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Zhang M, Zhang X, Xu Y, Xiang Y, Zhang B, Xie Z, Wu Q, Lou C. High-resolution and programmable RNA-IN and RNA-OUT genetic circuit in living mammalian cells. Nat Commun 2024; 15:8768. [PMID: 39384754 PMCID: PMC11464720 DOI: 10.1038/s41467-024-52962-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 09/26/2024] [Indexed: 10/11/2024] Open
Abstract
RNAs and their encoded proteins intricately regulate diverse cell types and states within the human body. Dysregulated RNA expressions or mutations can lead to various diseased cell states, including tumorigenesis. Detecting and manipulating these endogenous RNAs offers significant promise for restoring healthy cell states and targeting tumors both in research and clinical contexts. This study presents an RNA-IN and RNA-OUT genetic circuit capable dynamically sensing and manipulating any RNA target in a programmable manner. The RNA-IN module employes a programmable CRISPR-associated protease (CASP) complex for RNA detection, while the RNA-OUT module utilizes an engineered protease-responsive dCas9-VPR activator. Additionally, the CASP module can detect point mutations by harnessing an uncovered dual-nucleotide synergistic switching effect within the CASP complex, resulting in the amplification of point-mutation signals from initially undetectable levels (1.5-fold) to a remarkable 94-fold. We successfully showcase the circuit's ability to rewire endogenous RNA-IN signals to activate endogenous progesterone biosynthesis pathway, dynamically monitor adipogenic differentiation of mesenchymal stem cells (MSCs) and the epithelial-to-mesenchmal trans-differentiation, as well as selective killing of tumor cells. The programmable RNA-IN and RNA-OUT circuit exhibits tremendous potential for applications in gene therapy, biosensing and design of synthetic regulatory networks.
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Affiliation(s)
- Min Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xue Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yongyue Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yanhui Xiang
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Bo Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Chunbo Lou
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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van der Putten E, Wosikowski K, Beijnen JH, Imre G, Freund CR. Ritonavir reverses resistance to docetaxel and cabazitaxel in prostate cancer cells with acquired resistance to docetaxel. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2024; 7:3. [PMID: 38318527 PMCID: PMC10838382 DOI: 10.20517/cdr.2023.136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 01/08/2024] [Accepted: 01/29/2024] [Indexed: 02/07/2024]
Abstract
Aim: Docetaxel is a microtubule-stabilizing drug used for the treatment of several cancers, including prostate cancer. Resistance to docetaxel can either occur through intrinsic resistance or develop under therapeutic pressure, i.e., acquired resistance. A possible explanation for the occurrence of acquired resistance to docetaxel is increased drug efflux via P-glycoprotein (P-gp) drug transporters. Methods: We have generated docetaxel-resistant cell lines DU-145DOC10 and 22Rv1DOC8 by exposing parental cell lines DU-145DOC and 22Rv1 to increasing levels of docetaxel. Gene expression levels between DU-145DOC10 and 22Rv1DOC8 were compared with those of their respective originator cell lines. Both parental and resistant cell lines were treated with the taxane drugs docetaxel and cabazitaxel in combination with the P-gp/CYP3A4 inhibitor ritonavir and the P-gp inhibitor elacridar. Results: In the docetaxel-resistant cell lines DU-145DOC10 and 22Rv1DOC8, the ABCB1 (P-gp) gene was highly up-regulated. Expression of the P-gp protein was also significantly increased in the docetaxel-resistant cell lines in a Western blotting assay. The addition of ritonavir to docetaxel resulted in a return of the sensitivity to docetaxel in the DU-145DOC10 and 22Rv1DOC8 to a level similar to the sensitivity in the originator cells. We found that these docetaxel-resistant cell lines could also be re-sensitized to cabazitaxel in a similar manner. In a Caco-2 P-gp transporter assay, functional inhibition of P-gp-mediated transport of docetaxel with ritonavir was demonstrated. Conclusion: Our results demonstrate that ritonavir restores sensitivity to both docetaxel and cabazitaxel in docetaxel-resistant cell lines, most likely by inhibiting P-gp-mediated drug efflux.
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Affiliation(s)
| | | | - Jos H. Beijnen
- Department of Pharmacy & Pharmacology, Netherlands Cancer Institute - Antoni van Leeuwenhoek, Amsterdam 1066 CX, the Netherlands
| | - Gábor Imre
- SOLVO Biotechnology, Budapest H-1117, Hungary
| | - Colin R. Freund
- Modra Pharmaceuticals B.V., Amsterdam 1083 HN, the Netherlands
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Mukherjee S, Mukherjee SB, Frenkel-Morgenstern M. Functional and regulatory impact of chimeric RNAs in human normal and cancer cells. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1777. [PMID: 36633099 DOI: 10.1002/wrna.1777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023]
Abstract
Fusions of two genes can lead to the generation of chimeric RNAs, which may have a distinct functional role from their original molecules. Chimeric RNAs could encode novel functional proteins or serve as novel long noncoding RNAs (lncRNAs). The appearance of chimeric RNAs in a cell could help to generate new functionality and phenotypic diversity that might facilitate this cell to survive against new environmental stress. Several recent studies have demonstrated the functional roles of various chimeric RNAs in cancer progression and are considered as biomarkers for cancer diagnosis and sometimes even drug targets. Further, the growing evidence demonstrated the potential functional association of chimeric RNAs with cancer heterogeneity and drug resistance cancer evolution. Recent studies highlighted that chimeric RNAs also have functional potentiality in normal physiological processes. Several functionally potential chimeric RNAs were discovered in human cancer and normal cells in the last two decades. This could indicate that chimeric RNAs are the hidden layer of the human transcriptome that should be explored from the functional insights to better understand the functional evolution of the genome and disease development that could facilitate clinical practice improvements. This review summarizes the current knowledge of chimeric RNAs and highlights their functional, regulatory, and evolutionary impact on different cancers and normal physiological processes. Further, we will discuss the potential functional roles of a recently discovered novel class of chimeric RNAs named sense-antisense/cross-strand chimeric RNAs generated by the fusion of the bi-directional transcripts of the same gene. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Sunanda Biswas Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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Ma S, Liu JY, Zhang JT. eIF3d: A driver of noncanonical cap-dependent translation of specific mRNAs and a trigger of biological/pathological processes. J Biol Chem 2023; 299:104658. [PMID: 36997088 PMCID: PMC10165153 DOI: 10.1016/j.jbc.2023.104658] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/31/2023] Open
Abstract
Eukaryotic initiation factor 3d (eIF3d), a known RNA-binding subunit of the eIF3 complex, is a 66 to 68-kDa protein with an RNA-binding motif and a cap-binding domain. Compared with other eIF3 subunits, eIF3d is relatively understudied. However, recent progress in studying eIF3d has revealed a number of intriguing findings on its role in maintaining eIF3 complex integrity, global protein synthesis, and in biological and pathological processes. It has also been reported that eIF3d has noncanonical functions in regulating translation of a subset of mRNAs by binding to 5'-UTRs or interacting with other proteins independent of the eIF3 complex and additional functions in regulating protein stability. The noncanonical regulation of mRNA translation or protein stability may contribute to the role of eIF3d in biological processes such as metabolic stress adaptation and in disease onset and progression including severe acute respiratory syndrome coronavirus 2 infection, tumorigenesis, and acquired immune deficiency syndrome. In this review, we critically evaluate the recent studies on these aspects of eIF3d and assess prospects in understanding the function of eIF3d in regulating protein synthesis and in biological and pathological processes.
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Affiliation(s)
- Shijie Ma
- Department of Cell and Cancer Biology, The University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Jing-Yuan Liu
- Department of Medicine, The University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Jian-Ting Zhang
- Department of Cell and Cancer Biology, The University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA.
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Li C, Lu K, Yang C, Du W, Liang Z. EIF3D promotes resistance to 5-fluorouracil in colorectal cancer through upregulating RUVBL1. J Clin Lab Anal 2023; 37:e24825. [PMID: 36592991 PMCID: PMC9937894 DOI: 10.1002/jcla.24825] [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: 07/11/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND As EIF3D is oncogenic in colorectal cancer (CRC) and is associated with multidrug resistance, this study aims to investigate whether and how EIF3D regulates resistance to 5-fluorouracil (5-Fu) in CRC. METHODS EIF3D-associated genes in CRC were predicted using bioinformatics tools. CRC cells and nude mice received 5-Fu treatment. Then, the impacts of EIF3D and the interaction between EIF3D and RUVBL1 on cell viability, colony formation, apoptosis, and DNA damage were detected through MTT, colony formation, flow cytometry, and immunofluorescence assays, and those on in vivo tumorigenesis through murine xenograft assay. IC50 value of 5-Fu for CRC cells was determined by probit regression analysis. Expressions of EIF3D, eIF4E, EIF3D-associated genes, γH2AX, Bcl-2, Bax, and Cleaved Caspase-3/Caspase-3 in CRC tissues, cells, and/or xenograft tumors were analyzed by qRT-PCR and/or Western blot. RESULTS EIF3D and RUVBL1 were highly expressed and positively correlated with CRC tissues/cells. In CRC cells, except for eIF4E, both EIF3D and RUVBL1 levels were upregulated by 5-Fu treatment; in addition to that, RUVBL1 level was downregulated by EIF3D silencing rather than eIF4E. Meanwhile, EIF3D silencing diminished IC50 value of 5-Fu and potentiated 5-Fu-induced viability decrease, colony formation inhibition, apoptosis promotion, Bcl-2 downregulation, and γH2AX, Bax, and Cleaved Caspase-3/Caspase-3 upregulation but reversed 5-Fu-triggered RUVBL1 upregulation. RUVBL1 overexpression offsets EIF3D silencing-induced viability decrease and apoptosis promotion of 5-Fu-treated CRC cells, and tumorigenesis suppression and apoptosis promotion in 5-Fu-treated mice. CONCLUSION EIF3D promotes resistance to 5-Fu in CRC through upregulating RUVBL1 level.
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Affiliation(s)
- Chaobin Li
- Gastroenterology DepartmentLiaocheng People's HospitalLiaochengChina
| | - Kemei Lu
- Gastroenterology DepartmentLiaocheng People's HospitalLiaochengChina
| | - Chenggang Yang
- Gastrointestinal Surgery DepartmentLiaocheng People's HospitalLiaochengChina
| | - Wenfeng Du
- Gastrointestinal Surgery DepartmentLiaocheng People's HospitalLiaochengChina
| | - Zhengkai Liang
- Gastrointestinal Surgery DepartmentLiaocheng People's HospitalLiaochengChina
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The Landscape of Novel Expressed Chimeric RNAs in Rheumatoid Arthritis. Cells 2022; 11:cells11071092. [PMID: 35406656 PMCID: PMC8998144 DOI: 10.3390/cells11071092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
In cancers and other complex diseases, the fusion of two genes can lead to the production of chimeric RNAs, which are associated with disease development. Several recurrent chimeric RNAs are expressed in different cancers and are thus used for clinical cancer diagnosis. Rheumatoid arthritis (RA) is an immune-mediated joint disorder resulting in synovial inflammation and joint destruction. Despite advances in therapy, many patients do not respond to treatment and present persistent inflammation. Understanding the landscape of chimeric RNA expression in RA patients could provide a better insight into RA pathogenesis, which might provide better treatment strategies and tailored therapies. Accordingly, we analyzed the publicly available RNA-seq data of synovium tissue from 151 RA patients and 28 healthy controls and were able to identify 37 recurrent chimeric RNAs found to be expressed in at least 3 RA samples. Furthermore, the parental genes of these 37 recurrent chimeric RNAs were found to be differentially expressed and enriched in immune-related processes, such as adaptive immune response and the positive regulation of B-cell activation. Interestingly, the appearance of 5 coding and 23 non-coding chimeric RNAs might be associated with regulating their parental gene expression, leading to the generation of dysfunctional immune responses, such as inflammation and bone destruction. Therefore, in this paper, we present the first study to demonstrate the novel chimeric RNAs that are highly expressed and functional in RA.
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Mukherjee S, Frenkel-Morgenstern M. Evolutionary impact of chimeric RNAs on generating phenotypic plasticity in human cells. Trends Genet 2021; 38:4-7. [PMID: 34579972 DOI: 10.1016/j.tig.2021.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 11/18/2022]
Abstract
Chimeric RNAs are generated by the fusion of the exons or introns of two genes. The generation of chimeric RNAs is important for the functional expansion of cells. Here, we describe the functional implications of chimeric RNAs for generating phenotypic plasticity from an evolutionary perspective.
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Affiliation(s)
- Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel.
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel.
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8
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Mukherjee S, Heng HH, Frenkel-Morgenstern M. Emerging Role of Chimeric RNAs in Cell Plasticity and Adaptive Evolution of Cancer Cells. Cancers (Basel) 2021; 13:4328. [PMID: 34503137 PMCID: PMC8431553 DOI: 10.3390/cancers13174328] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022] Open
Abstract
Gene fusions can give rise to somatic alterations in cancers. Fusion genes have the potential to create chimeric RNAs, which can generate the phenotypic diversity of cancer cells, and could be associated with novel molecular functions related to cancer cell survival and proliferation. The expression of chimeric RNAs in cancer cells might impact diverse cancer-related functions, including loss of apoptosis and cancer cell plasticity, and promote oncogenesis. Due to their recurrence in cancers and functional association with oncogenic processes, chimeric RNAs are considered biomarkers for cancer diagnosis. Several recent studies demonstrated that chimeric RNAs could lead to the generation of new functionality for the resistance of cancer cells against drug therapy. Therefore, targeting chimeric RNAs in drug resistance cancer could be useful for developing precision medicine. So, understanding the functional impact of chimeric RNAs in cancer cells from an evolutionary perspective will be helpful to elucidate cancer evolution, which could provide a new insight to design more effective therapies for cancer patients in a personalized manner.
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Affiliation(s)
- Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel;
| | - Henry H. Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA;
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel;
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Panicker S, Venkatabalasubramanian S, Pathak S, Ramalingam S. The impact of fusion genes on cancer stem cells and drug resistance. Mol Cell Biochem 2021; 476:3771-3783. [PMID: 34095988 DOI: 10.1007/s11010-021-04203-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/29/2021] [Indexed: 12/12/2022]
Abstract
With ever increasing evidences on the role of fusion genes as the oncogenic protagonists in myriad cancers, it's time to explore if fusion genes can be the next generational drug targets in meeting the current demands of higher drug efficacy. Eliminating cancer stem cells (CSC) has become the current focus; however, we have reached a standstill in drug development owing to the lack of effective strategies to eradicate CSC. We believe that fusion genes could be the novel targets to overcome this limitation. The intriguing feature of fusion genes is that it dominantly impacts every aspect of CSC including self-renewal, differentiation, lineage commitment, tumorigenicity and stemness. Given the clinical success of fusion gene-based drugs in hematological cancers, our attempt to target fusion genes in eradicating CSC can be rewarding. As fusion genes are expressed explicitly in cancer cells, eradicating CSC by targeting fusion genes provides yet an another advantage of negligible patient side effects since normal cells remain unaffected by the drug. We hereby delineate the latest evidences on how fusion genes regulate CSC and drug resistance.
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Affiliation(s)
- Saurav Panicker
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kanchipuram, 603203, Tamil Nadu, India
| | | | - Surajit Pathak
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, Chennai, 603103, Tamil Nadu, India
| | - Satish Ramalingam
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kanchipuram, 603203, Tamil Nadu, India.
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Expanding the Molecular Spectrum of Secretory Carcinoma of Salivary Glands With a Novel VIM-RET Fusion. Am J Surg Pathol 2020; 44:1295-1307. [PMID: 32675658 DOI: 10.1097/pas.0000000000001535] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Secretory carcinoma (SC), originally described as mammary analogue SC, is a predominantly low-grade salivary gland neoplasm characterized by a recurrent t(12;15)(p13;q25) translocation, resulting in ETV6-NTRK3 gene fusion. Recently, alternative ETV6-RET, ETV6-MAML3, and ETV6-MET fusions have been found in a subset of SCs lacking the classic ETV6-NTRK3 fusion transcript, but still harboring ETV6 gene rearrangements. DESIGN Forty-nine cases of SC revealing typical histomorphology and immunoprofile were analyzed by next-generation sequencing using the FusionPlex Solid Tumor kit (ArcherDX). All 49 cases of SC were also tested for ETV6, RET, and NTRK3 break by fluorescence in situ hybridization and for the common ETV6-NTRK3 fusions using reverse transcription polymerase chain reaction. RESULTS Of the 49 cases studied, 37 (76%) occurred in the parotid gland, 7 (14%) in the submandibular gland, 2 (4%) in the minor salivary glands, and 1 (2%) each in the nasal mucosa, facial skin, and thyroid gland. SCs were diagnosed more frequently in males (27/49 cases; 55%). Patients' age at diagnosis varied from 15 to 80 years, with a mean age of 49.9 years. By molecular analysis, 40 cases (82%) presented the classic ETV6-NTRK3 fusion, whereas 9 cases (18%) revealed an alternate fusion. Of the 9 cases negative for the ETV6-NTRK3 fusion, 8 cases presented with ETV6-RET fusion. In the 1 remaining case in the parotid gland, next-generation sequencing analysis identified a novel VIM-RET fusion transcript. In addition, the analysis indicated that 1 recurrent high-grade case in the submandibular gland was positive for both ETV6-NTRK3 and MYB-SMR3B fusion transcripts. CONCLUSIONS A novel finding in our study was the discovery of a VIM-RET fusion in 1 patient with SC of the parotid gland who could possibly benefit from RET-targeted therapy. In addition, 1 recurrent high-grade case was shown to harbor 2 different fusions, namely, ETV6-NTRK3 and MYB-SMR3B. The expanded molecular spectrum provides a novel insight into SC oncogenesis and carries important implications for molecular diagnostics, as this is the first SC-associated translocation with a non-ETV6 5' fusion partner. This finding further expands the definition of SC while carrying implications for selecting the appropriate targeted therapy.
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Jonnalagadda B, Arockiasamy S, Krishnamoorthy S. Cellular growth factors as prospective therapeutic targets for combination therapy in androgen independent prostate cancer (AIPC). Life Sci 2020; 259:118208. [PMID: 32763294 DOI: 10.1016/j.lfs.2020.118208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/27/2020] [Accepted: 08/02/2020] [Indexed: 12/21/2022]
Abstract
Cancer is the second leading cause of death worldwide, with prostate cancer, the second most commonly diagnosed cancer among men. Prostate cancer develops in the peripheral zone of the prostate gland, and the initial progression largely depends on androgens, the male reproductive hormone that regulates the growth and development of the prostate gland and testis. The currently available treatments for androgen dependent prostate cancer are, however, effective for a limited period, where the patients show disease relapse, and develop androgen-independent prostate cancer (AIPC). Studies have shown various intricate cellular processes such as, deregulation in multiple biochemical and signaling pathways, intra-tumoral androgen synthesis; AR over-expression and mutations and AR activation via alternative growth pathways are involved in progression of AIPC. The currently approved treatment strategies target a single cellular protein or pathway, where the cells slowly develop resistance and adapt to proliferate via other cellular pathways over a period of time. Therefore, an increased research aims to understand the efficacy of combination therapy, which targets multiple interlinked pathways responsible for acquisition of resistance and survival. The combination therapy is also shown to enhance efficacy as well as reduce toxicity of the drugs. Thus, the present review focuses on the signaling pathways involved in the progression of AIPC, comprising a heterogeneous population of cells and the advantages of combination therapy. Several clinical and pre-clinical studies on a variety of combination treatments have shown beneficial outcomes, yet further research is needed to understand the potential of combination therapy and its diverse strategies.
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Affiliation(s)
- Bhavana Jonnalagadda
- Department of Biomedical Sciences, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Sumathy Arockiasamy
- Department of Biomedical Sciences, Sri Ramachandra Institute of Higher Education and Research, Chennai, India.
| | - Sriram Krishnamoorthy
- Department of Urology, Sri Ramachandra Medical Centre, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
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12
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GOLT1A-KISS1 fusion is associated with metastasis in adenoid cystic carcinomas. Biochem Biophys Res Commun 2020; 526:70-77. [PMID: 32192769 DOI: 10.1016/j.bbrc.2020.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/01/2020] [Indexed: 11/21/2022]
Abstract
Genetic alterations can drive carcinogenesis. Numerous studies have shown that gene fusion is associated with cancer progression and could provide valuable biomarkers for clinical diagnosis or targets for cancer therapy. Adenoid cystic carcinoma (ACC) is a rare form of adenocarcinoma, characterized by frequent local recurrence and high rates of distant metastasis, ultimately resulting in low survival rates. Owing to the lack of effective therapeutic targets and limited biomarkers for diagnosis, a deeper understanding of the molecular basis of ACC is urgently needed. Here, we show that gene fusion is associated with ACC metastasis. We identified a metastasis suppressor KISS1 fused with a close-by gene, GOLT1A, in highly metastatic ACC cell lines and human specimens. Such fusion blocks KISS1 translation, but not transcription, by introducing 5' upstream open reading frames (uORFs) in the GOLT1A-KISS1 fusion transcript. Deletion of these uORFs rescued KISS1 expression and reduced invasion and migration of metastatic ACC cells. We also detected GOLT1A-KISS1 fusion transcripts in other types of highly metastatic cancer cell lines. Taken together, our results highlight the significance of this novel GOLT1A-KISS1 gene fusion in tumor metastasis and provide a valuable biomarker for clinical diagnosis and future therapeutic targeting of ACC.
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13
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Eich ML, Chandrashekar DS, Rodriguez Pen A MDC, Robinson AD, Siddiqui J, Daignault-Newton S, Chakravarthi BVSK, Kunju LP, Netto GJ, Varambally S. Characterization of glycine-N-acyltransferase like 1 (GLYATL1) in prostate cancer. Prostate 2019; 79:1629-1639. [PMID: 31376196 DOI: 10.1002/pros.23887] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 07/09/2019] [Indexed: 01/08/2023]
Abstract
BACKGROUND Recent microarray and sequencing studies of prostate cancer showed multiple molecular alterations during cancer progression. It is critical to evaluate these molecular changes to identify new biomarkers and targets. We performed analysis of glycine-N-acyltransferase like 1 (GLYATL1) expression in various stages of prostate cancer in this study and evaluated the regulation of GLYATL1 by androgen. METHOD We performed in silico analysis of cancer gene expression profiling and transcriptome sequencing to evaluate GLYATL1 expression in prostate cancer. Furthermore, we performed immunohistochemistry using specific GLYATL1 antibody using high-density prostate cancer tissue microarray containing primary and metastatic prostate cancer. We also tested the regulation of GLYATL1 expression by androgen and ETS transcription factor ETV1. In addition, we performed RNA-sequencing of GLYATL1 modulated prostate cancer cells to evaluate the gene expression and changes in molecular pathways. RESULTS Our in silico analysis of cancer gene expression profiling and transcriptome sequencing we revealed an overexpression of GLYATL1 in primary prostate cancer. Confirming these findings by immunohistochemistry, we show that GLYATL1 is overexpressed in primary prostate cancer compared with metastatic prostate cancer and benign prostatic tissue. Low-grade cancers had higher GLYATL1 expression compared to high-grade prostate tumors. Our studies showed that GLYATL1 is upregulated upon androgen treatment in LNCaP prostate cancer cells which harbors ETV1 gene rearrangement. Furthermore, ETV1 knockdown in LNCaP cells showed downregulation of GLYATL1 suggesting potential regulation of GLYATL1 by ETS transcription factor ETV1. Transcriptome sequencing using the GLYATL1 knockdown prostate cancer cell lines LNCaP showed regulation of multiple metabolic pathways. CONCLUSIONS In summary, our study characterizes the expression of GLYATL1 in prostate cancer and explores the regulation of its regulation in prostate cancer showing role for androgen and ETS transcription factor ETV1. Future studies are needed to decipher the biological significance of these findings.
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Affiliation(s)
- Marie-Lisa Eich
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | | | | | - Alyncia D Robinson
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Javed Siddiqui
- Department of Pathology, The University of Michigan, Ann Arbor, Michigan
| | | | | | | | - George J Netto
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Sooryanarayana Varambally
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
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14
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Souza-Santos PTD, Soares Lima SC, Nicolau-Neto P, Boroni M, Meireles Da Costa N, Brewer L, Menezes AN, Furtado C, Moreira MAM, Seuanez HN, de Almeida Simão T, Ribeiro Pinto LF. Mutations, Differential Gene Expression, and Chimeric Transcripts in Esophageal Squamous Cell Carcinoma Show High Heterogeneity. Transl Oncol 2018; 11:1283-1291. [PMID: 30172240 PMCID: PMC6121831 DOI: 10.1016/j.tranon.2018.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 08/03/2018] [Accepted: 08/03/2018] [Indexed: 12/27/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a frequent and lethal neoplasia. As recent advances in targeted therapy have not improved ESCC prognosis, characterization of molecular alterations associated to this tumor is of foremost relevance. In this study, we analyze, for the first time, the complete genomic profile of ESCC by RNA-seq. TP53 was the most frequently mutated gene in the investigation and validation sets (78.6% and 67.4%, respectively). Differential expression analysis between tumor and nontumor adjacent mucosa showed 6698 differentially expressed genes, most of which were overexpressed (74%). Enrichment analysis identified overrepresentation of Wnt pathway, with overexpressed activators and underexpressed inactivators, suggesting activation of canonical and noncanonical Wnt signaling pathways. Higher WNT7B expression was associated with poor prognosis. Twenty-one gene fusions were identified in 50% of tumors, none of which involving the same genes in different patients; 71% of fusions involved syntenic genes. Comparisons with TCGA data showed co-amplification of seven gene pairs involved in fusions in the present study (~33%), suggesting that these rearrangements might have been driven by chromoanagenesis. In conclusion, genomic alterations in ESCC are highly heterogeneous, impacting negatively in target therapy development.
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Affiliation(s)
- Paulo Thiago de Souza-Santos
- Molecular Carcinogenesis Program, Instituto Nacional de Câncer-INCA, Rua Andre Cavalcanti, 37-6° andar, Centro, Rio de Janeiro, RJ, Brasil, 20231-050.
| | - Sheila Coelho Soares Lima
- Molecular Carcinogenesis Program, Instituto Nacional de Câncer-INCA, Rua Andre Cavalcanti, 37-6° andar, Centro, Rio de Janeiro, RJ, Brasil, 20231-050.
| | - Pedro Nicolau-Neto
- Molecular Carcinogenesis Program, Instituto Nacional de Câncer-INCA, Rua Andre Cavalcanti, 37-6° andar, Centro, Rio de Janeiro, RJ, Brasil, 20231-050.
| | - Mariana Boroni
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer-INCA, Rua Andre Cavalcanti, 37-1° andar, Centro, Rio de Janeiro, RJ, Brasil, 20231-050.
| | - Nathalia Meireles Da Costa
- Molecular Carcinogenesis Program, Instituto Nacional de Câncer-INCA, Rua Andre Cavalcanti, 37-6° andar, Centro, Rio de Janeiro, RJ, Brasil, 20231-050.
| | - Lilian Brewer
- Biochemistry Department, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard 28 de Setembro, 77-Maracanã, Rio de Janeiro, RJ, Brasil, 20551-030.
| | - Albert Nobre Menezes
- College of Medical and Dental Sciences, University of Birmingham, Vicent Drive, Edgbaston, Birmingham, B15 2TT, UK.
| | - Carolina Furtado
- Genetics Program, Instituto Nacional de Câncer-INCA, Rua Andre Cavalcanti, 37-4° andar, Centro, Rio de Janeiro, RJ, Brasil, 20231-050.
| | - Miguel Angelo Martins Moreira
- Genetics Program, Instituto Nacional de Câncer-INCA, Rua Andre Cavalcanti, 37-4° andar, Centro, Rio de Janeiro, RJ, Brasil, 20231-050.
| | - Hector N Seuanez
- Genetics Program, Instituto Nacional de Câncer-INCA, Rua Andre Cavalcanti, 37-4° andar, Centro, Rio de Janeiro, RJ, Brasil, 20231-050.
| | - Tatiana de Almeida Simão
- Biochemistry Department, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard 28 de Setembro, 77-Maracanã, Rio de Janeiro, RJ, Brasil, 20551-030.
| | - Luis Felipe Ribeiro Pinto
- Molecular Carcinogenesis Program, Instituto Nacional de Câncer-INCA, Rua Andre Cavalcanti, 37-6° andar, Centro, Rio de Janeiro, RJ, Brasil, 20231-050; Biochemistry Department, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard 28 de Setembro, 77-Maracanã, Rio de Janeiro, RJ, Brasil, 20551-030.
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15
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Mittal K, Donthamsetty S, Kaur R, Yang C, Gupta MV, Reid MD, Choi DH, Rida PCG, Aneja R. Multinucleated polyploidy drives resistance to Docetaxel chemotherapy in prostate cancer. Br J Cancer 2017; 116:1186-1194. [PMID: 28334734 PMCID: PMC5418452 DOI: 10.1038/bjc.2017.78] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 02/24/2017] [Accepted: 03/01/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Docetaxel is the only FDA-approved first-line treatment for castration-resistant prostate cancer (CRPC) patients. Docetaxel treatment inevitably leads to tumour recurrence after an initial therapeutic response with generation of multinucleated polyploid (MP) cells. Here we investigated role of MP cells in clinical relapse of CRPC. METHODS Prostate cancer (PC-3) cells were treated with docetaxel (5 nM) for 3 days followed by a washout and samples were collected at close intervals over 35 days post drug washout. The tumorigenic potential of the giant MP cells was studied by implanting MP cells subcutaneously as tumour xenografts in nude mice. RESULTS Docetaxel-induced polyploid cells undergo mitotic slippage and eventually spawn mononucleated cells via asymmetric cell division or neosis. Both MP and cells derived from polyploid cells had increased survival signals, were positive for CD44 and were resistant to docetaxel chemotherapy. Although MP cells were tumorigenic in nude mice, these cells took a significantly longer time to form tumours compared with parent PC-3 cells. CONCLUSIONS Generation of MP cells upon docetaxel therapy is an adaptive response of apoptosis-reluctant cells. These giant cells ultimately contribute to the generation of mononucleated aneuploid cells via neosis and may have a fundamental role precipitating clinical relapse and chemoresistance in CRPC.
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Affiliation(s)
- Karuna Mittal
- Department of Biology, Georgia State University, Atlanta, GA-30303, USA
| | | | - Ramneet Kaur
- Department of Biology, Georgia State University, Atlanta, GA-30303, USA
| | - Chunhua Yang
- Department of Biology, Georgia State University, Atlanta, GA-30303, USA
| | | | - Michelle D Reid
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
| | - Da Hoon Choi
- Department of Biology, Georgia State University, Atlanta, GA-30303, USA
| | - Padmashree C G Rida
- Department of Biology, Georgia State University, Atlanta, GA-30303, USA.,Novazoi Theranostics, Inc., Rolling Hills Estates, CA 90274, USA
| | - Ritu Aneja
- Department of Biology, Georgia State University, Atlanta, GA-30303, USA
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16
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Ma Y, Miao Y, Peng Z, Sandgren J, De Ståhl TD, Huss M, Lennartsson L, Liu Y, Nistér M, Nilsson S, Li C. Erratum to: Identification of mutations, gene expression changes and fusion transcripts by whole transcriptome RNAseq in docetaxel resistant prostate cancer cells. SPRINGERPLUS 2016; 5:2084. [PMID: 28018792 PMCID: PMC5143331 DOI: 10.1186/s40064-016-3759-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 11/28/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Yuanjun Ma
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Yali Miao
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden ; Department of Obstetrics and Gynecology, Beijing University People's Hospital, Beijing, China
| | - Zhuochun Peng
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Sandgren
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | - Mikael Huss
- SciLifeLab (Science for Life Laboratory), Stockholm, Sweden
| | - Lena Lennartsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Yanling Liu
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden ; Clinical Pathology/Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Sten Nilsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden ; Department of Clinical Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Chunde Li
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden ; Department of Clinical Oncology, Karolinska University Hospital, Stockholm, Sweden
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