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Herz M, Zarowiecki M, Wessels L, Pätzel K, Herrmann R, Braun C, Holroyd N, Huckvale T, Bergmann M, Spiliotis M, Koziol U, Berriman M, Brehm K. Genome-wide transcriptome analysis of Echinococcus multilocularis larvae and germinative cell cultures reveals genes involved in parasite stem cell function. Front Cell Infect Microbiol 2024; 14:1335946. [PMID: 38333034 PMCID: PMC10850878 DOI: 10.3389/fcimb.2024.1335946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/12/2024] [Indexed: 02/10/2024] Open
Abstract
The lethal zoonosis alveolar echinococcosis is caused by tumour-like growth of the metacestode stage of the tapeworm Echinococcus multilocularis within host organs. We previously demonstrated that metacestode proliferation is exclusively driven by somatic stem cells (germinative cells), which are the only mitotically active parasite cells that give rise to all differentiated cell types. The Echinococcus gene repertoire required for germinative cell maintenance and differentiation has not been characterised so far. We herein carried out Illumina sequencing on cDNA from Echinococcus metacestode vesicles, from metacestode tissue depleted of germinative cells, and from Echinococcus primary cell cultures. We identified a set of ~1,180 genes associated with germinative cells, which contained numerous known stem cell markers alongside genes involved in replication, cell cycle regulation, mitosis, meiosis, epigenetic modification, and nucleotide metabolism. Interestingly, we also identified 44 stem cell associated transcription factors that are likely involved in regulating germinative cell differentiation and/or pluripotency. By in situ hybridization and pulse-chase experiments, we also found a new general Echinococcus stem cell marker, EmCIP2Ah, and we provide evidence implying the presence of a slow cycling stem cell sub-population expressing the extracellular matrix factor Emkal1. RNA-Seq analyses on primary cell cultures revealed that metacestode-derived Echinococcus stem cells display an expanded differentiation capability and do not only form differentiated cell types of the metacestode, but also cells expressing genes specific for protoscoleces, adult worms, and oncospheres, including an ortholog of the schistosome praziquantel target, EmTRPMPZQ. Finally, we show that primary cell cultures contain a cell population expressing an ortholog of the tumour necrosis factor α receptor family and that mammalian TNFα accelerates the development of metacestode vesicles from germinative cells. Taken together, our analyses provide a robust and comprehensive characterization of the Echinococcus germinative cell transcriptome, demonstrate expanded differentiation capability of metacestode derived stem cells, and underscore the potential of primary germinative cell cultures to investigate developmental processes of the parasite. These data are relevant for studies into the role of Echinococcus stem cells in parasite development and will facilitate the design of anti-parasitic drugs that specifically act on the parasite germinative cell compartment.
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Affiliation(s)
- Michaela Herz
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | | | - Leonie Wessels
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Katharina Pätzel
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Ruth Herrmann
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Christiane Braun
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Nancy Holroyd
- Parasite Genomics, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Thomas Huckvale
- Parasite Genomics, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Monika Bergmann
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Markus Spiliotis
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Uriel Koziol
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Matthew Berriman
- Parasite Genomics, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Klaus Brehm
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
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Ryczek N, Łyś A, Makałowska I. The Functional Meaning of 5'UTR in Protein-Coding Genes. Int J Mol Sci 2023; 24:ijms24032976. [PMID: 36769304 PMCID: PMC9917990 DOI: 10.3390/ijms24032976] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
As it is well known, messenger RNA has many regulatory regions along its sequence length. One of them is the 5' untranslated region (5'UTR), which itself contains many regulatory elements such as upstream ORFs (uORFs), internal ribosome entry sites (IRESs), microRNA binding sites, and structural components involved in the regulation of mRNA stability, pre-mRNA splicing, and translation initiation. Activation of the alternative, more upstream transcription start site leads to an extension of 5'UTR. One of the consequences of 5'UTRs extension may be head-to-head gene overlap. This review describes elements in 5'UTR of protein-coding transcripts and the functional significance of protein-coding genes 5' overlap with implications for transcription, translation, and disease.
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Chen B, Hu H, Chen X. From Basic Science to Clinical Practice: The Role of Cancerous Inhibitor of Protein Phosphatase 2A (CIP2A)/p90 in Cancer. Front Genet 2023; 14:1110656. [PMID: 36911405 PMCID: PMC9998691 DOI: 10.3389/fgene.2023.1110656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/03/2023] [Indexed: 03/14/2023] Open
Abstract
Cancerous inhibitor of protein phosphatase 2A (CIP2A), initially reported as a tumor-associated antigen (known as p90), is highly expressed in most solid and hematological tumors. The interaction of CIP2A/p90, protein phosphatase 2A (PP2A), and c-Myc can hinder the function of PP2A toward c-Myc S62 induction, thus stabilizing c-Myc protein, which represents a potential role of CIP2A/p90 in tumorigeneses such as cell proliferation, invasion, and migration, as well as cancer drug resistance. The signaling pathways and regulation networks of CIP2A/p90 are complex and not yet fully understood. Many previous studies have also demonstrated that CIP2A/p90 can be used as a potential therapeutic cancer target. In addition, the autoantibody against CIP2A/p90 in sera may be used as a promising biomarker in the diagnosis of certain types of cancer. In this Review, we focus on recent advances relating to CIP2A/p90 and their implications for future research.
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Affiliation(s)
- Beibei Chen
- Department of Medical Oncology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China.,Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, Henan, China
| | - Huihui Hu
- Department of Medical Oncology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China.,Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, Henan, China
| | - Xiaobing Chen
- Department of Medical Oncology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China.,Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, Henan, China
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Tan L, Peng D, Cheng Y. Significant position of C-myc in colorectal cancer: a promising therapeutic target. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2022; 24:2295-2304. [PMID: 35972682 DOI: 10.1007/s12094-022-02910-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/23/2022] [Indexed: 12/17/2022]
Abstract
Colorectal cancer (CRC) is a malignant tumor initiating from the mucosa of the colorectum. According to the 2020 statistics from the World Health Organization, there are 10.0% CRC cases among all 19.3 million new cancers, followed by lung and breast cancer, and 9.4% CRC cases among all 9.9 million cancer deaths, ranking second. The population of CRC patients in China is large, and its incidence and mortality continue to increase each year. Despite the continuous development of surgical methods, chemotherapy, radiotherapy, targeted therapy and immunotherapy, the overall survival of CRC patients remains low. Past research has suggested that c-myc plays a pivotal role in the development of CRC. A higher expression level of c-Myc is a negative prognostic marker in CRC. However, there are few drugs targeting c-myc directly. Therefore, we focused on discovering the mechanism of c-myc in CRC to provide a reference for a better therapy choice for patients.
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Affiliation(s)
- Li Tan
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Dong Peng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
| | - Yong Cheng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
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Tarek MM, Yahia A, El-Nakib MM, Elhefnawi M. Integrative assessment of CIP2A overexpression and mutational effects in human malignancies identifies possible deleterious variants. Comput Biol Med 2021; 139:104986. [PMID: 34739970 DOI: 10.1016/j.compbiomed.2021.104986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/23/2021] [Accepted: 10/24/2021] [Indexed: 10/19/2022]
Abstract
KIAA1524 is the gene encoding the human cancerous inhibitor of PP2A (CIP2A) protein which is regarded as a novel target for cancer therapy. It is overexpressed in 65%-90% of tissues in almost all studied human cancers. CIP2A expression correlates with cancer progression, disease aggressivity in lung cancer besides poor survival and resistance to chemotherapy in breast cancer. Herein, a pan-cancer analysis of public gene expression datasets was conducted showing significant upregulation of CIP2A in cancerous and metastatic tissues. CIP2A overexpression also correlated with poor survival of cancer patients. To determine the non-coding variants associated with CIP2A overexpression, 5'UTR and 3'UTR variants were annotated and scored using RegulomeDB and Enformer deep learning model. The 5'UTR variants rs1239349555, rs1576326380, and rs1231839144 were predicted to be potential regulators of CIP2A overexpression scoring best on RegulomeDB annotations with a high "2a" rank of supporting experimental data. These variants also scored the highest on Enformer predictions. Analysis of the 3'UTR variants of CIP2A predicted rs56255137 and rs58758610 to alter binding sites of hsa-miR-500a-5 and (hsa-miR-3671, hsa-miR-5692a) respectively. Both variants were also found in linkage disequilibrium with rs11709183 and rs147863209 respectively at r2 ≥ 0.8. The aforementioned variants were found to be eQTL hits significantly associated with CIP2A overexpression. Further, analysis of rs11709183 and rs147863209 revealed a high "2b" rank on RegulomeDB annotations indicating a probable effect on DNAse transcription factors binding. The MuTarget analysis indicated that somatic mutations in TP53 are significantly associated with upregulated CIP2A in human cancers. Analysis of missense SNPs on CIP2A solved structure predicted seven deleterious effects. Four of these variants were also predicted as structurally and functionally destabilizing to CIP2A including; rs375108755, rs147942716, rs368722879, and rs367941403. Variant rs1193091427 was predicted as a potential intronic splicing mutation that might be responsible for the novel CIP2A variant (NOCIVA) in multiple myeloma. Finally, Enrichment of the Wnt/β-catenin pathway within the CIP2A regulatory gene network suggested potential of therapeutic combinations between FTY720 with Wnt/β-catenin, Plk1 and/or HDAC inhibitors to downregulate CIP2A which has been shown to be essential for the survival of different cancer cell lines.
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Affiliation(s)
- Mohammad M Tarek
- Bioinformatics Department, Armed Forces College of Medicine (AFCM) Cairo, Egypt.
| | - Ahmed Yahia
- Otolaryngology Department, Armed Forces College of Medicine (AFCM) Cairo, Egypt
| | | | - Mahmoud Elhefnawi
- Biomedical Informatics and Chemo-Informatics Group, Centre of Excellence for Medical Research, Informatics and Systems Department, National Research Centre, Cairo, Egypt
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