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Breunig K, Lei X, Montalbano M, Guardia GDA, Ostadrahimi S, Alers V, Kosti A, Chiou J, Klein N, Vinarov C, Wang L, Li M, Song W, Kraus WL, Libich DS, Tiziani S, Weintraub ST, Galante PAF, Penalva LOF. SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis. bioRxiv 2024:2024.03.22.586270. [PMID: 38585848 PMCID: PMC10996453 DOI: 10.1101/2024.03.22.586270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
RNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase separation (LLPS) and the formation of membraneless organelles such as stress granules and nucleoli. IDR-RBPs are particularly relevant in the nervous system and their dysfunction is associated with neurodegenerative diseases and brain tumor development. SERBP1 is a unique member of this group, being mostly disordered and lacking canonical RNA-binding domains. Using a proteomics approach followed by functional analysis, we defined SERBP1's interactome. We uncovered novel SERBP1 roles in splicing, cell division, and ribosomal biogenesis and showed its participation in pathological stress granules and Tau aggregates in Alzheimer's disease brains. SERBP1 preferentially interacts with other G-quadruplex (G4) binders, implicated in different stages of gene expression, suggesting that G4 binding is a critical component of SERBP1 function in different settings. Similarly, we identified important associations between SERBP1 and PARP1/polyADP-ribosylation (PARylation). SERBP1 interacts with PARP1 and its associated factors and influences PARylation. Moreover, protein complexes in which SERBP1 participates contain mostly PARylated proteins and PAR binders. Based on these results, we propose a feedback regulatory model in which SERBP1 influences PARP1 function and PARylation, while PARylation modulates SERBP1 functions and participation in regulatory complexes.
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Rangel-Pozzo A, Dos Santos FF, Dettori T, Giulietti M, Frau DV, Galante PAF, Vanni R, Pathak A, Fischer G, Gartner J, Caria P, Mai S. Three-dimensional nuclear architecture distinguishes thyroid cancer histotypes. Int J Cancer 2023; 153:1842-1853. [PMID: 37539710 DOI: 10.1002/ijc.34667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023]
Abstract
Molecular markers can serve as diagnostic tools to support pathological analysis in thyroid neoplasms. However, because the same markers can be observed in some benign thyroid lesions, additional approaches are necessary to differentiate thyroid tumor subtypes, prevent overtreatment and tailor specific clinical management. This applies particularly to the recently described variant of thyroid cancer referred to as noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP). This variant has an estimated prevalence of 4.4% to 9.1% of all papillary thyroid carcinomas worldwide. We studied 60 thyroid lesions: 20 classical papillary thyroid carcinoma (CPTC), 20 follicular variant of PTC (FVPTC) and 20 NIFTP. We examined morphological and molecular features to identify parameters that can differentiate NIFTP from the other PTC subtypes. When blindly investigating the nuclear architecture of thyroid neoplasms, we observed that NIFTP has significantly longer telomeres than CPTC and FVPTC. Super-resolved 3D-structured illumination microscopy demonstrated that NIFTP is heterogeneous and that its nuclei contain more densely packed DNA and smaller interchromatin spaces than CPTC and FVPTC, a pattern that resembles normal thyroid tissue. These data are consistent with the observed indolent biological behavior and favorable prognosis associated with NIFTP, which lacks BRAFV600E mutations. Of note, next-generation thyroid oncopanel sequencing was unable to distinguish the thyroid cancer histotypes in our study cohort. In summary, our data suggest that 3D nuclear architecture can be a powerful analytical tool to diagnose and guide clinical management of NIFTP.
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Affiliation(s)
- Aline Rangel-Pozzo
- CancerCare Manitoba Research Institute, CancerCare Manitoba, University of Manitoba, Winnipeg, Canada
| | - Filipe F Dos Santos
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, Brazil
- Department of Biochemistry, Chemistry Institute, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Tinuccia Dettori
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona, Italy
| | | | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, Brazil
| | - Roberta Vanni
- University of Cagliari, Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Alok Pathak
- Department of Surgery, University of Manitoba, Winnipeg, Canada
| | - Gabor Fischer
- Department of Pathology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
| | - John Gartner
- Department of Pathology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Paola Caria
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Sabine Mai
- CancerCare Manitoba Research Institute, CancerCare Manitoba, University of Manitoba, Winnipeg, Canada
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Lopes CDH, Antonacio FF, Moraes PMG, Asprino PF, Galante PAF, Jardim DL, de Macedo MP, Sandoval RL, Katz A, de Castro G, Achatz MI. The Clinical and Molecular Profile of Lung Cancer Patients Harboring the TP53 R337H Germline Variant in a Brazilian Cancer Center: The Possible Mechanism of Carcinogenesis. Int J Mol Sci 2023; 24:15035. [PMID: 37894716 PMCID: PMC10606350 DOI: 10.3390/ijms242015035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
In southern and southeastern Brazil, the TP53 founder variant c.1010G>A (R337H) has been previously documented with a prevalence of 0.3% within the general population and linked to a heightened incidence of lung adenocarcinomas (LUADs). In the present investigation, we cover clinical and molecular characterizations of lung cancer patients from the Brazilian Li-Fraumeni Syndrome Study (BLISS) database. Among the 175 diagnosed malignant neoplasms, 28 (16%) were classified as LUADs, predominantly occurring in females (68%), aged above 50 years, and never-smokers (78.6%). Significantly, LUADs manifested as the initial clinical presentation of Li-Fraumeni Syndrome in 78.6% of cases. Molecular profiling was available for 20 patients, with 14 (70%) revealing EGFR family alterations. In total, 23 alterations in cancer driver genes were identified, comprising 7 actionable mutations and 4 linked to resistance against systemic treatments. In conclusion, the carriers of TP53 R337H demonstrate a predisposition to LUAD development. Furthermore, our results indicate that environmental pollution potentially impacts the carcinogenesis of lung tumors in the carriers of TP53 R337H.
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Affiliation(s)
- Carlos D. H. Lopes
- Hospital Sirio Libanes, São Paulo 01308-050, Brazil; (F.F.A.); (P.M.G.M.); (P.F.A.); (P.A.F.G.); (D.L.J.); (M.P.d.M.); (R.L.S.); (A.K.); (G.d.C.J.)
| | - Fernanda F. Antonacio
- Hospital Sirio Libanes, São Paulo 01308-050, Brazil; (F.F.A.); (P.M.G.M.); (P.F.A.); (P.A.F.G.); (D.L.J.); (M.P.d.M.); (R.L.S.); (A.K.); (G.d.C.J.)
| | - Priscila M. G. Moraes
- Hospital Sirio Libanes, São Paulo 01308-050, Brazil; (F.F.A.); (P.M.G.M.); (P.F.A.); (P.A.F.G.); (D.L.J.); (M.P.d.M.); (R.L.S.); (A.K.); (G.d.C.J.)
| | - Paula F. Asprino
- Hospital Sirio Libanes, São Paulo 01308-050, Brazil; (F.F.A.); (P.M.G.M.); (P.F.A.); (P.A.F.G.); (D.L.J.); (M.P.d.M.); (R.L.S.); (A.K.); (G.d.C.J.)
| | - Pedro A. F. Galante
- Hospital Sirio Libanes, São Paulo 01308-050, Brazil; (F.F.A.); (P.M.G.M.); (P.F.A.); (P.A.F.G.); (D.L.J.); (M.P.d.M.); (R.L.S.); (A.K.); (G.d.C.J.)
| | - Denis L. Jardim
- Hospital Sirio Libanes, São Paulo 01308-050, Brazil; (F.F.A.); (P.M.G.M.); (P.F.A.); (P.A.F.G.); (D.L.J.); (M.P.d.M.); (R.L.S.); (A.K.); (G.d.C.J.)
- Oncoclínicas, São Paulo 04543-906, Brazil
| | - Mariana P. de Macedo
- Hospital Sirio Libanes, São Paulo 01308-050, Brazil; (F.F.A.); (P.M.G.M.); (P.F.A.); (P.A.F.G.); (D.L.J.); (M.P.d.M.); (R.L.S.); (A.K.); (G.d.C.J.)
| | - Renata L. Sandoval
- Hospital Sirio Libanes, São Paulo 01308-050, Brazil; (F.F.A.); (P.M.G.M.); (P.F.A.); (P.A.F.G.); (D.L.J.); (M.P.d.M.); (R.L.S.); (A.K.); (G.d.C.J.)
| | - Artur Katz
- Hospital Sirio Libanes, São Paulo 01308-050, Brazil; (F.F.A.); (P.M.G.M.); (P.F.A.); (P.A.F.G.); (D.L.J.); (M.P.d.M.); (R.L.S.); (A.K.); (G.d.C.J.)
| | - Gilberto de Castro
- Hospital Sirio Libanes, São Paulo 01308-050, Brazil; (F.F.A.); (P.M.G.M.); (P.F.A.); (P.A.F.G.); (D.L.J.); (M.P.d.M.); (R.L.S.); (A.K.); (G.d.C.J.)
| | - Maria Isabel Achatz
- Hospital Sirio Libanes, São Paulo 01308-050, Brazil; (F.F.A.); (P.M.G.M.); (P.F.A.); (P.A.F.G.); (D.L.J.); (M.P.d.M.); (R.L.S.); (A.K.); (G.d.C.J.)
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Corradi C, Vilar JB, Buzatto VC, de Souza TA, Castro LP, Munford V, De Vecchi R, Galante PAF, Orpinelli F, Miller TLA, Buzzo JL, Sotto MN, Saldiva P, de Oliveira JW, Chaibub SCW, Sarasin A, Menck CFM. Mutational signatures and increased retrotransposon insertions in xeroderma pigmentosum variant skin tumors. Carcinogenesis 2023; 44:511-524. [PMID: 37195263 DOI: 10.1093/carcin/bgad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/06/2023] [Accepted: 05/05/2023] [Indexed: 05/18/2023] Open
Abstract
Xeroderma pigmentosum variant (XP-V) is an autosomal recessive disease with an increased risk of developing cutaneous neoplasms in sunlight-exposed regions. These cells are deficient in the translesion synthesis (TLS) DNA polymerase eta, responsible for bypassing different types of DNA lesions. From the exome sequencing of 11 skin tumors of a genetic XP-V patients' cluster, classical mutational signatures related to sunlight exposure, such as C>T transitions targeted to pyrimidine dimers, were identified. However, basal cell carcinomas also showed distinct C>A mutation spectra reflecting a mutational signature possibly related to sunlight-induced oxidative stress. Moreover, four samples carry different mutational signatures, with C>A mutations associated with tobacco chewing or smoking usage. Thus, XP-V patients should be warned of the risk of these habits. Surprisingly, higher levels of retrotransposon somatic insertions were also detected when the tumors were compared with non-XP skin tumors, revealing other possible causes for XP-V tumors and novel functions for the TLS polymerase eta in suppressing retrotransposition. Finally, the expected high mutation burden found in most of these tumors renders these XP patients good candidates for checkpoint blockade immunotherapy.
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Affiliation(s)
- Camila Corradi
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Juliana B Vilar
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Vanessa C Buzatto
- Molecular Oncology Center, Bioinformatics Laboratory, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Tiago A de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
- Tau GC Bioinformatics, Cotia, SP 06711-020, Brazil
| | - Ligia P Castro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Veridiana Munford
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | | | - Pedro A F Galante
- Molecular Oncology Center, Bioinformatics Laboratory, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Fernanda Orpinelli
- Molecular Oncology Center, Bioinformatics Laboratory, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Thiago L A Miller
- Molecular Oncology Center, Bioinformatics Laboratory, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, SP 05508-000, Brazil
| | - José L Buzzo
- Molecular Oncology Center, Bioinformatics Laboratory, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Mirian N Sotto
- Medical School, University of Sao Paulo, Sao Paulo, SP 01246-903, Brazil
| | - Paulo Saldiva
- Medical School, University of Sao Paulo, Sao Paulo, SP 01246-903, Brazil
| | - Jocelânio W de Oliveira
- Institute of Mathematics and Statistics, University of São Paulo, São Paulo, SP 05508-090, Brazil
| | | | - Alain Sarasin
- Laboratory of Genetic Instability and Oncogenesis, UMR8200 CNRS, Gustave Roussy, Université Paris-Sud, Villejuif, France
| | - Carlos F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
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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] [What about the content of this article? (0)] [Affiliation(s)] [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, Link R, Abreu L, Bettoni F, Marson F, Galante PAF, Masotti C, Amano MT, de Molla V, Camargo AA, Asprino PF, Sabbaga J. Suspected Germline TP53 Variants and Clonal Hematopoiesis of Indeterminate Potential: Lessons Learned From a Molecular Tumor Board. Oncologist 2023:7158600. [PMID: 37159554 DOI: 10.1093/oncolo/oyad105] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/10/2023] [Indexed: 05/11/2023] Open
Abstract
OBJECTIVE Li-Fraumeni syndrome (LFS) is a pan-cancer predisposition syndrome caused by germline pathogenic variants in the gene TP53. The interpretation of TP53 variants in clinical scenarios outside the classic LFS criteria may be challenging. Here, we report a patient affected by 2 primary cancers at later ages, who harbored a likely pathogenic TP53 at low allele frequency detected in a blood sample. METHODS The Molecular Tumor Board committee at our institution revisited the case of a patient who was enrolled in a research protocol for the investigation of genetic conditions associated with neuroendocrine tumors. Clinical, familial, and molecular data were reviewed. The patient received germline testing using a next generation sequencing multi-gene panel and was incidentally found to harbor a TP53 likely pathogenic variant, with 22% of variant allele fraction. Additional samples, including a second blood sample, oral swab, and saliva, were collected for DNA analysis. A new TP53 sequencing round was performed with the attempt to distinguish between a true constitutional germline variant and a somatically acquired variant due to aberrant clonal expansion of bone marrow precursors. RESULTS Patient's personal and familial history of cancer did not meet classic nor Chompret LFS criteria. Environmental risk factors for cancer were identified, such as alcohol abuse and tobacco exposure. The TP53 variant initially found in the next-generation sequencing was confirmed by Sanger sequencing in the previous DNA sample extracted from blood for the first analysis and in a second blood sample collected 6 years later. The TP53 variant was not detected in the DNA extracted from the oral swab and saliva samples. CONCLUSION Considering the low TP53 variant allele fraction in blood, absence of variant detection in oral swab and saliva samples, the lack of LFS clinical criteria, and history of exposure to environmental risk factors for cancer, the main hypothesis for this case was aberrant clonal expansion due to clonal hematopoiesis. Oncologists should interpret TP53 findings during germline testing with caution.
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Affiliation(s)
- Camila B Xavier
- Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Rudinei Link
- Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Leonília Abreu
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Fabiana Bettoni
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Fabiane Marson
- Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Pedro A F Galante
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Cibele Masotti
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Mariane T Amano
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | | | - Anamaria A Camargo
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Paula F Asprino
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Jorge Sabbaga
- Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
- Instituto do Câncer do Estado de São Paulo, Universidade de São Paulo, São Paulo, SP, Brazil
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8
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Kosti A, Chiou J, Guardia GDA, Lei X, Balinda H, Landry T, Lu X, Qiao M, Gilbert A, Brenner A, Galante PAF, Tiziani S, Penalva LOF. ELF4 is a critical component of a miRNA-transcription factor network and is a bridge regulator of glioblastoma receptor signaling and lipid dynamics. Neuro Oncol 2023; 25:459-470. [PMID: 35862252 PMCID: PMC10013642 DOI: 10.1093/neuonc/noac179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The loss of neurogenic tumor suppressor microRNAs miR-124, miR-128, and miR-137 is associated with glioblastoma's undifferentiated state. Most of their impact comes via the repression of a network of oncogenic transcription factors. We conducted a high-throughput functional siRNA screen in glioblastoma cells and identify E74 like ETS transcription factor 4 (ELF4) as the leading contributor to oncogenic phenotypes. METHODS In vitro and in vivo assays were used to assess ELF4 impact on cancer phenotypes. We characterized ELF4's mechanism of action via genomic and lipidomic analyses. A MAPK reporter assay verified ELF4's impact on MAPK signaling, and qRT-PCR and western blotting were used to corroborate ELF4 regulatory role on most relevant target genes. RESULTS ELF4 knockdown resulted in significant proliferation delay and apoptosis in GBM cells and long-term growth delay and morphological changes in glioma stem cells (GSCs). Transcriptomic analyses revealed that ELF4 controls two interlinked pathways: 1) Receptor tyrosine kinase signaling and 2) Lipid dynamics. ELF4 modulation directly affected receptor tyrosine kinase (RTK) signaling, as mitogen-activated protein kinase (MAPK) activity was dependent upon ELF4 levels. Furthermore, shotgun lipidomics revealed that ELF4 depletion disrupted several phospholipid classes, highlighting ELF4's importance in lipid homeostasis. CONCLUSIONS We found that ELF4 is critical for the GBM cell identity by controlling genes of two dependent pathways: RTK signaling (SRC, PTK2B, and TNK2) and lipid dynamics (LRP1, APOE, ABCA7, PLA2G6, and PITPNM2). Our data suggest that targeting these two pathways simultaneously may be therapeutically beneficial to GBM patients.
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Affiliation(s)
- Adam Kosti
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas,USA.,Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Jennifer Chiou
- Department of Nutritional Sciences, Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, Texas, USA
| | | | - Xiufen Lei
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas,USA.,Department of Nutritional Sciences, Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, Texas, USA
| | - Henriette Balinda
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas,USA
| | - Tesha Landry
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas,USA
| | - Xiyuan Lu
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas,USA.,Department of Nutritional Sciences, Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, Texas, USA
| | - Mei Qiao
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas,USA
| | - Andrea Gilbert
- Department of Pathology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Andrew Brenner
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas,USA
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, São Paulo, Brazil.,Departamento de Bioquimica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Stefano Tiziani
- Department of Nutritional Sciences, Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, Texas, USA
| | - Luiz O F Penalva
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas,USA.,Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
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9
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Rocha BGS, Picoli CC, Gonçalves BOP, Silva WN, Costa AC, Moraes MM, Costa PAC, Santos GSP, Almeida MR, Silva LM, Singh Y, Falchetti M, Guardia GDA, Guimarães PPG, Russo RC, Resende RR, Pinto MCX, Amorim JH, Azevedo VAC, Kanashiro A, Nakaya HI, Rocha EL, Galante PAF, Mintz A, Frenette PS, Birbrair A. Tissue-resident glial cells associate with tumoral vasculature and promote cancer progression. Angiogenesis 2023; 26:129-166. [PMID: 36183032 DOI: 10.1007/s10456-022-09858-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/08/2022] [Indexed: 11/01/2022]
Abstract
Cancer cells are embedded within the tissue and interact dynamically with its components during cancer progression. Understanding the contribution of cellular components within the tumor microenvironment is crucial for the success of therapeutic applications. Here, we reveal the presence of perivascular GFAP+/Plp1+ cells within the tumor microenvironment. Using in vivo inducible Cre/loxP mediated systems, we demonstrated that these cells derive from tissue-resident Schwann cells. Genetic ablation of endogenous Schwann cells slowed down tumor growth and angiogenesis. Schwann cell-specific depletion 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 tumor biopsies revealed that increased expression of Schwann cell-related genes within melanoma was associated with improved survival. Collectively, our study suggests that Schwann cells regulate tumor progression, indicating that manipulation of Schwann cells may provide a valuable tool to improve cancer patients' outcomes.
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Affiliation(s)
- Beatriz G S Rocha
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Caroline C Picoli
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bryan O P Gonçalves
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Walison N Silva
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alinne C Costa
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Michele M Moraes
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Pedro A C Costa
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gabryella S P Santos
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Milla R Almeida
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luciana M Silva
- Department of Cell Biology, Ezequiel Dias Foundation, Belo Horizonte, MG, Brazil
| | - Youvika Singh
- Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Marcelo Falchetti
- Department of Microbiology and Immunology, Federal University of Santa Catarina, Florianópolis, Brazil
| | | | - Pedro P G Guimarães
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Remo C Russo
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rodrigo R Resende
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Mauro C X Pinto
- Institute of Biological Sciences, Federal University of Goiás, Goiânia, GO, Brazil
| | - Jaime H Amorim
- Center of Biological Sciences and Health, Federal University of Western Bahia, Barreiras, BA, Brazil
| | - Vasco A C Azevedo
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alexandre Kanashiro
- Department of Dermatology, University of Wisconsin-Madison, Medical Sciences Center, Rm 4385, 1300 University Avenue, Madison, WI, 53706, USA
| | | | - Edroaldo L Rocha
- Department of Microbiology and Immunology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP, Brazil
| | - Akiva Mintz
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Paul S Frenette
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, NY, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
- Department of Dermatology, University of Wisconsin-Madison, Medical Sciences Center, Rm 4385, 1300 University Avenue, Madison, WI, 53706, USA.
- Department of Radiology, Columbia University Medical Center, New York, NY, USA.
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10
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Barreiro RAS, Guardia GDA, Meliso FM, Lei X, Li WQ, Savio A, Fellermeyer M, Conceição HB, Mercuri RLV, Landry T, Qiao M, Blazquez L, Ule J, Penalva LOF, Galante PAF. The paralogues MAGOH and MAGOHB are oncogenic factors in high-grade gliomas and safeguard the splicing of cell division and cell cycle genes. RNA Biol 2023; 20:311-322. [PMID: 37294214 DOI: 10.1080/15476286.2023.2221511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023] Open
Abstract
The exon junction complex (EJC) plays key roles throughout the lifespan of RNA and is particularly relevant in the nervous system. We investigated the roles of two EJC members, the paralogs MAGOH and MAGOHB, with respect to brain tumour development. High MAGOH/MAGOHB expression was observed in 14 tumour types; glioblastoma (GBM) showed the greatest difference compared to normal tissue. Increased MAGOH/MAGOHB expression was associated with poor prognosis in glioma patients, while knockdown of MAGOH/MAGOHB affected different cancer phenotypes. Reduced MAGOH/MAGOHB expression in GBM cells caused alterations in the splicing profile, including re-splicing and skipping of multiple exons. The binding profiles of EJC proteins indicated that exons affected by MAGOH/MAGOHB knockdown accumulated fewer complexes on average, providing a possible explanation for their sensitivity to MAGOH/MAGOHB knockdown. Transcripts (genes) showing alterations in the splicing profile are mainly implicated in cell division, cell cycle, splicing, and translation. We propose that high MAGOH/MAGOHB levels are required to safeguard the splicing of genes in high demand in scenarios requiring increased cell proliferation (brain development and GBM growth), ensuring efficient cell division, cell cycle regulation, and gene expression (splicing and translation). Since differentiated neuronal cells do not require increased MAGOH/MAGOHB expression, targeting these paralogs is a potential option for treating GBM.
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Affiliation(s)
- Rodrigo A S Barreiro
- Molecular Oncology Center, Hospital Sirio-Libanes, São Paulo, Brazil
- Departamento de Bioquimica, Instituto de Química - Universidade de São Paulo, São Paulo, Brazil
| | | | - Fabiana M Meliso
- Molecular Oncology Center, Hospital Sirio-Libanes, São Paulo, Brazil
| | - Xiufen Lei
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Wei-Qing Li
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Andre Savio
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Martin Fellermeyer
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Helena B Conceição
- Molecular Oncology Center, Hospital Sirio-Libanes, São Paulo, Brazil
- Programa Interunidades Em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - Rafael L V Mercuri
- Molecular Oncology Center, Hospital Sirio-Libanes, São Paulo, Brazil
- Programa Interunidades Em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - Tesha Landry
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Mei Qiao
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Lorea Blazquez
- The Francis Crick Institute, London, UK
- UK Dementia Research Institute, King's College London, London, UK
| | - Jernej Ule
- The Francis Crick Institute, London, UK
- UK Dementia Research Institute, King's College London, London, UK
| | - Luiz O F Penalva
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Pedro A F Galante
- Molecular Oncology Center, Hospital Sirio-Libanes, São Paulo, Brazil
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11
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Giolito MV, La Rosa T, Farhat D, Bodoirat S, Guardia GDA, Domon‐Dell C, Galante PAF, Freund J, Plateroti M. Regulation of the THRA gene, encoding the thyroid hormone nuclear receptor TRα1, in intestinal lesions. Mol Oncol 2022; 16:3975-3993. [PMID: 36217307 PMCID: PMC9718118 DOI: 10.1002/1878-0261.13298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 07/05/2022] [Accepted: 07/29/2022] [Indexed: 12/24/2022] Open
Abstract
The THRA gene, encoding the thyroid hormone nuclear receptor TRα1, is expressed in an increasing gradient at the bottom of intestinal crypts, overlapping with high Wnt and Notch activities. Importantly, THRA is upregulated in colorectal cancers, particularly in the high-Wnt molecular subtype. The basis of this specific and/or altered expression pattern has remained unknown. To define the mechanisms controlling THRA transcription and TRα1 expression, we used multiple in vitro and ex vivo approaches. Promoter analysis demonstrated that transcription factors important for crypt homeostasis and altered in colorectal cancers, such as transcription factor 7-like 2 (TCF7L2; Wnt pathway), recombining binding protein suppressor of hairless (RBPJ; Notch pathway), and homeobox protein CDX2 (epithelial cell identity), modulate THRA activity. Specifically, although TCF7L2 and CDX2 stimulated THRA, RBPJ induced its repression. In-depth analysis of the Wnt-dependent increase showed direct regulation of the THRA promoter in cells and of TRα1 expression in murine enteroids. Given our previous results on the control of the Wnt pathway by TRα1, our new results unveil a complex regulatory loop and synergy between these endocrine and epithelial-cell-intrinsic signals. Our work describes, for the first time, the regulation of the THRA gene in specific cell and tumor contexts.
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Affiliation(s)
- Maria Virginia Giolito
- Inserm, IRFAC/UMR‐S1113, FMTS, Université de StrasbourgFrance,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de LyonFrance
| | - Théo La Rosa
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de LyonFrance,Present address:
Stem‐Cell and Brain Research Institute, U1208 INSERM, USC1361 INRABronFrance
| | - Diana Farhat
- Inserm, IRFAC/UMR‐S1113, FMTS, Université de StrasbourgFrance,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de LyonFrance
| | | | | | | | | | | | - Michelina Plateroti
- Inserm, IRFAC/UMR‐S1113, FMTS, Université de StrasbourgFrance,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de LyonFrance
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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de Souza A, de Freitas Amorim VM, Guardia GDA, dos Santos FRC, dos Santos FF, de Souza RF, de Araujo Juvenal G, Huang Y, Ge P, Jiang Y, Li C, Paudel P, Ulrich H, Galante PAF, Guzzo CR. Molecular Dynamics Analysis of Fast-Spreading Severe Acute Respiratory Syndrome Coronavirus 2 Variants and Their Effects on the Interaction with Human Angiotensin-Converting Enzyme 2. ACS Omega 2022; 7:30700-30709. [PMID: 36068861 PMCID: PMC9437663 DOI: 10.1021/acsomega.1c07240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is evolving with mutations in the spike protein, especially in the receptor-binding domain (RBD). The failure of public health measures in some countries to contain the spread of the disease has given rise to novel viral variants with increased transmissibility. However, key questions about how quickly the variants can spread remain unclear. Herein, we performed a structural investigation using molecular dynamics simulations and determined dissociation constant (K D) values using surface plasmon resonance assays of three fast-spreading SARS-CoV-2 variants, alpha, beta, and gamma, as well as genetic factors in host cells that may be related to the viral infection. Our results suggest that the SARS-CoV-2 variants facilitate their entry into the host cell by moderately increased binding affinities to the human ACE2 receptor, different torsions in hACE2 mediated by RBD variants, and an increased spike exposure time to proteolytic enzymes. We also found that other host cell aspects, such as gene and isoform expression of key genes for the infection (ACE2, FURIN, and TMPRSS2), may have few contributions to the SARS-CoV-2 variant infectivity. In summary, we concluded that a combination of viral and host cell factors allows SARS-CoV-2 variants to increase their abilities to spread faster than the wild type.
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Affiliation(s)
- Anacleto
Silva de Souza
- Department
of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-900, Brazil
| | | | | | - Felipe R. C. dos Santos
- Molecular
Oncology Center, Hospital Sírio Libanes, São Paulo 01308-050, Brazil
- Programa
Interunidades Em Bioinformática, University of São Paulo, São Paulo 05508-900, Brazil
| | - Filipe F. dos Santos
- Molecular
Oncology Center, Hospital Sírio Libanes, São Paulo 01308-050, Brazil
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-900, Brazil
| | - Robson Francisco de Souza
- Department
of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-900, Brazil
| | | | - Yihua Huang
- ACROBiosystems
Inc., 8 N. Hongda Rd.,
Beijing Economic-Technological Development Area, Beijing 100176, China
| | - Pingju Ge
- ACROBiosystems
Inc., 8 N. Hongda Rd.,
Beijing Economic-Technological Development Area, Beijing 100176, China
| | - Yinan Jiang
- ACROBiosystems
Inc., 8 N. Hongda Rd.,
Beijing Economic-Technological Development Area, Beijing 100176, China
| | - Coco Li
- ACROBiosystems
Inc., 8 N. Hongda Rd.,
Beijing Economic-Technological Development Area, Beijing 100176, China
| | - Prajwal Paudel
- ACROBiosystems
Inc., 8 N. Hongda Rd.,
Beijing Economic-Technological Development Area, Beijing 100176, China
| | - Henning Ulrich
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-900, Brazil
| | - Pedro A. F. Galante
- Molecular
Oncology Center, Hospital Sírio Libanes, São Paulo 01308-050, Brazil
| | - Cristiane Rodrigues Guzzo
- Department
of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-900, Brazil
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14
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Lima ARJ, de Sousa Silva HG, Poubel SB, Rosón JN, de Lima LPO, Costa-Silva HM, Gonçalves CS, Galante PAF, Holetz F, Motta MCM, Silber AM, Elias MC, da Cunha JPC. Correction to: Open chromatin analysis in Trypanosoma cruzi life forms highlights critical differences in genomic compartments and developmental regulation at tDNA loci. Epigenetics Chromatin 2022; 15:25. [PMID: 35794678 PMCID: PMC9258163 DOI: 10.1186/s13072-022-00459-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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15
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Lima ARJ, Silva HGD, Poubel S, Rosón JN, de Lima LPO, Costa-Silva HM, Gonçalves CS, Galante PAF, Holetz F, Motta MCMM, Silber AM, Elias MC, da Cunha JPC. Open chromatin analysis in Trypanosoma cruzi life forms highlights critical differences in genomic compartments and developmental regulation at tDNA loci. Epigenetics Chromatin 2022; 15:22. [PMID: 35650626 PMCID: PMC9158160 DOI: 10.1186/s13072-022-00450-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/18/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Genomic organization and gene expression regulation in trypanosomes are remarkable because protein-coding genes are organized into codirectional gene clusters with unrelated functions. Moreover, there is no dedicated promoter for each gene, resulting in polycistronic gene transcription, with posttranscriptional control playing a major role. Nonetheless, these parasites harbor epigenetic modifications at critical regulatory genome features that dynamically change among parasite stages, which are not fully understood. RESULTS Here, we investigated the impact of chromatin changes in a scenario commanded by posttranscriptional control exploring the parasite Trypanosoma cruzi and its differentiation program using FAIRE-seq approach supported by transmission electron microscopy. We identified differences in T. cruzi genome compartments, putative transcriptional start regions, and virulence factors. In addition, we also detected a developmental chromatin regulation at tRNA loci (tDNA), which could be linked to the intense chromatin remodeling and/or the translation regulatory mechanism required for parasite differentiation. We further integrated the open chromatin profile with public transcriptomic and MNase-seq datasets. Strikingly, a positive correlation was observed between active chromatin and steady-state transcription levels. CONCLUSION Taken together, our results indicate that chromatin changes reflect the unusual gene expression regulation of trypanosomes and the differences among parasite developmental stages, even in the context of a lack of canonical transcriptional control of protein-coding genes.
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Affiliation(s)
- Alex Ranieri Jerônimo Lima
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Herbert Guimarães de
Sousa Silva
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil ,grid.411249.b0000 0001 0514 7202Departamento de Microbiologia, Universidade Federal de São Paulo, Escola Paulista de Medicina, Imunologia E Parasitologia, São Paulo, SP Brazil
| | - Saloe Poubel
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Juliana Nunes Rosón
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil ,grid.411249.b0000 0001 0514 7202Departamento de Microbiologia, Universidade Federal de São Paulo, Escola Paulista de Medicina, Imunologia E Parasitologia, São Paulo, SP Brazil
| | - Loyze Paola Oliveira de Lima
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Héllida Marina Costa-Silva
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Camila Silva Gonçalves
- grid.8536.80000 0001 2294 473XLaboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal Do Rio de Janeiro, IBCCF, CCS, UFRJ, Cidade Universitária, Rio de Janeiro, RJ Brazil ,Centro Nacional de Biologia Estrutural E Bioimagem, Rio de Janeiro, RJ Brazil
| | - Pedro A. F. Galante
- grid.413471.40000 0000 9080 8521Centro de Oncologia Molecular, Hospital Sírio Libanês, São Paulo, SP Brazil
| | - Fabiola Holetz
- grid.418068.30000 0001 0723 0931Instituto Carlos Chagas, Fiocruz, Curitiba, PR Brazil
| | - Maria Cristina Machado M. Motta
- grid.8536.80000 0001 2294 473XLaboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal Do Rio de Janeiro, IBCCF, CCS, UFRJ, Cidade Universitária, Rio de Janeiro, RJ Brazil ,Centro Nacional de Biologia Estrutural E Bioimagem, Rio de Janeiro, RJ Brazil
| | - Ariel M. Silber
- grid.11899.380000 0004 1937 0722Universidade de São Paulo, São Paulo, SP Brazil
| | - M. Carolina Elias
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil. .,Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil.
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16
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de Souza AS, de Freitas Amorim VM, Guardia GDA, dos Santos FF, Ulrich H, Galante PAF, de Souza RF, Guzzo CR. Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern: A Perspective for Emerging More Transmissible and Vaccine-Resistant Strains. Viruses 2022; 14:827. [PMID: 35458557 PMCID: PMC9029021 DOI: 10.3390/v14040827] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 02/06/2023] Open
Abstract
Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) are constantly threatening global public health. With no end date, the pandemic persists with the emergence of novel variants that threaten the effectiveness of diagnostic tests and vaccines. Mutations in the Spike surface protein of the virus are regularly observed in the new variants, potentializing the emergence of novel viruses with different tropism from the current ones, which may change the severity and symptoms of the disease. Growing evidence has shown that mutations are being selected in favor of variants that are more capable of evading the action of neutralizing antibodies. In this context, the most important factor guiding the evolution of SARS-CoV-2 is its interaction with the host's immune system. Thus, as current vaccines cannot block the transmission of the virus, measures complementary to vaccination, such as the use of masks, hand hygiene, and keeping environments ventilated remain essential to delay the emergence of new variants. Importantly, in addition to the involvement of the immune system in the evolution of the virus, we highlight several chemical parameters that influence the molecular interactions between viruses and host cells during invasion and are also critical tools making novel variants more transmissible. In this review, we dissect the impacts of the Spike mutations on biological parameters such as (1) the increase in Spike binding affinity to hACE2; (2) bound time for the receptor to be cleaved by the proteases; (3) how mutations associate with the increase in RBD up-conformation state in the Spike ectodomain; (4) expansion of uncleaved Spike protein in the virion particles; (5) increment in Spike concentration per virion particles; and (6) evasion of the immune system. These factors play key roles in the fast spreading of SARS-CoV-2 variants of concern, including the Omicron.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Vitor Martins de Freitas Amorim
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Gabriela D. A. Guardia
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Filipe F. dos Santos
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Pedro A. F. Galante
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
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17
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Barreiro RAS, Sabbaga J, Rossi BM, Achatz MIW, Bettoni F, Camargo AA, Asprino PF, A F Galante P. Monoallelic deleterious MUTYH germline variants as a driver for tumorigenesis. J Pathol 2021; 256:214-222. [PMID: 34816434 DOI: 10.1002/path.5829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/14/2021] [Accepted: 10/28/2021] [Indexed: 01/06/2023]
Abstract
MUTYH encodes a glycosylase involved in the base excision repair of DNA. Biallelic pathogenic germline variants in MUTYH cause an autosomal recessive condition known as MUTYH-associated adenomatous polyposis and consequently increase the risk of colorectal cancer. However, reports of increased cancer risk in individuals carrying only one defective MUTYH allele are controversial and based on studies involving few individuals. Here, we describe a comprehensive investigation of monoallelic pathogenic MUTYH germline variants in 10,389 cancer patients across 33 different tumour types and 117,000 healthy individuals. Our results indicate that monoallelic pathogenic MUTYH germline variants can lead to tumorigenesis through a mechanism of somatic loss of heterozygosity of the functional MUTYH allele in the tumour. We confirmed that the frequency of monoallelic pathogenic MUTYH germline variants is higher in individuals with cancer than in the general population, although this frequency is not homogeneous among tumour types. We also demonstrated that the MUTYH mutational signature is present only in tumours with loss of the functional allele and found that the characteristic MUTYH base substitution (C>A) increases stop-codon generation. We identified key genes that are affected during tumorigenesis. In conclusion, we propose that carriers of the monoallelic pathogenic MUTYH germline variant are at a higher risk of developing tumours, especially those with frequent loss of heterozygosity events, such as adrenal adenocarcinoma, although the overall risk is still low. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Rodrigo Araujo Sequeira Barreiro
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, Brazil
| | - Jorge Sabbaga
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Benedito M Rossi
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | | | - Fabiana Bettoni
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Anamaria A Camargo
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Paula F Asprino
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
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18
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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: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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
- grid.8430.f0000 0001 2181 4888Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Walison N. Silva
- grid.8430.f0000 0001 2181 4888Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Pedro H. D. M. Prazeres
- grid.8430.f0000 0001 2181 4888Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Caroline C. Picoli
- grid.8430.f0000 0001 2181 4888Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Gabriela D. A. Guardia
- grid.413471.40000 0000 9080 8521Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP Brasil
| | - Alinne C. Costa
- grid.8430.f0000 0001 2181 4888Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Mariana A. Oliveira
- grid.8430.f0000 0001 2181 4888Departamento de Bioquimica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Pedro P. G. Guimarães
- grid.8430.f0000 0001 2181 4888Departamento de Fisiologia e Biofísica, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Ricardo Gonçalves
- grid.8430.f0000 0001 2181 4888Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Mauro C. X. Pinto
- grid.411195.90000 0001 2192 5801Departamento de Farmacologia, Universidade Federal de Goiás, Goiânia, GO Brasil
| | - Jaime H. Amorim
- grid.472638.c0000 0004 4685 7608Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Barreiras, BA Brasil
| | - Vasco A. C. Azevedo
- grid.8430.f0000 0001 2181 4888Departamento de Genetica, Ecologia e Evolucao, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Rodrigo R. Resende
- grid.8430.f0000 0001 2181 4888Departamento de Bioquimica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Remo C. Russo
- grid.8430.f0000 0001 2181 4888Departamento de Fisiologia e Biofísica, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Thiago M. Cunha
- grid.11899.380000 0004 1937 0722Departamento de Farmacologia, Universidade de São Paulo, Ribeirão Preto, SP Brasil
| | - Pedro A. F. Galante
- grid.413471.40000 0000 9080 8521Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP Brasil
| | - Akiva Mintz
- grid.239585.00000 0001 2285 2675Department 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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19
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dos Santos FRC, Guardia GDA, dos Santos FF, Ohara D, Galante PAF. Reboot: a straightforward approach to identify genes and splicing isoforms associated with cancer patient prognosis. NAR Cancer 2021; 3:zcab024. [PMID: 34316711 PMCID: PMC8210018 DOI: 10.1093/narcan/zcab024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/26/2021] [Accepted: 06/03/2021] [Indexed: 12/20/2022] Open
Abstract
Nowadays, the massive amount of data generated by modern sequencing technologies provides an unprecedented opportunity to find genes associated with cancer patient prognosis, connecting basic and translational research. However, treating high dimensionality of gene expression data and integrating it with clinical variables are major challenges to perform these analyses. Here, we present Reboot, an integrative approach to find and validate genes and transcripts (splicing isoforms) associated with cancer patient prognosis from high dimensional expression datasets. Reboot innovates by using a multivariate strategy with penalized Cox regression (LASSO method) combined with a bootstrap approach, in addition to statistical tests and plots to support the findings. Applying Reboot on data from 154 glioblastoma patients, we identified a three-gene signature (IKBIP, OSMR, PODNL1) whose increased derived risk score was significantly associated with worse patients' prognosis. Similarly, Reboot was able to find a seven-splicing isoforms signature related to worse overall survival in 177 pancreatic adenocarcinoma patients with elevated risk scores after uni- and multivariate analyses. In summary, Reboot is an efficient, intuitive and straightforward way of finding genes or splicing isoforms signatures relevant to patient prognosis, which can democratize this kind of analysis and shed light on still under-investigated cancer-related genes and splicing isoforms.
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Affiliation(s)
- Felipe R C dos Santos
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP 01308-060, Brazil
- Programa Interunidades em Bioinformatica, Universidade de São Paulo, Sao Paulo, SP 05508-090, Brazil
| | - Gabriela D A Guardia
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP 01308-060, Brazil
| | - Filipe F dos Santos
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP 01308-060, Brazil
- Departamento de Bioquimica, Universidade de Sao Paulo, SP 05508-000, Brazil
| | - Daniel T Ohara
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP 01308-060, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP 01308-060, Brazil
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20
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Miller TLA, Orpinelli Rego F, Buzzo JLL, Galante PAF. sideRETRO: a pipeline for identifying somatic and polymorphic insertions of processed pseudogenes or retrocopies. Bioinformatics 2021; 37:419-421. [PMID: 32717039 DOI: 10.1093/bioinformatics/btaa689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/29/2020] [Accepted: 07/23/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Retrocopies or processed pseudogenes are gene copies resulting from mRNA retrotransposition. These gene duplicates can be fixed, somatically inserted or polymorphic in the genome. However, knowledge regarding unfixed retrocopies (retroCNVs) is still limited, and the development of computational tools for effectively identifying and genotyping them is an urgent need. RESULTS Here, we present sideRETRO, a pipeline dedicated not only to detecting retroCNVs in whole-genome or whole-exome sequencing data but also to revealing their insertion sites, zygosity and genomic context and classifying them as somatic or polymorphic events. We show that sideRETRO can identify novel retroCNVs and genotype them, in addition to finding polymorphic retroCNVs in whole-genome and whole-exome data. Therefore, sideRETRO fills a gap in the literature and presents an efficient and straightforward algorithm to accelerate the study of bona fide retroCNVs. AVAILABILITY AND IMPLEMENTATION sideRETRO is available at https://github.com/galantelab/sideRETRO. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Thiago L A Miller
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo 01308-060, Brazil.,Departmento de Bioquímica, Universidade de São Paulo, São Paulo 05508-000, Brazil
| | | | - José Leonel L Buzzo
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo 01308-060, Brazil.,Departmento de Bioquímica, Universidade de São Paulo, São Paulo 05508-000, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo 01308-060, Brazil
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21
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Frau C, Jamard C, Delpouve G, Guardia GDA, Machon C, Pilati C, Nevé CL, Laurent-Puig P, Guitton J, Galante PAF, Penalva LO, Freund JN, de la Fouchardiere C, Plateroti M. Deciphering the Role of Intestinal Crypt Cell Populations in Resistance to Chemotherapy. Cancer Res 2021; 81:2730-2744. [PMID: 33741693 DOI: 10.1158/0008-5472.can-20-2450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 02/11/2021] [Accepted: 03/18/2021] [Indexed: 12/24/2022]
Abstract
Intestinal crypts are composed of heterogeneous and highly plastic cell populations. Lgr5high-stem cells (SC) are responsible for homeostatic renewal, but other cells can revert to an SC-like phenotype to maintain epithelial integrity. Despite their distinct roles in orchestrating homeostasis, both populations have been designated as the putative "cell-of-origin" of colorectal cancer. However, their respective involvement in the emergence of drug-resistant cancer SCs (CSC), responsible for tumor relapse and associated with poor outcome of colorectal cancer, remains elusive. In this context, the intestinal SC/progenitor-marker Musashi1 (MSI1) is interesting as it plays important functions in intestinal homeostasis and is frequently overexpressed in human colorectal cancer. Therefore, our aims were: (i) to study the impact of chemotherapy on Lgr5-expressing and MSI1-expressing cell populations, (ii) to explore the effect of increased MSI1 levels in response to treatment, and (iii) to evaluate the relevance in human colorectal cancer. Engineered mouse models treated with the therapeutic agent 5-fluorouracil showed that upon increased MSI1 levels, Lgr5high SCs remain sensitive while Lgr5low progenitors reprogram to a drug-resistant phenotype. This resulted in the expansion of an MSI1-expressing cell subpopulation with improved resistance to DNA damage and increased detoxification, typical properties of dormant-CSCs that can reactivate after chemotherapy. Analysis in patients with colorectal cancer revealed a correlation between MSI1 levels and tumor grading, CSC phenotype, and chemoresistance. Altogether, these results shed new light on the biology and plasticity of normal crypt and cancer cell populations and also open new perspectives to target MSI1 to improve chemotherapy outcome. SIGNIFICANCE: This study unveils paradoxical roles for MSI1, underlining its importance in facilitating intestinal regeneration upon injury but also unraveling its new function in drug-resistant colorectal cancer stem cells.
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Affiliation(s)
- Carla Frau
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Lyon, France
| | - Catherine Jamard
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Lyon, France
| | - Gaspard Delpouve
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Lyon, France
| | | | - Christelle Machon
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Lyon, France.,Hospices Civils de Lyon, Service de Biochimie et Pharmaco-toxicologie, Centre Hospitalier Lyon-Sud, Pierre Bénite, France
| | - Camilla Pilati
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Paris, France
| | - Clémentine Le Nevé
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Lyon, France
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Paris, France.,Department of Biology, AP-HP, Hôpital Européen Georges Pompidou, Paris, France
| | - Jérôme Guitton
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Lyon, France.,Hospices Civils de Lyon, Service de Biochimie et Pharmaco-toxicologie, Centre Hospitalier Lyon-Sud, Pierre Bénite, France
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Luiz O Penalva
- Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Jean-Noel Freund
- Université de Strasbourg, Inserm, IRFAC/UMR-S1113, Strasbourg, France
| | | | - Michelina Plateroti
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Lyon, France.
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22
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Kosti A, de Araujo PR, Li WQ, Guardia GDA, Chiou J, Yi C, Ray D, Meliso F, Li YM, Delambre T, Qiao M, Burns SS, Lorbeer FK, Georgi F, Flosbach M, Klinnert S, Jenseit A, Lei X, Sandoval CR, Ha K, Zheng H, Pandey R, Gruslova A, Gupta YK, Brenner A, Kokovay E, Hughes TR, Morris QD, Galante PAF, Tiziani S, Penalva LOF. The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation. Genome Biol 2020; 21:195. [PMID: 32762776 PMCID: PMC7412812 DOI: 10.1186/s13059-020-02115-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/22/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND RNA-binding proteins (RBPs) function as master regulators of gene expression. Alterations in RBP expression and function are often observed in cancer and influence critical pathways implicated in tumor initiation and growth. Identification and characterization of oncogenic RBPs and their regulatory networks provide new opportunities for targeted therapy. RESULTS We identify the RNA-binding protein SERBP1 as a novel regulator of glioblastoma (GBM) development. High SERBP1 expression is prevalent in GBMs and correlates with poor patient survival and poor response to chemo- and radiotherapy. SERBP1 knockdown causes delay in tumor growth and impacts cancer-relevant phenotypes in GBM and glioma stem cell lines. RNAcompete identifies a GC-rich region as SERBP1-binding motif; subsequent genomic and functional analyses establish SERBP1 regulation role in metabolic routes preferentially used by cancer cells. An important consequence of these functions is SERBP1 impact on methionine production. SERBP1 knockdown decreases methionine levels causing a subsequent reduction in histone methylation as shown for H3K27me3 and upregulation of genes associated with neurogenesis, neuronal differentiation, and function. Further analysis demonstrates that several of these genes are downregulated in GBM, potentially through epigenetic silencing as indicated by the presence of H3K27me3 sites. CONCLUSIONS SERBP1 is the first example of an RNA-binding protein functioning as a central regulator of cancer metabolism and indirect modulator of epigenetic regulation in GBM. By bridging these two processes, SERBP1 enhances glioma stem cell phenotypes and contributes to GBM poorly differentiated state.
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Affiliation(s)
- Adam Kosti
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Patricia Rosa de Araujo
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Wei-Qing Li
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
- Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Gabriela D. A. Guardia
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil
| | - Jennifer Chiou
- Department of Nutritional Sciences, Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, TX 78712 USA
| | - Caihong Yi
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1 Canada
| | - Fabiana Meliso
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil
| | - Yi-Ming Li
- Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Talia Delambre
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Mei Qiao
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Suzanne S. Burns
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Franziska K. Lorbeer
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Fanny Georgi
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Markus Flosbach
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Sarah Klinnert
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Anne Jenseit
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Xiufen Lei
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | | | - Kevin Ha
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1 Canada
| | - Hong Zheng
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1 Canada
| | - Renu Pandey
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | | | - Yogesh K. Gupta
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Andrew Brenner
- Mays Cancer Center, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Erzsebet Kokovay
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Timothy R. Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8 Canada
- Canadian Institute for Advanced Research, MaRS Centre, West Tower, 661 University Avenue, Suite 505, Toronto, ON M5G 1M1 Canada
| | - Quaid D. Morris
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8 Canada
- Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1 Canada
| | - Pedro A. F. Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil
| | - Stefano Tiziani
- Department of Nutritional Sciences, Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, TX 78712 USA
| | - Luiz O. F. Penalva
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229 USA
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23
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Bastos DA, Mattedi RL, Barreiro R, dos Santos FF, Buzatto V, Masotti C, Souza JM, de Lima MZT, Friguglietti GW, Dzik C, Jardim DLF, Coelho R, Ribeiro Filho LA, Cordeiro MD, Nahas WC, de Mello ES, Chammas R, Reis LFL, Bettoni F, Galante PAF, Camargo AA. Genomic Biomarkers and Underlying Mechanism of Benefit from BCG Immunotherapy in Non-Muscle Invasive Bladder Cancer. Bladder Cancer 2020. [DOI: 10.3233/blc-200289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND: Optimal therapy for high-risk non-muscle invasive bladder cancer (NMIBC) includes intravesical instillation of Bacillus Calmette-Guérin (BCG). However, about 25-45% of patients do not benefit from BCG immunotherapy, and there is no biomarker to guide therapy. Also, many questions regarding BCG mechanisms of action remain unanswered. OBJECTIVE: To identify genomic biomarkers and characterize the underlying mechanism of benefit from BCG in NMIBC. PATIENTS AND METHODS: Pre-treatment archival index-tumors of 35 patients with NMIBC treated with BCG were analyzed by whole-exome sequencing (WES). Tumor mutation burden (TMB) and neoantigen load (NAL) were correlated with BCG response rate (RR) and recurrence-free survival (RFS). The presence of deleterious mutations in DNA damage response (DDR) genes was also compared between BCG-responsive (BCG-R, N = 17) and unresponsive (BCG-UR, N = 18) subgroups. RESULTS: TMB and NAL were higher in BCG-R compared to BCG-UR patients (median TMB 4.9 vs. 2.8 mutations/Mb, P = 0.017 and median NAL 100 vs. 65 neoantigens, P = 0.032). Improved RR and RFS were observed in patients with high vs. low TMB (RR 71% vs. 28%, P = 0.011 and mRFS 38.0 vs. 15.0 months, P = 0.009) and with high vs. low NAL (RR 71% vs. 28%, P = 0.011 and mRFS 36.0 vs. 18.5 months, P = 0.016). The presence of deleterious mutations in DDR genes was associated with improved RFS (mRFS 35.5 vs. 11.0 months, P = 0.017). CONCLUSIONS: In our cohort, improved outcomes after BCG immunotherapy were observed in patients with high TMB, high NAL and deleterious mutations in DDR genes. BCG may induce tumor-specific immune response by enhancing the recognition of neoantigens.
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Affiliation(s)
- Diogo A. Bastos
- Medical Oncology, Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
- Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Romulo L. Mattedi
- Department of Pathology, Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | - Rodrigo Barreiro
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
- Department of Biochemistry, Chemistry Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Vanessa Buzatto
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Cibele Masotti
- Translational Oncology Center, Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | - Jussara M. Souza
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | | | | | - Carlos Dzik
- Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | | | - Rafael Coelho
- Department of Urology, Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | | | - Maurício D. Cordeiro
- Department of Urology, Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | - William C. Nahas
- Department of Urology, Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | - Evandro S. de Mello
- Department of Pathology, Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | - Roger Chammas
- Translational Oncology Center, Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | | | - Fabiana Bettoni
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
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24
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Santiago KM, Castro LP, Neto JPD, de Nóbrega AF, Pinto CAL, Ashton-Prolla P, Pinto E Vairo F, de Medeiros PFV, Ribeiro EM, Ribeiro BFR, do Valle FF, Doriqui MJR, Leite CHB, Rocha RM, Moura LMS, Munford V, Galante PAF, Menck CFM, Rogatto SR, Achatz MI. Comprehensive germline mutation analysis and clinical profile in a large cohort of Brazilian xeroderma pigmentosum patients. J Eur Acad Dermatol Venereol 2020; 34:2392-2401. [PMID: 32239545 DOI: 10.1111/jdv.16405] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/05/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Xeroderma pigmentosum (XP) patients present a high risk of developing skin cancer and other complications at an early age. This disease is characterized by mutations in the genes related to the DNA repair system. OBJECTIVES To describe the clinical and molecular findings in a cohort of 32 Brazilian individuals who received a clinical diagnosis of XP. METHODS Twenty-seven families were screened for germline variants in eight XP-related genes. RESULTS All patients (N = 32) were diagnosed with bi-allelic germline pathogenic or potentially pathogenic variants, including nine variants previously undescribed. The c.2251-1G>C XPC pathogenic variant, reported as the founder mutation in Comorian and Pakistani patients, was observed in 15 cases in homozygous or compound heterozygous. Seven homozygous patients for POLH/XPV variants developed their symptoms by an average age of 7.7 years. ERCC2/XPD, DDB2/XPE and ERCC5/XPG variants were found in a few patients. Aside from melanoma and non-melanoma skin tumours, a set of patients developed skin sebaceous carcinoma, leiomyosarcoma, angiosarcoma, mucoepidermoid carcinoma, gastric adenocarcinoma and serous ovarian carcinoma. CONCLUSIONS We reported a high frequency of XPC variants in 32 XP Brazilian patients. Nine new variants in XP-related genes, unexpected non-skin cancer lesions and an anticipation of the clinical manifestation in POLH/XPV cases were also described.
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Affiliation(s)
- K M Santiago
- Department of Oncogenetics, A.C.Camargo Cancer Center, São Paulo, São Paulo, Brazil.,International Research Center (CIPE), A.C.Camargo Cancer Center, São Paulo, São Paulo, Brazil
| | - L P Castro
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, São Paulo, Brazil
| | - J P D Neto
- Department of Skin Cancer, A.C.Camargo Cancer Center, São Paulo, São Paulo, Brazil
| | - A F de Nóbrega
- Department of Oncogenetics, A.C.Camargo Cancer Center, São Paulo, São Paulo, Brazil.,International Research Center (CIPE), A.C.Camargo Cancer Center, São Paulo, São Paulo, Brazil
| | - C A L Pinto
- Department of Pathology, A.C.Camargo Cancer Center, São Paulo, São Paulo, Brazil
| | - P Ashton-Prolla
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil.,Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - F Pinto E Vairo
- Center for Individualized Medicine and Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - P F V de Medeiros
- University Hospital Alcides Carneiro, Federal University of Campina Grande, Campina Grande, Paraíba, Brazil
| | - E M Ribeiro
- Associação Cearense de Doenças Genéticas, Fortaleza, Ceará, Brazil
| | - B F R Ribeiro
- Children's Hospital, Secretaria de Estado de Saúde do Acre, Rio Branco, Acre, Brazil
| | - F F do Valle
- Amazonas Federal University, Manaus, Amazonas, Brazil
| | - M J R Doriqui
- Hospital Infantil Dr Juvêncio Mattos, São Luís, Maranhão, Brazil
| | - C H B Leite
- Department of Radiation Oncology, Instituto do Câncer do Ceará, Fortaleza, Ceará, Brazil
| | - R M Rocha
- Gynecology Department, Paulista Medicine School, Federal University of São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| | - L M S Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, São Paulo, Brazil
| | - V Munford
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, São Paulo, Brazil
| | - P A F Galante
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, São Paulo, Brazil
| | - C F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, São Paulo, Brazil
| | - S R Rogatto
- Department of Clinical Genetics, University Hospital, Institute of Regional Health Research, University of Southern Denmark, Vejle, Denmark
| | - M I Achatz
- Centro de Oncologia, Hospital Sírio-Libanês, São Paulo, São Paulo, Brazil
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25
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Nagai MH, Xavier VPS, Gutiyama LM, Machado CF, Reis AH, Donnard ER, Galante PAF, Abreu JG, Festuccia WT, Malnic B. Depletion of Ric-8B leads to reduced mTORC2 activity. PLoS Genet 2020; 16:e1008255. [PMID: 32392211 PMCID: PMC7252638 DOI: 10.1371/journal.pgen.1008255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 05/27/2020] [Accepted: 02/24/2020] [Indexed: 11/19/2022] Open
Abstract
mTOR, a serine/threonine protein kinase that is involved in a series of critical cellular processes, can be found in two functionally distinct complexes, mTORC1 and mTORC2. In contrast to mTORC1, little is known about the mechanisms that regulate mTORC2. Here we show that mTORC2 activity is reduced in mice with a hypomorphic mutation of the Ric-8B gene. Ric-8B is a highly conserved protein that acts as a non-canonical guanine nucleotide exchange factor (GEF) for heterotrimeric Gαs/olf type subunits. We found that Ric-8B hypomorph embryos are smaller than their wild type littermates, fail to close the neural tube in the cephalic region and die during mid-embryogenesis. Comparative transcriptome analysis revealed that signaling pathways involving GPCRs and G proteins are dysregulated in the Ric-8B mutant embryos. Interestingly, this analysis also revealed an unexpected impairment of the mTOR signaling pathway. Phosphorylation of Akt at Ser473 is downregulated in the Ric-8B mutant embryos, indicating a decreased activity of mTORC2. Knockdown of the endogenous Ric-8B gene in cultured cell lines leads to reduced phosphorylation levels of Akt (Ser473), further supporting the involvement of Ric-8B in mTORC2 activity. Our results reveal a crucial role for Ric-8B in development and provide novel insights into the signals that regulate mTORC2. Gene inactivation in mice can be used to identify genes that are involved in important biological processes and that may contribute to disease. We used this approach to study the Ric-8B gene, which is highly conserved in mammals, including humans. We found that Ric-8B is essential for embryogenesis and for the proper development of the nervous system. Ric-8B mutant mouse embryos are smaller than their wild type littermates and show neural tube defects at the cranial region. This approach also allowed us to identify the biological pathways that potentially contribute to the observed phenotypes, and uncover a novel role for Ric-8B in the mTORC2 signaling pathway. mTORC2 plays particular important roles in the adult brain, and has been implicated in neurological disorders. Our mutant mice provide a model to study the complex molecular and cellular processes underlying the interplay between Ric-8B and mTORC2 in neuronal function.
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Affiliation(s)
- Maíra H. Nagai
- Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | | | | | | | - Alice H. Reis
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elisa R. Donnard
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | | | - Jose G. Abreu
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - William T. Festuccia
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Bettina Malnic
- Department of Biochemistry, University of São Paulo, São Paulo, Brazil
- * E-mail:
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26
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Guardia GDA, Correa BR, Araujo PR, Qiao M, Burns S, Penalva LOF, Galante PAF. Proneural and mesenchymal glioma stem cells display major differences in splicing and lncRNA profiles. NPJ Genom Med 2020; 5:2. [PMID: 31969990 PMCID: PMC6965107 DOI: 10.1038/s41525-019-0108-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
Therapy resistance and recurrence in high-grade gliomas are driven by their populations of glioma stem cells (GSCs). Thus, detailed molecular characterization of GSCs is needed to develop more effective therapies. We conducted a study to identify differences in the splicing profile and expression of long non-coding RNAs in proneural and mesenchymal GSC cell lines. Genes related to cell cycle, DNA repair, cilium assembly, and splicing showed the most differences between GSC subgroups. We also identified genes distinctly associated with survival among patients of mesenchymal or proneural subgroups. We determined that multiple long non-coding RNAs with increased expression in mesenchymal GSCs are associated with poor survival of glioblastoma patients. In summary, our study established critical differences between proneural and mesenchymal GSCs in splicing profiles and expression of long non-coding RNA. These splicing isoforms and lncRNA signatures may contribute to the uniqueness of GSC subgroups, thus contributing to cancer phenotypes and explaining differences in therapeutic responses.
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Affiliation(s)
- Gabriela D A Guardia
- 1Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil
| | - Bruna R Correa
- 1Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil.,4Present Address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003 Catalonia Spain
| | - Patricia Rosa Araujo
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Mei Qiao
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Suzanne Burns
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Luiz O F Penalva
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA.,Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Pedro A F Galante
- 1Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil
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27
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Camargo AP, Nakahara TS, Firmino LER, Netto PHM, do Nascimento JBP, Donnard ER, Galante PAF, Carazzolle MF, Malnic B, Papes F. Uncovering the mouse olfactory long non-coding transcriptome with a novel machine-learning model. DNA Res 2020; 26:365-378. [PMID: 31321403 PMCID: PMC6704403 DOI: 10.1093/dnares/dsz015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Very little is known about long non-coding RNAs (lncRNAs) in the mammalian olfactory sensory epithelia. Deciphering the non-coding transcriptome in olfaction is relevant because these RNAs have been shown to play a role in chromatin modification and nuclear architecture reorganization, processes that accompany olfactory differentiation and olfactory receptor gene choice, one of the most poorly understood gene regulatory processes in mammals. In this study, we used a combination of in silico and ex vivo approaches to uncover a comprehensive catalogue of olfactory lncRNAs and to investigate their expression in the mouse olfactory organs. Initially, we used a novel machine-learning lncRNA classifier to discover hundreds of annotated and unannotated lncRNAs, some of which were predicted to be preferentially expressed in the main olfactory epithelium and the vomeronasal organ, the most important olfactory structures in the mouse. Moreover, we used whole-tissue and single-cell RNA sequencing data to discover lncRNAs expressed in mature sensory neurons of the main epithelium. Candidate lncRNAs were further validated by in situ hybridization and RT-PCR, leading to the identification of lncRNAs found throughout the olfactory epithelia, as well as others exquisitely expressed in subsets of mature olfactory neurons or progenitor cells.
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Affiliation(s)
- Antonio P Camargo
- Department of Genetics and Evolution, Institute of Biology, University of Campinas, Campinas, SP, Brazil.,Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Thiago S Nakahara
- Department of Genetics and Evolution, Institute of Biology, University of Campinas, Campinas, SP, Brazil.,Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Luiz E R Firmino
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Paulo H M Netto
- Department of Genetics and Evolution, Institute of Biology, University of Campinas, Campinas, SP, Brazil.,Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - João B P do Nascimento
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Elisa R Donnard
- Molecular Oncology Center, Hospital Sirio-Libanes, Sao Paulo, SP, Brazil
| | - Pedro A F Galante
- Molecular Oncology Center, Hospital Sirio-Libanes, Sao Paulo, SP, Brazil
| | - Marcelo F Carazzolle
- Department of Genetics and Evolution, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Bettina Malnic
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Fabio Papes
- Department of Genetics and Evolution, Institute of Biology, University of Campinas, Campinas, SP, Brazil
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28
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Bettoni F, Masotti C, Corrêa BR, Donnard E, Dos Santos FF, São Julião GP, Vailati BB, Habr-Gama A, Galante PAF, Perez RO, Camargo AA. The Effects of Neoadjuvant Chemoradiation in Locally Advanced Rectal Cancer-The Impact in Intratumoral Heterogeneity. Front Oncol 2019; 9:974. [PMID: 31612112 PMCID: PMC6776613 DOI: 10.3389/fonc.2019.00974] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/13/2019] [Indexed: 12/22/2022] Open
Abstract
Purpose: Intratumoral genetic heterogeneity (ITGH) is a common feature of solid tumors. However, little is known about the effect of neoadjuvant chemoradiation (nCRT) in ITGH of rectal tumors that exhibit poor response to nCRT. Here, we examined the impact of nCRT in the mutational profile and ITGH of rectal tumors and its adjacent irradiated normal mucosa in the setting of incomplete response to nCRT. Methods and Materials: To evaluate ITGH in rectal tumors, we analyzed whole-exome sequencing (WES) data from 79 tumors obtained from The Cancer Genome Atlas (TCGA). We also compared matched peripheral blood cells, irradiated normal rectal mucosa and pre and post-treatment tumor samples (PRE-T and POS-T) from one individual to examine the iatrogenic effects of nCRT. Finally, we performed WES of 7 PRE-T/POST-T matched samples to examine how nCRT affects ITGH. ITGH was assessed by quantifying subclonal mutations within individual tumors using the Mutant-Allele Tumor Heterogeneity score (MATH score). Results: Rectal tumors exhibit remarkable ITGH that is ultimately associated with disease stage (MATH score stage I/II 35.54 vs. stage III/IV 44.39, p = 0.047) and lymph node metastasis (MATH score N0 35.87 vs. N+ 45.79, p = 0.026). We also showed that nCRT does not seem to introduce detectable somatic mutations in the irradiated mucosa. Comparison of PRE-T and POST-T matched samples revealed a significant increase in ITGH in 5 out 7 patients and MATH scores were significantly higher after nCRT (median 41.7 vs. 28.8, p = 0.04). Finally, we were able to identify a subset of “enriched mutations” with significant changes in MAFs between PRE-T and POST-T samples. These “enriched mutations” were significantly more frequent in POST-T compared to PRE-T samples (92.9% vs. 7.1% p < 0.00001) and include mutations in genes associated with genetic instability and drug resistance in colorectal cancer, indicating the expansion of tumor cell subpopulations more prone to resist to nCRT. Conclusions: nCRT increases ITGH and may result in the expansion of resistant tumor cell populations in residual tumors. The risk of introducing relevant somatic mutations in the adjacent mucosa is minimal but non-responsive tumors may have potentially worse biological behavior when compared to their untreated counterparts. This was an exploratory study, and due to the limited number of samples analyzed, our results need to be validated in larger cohorts.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Anamaria A Camargo
- Hospital Sírio Libanês, São Paulo, Brazil.,Ludwig Institute for Cancer Research, São Paulo, Brazil
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29
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Bim LV, Navarro FCP, Valente FOF, Lima-Junior JV, Delcelo R, Dias-da-Silva MR, Maciel RMB, Galante PAF, Cerutti JM. Retroposed copies of RET gene: a somatically acquired event in medullary thyroid carcinoma. BMC Med Genomics 2019; 12:104. [PMID: 31288802 PMCID: PMC6617568 DOI: 10.1186/s12920-019-0552-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/17/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Different pathogenic germline mutations in the RET oncogene are identified in MEN 2, a hereditary syndrome characterized by medullary thyroid carcinoma (MTC) and other endocrine tumors. Although genetic predisposition is recognized, not all RET mutation carriers will develop the disease during their lifetime or, likewise, RET mutation carriers belonging to the same family may present clinical heterogeneity. It has been suggested that a single germline mutation might not be sufficient for development of MEN 2-associated tumors and a somatic bi-allelic alteration might be required. Here we investigated the presence of somatic second hit mutation in the RET gene in MTC. METHODS We integrated Multiplex Ligation-dependent Probe Amplification (MLPA) and whole exome sequencing (WES) to search for copy number alteration (CNA) in the RET gene in MTC samples and medullary thyroid cell lines (TT and MZ-CR-1). We next found reads spanning exon-exon boundaries on RET, an indicative of retrocopy. We subsequently searched for RET retrocopies in the human reference genome (GRCh37) and in the 1000 Genomes Project data, by looking for reads reporting joined exons in the RET locus or distinct genomic regions. To determine RET retrocopy specificity and recurrence, DNA isolated from sporadic and MEN 2-associated MTC (n = 37), peripheral blood (n = 3) and papillary thyroid carcinomas with RET fusion (n = 10) samples were tested using PCR-sequencing methodology. RESULTS Through MLPA we have found evidence of CNA in the RET gene in MTC samples and MTC cell lines. WES analysis reinforced the presence of the CNA and hinted for a retroposed copy of RET not found in the human reference genome and 1.000 Genomes Project. Extended analysis confirmed the presence of a somatic MTC-related retrocopy of RET in both sporadic and hereditary tumors. We further unveiled a recurrent (28%) novel point mutation (p.G548 V) found exclusively in the retrocopy of RET. The mutation was also found in cDNA of mutated samples, suggesting it might be functional. CONCLUSION We here report a somatic specific RET retroposed copy in MTC samples and cell lines. Our results support the idea that generation of retrocopies in somatic cells is likely to contribute to MTC genesis and progression.
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Affiliation(s)
- Larissa V Bim
- Laboratório As Bases Genéticas dos Tumores da Tiroide, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Fábio C P Navarro
- Centro de Oncologia Molecular, Hospital Sírio-libanês, São Paulo, SP, Brazil.,Departamento de Bioquímica, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Flávia O F Valente
- Laboratório de Endocrinologia Molecular e Translacional, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - José V Lima-Junior
- Laboratório As Bases Genéticas dos Tumores da Tiroide, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Rosana Delcelo
- Departamento de Patologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Magnus R Dias-da-Silva
- Laboratório de Endocrinologia Molecular e Translacional, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Rui M B Maciel
- Laboratório de Endocrinologia Molecular e Translacional, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-libanês, São Paulo, SP, Brazil
| | - Janete M Cerutti
- Laboratório As Bases Genéticas dos Tumores da Tiroide, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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30
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Velasco MX, Kosti A, Guardia GDA, Santos MC, Tegge A, Qiao M, Correa BRS, Hernández G, Kokovay E, Galante PAF, Penalva LOF. Antagonism between the RNA-binding protein Musashi1 and miR-137 and its potential impact on neurogenesis and glioblastoma development. RNA 2019; 25:768-782. [PMID: 31004009 PMCID: PMC6573790 DOI: 10.1261/rna.069211.118] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
RNA-binding proteins (RBPs) and miRNAs are critical gene expression regulators that interact with one another in cooperative and antagonistic fashions. We identified Musashi1 (Msi1) and miR-137 as regulators of a molecular switch between self-renewal and differentiation. Msi1 and miR-137 have opposite expression patterns and functions, and Msi1 is repressed by miR-137. Msi1 is a stem-cell protein implicated in self-renewal while miR-137 functions as a proneuronal differentiation miRNA. In gliomas, miR-137 functions as a tumor suppressor while Msi1 is a prooncogenic factor. We suggest that the balance between Msi1 and miR-137 is a key determinant in cell fate decisions and disruption of this balance could contribute to neurodegenerative diseases and glioma development. Genomic analyses revealed that Msi1 and miR-137 share 141 target genes associated with differentiation, development, and morphogenesis. Initial results pointed out that these two regulators have an opposite impact on the expression of their target genes. Therefore, we propose an antagonistic model in which this network of shared targets could be either repressed by miR-137 or activated by Msi1, leading to different outcomes (self-renewal, proliferation, tumorigenesis).
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Affiliation(s)
- Mitzli X Velasco
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
- Translation and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (INCan), Mexico City 14080, Mexico
| | - Adam Kosti
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Gabriela D A Guardia
- Centro de Oncologia Molecular-Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | - Marcia C Santos
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Allison Tegge
- Department of Statistics, Virginia Tech, Blacksburg, Virginia 14080, USA
| | - Mei Qiao
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Bruna R S Correa
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
- Centro de Oncologia Molecular-Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | - Greco Hernández
- Translation and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (INCan), Mexico City 14080, Mexico
| | - Erzsebet Kokovay
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Pedro A F Galante
- Centro de Oncologia Molecular-Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | - Luiz O F Penalva
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
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31
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Steranka JP, Tang Z, Grivainis M, Huang CRL, Payer LM, Rego FOR, Miller TLA, Galante PAF, Ramaswami S, Heguy A, Fenyö D, Boeke JD, Burns KH. Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome. Mob DNA 2019; 10:8. [PMID: 30899333 PMCID: PMC6407172 DOI: 10.1186/s13100-019-0148-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/14/2019] [Indexed: 12/14/2022] Open
Abstract
Background Transposable elements make up a significant portion of the human genome. Accurately locating these mobile DNAs is vital to understand their role as a source of structural variation and somatic mutation. To this end, laboratories have developed strategies to selectively amplify or otherwise enrich transposable element insertion sites in genomic DNA. Results Here we describe a technique, Transposon Insertion Profiling by sequencing (TIPseq), to map Long INterspersed Element 1 (LINE-1, L1) retrotransposon insertions in the human genome. This method uses vectorette PCR to amplify species-specific L1 (L1PA1) insertion sites followed by paired-end Illumina sequencing. In addition to providing a step-by-step molecular biology protocol, we offer users a guide to our pipeline for data analysis, TIPseqHunter. Our recent studies in pancreatic and ovarian cancer demonstrate the ability of TIPseq to identify invariant (fixed), polymorphic (inherited variants), as well as somatically-acquired L1 insertions that distinguish cancer genomes from a patient’s constitutional make-up. Conclusions TIPseq provides an approach for amplifying evolutionarily young, active transposable element insertion sites from genomic DNA. Our rationale and variations on this protocol may be useful to those mapping L1 and other mobile elements in complex genomes. Electronic supplementary material The online version of this article (10.1186/s13100-019-0148-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jared P Steranka
- 1Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,2McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Zuojian Tang
- 3Department for Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016 USA.,4Institute for Systems Genetics, NYU Langone Health, New York, NY 10016 USA
| | - Mark Grivainis
- 3Department for Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016 USA.,4Institute for Systems Genetics, NYU Langone Health, New York, NY 10016 USA
| | - Cheng Ran Lisa Huang
- 2McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Lindsay M Payer
- 1Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Fernanda O R Rego
- 5Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Thiago Luiz Araujo Miller
- 5Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paul, São Paulo, Brazil
| | - Pedro A F Galante
- 5Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Sitharam Ramaswami
- 7Genome Technology Center, Division of Advanced Research Technologies, NYU Langone Health, New York, NY USA
| | - Adriana Heguy
- 7Genome Technology Center, Division of Advanced Research Technologies, NYU Langone Health, New York, NY USA
| | - David Fenyö
- 3Department for Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016 USA.,4Institute for Systems Genetics, NYU Langone Health, New York, NY 10016 USA
| | - Jef D Boeke
- 4Institute for Systems Genetics, NYU Langone Health, New York, NY 10016 USA
| | - Kathleen H Burns
- 1Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,2McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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32
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Dos Santos MCT, Barreto-Sanz MA, Correia BRS, Bell R, Widnall C, Perez LT, Berteau C, Schulte C, Scheller D, Berg D, Maetzler W, Galante PAF, Nogueira da Costa A. miRNA-based signatures in cerebrospinal fluid as potential diagnostic tools for early stage Parkinson's disease. Oncotarget 2018; 9:17455-17465. [PMID: 29707120 PMCID: PMC5915128 DOI: 10.18632/oncotarget.24736] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 02/25/2018] [Indexed: 12/20/2022] Open
Abstract
Parkinson’s Disease is the second most common neurodegenerative disorder, affecting 1–2% of the elderly population. Its diagnosis is still based on the identification of motor symptoms when a considerable number of dopaminergic neurons are already lost. The development of translatable biomarkers for accurate diagnosis at the earliest stages of PD is of extreme interest. Several microRNAs have been associated with PD pathophysiology. Consequently, microRNAs are emerging as potential biomarkers, especially due to their presence in Cerebrospinal Fluid and peripheral circulation. This study employed small RNA sequencing, protein binding ligand assays and machine learning in a cross-sectional cohort comprising 40 early stage PD patients and 40 well-matched controls. We identified a panel comprising 5 microRNAs (Let-7f-5p, miR-27a-3p, miR-125a-5p, miR-151a-3p and miR-423-5p), with 90% sensitivity, 80% specificity and 82% area under the curve (AUC) for the differentiation of the cohorts. Moreover, we combined miRNA profiles with hallmark-proteins of PD and identified a panel (miR-10b-5p, miR-22-3p, miR-151a-3p and α-synuclein) reaching 97% sensitivity, 90% specificity and 96% AUC. We performed a gene ontology analysis for the genes targeted by the microRNAs present in each panel and showed the likely association of the models with pathways involved in PD pathogenesis.
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Affiliation(s)
- Marcia Cristina T Dos Santos
- Experimental Medicine and Diagnostics, Global Exploratory Development, UCB Biopharma SPRL, Braine-l'Alleud, Belgium
| | | | | | - Rosie Bell
- Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Catherine Widnall
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, UK
| | - Luis Tosar Perez
- Bioanalytical Sciences, Non Clinical Development, UCB Biopharma SPRL, Belgium
| | - Caroline Berteau
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, UK
| | - Claudia Schulte
- Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen and German Center for Neurodegenerative Diseases, Tuebingen, Germany
| | | | - Daniela Berg
- Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen and German Center for Neurodegenerative Diseases, Tuebingen, Germany.,Department of Neurology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Walter Maetzler
- Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen and German Center for Neurodegenerative Diseases, Tuebingen, Germany.,Department of Neurology, Christian-Albrechts-University Kiel, Kiel, Germany
| | | | - Andre Nogueira da Costa
- Experimental Medicine and Diagnostics, Global Exploratory Development, UCB Biopharma SPRL, Braine-l'Alleud, Belgium
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33
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Hinske LC, Dos Santos FRC, Ohara DT, Ohno-Machado L, Kreth S, Galante PAF. MiRIAD update: using alternative polyadenylation, protein interaction network analysis and additional species to enhance exploration of the role of intragenic miRNAs and their host genes. Database (Oxford) 2018; 2017:4060447. [PMID: 29220447 PMCID: PMC5569676 DOI: 10.1093/database/bax053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 06/20/2017] [Indexed: 01/23/2023]
Abstract
MicroRNAs have established their role as potent regulators of the epigenome. Interestingly, most miRNAs are located within protein-coding genes with functional consequences that have yet to be fully investigated. MiRIAD is a database with an interactive and user-friendly online interface that has been facilitating research on intragenic miRNAs. In this article, we present a major update. First, data for five additional species (chimpanzee, rat, dog, cow and frog) were added to support the exploration of evolutionary aspects of the relationship between host genes and intragenic miRNAs. Moreover, we integrated data from two different sources to generate a comprehensive alternative polyadenylation dataset. The miRIAD interface was therefore redesigned and provides a completely new gene model representation, including an interactive visualization of the 3′ untranslated region (UTR) with alternative polyadenylation sites, corresponding signals and potential miRNA binding sites. Furthermore, we expanded on functional host gene network analysis. Although the previous version solely reported protein interactions, the update features a separate network analysis view that can either be accessed through the submission of a list of genes of interest or directly from a gene’s list of protein interactions. In addition to statistical properties of the submitted gene set, the interaction network graph is presented and miRNAs with seed site over- and underrepresentation are identified. In summary, the update of miRIAD provides novel datasets and bioinformatics resources with a significant increase in functionality to facilitate intragenic miRNA research in a user-friendly and interactive way. Database URL:http://www.miriad-database.org
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Affiliation(s)
- Ludwig C Hinske
- Department of Anaesthesiology, University Hospital of the Ludwig-Maximilians-University Munich, Munich, Germany
| | - Felipe R C Dos Santos
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo SP 01308-060, Brazil.,Inter Unidades em Bioinformática, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Daniel T Ohara
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo SP 01308-060, Brazil
| | - Lucila Ohno-Machado
- Health System Department of Biomedical Informatics, University of California San Diego, La Jolla, CA 93093, USA
| | - Simone Kreth
- Department of Anaesthesiology, University Hospital of the Ludwig-Maximilians-University Munich, Munich, Germany
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo SP 01308-060, Brazil
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34
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Masotti C, Bettoni F, Correa BR, Habr-Gama A, Gama-Rodrigues J, Viana M, Vailati BB, Juliao GPS, Fernandez LM, Galante PAF, Perez RO, Camargo AA. Abstract B62: Intratumoral genetic heterogeneity in rectal cancer and response to neoadjuvant chemoradiotherapy. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.tcm17-b62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Response to neoadjuvant chemoradiotherapy (nCRT) varies substantially among patients with locally advanced rectal cancer, but key determinants of treatment response are not fully understood. Intratumoral genetic heterogeneity (ITGH) is a common feature of solid tumors and has been proposed to drive disease progression and treatment response. Others and we have recently demonstrated that primary nontreated rectal tumors exhibit significant ITGH, but the effect of nCRT in shaping the clonal architecture of rectal cancer has not yet been addressed. In the present work, we further expanded the analysis of ITGH in rectal cancer by analyzing whole-exome sequencing (WES) and clinical data from 79 primary nontreated rectal cancers obtained from The Cancer Genome Atlas. We show that primary rectal tumors exhibit a remarkable variability in the degree of ITH. We also analyzed the effect of nCRT on ITGH and monitored tumor cell subpopulation dynamics after treatment through WES of paired tumor samples collected at diagnosis (pretreatment) and at surgery following nCRT (post-treatment) from seven patients. We show that treatment exposure does not introduce novel somatic mutations or significantly alter tissue genetic heterogeneity. Instead, nCRT acts as a potent selective pressure, shaping the mutational landscape of rectal tumors and allowing the selection and expansion of tumor cell subpopulations, which are more prone to resist nCRT. Our results shed light on the highly heterogeneous and dynamic mutational landscape of rectal tumors and indicate that ITGH may directly affect response to nCRT.
Citation Format: Cibele Masotti, Fabiana Bettoni, Bruna R. Correa, Angelita Habr-Gama, Joaquim Gama-Rodrigues, Maria Viana, Bruna B. Vailati, Guilherme P. Sao Juliao, Laura M. Fernandez, Pedro A. F. Galante, Rodrigo O. Perez, Anamaria A. Camargo. Intratumoral genetic heterogeneity in rectal cancer and response to neoadjuvant chemoradiotherapy [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr B62.
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Affiliation(s)
- Cibele Masotti
- 1Centro de Oncologia Molecular, Instituto de Ensino e Pesquisa do Hospital Sirio-Libanes, São Paulo, SP, Brazil,
| | - Fabiana Bettoni
- 1Centro de Oncologia Molecular, Instituto de Ensino e Pesquisa do Hospital Sirio-Libanes, São Paulo, SP, Brazil,
| | - Bruna R. Correa
- 1Centro de Oncologia Molecular, Instituto de Ensino e Pesquisa do Hospital Sirio-Libanes, São Paulo, SP, Brazil,
| | | | | | - Maria Viana
- 3CICAP, Pathology Division, São Paulo, SP, Brazil
| | | | | | | | - Pedro A. F. Galante
- 1Centro de Oncologia Molecular, Instituto de Ensino e Pesquisa do Hospital Sirio-Libanes, São Paulo, SP, Brazil,
| | | | - Anamaria A. Camargo
- 1Centro de Oncologia Molecular, Instituto de Ensino e Pesquisa do Hospital Sirio-Libanes, São Paulo, SP, Brazil,
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35
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Munford V, Castro LP, Souto R, Lerner LK, Vilar JB, Quayle C, Asif H, Schuch AP, de Souza TA, Ienne S, Alves FIA, Moura LMS, Galante PAF, Camargo AA, Liboredo R, Pena SDJ, Sarasin A, Chaibub SC, Menck CFM. A genetic cluster of patients with variant xeroderma pigmentosum with two different founder mutations. Br J Dermatol 2017; 176:1270-1278. [PMID: 27664908 DOI: 10.1111/bjd.15084] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2016] [Indexed: 01/04/2023]
Abstract
BACKGROUND Xeroderma pigmentosum (XP) is a rare human syndrome associated with hypersensitivity to sunlight and a high frequency of skin tumours at an early age. We identified a community in the state of Goias (central Brazil), a sunny and tropical region, with a high incidence of XP (17 patients among approximately 1000 inhabitants). OBJECTIVES To identify gene mutations in the affected community and map the distribution of the affected alleles, correlating the mutations with clinical phenotypes. METHODS Functional analyses of DNA repair capacity and cell-cycle responses after ultraviolet exposure were investigated in cells from local patients with XP, allowing the identification of the mutated gene, which was then sequenced to locate the mutations. A specific assay was designed for mapping the distribution of these mutations in the community. RESULTS Skin primary fibroblasts showed normal DNA damage removal but abnormal DNA synthesis after ultraviolet irradiation and deficient expression of the Polη protein, which is encoded by POLH. We detected two different POLH mutations: one at the splice donor site of intron 6 (c.764 +1 G>A), and the other in exon 8 (c.907 C>T, p.Arg303X). The mutation at intron 6 is novel, whereas the mutation at exon 8 has been previously described in Europe. Thus, these mutations were likely brought to the community long ago, suggesting two founder effects for this rare disease. CONCLUSIONS This work describes a genetic cluster involving POLH, and, particularly unexpected, with two independent founder mutations, including one that likely originated in Europe.
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Affiliation(s)
- V Munford
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - L P Castro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - R Souto
- Secretariat of Health, Goiania, GO, Brazil
| | - L K Lerner
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - J B Vilar
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - C Quayle
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - H Asif
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - A P Schuch
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - T A de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - S Ienne
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - F I A Alves
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - L M S Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - P A F Galante
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - A A Camargo
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - R Liboredo
- Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - S D J Pena
- Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - A Sarasin
- UMR 8200 CNRS, Institut Gustave Roussy and University Paris-Saclay, Villejuif, France
| | - S C Chaibub
- General Hospital of Goiania, Goiania, GO, Brazil
| | - C F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
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36
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França GS, Hinske LC, Galante PAF, Vibranovski MD. Unveiling the Impact of the Genomic Architecture on the Evolution of Vertebrate microRNAs. Front Genet 2017; 8:34. [PMID: 28377786 PMCID: PMC5359303 DOI: 10.3389/fgene.2017.00034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/09/2017] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic genomes frequently exhibit interdependency between transcriptional units, as evidenced by regions of high gene density. It is well recognized that vertebrate microRNAs (miRNAs) are usually embedded in those regions. Recent work has shown that the genomic context is of utmost importance to determine miRNA expression in time and space, thus affecting their evolutionary fates over long and short terms. Consequently, understanding the inter- and intraspecific changes on miRNA genomic architecture may bring novel insights on the basic cellular processes regulated by miRNAs, as well as phenotypic evolution and disease-related mechanisms.
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Affiliation(s)
- Gustavo S França
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo São Paulo, Brazil
| | - Ludwig C Hinske
- Department of Anesthesiology, Clinic of the University of Munich, Ludwig Maximilian University of Munich Munich, Germany
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês São Paulo, Brazil
| | - Maria D Vibranovski
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo São Paulo, Brazil
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37
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Lima WR, Tessarin-Almeida G, Rozanski A, Parreira KS, Moraes MS, Martins DC, Hashimoto RF, Galante PAF, Garcia CRS. Signaling transcript profile of the asexual intraerythrocytic development cycle of Plasmodium falciparum induced by melatonin and cAMP. Genes Cancer 2016; 7:323-339. [PMID: 28050233 PMCID: PMC5115173 DOI: 10.18632/genesandcancer.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
According to the World Health Organization (WHO), Plasmodium falciparum is the deadliest parasite among all species. This parasite possesses the ability to sense molecules, including melatonin (MEL) and cAMP, and modulate its cell cycle accordingly. MEL synchronizes the development of this malaria parasite by activating several cascades, including the generation of the second messenger cAMP. Therefore, we performed RNA sequencing (RNA-Seq) analysis in P. falciparum erythrocytic stages (ring, trophozoite and schizont) treated with MEL and cAMP. To investigate the expression profile of P. falciparum genes regulated by MEL and cAMP, we performed RNA-Seq analysis in three P. falciparum strains (control, 3D7; protein kinase 7 knockout, PfPK7-; and PfPK7 complement, PfPK7C). In the 3D7 strain, 38 genes were differentially expressed upon MEL treatment; however, none of the genes in the trophozoite (T) stage PfPK7- knockout parasites were differentially expressed upon MEL treatment for 5 hours compared to untreated controls, suggesting that PfPK7 may be involved in the signaling leading to differential gene expression. Moreover, we found that MEL modified the mRNA expression of genes encoding membrane proteins, zinc ion-binding proteins and nucleic acid-binding proteins, which might influence numerous functions in the parasite. The RNA-Seq data following treatment with cAMP show that this molecule modulates different genes throughout the intraerythrocytic cycle, namely, 75, 101 and 141 genes, respectively, in the ring (R), T and schizont (S) stages. Our results highlight P. falciparum's perception of the external milieu through the signaling molecules MEL and cAMP, which are able to drive to changes in gene expression in the parasite.
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Affiliation(s)
- Wânia Rezende Lima
- Departamento de Fisiologia, Instituto de Biociências, Universidade de Sao Paulo, Sao Paulo, Brazil.,Instituto de Ciências Exatas e Naturais (ICEN)- Medicina, Universidade Federal do Mato Grosso - Campus Rondonópolis, Brazil
| | | | - Andrei Rozanski
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, Sao Paulo, Brazil
| | - Kleber S Parreira
- Departamento de Imunologia e Parasitologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Brazil
| | - Miriam S Moraes
- Departamento de Fisiologia, Instituto de Biociências, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - David C Martins
- Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Paulo, Brazil
| | - Ronaldo F Hashimoto
- Departamento de Ciência da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, Sao Paulo, Brazil
| | - Célia R S Garcia
- Departamento de Fisiologia, Instituto de Biociências, Universidade de Sao Paulo, Sao Paulo, Brazil
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38
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Carpinetti P, Donnard E, Bettoni F, Asprino P, Koyama F, Rozanski A, Sabbaga J, Habr-Gama A, Parmigiani RB, Galante PAF, Perez RO, Camargo AA. The use of personalized biomarkers and liquid biopsies to monitor treatment response and disease recurrence in locally advanced rectal cancer after neoadjuvant chemoradiation. Oncotarget 2016; 6:38360-71. [PMID: 26451609 PMCID: PMC4742005 DOI: 10.18632/oncotarget.5256] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/24/2015] [Indexed: 12/18/2022] Open
Abstract
Neoadjuvant chemoradiotherapy (nCRT) followed by surgery is the mainstay treatment for locally advanced rectal cancer. Variable degrees of tumor regression are observed after nCRT and alternative treatment strategies, including close surveillance without immediate surgery, have been investigated to spare patients with complete tumor regression from potentially adverse outcomes of radical surgery. However, clinical and radiological assessment of response does not allow accurate identification of patients with complete response. In addition, surveillance for recurrence is similarly important for these patients, as early detection of recurrence allows salvage resections and adjuvant interventions. We report the use of liquid biopsies and personalized biomarkers for monitoring treatment response to nCRT and detecting residual disease and recurrence in patients with rectal cancer. We sequenced the whole-genome of four rectal tumors to identify patient-specific chromosomal rearrangements that were used to monitor circulating tumor DNA (ctDNA) in liquid biopsies collected at diagnosis and during nCRT and follow-up. We compared ctDNA levels to clinical, radiological and pathological response to nCRT. Our results indicate that personalized biomarkers and liquid biopsies may not be sensitive for the detection of microscopic residual disease. However, it can be efficiently used to monitor treatment response to nCRT and detect disease recurrence, preceding increases in CEA levels and radiological diagnosis. Similar good results were observed when assessing tumor response to systemic therapy and disease progression. Our study supports the use of personalized biomarkers and liquid biopsies to tailor the management of rectal cancer patients, however, replication in a larger cohort is necessary to introduce this strategy into clinical practice.
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Affiliation(s)
- Paola Carpinetti
- Ludwig Institute for Cancer Research, São Paulo, SP, Brazil.,Centro de Oncologia Molecular Hospital Sírio Libanês, São Paulo, SP, Brazil.,Programa de Pós Graduação em Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil
| | - Elisa Donnard
- Ludwig Institute for Cancer Research, São Paulo, SP, Brazil.,Centro de Oncologia Molecular Hospital Sírio Libanês, São Paulo, SP, Brazil.,Programa de Pós Graduação em Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil
| | - Fabiana Bettoni
- Centro de Oncologia Molecular Hospital Sírio Libanês, São Paulo, SP, Brazil
| | - Paula Asprino
- Centro de Oncologia Molecular Hospital Sírio Libanês, São Paulo, SP, Brazil
| | | | - Andrei Rozanski
- Centro de Oncologia Molecular Hospital Sírio Libanês, São Paulo, SP, Brazil
| | - Jorge Sabbaga
- Centro de Oncologia Clínica, Hospital Sírio Libanês, São Paulo, SP, Brazil
| | - Angelita Habr-Gama
- Angelita & Joaquim Gama Institute, São Paulo, SP, Brazil.,University of São Paulo, School of Medicine, São Paulo, SP, Brazil
| | | | - Pedro A F Galante
- Centro de Oncologia Molecular Hospital Sírio Libanês, São Paulo, SP, Brazil
| | - Rodrigo O Perez
- Ludwig Institute for Cancer Research, São Paulo, SP, Brazil.,Angelita & Joaquim Gama Institute, São Paulo, SP, Brazil.,University of São Paulo, School of Medicine, São Paulo, SP, Brazil
| | - Anamaria A Camargo
- Ludwig Institute for Cancer Research, São Paulo, SP, Brazil.,Centro de Oncologia Molecular Hospital Sírio Libanês, São Paulo, SP, Brazil
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39
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Correa BR, de Araujo PR, Qiao M, Burns SC, Chen C, Schlegel R, Agarwal S, Galante PAF, Penalva LOF. Functional genomics analyses of RNA-binding proteins reveal the splicing regulator SNRPB as an oncogenic candidate in glioblastoma. Genome Biol 2016; 17:125. [PMID: 27287018 PMCID: PMC4901439 DOI: 10.1186/s13059-016-0990-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/24/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most common and aggressive type of brain tumor. Currently, GBM has an extremely poor outcome and there is no effective treatment. In this context, genomic and transcriptomic analyses have become important tools to identify new avenues for therapies. RNA-binding proteins (RBPs) are master regulators of co- and post-transcriptional events; however, their role in GBM remains poorly understood. To further our knowledge of novel regulatory pathways that could contribute to gliomagenesis, we have conducted a systematic study of RBPs in GBM. RESULTS By measuring expression levels of 1542 human RBPs in GBM samples and glioma stem cell samples, we identified 58 consistently upregulated RBPs. Survival analysis revealed that increased expression of 21 RBPs was also associated with a poor prognosis. To assess the functional impact of those RBPs, we modulated their expression in GBM cell lines and performed viability, proliferation, and apoptosis assays. Combined results revealed a prominent oncogenic candidate, SNRPB, which encodes core spliceosome machinery components. To reveal the impact of SNRPB on splicing and gene expression, we performed its knockdown in a GBM cell line followed by RNA sequencing. We found that the affected genes were involved in RNA processing, DNA repair, and chromatin remodeling. Additionally, genes and pathways already associated with gliomagenesis, as well as a set of general cancer genes, also presented with splicing and expression alterations. CONCLUSIONS Our study provides new insights into how RBPs, and specifically SNRPB, regulate gene expression and directly impact GBM development.
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Affiliation(s)
- Bruna R Correa
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
- Children's Cancer Research Institute, UTHSCSA, San Antonio, TX, USA
| | | | - Mei Qiao
- Children's Cancer Research Institute, UTHSCSA, San Antonio, TX, USA
| | - Suzanne C Burns
- Children's Cancer Research Institute, UTHSCSA, San Antonio, TX, USA
| | - Chen Chen
- Georgetown University Medical Center, Washington, DC, USA
| | | | - Seema Agarwal
- Georgetown University Medical Center, Washington, DC, USA
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil.
| | - Luiz O F Penalva
- Children's Cancer Research Institute, UTHSCSA, San Antonio, TX, USA.
- Department of Cellular and Structural Biology, UTHSCSA, San Antonio, TX, USA.
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40
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França GS, Vibranovski MD, Galante PAF. Host gene constraints and genomic context impact the expression and evolution of human microRNAs. Nat Commun 2016; 7:11438. [PMID: 27109497 PMCID: PMC4848552 DOI: 10.1038/ncomms11438] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/25/2016] [Indexed: 12/16/2022] Open
Abstract
Increasing evidence has shown that recent miRNAs tend to emerge within coding genes. Here we conjecture that human miRNA evolution is tightly influenced by the genomic context, especially by host genes. Our findings show a preferential emergence of intragenic miRNAs within old genes. We found that miRNAs within old host genes are significantly more broadly expressed than those within young ones. Young miRNAs within old genes are more broadly expressed than their intergenic counterparts, suggesting that young miRNAs have an initial advantage by residing in old genes, and benefit from their hosts' expression control and from the exposure to diverse cellular contexts and target genes. Our results demonstrate that host genes may provide stronger expression constraints to intragenic miRNAs in the long run. We also report associated functional implications, highlighting the genomic context and host genes as driving factors for the expression and evolution of human miRNAs. Recent miRNAs tend to emerge within coding genes. Here, by analysing miRNA expression data from six species and comparing genomes from 13 species, the authors report that host genes may provide stronger expression constraints to intragenic miRNAs in the long run.
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Affiliation(s)
- Gustavo S França
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, Rua Daher Cutait 69, 01308-060 São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, Brazil
| | - Maria D Vibranovski
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matao 277, 05508-090 São Paulo, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, Rua Daher Cutait 69, 01308-060 São Paulo, Brazil
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41
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Bettoni F, Donnard ER, Correa BRS, Asprino PF, Koyama FC, Felício NM, Hessel BH, Galante PAF, Camargo AA, Habr-Gama A, Perez RO. Abstract 05: Genetic heterogeneity in rectal cancer - Identification of subpopulations of tumor cells resistant to neoadjuvant CRT. Clin Cancer Res 2016. [DOI: 10.1158/1557-3265.pmsclingen15-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
One of the benefits of neoadjuvant chemotherapy and radiation therapy (CRT) for the management of rectal cancer is tumor downstaging that can ultimately lead to complete tumor regression (known as complete pathological response - pCR). In a previous study using PET/CT imaging to assess tumor response to CRT, 50% of rectal cancers showed a continuous decrease in metabolic activity (estimated by standard uptake value measurements) between 6 and 12 weeks from CRT completion. However the remaining 50% of the cases showed increased metabolic activity within that period. We reasoned that the increased metabolic activity observed in these later patients could be determined by the clonal expansion of a genetically distinct subpopulation of tumor cells resistant to CRT. To address this question we performed exome sequencing and mutation detection analysis on normal tissue, primary tumor and residual tumor from 7 patients with rectal cancer that exhibited an increase in metabolic activity after CRT. Overall, about 20Gb of unambiguously mapped sequences were generated for each sample resulting in an average fold-coverage of 30X. Captured sequences mapped to the reference human genome were then used for the detection of SNPs and non-synonymous somatic point mutations in all three samples from each patient. Approximately 30,000 single nucleotide variants (SNVs) were identified in each sample and most of these SNVs were common to all samples. As expected, the majority of these common inherited variants (96%) have already been described in dbSNP. To identify non-synonymous somatic mutations occurring in primary and residual tumor samples, we excluded those present in the normal sample and those already described as a known SNP in dbSNP resulting in a mean of 243 SNVs per patient. Noteworthy, a significant number of non-synonymous somatic mutations were exclusively found in the primary and residual tumor samples of each patient, 30 and 32 SNVs on average respectively, revealing a high degree of tumor genetic heterogeneity. Furthermore, we were able to identify non-synonymous somatic mutations that were presented in both samples (mean of 107 SNVs), and for these mutations we determined the mutant allele frequency (number of reads representing the mutation/total number of reads covering the mutated base) in the primary and the residual tumor. We then searched for mutations with significantly different allele frequencies in the two samples, as these mutations would likely represent genetically distinct subpopulations of tumor cells selected during CRT. We were able to identify, on average, 4 SNVs enriched in primary tumor and 37 SNVs enriched in residual tumor per patient. In conclusion, based on exome sequencing of rectal tumors that exhibit incomplete response to CRT and have increased tumor metabolism we were able to identify non-synonymous mutations that may be associated with specific mechanisms of resistance or sensitivity to CRT. Functional analysis of these mutations and mutated genes will be presented, providing new insights into the molecular events influencing response to neoadjuvant CRT in rectal cancer.
Citation Format: Fabiana Bettoni, Elisa R. Donnard, Bruna R. S. Correa, Paula F. Asprino, Fernanda C. Koyama, Natália M. Felício, Bruna H. Hessel, Pedro A. F. Galante, Anamaria A. Camargo, Angelita Habr-Gama, Rodrigo O. Perez. Genetic heterogeneity in rectal cancer - Identification of subpopulations of tumor cells resistant to neoadjuvant CRT. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 05.
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42
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Cambuli FM, Correa BR, Rezza A, Burns SC, Qiao M, Uren PJ, Kress E, Boussouar A, Galante PAF, Penalva LOF, Plateroti M. A Mouse Model of Targeted Musashi1 Expression in Whole Intestinal Epithelium Suggests Regulatory Roles in Cell Cycle and Stemness. Stem Cells 2015; 33:3621-34. [PMID: 26303183 DOI: 10.1002/stem.2202] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 06/30/2015] [Accepted: 07/28/2015] [Indexed: 12/21/2022]
Abstract
The intestinal epithelium is very peculiar for its continuous cell renewal, fuelled by multipotent stem cells localized within the crypts of Lieberkühn. Several lines of evidence have established the evolutionary conserved RNA-binding protein Musashi1 as a marker of adult stem cells, including those of the intestinal epithelium, and revealed its roles in stem cell self-renewal and cell fate determination. Previous studies from our laboratories have shown that Musashi1 controls stem cell-like features in medulloblastoma, glioblastoma, and breast cancer cells, and has pro-proliferative and pro-tumorigenic properties in intestinal epithelial progenitor cells in vitro. To undertake a detailed study of Musashi1's function in the intestinal epithelium in vivo, we have generated a mouse model, referred to as v-Msi, overexpressing Musashi1 specifically in the entire intestinal epithelium. Compared with wild type litters, v-Msi1 mice exhibited increased intestinal crypt size accompanied by enhanced proliferation. Comparative transcriptomics by RNA-seq revealed Musashi1's association with gut stem cell signature, cell cycle, DNA replication, and drug metabolism. Finally, we identified and validated three novel mRNA targets that are stabilized by Musashi1, Ccnd1 (Cyclin D1), Cdk6, and Sox4. In conclusion, the targeted expression of Musashi1 in the intestinal epithelium in vivo increases the cell proliferation rate and strongly suggests its action on stem cells activity. This is due to the modulation of a complex network of gene functions and pathways including drug metabolism, cell cycle, and DNA synthesis and repair.
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Affiliation(s)
- F M Cambuli
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, Université Lyon, France
| | - B R Correa
- Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, Texas, USA.,Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - A Rezza
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, Université Lyon, France
| | - S C Burns
- Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, Texas, USA
| | - M Qiao
- Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, Texas, USA
| | - P J Uren
- Molecular and Computational Biology Section, Division of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - E Kress
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, Université Lyon, France
| | - A Boussouar
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, Université Lyon, France
| | - P A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - L O F Penalva
- Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, Texas, USA.,Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, Texas, USA
| | - M Plateroti
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, Université Lyon, France
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43
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Abstract
Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (∼7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (∼10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes.
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Affiliation(s)
- Fábio C P Navarro
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil Dep. de Bioquímica, Universidade de São Paulo, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
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44
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Hinske LC, Galante PAF, Limbeck E, Möhnle P, Parmigiani RB, Ohno-Machado L, Camargo AA, Kreth S. Alternative polyadenylation allows differential negative feedback of human miRNA miR-579 on its host gene ZFR. PLoS One 2015; 10:e0121507. [PMID: 25799583 PMCID: PMC4370670 DOI: 10.1371/journal.pone.0121507] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/31/2015] [Indexed: 02/02/2023] Open
Abstract
About half of the known miRNA genes are located within protein-coding host genes, and are thus subject to co-transcription. Accumulating data indicate that this coupling may be an intrinsic mechanism to directly regulate the host gene's expression, constituting a negative feedback loop. Inevitably, the cell requires a yet largely unknown repertoire of methods to regulate this control mechanism. We propose APA as one possible mechanism by which negative feedback of intronic miRNA on their host genes might be regulated. Using in-silico analyses, we found that host genes that contain seed matching sites for their intronic miRNAs yield longer 32UTRs with more polyadenylation sites. Additionally, the distribution of polyadenylation signals differed significantly between these host genes and host genes of miRNAs that do not contain potential miRNA binding sites. We then transferred these in-silico results to a biological example and investigated the relationship between ZFR and its intronic miRNA miR-579 in a U87 cell line model. We found that ZFR is targeted by its intronic miRNA miR-579 and that alternative polyadenylation allows differential targeting. We additionally used bioinformatics analyses and RNA-Seq to evaluate a potential cross-talk between intronic miRNAs and alternative polyadenylation. CPSF2, a gene previously associated with alternative polyadenylation signal recognition, might be linked to intronic miRNA negative feedback by altering polyadenylation signal utilization.
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Affiliation(s)
- Ludwig Christian Hinske
- Research Group Molecular Medicine, Department of Anaesthesiology, Clinic of the University of Munich, Munich, Germany
| | | | - Elisabeth Limbeck
- Molecular Oncology Center, Sírio Libanês Hospital, São Paulo, Brazil
| | - Patrick Möhnle
- Research Group Molecular Medicine, Department of Anaesthesiology, Clinic of the University of Munich, Munich, Germany
| | | | - Lucila Ohno-Machado
- Division of Biomedical Informatics, University of California San Diego, La Jolla, California, United States of America
| | | | - Simone Kreth
- Research Group Molecular Medicine, Department of Anaesthesiology, Clinic of the University of Munich, Munich, Germany
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45
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Gonzalez-Kristeller DC, do Nascimento JBP, Galante PAF, Malnic B. Identification of agonists for a group of human odorant receptors. Front Pharmacol 2015; 6:35. [PMID: 25784876 PMCID: PMC4347425 DOI: 10.3389/fphar.2015.00035] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/11/2015] [Indexed: 11/13/2022] Open
Abstract
Olfaction plays a critical role in several aspects of the human life. Odorants are detected by hundreds of odorant receptors (ORs) which belong to the superfamily of G protein-coupled receptors. These receptors are expressed in the olfactory sensory neurons of the nose. The information provided by the activation of different combinations of ORs in the nose is transmitted to the brain, leading to odorant perception and emotional and behavioral responses. There are ~400 intact human ORs, and to date only a small percentage of these receptors (~10%) have known agonists. The determination of the specificity of the human ORs will contribute to a better understanding of how odorants are discriminated by the olfactory system. In this work, we aimed to identify human specific ORs, that is, ORs that are present in humans but absent from other species, and their corresponding agonists. To do this, we first selected 22 OR gene sequences from the human genome with no counterparts in the mouse, rat or dog genomes. Then we used a heterologous expression system to screen a subset of these human ORs against a panel of odorants of biological relevance, including foodborne aroma volatiles. We found that different types of odorants are able to activate some of these previously uncharacterized human ORs.
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Affiliation(s)
| | - João B P do Nascimento
- Department of Biochemistry, Institute of Chemistry, University of São Paulo São Paulo, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês São Paulo, Brazil
| | - Bettina Malnic
- Department of Biochemistry, Institute of Chemistry, University of São Paulo São Paulo, Brazil
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46
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Hinske LC, França GS, Torres HAM, Ohara DT, Lopes-Ramos CM, Heyn J, Reis LFL, Ohno-Machado L, Kreth S, Galante PAF. miRIAD-integrating microRNA inter- and intragenic data. Database (Oxford) 2014; 2014:bau099. [PMID: 25288656 PMCID: PMC4186326 DOI: 10.1093/database/bau099] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs) are a class of small (∼22 nucleotides) non-coding RNAs that post-transcriptionally regulate gene expression by interacting with target mRNAs. A majority of miRNAs is located within intronic or exonic regions of protein-coding genes (host genes), and increasing evidence suggests a functional relationship between these miRNAs and their host genes. Here, we introduce miRIAD, a web-service to facilitate the analysis of genomic and structural features of intragenic miRNAs and their host genes for five species (human, rhesus monkey, mouse, chicken and opossum). miRIAD contains the genomic classification of all miRNAs (inter- and intragenic), as well as classification of all protein-coding genes into host or non-host genes (depending on whether they contain an intragenic miRNA or not). We collected and processed public data from several sources to provide a clear visualization of relevant knowledge related to intragenic miRNAs, such as host gene function, genomic context, names of and references to intragenic miRNAs, miRNA binding sites, clusters of intragenic miRNAs, miRNA and host gene expression across different tissues and expression correlation for intragenic miRNAs and their host genes. Protein–protein interaction data are also presented for functional network analysis of host genes. In summary, miRIAD was designed to help the research community to explore, in a user-friendly environment, intragenic miRNAs, their host genes and functional annotations with minimal effort, facilitating hypothesis generation and in-silico validations. Database URL:http://www.miriad-database.org
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Affiliation(s)
| | - Gustavo S França
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Hugo A M Torres
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Daniel T Ohara
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Camila M Lopes-Ramos
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Jens Heyn
- Clinic of Anaesthesiology, Clinic of the University of Munich, Munich, Germany
| | - Luiz F L Reis
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Lucila Ohno-Machado
- Division of Medial Informatics, University of California San Diego, La Jolla, CA 93093-0505, USA
| | - Simone Kreth
- Clinic of Anaesthesiology, Clinic of the University of Munich, Munich, Germany
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
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Torrezan GT, Ferreira EN, Nakahata AM, Barros BDF, Castro MTM, Correa BR, Krepischi ACV, Olivieri EHR, Cunha IW, Tabori U, Grundy PE, Costa CML, de Camargo B, Galante PAF, Carraro DM. Recurrent somatic mutation in DROSHA induces microRNA profile changes in Wilms tumour. Nat Commun 2014; 5:4039. [PMID: 24909261 PMCID: PMC4062040 DOI: 10.1038/ncomms5039] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 05/06/2014] [Indexed: 12/16/2022] Open
Abstract
Wilms tumour (WT) is an embryonal kidney neoplasia for which very few driver genes have
been identified. Here we identify DROSHA mutations in 12% of WT samples (26/222) using whole-exome
sequencing and targeted sequencing of 10 microRNA (miRNA)-processing genes. A recurrent
mutation (E1147K) affecting a metal-binding residue of the RNase IIIb domain is detected in
81% of the DROSHA-mutated tumours.
In addition, we identify non-recurrent mutations in other genes of this pathway
(DGCR8, DICER1, XPO5 and TARBP2). By assessing the miRNA expression pattern of the
DROSHA-E1147K-mutated tumours
and cell lines expressing this mutation, we determine that this variant leads to a
predominant downregulation of a subset of miRNAs. We confirm that the downregulation occurs
exclusively in mature miRNAs and not in primary miRNA transcripts, suggesting that the
DROSHA E1147K mutation affects
processing of primary miRNAs. Our data underscore the pivotal role of the miRNA biogenesis
pathway in WT tumorigenesis, particularly the major miRNA-processing gene DROSHA. Wilms tumour (WT) is the most common paediatric kidney cancer and few driver
genes related to its development have been identified. Here, the authors identify
DROSHA mutations that may contribute to WT tumorigenesis through their effect on
primary microRNA processing.
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Affiliation(s)
- Giovana T Torrezan
- 1] Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil [2]
| | - Elisa N Ferreira
- 1] Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil [2]
| | - Adriana M Nakahata
- Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil
| | - Bruna D F Barros
- Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil
| | - Mayra T M Castro
- Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil
| | - Bruna R Correa
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, S.P., 01308-060, Brazil
| | - Ana C V Krepischi
- Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil
| | - Eloisa H R Olivieri
- Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil
| | - Isabela W Cunha
- Department of Pathology, A. C. Camargo Cancer Center, São Paulo, S.P., 01509-900, Brazil
| | - Uri Tabori
- Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
| | - Paul E Grundy
- Cancer Control Alberta, Alberta Health Services, Edmonton, Alberta, Canada AB T5J 3H1
| | - Cecilia M L Costa
- Department of Pediatrics, A. C. Camargo Cancer Center, São Paulo, S.P., 01509-010, Brazil
| | - Beatriz de Camargo
- Pediatric Hematology-Oncology Research Program, Instituto Nacional de Cancer, INCA, Rio de Janeiro, R.J., 20231-050, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, S.P., 01308-060, Brazil
| | - Dirce M Carraro
- Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil
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48
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Bettoni F, Donnard ER, Correa BRS, Asprino PF, Koyama FC, Felício NM, Hessel BH, Galante PAF, Camargo AA, Habr-Gama A, Perez RO. Abstract A133: Genetic heterogeneity in rectal cancer: Identification of subpopulations of tumor cells resistant to neoadjuvant CRT. Mol Cancer Ther 2013. [DOI: 10.1158/1535-7163.targ-13-a133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
One of the benefits of neoadjuvant chemotherapy and radiation therapy (CRT) for the management of rectal cancer is tumor downstaging that can ultimately lead to complete tumor regression (known as complete pathological response - pCR). In a previous study using PET/CT imaging to assess tumor response to CRT, 50% of rectal cancers showed a continuous decrease in metabolic activity (estimated by standard uptake value measurements) between 6 and 12 weeks from CRT completion. However the remaining 50% of the cases showed increased metabolic activity within that period. We reasoned that the increased metabolic activity observed in these later patients could be determined by the clonal expansion of a genetically distinct subpopulation of tumor cells resistant to CRT. To address this question we performed exome sequencing and mutation detection analysis on normal tissue, primary tumor and residual tumor from one patient with rectal cancer that exhibited an increase in metabolic activity after CRT. Approximately, 15Gb of unambiguously mapped sequences were generated for each normal tissue and residual tumor and 25Gb of mapped sequences were generated for primary tumor. Over 51% of the bases mapped to the targeted regions, resulting in an average fold-coverage of 30X. Captured sequences mapped to the reference human genome were then used for the detection of SNPs and non-synonymous somatic point mutations in all three samples from this patient. Approximately 30,000 single nucleotide variants (SNVs) were identified in each sample and most of the SNVs were common to all samples. As expected, the majority of these common inherited variants (96%) have already been described in dbSNP. To identify non-synonymous somatic mutations occurring in primary and residual tumor samples, we excluded those present in the normal sample and those already described as a known SNP in dbSNP. Noteworthy, a significant number of non-synonymous somatic mutations were exclusively found in the primary and residual tumor samples revealing a high degree of tumor genetic heterogeneity. A total of 80 non-synonymous somatic mutations were present in both samples, and for these mutations we determined the mutant allele frequency (number of reads representing the mutation/total number of reads covering the mutated base) in the primary and the residual tumor. We then searched for mutations with significantly different allele frequencies in the two samples, as these mutations would likely represent genetically distinct subpopulations of tumor cells selected during CRT. Functional analysis of these mutations and mutated genes will be presented, providing new insights into the molecular events influencing response to neoadjuvant CRT in rectal cancer.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A133.
Citation Format: Fabiana Bettoni, Elisa R. Donnard, Bruna R. S. Correa, Paula F. Asprino, Fernanda C. Koyama, Natália M. Felício, Bruna H. Hessel, Pedro A. F. Galante, Anamaria A. Camargo, Angelita Habr-Gama, Rodrigo O. Perez. Genetic heterogeneity in rectal cancer: Identification of subpopulations of tumor cells resistant to neoadjuvant CRT. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A133.
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Affiliation(s)
- Fabiana Bettoni
- 1Centro de Oncologia Molecular - Hospital Sírio-Libanês, Sao Paulo, Brazil
| | - Elisa R. Donnard
- 1Centro de Oncologia Molecular - Hospital Sírio-Libanês, Sao Paulo, Brazil
| | - Bruna R. S. Correa
- 1Centro de Oncologia Molecular - Hospital Sírio-Libanês, Sao Paulo, Brazil
| | - Paula F. Asprino
- 1Centro de Oncologia Molecular - Hospital Sírio-Libanês, Sao Paulo, Brazil
| | - Fernanda C. Koyama
- 2Centro de Oncologia Molecular - Hospital Sírio-Libanês / Instituto Ludwig de Pesquisa sobre o Câncer, Sao Paulo, Brazil
| | - Natália M. Felício
- 3Instituto Angelita & Joaquim Gama / Hospital Alemão Oswaldo Cruz, Sao Paulo, Brazil
| | | | | | - Anamaria A. Camargo
- 2Centro de Oncologia Molecular - Hospital Sírio-Libanês / Instituto Ludwig de Pesquisa sobre o Câncer, Sao Paulo, Brazil
| | | | - Rodrigo O. Perez
- 5Instituto Angelita & Joaquim Gama / Instituto Ludwig de Pesquisa sobre o Câncer, Sao Paulo, Brazil
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49
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Abstract
Motivation: Retrocopies are copies of mature RNAs that are usually devoid of regulatory sequences and introns. They have routinely been classified as processed pseudo-genes with little or no biological relevance. However, recent findings have revealed functional roles for retrocopies, as well as their high frequency in some organisms, such as primates. Despite their increasing importance, there is no user-friendly and publicly available resource for the study of retrocopies. Results: Here, we present RCPedia, an integrative and user-friendly database designed for the study of retrocopied genes. RCPedia contains a complete catalogue of the retrocopies that are known to be present in human and five other primate genomes, their genomic context, inter-species conservation and gene expression data. RCPedia also offers a streamlined data representation and an efficient query system. Availability and implementation: RCPedia is available at http://www.bioinfo.mochsl.org.br/rcpedia. Contact:pgalante@mochsl.org.br Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Fábio C P Navarro
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo 01308-060, Brazil
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50
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Schrider DR, Navarro FCP, Galante PAF, Parmigiani RB, Camargo AA, Hahn MW, de Souza SJ. Gene copy-number polymorphism caused by retrotransposition in humans. PLoS Genet 2013; 9:e1003242. [PMID: 23359205 PMCID: PMC3554589 DOI: 10.1371/journal.pgen.1003242] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 11/28/2012] [Indexed: 01/05/2023] Open
Abstract
The era of whole-genome sequencing has revealed that gene copy-number changes caused by duplication and deletion events have important evolutionary, functional, and phenotypic consequences. Recent studies have therefore focused on revealing the extent of variation in copy-number within natural populations of humans and other species. These studies have found a large number of copy-number variants (CNVs) in humans, many of which have been shown to have clinical or evolutionary importance. For the most part, these studies have failed to detect an important class of gene copy-number polymorphism: gene duplications caused by retrotransposition, which result in a new intron-less copy of the parental gene being inserted into a random location in the genome. Here we describe a computational approach leveraging next-generation sequence data to detect gene copy-number variants caused by retrotransposition (retroCNVs), and we report the first genome-wide analysis of these variants in humans. We find that retroCNVs account for a substantial fraction of gene copy-number differences between any two individuals. Moreover, we show that these variants may often result in expressed chimeric transcripts, underscoring their potential for the evolution of novel gene functions. By locating the insertion sites of these duplicates, we are able to show that retroCNVs have had an important role in recent human adaptation, and we also uncover evidence that positive selection may currently be driving multiple retroCNVs toward fixation. Together these findings imply that retroCNVs are an especially important class of polymorphism, and that future studies of copy-number variation should search for these variants in order to illuminate their potential evolutionary and functional relevance. Recent studies of human genetic variation have revealed that, in addition to differing at single nucleotide polymorphisms, individuals differ in copy-number at many regions of the genome. These copy-number variants (CNVs) are caused by duplication or deletion events and often affect functional sequences such as genes. Efforts to reveal the functional impact of CNVs have identified many variants increasing the risk of various disorders, and some that are adaptive. However, these studies mostly fail to detect gene duplications caused by retrotransposition, in which an mRNA transcript is reverse-transcribed and reinserted into the genome, yielding a new intron-less gene copy. Here we describe a method leveraging next-generation sequence data to accurately detect gene copy-number variants caused by retrotransposition, or retroCNVs, and apply this method to hundreds of whole-genome sequences from three different human subpopulations. We find that these variants account for a substantial number of gene copy-number differences between individuals, and that gene retrotransposition may often result in both deleterious and beneficial mutations. Indeed, we present evidence that two of these new gene duplications may be adaptive. These results imply that retroCNVs are an especially important class of CNV and should be included in future studies of human copy-number variation.
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Affiliation(s)
- Daniel R. Schrider
- Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America
- * E-mail: (DRS); (FCPN)
| | - Fabio C. P. Navarro
- São Paulo Branch, Ludwig Institute for Cancer Research, São Paulo, Brazil
- Departamento de Bioquímica, Universidade de São Paulo, São Paulo, Brazil
- Centro de Oncologia Molecular–Hospital Sírio-Libanês, São Paulo, Brazil
- * E-mail: (DRS); (FCPN)
| | - Pedro A. F. Galante
- São Paulo Branch, Ludwig Institute for Cancer Research, São Paulo, Brazil
- Centro de Oncologia Molecular–Hospital Sírio-Libanês, São Paulo, Brazil
| | - Raphael B. Parmigiani
- São Paulo Branch, Ludwig Institute for Cancer Research, São Paulo, Brazil
- Centro de Oncologia Molecular–Hospital Sírio-Libanês, São Paulo, Brazil
| | - Anamaria A. Camargo
- São Paulo Branch, Ludwig Institute for Cancer Research, São Paulo, Brazil
- Centro de Oncologia Molecular–Hospital Sírio-Libanês, São Paulo, Brazil
| | - Matthew W. Hahn
- Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America
| | - Sandro J. de Souza
- São Paulo Branch, Ludwig Institute for Cancer Research, São Paulo, Brazil
- Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
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