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Dong SXM, Vizeacoumar FS, Bhanumathy KK, Alli N, Gonzalez-Lopez C, Gajanayaka N, Caballero R, Ali H, Freywald A, Cassol E, Angel JB, Vizeacoumar FJ, Kumar A. Identification of novel genes involved in apoptosis of HIV-infected macrophages using unbiased genome-wide screening. BMC Infect Dis 2021; 21:655. [PMID: 34233649 PMCID: PMC8261936 DOI: 10.1186/s12879-021-06346-7] [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: 11/15/2020] [Accepted: 06/15/2021] [Indexed: 12/01/2022] Open
Abstract
Background Macrophages, besides resting latently infected CD4+ T cells, constitute the predominant stable, major non-T cell HIV reservoirs. Therefore, it is essential to eliminate both latently infected CD4+ T cells and tissue macrophages to completely eradicate HIV in patients. Until now, most of the research focus is directed towards eliminating latently infected CD4+ T cells. However, few approaches have been directed at killing of HIV-infected macrophages either in vitro or in vivo. HIV infection dysregulates the expression of many host genes essential for the survival of infected cells. We postulated that exploiting this alteration may yield novel targets for the selective killing of infected macrophages. Methods We applied a pooled shRNA-based genome-wide approach by employing a lentivirus-based library of shRNAs to screen novel gene targets whose inhibition should selectively induce apoptosis in HIV-infected macrophages. Primary human MDMs were infected with HIV-eGFP and HIV-HSA viruses. Infected MDMs were transfected with siRNAs specific for the promising genes followed by analysis of apoptosis by flow cytometry using labelled Annexin-V in HIV-infected, HIV-exposed but uninfected bystander MDMs and uninfected MDMs. The results were analyzed using student’s t-test from at least four independent experiments. Results We validated 28 top hits in two independent HIV infection models. This culminated in the identification of four target genes, Cox7a2, Znf484, Cstf2t, and Cdk2, whose loss-of-function induced apoptosis preferentially in HIV-infected macrophages. Silencing these single genes killed significantly higher number of HIV-HSA-infected MDMs compared to the HIV-HSA-exposed, uninfected bystander macrophages, indicating the specificity in the killing of HIV-infected macrophages. The mechanism governing Cox7a2-mediated apoptosis of HIV-infected macrophages revealed that targeting respiratory chain complex II and IV genes also selectively induced apoptosis of HIV-infected macrophages possibly through enhanced ROS production. Conclusions We have identified above-mentioned novel genes and specifically the respiratory chain complex II and IV genes whose silencing may cause selective elimination of HIV-infected macrophages and eventually the HIV-macrophage reservoirs. The results highlight the potential of the identified genes as targets for eliminating HIV-infected macrophages in physiological environment as part of an HIV cure strategy. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06346-7.
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Affiliation(s)
- Simon X M Dong
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kalpana K Bhanumathy
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Nezeka Alli
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Niranjala Gajanayaka
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Ramon Caballero
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hamza Ali
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Andrew Freywald
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Edana Cassol
- Department of Health Sciences, Carleton University, Ottawa, ON, Canada
| | - Jonathan B Angel
- Department of Medicine, the Ottawa Health Research Institute, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Franco J Vizeacoumar
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada. .,Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, SK, Canada.
| | - Ashok Kumar
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada. .,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada. .,Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
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Carron J, Torricelli C, Silva JK, Coser LDO, Lima CSP, Lourenço GJ. Intronic variants of MITF (rs7623610) and CREB1 (rs10932201) genes may enhance splicing efficiency in human melanoma cell line. Mutat Res 2021; 823:111763. [PMID: 34710701 DOI: 10.1016/j.mrfmmm.2021.111763] [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: 07/27/2021] [Revised: 09/24/2021] [Accepted: 10/17/2021] [Indexed: 11/20/2022]
Abstract
We previously reported that intronic single nucleotide variations (SNVs) in MITF (c.938-325G>A, rs7623610) and CREB1 (c.303+373G>A, rs10932201) genes were associated with risk, aggressiveness, and prognosis of cutaneous melanoma (CM). In this study, we investigated the influence of the above SNVs in splicing patterns and efficiency. We constructed minigenes with wild type and variant alleles from MITF and CREB1 to assess the effect of the SNVs on splicing. The minigenes were transfected in the human melanoma cell line (SK-MEL-28). RT-PCR and DNA sequencing investigated the constructs' splicing patterns. Minigenes constructs' splicing efficiency and HNRNPA1 and SF1 splicing genes' expression were investigated by qPCR. We found that MITF and CREB1 SNVs did not alter the splicing pattern, but they influenced the splicing efficiency. MITF-A (p= 0.03) and CREB1-A (p= 0.005) variant minigenes yielded an increase of mRNA generated from the constructions. Additionally, lower mRNA levels of HNRNPA1 and SF1 were seen in the variant minigenes MITF-A (p= 0.04) and CREB1-A (p= 0.005). We described for the first time the potential importance of MITF rs7623610 and CREB1 rs10932201 SNVs in splicing efficiency and its relationship with CM.
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Affiliation(s)
- Juliana Carron
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Caroline Torricelli
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Janet Keller Silva
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Lilian de Oliveira Coser
- Laboratory of Nerve Regeneration, Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Carmen Silvia Passos Lima
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil; Department of Radiology, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Gustavo Jacob Lourenço
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil.
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Lourenço GJ, Oliveira C, Carvalho BS, Torricelli C, Silva JK, Gomez GVB, Rinck-Junior JA, Oliveira WL, Vazquez VL, Serrano SV, Moraes AM, Lima CSP. Inherited variations in human pigmentation-related genes modulate cutaneous melanoma risk and clinicopathological features in Brazilian population. Sci Rep 2020; 10:12129. [PMID: 32699307 PMCID: PMC7376158 DOI: 10.1038/s41598-020-68945-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 05/04/2020] [Indexed: 01/29/2023] Open
Abstract
Ultraviolet light exposure and cutaneous pigmentation are important host risk factors for cutaneous melanoma (CM), and it is well known that inherited ability to produce melanin varies in humans. The study aimed to identify single-nucleotide variants (SNVs) on pigmentation-related genes with importance in risk and clinicopathological aspects of CM. The study was conducted in two stages. In stage 1, 103 CM patients and 103 controls were analyzed using Genome-Wide Human SNV Arrays in order to identify SNVs in pigmentation-related genes, and the most important SNVs were selected for data validation in stage 2 by real-time polymerase-chain reaction in 247 CM patients and 280 controls. ADCY3 c.675+9196T>G, CREB1 c.303+373G>A, and MITF c.938-325G>A were selected for data validation among 74 SNVs. Individuals with CREB1 GA or AA genotype and allele "A" were under 1.79 and 1.47-fold increased risks of CM than others, respectively. Excesses of CREB1 AA and MITF AA genotype were seen in patients with tumors at Clark levels III to V (27.8% versus 13.7%) and at III or IV stages (46.1% versus 24.9%) compared to others, respectively. When compared to others, patients with ADCY3 TT had 1.89 more chances of presenting CM progression, and those with MITF GA or AA had 2.20 more chances of evolving to death by CM. Our data provide, for the first time, preliminary evidence that inherited abnormalities in ADCY3, CREB1, and MITF pigmentation-related genes, not only can increase the risk to CM, but also influence CM patients' clinicopathological features.
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Affiliation(s)
- Gustavo Jacob Lourenço
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Cristiane Oliveira
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Benilton Sá Carvalho
- Department of Statistics, Institute of Mathematics, Statistic, and Computer Science, University of Campinas, Campinas, São Paulo, Brazil
| | - Caroline Torricelli
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Janet Keller Silva
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Gabriela Vilas Bôas Gomez
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - José Augusto Rinck-Junior
- Clinical Oncology Service, Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas, Rua Alexander Fleming, 181, Cidade Universitária "Zeferino Vaz", Barão Geraldo, Campinas, São Paulo, Brazil
- A.C. Camargo Cancer Center, São Paulo, São Paulo, Brazil
| | - Wesley Lima Oliveira
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Vinicius Lima Vazquez
- Melanoma and Sarcoma Surgery Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | | | - Aparecida Machado Moraes
- Clinical Oncology Service, Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas, Rua Alexander Fleming, 181, Cidade Universitária "Zeferino Vaz", Barão Geraldo, Campinas, São Paulo, Brazil
| | - Carmen Silvia Passos Lima
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil.
- Clinical Oncology Service, Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas, Rua Alexander Fleming, 181, Cidade Universitária "Zeferino Vaz", Barão Geraldo, Campinas, São Paulo, Brazil.
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Identification and Validation of Prognostically Relevant Gene Signature in Melanoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5323614. [PMID: 32462000 PMCID: PMC7238332 DOI: 10.1155/2020/5323614] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/08/2020] [Accepted: 04/15/2020] [Indexed: 12/19/2022]
Abstract
Background Currently, effective genetic markers are limited to predict the clinical outcome of melanoma. High-throughput multiomics sequencing data have provided a valuable approach for the identification of genes associated with cancer prognosis. Method The multidimensional data of melanoma patients, including clinical, genomic, and transcriptomic data, were obtained from The Cancer Genome Atlas (TCGA). These samples were then randomly divided into two groups, one for training dataset and the other for validation dataset. In order to select reliable biomarkers, we screened prognosis-related genes, copy number variation genes, and SNP variation genes and integrated these genes to further select features using random forests in the training dataset. We screened for robust biomarkers and established a gene-related prognostic model. Finally, we verified the selected biomarkers in the test sets (GSE19234 and GSE65904) and on clinical samples extracted from melanoma patients using qRT-PCR and immunohistochemistry analysis. Results We obtained 1569 prognostic-related genes and 1101 copy-amplification, 1093 copy-deletions, and 92 significant mutations in genomic variants. These genomic variant genes were closely related to the development of tumors and genes that integrate genomic variation. A total of 141 candidate genes were obtained from prognosis-related genes. Six characteristic genes (IQCE, RFX6, GPAA1, BAHCC1, CLEC2B, and AGAP2) were selected by random forest feature selection, many of which have been reported to be associated with tumor progression. Cox regression analysis was used to establish a 6-gene signature. Experimental verification with qRT-PCR and immunohistochemical staining proved that these selected genes were indeed expressed at a significantly higher level compared with the normal tissues. This signature comprised an independent prognostic factor for melanoma patients. Conclusions We constructed a 6-gene signature (IQCE, RFX6, GPAA1, BAHCC1, CLEC2B, and AGAP2) as a novel prognostic marker for predicting the survival of melanoma patients.
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