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Zhang LM, Chen L, Zhao YF, Duan WM, Zhong LM, Liu MW. Identification of key potassium channel genes of temporal lobe epilepsy by bioinformatics analyses and experimental verification. Front Neurol 2023; 14:1175007. [PMID: 37483435 PMCID: PMC10361730 DOI: 10.3389/fneur.2023.1175007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/16/2023] [Indexed: 07/25/2023] Open
Abstract
One of the most prevalent types of epilepsy is temporal lobe epilepsy (TLE), which has unknown etiological factors and drug resistance. The detailed mechanisms underlying potassium channels in human TLE have not yet been elucidated. Hence, this study aimed to mine potassium channel genes linked to TLE using a bioinformatic approach. The results found that Four key TLE-related potassium channel genes (TERKPCGs) were identified: potassium voltage-gated channel subfamily E member (KCNA) 1, KCNA2, potassium inwardly rectifying channel, subfamily J, member 11 (KCNJ11), and KCNS1. A protein-protein interaction (PPI) network was constructed to analyze the relationship between TERKPCGs and other key module genes. The results of gene set enrichment analysis (GSEA) for a single gene indicated that the four TERKPCGs were highly linked to the cation channel, potassium channel, respiratory chain, and oxidative phosphorylation. The mRNA-TF network was established using four mRNAs and 113 predicted transcription factors. A ceRNA network containing seven miRNAs, two mRNAs, and 244 lncRNAs was constructed based on the TERKPCGs. Three common small-molecule drugs (enflurane, promethazine, and miconazole) target KCNA1, KCNA2, and KCNS1. Ten small-molecule drugs (glimepiride, diazoxide, levosimendan, and thiamylal et al.) were retrieved for KCNJ11. Compared to normal mice, the expression of KCNA1, KCNA2, KCNJ11, and KCNS1 was downregulated in the brain tissue of the epilepsy mouse model at both the transcriptional and translational levels, which was consistent with the trend of human data from the public database. The results indicated that key potassium channel genes linked to TLE were identified based on bioinformatics analysis to investigate the potential significance of potassium channel genes in the development and treatment of TLE.
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Affiliation(s)
- Lin-ming Zhang
- Department of Neurology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Provincial Clinical Research Center for Neurological Disease, Kunming, Yunnan, China
| | - Ling Chen
- Department of Neurology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Provincial Clinical Research Center for Neurological Disease, Kunming, Yunnan, China
| | - Yi-fei Zhao
- Department of Neurology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Provincial Clinical Research Center for Neurological Disease, Kunming, Yunnan, China
| | - Wei-mei Duan
- Department of Neurology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Provincial Clinical Research Center for Neurological Disease, Kunming, Yunnan, China
| | - Lian-mei Zhong
- Department of Neurology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Provincial Clinical Research Center for Neurological Disease, Kunming, Yunnan, China
| | - Ming-wei Liu
- Department of Emergency, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
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2
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Qian H, Qian Y, Liu Y, Cao J, Wang Y, Yang A, Zhao W, Lu Y, Liu H, Zhu W. Identification of novel biomarkers involved in doxorubicin-induced acute and chronic cardiotoxicity, respectively, by integrated bioinformatics. Front Cardiovasc Med 2023; 9:996809. [PMID: 36712272 PMCID: PMC9874088 DOI: 10.3389/fcvm.2022.996809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023] Open
Abstract
Background The mechanisms of doxorubicin (DOX) cardiotoxicity were complex and controversial, with various contradictions between experimental and clinical data. Understanding the differences in the molecular mechanism between DOX-induced acute and chronic cardiotoxicity may be an ideal entry point to solve this dilemma. Methods Mice were injected intraperitoneally with DOX [(20 mg/kg, once) or (5 mg/kg/week, three times)] to construct acute and chronic cardiotoxicity models, respectively. Survival record and ultrasound monitored the cardiac function. The corresponding left ventricular (LV) myocardium tissues were analyzed by RNA-seq to identify differentially expressed genes (DEGs). Gene Ontology (GO), Kyoto Encyclopedia of Gene and Genome (KEGG), and Gene Set Enrichment Analysis (GSEA) found the key biological processes and signaling pathways. DOX cardiotoxicity datasets from the Gene expression omnibus (GEO) database were combined with RNA-seq to identify the common genes. Cytoscape analyzed the hub genes, which were validated by quantitative real-time PCR. ImmuCo and ImmGen databases analyzed the correlations between hub genes and immunity-relative markers in immune cells. Cibersort analyzed the immune infiltration and correlations between the hub genes and the immune cells. Logistic regression, receiver operator characteristic curve, and artificial neural network analysis evaluated the diagnosis ability of hub genes for clinical data in the GEO dataset. Results The survival curves and ultrasound monitoring demonstrated that cardiotoxicity models were constructed successfully. In the acute model, 788 DEGs were enriched in the activated metabolism and the suppressed immunity-associated signaling pathways. Three hub genes (Alas1, Atp5g1, and Ptgds) were upregulated and were negatively correlated with a colony of immune-activating cells. However, in the chronic model, 281 DEGs showed that G protein-coupled receptor (GPCR)-related signaling pathways were the critical events. Three hub genes (Hsph1, Abcb1a, and Vegfa) were increased in the chronic model. Furthermore, Hsph1 combined with Vegfa was positively correlated with dilated cardiomyopathy (DCM)-induced heart failure (HF) and had high accuracy in the diagnosis of DCM-induced HF (AUC = 0.898, P = 0.000). Conclusion Alas1, Atp5g1, and Ptgds were ideal biomarkers in DOX acute cardiotoxicity. However, Hsph1 and Vegfa were potential biomarkers in the myocardium in the chronic model. Our research, first, provided bioinformatics and clinical evidence for the discovery of the differences in mechanism and potential biomarkers of DOX-induced acute and chronic cardiotoxicity to find a therapeutic strategy precisely.
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Affiliation(s)
- Hongyan Qian
- Department of Pharmacology, School of Medicine and School of Pharmacy Nantong University, Nantong, China,Cancer Research Center Nantong, Nantong Tumor Hospital and Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Yi Qian
- Department of Pharmacology, School of Medicine and School of Pharmacy Nantong University, Nantong, China
| | - Yi Liu
- Department of Pharmacology, School of Medicine and School of Pharmacy Nantong University, Nantong, China
| | - Jiaxin Cao
- Department of Pharmacology, School of Medicine and School of Pharmacy Nantong University, Nantong, China
| | - Yuhang Wang
- Department of Pharmacology, School of Medicine and School of Pharmacy Nantong University, Nantong, China
| | - Aihua Yang
- Department of Pharmacology, School of Medicine and School of Pharmacy Nantong University, Nantong, China
| | - Wenjing Zhao
- Department of Pharmacology, School of Medicine and School of Pharmacy Nantong University, Nantong, China
| | - Yingnan Lu
- School of Overseas Education, Changzhou University, Changzhou, China
| | - Huanxin Liu
- Shanghai Labway Medical Laboratory, Shanghai, China
| | - Weizhong Zhu
- Department of Pharmacology, School of Medicine and School of Pharmacy Nantong University, Nantong, China,*Correspondence: Weizhong Zhu, ; orcid.org/0000-0002-8740-3210
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3
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Xie T, Feng W, He M, Zhan X, Liao S, He J, Qin Z, Li F, Xu J, Liu Y, Wei Q. Analysis of scRNA-seq and bulk RNA-seq demonstrates the effects of EVI2B or CD361 on CD8 + T cells in osteosarcoma. Exp Biol Med (Maywood) 2023; 248:130-145. [PMID: 36511103 PMCID: PMC10041056 DOI: 10.1177/15353702221142607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Osteosarcoma (OS) is a common primary malignant tumor of the bone in children and adolescents. The five-year survival rate is estimated to be ~70% based on the currently available treatment modalities. It is well known that tumor-infiltrating immune cells (TIICs) that are the most important components in the tumor microenvironment can exert a killing effect on tumor cells. Therefore, in the present study, 85 RNA-sequencing OS samples were categorized into high- and low-immune score groups with ESTIAMATE. Based on the immune score groups, 474 differentially expressed genes (DEGs) were acquired using the LIMMA package of R language. Subsequently, 86 DEGs were taken through univariate COX regression analysis, of which 14 were screened out by least absolute shrinkage and selection operator regression analysis. Furthermore, multivariate COX regression analysis was performed to obtain 4 DEGs. Finally, ecotropic virus integration site 2B (EVI2B) or CD361 gene was screened out via Kaplan-Meier analysis. In addition, CIBERSORT algorithm was used to evaluate the proportion of 22 kinds of TIICs in OS. Correlation analysis revealed that the high expression level of EVI2B can elevate the infiltrated proportion of CD8+ T cells. Moreover, analysis of single cell RNA-sequencing transcriptome datasets and immunohistochemical staining uncovered that EVI2B was mainly expressed on CD8+ T cells and that EVI2B could promote the expression of granzyme A and K of CD8+ T cells to exhibit a potent killing effect on tumor cells. Therefore, EVI2B was identified as a protective immune-related gene and contributed to good prognosis in OS patients.
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Affiliation(s)
- Tianyu Xie
- Department of Traumatic Orthopaedic, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Wenyu Feng
- Department of Orthopaedic, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530005, China
| | - Mingwei He
- Department of Traumatic Orthopaedic, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Xinli Zhan
- Department of Spine and Bone Diseases, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Shijie Liao
- Department of Traumatic Orthopaedic, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Juliang He
- Department of Bone and Soft Tissue, Affiliated Tumour Hospital of Guangxi Medical University, Nanning 530021, China
| | - Zhaojie Qin
- Department of Spine and Bone Diseases, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Feicui Li
- Department of Spine and Bone Diseases, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Jiake Xu
- School of Biomedical Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Yun Liu
- Department of Spine and Bone Diseases, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Qingjun Wei
- Department of Traumatic Orthopaedic, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
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4
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Bheemareddy BR, Reddy PN, Vemparala K, Dirisala VR. Enhancement of effector functions of anti-CD20 monoclonal antibody by increased afucosylation in CHO cell line through cell culture medium optimization. J Genet Eng Biotechnol 2022; 20:141. [PMID: 36194313 PMCID: PMC9532503 DOI: 10.1186/s43141-022-00421-5] [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: 04/19/2022] [Accepted: 09/23/2022] [Indexed: 11/12/2022]
Abstract
Background Recombinant therapeutic anti-CD20 monoclonal antibody (mAb) is used for the treatment of non-Hodgkin’s lymphoma, a common B cell lymphoma constituting 80% of all lymphomas. Anti-CD20 mAb contains an Fc-linked biantennary glycan. Although, anti-CD20 monoclonal antibodies are being increasingly used for immunotherapy, their efficacy is limited in a section of patients with drug resistance to immunotherapy. There is a need to improve the efficacy by increasing the effector functions, such as the antibody-dependent cellular cytotoxicity (ADCC) activity of anti-CD20 monoclonal antibodies. Results We developed a simple and cost-effective approach to enhance ADCC effector activity in an in-house developed clone of anti-CD20 monoclonal antibody by increasing afucosylation in a new clone of Chinese Hamster Ovary (CHO) cells using 8X uridine, manganese, and galactose (UMG) to modulate the osmolality of the medium. The purified anti-CD20 monoclonal antibody from 8X UMG-containing medium showed a 2-fold increase in afucose content and 203% ADCC activity in comparison to control antibody. Conclusions Our study reports enhanced ADCC activity by modulating afucosylation using osmolality by altering simple feed additives in the culture medium. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00421-5.
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Affiliation(s)
- Bala Reddy Bheemareddy
- R&D Division, Hetero Biopharma Limited, Jadcherla, Mahbubnagar, Telangana, 509301, India
| | - Prakash Narayana Reddy
- Microbiology Department, Dr. V.S. Krishna Government Degree College (Autonomous), Visakhapatnam, Andhra Pradesh, 530013, India
| | - Kranthi Vemparala
- R&D Division, Hetero Biopharma Limited, Jadcherla, Mahbubnagar, Telangana, 509301, India
| | - Vijaya R Dirisala
- Department of Biotechnology, Vignan's Foundation for Science, Technology and Research (Deemed to be University), Guntur, Andhra Pradesh, 522213, India.
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5
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Mu D, Long S, Guo L, Liu W. High Expression of VAV Gene Family Predicts Poor Prognosis of Acute Myeloid Leukemia. Technol Cancer Res Treat 2021; 20:15330338211065877. [PMID: 34894858 PMCID: PMC8679409 DOI: 10.1177/15330338211065877] [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] [Indexed: 12/05/2022] Open
Abstract
Objectives: VAV family genes (VAV1, VAV2, and
VAV3) are associated with prognosis in various cancers;
however, they have not been evaluated in acute myeloid leukemia (AML). In this
study, the prognostic value of VAV expression in AML was evaluated by a
single-center study in combination with bioinformatics analyses.
Methods: The expression and prognostic value of VAVs in
patients with AML were investigated using various databases, including GEPIA,
CCLE, EMBL-EBI, UALCAN, cBioPortal, STRING, and DAVID. Blood samples from 35
patients with AML (non-M3 subtype) and 13 benigh individuals were collected at
our center. VAV expression levels were detected by real-time quantitative PCR
(RT-qPCR) and western blotting. Clinical data were derived from medical records.
Results: Based on data from multiple databases, the expression
levels of VAV1, VAV2, and VAV3 were significantly higher in AML than in control
tissues (P < 0.05). RT-qPCR and western blotting results
showed that VAV expression in mRNA and protein levels were
higher in patients with AML that in the control group (P <
0.05). Complete remission rates were lower and risks were higher in patients
with AML with high VAV1 expression than with low
VAV1 expression (P < 0.05). High levels
of VAV2, VAV3, and VAV1 were related to a poor overall survival, and this
relationship was significant for VAV1 (P < 0.05). High
expression levels of genes correlated with VAV1, such as
SIPA1, SH2D3C, and HMHA1
were also related to a poor prognosis in AML. Functional and pathways enrichment
analyses indicated that the contribution of the VAV family to AML may be
mediated by the NF-κB, cAMP, and other pathways. Conclusion: VAVs
were highly expressed in AML. In particular, VAV1 has prognostic value and is a
promising therapeutic target for AML.
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Affiliation(s)
- Dan Mu
- 556508Department of Pediatrics Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China.,556508Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Sili Long
- 556508Department of Pediatrics Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China.,556508Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China.,Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, 646000, China
| | - Ling Guo
- 556508Department of Pediatrics Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China.,556508Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China.,Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, 646000, China
| | - Wenjun Liu
- 556508Department of Pediatrics Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China.,556508Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China.,Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, 646000, China
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6
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Piris MA. SPARC macrophages in lymphoma. Ann Oncol 2021; 32:1314-1315. [PMID: 34492312 DOI: 10.1016/j.annonc.2021.08.2152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022] Open
Affiliation(s)
- M A Piris
- Pathology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Madrid, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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7
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Sun J, Zhu X, Zhao Y, Zhou Q, Qi R, Liu H. CHN1 is a Novel Prognostic Marker for Diffuse Large B-Cell Lymphoma. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:397-408. [PMID: 33833551 PMCID: PMC8021264 DOI: 10.2147/pgpm.s301718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/15/2021] [Indexed: 12/14/2022]
Abstract
Purpose Diffuse large B-cell lymphoma (DLBCL) is the most common B-cell malignancy. Thirty to forty percent of DLBCL patients still experience relapse or develop refractory disease even with standard immunochemotherapy, leading to a poor prognosis. Currently, although several gene-based classification methods can be used to predict the prognosis of DLBCL, some patients are still unable to be classified. This study was performed to identify a novel prognostic biomarker for DLBCL. Patients and Methods A total of 1850 B-cell non-Hodgkin lymphoma (B-NHL) patients in 8 independent datasets with microarray gene expression profiles were retrieved from the Gene Expression Omnibus (GEO) database and Lymphoma/Leukemia Molecular Profiling Project (LLMPP). The candidate genes were selected through three filters in a strict pipeline. Survival analysis was performed in two independent datasets of patients with both gene expression data and clinical information. Gene set enrichment analysis (GSEA) and the CIBERSORT algorithm were used to explore the biological functions of the genes. Results We identified 6 candidate genes associated with the clinical outcome of DLBCL patients: CHN1, CD3D, CLU, ICOS, KLRB1 and LAT. Unlike the other five genes, CHN1 has not been previously reported to be implicated in lymphoma. We also observed that CHN1 had prognostic significance in important clinical subgroups; in particular, high CHN1 expression was significantly related to good outcomes in DLBCL patients with the germinal center B-cell-like (GCB) subtype, stage III–IV, or an International Prognostic Index (IPI) score > 2. Multivariate Cox regression analysis of the two datasets showed that CHN1 was an independent prognostic factor for DLBCL. Additionally, GSEA and CIBERSORT indicated that CHN1 was correlated with cell adhesion and T cell immune infiltration. Conclusion Our data indicate for the first time that high CHN1 expression is associated with favorable outcomes in DLBCL patients, suggesting its potential utility as a prognostic marker in DLBCL.
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Affiliation(s)
- Jie Sun
- Department of Hematology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Xiaoquan Zhu
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Yanyang Zhao
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Qi Zhou
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Ruomei Qi
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Hui Liu
- Department of Hematology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
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8
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Raboso-Gallego J, Casado-García A, Jiang X, Isidro-Hernández M, Gentles AJ, Zhao S, Natkunam Y, Blanco O, Domínguez V, Pintado B, Alonso-López D, De Las Rivas J, Vicente-Dueñas C, Lossos IS, Sanchez-Garcia I. Conditional expression of HGAL leads to the development of diffuse large B-cell lymphoma in mice. Blood 2021; 137:1741-1753. [PMID: 33024996 PMCID: PMC8020264 DOI: 10.1182/blood.2020004996] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 09/22/2020] [Indexed: 12/23/2022] Open
Abstract
Diffuse large B-cell lymphomas (DLBCLs) are clinically and genetically heterogeneous tumors. Deregulation of diverse biological processes specific to B cells, such as B-cell receptor (BCR) signaling and motility regulation, contribute to lymphomagenesis. Human germinal center associated lymphoma (HGAL) is a B-cell-specific adaptor protein controlling BCR signaling and B lymphocyte motility. In normal B cells, it is expressed in germinal center (GC) B lymphocytes and promptly downregulated upon further differentiation. The majority of DLBCL tumors, primarily GC B-cell types, but also activated types, express HGAL. To investigate the consequences of constitutive expression of HGAL in vivo, we generated mice that conditionally express human HGAL at different stages of hematopoietic development using 3 restricted Cre-mediated approaches to initiate expression of HGAL in hematopoietic stem cells, pro-B cells, or GC B cells. Following immune stimulation, we observed larger GCs in mice in which HGAL expression was initiated in GC B cells. All 3 mouse strains developed DLBCL at a frequency of 12% to 30% starting at age 13 months, leading to shorter survival. Immunohistochemical studies showed that all analyzed tumors were of the GC B-cell type. Exon sequencing revealed mutations reported in human DLBCL. Our data demonstrate that constitutive enforced expression of HGAL leads to DLBCL development.
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Affiliation(s)
- Javier Raboso-Gallego
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, Centro Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca (USAL), Salamanca, Spain
- Institute for Biomedical Research of Salamanca, Salamanca, Spain
| | - Ana Casado-García
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, Centro Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca (USAL), Salamanca, Spain
- Institute for Biomedical Research of Salamanca, Salamanca, Spain
| | - Xiaoyu Jiang
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL
| | - Marta Isidro-Hernández
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, Centro Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca (USAL), Salamanca, Spain
- Institute for Biomedical Research of Salamanca, Salamanca, Spain
| | - Andrew J Gentles
- Department of Medicine
- Department of Biomedical Data Science, and
| | - Shuchun Zhao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Yaso Natkunam
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Oscar Blanco
- Institute for Biomedical Research of Salamanca, Salamanca, Spain
- Departamento de Anatomía Patológica, USAL, Salamanca, Spain
| | - Verónica Domínguez
- Transgenesis Facility Centro Nacional de Biotecnología-Centro de Biología Molecular Severo Ochoa (CNB-CBMSO), Consejo Superior de Investigaciones Cientificas-Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
| | - Belén Pintado
- Transgenesis Facility Centro Nacional de Biotecnología-Centro de Biología Molecular Severo Ochoa (CNB-CBMSO), Consejo Superior de Investigaciones Cientificas-Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
| | | | - Javier De Las Rivas
- Institute for Biomedical Research of Salamanca, Salamanca, Spain
- Bioinformatics and Functional Genomics Research Group, Cancer Research Center, CSIC-USAL, Salamanca, Spain; and
| | | | - Izidore S Lossos
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL
| | - Isidro Sanchez-Garcia
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, Centro Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca (USAL), Salamanca, Spain
- Institute for Biomedical Research of Salamanca, Salamanca, Spain
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9
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Baumgarten N, Schmidt F, Wegner M, Hebel M, Kaulich M, Schulz MH. Computational prediction of CRISPR-impaired non-coding regulatory regions. Biol Chem 2021; 402:973-982. [PMID: 33660495 DOI: 10.1515/hsz-2020-0392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/18/2021] [Indexed: 12/14/2022]
Abstract
Genome-wide CRISPR screens are becoming more widespread and allow the simultaneous interrogation of thousands of genomic regions. Although recent progress has been made in the analysis of CRISPR screens, it is still an open problem how to interpret CRISPR mutations in non-coding regions of the genome. Most of the tools concentrate on the interpretation of mutations introduced in gene coding regions. We introduce a computational pipeline that uses epigenomic information about regulatory elements for the interpretation of CRISPR mutations in non-coding regions. We illustrate our analysis protocol on the analysis of a genome-wide CRISPR screen in hTERT-RPE1 cells and reveal novel regulatory elements that mediate chemoresistance against doxorubicin in these cells. We infer links to established and to novel chemoresistance genes. Our analysis protocol is general and can be applied on any cell type and with different CRISPR enzymes.
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Affiliation(s)
- Nina Baumgarten
- Institute for Cardiovascular Regeneration, Goethe University, 60590Frankfurt am Main, Germany.,German Center for Cardiovascular Research, Partner site Rhein-Main, 60590Frankfurt am Main, Germany.,Cluster of Excellence MMCI, Saarland University, and Max Planck Institute for Informatics, Saarland Informatics Campus, 66123Saarbrücken, Germany.,Cardiopulmonary Institute (CPI), Goethe University, 60590 Frankfurt am Main, Germany
| | - Florian Schmidt
- Institute for Cardiovascular Regeneration, Goethe University, 60590Frankfurt am Main, Germany.,German Center for Cardiovascular Research, Partner site Rhein-Main, 60590Frankfurt am Main, Germany.,Cluster of Excellence MMCI, Saarland University, and Max Planck Institute for Informatics, Saarland Informatics Campus, 66123Saarbrücken, Germany.,Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore, Singapore
| | - Martin Wegner
- Institute of Biochemistry II, Goethe University - Medical Faculty, University Hospital, 60590Frankfurt am Main, Germany.,Frankfurt Cancer Institute, Goethe University, 60590Frankfurt am Main, Germany
| | - Marie Hebel
- Institute of Biochemistry II, Goethe University - Medical Faculty, University Hospital, 60590Frankfurt am Main, Germany.,Frankfurt Cancer Institute, Goethe University, 60590Frankfurt am Main, Germany
| | - Manuel Kaulich
- Institute of Biochemistry II, Goethe University - Medical Faculty, University Hospital, 60590Frankfurt am Main, Germany.,Frankfurt Cancer Institute, Goethe University, 60590Frankfurt am Main, Germany
| | - Marcel H Schulz
- Institute for Cardiovascular Regeneration, Goethe University, 60590Frankfurt am Main, Germany.,German Center for Cardiovascular Research, Partner site Rhein-Main, 60590Frankfurt am Main, Germany.,Cluster of Excellence MMCI, Saarland University, and Max Planck Institute for Informatics, Saarland Informatics Campus, 66123Saarbrücken, Germany.,Cardiopulmonary Institute (CPI), Goethe University, 60590 Frankfurt am Main, Germany
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