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Toyoda H, Tani A, Goto-Koshino Y, Motegi T, Sakamoto M, Mochizuki T, Harada K, Kobayashi T, Setoguchi A, Shizuta Y, Mizuno T, Irie M, Nakamichi J, Tsujimoto H, Ohmi A, Fukuoka R, Nakamura Y, Tomiyasu H. Gene expression profiles associated with early relapse during first remission induction in canine multicentric high-grade B-cell lymphoma. J Vet Med Sci 2024; 86:18-27. [PMID: 37952972 PMCID: PMC10849849 DOI: 10.1292/jvms.23-0269] [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: 06/26/2023] [Accepted: 10/29/2023] [Indexed: 11/14/2023] Open
Abstract
Although chemotherapy using CHOP-based protocol induces remission in most cases of canine multicentric high-grade B-cell lymphoma (mhBCL), some cases develop early relapse during the first induction protocol. In this study, we examined the gene expression profiles of canine mhBCL before chemotherapy and investigated their associations with early relapse during the first whole CHOP-based protocol. Twenty-five cases of mhBCL treated with CHOP-based protocol as first induction chemotherapy were included in this study. Sixteen cases completed the first whole CHOP-based protocol without relapse (S-group), and nine developed relapse during the chemotherapy (R-group). RNA-seq was performed on samples from neoplastic lymph nodes. Differentially expressed genes (DEGs) were extracted by the comparison of gene expression profiles between S- and R-groups, and the differences in the expression levels of these genes were validated by RT-qPCR. Extracted 179 DEGs included the genes related to chemokine CC motif ligand, T-cell receptor signaling pathway, and PD-L1 expression and PD-1 checkpoint pathway. We focused on chemokine CC motif ligand, and CCL4 was confirmed to be significantly downregulated in the R-group (P=0.039). We also focused on the genes related to T-cell signaling pathway, and CD3E (P=0.039), ITK (P=0.023), and LAT (P=0.023) genes were confirmed to be significantly upregulated in the R-group. The current results suggest that both changes in tumor cells and the interactions between tumor cells and immune cells are associated with the efficacy of the chemotherapy for first remission induction.
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Affiliation(s)
- Hiroto Toyoda
- Department of Veterinary Internal Medicine, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Akiyoshi Tani
- Department of Veterinary Internal Medicine, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuko Goto-Koshino
- Veterinary Medical Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tomoki Motegi
- Boston University School of Medicine, Department of Medicine, Division of Computational Biomedicine, Boston, MA, USA
| | - Mika Sakamoto
- Genome Informatics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Takako Mochizuki
- Genome Informatics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Kei Harada
- Japan Small Animal Cancer Center, Saitama, Japan
| | | | | | | | - Takuya Mizuno
- Laboratory of Molecular Diagnostics and Therapeutics, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | | | - Jun Nakamichi
- Japan Animal Referral Medical Center, Kanagawa, Japan
| | | | - Aki Ohmi
- Veterinary Medical Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ray Fukuoka
- Veterinary Medical Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasukazu Nakamura
- Genome Informatics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Hirotaka Tomiyasu
- Department of Veterinary Internal Medicine, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Ribeiro ML, Sánchez Vinces S, Mondragon L, Roué G. Epigenetic targets in B- and T-cell lymphomas: latest developments. Ther Adv Hematol 2023; 14:20406207231173485. [PMID: 37273421 PMCID: PMC10236259 DOI: 10.1177/20406207231173485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 04/17/2023] [Indexed: 06/06/2023] Open
Abstract
Non-Hodgkin's lymphomas (NHLs) comprise a diverse group of diseases, either of mature B-cell or of T-cell derivation, characterized by heterogeneous molecular features and clinical manifestations. While most of the patients are responsive to standard chemotherapy, immunotherapy, radiation and/or stem cell transplantation, relapsed and/or refractory cases still have a dismal outcome. Deep sequencing analysis have pointed out that epigenetic dysregulations, including mutations in epigenetic enzymes, such as chromatin modifiers and DNA methyltransferases (DNMTs), are prevalent in both B- cell and T-cell lymphomas. Accordingly, over the past decade, a large number of epigenetic-modifying agents have been developed and introduced into the clinical management of these entities, and a few specific inhibitors have already been approved for clinical use. Here we summarize the main epigenetic alterations described in B- and T-NHL, that further supported the clinical development of a selected set of epidrugs in determined diseases, including inhibitors of DNMTs, histone deacetylases (HDACs), and extra-terminal domain proteins (bromodomain and extra-terminal motif; BETs). Finally, we highlight the most promising future directions of research in this area, explaining how bioinformatics approaches can help to identify new epigenetic targets in B- and T-cell lymphoid neoplasms.
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Affiliation(s)
- Marcelo Lima Ribeiro
- Lymphoma Translational Group, Josep Carreras
Leukaemia Research Institute, Badalona, Spain
- Laboratory of Immunopharmacology and Molecular
Biology, Sao Francisco University Medical School, Braganca Paulista,
Brazil
| | - Salvador Sánchez Vinces
- Laboratory of Immunopharmacology and Molecular
Biology, Sao Francisco University Medical School, Braganca Paulista,
Brazil
| | - Laura Mondragon
- T Cell Lymphoma Group, Josep Carreras Leukaemia
Research Institute, IJC. Ctra de Can Ruti, Camí de les Escoles s/n, 08916
Badalona, Barcelona, Spain
| | - Gael Roué
- Lymphoma Translational Group, Josep Carreras
Leukaemia Research Institute, IJC. Ctra de Can Ruti, Camí de les Escoles
s/n, 08916 Badalona, Barcelona, Spain
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Nguyen N, Jennen D, Kleinjans J. Omics technologies to understand drug toxicity mechanisms. Drug Discov Today 2022; 27:103348. [PMID: 36089240 DOI: 10.1016/j.drudis.2022.103348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/18/2022] [Accepted: 09/04/2022] [Indexed: 11/26/2022]
Abstract
Drug side effects are an important study subject in pharmacology. Recent omics technologies provide a range of omics data and help to understand the biological mechanisms involved in drug effects. These modern technologies provide significant support to all biological disciplines, including drug toxicology. In this review, we provide an overview the use of omics applications to understand drug side effects at the molecular level. We discuss by available omics technologies, their possible uses, as well as their advantages and limitations.
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Affiliation(s)
- Nhan Nguyen
- Department of Toxicogenomics, GROW School for Oncology and Reproduction, Maastricht University, Maastricht 6229ER, the Netherlands
| | - Danyel Jennen
- Department of Toxicogenomics, GROW School for Oncology and Reproduction, Maastricht University, Maastricht 6229ER, the Netherlands.
| | - Jos Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Reproduction, Maastricht University, Maastricht 6229ER, the Netherlands
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Insight into the potential candidate genes and signaling pathways involved in lymphoma disease in dogs using a comprehensive whole blood transcriptome analysis. Gene 2022; 838:146735. [PMID: 35835403 DOI: 10.1016/j.gene.2022.146735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/20/2022] [Accepted: 07/08/2022] [Indexed: 11/04/2022]
Abstract
Lymphoma is one of the most prevalent hematological cancers, accounting for 15-20 % of new cancer diagnoses in dogs. Therefore, this study aims to explore the important genes and pathways involved in canine lymphoma progression and understand the underlying molecular mechanisms using RNA sequencing. In this study, RNAs acquired from seven pairs of lymphoma and non-lymphoma blood samples were sequenced from different breeds of dogs. Sequencing reads were preprocessed, aligned with the reference genome, assembled and expressions were estimated through bioinformatics approaches. At a false discovery rate (FDR) < 0.05 and fold change (FC) ≥ 1.5, a total of 625 differentially expressed genes (DEGs) were identified between lymphoma and non-lymphoma samples, including 347 up-regulated DEGs such as SLC38A11, SCN3A, ZIC5 etc. and 278 down-regulated DEGs such as LOC475937, CSMD1, KRT14 etc. GO enrichment analysis showed that these DEGs were highly enriched for molecular function of ATP binding and calcium ion binding, cellular process of focal adhesion, and biological process of immune response, and defense response to virus. Similarly, KEGG pathways analysis revealed 11 significantly enriched pathways such as ECM-receptor interaction, cell cycle, PI3K-Akt signaling pathway, ABC transporters etc. In the protein-protein interaction (PPI) network, CDK1 was found to be a top hub gene with highest degree of connectivity. Three modules selected from the PPI network showed that canine lymphoma was highly associated with cell cycle, ECM-receptor interaction, hypertrophic cardiomyopathy, dilated cardiomyopathy and RIG-I-like receptor signaling pathway. Overall, our findings highlighted new candidate therapeutic targets for further testing in canine lymphoma and facilitate the understanding of molecular mechanism of lymphoma's progression in dogs.
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