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Mercuri RLV, Conceição HB, Guardia GDA, Goldstein G, Vibranovski MD, Hinske LC, Galante PAF. Retro-miRs: novel and functional miRNAs originating from mRNA retrotransposition. Mob DNA 2023; 14:12. [PMID: 37684690 PMCID: PMC10486083 DOI: 10.1186/s13100-023-00301-w] [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: 03/11/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Reverse-transcribed gene copies (retrocopies) have emerged as major sources of evolutionary novelty. MicroRNAs (miRNAs) are small and highly conserved RNA molecules that serve as key post-transcriptional regulators of gene expression. The origin and subsequent evolution of miRNAs have been addressed but not fully elucidated. RESULTS In this study, we performed a comprehensive investigation of miRNA origination through retroduplicated mRNA sequences (retro-miRs). We identified 17 retro-miRs that emerged from the mRNA retrocopies. Four of these retro-miRs had de novo origins within retrocopied sequences, while 13 retro-miRNAs were located within exon regions and duplicated along with their host mRNAs. We found that retro-miRs were primate-specific, including five retro-miRs conserved among all primates and two human-specific retro-miRs. All retro-miRs were expressed, with predicted and experimentally validated target genes except miR-10527. Notably, the target genes of retro-miRs are involved in key biological processes such as metabolic processes, cell signaling, and regulation of neurotransmitters in the central nervous system. Additionally, we found that these retro-miRs play a potential oncogenic role in cancer by targeting key cancer genes and are overexpressed in several cancer types, including liver hepatocellular carcinoma and stomach adenocarcinoma. CONCLUSIONS Our findings demonstrated that mRNA retrotransposition is a key mechanism for the generation of novel miRNAs (retro-miRs) in primates. These retro-miRs are expressed, conserved, have target genes with important cellular functions, and play important roles in cancer.
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Affiliation(s)
- Rafael L V Mercuri
- Hospital Sirio-Libanes, São Paulo, 01308-060, Brazil
- Interunidades Em Bioinformática, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Helena B Conceição
- Hospital Sirio-Libanes, São Paulo, 01308-060, Brazil
- Interunidades Em Bioinformática, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | | | - Gabriel Goldstein
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Maria D Vibranovski
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University, Tempe, AZ, USA
| | - Ludwig C Hinske
- Institute for Digital Medicine/Clinic of Anaesthesiology, University of Augsburg, Augsburg, Germany
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Guardia GDA, Naressi RG, Buzzato VC, da Costa JB, Zalcberg I, Ramires J, Malnic B, Gutiyama LM, Galante PAF. Acute Myeloid Leukemia Expresses a Specific Group of Olfactory Receptors. Cancers (Basel) 2023; 15:3073. [PMID: 37370684 DOI: 10.3390/cancers15123073] [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: 04/12/2023] [Revised: 05/23/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Acute myeloid leukemia (AML) is the most common form of acute leukemia in adults, with a 5-year overall survival rate of approximately 30%. Despite recent advances in therapeutic options, relapse remains the leading cause of death and poor survival outcomes. New drugs benefit specific small subgroups of patients with actionable therapeutic targets. Thus, finding new targets with greater applicability should be pursued. Olfactory receptors (ORs) are seven transmembrane G-protein coupled receptors preferentially expressed in sensory neurons with a critical role in recognizing odorant molecules. Recent studies have revealed ectopic expression and putative function of ORs in nonolfactory tissues and pathologies, including AML. Here, we investigated OR expression in 151 AML samples, 6400 samples of 15 other cancer types, and 11,200 samples of 51 types of healthy tissues. First, we identified 19 ORs with a distinct and major expression pattern in AML, which were experimentally validated by RT-PCR in an independent set of 13 AML samples, 13 healthy donors, and 8 leukemia cell lines. We also identified an OR signature with prognostic potential for AML patients. Finally, we found cancer-related genes coexpressed with the ORs in the AML samples. In summary, we conducted an extensive study to identify ORs that can be used as novel biomarkers for the diagnosis of AML and as potential drug targets.
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Affiliation(s)
- Gabriela D A Guardia
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo 01308-060, SP, Brazil
| | - Rafaella G Naressi
- Centro de Transplante de Medula Óssea, Instituto Nacional do Câncer, Rio de Janeiro 20230-130, RJ, Brazil
- Department of Biochemistry, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Vanessa C Buzzato
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo 01308-060, SP, Brazil
| | - Juliana B da Costa
- Centro de Transplante de Medula Óssea, Instituto Nacional do Câncer, Rio de Janeiro 20230-130, RJ, Brazil
| | - Ilana Zalcberg
- Centro de Transplante de Medula Óssea, Instituto Nacional do Câncer, Rio de Janeiro 20230-130, RJ, Brazil
| | - Jordana Ramires
- Centro de Transplante de Medula Óssea, Instituto Nacional do Câncer, Rio de Janeiro 20230-130, RJ, Brazil
| | - Bettina Malnic
- Department of Biochemistry, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Luciana M Gutiyama
- Centro de Transplante de Medula Óssea, Instituto Nacional do Câncer, Rio de Janeiro 20230-130, RJ, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo 01308-060, SP, Brazil
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Xavier CB, Lopes CDH, Awni BM, Campos EF, Alves JPB, Camargo AA, Guardia GDA, Galante PAF, Jardim DL. Interplay between Tumor Mutational Burden and Mutational Profile and Its Effect on Overall Survival: A Pilot Study of Metastatic Patients Treated with Immune Checkpoint Inhibitors. Cancers (Basel) 2022; 14:cancers14215433. [PMID: 36358851 PMCID: PMC9657500 DOI: 10.3390/cancers14215433] [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: 08/27/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/06/2022] Open
Abstract
Purpose: Solid tumors harboring tumor mutational burden (TMB) ≥10 mutations per megabase (mut/Mb) received agnostic approval for pembrolizumab. This work aims to analyze the somatic mutational profile’s influence on the outcomes of patients with TMB-high tumors treated with immune checkpoint inhibitors (ICIs). Methods: This post-hoc analysis evaluated clinical and molecular features of patients with solid tumors treated with ICIs that could be either monoclonal antibody directed against programmed cell death protein-1 or monoclonal antibody directed against programmed cell death ligand 1 (anti-PD-1/anti-PD-L1), monoclonal antibody directed against cytotoxic T lymphocyte-associated antigen (anti-CTLA-4) or a combined treatment regimen including one anti-PD-1/anti-PD-L1 and one anti-CTLA-4 (ICIs combination). We performed OS analysis for TMB thresholds of ≥10, ≥20, and <10 mut/Mb. We assessed OS according to the mutational profile for a TMB ≥ 10 mut/Mb cutoff. For genes correlated with OS at the univariate assessment, we conducted a Cox multivariate analysis adjusted by median TMB, sex, age, microsatellite instability (MSI), and histology. Results: A total of 1661 patients were investigated; 488 with a TMB ≥10 mut/Mb (29.4%). The median OS was 42 months for TMB ≥10 or 20 mut/Mb, and 15 months for TMB <10 mut/Mb (p < 0.005). Among TMB ≥10 mut/Mb patients, mutations in E2F3 or STK11 correlated with worse OS, and mutations in NTRK3, PTPRD, RNF43, TENT5C, TET1, or ZFHX3 with better OS. These associations were confirmed with univariate and multivariate analyses (p < 0.05). Melanoma histology and TMB above the median endowed patients with better OS (p < 0.05), while MSI status, age, and gender did not have a statistically significant effect on OS. Conclusion: Combining TMB and mutation profiles in key cancer genes can better qualify patients for ICI treatment and predict their OS.
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Affiliation(s)
- Camila B. Xavier
- Oncology Center, Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | | | - Beatriz M. Awni
- Oncology Center, Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | - Eduardo F. Campos
- Oncology Center, Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | | | - Anamaria A. Camargo
- Molecular Oncology Center, Instituto de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | - Gabriela D. A. Guardia
- Molecular Oncology Center, Instituto de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | - Pedro A. F. Galante
- Molecular Oncology Center, Instituto de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | - Denis L. Jardim
- Oncology Center, Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
- Correspondence: ; Tel.: +55-11-99-707-2594
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Costa PAC, Silva WN, Prazeres PHDM, Picoli CC, Guardia GDA, Costa AC, Oliveira MA, Guimarães PPG, Gonçalves R, Pinto MCX, Amorim JH, Azevedo VAC, Resende RR, Russo RC, Cunha TM, Galante PAF, Mintz A, Birbrair A. Chemogenetic modulation of sensory neurons reveals their regulating role in melanoma progression. Acta Neuropathol Commun 2021; 9:183. [PMID: 34784974 PMCID: PMC8594104 DOI: 10.1186/s40478-021-01273-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/10/2021] [Indexed: 02/08/2023] Open
Abstract
Sensory neurons have recently emerged as components of the tumor microenvironment. Nevertheless, whether sensory neuronal activity is important for tumor progression remains unknown. Here we used Designer Receptors Exclusively Activated by a Designer Drug (DREADD) technology to inhibit or activate sensory neurons' firing within the melanoma tumor. Melanoma growth and angiogenesis were accelerated following inhibition of sensory neurons' activity and were reduced following overstimulation of these neurons. Sensory neuron-specific overactivation also induced a boost in the immune surveillance by increasing tumor-infiltrating anti-tumor lymphocytes, while reducing immune-suppressor cells. In humans, a retrospective in silico analysis of melanoma biopsies revealed that increased expression of sensory neurons-related genes within melanoma was associated with improved survival. These findings suggest that sensory innervations regulate melanoma progression, indicating that manipulation of sensory neurons' activity may provide a valuable tool to improve melanoma patients' outcomes.
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Affiliation(s)
- Pedro A C Costa
- Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Walison N Silva
- Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Pedro H D M Prazeres
- Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Caroline C Picoli
- Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | | | - Alinne C Costa
- Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Mariana A Oliveira
- Departamento de Bioquimica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Pedro P G Guimarães
- Departamento de Fisiologia e Biofísica, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Ricardo Gonçalves
- Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Mauro C X Pinto
- Departamento de Farmacologia, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - Jaime H Amorim
- Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Barreiras, BA, Brasil
| | - Vasco A C Azevedo
- Departamento de Genetica, Ecologia e Evolucao, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Rodrigo R Resende
- Departamento de Bioquimica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Remo C Russo
- Departamento de Fisiologia e Biofísica, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Thiago M Cunha
- Departamento de Farmacologia, Universidade de São Paulo, Ribeirão Preto, SP, Brasil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP, Brasil
| | - Akiva Mintz
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Alexander Birbrair
- Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil.
- Department of Radiology, Columbia University Medical Center, New York, NY, USA.
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