1
|
Furuya TK, Murta CB, Murillo Carrasco AG, Uno M, Sichero L, Villa LL, Cardilli L, Coelho RF, Guglielmetti GB, Cordeiro MD, Leite KRM, Nahas WC, Chammas R, Pontes J. Disruption of miRNA-mRNA Networks Defines Novel Molecular Signatures for Penile Carcinogenesis. Cancers (Basel) 2021; 13:cancers13194745. [PMID: 34638231 PMCID: PMC8507530 DOI: 10.3390/cancers13194745] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 09/01/2021] [Revised: 09/13/2021] [Accepted: 09/18/2021] [Indexed: 11/16/2022] Open
Abstract
Penile cancer (PeC) carcinogenesis is not fully understood, and no biomarkers are reported in clinical practice. We aimed to investigate molecular signatures based on miRNA and mRNA and perform an integrative analysis to identify molecular drivers and pathways for PeC development. Affymetrix miRNA microarray was used to identify differentially expressed miRNAs (DEmiRs) comparing 11 tumoral tissues (TT) paired with non-neoplastic tissues (NNT) with further validation in an independent cohort (n = 13). We also investigated the mRNA expression of 83 genes in the total sample. Experimentally validated targets of DEmiRs, miRNA-mRNA networks, and enriched pathways were evaluated in silico. Eight out of 69 DEmiRs identified by microarray analysis were validated by qRT-PCR (miR-145-5p, miR-432-5p, miR-487b-3p, miR-30a-5p, miR-200a-5p, miR-224-5p, miR-31-3p and miR-31-5p). Furthermore, 37 differentially expressed genes (DEGs) were identified when comparing TT and NNT. We identified four downregulated DEmiRs (miR-30a-5p, miR-432-5p, miR-487b-3p, and miR-145-5p) and six upregulated DEGs (IL1A, MCM2, MMP1, MMP12, SFN and VEGFA) as potential biomarkers in PeC by their capacity of discriminating TT and NNT with accuracy. The integration analysis showed eight dysregulated miRNA-mRNA pairs in penile carcinogenesis. Taken together, our findings contribute to a better understanding of the regulatory roles of miRNAs and altered transcripts levels in penile carcinogenesis.
Collapse
Affiliation(s)
- Tatiane Katsue Furuya
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), Sao Paulo CEP 01246-000, SP, Brazil; (A.G.M.C.); (M.U.); (L.S.); (L.L.V.); (R.C.)
- Correspondence: (T.K.F.); (C.B.M.)
| | - Claudio Bovolenta Murta
- Departamento de Urologia, ICESP, HCFMUSP, Sao Paulo CEP 01246-000, SP, Brazil; (R.F.C.); (G.B.G.); (M.D.C.); (K.R.M.L.); (W.C.N.); (J.P.J.)
- Correspondence: (T.K.F.); (C.B.M.)
| | - Alexis Germán Murillo Carrasco
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), Sao Paulo CEP 01246-000, SP, Brazil; (A.G.M.C.); (M.U.); (L.S.); (L.L.V.); (R.C.)
| | - Miyuki Uno
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), Sao Paulo CEP 01246-000, SP, Brazil; (A.G.M.C.); (M.U.); (L.S.); (L.L.V.); (R.C.)
| | - Laura Sichero
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), Sao Paulo CEP 01246-000, SP, Brazil; (A.G.M.C.); (M.U.); (L.S.); (L.L.V.); (R.C.)
| | - Luisa Lina Villa
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), Sao Paulo CEP 01246-000, SP, Brazil; (A.G.M.C.); (M.U.); (L.S.); (L.L.V.); (R.C.)
| | - Leonardo Cardilli
- Departamento de Patologia, ICESP, HCFMUSP, Sao Paulo CEP 01246-000, SP, Brazil;
| | - Rafael Ferreira Coelho
- Departamento de Urologia, ICESP, HCFMUSP, Sao Paulo CEP 01246-000, SP, Brazil; (R.F.C.); (G.B.G.); (M.D.C.); (K.R.M.L.); (W.C.N.); (J.P.J.)
| | - Giuliano Betoni Guglielmetti
- Departamento de Urologia, ICESP, HCFMUSP, Sao Paulo CEP 01246-000, SP, Brazil; (R.F.C.); (G.B.G.); (M.D.C.); (K.R.M.L.); (W.C.N.); (J.P.J.)
| | - Mauricio Dener Cordeiro
- Departamento de Urologia, ICESP, HCFMUSP, Sao Paulo CEP 01246-000, SP, Brazil; (R.F.C.); (G.B.G.); (M.D.C.); (K.R.M.L.); (W.C.N.); (J.P.J.)
| | - Katia Ramos Moreira Leite
- Departamento de Urologia, ICESP, HCFMUSP, Sao Paulo CEP 01246-000, SP, Brazil; (R.F.C.); (G.B.G.); (M.D.C.); (K.R.M.L.); (W.C.N.); (J.P.J.)
| | - William Carlos Nahas
- Departamento de Urologia, ICESP, HCFMUSP, Sao Paulo CEP 01246-000, SP, Brazil; (R.F.C.); (G.B.G.); (M.D.C.); (K.R.M.L.); (W.C.N.); (J.P.J.)
| | - Roger Chammas
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), Sao Paulo CEP 01246-000, SP, Brazil; (A.G.M.C.); (M.U.); (L.S.); (L.L.V.); (R.C.)
| | - José Pontes
- Departamento de Urologia, ICESP, HCFMUSP, Sao Paulo CEP 01246-000, SP, Brazil; (R.F.C.); (G.B.G.); (M.D.C.); (K.R.M.L.); (W.C.N.); (J.P.J.)
| |
Collapse
|
2
|
Martínez-Pacheco M, Tenorio M, Almonte L, Fajardo V, Godínez A, Fernández D, Cornejo-Páramo P, Díaz-Barba K, Halbert J, Liechti A, Székely T, Urrutia AO, Cortez D. Expression Evolution of Ancestral XY Gametologs across All Major Groups of Placental Mammals. Genome Biol Evol 2020; 12:2015-2028. [PMID: 32790864 PMCID: PMC7674692 DOI: 10.1093/gbe/evaa173] [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] [Accepted: 08/10/2020] [Indexed: 12/14/2022] Open
Abstract
Placental mammals present 180 million-year-old Y chromosomes that have retained a handful of dosage-sensitive genes. However, the expression evolution of Y-linked genes across placental groups has remained largely unexplored. Here, we expanded the number of Y gametolog sequences by analyzing ten additional species from previously unexplored groups. We detected seven remarkably conserved genes across 25 placental species with known Y repertoires. We then used RNA-seq data from 17 placental mammals to unveil the expression evolution of XY gametologs. We found that Y gametologs followed, on average, a 3-fold expression loss and that X gametologs also experienced some expression reduction, particularly in primates. Y gametologs gained testis specificity through an accelerated expression decay in somatic tissues. Moreover, despite the substantial expression decay of Y genes, the combined expression of XY gametologs in males is higher than that of both X gametologs in females. Finally, our work describes several features of the Y chromosome in the last common mammalian ancestor.
Collapse
Affiliation(s)
| | | | - Laura Almonte
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
| | | | - Alan Godínez
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
| | | | | | | | - Jean Halbert
- Center for Integrative Genomics, University of Lausanne, Switzerland
| | - Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, Switzerland
| | - Tamas Székely
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Araxi O Urrutia
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom.,Ecology Institute, UNAM, Mexico
| | - Diego Cortez
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
| |
Collapse
|
3
|
Abstract
We use simple models of the costs and benefits of microbial gene expression to show that changing a protein's expression away from its optimum by 2-fold should reduce fitness by at least [Formula: see text], where P is the fraction the cell's protein that the gene accounts for. As microbial genes are usually expressed at above 5 parts per million, and effective population sizes are likely to be above 10(6), this implies that 2-fold changes to gene expression levels are under strong selection, as [Formula: see text], where Ne is the effective population size and s is the selection coefficient. Thus, most gene duplications should be selected against. On the other hand, we predict that for most genes, small changes in the expression will be effectively neutral.
Collapse
Affiliation(s)
- Morgan N Price
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Lab
| | - Adam P Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Lab
| |
Collapse
|
4
|
Zhao Y, Yuan NA, Li K, Geng YI, Zhou H, Wang H, Hou J, Zhang B, Cai Y, Zhao X. Bilateral breast cancer following augmentation mammaplasty with polyacrylamide hydrogel injection: A case report. Oncol Lett 2015; 9:2687-93. [PMID: 26137129 DOI: 10.3892/ol.2015.3116] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 02/13/2015] [Indexed: 11/05/2022] Open
Abstract
Breast cancer occurring following injection with polyacrylamide hydrogel (PAMG) for augmentation mammaplasty is rare. The present study reports the case of a 43-year-old female presenting with bilateral breast cancer 10 years after augmentation mammaplasty with PAMG injection and no family history of breast cancer. A 5.5×6.0-cm mass in the right breast with multiple intumescent axillary lymph nodes was revealed and a palpable mass of ~1.0 cm was identified in the outer upper quadrant of the left breast. Multiple smaller nodules were observed in the pulmonary field. Pathological examination revealed invasive lobular grade II carcinoma in both breasts with ER(+++), PR(+++), C-erbB2(-), Top-2(+), in the right breast and ER(++), PR(++), c-erb-B2(-), Top-2(+) in the left. Preoperative chemotherapy, modified radical bilateral mastectomy with axillary clearance, postoperative chemotherapy, and an oophorectomy were conducted, followed by treatment with Arimedex® until the present date A number of valuable insights can be garnered from this case. First, close follow-up is required for female patients who receive an injection of PAMG for augmentation mammaplasty in order to achieve an early diagnosis and to intervene in any incidences of breast cancer. Second, the differential diagnosis of dual primary carcinoma versus metastatic breast cancer is important and may be aided by the use of molecular technology. Third, it remains difficult to determine gene expression values for the prediction of chemotherapy sensitivity. Thus, discrimination between primary and secondary carcinomas is the principle barrier for identifying an appropriate treatment strategy when a patient is diagnosed with bilateral breast cancer.
Collapse
|
5
|
Prabha R, Singh DP, Rai A. Looking into the genome of Thermosynechococcus elongatus (thermophilic cyanobacteria) with codon selection and usage perspective. Int J Bioinform Res Appl 2015; 11:130-41. [PMID: 25786792 DOI: 10.1504/ijbra.2015.068088] [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] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Genome analysis of thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1 revealed factors ruling choices of codons in this organism. Multiple parameters like Nc, GC3s, RSCU, Codon Adaptation Index (CAI), optimal and rare codons, codon-pair context and amino acid usage were analysed and compositional constraint was identified as major factor. Wide range of Nc values for the same GC3 content suggested the role of translational selection. Mutational bias is suggested at synonymous position. Among optimal codons for translation, most were GC-ending. Seven codons (AGA, AGG, AUA, UAA, UAG, UCA and UGA) were found to have least occurrence in the entire genome and except stop codons all were A-ending (exception AGG). Most widely used codon-pair in the genome are G-ending or C-ending and A-ending or U-ending codons make pair with G-ending or C-ending codons. Amino acids which are largely distributed in T. elongatus tend to use G-ending or C-ending codons most frequently. Findings showed cumulative role of translational selection, translational accuracy and gene expression levels with mutational bias as key player in codon selection pattern of this organism.
Collapse
Affiliation(s)
- Ratna Prabha
- National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275103, Uttar Pradesh, India; Department of Biotechnology, Mewar University, Chittorgarh, Rajasthan, India
| | - Dhananjaya P Singh
- National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275103, Uttar Pradesh, India
| | - Anil Rai
- Indian Agricultural Statistical Research Institute, Indian Council of Agricultural Research, Pusa, New Delhi 110012, India
| |
Collapse
|
6
|
Al Kaddissi S, Legeay A, Elia AC, Gonzalez P, Floriani M, Cavalie I, Massabuau JC, Gilbin R, Simon O. Mitochondrial gene expression, antioxidant responses, and histopathology after cadmium exposure. Environ Toxicol 2014; 29:893-907. [PMID: 23065898 DOI: 10.1002/tox.21817] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 08/27/2012] [Accepted: 08/29/2012] [Indexed: 05/29/2023]
Abstract
The present study investigates cadmium effects on the transcription of mitochondrial genes of Procambarus clarkii after acute (0.05, 0.5, and 5 mg Cd/L; 4-10 days) and chronic exposures (10 μg Cd/L; 30-60 days). Transcriptional responses of cox1, atp6, and 12S using quantitative real-time RT-PCR were assessed in gills and hepatopancreas. Additionally, the expression levels of genes involved in detoxification and/or oxidative stress responses [mt, sod(Mn)] and enzymatic activities of antioxidants (SOD, CAT, GPX, and GST) were analyzed. The histopathological effects in hepatopancreas of crayfish were evaluated by light microscopy. Relationships between endpoints at different levels of biological organization and Cd bioaccumulation were also examined. Cd induced high levels of bioaccumulation, which was followed by mitochondrial dysfunction and histological alterations in both experiments. Moreover, perturbations in the defence mechanisms against oxidative stress tended to increase with time. Results also showed that molecular responses can vary depending on the intensity and duration of the chemical stress applied to the organisms and that the study of mt gene expression levels seemed to be the best tool to assess Cd intoxication.
Collapse
Affiliation(s)
- Simone Al Kaddissi
- Laboratory of Radioecology and Ecotoxicology (LRE), Institute of Radioprotection and Nuclear Safety (IRSN), Bd 186, BP 3, 13115 Saint-Paul-Lez-Durance, France; Laboratory of Aquatic Ecotoxicology (EA), University of Bordeaux1/UMR CNRS 5805, Dr Peyneau Square, 33120 Arcachon, France
| | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Verne S, Jaquish B, White R, Ritland C, Ritland K. Global transcriptome analysis of constitutive resistance to the white pine weevil in spruce. Genome Biol Evol 2011; 3:851-67. [PMID: 21852250 PMCID: PMC3296464 DOI: 10.1093/gbe/evr069] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [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] [Accepted: 06/30/2011] [Indexed: 01/06/2023] Open
Abstract
Constitutive defense mechanisms are critical to the understanding of defense mechanisms in conifers because they constitute the first barrier to attacks by insect pests. In interior spruce, trees that are putatively resistant and susceptible to attacks by white pine weevil (Pissodes strobi) typically exhibit constitutive differences in traits such as resin duct size and number, bark thickness, and terpene content. To improve our knowledge of their genetic basis, we compared globally the constitutive expression levels of 17,825 genes between 20 putatively resistant and 20 putatively susceptible interior spruce trees from the British Columbia tree improvement program. We identified 54 upregulated and 137 downregulated genes in resistant phenotypes, relative to susceptible phenotypes, with a maximum fold change of 2.24 and 3.91, respectively. We found a puzzling increase of resistance by downregulated genes, as one would think that "procuring armaments" is the best defense. Also, although terpenes and phenolic compounds play an important role in conifer defense, we found few of these genes to be differentially expressed. We found 15 putative small heat-shock proteins (sHSP) and several other stress-related proteins to be downregulated in resistant trees. Downregulated putative sHSP belong to several sHSP classes and represented 58% of all tested putative sHSP. These proteins are well known to be involved in plant response to various kinds of abiotic stress; however, their role in constitutive resistance is not yet understood. The lack of correspondence between transcriptome profile clusters and phenotype classifications suggests that weevil resistance in spruce is a complex trait.
Collapse
Affiliation(s)
- Sébastien Verne
- Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Barry Jaquish
- Kalamalka Forestry Centre, British Columbia Ministry of Forests, Lands and Natural Resource Operations, Vernon, British Columbia, Canada
| | - Rick White
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carol Ritland
- Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kermit Ritland
- Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|