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Gonzalez‐Molina J, Hahn P, Falcão RM, Gultekin O, Kokaraki G, Zanfagnin V, Braz Petta T, Lehti K, Carlson JW. MMP14 expression and collagen remodelling support uterine leiomyosarcoma aggressiveness. Mol Oncol 2024; 18:850-865. [PMID: 37078535 PMCID: PMC10994236 DOI: 10.1002/1878-0261.13440] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 03/14/2023] [Accepted: 04/18/2023] [Indexed: 04/21/2023] Open
Abstract
Fibrillar collagen deposition, stiffness and downstream signalling support the development of leiomyomas (LMs), common benign mesenchymal tumours of the uterus, and are associated with aggressiveness in multiple carcinomas. Compared with epithelial carcinomas, however, the impact of fibrillar collagens on malignant mesenchymal tumours, including uterine leiomyosarcoma (uLMS), remains elusive. In this study, we analyse the network morphology and density of fibrillar collagens combined with the gene expression within uLMS, LM and normal myometrium (MM). We find that, in contrast to LM, uLMS tumours present low collagen density and increased expression of collagen-remodelling genes, features associated with tumour aggressiveness. Using collagen-based 3D matrices, we show that matrix metalloproteinase-14 (MMP14), a central protein with collagen-remodelling functions that is particularly overexpressed in uLMS, supports uLMS cell proliferation. In addition, we find that, unlike MM and LM cells, uLMS proliferation and migration are less sensitive to changes in collagen substrate stiffness. We demonstrate that uLMS cell growth in low-stiffness substrates is sustained by an enhanced basal yes-associated protein 1 (YAP) activity. Altogether, our results indicate that uLMS cells acquire increased collagen remodelling capabilities and are adapted to grow and migrate in low collagen and soft microenvironments. These results further suggest that matrix remodelling and YAP are potential therapeutic targets for this deadly disease.
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Affiliation(s)
- Jordi Gonzalez‐Molina
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
- Department of Oncology‐PathologyKarolinska InstitutetStockholmSweden
| | - Paula Hahn
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Raul Maia Falcão
- Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
- Department of Cellular Biology and GeneticsFederal University of Rio Grande do NorteNatalBrazil
| | - Okan Gultekin
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Georgia Kokaraki
- Department of Oncology‐PathologyKarolinska InstitutetStockholmSweden
- Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | | | - Tirzah Braz Petta
- Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
- Department of Cellular Biology and GeneticsFederal University of Rio Grande do NorteNatalBrazil
| | - Kaisa Lehti
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
- Department of Biomedical Laboratory ScienceNorwegian University of Science and TechnologyTrondheimNorway
| | - Joseph W. Carlson
- Department of Oncology‐PathologyKarolinska InstitutetStockholmSweden
- Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
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Maia Falcão R, Kokaraki G, De Wispelaere W, Amant F, De Souza GA, de Souza JES, Carlson JW, Petta TB. The Expression of the Immunoproteasome Subunit PSMB9 Is Related to Distinct Molecular Subtypes of Uterine Leiomyosarcoma. Cancers (Basel) 2022; 14:cancers14205007. [PMID: 36291793 PMCID: PMC9600211 DOI: 10.3390/cancers14205007] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Uterine leiomyosarcoma (uLMS) is a rare, aggressive, and highly heterogeneous tumor. Knockout female mice for the catalytic subunit of the immunoproteasome PSMB9 develops spontaneous uLMS. In this study, we used molecular data from 3 non-related uLMS cohorts that were integrated and analyzed by proteotranscriptomics. We observed overexpression of the immunoproteasome pathway in uLMS, and then further classified the samples as low or high PSMB9 gene expression levels and we provide evidence that; (i) in the group high there is an enrichment of pathways related to the immune system and in the group low, the ECM formation; (ii) samples with high CD8+/PSMB9 ratio shows better OS; and (iii) the main regulator in the high group is IFNγ and in the low, the proto-oncogene SRC. These findings contribute to the understanding of potential therapeutic or prognostic markers in uLMS. Abstract Background: Uterine leiomyosarcoma (uLMS) are rare and malignant tumors that arise in the myometrium cells and whose diagnosis is based on histopathological features. Identifying diagnostic biomarkers for uLMS is a challenge due to molecular heterogeneity and the scarcity of samples. In vivo and in vitro models for uLMS are urgently needed. Knockout female mice for the catalytic subunit of the immunoproteasome PSMB9 (MIM:177045) develop spontaneous uLMS. This study aimed to analyze the role of PSMB9 in uLMS tumorigenesis and patient outcome. Methods: Molecular data from 3 non-related uLMS cohorts were integrated and analyzed by proteotranscriptomic using gene expression and protein abundance levels in 68 normal adjacent myometrium (MM), 66 uterine leiomyoma (LM), and 67 uLMS. Results: the immunoproteasome pathway is upregulated and the gene PMSB9 shows heterogeneous expression values in uLMS. Quartile group analysis showed no significant difference between groups high and low PSMB9 expression groups at 3-years overall survival (OS). Using CYBERSORTx analysis we observed 9 out of 17 samples in the high group clustering together due to high M2 macrophages and CD4 memory resting, and high CD8+/PSMB9 ratio was associated with better OS. The main pathway regulated in the high group is IFNγ and in the low is the ECM pathway dependent on the proto-oncogene SRC. Conclusion: these findings suggest 2 subtypes of uLMS (immune-related and ECM-related) with different candidate mechanisms of malignancy.
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Affiliation(s)
- Raul Maia Falcão
- Bioinformatics Graduate Program, Instituto Metropole Digital, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
- University of Southern California Keck School of Medicine, University of Southern California, Los Angeles, CA 90007, USA
| | - Georgia Kokaraki
- University of Southern California Keck School of Medicine, University of Southern California, Los Angeles, CA 90007, USA
| | - Wout De Wispelaere
- Department of Oncology, Leuven and Leuven Cancer Institute, Katholieke Universiteit, 3000 Leuven, Belgium
| | - Frédéric Amant
- Department of Oncology, Leuven and Leuven Cancer Institute, Katholieke Universiteit, 3000 Leuven, Belgium
- Department of Surgery, The Netherlands Cancer Institute, 1066 Amsterdam, The Netherlands
| | - Gustavo Antônio De Souza
- Bioinformatics Graduate Program, Instituto Metropole Digital, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
| | - Jorge Estefano Santana de Souza
- Bioinformatics Graduate Program, Instituto Metropole Digital, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
- University of Southern California Keck School of Medicine, University of Southern California, Los Angeles, CA 90007, USA
| | - Joseph Woodward Carlson
- University of Southern California Keck School of Medicine, University of Southern California, Los Angeles, CA 90007, USA
- K7 Onkologi-Patologi, Karolinska Institute, 17177 Stockholm, Sweden
| | - Tirzah Braz Petta
- Bioinformatics Graduate Program, Instituto Metropole Digital, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
- University of Southern California Keck School of Medicine, University of Southern California, Los Angeles, CA 90007, USA
- K7 Onkologi-Patologi, Karolinska Institute, 17177 Stockholm, Sweden
- Correspondence: ; Tel.: +1-323-442-1153
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Gonzalez-Molina J, Hahn P, Falcão RM, Kokaraki G, de Souza JE, Lajus TBP, Lehti K, Carlson JW. Abstract 6096: The microarchitecture and fibrillar collagen expression of leiomyosarcoma are associated with malignancy. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-6096] [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
The expression, abundance, and microarchitecture of fibrillar collagens are associated with tumor development and aggressiveness in various carcinomas. However, the impact of fibrillar collagens on mesenchymal tumors is less understood. While uterine leiomyomas, also known as fibroids, are characterized by high fibrillar collagen deposition and depend on ECM signaling for cell proliferation, the impact of fibrillar collagens on malignant uterine leiomyosarcomas has not been explored. Thus, identifying malignancy and aggressiveness-associated features of the fibrillar collagen-leiomyosarcoma crosstalk may provide novel biomarkers and therapeutic targets for these aggressive tumors. We used publicly available RNAseq data and performed RNAseq and picrosirius red analysis of fiber microarchitecture in a cohort of normal myometrium (MM; n =68 ), leiomyoma (LM; n = 66), and leiomyosarcoma (LMS; n = 67) tissues. Furthermore, we cultured patient-derived primary cells (4 MM, 3 LM, and 4 LMS) on collagen I-functionalized polyacrylamide gels at stiffness ranging from 0.5 to 115 kPa, covering the physiological and pathological stiffness, to investigate distinct behaviors between cell types, including proliferation, migration, and activity of the ECM stiffness molecular rheostat YAP/TAZ. At the protein level, analysis of fibrillar collagen microarchitecture revealed that LMS tumors present reduced fibrillar collagen density and hyphal growth units and enhanced fiber endpoints compared to both MM and LM. At the gene expression level, however, LMS tumors did not show reduced fibrillar collagen expression, instead they exhibited enhanced matrix metalloproteinase expression, particularly of MMP14. Furthermore, COL11A1 was specifically upregulated in LMS tumors and its expression was associated with poor prognosis. Finally, in vitro response of MM, LM, and LMS cells to collagen I at defined stiffness showed that LMS cell migration, proliferation, and subcellular localization of YAP/TAZ are less sensitive to substrate stiffness than in MM and LM cells, although the response varied between distinct donors. In conclusion, we show that LMS tumors typically present low fibrillar collagen protein expression likely due to enhanced degradation. In addition, collagen I adhesion and stiffness have a lower impact on malignant LMS cells than on MM and LM, which may explain their ability to grow in low-collagen microenvironments. Furthermore, this study shows that COL11A1 is a potential biomarker with prognostic value in leiomyosarcoma.
Citation Format: Jordi Gonzalez-Molina, Paula Hahn, Raul Maia Falcão, Georgia Kokaraki, Jorge Estefano de Souza, Tirzah Braz Petta Lajus, Kaisa Lehti, Joseph W. Carlson. The microarchitecture and fibrillar collagen expression of leiomyosarcoma are associated with malignancy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6096.
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Affiliation(s)
| | | | | | | | | | | | - Kaisa Lehti
- 3Norwegian University of Science and Technology, Trondheim, Norway
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Passarini MRZ, Ottoni JR, Costa PEDS, Hissa DC, Falcão RM, Melo VMM, Balbino VQ, Mendonça LAR, Lima MGDS, Coutinho HDM, Verde LCL. Fungal community diversity of heavy metal contaminated soils revealed by metagenomics. Arch Microbiol 2022; 204:255. [PMID: 35412096 DOI: 10.1007/s00203-022-02860-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 07/18/2021] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 11/29/2022]
Abstract
The inappropriate disposal of toxic compounds generated by industrial activity has been impacting the environment considerably. Microbial communities inhabiting contaminated sites may represent interesting ecological alternatives for the decontamination of environments. The present work aimed to investigate the fungal diversity and its functionality contained in stream sediments with industrial waste contaminated with heavy metals by using metagenomic approach. A total of 12 fungal orders were retrieved from datasets and, at phylum level, Ascomycota was the most abundant, followed by Basidiomycota, Chytridiomycota and Blastocladiomycota. Higher abundance of sequences was encountered within the less contaminated site, while the lower abundance was found in the sample with the higher contamination with lead. Gene sequences related to DNA repair and heavy metals biosorption processes were found in the four samples analyzed. The genera Aspergillus and Chaetomium, and Saccharomycetales order were highly present within all samples, showing their potential to be used for bioremediation studies. The present work demonstrated the importance of using the metagenomic approach to understand the dynamics and the possible metabolic pathways associated with fungal communities related to environmental samples containing heavy metals, as well as evidenced the importance of improving culturomics techniques for isolating strains with potential application in bioremediation processes of environments contaminated with heavy metals.
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Affiliation(s)
- Michel Rodrigo Zambrano Passarini
- UNILA-Universidade Federal da Integração Latino-Americana, Av. Tarquínio Joslin Dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil.
| | - Júlia Ronzella Ottoni
- UNILA-Universidade Federal da Integração Latino-Americana, Av. Tarquínio Joslin Dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | | | | | - Raul Maia Falcão
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil
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do Nascimento PM, Medeiros IG, Falcão RM, Stransky B, de Souza JES. A decision tree to improve identification of pathogenic mutations in clinical practice. BMC Med Inform Decis Mak 2020; 20:52. [PMID: 32151256 PMCID: PMC7063785 DOI: 10.1186/s12911-020-1060-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 04/30/2019] [Accepted: 02/21/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND A variant of unknown significance (VUS) is a variant form of a gene that has been identified through genetic testing, but whose significance to the organism function is not known. An actual challenge in precision medicine is to precisely identify which detected mutations from a sequencing process have a suitable role in the treatment or diagnosis of a disease. The average accuracy of pathogenicity predictors is 85%. However, there is a significant discordance about the identification of mutational impact and pathogenicity among them. Therefore, manual verification is necessary for confirming the real effect of a mutation in its casuistic. METHODS In this work, we use variables categorization and selection for building a decision tree model, and later we measure and compare its accuracy with four known mutation predictors and seventeen supervised machine-learning (ML) algorithms. RESULTS The results showed that the proposed tree reached the highest precision among all tested variables: 91% for True Neutrals, 8% for False Neutrals, 9% for False Pathogenic, and 92% for True Pathogenic. CONCLUSIONS The decision tree exceptionally demonstrated high classification precision with cancer data, producing consistently relevant forecasts for the sample tests with an accuracy close to the best ones achieved from supervised ML algorithms. Besides, the decision tree algorithm is easier to apply in clinical practice by non-IT experts. From the cancer research community perspective, this approach can be successfully applied as an alternative for the determination of potential pathogenicity of VOUS.
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Affiliation(s)
| | - Inácio Gomes Medeiros
- Bioinformatics Postgraduate Program, Metrópole Digital Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Raul Maia Falcão
- Bioinformatics Postgraduate Program, Metrópole Digital Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Beatriz Stransky
- Biomedical Engineering Department, Center of Technology, Federal University of Rio Grande do Norte, Natal, Brazil
- Bioinformatics Multidisciplinary Environment (BioME), Metrópole Digital Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Jorge Estefano Santana de Souza
- Bioinformatics Postgraduate Program, Metrópole Digital Institute, Federal University of Rio Grande do Norte, Natal, Brazil.
- Bioinformatics Multidisciplinary Environment (BioME), Metrópole Digital Institute, Federal University of Rio Grande do Norte, Natal, Brazil.
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Silva Junior WJ, Farias ARG, Lima NB, Benko-Iseppon AM, Aburjaile F, Balbino VQ, Falcão RM, Leitão Paiva Júnior SDS, Sousa-Paula LC, Mariano RLR, Souza EB, Gama MAS. Complete Genome Sequence of Xanthomonas citri pv. anacardii Strain IBSBF2579 from Brazil. Genome Announc 2018; 6:e01574-17. [PMID: 29437111 PMCID: PMC5794958 DOI: 10.1128/genomea.01574-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 12/19/2017] [Indexed: 11/29/2022]
Abstract
The bacterium Xanthomonas citri pv. anacardii is the agent of angular leaf spot of the cashew tree (Anacardium occidentale L.). The complete genome sequencing of the strain IBSBF2579 was done on an Illumina HiSeq 2500 platform. The de novo assembly of the X. citri pv. anacardii strain IBSBF2579 genome yielded 133 contigs, with a size of 5,329,247 bp and a G+C content of 64.03%. The prediction was performed by GeneMarkS and the automatic annotation by Rapid Annotations using Subsystems Technology (RAST), with 4,406 identified genes.
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Affiliation(s)
| | | | | | | | - Flávia Aburjaile
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil
| | | | - Raul Maia Falcão
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil
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Silva Junior WJD, Falcão RM, Sousa-Paula LCD, Sbaraini N, Vieira WADS, Lima WG, Paiva Junior SDSL, Staats CC, Schrank A, Benko-Iseppon AM, Balbino VDQ, Câmara MPS. Draft genome assembly of Colletotrichum musae, the pathogen of banana fruit. Data Brief 2018; 17:256-260. [PMID: 29387740 PMCID: PMC5790810 DOI: 10.1016/j.dib.2018.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 12/19/2017] [Accepted: 01/02/2018] [Indexed: 11/28/2022] Open
Abstract
Colletotrichum musae is an important cosmopolitan pathogenic fungus that causes anthracnose in banana fruit. The entire genome of C. musae isolate GM20 (CMM 4420), originally isolated from infected banana fruit from Alagoas State, Brazil, was sequenced and annotated. The pathogen genomic DNA was sequenced on HiSeq Illumina platform. The C. musae GM20 genome has 50,635,197 bp with G + C content of 53.74% and in its present assembly has 2763 scaffolds, harboring 13,451 putative genes with an average length of 1626 bp. Gene prediction and annotation was performed by Funannotate pipeline, using a pattern for gene identification based on BUSCO.
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Affiliation(s)
| | - Raul Maia Falcão
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | - Nicolau Sbaraini
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil
| | | | | | | | - Charley Christian Staats
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil
| | - Augusto Schrank
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil
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