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Kowalski TW, Feira MF, Lord VO, Gomes JDA, Giudicelli GC, Fraga LR, Sanseverino MTV, Recamonde-Mendoza M, Schuler-Faccini L, Vianna FSL. A New Strategy for the Old Challenge of Thalidomide: Systems Biology Prioritization of Potential Immunomodulatory Drug (IMiD)-Targeted Transcription Factors. Int J Mol Sci 2023; 24:11515. [PMID: 37511270 PMCID: PMC10380514 DOI: 10.3390/ijms241411515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Several molecular mechanisms of thalidomide embryopathy (TE) have been investigated, from anti-angiogenesis to oxidative stress to cereblon binding. Recently, it was discovered that thalidomide and its analogs, named immunomodulatory drugs (IMiDs), induced the degradation of C2H2 transcription factors (TFs). This mechanism might impact the strict transcriptional regulation of the developing embryo. Hence, this study aims to evaluate the TFs altered by IMiDs, prioritizing the ones associated with embryogenesis through transcriptome and systems biology-allied analyses. This study comprises only the experimental data accessed through bioinformatics databases. First, proteins and genes reported in the literature as altered/affected by the IMiDs were annotated. A protein systems biology network was evaluated. TFs beta-catenin (CTNNB1) and SP1 play more central roles: beta-catenin is an essential protein in the network, while SP1 is a putative C2H2 candidate for IMiD-induced degradation. Separately, the differential expressions of the annotated genes were analyzed through 23 publicly available transcriptomes, presenting 8624 differentially expressed genes (2947 in two or more datasets). Seventeen C2H2 TFs were identified as related to embryonic development but not studied for IMiD exposure; these TFs are potential IMiDs degradation neosubstrates. This is the first study to suggest an integration of IMiD molecular mechanisms through C2H2 TF degradation.
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Affiliation(s)
- Thayne Woycinck Kowalski
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Biomedical Sciences Course, Centro Universitário CESUCA, Cachoeirinha 94935-630, Brazil
| | - Mariléa Furtado Feira
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Vinícius Oliveira Lord
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Biomedical Sciences Course, Centro Universitário CESUCA, Cachoeirinha 94935-630, Brazil
| | - Julia do Amaral Gomes
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Giovanna Câmara Giudicelli
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Lucas Rosa Fraga
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Post-Graduation Program in Medicine, Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-003, Brazil
- Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90010-150, Brazil
| | - Maria Teresa Vieira Sanseverino
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, Brazil
| | - Mariana Recamonde-Mendoza
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Post-Graduation Program in Computer Science, Institute of Informatics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
| | - Lavinia Schuler-Faccini
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Fernanda Sales Luiz Vianna
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Post-Graduation Program in Medicine, Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-003, Brazil
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Huang Q, Wang CC, Liu YG, Zhao CM, Zhang TP, Liu Y, Wang H. Clinical relevance of genetic polymorphisms in WNT signaling pathway ( SFRP1, WNT3A, CTNNB1, WIF-1, DKK-1, LRP5, LRP6) on pulmonary tuberculosis in a Chinese population. Front Immunol 2022; 13:1011700. [PMID: 36569862 PMCID: PMC9768481 DOI: 10.3389/fimmu.2022.1011700] [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: 08/04/2022] [Accepted: 10/21/2022] [Indexed: 12/13/2022] Open
Abstract
The present study was performed to evaluate the association of WNT signaling pathway genes variants with pulmonary tuberculosis (PTB) risk in Chinese Han population. Our study subjects were composed of 452 PTB patients and 465 normal controls, and seventeen SNPs of seven genes in WNT signaling pathway (SFRP1, WNT3A, CTNNB1, WIF-1, DKK-1, LRP5, LRP6) were genotyped by SNPscan technique. We found no significant relationship of SFRP1 rs10088390, rs4736958, rs3242, WNT3A rs752107, rs3121310, CTNNB1 rs2293303, rs1798802, rs4135385, WIF-1 rs1026024, rs3782499, DKK-1 rs2241529, rs1569198, LRP5 rs3736228, rs556442, LRP6 rs2302685, rs11054697, rs10743980 polymorphisms with PTB susceptibility. While, WIF-1 rs3782499 variant was associated with susceptibility to PTB under recessive model, and haplotype analysis showed that DKK-1 GA haplotype frequency was significantly increased in PTB patients. The WNT3A rs3121310, CTNNB1 rs2293303 polymorphisms were respectively associated with drug-induced liver injury (DILI), sputum smear-positive in PTB patients. The rs3782499 in WIF-1 gene was related to fever, leukopenia, and the rs1569198 in DKK-1 was linked to sputum smear-positive in PTB patients. In LRP5 gene, rs3736228, rs556442 variants respectively affected the occurrence of DILI, fever, and LRP6 gene rs2302685, rs10743980 variants respectively influenced the development of hypoproteinemia, sputum smear-positive in PTB patients. Our results revealed that WNT signaling pathway genes variation were not associated with the susceptibility to PTB, while WNT3A, CTNNB1, WIF-1, DKK-1, LRP5, LRP6 genetic variations might be closely related to the occurrence of several clinical characteristics of PTB patients.
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Affiliation(s)
- Qian Huang
- Department of Public Health, Medical College of Qinghai University, Xining, China
| | - Chao-Cai Wang
- Department of Infection Disease, Qinghai Center for Disease Prevention and Control, Xining, China
| | - Yun-Guang Liu
- Department of Public Health, Medical College of Qinghai University, Xining, China
| | - Chang-Ming Zhao
- Department of Public Health, Medical College of Qinghai University, Xining, China
| | - Tian-Ping Zhang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yan Liu
- Department of Public Health, Medical College of Qinghai University, Xining, China,*Correspondence: Yan Liu, ; Hua Wang,
| | - Hua Wang
- Department of Tuberculosis, Anhui Chest Hospital, Hefei, Anhui, China,*Correspondence: Yan Liu, ; Hua Wang,
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Zuo X, Liu D. Mechanism of immunomodulatory drug resistance and novel therapeutic strategies in multiple myeloma. HEMATOLOGY (AMSTERDAM, NETHERLANDS) 2022; 27:1110-1121. [PMID: 36121114 DOI: 10.1080/16078454.2022.2124694] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The mechanism of immunomodulatory drugs (IMiDs) resistance to multiple myeloma (MM) cells has been gradually demonstrated by recently studies, and some potential novel strategies have been confirmed to have antimyeloma activity and be associated with IMiD activity in MM. METHODS This article searched the Pubmed library, reviewed some recently studies related to IMiD resistance to MM cells and summarized some potent agents to improve IMiD resistance to MM cells. RESULTS Studies have confirmed that cereblon is a primary direct protein target of IMiDs. IRF4 not only is affected by the IKZF protein but also can directly inhibit the expression of BMF and BIM, thereby promoting the survival of MM cells. Additionally, the expression of IRF4 and MYC also plays an important role in three important signaling pathways (Wnt, STAT3 and MAPK/ERK) related to IMiD resistance. Notably, MYC, a downstream factor of IRF4, may be upregulated by BRD4, and upregulation of MYC promotes cell proliferation in MM and disease progression. Recently, some novel therapeutic agents targeting BRD4, a histone modification-related 'reader' of epigenetic marks, or other important factors (e.g. TAK1) in relevant signaling pathways have been developed and they may provide new options for relapse/refractory MM therapy, such as BET inhibitors, CBP/EP300 inhibitors, dual-target BET-CBP/EP300 inhibitors, TAK1 inhibitors, and they may provide new options for relapsed/refractory MM therapy. CONCLUSIONS Accumulated studies have revealed that some key factors associated with the mechanism of IMiD resistance to MM cells. Some agents represent promising new therapeutics of MM to regulate the IRF4/MYC axis by inhibiting BRD4 expression or signaling pathway activation.
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Affiliation(s)
- Xiaojia Zuo
- Department of Hematology, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai, People's Republic of China.,Department of Oncology and Hematology, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, People's Republic of China.,Guizhou Medical University, Guiyang, People's Republic of China
| | - Dingsheng Liu
- Department of Hematology, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai, People's Republic of China
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4
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Costa PDSS, Maciel-Fiuza MF, Kowalski TW, Fraga LR, Feira MF, Camargo LMA, Caldoncelli DIDO, Silveira MIDS, Schuler-Faccini L, Vianna FSL. Evaluation of the influence of genetic variants in Cereblon gene on the response to the treatment of erythema nodosum leprosum with thalidomide. Mem Inst Oswaldo Cruz 2022; 117:e220039. [DOI: 10.1590/0074-02760220039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Perpétua do Socorro Silva Costa
- Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Genética Médica Populacional, Brasil; Universidade Federal do Maranhão, Brazil
| | - Miriãn Ferrão Maciel-Fiuza
- Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Genética Médica Populacional, Brasil; Hospital de Clínicas de Porto Alegre, Brasil; Universidade Federal do Rio Grande do Sul, Brazil
| | - Thayne Woycinck Kowalski
- Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Genética Médica Populacional, Brasil; Hospital de Clínicas de Porto Alegre, Brasil; Universidade Federal do Rio Grande do Sul, Brazil; Hospital de Clínicas de Porto Alegre, Brasil
| | - Lucas Rosa Fraga
- Hospital de Clínicas de Porto Alegre, Brasil; Universidade Federal do Rio Grande do Sul, Brazil; Hospital de Clínicas de Porto Alegre, Brasil; Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil
| | - Mariléa Furtado Feira
- Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Genética Médica Populacional, Brasil; Hospital de Clínicas de Porto Alegre, Brasil; Universidade Federal do Rio Grande do Sul, Brazil
| | - Luís Marcelo Aranha Camargo
- Universidade de São Paulo, Brazil; Centro de Pesquisa em Medicina Tropical, Brasil; Instituto Nacional de Ciência e Tecnologia de Epidemiologia da Amazônia Ocidental, Brasil; Centro Universitário São Lucas, Brazil
| | | | | | - Lavínia Schuler-Faccini
- Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Genética Médica Populacional, Brasil; Hospital de Clínicas de Porto Alegre, Brasil
| | - Fernanda Sales Luiz Vianna
- Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Genética Médica Populacional, Brasil; Hospital de Clínicas de Porto Alegre, Brasil; Universidade Federal do Rio Grande do Sul, Brazil; Hospital de Clínicas de Porto Alegre, Brasil; Universidade Federal do Rio Grande do Sul, Brazil
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5
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Vohra M, Sharma AR, Satyamoorthy K, Rai PS. Pharmacogenomic considerations for repurposing of dexamethasone as a potential drug against SARS-CoV-2 infection. Per Med 2021; 18:389-398. [PMID: 34086487 PMCID: PMC8186476 DOI: 10.2217/pme-2020-0183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/27/2021] [Indexed: 12/15/2022]
Abstract
Immunomodulatory and analgesic effects of dexamethasone are clinically well established, and this synthetic corticosteroid acts as an agonist of glucocorticoid receptors. Early results of the RECOVERY Trial from the United Kingdom and others suggest certain benefits of dexamethasone against COVID-19 chronic patients. The efforts have been acknowledged by World Health Organization with an interim guideline to use in patients with a severe and critical illness. The inherent genetic variations in genes such as CYP3A5, NR3C1, NR3C2, etc., involved in the pharmacokinetic and pharmacodynamic processes may influence dexamethasone's effects as an anti-inflammatory drug. Besides, the drug may influence transcriptome or metabolic changes in the individuals. In the present review, we summarize the reported genetic variations that impact dexamethasone response and discuss dexamethasone-induced changes in transcriptome and metabolome that may influence potential treatment outcome against COVID-19.
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Affiliation(s)
- Manik Vohra
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Anu Radha Sharma
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Kapaettu Satyamoorthy
- Department of Cell & Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Padmalatha S Rai
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
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6
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Zhao XY, Hu SY, Yang JL, Chen XM, Huang XL, Tang LJ, Gu L, Su L. A 3' Untranslated Region Polymorphism of CTNNB1 (Rs2953) Alters MiR-3161 Binding and Affects the Risk of Ischemic Stroke and Coronary Artery Disease in Chinese Han Population. Eur Neurol 2021; 84:85-95. [PMID: 33789307 DOI: 10.1159/000514543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 12/31/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND CTNNB1 is reported to be related to the pathological process of ischemic stroke (IS) and coronary artery disease (CAD). Polymorphism located in the 3' untranslated region (3'UTR) of a gene might affect gene expression by modifying binding sites for microRNAs (miRNAs). This study aimed to analyze the association between polymorphism rs2953, which locates in the 3'UTR of CTNNB1, and the risk of IS and CAD. METHODS The CTNNB1 messenger RNA (mRNA) expression level in peripheral venous blood was measured. In total, 533 patients with IS, 500 patients with CAD, and 531 healthy individuals were genotyped by Sequenom Mass-Array technology. The binding of miR-3161 to CTNNB1 was determined by dual-luciferase reporter assay. RESULTS The CTNNB1 mRNA expression level for the IS group was significantly lower than that for the control group. Rs2953 was significantly associated with both IS risk and CAD risk. Significant association was also found between polymorphism rs2953 and many conventional factors, such as serum lipid level, blood coagulation markers, blood glucose level, and homocysteine level in patients. Rs2953 T allele introduced a binding site to miRNA-3161 and thus decreased luciferase activity. CONCLUSION Polymorphism rs2953 is associated with the risk of both IS and CAD. Moreover, polymorphism rs2953 (T) introduces a binding site to miRNA-3161 and thus decreases luciferase activity in cell lines.
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Affiliation(s)
- Xin-Yi Zhao
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China
| | - Shu-Yan Hu
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China
| | - Jia-Lei Yang
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Xing-Mei Chen
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China
| | - Xian-Li Huang
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China
| | - Lue-Jun Tang
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China
| | - Lian Gu
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China
| | - Li Su
- School of Public Health, Guangxi Medical University, Nanning, China.,Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Nanning, China
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7
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Pál I, Szilágyi B, Nagy B, Pál T, Hodosi K, Illés Á, Váróczy L. The Impact of Beta-Catenin and glutathione-S-transferase Gene Polymorphisms on the Treatment Results and Survival of Multiple Myeloma Patients. Pathol Oncol Res 2020; 26:1633-1638. [PMID: 31506802 PMCID: PMC7297842 DOI: 10.1007/s12253-019-00747-5] [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: 04/12/2019] [Accepted: 09/03/2019] [Indexed: 11/09/2022]
Abstract
Multiple myeloma (MM) is an incurable disease, however, novel therapeutic agents has significantly improved its prognosis. In this study we analyzed if polymorphisms in the genes of β-catenin and glutathione-S-transferase have affected the clinical course, treatment response and progression-free survival (PFS) of MM patients. Ninety-seven MM patients were involved who were administered immunomodulatory drug (Imid) or alkylating agent-based therapy. β-catenin (CTNNB1, rs4135385 A > G, rs4533622 A > C) and glutathione-S-transferase (GSTP1 105, GSTP1 114) gene polymorphisms were analyzed by Light SNiP assays. The distribution of CTNNB1 (rs4135385) AA, AG and GG genotypes were 48.4%, 47.4% and 4,1%, respectively. Patients with AA genotype were older than those who carried G allele (64.5 vs. 61.0 years of age, p < 0.05). Response to Imid-based therapies (p < 0.05) and PFS (p = 0.032) were significantly more favourable in the AA homozygous group. The other polymorphism (rs4533622) of β-catenin gene did not markedly influence these clinical parameters, although MM was diagnosed at significantly younger age in subjects with CC genotype compared to AG/AA combined genotypes (59.1 vs. 65.7 years, p = 0.015). When GSTP1 polymorphisms were investigated, no such significant associations were observed. Our results demonstrate that the polymorphism of β-catenin gene (rs4135385) may be an independent predictive factor in MM.
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8
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Iskierka-Jażdżewska E, Canzian F, Stępień A, Martino A, Campa D, Stein A, Krawczyk-Kuliś M, Rybicka-Ramos M, Kyrcz-Krzemień S, Butrym A, Mazur G, Jurczyszyn A, Zawirska D, Grząśko N, Tomczak W, Subocz E, Wątek M, Pasiarski M, Rymko M, Całbecka M, Druzd-Sitek A, Walewski J, Kruszewski M, Raźny M, Zaucha JM, Dudziński M, Gaj P, Robak T, Warzocha K, Jamroziak K. Cereblon ( CRBN) gene polymorphisms predict clinical response and progression-free survival in relapsed/refractory multiple myeloma patients treated with lenalidomide: a pharmacogenetic study from the IMMEnSE consortium. Leuk Lymphoma 2019; 61:699-706. [PMID: 31746254 DOI: 10.1080/10428194.2019.1689391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Cereblon (CRBN) is crucial for antiproliferative and immunomodulatory properties of immunomodulatory drugs. The objective of this study was to verify whether germline single nucleotide polymorphisms (SNPs) in the CRBN gene may influence response to lenalidomide in multiple myeloma (MM). Fourteen tagging SNPs covering the genetic variability in the CRBN gene region were genotyped in 167 Polish patients with refractory/relapsed MM treated with lenalidomide-based regimens. We found that carriers of minor alleles of two studied CRBN SNPs rs1714327G > C (OR = 0.26; 95% CI = 0.1-0.67; p = .0055, Bonferroni corrected p = .033) and rs1705814T > C (OR = 0.22; 95% CI = 0.07-0.65; p = .0063, Bonferroni corrected p = .037) were significantly associated with lower probability of achievement at least partial remission while treated with lenalidomide-based regimens, using the dominant inheritance model. Moreover, one of these SNPs, namely rs1705814T > C, was correlated with shorter progression-free survival (HR = 2.49; 95%CI = 1.31-4.74, p = .0054, Bonferroni corrected p = .033). It is suggested that selected germline CRBN allelic variants (rs1714327G > C and rs1705814T > C) affect lenalidomide efficacy in patients with relapsed/refractory MM.
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Affiliation(s)
| | | | - Anna Stępień
- Laboratory of Clinical and Transplant Immunology and Genetics, Copernicus Memorial Hospital, Lodz, Poland
| | | | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| | - Angelica Stein
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | | | - Aleksandra Butrym
- Department of Cancer Prevention and Therapy, Wroclaw Medical University, Wroclaw, Poland
| | - Grzegorz Mazur
- Department of Cancer Prevention and Therapy, Wroclaw Medical University, Wroclaw, Poland
| | - Artur Jurczyszyn
- Department and Clinic of Internal and Occupational Diseases and Hypertension, Wroclaw Medical University, Wroclaw, Poland
| | - Daria Zawirska
- Department and Clinic of Internal and Occupational Diseases and Hypertension, Wroclaw Medical University, Wroclaw, Poland
| | - Norbert Grząśko
- Department of Haematology, Jagiellonian University Medical College, Cracow, Poland
| | - Waldemar Tomczak
- Department of Haematooncology and Bone Marrow Transplantation, Medical University of Lublin, Lublin, Poland
| | - Edyta Subocz
- Department of Hematology, Military Institute of Medicine, Warsaw, Poland
| | - Marzena Wątek
- Department of Hematology, Holycross Cancer Center, Kielce, Poland
| | - Marcin Pasiarski
- Department of Hematology, Holycross Cancer Center, Kielce, Poland
| | - Marcin Rymko
- Department of Hematology, Copernicus Hospital, Torun, Poland
| | | | - Agnieszka Druzd-Sitek
- Department of Lymphoid Malignancies, Maria Sklodowska-Curie Institute Oncology Centre, Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoid Malignancies, Maria Sklodowska-Curie Institute Oncology Centre, Warsaw, Poland
| | | | - Małgorzata Raźny
- Department of Haematology, Rydygier Memorial Hospital, Cracow, Poland
| | - Jan Maciej Zaucha
- Department of Oncological Propaedeutics, Medical University of Gdansk, Gdansk, Poland.,Gdynia Oncology Center, Gdynia, Poland
| | | | - Paweł Gaj
- Laboratory of Human Cancer Genetics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Tadeusz Robak
- Department of Hematology, Copernicus Memorial Hospital, Medical University, Lodz, Poland
| | - Krzysztof Warzocha
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Krzysztof Jamroziak
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
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9
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Huang PA, Beedie SL, Chau CH, Venzon DJ, Gere S, Kazandjian D, Korde N, Mailankody S, Landgren O, Figg WD. Cereblon gene variants and clinical outcome in multiple myeloma patients treated with lenalidomide. Sci Rep 2019; 9:14884. [PMID: 31619706 PMCID: PMC6795854 DOI: 10.1038/s41598-019-51446-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/03/2019] [Indexed: 12/20/2022] Open
Abstract
Carfilzomib-lenalidomide-dexamethasone (KRd) therapy has yielded promising results in patients with newly diagnosed multiple myeloma (NDMM). Cereblon (CRBN) is the direct molecular target of lenalidomide and genetic polymorphisms in CRBN have been associated with lenalidomide efficacy. In this study, we assessed the correlation of five single nucleotide variants (SNVs) in the CRBN gene with clinical response and outcomes in patients with NDMM administered KRd therapy with lenalidomide maintenance, achieving favorable trial endpoints in a prospective Phase II study (NCT01402284). Of the observed SNVs, no associations with KRd therapy response were found in this patient cohort, although strong trends in hypoalbuminemia grade and hyperbilirubinemia grade emerged across the CRBN rs1672753 genotype (P = 0.0008) and the rs1714327 genotype (P = 0.0010), respectively. Our results do not provide conclusive support for the predictive utility of CRBN gene polymorphisms as potential biomarkers of clinical response to lenalidomide-based therapy in our patient population. However, these findings remain to be validated in prospective studies using larger patient populations.
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Affiliation(s)
- Phoebe A Huang
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Shaunna L Beedie
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Cindy H Chau
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - David J Venzon
- Biostatistics and Data Management Section, National Cancer Institute, Bethesda, MD, USA
| | - Sheryl Gere
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Dickran Kazandjian
- Myeloma Program, Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Neha Korde
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sham Mailankody
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ola Landgren
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William D Figg
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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10
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Mlak R, Szudy‐Szczyrek A, Mazurek M, Szczyrek M, Homa‐Mlak I, Mielnik M, Chocholska S, Jankowska‐Łęcka O, Małecka‐Massalska T, Hus M. Polymorphisms in the promotor region of theCRBNgene as a predictive factor for peripheral neuropathy in the course of thalidomide‐based chemotherapy in multiple myeloma patients. Br J Haematol 2019; 186:695-705. [DOI: 10.1111/bjh.15972] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/19/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Radosław Mlak
- Department of Human Physiology Medical University of Lublin Lublin Poland
| | - Aneta Szudy‐Szczyrek
- Department of Haemato‐oncology and Bone Marrow Transplantation Medical University of Lublin Lublin Poland
| | - Marcin Mazurek
- Department of Human Physiology Medical University of Lublin Lublin Poland
| | - Michał Szczyrek
- Department of Pneumonology, Oncology and Allergology Medical University of Lublin Lublin Poland
| | - Iwona Homa‐Mlak
- Department of Human Physiology Medical University of Lublin Lublin Poland
| | - Michał Mielnik
- Department of Haemato‐oncology and Bone Marrow Transplantation Medical University of Lublin Lublin Poland
| | - Sylwia Chocholska
- Department of Haemato‐oncology and Bone Marrow Transplantation Medical University of Lublin Lublin Poland
| | - Olga Jankowska‐Łęcka
- Department of Haemato‐oncology and Bone Marrow Transplantation Medical University of Lublin Lublin Poland
| | | | - Marek Hus
- Department of Haemato‐oncology and Bone Marrow Transplantation Medical University of Lublin Lublin Poland
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11
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Dharanipragada P, Seelam SR, Parekh N. SeqVItA: Sequence Variant Identification and Annotation Platform for Next Generation Sequencing Data. Front Genet 2018; 9:537. [PMID: 30487811 PMCID: PMC6247818 DOI: 10.3389/fgene.2018.00537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/23/2018] [Indexed: 12/20/2022] Open
Abstract
The current trend in clinical data analysis is to understand how individuals respond to therapies and drug interactions based on their genetic makeup. This has led to a paradigm shift in healthcare; caring for patients is now 99% information and 1% intervention. Reducing costs of next generation sequencing (NGS) technologies has made it possible to take genetic profiling to the clinical setting. This requires not just fast and accurate algorithms for variant detection, but also a knowledge-base for variant annotation and prioritization to facilitate tailored therapeutics based on an individual's genetic profile. Here we show that it is possible to provide a fast and easy access to all possible information about a variant and its impact on the gene, its protein product, associated pathways and drug-variant interactions by integrating previously reported knowledge from various databases. With this objective, we have developed a pipeline, Sequence Variants Identification and Annotation (SeqVItA) that provides end-to-end solution for small sequence variants detection, annotation and prioritization on a single platform. Parallelization of the variant detection step and with numerous resources incorporated to infer functional impact, clinical relevance and drug-variant associations, SeqVItA will benefit the clinical and research communities alike. Its open-source platform and modular framework allows for easy customization of the workflow depending on the data type (single, paired, or pooled samples), variant type (germline and somatic), and variant annotation and prioritization. Performance comparison of SeqVItA on simulated data and detection, interpretation and analysis of somatic variants on real data (24 liver cancer patients) is carried out. We demonstrate the efficacy of annotation module in facilitating personalized medicine based on patient's mutational landscape. SeqVItA is freely available at https://bioinf.iiit.ac.in/seqvita.
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Affiliation(s)
- Prashanthi Dharanipragada
- Center for Computational Natural Science and Bioinformatics, International Institute of Information Technology, Hyderabad, India
| | - Sampreeth Reddy Seelam
- Center for Computational Natural Science and Bioinformatics, International Institute of Information Technology, Hyderabad, India
| | - Nita Parekh
- Center for Computational Natural Science and Bioinformatics, International Institute of Information Technology, Hyderabad, India
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12
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Łacina P, Butrym A, Mazur G, Bogunia-Kubik K. BSG and MCT1 Genetic Variants Influence Survival in Multiple Myeloma Patients. Genes (Basel) 2018; 9:genes9050226. [PMID: 29695106 PMCID: PMC5977166 DOI: 10.3390/genes9050226] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 01/20/2023] Open
Abstract
Multiple myeloma (MM) is a haematologic malignancy characterized by the presence of atypical plasma cells. Basigin (BSG, CD147) controls lactate export through the monocarboxylic acid transporter 1 (MCT1, SLC16A1) and supports MM survival and proliferation. Additionally, BSG is implicated in response to treatment with immunomodulatory drugs (thalidomide and its derivatives). We investigated the role of single nucleotide polymorphisms (SNPs) in the gene coding for BSG and SLC16A1 in MM. Following an in silico analysis, eight SNPs (four in BSG and four in SLC16A1) predicted to have a functional effect were selected and analyzed in 135 MM patients and 135 healthy individuals. Alleles rs4919859 C, rs8637 G, and haplotype CG were associated with worse progression-free survival (p = 0.006, p = 0.017, p = 0.002, respectively), while rs7556664 A, rs7169 T and rs1049434 A (all in linkage disequilibrium (LD), r² > 0.98) were associated with better overall survival (p = 0.021). Similar relationships were observed in thalidomide-treated patients. Moreover, rs4919859 C, rs8637 G, rs8259 A and the CG haplotype were more common in patients in stages II⁻III of the International Staging System (p < 0.05), while rs8259 A correlated with higher levels of β-2-microglobulin and creatinine (p < 0.05). Taken together, our results show that BSG and SLC16A1 variants affect survival, and may play an important role in MM.
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Affiliation(s)
- Piotr Łacina
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland.
| | - Aleksandra Butrym
- Department of Internal, Occupational Diseases, Hypertension and Clinical Oncology, Wroclaw Medical University, 50-556 Wrocław, Poland.
| | - Grzegorz Mazur
- Department of Internal, Occupational Diseases, Hypertension and Clinical Oncology, Wroclaw Medical University, 50-556 Wrocław, Poland.
| | - Katarzyna Bogunia-Kubik
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland.
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13
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Butrym A, Łacina P, Rybka J, Chaszczewska-Markowska M, Mazur G, Bogunia-Kubik K. Cereblon and IRF4 Variants Affect Risk and Response to Treatment in Multiple Myeloma. Arch Immunol Ther Exp (Warsz) 2017; 64:151-156. [PMID: 28083618 PMCID: PMC5334380 DOI: 10.1007/s00005-016-0442-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/24/2016] [Indexed: 11/27/2022]
Abstract
Multiple myeloma (MM) is a plasma-cell malignancy derived from an early precursor of the B-cell lineage characterised by bone-marrow infiltration, lytic bone lesions, and the presence of a monoclonal protein in serum and/or urine. Interferon regulatory factor 4 (IRF4) is a critical transcriptional regulator in B-cell development and function that is required during immune response for lymphocyte activation and the generation of immunoglobulin-secreting plasma cells. Immunomodulatory drugs, derivatives of thalidomide, are commonly used in therapy against MM. They are known to target a protein called cereblon (CRBN); however, the exact mechanism remains unknown. The present study aimed to assess the association of two (rs12203592 and rs872071) polymorphisms within the IRF4 gene and two (rs711613 and rs1045433) in the CRBN gene with MM susceptibility, progression, and response to treatment. For this purpose, 144 MM patients and 126 healthy individuals were genotyped for the IRF4 and CRBN alleles. The presence of the IRF4 (rs872071) G allele was more frequently detected in patients than healthy individuals (OR 1.78; P = 0.034), and this relationship was especially pronounced in women (OR 2.83; P = 0.012). The CRBN (rs711613) A allele-carriers were better responders to the treatment (P = 0.012), in particular to thalidomide including therapy (P = 0.023). These results underline the prognostic significance of the IRF4 and CRBN polymorphisms in patients with MM.
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Affiliation(s)
- Aleksandra Butrym
- Department of Physiology, Wroclaw Medical University, Wroclaw, Poland
| | - Piotr Łacina
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Justyna Rybka
- Department of Haematology, Blood Neoplasms and Bone Marrow Transplantation, Wroclaw Medical University, Borowska 213, 50-556, Wroclaw, Poland
| | - Monika Chaszczewska-Markowska
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Grzegorz Mazur
- Department and Clinic of Internal and Occupational Diseases, Hypertension and Clinical Oncology, Wroclaw Medical University, Wroclaw, Poland.
| | - Katarzyna Bogunia-Kubik
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
- Department and Clinic of Internal and Occupational Diseases, Hypertension and Clinical Oncology, Wroclaw Medical University, Wroclaw, Poland
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14
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Yu J, Huang Y, Liu L, Wang J, Yin J, Huang L, Chen S, Li J, Yuan H, Yang G, Liu W, Wang H, Pei Q, Guo C. Genetic polymorphisms of Wnt/β-catenin pathway genes are associated with the efficacy and toxicities of radiotherapy in patients with nasopharyngeal carcinoma. Oncotarget 2016; 7:82528-82537. [PMID: 27769064 PMCID: PMC5347711 DOI: 10.18632/oncotarget.12754] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/14/2016] [Indexed: 12/14/2022] Open
Abstract
Radiotherapy (RT) is the normative therapeutic treatment for primary nasopharyngeal carcinoma (NPC). Single nucleotide polymorphisms (SNPs) of genes in Wnt/β-catenin pathway are correlated to the development, prognosis, and treatment benefit of various cancers. However, it has not been established whether SNPs of Wnt/β-catenin pathway are associated with nasopharyngeal tumorigenesis and the efficacy of RT in NPC patients. Therefore, in this study, we aimed to investigate the nine potentially functional SNPs of four genes in the Wnt/β-catenin pathway and genotyped these in 188 NPC patients treated with RT. To achieve this goal, associations between these SNPs and the RT's curative efficacy, as well as acute radiation-induced toxic reaction were determined by multifactorial logistic regression. We observed that catenin beta 1 gene (CTNNB1) rs1880481 and rs3864004, and glycogen synthase kinase 3 beta gene (GSK3β) rs3755557 polymorphisms were significantly associated with poorer efficacy of RT in NPC patients. Moreover, GSK3β rs375557 and adenomatous polyposis coli gene (APC) rs454886 polymorphisms were correlated with acute grade 3-4 radiation-induced dermatitis and oral mucositis, respectively. In conclusion, this study suggests that gene polymorphisms of Wnt/β-catenin may be novel prognostic factors for NPC patients treated with RT.
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Affiliation(s)
- Jingjing Yu
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Yuling Huang
- Department of Radiation Oncology, Jiangxi Province Tumor Hospital, Nanchang, Jiangxi 330029, China
| | - Lijuan Liu
- Department of Pharmacy, Jiangxi Cancer Hospital, Nanchang 330029, China
| | - Jing Wang
- Department of Radiation Oncology, Jiangxi Province Tumor Hospital, Nanchang, Jiangxi 330029, China
| | - Jiye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lihua Huang
- Center for Medical Experiments, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Shaojun Chen
- Department of Oncology, Fourth Affiliated Hospital, Guangxi Medical University, Liuzhou, Guangxi 545005, China
| | - Jingao Li
- Department of Radiation Oncology, Jiangxi Province Tumor Hospital, Nanchang, Jiangxi 330029, China
| | - Hong Yuan
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Guoping Yang
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Wenyu Liu
- College of Pharmacy, Central South University, Changsha, Hunan 410008, China
| | - Hai Wang
- Xiangya Medical College, Central South University, Changsha, Hunan 410008, China
| | - Qi Pei
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Chengxian Guo
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
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