruyenaere
- Department of Hematology, Ghent University Hospital, 9K12, Campus UZ Ghent, Corneel Heymanslaan 10, 9000 Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Fritz Offner
- Department of Hematology, Ghent University Hospital, 9K12, Campus UZ Ghent, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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18
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Wuu YR, Hu B, Okunola H, Paul AM, Blaber EA, Cheng-Campbell M, Beheshti A, Grabham P. LET-Dependent Low Dose and Synergistic Inhibition of Human Angiogenesis by Charged Particles: Validation of miRNAs that Drive Inhibition. iScience 2020; 23:101771. [PMID: 33376971 PMCID: PMC7756138 DOI: 10.1016/j.isci.2020.101771] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/19/2020] [Accepted: 10/31/2020] [Indexed: 12/17/2022] Open
Abstract
Space radiation inhibits angiogenesis by two mechanisms depending on the linear energy transfer (LET). Using human 3D micro-vessel models, blockage of the early motile stage of angiogenesis was determined to occur after exposure to low LET ions (<3 KeV/AMU), whereas inhibition of the later stages occurs after exposure to high LET ions (>8 KeV/AMU). Strikingly, the combined effect is synergistic, detectible as low as 0.06 Gy making mixed ion space radiation more potent. Candidates for bystander transmission are microRNAs (miRNAs), and analysis on miRNA-seq data from irradiated mice shows that angiogenesis would in theory be downregulated. Further analysis of three previously identified miRNAs showed downregulation of their targets associated with angiogenesis and confirmed their involvement in angiogenesis pathways and increased health risks associated with cardiovascular disease. Finally, synthetic molecules (antagomirs) designed to inhibit the predicted miRNAs were successfully used to reverse the inhibition of angiogenesis.
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Affiliation(s)
- Yen-Ruh Wuu
- Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Burong Hu
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Hazeem Okunola
- Center for Radiological Research, Department of Radiation Oncology, College of Physicians and Surgeons, Columbia University, VC 11-243, 630 West 168 Street, New York, NY 10032, USA
| | - Amber M. Paul
- Universities Space Research Association, Columbia, MD 21046, USA
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Elizabeth A. Blaber
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Department of Bioengineering, Center for Biotechnology & InterdisciplinaryStudies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Margareth Cheng-Campbell
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Department of Bioengineering, Center for Biotechnology & InterdisciplinaryStudies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Peter Grabham
- Center for Radiological Research, Department of Radiation Oncology, College of Physicians and Surgeons, Columbia University, VC 11-243, 630 West 168 Street, New York, NY 10032, USA
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19
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Paul AM, Cheng-Campbell M, Blaber EA, Anand S, Bhattacharya S, Zwart SR, Crucian BE, Smith SM, Meller R, Grabham P, Beheshti A. Beyond Low-Earth Orbit: Characterizing Immune and microRNA Differentials following Simulated Deep Spaceflight Conditions in Mice. iScience 2020; 23:101747. [PMID: 33376970 PMCID: PMC7756144 DOI: 10.1016/j.isci.2020.101747] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 12/21/2022] Open
Abstract
Spaceflight missions can cause immune system dysfunction in astronauts with little understanding of immune outcomes in deep space. This study assessed immune responses in mice following ground-based, simulated deep spaceflight conditions, compared with data from astronauts on International Space Station missions. For ground studies, we simulated microgravity using the hindlimb unloaded mouse model alone or in combination with acute simulated galactic cosmic rays or solar particle events irradiation. Immune profiling results revealed unique immune diversity following each experimental condition, suggesting each stressor results in distinct circulating immune responses, with clear consequences for deep spaceflight. Circulating plasma microRNA sequence analysis revealed involvement in immune system dysregulation. Furthermore, a large astronaut cohort showed elevated inflammation during low-Earth orbit missions, thereby supporting our simulated ground experiments in mice. Herein, circulating immune biomarkers are defined by distinct deep space irradiation types coupled to simulated microgravity and could be targets for future space health initiatives.
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Affiliation(s)
- Amber M. Paul
- Universities Space Research Association, Columbia, MD 21046, USA
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94043, USA
| | - Margareth Cheng-Campbell
- Department of Biomedical Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Elizabeth A. Blaber
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94043, USA
- Department of Biomedical Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Sulekha Anand
- Department of Biological Sciences, San Jose State University, San Jose, CA 95112, USA
| | | | - Sara R. Zwart
- Department of Preventive Medicine and Community Health, University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | | | - Robert Meller
- Department of Neurobiology/Pharmacology, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Peter Grabham
- Center for Radiological Research, Columbia University, New York, NY 10027, USA
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94043, USA
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20
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Chebly A, Chouery E, Ropio J, Kourie HR, Beylot-Barry M, Merlio JP, Tomb R, Chevret E. Diagnosis and treatment of lymphomas in the era of epigenetics. Blood Rev 2020; 48:100782. [PMID: 33229141 DOI: 10.1016/j.blre.2020.100782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/05/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022]
Abstract
Lymphomas represent a heterogeneous group of cancers characterized by clonal lymphoproliferation. Over the past decades, frequent epigenetic dysregulations have been identified in hematologic malignancies including lymphomas. Many of these impairments occur in genes with established roles and well-known functions in the regulation and maintenance of the epigenome. In hematopoietic cells, these dysfunctions can result in abnormal DNA methylation, erroneous chromatin state and/or altered miRNA expression, affecting many different cellular functions. Nowadays, it is evident that epigenetic dysregulations in lymphoid neoplasms are mainly caused by genetic alterations in genes encoding for enzymes responsible for histone or chromatin modifications. We summarize herein the recent epigenetic modifiers findings in lymphomas. We focus also on the most commonly mutated epigenetic regulators and emphasize on actual epigenetic therapies.
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Affiliation(s)
- Alain Chebly
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon
| | - Eliane Chouery
- Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon
| | - Joana Ropio
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Porto University, Institute of Biomedical Sciences of Abel Salazar, 4050-313 Porto, Instituto de Investigação e Inovação em Saúde, 4200-135 Porto, Institute of Molecular Pathology and Immunology (Ipatimup), Cancer Biology group, 4200-465 Porto, Portugal
| | - Hampig Raphael Kourie
- Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon; Saint Joseph University, Faculty of Medicine, Hematology-Oncology Department, Beirut, Lebanon
| | - Marie Beylot-Barry
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Bordeaux University Hospital Center, Dermatology Department, 33000 Bordeaux, France
| | - Jean-Philippe Merlio
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Bordeaux University Hospital Center, Tumor Bank and Tumor Biology Laboratory, 33600 Pessac, France
| | - Roland Tomb
- Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon; Saint Joseph University, Faculty of Medicine, Dermatology Department, Beirut, Lebanon
| | - Edith Chevret
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France.
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21
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miRNA signature associated with R-CHOP refractoriness in patients diagnosed with diffuse large B cell lymphoma. Noncoding RNA Res 2020; 5:185-190. [PMID: 33134613 PMCID: PMC7585044 DOI: 10.1016/j.ncrna.2020.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 12/24/2022] Open
Abstract
Refractoriness remains as one of the challenges in patients with lymphoma under chemotherapy, and among biological regulators in cells driving this type of response are microRNAs (miRNAs). Different genes are constantly turned on or off according to the miRNAs expression profiles affecting the drug response in patients and their stability in serum and plasma makes them potential prognostic biomarkers in several diseases. Here we described a profile of miRNAs in plasma of diffuse large B cell lymphoma (DLBCL) patients. miRNA expression arrays were carried using pre-treatment plasma samples of sixteen patients, followed by a comparison between the responder and the non-responders. After six cycles of R–CHOP treatment, twelve out of sixteen patients were clinically diagnosed with complete response while in four patients no clinical response was observed. Between these groups, a signature of fifteen differential expressed miRNAs was found. The circulating miRNAs in plasma of patients with no response were related to the drug resistance in other types of cancer, by targeting genes involved in cell proliferation and apoptosis, among other cell processes.
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22
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Li J, Zou J, Wan X, Sun C, Peng F, Chu Z, Hu Y. The Role of Noncoding RNAs in B-Cell Lymphoma. Front Oncol 2020; 10:577890. [PMID: 33194698 PMCID: PMC7645065 DOI: 10.3389/fonc.2020.577890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/20/2020] [Indexed: 12/19/2022] Open
Abstract
In recent years, emerging evidence has suggested that noncoding RNAs (ncRNAs) participate in nearly every aspect of biological processes and play a crucial role in the genesis and progression of numerous tumors, including B-cell lymphoma. The exploration of ncRNA dysregulations and their functions in B-cell lymphoma provides new insights into lymphoma pathogenesis and is essential for indicating future clinical trials and optimizing the diagnostic and therapeutic strategies. In this review, we summarize the role of ncRNAs in B-cell lymphoma and discuss their potential in clinical applications.
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Affiliation(s)
- Jingwen Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Zou
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyue Wan
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunyan Sun
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Peng
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhangbo Chu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, China
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23
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Drees EEE, Pegtel DM. Circulating miRNAs as Biomarkers in Aggressive B Cell Lymphomas. Trends Cancer 2020; 6:910-923. [PMID: 32660885 DOI: 10.1016/j.trecan.2020.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 04/23/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023]
Abstract
B cell lymphomas are heterogeneous malignancies of hematological origin with vastly different biology and clinical outcomes. Histopathology of tissue biopsies and image-based assessment guide clinical decisions. Given that tissue biopsies cannot be frequently repeated and will not inform on systemic responses to the treatment, more accessible biomarkers, such as circulating miRNAs, are considered. Aberrant miRNA expression in lymphoma tissues and ongoing immune reactions may lead to miRNA alterations in circulation. miRNAs bound to extracellular vesicles (EVs) are of interest because of their role in intercellular communication and organ crosstalk. Herein, we highlight the role of miRNAs and EVs in B cell lymphomagenesis and explain how circulating miRNAs may be turned into robust liquid biopsy tests for aggressive B cell lymphoma.
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Affiliation(s)
- Esther E E Drees
- Amsterdam UMC, Vrije Universiteit Amsterdam, Exosomes Research Group, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - D Michiel Pegtel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Exosomes Research Group, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands.
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