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Murphy RG, Gilmore A, Senevirathne S, O'Reilly PG, LaBonte Wilson M, Jain S, McArt DG. Particle Swarm Optimization Artificial Intelligence technique for gene signature discovery in transcriptomic cohorts. Comput Struct Biotechnol J 2022; 20:5547-5563. [PMID: 36249564 PMCID: PMC9556859 DOI: 10.1016/j.csbj.2022.09.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/22/2022] [Accepted: 09/22/2022] [Indexed: 11/12/2022] Open
Abstract
EBPSO identifies unique, accurate, and succinct gene signatures. Key genes within the signatures provide biological insights its associated functions. A web-based micro-framework developed for ease of use and real-time visualizations. A promising alternative to traditional single gene signature generation. Downstream analysis will better translate these signatures towards clinical translation.
The development of gene signatures is key for delivering personalized medicine, despite only a few signatures being available for use in the clinic for cancer patients. Gene signature discovery tends to revolve around identifying a single signature. However, it has been shown that various highly predictive signatures can be produced from the same dataset. This study assumes that the presentation of top ranked signatures will allow greater efforts in the selection of gene signatures for validation on external datasets and for their clinical translation. Particle swarm optimization (PSO) is an evolutionary algorithm often used as a search strategy and largely represented as binary PSO (BPSO) in this domain. BPSO, however, fails to produce succinct feature sets for complex optimization problems, thus affecting its overall runtime and optimization performance. Enhanced BPSO (EBPSO) was developed to overcome these shortcomings. Thus, this study will validate unique candidate gene signatures for different underlying biology from EBPSO on transcriptomics cohorts. EBPSO was consistently seen to be as accurate as BPSO with substantially smaller feature signatures and significantly faster runtimes. 100% accuracy was achieved in all but two of the selected data sets. Using clinical transcriptomics cohorts, EBPSO has demonstrated the ability to identify accurate, succinct, and significantly prognostic signatures that are unique from one another. This has been proposed as a promising alternative to overcome the issues regarding traditional single gene signature generation. Interpretation of key genes within the signatures provided biological insights into the associated functions that were well correlated to their cancer type.
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Wang Z, Pascal LE, Chandran UR, Chaparala S, Lv S, Ding H, Qi L, Wang Z. ELL2 Is Required for the Growth and Survival of AR-Negative Prostate Cancer Cells. Cancer Manag Res 2020; 12:4411-4427. [PMID: 32606936 PMCID: PMC7294050 DOI: 10.2147/cmar.s248854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 05/01/2020] [Indexed: 12/20/2022] Open
Abstract
Background Elongation factor for RNA polymerase II 2 (ELL2) was reported as a putative tumor suppressor in the prostate. ELL2 is frequently down-regulated in prostatic adenocarcinoma specimens, and loss of ELL2 induced murine prostatic intraepithelial neoplasia and enhanced AR-positive prostate cancer cell proliferation. However, the ELL2 gene appears to be amplified in AR-negative neuroendocrine prostate tumors, suggesting a potential oncogenic role for ELL2 in AR-negative prostate cancer cells. In this study, we explored the potential function of ELL2 in PC-3 and DU145, two AR-negative prostate cancer cell lines. Materials and Methods The role of ELL2 in PC-3 and DU145 cells was studied using siRNA-mediated ELL2 knockdown. Genes regulated by ELL2 knockdown in PC-3 cells were identified and analyzed using RNA-Seq and bioinformatics. The expression of representative genes was confirmed by Western blot and/or quantitative PCR. Cell growth was determined by BrdU, MTT and colony formation assays. Cell death was analyzed by 7-AAD/Annexin V staining and trypan blue exclusion staining. Cell cycle was determined by PI staining and flow cytometry. Results ELL2 knockdown inhibited the proliferation of PC-3 and DU145 cells. RNA-Seq analysis showed an enrichment in genes associated with cell death and survival following ELL2 knockdown. The interferon-γ pathway was identified as the top canonical pathway comprising of 55.6% of the genes regulated by ELL2. ELL2 knockdown induced an increase in STAT1 and IRF1 mRNA and an induction of total STAT1 and phosphorylated STAT1 protein. Inhibition of cell proliferation by ELL2 knockdown was partly abrogated by STAT1 knockdown. ELL2 knockdown inhibited colony formation and induced apoptosis in both PC-3 and DU145 cells. Furthermore, knockdown of ELL2 caused S-phase cell cycle arrest, inhibition of CDK2 phosphorylation and cyclin D1 expression, and increased expression of cyclin E. Conclusion ELL2 knockdown in PC-3 and DU145 cells induced S-phase cell cycle arrest and profound apoptosis, which was accompanied by the induction of genes associated with cell death and survival pathways. These observations suggest that ELL2 is a potential oncogenic protein required for survival and proliferation in AR-negative prostate cancer cells.
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Affiliation(s)
- Zhi Wang
- Department of Urology, Xiangya Hospital of Central South University, Changsha, People's Republic of China.,Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Laura E Pascal
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Uma R Chandran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Srilakshmi Chaparala
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shidong Lv
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Hui Ding
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lin Qi
- Department of Urology, Xiangya Hospital of Central South University, Changsha, People's Republic of China
| | - Zhou Wang
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Wang Z, Zhong M, Song Q, Pascal LE, Yang Z, Wu Z, Wang K, Wang Z. Anti-apoptotic factor Birc3 is up-regulated by ELL2 knockdown and stimulates proliferation in LNCaP cells. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2019; 7:223-231. [PMID: 31511829 PMCID: PMC6734035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 07/02/2019] [Indexed: 06/10/2023]
Abstract
ELL2 is a potential tumor suppressor in prostate cancer. ELL2 knockout in mice induced mPIN, the putative precursor of prostate cancer and ELL2 knockdown enhanced proliferation in cultured prostate cancer cells. To explore the mechanism of ELL2 action in prostate cancer, we investigated the role of Birc3, an apoptosis inhibitor, in prostate cancer cells and the regulation of its expression by ELL2. ELL2 knockdown enhanced Birc3 expression in LNCaP and C4-2 cell line models. BrdU assay showed that Birc3 knockdown inhibited proliferation, ELL2 knockdown enhanced proliferation, and Birc3 knockdown counteracted ELL2 knockdown-induced proliferation in LNCaP cells. Trypan blue assay suggested that Birc3 knockout did not induce cell death in LNCaP cells. These findings suggested that Birc3 is a downstream gene of ELL2 and may play a role in driving prostate cancer proliferation.
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Affiliation(s)
- Zhi Wang
- Department of Urology, Xiangya Hospital of Central South UniversityChangsha, China
- Department of Urology, University of Pittsburgh School of MedicinePittsburgh, PA, USA
| | - Mingming Zhong
- Department of Urology, University of Pittsburgh School of MedicinePittsburgh, PA, USA
| | - Qiong Song
- Department of Urology, University of Pittsburgh School of MedicinePittsburgh, PA, USA
- Center for Translational Medicine, Guangxi Medical UniversityNanning, Guangxi, China
| | - Laura E Pascal
- Department of Urology, University of Pittsburgh School of MedicinePittsburgh, PA, USA
| | - Zhenyu Yang
- Department of Urology, Xiangya Hospital of Central South UniversityChangsha, China
- Department of Urology, University of Pittsburgh School of MedicinePittsburgh, PA, USA
| | - Zeyu Wu
- Department of Urology, Xiangya Hospital of Central South UniversityChangsha, China
- Department of Urology, University of Pittsburgh School of MedicinePittsburgh, PA, USA
| | - Ke Wang
- Department of Urology, University of Pittsburgh School of MedicinePittsburgh, PA, USA
- Department of Urology, First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, China
| | - Zhou Wang
- Department of Urology, University of Pittsburgh School of MedicinePittsburgh, PA, USA
- UPMC Hillman Cancer Center, University of Pittsburgh School of MedicinePittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, and University of Pittsburgh School of MedicinePittsburgh, PA, USA
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Pascal LE, Su F, Wang D, Ai J, Song Q, Wang Y, O'Malley KJ, Cross B, Rigatti LH, Green A, Dhir R, Wang Z. Conditional Deletion of Eaf1 Induces Murine Prostatic Intraepithelial Neoplasia in Mice. Neoplasia 2019; 21:752-764. [PMID: 31229879 PMCID: PMC6593215 DOI: 10.1016/j.neo.2019.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 01/03/2023]
Abstract
ELL-associated factor 1 is a transcription elongation factor that shares significant homology and functional similarity to the androgen-responsive prostate tumor suppressor ELL-associated factor 2. EAF2 is frequently down-regulated in advanced prostate cancer and Eaf2 deletion in the mouse induced the development of murine prostatic intraepithelial neoplasia. Here we show that similar to EAF2, EAF1 is frequently down-regulated in advanced prostate cancer. Co-downregulation of EAF1 and EAF2 occurred in 40% of clinical specimens with Gleason score >7. We developed and characterized a murine model of prostate-epithelial specific deletion of Eaf1 in the prostate and crossed it with our previously generated mouse with conventional deletion of Eaf2. The prostates of Eaf1 deletion mice displayed murine prostatic intraepithelial neoplasia lesions with increased proliferation and inflammation. Combined deletion of Eaf1 and Eaf2 in the murine model induced an increased incidence in mPIN lesions characterized by increased proliferation and CD3+ T cells and CD19+ B cells infiltration compared to individual deletion of either Eaf1 or Eaf2 in the murine prostate. These results suggest that EAF1 may play a tumor suppressive role in the prostate. Cooperation between EAF1 and EAF2 may be important for prostate maintaining prostate epithelial homeostasis, and concurrent loss of these two tumor suppressors may promote prostate tumorigenesis and progression.
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Affiliation(s)
- Laura E Pascal
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
| | - Fei Su
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA; The Center for Metabolic and Degenerative Diseases, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Dan Wang
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
| | - Junkui Ai
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
| | - Qiong Song
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA; Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Center for Translational Medicine & School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Yujuan Wang
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
| | - Katherine J O'Malley
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
| | - Brian Cross
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
| | - Lora H Rigatti
- Division of Laboratory Animal Resources, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Anthony Green
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rajiv Dhir
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zhou Wang
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA; Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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ELL2 Is Downregulated and Associated with Galactose-Deficient IgA1 in IgA Nephropathy. DISEASE MARKERS 2019; 2019:2407067. [PMID: 31275443 PMCID: PMC6589307 DOI: 10.1155/2019/2407067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/23/2019] [Accepted: 02/15/2019] [Indexed: 11/25/2022]
Abstract
Background Galactose-deficient IgA1 (Gd-IgA1) is an important causal factor in IgA nephropathy; however, the underlying mechanism for the production of Gd-IgA1 is unknown. The elongation factor for RNA polymerase II (ELL2), which encoded a key component of the superelongation complex (SEC), drives secretory-specific Ig mRNA production. Methods We enrolled 21 patients with IgAN, 18 healthy controls, and 20 patients with non-IgAN glomerulonephritis. The differential expression of ELL2 was compared using publically available data from Gene Expression Omnibus (GEO) datasets. The relationship between ELL2 expressions and galactose-deficient IgA1 (Gd-IgA1) levels in serum were also studied. At last, the results were validated by shELL2 treatment experiment. Results We found that the number of CD19+ B cells was increased in IgAN patients compared to healthy controls. The expression level of ELL2 in patients with IgAN was significantly lower than that of healthy control and disease control. Consistent with present results, the lower ELL2 expression in IgAN patients was observed in microarray expression profiles from GEO datasets. Pearson correlation analysis showed that ELL2 expression negatively correlated with Gd-IgA1 levels. Furthermore, in an in vitro experiment, we found that loss of ELL2 function in human B lymphoma DAKIKI cells, an IgA1-producing cell line, increased the levels of Gd-IgA1, which confirmed that ELL2 modulated the levels of Gd-IgA1. Conclusion Our findings implied that decreased ELL2 expression was negatively correlated with the numbers of B cells and aberrant glycosylation of IgA1 in IgAN.
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