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Chen J, Wen B. Bi-level gene selection of cancer by combining clustering and sparse learning. Comput Biol Med 2024; 172:108236. [PMID: 38471351 DOI: 10.1016/j.compbiomed.2024.108236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 02/07/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024]
Abstract
The diagnosis of cancer based on gene expression profile data has attracted extensive attention in the field of biomedical science. This type of data usually has the characteristics of high dimensionality and noise. In this paper, a hybrid gene selection method based on clustering and sparse learning is proposed to choose the key genes with high precision. We first propose a filter method, which combines the k-means clustering algorithm and signal-to-noise ratio ranking method, and then, a weighted gene co-expression network has been applied to the reduced data set to identify modules corresponding to biological pathways. Moreover, we choose the key genes by using group bridge and sparse group lasso as wrapper methods. Finally, we conduct some numerical experiments on six cancer datasets. The numerical results show that our proposed method has achieved good performance in gene selection and cancer classification.
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Affiliation(s)
- Junnan Chen
- School of Science, Hebei University of Technology, Tianjin, PR China.
| | - Bo Wen
- Institute of Mathematics, Hebei University of Technology, Tianjin, PR China.
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Novel Approach Combining Transcriptional and Evolutionary Signatures to Identify New Multiciliation Genes. Genes (Basel) 2021; 12:genes12091452. [PMID: 34573434 PMCID: PMC8470418 DOI: 10.3390/genes12091452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 11/19/2022] Open
Abstract
Multiciliogenesis is a complex process that allows the generation of hundreds of motile cilia on the surface of specialized cells, to create fluid flow across epithelial surfaces. Dysfunction of human multiciliated cells is associated with diseases of the brain, airway and reproductive tracts. Despite recent efforts to characterize the transcriptional events responsible for the differentiation of multiciliated cells, a lot of actors remain to be identified. In this work, we capitalize on the ever-growing quantity of high-throughput data to search for new candidate genes involved in multiciliation. After performing a large-scale screening using 10 transcriptomics datasets dedicated to multiciliation, we established a specific evolutionary signature involving Otomorpha fish to use as a criterion to select the most likely targets. Combining both approaches highlighted a list of 114 potential multiciliated candidates. We characterized these genes first by generating protein interaction networks, which showed various clusters of ciliated and multiciliated genes, and then by computing phylogenetic profiles. In the end, we selected 11 poorly characterized genes that seem like particularly promising multiciliated candidates. By combining functional and comparative genomics methods, we developed a novel type of approach to study biological processes and identify new promising candidates linked to that process.
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Coan M, Rampioni Vinciguerra GL, Cesaratto L, Gardenal E, Bianchet R, Dassi E, Vecchione A, Baldassarre G, Spizzo R, Nicoloso MS. Exploring the Role of Fallopian Ciliated Cells in the Pathogenesis of High-Grade Serous Ovarian Cancer. Int J Mol Sci 2018; 19:ijms19092512. [PMID: 30149579 PMCID: PMC6163198 DOI: 10.3390/ijms19092512] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 08/20/2018] [Accepted: 08/20/2018] [Indexed: 12/22/2022] Open
Abstract
High-grade serous epithelial ovarian cancer (HGSOC) is the fifth leading cause of cancer death in women and the first among gynecological malignancies. Despite an initial response to standard chemotherapy, most HGSOC patients relapse. To improve treatment options, we must continue investigating tumor biology. Tumor characteristics (e.g., risk factors and epidemiology) are valuable clues to accomplish this task. The two most frequent risk factors for HGSOC are the lifetime number of ovulations, which is associated with increased oxidative stress in the pelvic area caused by ovulation fluid, and a positive family history due to genetic factors. In the attempt to identify novel genetic factors (i.e., genes) associated with HGSOC, we observed that several genes in linkage with HGSOC are expressed in the ciliated cells of the fallopian tube. This finding made us hypothesize that ciliated cells, despite not being the cell of origin for HGSOC, may take part in HGSOC tumor initiation. Specifically, malfunction of the ciliary beat impairs the laminar fluid flow above the fallopian tube epithelia, thus likely reducing the clearance of oxidative stress caused by follicular fluid. Herein, we review the up-to-date findings dealing with HGSOC predisposition with the hypothesis that fallopian ciliated cells take part in HGSOC onset. Finally, we review the up-to-date literature concerning genes that are located in genomic loci associated with epithelial ovarian cancer (EOC) predisposition that are expressed by the fallopian ciliated cells.
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Affiliation(s)
- Michela Coan
- Division of Molecular Oncology, Department of Translational Research, IRCCS CRO Aviano-National Cancer Institute, Via Franco Gallini, 2 33081 Aviano PN, Italy.
| | - Gian Luca Rampioni Vinciguerra
- Division of Molecular Oncology, Department of Translational Research, IRCCS CRO Aviano-National Cancer Institute, Via Franco Gallini, 2 33081 Aviano PN, Italy.
| | - Laura Cesaratto
- Division of Molecular Oncology, Department of Translational Research, IRCCS CRO Aviano-National Cancer Institute, Via Franco Gallini, 2 33081 Aviano PN, Italy.
| | - Emanuela Gardenal
- Azienda Ospedaliera Universitaria Integrata, University of Verona, 37129 Verona, Italy.
| | - Riccardo Bianchet
- Scientific Direction, CRO Aviano Italy, Via Franco Gallini, 2 33081 Aviano, Italy.
| | - Erik Dassi
- Centre for Integrative Biology, University of Trento, 38122 Trento, Italy.
| | - Andrea Vecchione
- Department of clinical and molecular medicine, university of Rome "Sapienza", c/o sant andrea hospital, Via di Grottarossa 1035, 00189 Rome, Italy.
| | - Gustavo Baldassarre
- Division of Molecular Oncology, Department of Translational Research, IRCCS CRO Aviano-National Cancer Institute, Via Franco Gallini, 2 33081 Aviano PN, Italy.
| | - Riccardo Spizzo
- Division of Molecular Oncology, Department of Translational Research, IRCCS CRO Aviano-National Cancer Institute, Via Franco Gallini, 2 33081 Aviano PN, Italy.
| | - Milena Sabrina Nicoloso
- Division of Molecular Oncology, Department of Translational Research, IRCCS CRO Aviano-National Cancer Institute, Via Franco Gallini, 2 33081 Aviano PN, Italy.
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Anderson L, Amaral MS, Beckedorff F, Silva LF, Dazzani B, Oliveira KC, Almeida GT, Gomes MR, Pires DS, Setubal JC, DeMarco R, Verjovski-Almeida S. Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq. PLoS Negl Trop Dis 2015; 9:e0004334. [PMID: 26719891 PMCID: PMC4699917 DOI: 10.1371/journal.pntd.0004334] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/06/2015] [Indexed: 12/28/2022] Open
Abstract
Background Schistosomiasis is one of the most prevalent parasitic diseases worldwide and is a public health problem. Schistosoma mansoni is the most widespread species responsible for schistosomiasis in the Americas, Middle East and Africa. Adult female worms (mated to males) release eggs in the hepatic portal vasculature and are the principal cause of morbidity. Comparative separate transcriptomes of female and male adult worms were previously assessed with using microarrays and Serial Analysis of Gene Expression (SAGE), thus limiting the possibility of finding novel genes. Moreover, the egg transcriptome was analyzed only once with limited bacterially cloned cDNA libraries. Methodology/Principal findings To compare the gene expression of S. mansoni eggs, females, and males, we performed RNA-Seq on these three parasite forms using 454/Roche technology and reconstructed the transcriptome using Trinity de novo assembly. The resulting contigs were mapped to the genome and were cross-referenced with predicted Smp genes and H3K4me3 ChIP-Seq public data. For the first time, we obtained separate, unbiased gene expression profiles for S. mansoni eggs and female and male adult worms, identifying enriched biological processes and specific enriched functions for each of the three parasite forms. Transcripts with no match to predicted genes were analyzed for their protein-coding potential and the presence of an encoded conserved protein domain. A set of 232 novel protein-coding genes with putative functions related to reproduction, metabolism, and cell biogenesis was detected, which contributes to the understanding of parasite biology. Conclusions/Significance Large-scale RNA-Seq analysis using de novo assembly associated with genome-wide information for histone marks in the vicinity of gene models constitutes a new approach to transcriptome analysis that has not yet been explored in schistosomes. Importantly, all data have been consolidated into a UCSC Genome Browser search- and download-tool (http://schistosoma.usp.br/). This database provides new ways to explore the schistosome genome and transcriptome and will facilitate molecular research on this important parasite. Schistosomiasis is a public health problem caused by parasites of the genus Schistosoma, of which S. mansoni is the primary causative agent. The parasite has a complex life cycle; their sexual reproductive stage is dependent on female and male adult worms mating inside the mesenteric circulation of the human host, with the female releasing hundreds of eggs daily. This phase of the life cycle is responsible for the development of pathology, which is proportional to the number of eggs accumulating in the liver and intestine of the human host. Genome and transcriptome sequencing of this parasite represent important advances in schistosome research, but there is still a need for integrated analyses to better understand the biology of this parasite. In this study, we describe the first large-scale transcriptomes of eggs, and female and male adult worms, the parasite forms that are mainly responsible for the pathology of schistosomiasis. We were able to cross-reference the gene transcription regions with promoter regions, thus improving the gene annotations. Moreover, we identified the expression of novel protein-coding genes not yet described in the current genome annotation, advancing the biological knowledge regarding this parasite.
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Affiliation(s)
- Letícia Anderson
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Murilo S. Amaral
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Instituto Butantan, São Paulo, SP, Brazil
| | - Felipe Beckedorff
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Lucas F. Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Bianca Dazzani
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Katia C. Oliveira
- Núcleo de Enteroparasitas, Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, São Paulo, SP, Brazil
| | - Giulliana T. Almeida
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Monete R. Gomes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - David S. Pires
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Instituto Butantan, São Paulo, SP, Brazil
| | - João C. Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Ricardo DeMarco
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Sergio Verjovski-Almeida
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Instituto Butantan, São Paulo, SP, Brazil
- * E-mail:
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Li N, Li S. Epigenetic inactivation of SOX1 promotes cell migration in lung cancer. Tumour Biol 2015; 36:4603-10. [DOI: 10.1007/s13277-015-3107-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 01/14/2015] [Indexed: 11/28/2022] Open
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Li N, Li S. RASAL2 promotes lung cancer metastasis through epithelial-mesenchymal transition. Biochem Biophys Res Commun 2014; 455:358-62. [PMID: 25446096 DOI: 10.1016/j.bbrc.2014.11.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 11/08/2014] [Indexed: 11/20/2022]
Abstract
It was reported that genetically-engineered RASAL2 knockout mice are prone to development of several sporadic tumor, including lung adenocarcinoma. However, a causative relationship between RASAL2 deficiency and lung adenocarcinoma development still remains unknown. In the present study, RASAL2 level was determined in patients with lung adenocarcinoma and control subjects in an attempt to explore its potential clinical diagnostic and prognostic value. Low RASAL2 expression levels were found in 71% (37 of 52) of lung adenocarcinoma, which were correlated with lymph node metastasis in lung adenocarcinoma. Moreover, Low RASAL2 expression levels were correlated with reduced overall survival (OS) in lung adenocarcinoma. We find that inactivation of RASAL2 promotes lung cancer cell migration through the induction of epithelial mesenchymal transition (EMT) and promoted lung metastasis in nude mice. Our results suggest that the down-regulation of RASAL2 promotes metastatic progression of lung adenocarcinoma, hence it could serve as a potential target for the development of lung cancer therapies.
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Affiliation(s)
- Ning Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
| | - Suyun Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China.
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Li N, Zhang F, Li S, Zhou S. Epigenetic silencing of MicroRNA-503 regulates FANCA expression in non-small cell lung cancer cell. Biochem Biophys Res Commun 2014; 444:611-6. [PMID: 24486548 DOI: 10.1016/j.bbrc.2014.01.103] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 01/22/2014] [Indexed: 12/16/2022]
Abstract
It is reported that MicroRNA-503 (miR-503) regulates cell apoptosis, and thus modulates the resistance of non-small cell lung cancer cells (NSCLC) to cisplatin. However, the exact role of miR-503 in NSCLC remains unknown. In the present study, the level of miR-503 expression in NSCLC was evaluated using realtime PCR, and the DNA methylation status within miR-503 promoter was analyzed by Combined Bisulfite Restriction Analysis (COBRA) or bisulfite-treated DNA sequencing assays (BSP). We found that the expression of miR-503 was significantly decreased in NSCLC tissues compared to normal tissues. A statistically significant inverse association was found between miR-503 methylation status and expression of the miR-503 in tumor tissues (P<0.001), and expression of miR-503 was restored by the demethylating agent 5-aza-2'-deoxycytidine, suggesting that methylation was associated with the transcriptional silencing. Then, we show that miR-503 targets a homologous DNA region in the 3'-UTR region of the Fanconi anemia complementation group A protein (FANCA) gene and represses its expression at the transcriptional level. Taken together, our results suggest that miR-503 regulates the resistance of non-small cell lung cancer cells to cisplatin at least in part by targeting FANCA.
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Affiliation(s)
- Ning Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
| | - Fangfang Zhang
- Department of Internal Medicine-Oncology, The First Affiliated Hospital, Zhengzhou University, China
| | - Suyun Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China.
| | - Suzhen Zhou
- Department of Respiratory Medicine, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
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Downregulation of BTG3 in non-small cell lung cancer. Biochem Biophys Res Commun 2013; 437:173-8. [PMID: 23810394 DOI: 10.1016/j.bbrc.2013.06.062] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 06/17/2013] [Indexed: 11/21/2022]
Abstract
BTG3 is identified as a tumor suppressor gene in some malignancies. Btg3-deficient mice display a higher incidence of lung cancer. These results suggest that BTG3 plays an important role in lung tumorigenesis, although the underlying mechanisms are unknown. The BTG3 expression was detected using immunohistochemical staining and our results showed that the expression of BTG3 was reduced in lung cancer compared to benign lung tissues. We identified two BTG3 isoforms present in lung cancer: Full-length BTG3 and BTG3b lacking the 44 amino acids. BTG3 was predominantly expressed in benign lung tissues, whereas its expression was generally undetectable in lung cancer and cancer cell lines. Functional analysis revealed that BTG3 but not BTG3b inhibited lung cancer growth. Our results disclosed an important role of BTG3 in lung tumorigenesis.
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Comparative analysis of methods for identifying recurrent copy number alterations in cancer. PLoS One 2012; 7:e52516. [PMID: 23285074 PMCID: PMC3527554 DOI: 10.1371/journal.pone.0052516] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 11/14/2012] [Indexed: 11/19/2022] Open
Abstract
Recurrent copy number alterations (CNAs) play an important role in cancer genesis. While a number of computational methods have been proposed for identifying such CNAs, their relative merits remain largely unknown in practice since very few efforts have been focused on comparative analysis of the methods. To facilitate studies of recurrent CNA identification in cancer genome, it is imperative to conduct a comprehensive comparison of performance and limitations among existing methods. In this paper, six representative methods proposed in the latest six years are compared. These include one-stage and two-stage approaches, working with raw intensity ratio data and discretized data respectively. They are based on various techniques such as kernel regression, correlation matrix diagonal segmentation, semi-parametric permutation and cyclic permutation schemes. We explore multiple criteria including type I error rate, detection power, Receiver Operating Characteristics (ROC) curve and the area under curve (AUC), and computational complexity, to evaluate performance of the methods under multiple simulation scenarios. We also characterize their abilities on applications to two real datasets obtained from cancers with lung adenocarcinoma and glioblastoma. This comparison study reveals general characteristics of the existing methods for identifying recurrent CNAs, and further provides new insights into their strengths and weaknesses. It is believed helpful to accelerate the development of novel and improved methods.
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Park KS, Kim HK, Lee JH, Choi YB, Park SY, Yang SH, Kim SY, Hong KM. Transglutaminase 2 as a cisplatin resistance marker in non-small cell lung cancer. J Cancer Res Clin Oncol 2009; 136:493-502. [PMID: 19763620 DOI: 10.1007/s00432-009-0681-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 09/02/2009] [Indexed: 01/06/2023]
Abstract
PURPOSE Recently, it was reported that expression of transglutaminase 2 plays an important role in doxorubicin/cisplatin resistance in breast and ovarian cancer. The aims of this study were to verify the role of transglutaminase 2 in cisplatin response in non-small cell lung cancer (NSCLC) and to study if transglutaminase 2 gene (TGM2) methylation can be a molecular marker for good response to cisplatin. METHODS TGM2 promoter methylation was analyzed by sodium bisulfite sequencing. Cisplatin sensitivity was analyzed by treatment of cisplatin in NSCLC cell lines with/without TGM2 or TGM2 siRNA transfection. RESULTS In one-third of NSCLC cell lines, TGase 2 gene (TGM2) was silenced by promoter methylation. The TGM2 promoter-methylated cell lines (HCC-95 and HCC-1588) showed relatively higher sensitivity to cisplatin than the TGM2-expressing cell lines (NCI-H1299 and HCC-1195). Down-regulation and over-expression of TGM2 in those NSCLC cells also suggested a positive correlation of cisplatin sensitivity and TGM2 inhibition. With doxorubicin, the relationship was quite similar. CONCLUSIONS We showed that good responders of cisplatin in NSCLC could be identified by the promoter methylation of TGM2 and that TGase 2 inhibition appears to be an effective cisplatin-sensitizing modality in NSCLC.
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Affiliation(s)
- Kang-Seo Park
- Research Institute, National Cancer Center, 111 Jungbalsan-ro, Ilsandong-gu, Goyang, 410-769, Korea
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