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Liu Y, Edrisi M, Yan Z, A Ogilvie H, Nakhleh L. NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model. Algorithms Mol Biol 2024; 19:18. [PMID: 38685065 PMCID: PMC11059640 DOI: 10.1186/s13015-024-00264-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/27/2024] [Indexed: 05/02/2024] Open
Abstract
Copy number aberrations (CNAs) are ubiquitous in many types of cancer. Inferring CNAs from cancer genomic data could help shed light on the initiation, progression, and potential treatment of cancer. While such data have traditionally been available via "bulk sequencing," the more recently introduced techniques for single-cell DNA sequencing (scDNAseq) provide the type of data that makes CNA inference possible at the single-cell resolution. We introduce a new birth-death evolutionary model of CNAs and a Bayesian method, NestedBD, for the inference of evolutionary trees (topologies and branch lengths with relative mutation rates) from single-cell data. We evaluated NestedBD's performance using simulated data sets, benchmarking its accuracy against traditional phylogenetic tools as well as state-of-the-art methods. The results show that NestedBD infers more accurate topologies and branch lengths, and that the birth-death model can improve the accuracy of copy number estimation. And when applied to biological data sets, NestedBD infers plausible evolutionary histories of two colorectal cancer samples. NestedBD is available at https://github.com/Androstane/NestedBD .
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Affiliation(s)
- Yushu Liu
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, USA.
| | - Mohammadamin Edrisi
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, USA
| | - Zhi Yan
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, USA
| | - Huw A Ogilvie
- Department of Genetics, University of Texas MD Anderson Cancer Center, TX, 77030, Houston, USA
| | - Luay Nakhleh
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, USA
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Srivastava A, Srivastava S. Multiomics data identifies RSPO2 as a prognostic biomarker in human tumors associated with pan-cancer. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:469-499. [PMID: 38448143 DOI: 10.1016/bs.apcsb.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
RSPO2 protein may provide valuable insights into the mechanism underlying various types of tumorigenesis. The role of RSPO2 in pan-cancer has not been reported so far. Therefore, this study aimed to provide a comprehensive analysis of RSPO2 from a pan-cancer perspective employing multiomics data. The expression profile and function of RSPO2 across different tumors were investigated using various web-based tools UALCAN, GEPIA, TIMER, Human Protein Atlas, cBioPortal, TISIDB, STRING, and Metascape to interpret the expression profile, promoter methylation status, genomic alterations, survival analysis, protein-protein interaction, correlation with immune cell subtypes, tumor immune microenvironment and enrichment analysis. Comprehensive pan-cancer analysis indicated that RSPO2 was significantly downregulated in eleven and upregulated in five tumor types compared to normal tissues, validation results further suggest RSPO2 was downregulated in most of the tumors. The protein level expression of RSPO2 was mostly low in malignant tissues. We found that RSPO2 was significantly related to individual pathological stages in BLCA, COAD, LUAD and LUSC. Prognostic analysis indicates that the high RSPO2 expression was significantly correlated with the poor prognosis in BRCA, KICH, KIRP, READ, and UCES. Furthermore, RSPO2 is frequently amplified, exhibits hypermethylated promoter in most cancers, and is associated with immune subtypes, molecular subtypes and immune cell infiltration. Finally, enrichment analysis showed that RSPO2 is involved in the regulation of the canonical Wnt pathway and neuronal development. The overall comprehensive pan-cancer analysis affirms that RSPO2 could be a promising diagnostic and prognostic biomarker and latent therapy target in the future.
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Affiliation(s)
- Ankit Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Uttar Pradesh, India
| | - Sameer Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Uttar Pradesh, India.
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Tan L, Yan M, Su Z, Wang H, Li H, Zhao X, Liu S, Zhang L, Sun Q, Lu D. R-spondin-1 induces Axin degradation via the LRP6-CK1ε axis. Cell Commun Signal 2024; 22:14. [PMID: 38183076 PMCID: PMC10768284 DOI: 10.1186/s12964-023-01456-y] [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: 08/09/2023] [Accepted: 12/21/2023] [Indexed: 01/07/2024] Open
Abstract
R-spondins (RSPOs) are secreted signaling molecules that potentiate the Wnt/β-catenin pathway by cooperating with Wnt ligands. RSPO1 is crucial in tissue development and tissue homeostasis. However, the molecular mechanism by which RSPOs activate Wnt/β-catenin signaling remains elusive. In this study, we found that RSPOs could mediate the degradation of Axin through the ubiquitin-proteasome pathway. The results of Co-IP showed that the recombinant RSPO1 protein promoted the interaction between Axin1 and CK1ε. Either knockout of the CK1ε gene or treatment with the CK1δ/CK1ε inhibitor SR3029 caused an increase in Axin1 protein levels and attenuated RSPO1-induced degradation of the Axin1 protein. Moreover, we observed an increase in the number of associations of LRP6 with CK1ε and Axin1 following RSPO1 stimulation. Overexpression of LRP6 further potentiated Axin1 degradation mediated by RSPO1 or CK1ε. In addition, recombinant RSPO1 and Wnt3A proteins synergistically downregulated the protein expression of Axin1 and enhanced the transcriptional activity of the SuperTOPFlash reporter. Taken together, these results uncover the novel mechanism by which RSPOs activate Wnt/β-catenin signaling through LRP6/CK1ε-mediated degradation of Axin.
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Affiliation(s)
- Lifeng Tan
- Guangdong Provincial Key Laboratory of Regional Immunity and Disease, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Pharmacology, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, Guangdong, China
| | - Mengfang Yan
- Guangdong Provincial Key Laboratory of Regional Immunity and Disease, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Pharmacology, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, Guangdong, China
| | - Zijie Su
- Guangdong Provincial Key Laboratory of Regional Immunity and Disease, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Pharmacology, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, Guangdong, China
- Department of Research, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Hanbin Wang
- Guangdong Provincial Key Laboratory of Regional Immunity and Disease, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Pharmacology, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, Guangdong, China
| | - Huan Li
- Guangdong Provincial Key Laboratory of Regional Immunity and Disease, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Pharmacology, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, Guangdong, China
| | - Xibao Zhao
- Guangdong Provincial Key Laboratory of Regional Immunity and Disease, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Pharmacology, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, Guangdong, China
| | - Shanshan Liu
- Guangdong Provincial Key Laboratory of Regional Immunity and Disease, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Pharmacology, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, Guangdong, China
| | - Long Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Qi Sun
- Guangdong Provincial Key Laboratory of Regional Immunity and Disease, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Pharmacology, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, Guangdong, China.
| | - Desheng Lu
- Guangdong Provincial Key Laboratory of Regional Immunity and Disease, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Pharmacology, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, Guangdong, China.
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