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Bae SH, Lee KY, Han S, Yun CW, Park C, Jang H. SOX2 Expression Does Not Guarantee Cancer Stem Cell-like Characteristics in Lung Adenocarcinoma. Cells 2024; 13:216. [PMID: 38334608 PMCID: PMC10854781 DOI: 10.3390/cells13030216] [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: 11/17/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Effectively targeting cancer stemness is essential for successful cancer therapy. Recent studies have revealed that SOX2, a pluripotent stem cell factor, significantly contributes to cancer stem cell (CSC)-like characteristics closely associated with cancer malignancy. However, its contradictory impact on patient survival in specific cancer types, including lung adenocarcinoma (LUAD), underscores the need for more comprehensive research to clarify its functional effect on cancer stemness. In this study, we demonstrate that SOX2 is not universally required for the regulation of CSC-like properties in LUAD. We generated SOX2 knockouts in A549, H358, and HCC827 LUAD cells using the CRISPR/Cas9 system. Our results reveal unchanged CSC characteristics, including sustained proliferation, tumor sphere formation, invasion, migration, and therapy resistance, compared to normal cells. Conversely, SOX2 knockdown using conditional shRNA targeting SOX2, significantly reduced CSC traits. However, these loss-of-function effects were not rescued by SOX2 resistant to shRNA, underscoring the potential for SOX2 protein level-independent results in prior siRNA- or shRNA-based research. Ultimately, our findings demonstrate that SOX2 is not absolutely essential in LUAD cancer cells. This emphasizes the necessity of considering cancer subtype-dependent and context-dependent factors when targeting SOX2 overexpression as a potential therapeutic vulnerability in diverse cancers.
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Affiliation(s)
- Seung-Hyun Bae
- Division of Rare and Refractory Cancer, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea; (S.-H.B.)
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang 10408, Republic of Korea;
| | - Kyung Yong Lee
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang 10408, Republic of Korea;
- Division of Cancer Biology, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea
| | - Suji Han
- Division of Rare and Refractory Cancer, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea; (S.-H.B.)
| | - Chul Won Yun
- Division of Rare and Refractory Cancer, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea; (S.-H.B.)
| | - ChanHyeok Park
- Division of Rare and Refractory Cancer, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea; (S.-H.B.)
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang 10408, Republic of Korea;
| | - Hyonchol Jang
- Division of Rare and Refractory Cancer, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea; (S.-H.B.)
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang 10408, Republic of Korea;
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Li YR, Lyu Z, Tian Y, Fang Y, Zhu Y, Chen Y, Yang L. Advancements in CRISPR screens for the development of cancer immunotherapy strategies. Mol Ther Oncolytics 2023; 31:100733. [PMID: 37876793 PMCID: PMC10591018 DOI: 10.1016/j.omto.2023.100733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
CRISPR screen technology enables systematic and scalable interrogation of gene function by using the CRISPR-Cas9 system to perturb gene expression. In the field of cancer immunotherapy, this technology has empowered the discovery of genes, biomarkers, and pathways that regulate tumor development and progression, immune reactivity, and the effectiveness of immunotherapeutic interventions. By conducting large-scale genetic screens, researchers have successfully identified novel targets to impede tumor growth, enhance anti-tumor immune responses, and surmount immunosuppression within the tumor microenvironment (TME). Here, we present an overview of CRISPR screens conducted in tumor cells for the purpose of identifying novel therapeutic targets. We also explore the application of CRISPR screens in immune cells to propel the advancement of cell-based therapies, encompassing T cells, natural killer cells, dendritic cells, and macrophages. Furthermore, we outline the crucial components necessary for the successful implementation of immune-specific CRISPR screens and explore potential directions for future research.
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Affiliation(s)
- Yan-Ruide Li
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zibai Lyu
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yanxin Tian
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ying Fang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yichen Zhu
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yuning Chen
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lili Yang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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3
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Wolffhardt TM, Ketzer F, Telese S, Wirth T, Ushmorov A. Dependency of B-Cell Acute Lymphoblastic Leukemia and Multiple Myeloma Cell Lines on MEN1 Extends beyond MEN1-KMT2A Interaction. Int J Mol Sci 2023; 24:16472. [PMID: 38003662 PMCID: PMC10670986 DOI: 10.3390/ijms242216472] [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: 10/20/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Menin/MEN1 is a scaffold protein that participates in proliferation, regulation of gene transcription, DNA damage repair, and signal transduction. In hematological malignancies harboring the KMT2A/MLL1 (MLLr) chromosomal rearrangements, the interaction of the oncogenic fusion protein MLLr with MEN1 has been shown to be essential. MEN1 binders inhibiting the MEN1 and KMT2A interaction have been shown to be effective against MLLr AML and B-ALL in experimental models and clinical studies. We hypothesized that in addition to the MEN1-KMT2A interaction, alternative mechanisms might be instrumental in the MEN1 dependency of leukemia. We first mined and analyzed data from publicly available gene expression databases, finding that the dependency of B-ALL cell lines on MEN1 did not correlate with the presence of MLLr. Using shRNA-mediated knockdown, we found that all tested B-ALL cell lines were sensitive to MEN1 depletion, independent of the underlying driver mutations. Most multiple myeloma cell lines that did not harbor MLLr were also sensitive to the genetic depletion of MEN1. We conclude that the oncogenic role of MEN1 is not limited to the interaction with KMT2A. Our results suggest that targeted degradation of MEN1 or the development of binders that induce global changes in the MEN1 protein structure may be more efficient than the inhibition of individual MEN1 protein interactions.
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Affiliation(s)
- Tatjana Magdalena Wolffhardt
- Institute of Physiological Chemistry, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (T.M.W.); (S.T.)
| | - Franz Ketzer
- Center for Molecular and Cellular Oncology, Yale School of Medicine, New Haven, CT 06510, USA;
| | - Stefano Telese
- Institute of Physiological Chemistry, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (T.M.W.); (S.T.)
| | - Thomas Wirth
- Institute of Physiological Chemistry, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (T.M.W.); (S.T.)
| | - Alexey Ushmorov
- Institute of Physiological Chemistry, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (T.M.W.); (S.T.)
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4
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Progresses, Challenges, and Prospects of CRISPR/Cas9 Gene-Editing in Glioma Studies. Cancers (Basel) 2023; 15:cancers15020396. [PMID: 36672345 PMCID: PMC9856991 DOI: 10.3390/cancers15020396] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/11/2023] Open
Abstract
Glioma refers to a tumor that is derived from brain glial stem cells or progenitor cells and is the most common primary intracranial tumor. Due to its complex cellular components, as well as the aggressiveness and specificity of the pathogenic site of glioma, most patients with malignant glioma have poor prognoses following surgeries, radiotherapies, and chemotherapies. In recent years, an increasing amount of research has focused on the use of CRISPR/Cas9 gene-editing technology in the treatment of glioma. As an emerging gene-editing technology, CRISPR/Cas9 utilizes the expression of certain functional proteins to repair tissues or treat gene-deficient diseases and could be applied to immunotherapies through the expression of antigens, antibodies, or receptors. In addition, some research also utilized CRISPR/Cas9 to establish tumor models so as to study tumor pathogenesis and screen tumor prognostic targets. This paper mainly discusses the roles of CRISPR/Cas9 in the treatment of glioma patients, the exploration of the pathogenesis of neuroglioma, and the screening targets for clinical prognosis. This paper also raises the future research prospects of CRISPR/Cas9 in glioma, as well as the opportunities and challenges that it will face in clinical treatment in the future.
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Veras FP, Publio GA, Melo BM, Prado DS, Norbiato T, Cecilio NT, Hiroki C, Damasceno LEA, Jung R, Toller-Kawahisa JE, Martins TV, Assunção SF, Lima D, Alves MG, Vieira GV, Tavares LA, Alves-Rezende ALR, Karbach SH, Nakaya HI, Cunha TM, Souza CS, Cunha FQ, Sales KU, Waisman A, Alves-Filho JC. Pyruvate kinase M2 mediates IL-17 signaling in keratinocytes driving psoriatic skin inflammation. Cell Rep 2022; 41:111897. [PMID: 36577385 DOI: 10.1016/j.celrep.2022.111897] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 11/17/2022] [Accepted: 12/08/2022] [Indexed: 12/28/2022] Open
Abstract
Psoriasis is an inflammatory skin disease characterized by keratinocyte proliferation and inflammatory cell infiltration induced by IL-17. However, the molecular mechanism through which IL-17 signaling in keratinocytes triggers skin inflammation remains not fully understood. Pyruvate kinase M2 (PKM2), a glycolytic enzyme, has been shown to have non-metabolic functions. Here, we report that PKM2 mediates IL-17A signaling in keratinocytes triggering skin psoriatic inflammation. We find high expression of PKM2 in the epidermis of psoriatic patients and mice undergoing psoriasis models. Specific depletion of PKM2 in keratinocytes attenuates the development of experimental psoriasis by reducing the production of pro-inflammatory mediators. Mechanistically, PKM2 forms a complex with Act1 and TRAF6 regulating NF-κB transcriptional signaling downstream of the IL-17 receptor. As IL-17 also induces PKM2 expression in keratinocytes, our findings reveal a sustained signaling circuit critical for the psoriasis-driving effects of IL-17A, suggesting that PKM2 is a potential therapeutic target for psoriasis.
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Affiliation(s)
- Flávio P Veras
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg, University of Mainz, Mainz, Germany.
| | - Gabriel A Publio
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Bruno M Melo
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Douglas S Prado
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Thainá Norbiato
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Nerry T Cecilio
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Carlos Hiroki
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Luis Eduardo A Damasceno
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Rebecca Jung
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg, University of Mainz, Mainz, Germany; Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg, University of Mainz, Mainz, Germany
| | - Juliana E Toller-Kawahisa
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Timna V Martins
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Stella F Assunção
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Diogenes Lima
- Department of Clinical and Toxicological Analyses of the School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marcia G Alves
- Department of Cell Biology, Ribeirão Preto Medical School University of São Paulo, Ribeirão Preto, Brazil
| | - Gabriel V Vieira
- Department of Cell Biology, Ribeirão Preto Medical School University of São Paulo, Ribeirão Preto, Brazil
| | - Lucas A Tavares
- Department of Cell Biology, Ribeirão Preto Medical School University of São Paulo, Ribeirão Preto, Brazil
| | - Ana L R Alves-Rezende
- Division of Dermatology, Internal Medicine Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Susanne H Karbach
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg, University of Mainz, Mainz, Germany; Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg, University of Mainz, Mainz, Germany; Center for Cardiology, Cardiology I, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Helder I Nakaya
- Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Department of Clinical and Toxicological Analyses of the School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Thiago M Cunha
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Cacilda S Souza
- Division of Dermatology, Internal Medicine Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Fernando Q Cunha
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Katiuchia U Sales
- Department of Cell Biology, Ribeirão Preto Medical School University of São Paulo, Ribeirão Preto, Brazil
| | - Ari Waisman
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg, University of Mainz, Mainz, Germany
| | - José C Alves-Filho
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
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Jiang J, Lu Y, Zhang F, Pan T, Zhang Z, Wan Y, Ren X, Zhang R. Semaphorin 4B promotes tumor progression and associates with immune infiltrates in lung adenocarcinoma. BMC Cancer 2022; 22:632. [PMID: 35676688 PMCID: PMC9178879 DOI: 10.1186/s12885-022-09696-w] [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: 03/10/2022] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Semaphorins have been found to play important roles in multiple malignancy-related processes. However, the role of Semaphorin 4B (SEMA4B) in lung cancer remains unclear. Here, we aimed to explore the biological functions of SEMA4B in through bioinformatic analysis, in vitro and in vivo assays. In the present study, the possible mechanism by which SEMA4B affected the tumor growth and microenvironment of lung adenocarcinoma (LUAD) were investigated. METHODS The expression of SEMA4B in LUAD was analyzed by bioinformatic analysis and verified by the immunohistochemistry staining. The prognostic value of SEMA4B in LUAD was investigated using the Kaplan-Meier survival and Cox's regression model. After silencing SEMA4B expression, the functions of SEMA4B in LUAD cells were investigated by in vitro experiments, including CCK-8 and plate clone formation. And the effect of SEMA4B on tumor growth and immune infiltration was explored in C57BL/6 mice tumor-bearing models. RESULTS SEMA4B expression was upregulated in LUAD tissues and correlated with later pathological stages and poor prognosis of LUAD patients. Further study found that SEMA4B silencing suppressed the proliferation of lung cancer cells both in vitro and in vivo. Bioinformatic analysis showed that SEMA4B expression was correlated with the increased infiltration of myeloid-derived suppressor cells (MDSCs), T-regs and the decreased infiltration of CD8+ T cell in LUAD. Importantly, in vivo study verified that the infiltration of T-regs and MDSCs in tumor microenvironment (TME) of Xenograft tissues was decreased after SEMA4B silencing. CONCLUSIONS These findings demonstrated SEMA4B might play an oncogenic role in LUAD progression, and be a promising therapeutic target for lung cancer.
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Affiliation(s)
- Jun Jiang
- Department of Health Service, Base of Health Service, Fourth Military Medical University, Xi'an, China
| | - Yuan Lu
- Department of Respiratory and Critical Care Medicine, Zhongda Hospital, Southeast University, Nanjing, China
| | - Fang Zhang
- Department of Respiratory and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Tao Pan
- Department of Respiratory and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Translational Medicine Center, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhipei Zhang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Yi Wan
- Department of Health Service, Base of Health Service, Fourth Military Medical University, Xi'an, China
| | - Xinling Ren
- Department of Respiratory and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China. .,Department of Pulmonary Medicine, Shenzhen General Hospital, Shenzhen University, Shenzhen, 518055, Guangdong, China.
| | - Rui Zhang
- State Key Laboratory of Cancer Biology, Department of Immunology, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China.
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Interaction between TRPML1 and p62 in Regulating Autophagosome-Lysosome Fusion and Impeding Neuroaxonal Dystrophy in Alzheimer’s Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8096009. [PMID: 35116093 PMCID: PMC8807035 DOI: 10.1155/2022/8096009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022]
Abstract
The loss of transient receptor potential mucolipin 1 (TRPML1), an endosomal and lysosomal Ca2+-releasing channel, has been implicated in neurodegenerative disorders. Mounting evidence have shown that TRPML1 could clear intraneuronal amyloid-β (Aβ), which triggers a hypothesis that TRPML1 activation may be beneficial for axonal transport in Alzheimer's disease (AD). In this work, the functional roles of TRPML1 were studied in the APP/PS1 transgenic mice and Aβ1-42-stimulated hippocampal neurons HT22. We found that lentivirus-mediated overexpression of TRPML1 was shown to promote an accumulation of autolysosomes and increase brain-derived neurotrophic factor (BDNF) transportation to the nucleus, suggesting an axon-protective function. More importantly, we found that TRPML1 also increased p62 that interacted with dynein. Lentivirus-mediated knockdown of p62 or inhibition of dynein by ciliobrevin D stimulation was found to reduce autolysosome formation and nuclear accumulation of BDNF in HT22 cells with Aβ1-42 stimulation. Inhibition of p62 by XRK3F2 stimulation was observed to promote the death of hippocampal neurons of the APP/PS1 transgenic mice. TRPML1 recruited dynein by interacting with p62 to promote the autophagosome-lysosome fusion to mediate BDNF nuclear translocation to impede axon dystrophy in mice with Alzheimer-like phenotypes. In summary, these results demonstrate the presence of a TRPML1/p62/dynein regulatory network in AD, and activation of TRPML1 is required for axon protection to prevent neuroaxonal dystrophy.
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Zats LP, Ahmad L, Casden N, Lee MJ, Belzer V, Adato O, Bar Cohen S, Ko SHB, Filbin MG, Unger R, Lauffenburger DA, Segal RA, Behar O. An affinity for brainstem microglia in pediatric high-grade gliomas of brainstem origin. Neurooncol Adv 2022; 4:vdac117. [PMID: 35990702 PMCID: PMC9389428 DOI: 10.1093/noajnl/vdac117] [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] [Indexed: 11/24/2022] Open
Abstract
Background High-grade gliomas (HGG) in children have a devastating prognosis and occur in a remarkable spatiotemporal pattern. Diffuse midline gliomas (DMG), including diffuse intrinsic pontine gliomas (DIPG), typically occur in mid-childhood, while cortical HGGs are more frequent in older children and adults. The mechanisms behind this pattern are not clear. Methods We used mouse organotypic slice cultures and glial cell cultures to test the impact of the microenvironment on human DIPG cells. Comparing the expression between brainstem and cortical microglia identified differentially expressed secreted proteins. The impact of some of these proteins on DIPGs was tested. Results DIPGs, pediatric HGGs of brainstem origin, survive and divide more in organotypic slice cultures originating in the brainstem as compared to the cortex. Moreover, brainstem microglia are better able to support tumors of brainstem origin. A comparison between the two microglial populations revealed differentially expressed genes. One such gene, interleukin-33 (IL33), is highly expressed in the pons of young mice and its DIPG receptor is upregulated in this context. Consistent with this observation, the expression levels of IL33 and its receptor, IL1RL1, are higher in DIPG biopsies compared to low-grade cortical gliomas. Furthermore, IL33 can enhance proliferation and clonability of HGGs of brainstem origin, while blocking IL33 in brainstem organotypic slice cultures reduced the proliferation of these tumor cells. Conclusions Crosstalk between DIPGs and the brainstem microenvironment, in particular microglia, through IL33 and other secreted factors, modulates spatiotemporal patterning of this HGG and could prove to be an important future therapeutic target.
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Affiliation(s)
- Liat Peretz Zats
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, The Hebrew University , Jerusalem , Israel
| | - Labiba Ahmad
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, The Hebrew University , Jerusalem , Israel
| | - Natania Casden
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, The Hebrew University , Jerusalem , Israel
| | - Meelim J Lee
- Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, MA
| | - Vitali Belzer
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, The Hebrew University , Jerusalem , Israel
| | - Orit Adato
- Faculty of Life Sciences, Bar Ilan University , Ramat Gan , Israel
| | - Shaked Bar Cohen
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, The Hebrew University , Jerusalem , Israel
| | - Seung-Hyun B Ko
- Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, MA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center , Boston, MA
| | - Ron Unger
- Faculty of Life Sciences, Bar Ilan University , Ramat Gan , Israel
| | | | - Rosalind A Segal
- Department of Neurobiology, Harvard Medical School , Boston, MA , USA
- Departments of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute , Boston, MA
| | - Oded Behar
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, The Hebrew University , Jerusalem , Israel
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Gaudelet T, Day B, Jamasb AR, Soman J, Regep C, Liu G, Hayter JBR, Vickers R, Roberts C, Tang J, Roblin D, Blundell TL, Bronstein MM, Taylor-King JP. Utilizing graph machine learning within drug discovery and development. Brief Bioinform 2021; 22:bbab159. [PMID: 34013350 PMCID: PMC8574649 DOI: 10.1093/bib/bbab159] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 12/15/2022] Open
Abstract
Graph machine learning (GML) is receiving growing interest within the pharmaceutical and biotechnology industries for its ability to model biomolecular structures, the functional relationships between them, and integrate multi-omic datasets - amongst other data types. Herein, we present a multidisciplinary academic-industrial review of the topic within the context of drug discovery and development. After introducing key terms and modelling approaches, we move chronologically through the drug development pipeline to identify and summarize work incorporating: target identification, design of small molecules and biologics, and drug repurposing. Whilst the field is still emerging, key milestones including repurposed drugs entering in vivo studies, suggest GML will become a modelling framework of choice within biomedical machine learning.
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Affiliation(s)
| | - Ben Day
- Relation Therapeutics, London, UK
- The Computer Laboratory, University of Cambridge, UK
| | - Arian R Jamasb
- Relation Therapeutics, London, UK
- The Computer Laboratory, University of Cambridge, UK
- Department of Biochemistry, University of Cambridge, UK
| | | | | | | | | | | | | | - Jian Tang
- Mila, the Quebec AI Institute, Canada
- HEC Montreal, Canada
| | - David Roblin
- Relation Therapeutics, London, UK
- Juvenescence, London, UK
- The Francis Crick Institute, London, UK
| | | | - Michael M Bronstein
- Relation Therapeutics, London, UK
- Department of Computing, Imperial College London, UK
- Twitter, UK
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10
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Gao Y, Lin H, Guo D, Cheng S, Zhou Y, Zhang L, Yao J, Farooq MA, Ajmal I, Duan Y, He C, Tao L, Wu S, Liu M, Jiang W. Suppression of 4.1R enhances the potency of NKG2D-CAR T cells against pancreatic carcinoma via activating ERK signaling pathway. Oncogenesis 2021; 10:62. [PMID: 34548478 PMCID: PMC8455638 DOI: 10.1038/s41389-021-00353-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/12/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022] Open
Abstract
Pancreatic carcinoma (PC) is one of the most common malignancies. Chimeric antigen receptor (CAR)-modified T cells has achieved remarkable efficacy in the treatment of hematological malignancies. However, lack of tumor-specific targets and the existence of inhibitory factors limit the function of CAR T cells when treating solid tumors. 4.1R has been reported to suppress the anti-tumor activity of T cell responses. In this study, we investigated the anti-tumor activity of 4.1R deletion in natural killer group 2D (NKG2D)-CAR T cells against PC. The CAR T cells were obtained by transfecting T cells with lentiviral vector carrying NKG2D-CAR, NC-NKG2D-CAR, or KD2-NKG2D-CAR. In vitro, NKG2D-CAR T cells showed higher cytotoxicity than Mock T cells. However, compared to NKG2D-CAR T cells, furtherly higher cytotoxicity against PC cells in a dose-dependent manner was found in KD2-NKG2D-CAR T cells. In addition, the proliferation rate and cytotoxic activity of KD2-NKG2D-CAR T cells were significantly higher than those of NKG2D-CAR T cells. Besides, the inhibitory receptors PD-1 and TIM-3 were expressed in lower level on KD2-NKG2D-CAR T cells. In vivo, KD2-NKG2D-CAR T cells suppressed tumor growth more effectively in a xenograft model compared to NKG2D-CAR T cells. Mechanistically, 4.1R regulated CAR T cell function via activating ERK signaling pathway. Therefore, the study provides a new idea to enhance the anti-tumor efficiency of CAR T therapy.
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Affiliation(s)
- Yaoxin Gao
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Haizhen Lin
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Dandan Guo
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Sijia Cheng
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Ying Zhou
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Li Zhang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Jie Yao
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Muhammad Asad Farooq
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Iqra Ajmal
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Yixin Duan
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Cong He
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Lei Tao
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Shijia Wu
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Wenzheng Jiang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China.
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11
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Kenney J, Ndoye A, Lamar JM, DiPersio CM. Comparative use of CRISPR and RNAi to modulate integrin α3β1 in triple negative breast cancer cells reveals that some pro-invasive/pro-metastatic α3β1 functions are independent of global regulation of the transcriptome. PLoS One 2021; 16:e0254714. [PMID: 34270616 PMCID: PMC8284828 DOI: 10.1371/journal.pone.0254714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/01/2021] [Indexed: 12/13/2022] Open
Abstract
Integrin receptors for the extracellular matrix play critical roles at all stages of carcinogenesis, including tumor growth, tumor progression and metastasis. The laminin-binding integrin α3β1 is expressed in all epithelial tissues where it has important roles in cell survival, migration, proliferation, and gene expression programs during normal and pathological tissue remodeling. α3β1 signaling and adhesion functions promote tumor growth and metastasis in a number of different types of cancer cells. Previously, we used RNA interference (RNAi) technology to suppress the expression of the ITGA3 gene (encoding the α3 subunit) in the triple-negative breast cancer cell line, MDA-MB-231, thereby generating variants of this line with reduced expression of integrin α3β1. This approach revealed that α3β1 promotes pro-tumorigenic functions such as cell invasion, lung metastasis, and gene regulation. In the current study, we used CRISPR technology to knock out the ITGA3 gene in MDA-MB-231 cells, thereby ablating expression of integrin α3β1 entirely. RNA-seq analysis revealed that while the global transcriptome was altered substantially by RNAi-mediated suppression of α3β1, it was largely unaffected following CRISPR-mediated ablation of α3β1. Moreover, restoring α3β1 to the latter cells through inducible expression of α3 cDNA failed to alter gene expression substantially, suggesting that use of CRISPR to abolish α3β1 led to a decoupling of the integrin from its ability to regulate the transcriptome. Interestingly, both cell invasion in vitro and metastatic colonization in vivo were reduced when α3β1 was abolished using CRISPR, as we observed previously using RNAi to suppress α3β1. Taken together, our results show that pro-invasive/pro-metastatic roles for α3β1 are not dependent on its ability to regulate the transcriptome. Moreover, our finding that use of RNAi versus CRISPR to target α3β1 produced distinct effects on gene expression underlines the importance of using multiple approaches to obtain a complete picture of an integrin’s functions in cancer cells.
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Affiliation(s)
- James Kenney
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, United States of America
| | - Abibatou Ndoye
- Department of Surgery, Albany Medical College, Albany, New York, United States of America
| | - John M. Lamar
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York, United States of America
| | - C. Michael DiPersio
- Department of Surgery, Albany Medical College, Albany, New York, United States of America
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York, United States of America
- * E-mail:
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12
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Serine-Threonine Kinase Receptor-Associated Protein (STRAP) Knockout Decreases the Malignant Phenotype in Neuroblastoma Cell Lines. Cancers (Basel) 2021; 13:cancers13133201. [PMID: 34206917 PMCID: PMC8268080 DOI: 10.3390/cancers13133201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 12/21/2022] Open
Abstract
Background: Serine-threonine kinase receptor-associated protein (STRAP) plays an important role in neural development but also in tumor growth. Neuroblastoma, a tumor of neural crest origin, is the most common extracranial solid malignancy of childhood and it continues to carry a poor prognosis. The recent discovery of the role of STRAP in another pediatric solid tumor, osteosarcoma, and the known function of STRAP in neural development, led us to investigate the role of STRAP in neuroblastoma tumorigenesis. Methods: STRAP protein expression was abrogated in two human neuroblastoma cell lines, SK-N-AS and SK-N-BE(2), using transient knockdown with siRNA, stable knockdown with shRNA lentiviral transfection, and CRISPR-Cas9 genetic knockout. STRAP knockdown and knockout cells were examined for phenotypic alterations in vitro and tumor growth in vivo. Results: Cell proliferation, motility, and growth were significantly decreased in STRAP knockout compared to wild-type cells. Indicators of stemness, including mRNA abundance of common stem cell markers Oct4, Nanog, and Nestin, the percentage of cells expressing CD133 on their surface, and the ability to form tumorspheres were significantly decreased in the STRAP KO cells. In vivo, STRAP knockout cells formed tumors less readily than wild-type tumor cells. Conclusion: These novel findings demonstrated that STRAP plays a role in tumorigenesis and maintenance of neuroblastoma stemness.
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13
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Mandl M, Ritthammer H, Ejaz A, Wagner SA, Hatzmann FM, Baumgarten S, Viertler HP, Zwierzina ME, Mattesich M, Schiller V, Rauchenwald T, Ploner C, Waldegger P, Pierer G, Zwerschke W. CRISPR/Cas9-mediated gene knockout in human adipose stem/progenitor cells. Adipocyte 2020; 9:626-635. [PMID: 33070670 PMCID: PMC7575003 DOI: 10.1080/21623945.2020.1834230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The CRISPR/Cas9 system is a powerful tool to generate a specific loss-of-function phenotype by gene knockout (KO). However, this approach is challenging in primary human cells. In this technical report, we present a reliable protocol to achieve a functional KO in the genome of human adipose stem/progenitor cells (ASCs). Using Sprouty1 (SPRY1) as a model target gene for a CRISPR/Cas9 mediated KO, we particularize the procedure including the selection of the CRISPR/Cas9 target sequences and the employment of appropriate lentiviral vectors to obtain a functional gene KO. The efficiency of CRISPR/Cas9 to mutate the SPRY1 gene is determined by a PCR-based mutation detection assay and sequence analysis. Effects on mRNA and protein levels are studied by RT-qPCR and Western blotting. In addition, we demonstrate that CRISPR/Cas9 mediated SPRY1 KO and gene silencing by shRNA are similarly effective to deplete the Sprouty1 protein and to inhibit adipogenic differentiation. In summary, we show a reliable approach to achieve a gene KO in human ASCs, which could also apply to other primary cell types.
Abbreviations: ASC: Adipogenic Stem/Progenitor Cell; Cas: CRISPR-associated system; CRISPR: Clustered Regularly Interspaced Palindromic Repeat; gDNA: Genomic DNA; GOI: Gene of interest; gRNA: Guide RNA; NHEJ: Non-homologous end joining; Indel: Insertion/Deletion; PAM: Protospacer adjacent motif; sWAT: Subcutaneous white adipose tissue; TIDE: Tracking of indels by decomposition
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Affiliation(s)
- Markus Mandl
- Division of Cell Metabolism and Differentiation Research, Research Institute for Biomedical Aging Research, University of Innsbruck, Austria
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Austria
| | - Heike Ritthammer
- Division of Cell Metabolism and Differentiation Research, Research Institute for Biomedical Aging Research, University of Innsbruck, Austria
| | - Asim Ejaz
- Division of Cell Metabolism and Differentiation Research, Research Institute for Biomedical Aging Research, University of Innsbruck, Austria
- Adipose Stem Cell Center, Department of Plastic Surgery, University of Pittsburgh, PA, USA
| | - Sonja A. Wagner
- Division of Cell Metabolism and Differentiation Research, Research Institute for Biomedical Aging Research, University of Innsbruck, Austria
| | - Florian M. Hatzmann
- Division of Cell Metabolism and Differentiation Research, Research Institute for Biomedical Aging Research, University of Innsbruck, Austria
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Austria
| | - Saphira Baumgarten
- Division of Cell Metabolism and Differentiation Research, Research Institute for Biomedical Aging Research, University of Innsbruck, Austria
| | - Hans P. Viertler
- Division of Cell Metabolism and Differentiation Research, Research Institute for Biomedical Aging Research, University of Innsbruck, Austria
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Austria
| | - Marit E. Zwierzina
- Department of Plastic and Reconstructive Surgery, Innsbruck Medical University, Innsbruck, Austria
| | - Monika Mattesich
- Department of Plastic and Reconstructive Surgery, Innsbruck Medical University, Innsbruck, Austria
| | - Valerie Schiller
- Division of Cell Metabolism and Differentiation Research, Research Institute for Biomedical Aging Research, University of Innsbruck, Austria
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Austria
| | - Tina Rauchenwald
- Department of Plastic and Reconstructive Surgery, Innsbruck Medical University, Innsbruck, Austria
| | - Christian Ploner
- Department of Plastic and Reconstructive Surgery, Innsbruck Medical University, Innsbruck, Austria
| | - Petra Waldegger
- Division of Cell Metabolism and Differentiation Research, Research Institute for Biomedical Aging Research, University of Innsbruck, Austria
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Austria
| | - Gerhard Pierer
- Department of Plastic and Reconstructive Surgery, Innsbruck Medical University, Innsbruck, Austria
| | - Werner Zwerschke
- Division of Cell Metabolism and Differentiation Research, Research Institute for Biomedical Aging Research, University of Innsbruck, Austria
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Austria
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14
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Analysis of Cross-Association between mRNA Expression and RNAi Efficacy for Predictive Target Discovery in Colon Cancers. Cancers (Basel) 2020; 12:cancers12113091. [PMID: 33114107 PMCID: PMC7690798 DOI: 10.3390/cancers12113091] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/20/2022] Open
Abstract
Simple Summary This study focused on finding genes for which mRNA expression was able to predict the anticancer efficacy of its RNAi treatment. Predictive target discovery is of critical importance in developing biomarker-based strategies of precision medicine. We demonstrated this carrying out cross-association analysis on collateral mRNA expression and RNAi treatment data of ~12,000 genes on a colon cell line panel. The analysis revealed several genes with significant association between mRNA expression level and the inhibitory efficacy of its RNAi treatment. The experimental validation confirm that this simple approach has general applications for studying gene association between omics data from diverse cancer lineages. Abstract The availability of large-scale, collateral mRNA expression and RNAi data from diverse cancer cell types provides useful resources for the discovery of anticancer targets for which inhibitory efficacy can be predicted from gene expression. Here, we calculated bidirectional cross-association scores (predictivity and descriptivity) for each of approximately 18,000 genes identified from mRNA and RNAi (i.e., shRNA and sgRNA) data from colon cancer cell lines. The predictivity score measures the difference in RNAi efficacy between cell lines with high vs. low expression of the target gene, while the descriptivity score measures the differential mRNA expression between groups of cell lines exhibiting high vs. low RNAi efficacy. The mRNA expression of 90 and 74 genes showed significant (p < 0.01) cross-association scores with the shRNA and sgRNA data, respectively. The genes were found to be from diverse molecular classes and have different functions. Cross-association scores for the mRNA expression of six genes (CHAF1B, HNF1B, HTATSF1, IRS2, POLR2B and SATB2) with both shRNA and sgRNA efficacy were significant. These genes were interconnected in cancer-related transcriptional networks. Additional experimental validation confirmed that siHNF1B efficacy is correlated with HNF1B mRNA expression levels in diverse colon cancer cell lines. Furthermore, KIF26A and ZIC2 gene expression, with which shRNA efficacy displayed significant scores, were found to correlate with the survival rate from colon cancer patient data. This study demonstrates that bidirectional predictivity and descriptivity calculations between mRNA and RNAi data serve as useful resources for the discovery of predictive anticancer targets.
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15
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Xu Y, Bankhead A, Tian X, Tang J, Ljungman M, Neamati N. Deletion of Glutathione S-Transferase Omega 1 Activates Type I Interferon Genes and Downregulates Tissue Factor. Cancer Res 2020; 80:3692-3705. [PMID: 32571799 DOI: 10.1158/0008-5472.can-20-0530] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/16/2020] [Accepted: 06/17/2020] [Indexed: 12/18/2022]
Abstract
GST omega 1 (GSTO1) is an atypical GST isoform that is overexpressed in several cancers and has been implicated in drug resistance. Currently, no small-molecule drug targeting GSTO1 is under clinical development. Here we have validated GSTO1 as an impactful target in oncology. Transcriptional profiling coupled with proteomics uncovered novel pharmacodynamic markers and cellular pathways regulated by GSTO1. CRISPR/Cas9 GSTO1 knockout (KO) cell lines failed to form tumors or displayed growth delay in vivo; they also formed smaller 3D spheroids in vitro. Multiomics analysis in GSTO1 KO cells found a strong positive correlation with cell adhesion molecules and IFN response pathways and a strong negative correlation with Myc transcriptional signature. In addition, several clinically used drugs showed significant synthetic lethality with loss or inhibition of GSTO1. Transcription and protein expression of tissue factor (gene name, F3) were downregulated in response to GSTO1 KO. F3 is associated with poor patient survival and promotion of tumor progression in multiple cancers and is a known risk factor for metastasis. Transcription of F3 was regulated by IL1β, whose secretion decreased upon inhibition of GSTO1, suggesting that IL1β links GSTO1 expression and F3 transcription. In summary, our results implicate GSTO1 as a potential therapeutic target in cancer and offer new mechanistic insights into its significant role in cancer progression. SIGNIFICANCE: These findings validate GSTO1 as a therapeutic target in cancer and implicate GSTO1 in the modulation of tumor growth, immune responses, and expression of F3.
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Affiliation(s)
- Yibin Xu
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Armand Bankhead
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.,Department of Biostatistics and Department of Computational Medicine and Bioinformatics, Ann Arbor, Michigan
| | - Xiaoli Tian
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Jianming Tang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Mats Ljungman
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.,Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan.,Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan. .,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
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16
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Martínez-Arribas B, Requena CE, Pérez-Moreno G, Ruíz-Pérez LM, Vidal AE, González-Pacanowska D. DCTPP1 prevents a mutator phenotype through the modulation of dCTP, dTTP and dUTP pools. Cell Mol Life Sci 2020; 77:1645-1660. [PMID: 31377845 PMCID: PMC7162842 DOI: 10.1007/s00018-019-03250-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/05/2019] [Accepted: 07/23/2019] [Indexed: 12/02/2022]
Abstract
To maintain dNTP pool homeostasis and preserve genetic integrity of nuclear and mitochondrial genomes, the synthesis and degradation of DNA precursors must be precisely regulated. Human all-alpha dCTP pyrophosphatase 1 (DCTPP1) is a dNTP pyrophosphatase with high affinity for dCTP and 5'-modified dCTP derivatives, but its contribution to overall nucleotide metabolism is controversial. Here, we identify a central role for DCTPP1 in the homeostasis of dCTP, dTTP and dUTP. Nucleotide pools and the dUTP/dTTP ratio are severely altered in DCTPP1-deficient cells, which exhibit an accumulation of uracil in genomic DNA, the activation of the DNA damage response and both a mitochondrial and nuclear hypermutator phenotype. Notably, DNA damage can be reverted by incubation with thymidine, dUTPase overexpression or uracil-DNA glycosylase suppression. Moreover, DCTPP1-deficient cells are highly sensitive to down-regulation of nucleoside salvage. Our data indicate that DCTPP1 is crucially involved in the provision of dCMP for thymidylate biosynthesis, introducing a new player in the regulation of pyrimidine dNTP levels and the maintenance of genomic integrity.
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Affiliation(s)
- Blanca Martínez-Arribas
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Cristina E Requena
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Guiomar Pérez-Moreno
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Luis M Ruíz-Pérez
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Antonio E Vidal
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain.
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17
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Canonne M, Wanet A, Nguyen TTA, Khelfi A, Ayama-Canden S, Van Steenbrugge M, Fattaccioli A, Sokal E, Najimi M, Arnould T, Renard P. MPV17 does not control cancer cell proliferation. PLoS One 2020; 15:e0229834. [PMID: 32155188 PMCID: PMC7064194 DOI: 10.1371/journal.pone.0229834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/14/2020] [Indexed: 11/19/2022] Open
Abstract
MPV17 is described as a mitochondrial inner membrane channel. Although its function remains elusive, mutations in the MPV17 gene result in hepato-cerebral mitochondrial DNA depletion syndrome in humans. In this study, we show that MPV17 silencing does not induce depletion in mitochondrial DNA content in cancer cells. We also show that MPV17 does not control cancer cell proliferation despite the fact that we initially observed a reduced proliferation rate in five MPV17-silenced cancer cell lines with two different shRNAs. However, shRNA-mediated MPV17 knockdown performed in this work provided misguiding results regarding the resulting proliferation phenotype and only a rescue experiment was able to shed definitive light on the implication of MPV17 in cancer cell proliferation. Our results therefore emphasize the caution that is required when scientific conclusions are drawn from a work based on lentiviral vector-based gene silencing and clearly demonstrate the need to systematically perform a rescue experiment in order to ascertain the specific nature of the experimental results.
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Affiliation(s)
- Morgane Canonne
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Anaïs Wanet
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Thuy Truong An Nguyen
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Alexis Khelfi
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Sophie Ayama-Canden
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Martine Van Steenbrugge
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Antoine Fattaccioli
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Etienne Sokal
- Laboratory of Pediatric Hepatology and Cell Therapy, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium
| | - Mustapha Najimi
- Laboratory of Pediatric Hepatology and Cell Therapy, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium
| | - Thierry Arnould
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Patricia Renard
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
- * E-mail:
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18
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Feng L, Guo X, Li T, Yao C, Xia H, Jiang Z, Jia J, Fang Y, Shi L, Lu CA, Lou J. Novel DNA methylation biomarkers for hexavalent chromium exposure: an epigenome-wide analysis. Epigenomics 2020; 12:221-233. [DOI: 10.2217/epi-2019-0216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aim: We aimed to identify differential methylation of genes that could illuminate the biological mechanisms of chromium (VI) toxicity in this exposure-control study. Materials & methods: DNA methylation was measured in blood samples collected from electroplating workers and controls using a combination of Infinium Methylation450K Chip and targeted-bisulfite sequencing. QuantiGene assay was used to detect the mRNA expression of differentially methylated genes. Inductively coupled plasma–mass spectrometry was used to quantify metals in blood and urine samples. The cytosine–phosphate–guanine sites methylation and gene expression were confirmed in a human lymphoblastoid cell line. Results & conclusion: A total of 131 differentially methylated cytosine–phosphate–guanine sites were found between exposures and controls. DNA methylation of SEMA4B may serve as a potential biomarker for chromium (VI) exposure.
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Affiliation(s)
- Lingfang Feng
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou 310013, PR China
| | - Xinnian Guo
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou 310013, PR China
| | - Tao Li
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou 310013, PR China
| | - Chunji Yao
- Institute of Hygiene, Zhejiang Academy of Medical Sciences, Hangzhou 310013, PR China
| | - Hailing Xia
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou 310013, PR China
| | - Zhaoqiang Jiang
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou 310013, PR China
| | - Junlin Jia
- Center for Biostatistics, Bioinformatics & Big Data, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, PR China
| | - Yuan Fang
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou 310013, PR China
| | - Li Shi
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou 310013, PR China
| | - Chensheng Alex Lu
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Jianlin Lou
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou 310013, PR China
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Combined gene essentiality scoring improves the prediction of cancer dependency maps. EBioMedicine 2019; 50:67-80. [PMID: 31732481 PMCID: PMC6923492 DOI: 10.1016/j.ebiom.2019.10.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 12/22/2022] Open
Abstract
Background Probing genetic dependencies of cancer cells can improve our understanding of tumour development and progression, as well as identify potential drug targets. CRISPR-Cas9-based and shRNA-based genetic screening are commonly utilized to identify essential genes that affect cancer growth. However, systematic methods leveraging these genetic screening techniques to derive consensus cancer dependency maps for individual cancer cell lines are lacking. Finding In this work, we first explored the CRISPR-Cas9 and shRNA gene essentiality profiles in 42 cancer cell lines representing 10 cancer types. We observed limited consistency between the essentiality profiles of these two screens at the genome scale. To improve consensus on the cancer dependence map, we developed a computational model called combined essentiality score (CES) to integrate the genetic essentiality profiles from CRISPR-Cas9 and shRNA screens, while accounting for the molecular features of the genes. We found that the CES method outperformed the existing gene essentiality scoring approaches in terms of ability to detect cancer essential genes. We further demonstrated the power of the CES method in adjusting for screen-specific biases and predicting genetic dependencies in individual cancer cell lines. Interpretation Systematic comparison of the CRISPR-Cas9 and shRNA gene essentiality profiles showed the limitation of relying on a single technique to identify cancer essential genes. The CES method provides an integrated framework to leverage both genetic screening techniques as well as molecular feature data to determine gene essentiality more accurately for cancer cells.
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Giuliano CJ, Lin A, Girish V, Sheltzer JM. Generating Single Cell-Derived Knockout Clones in Mammalian Cells with CRISPR/Cas9. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2019; 128:e100. [PMID: 31503414 PMCID: PMC6741428 DOI: 10.1002/cpmb.100] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9 technology enables the rapid generation of loss-of-function mutations in a targeted gene in mammalian cells. A single cell harboring those mutations can be used to establish a new cell line, thereby creating a CRISPR-induced knockout clone. These clonal cell lines serve as crucial tools for exploring protein function, analyzing the consequences of gene loss, and investigating the specificity of biological reagents. However, the successful derivation of knockout clones can be technically challenging and may be complicated by multiple factors, including incomplete target ablation and interclonal heterogeneity. Here, we describe optimized protocols and plasmids for generating clonal knockouts in mammalian cell lines. We provide strategies for guide RNA design, CRISPR delivery, and knockout validation that facilitate the derivation of true knockout clones and are amenable to multiplexed gene targeting. These protocols will be broadly useful for researchers seeking to apply CRISPR to study gene function in mammalian cells. © 2019 The Authors.
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Affiliation(s)
- Christopher J. Giuliano
- Cold Spring Harbor LaboratoryCold Spring HarborNew York
- Stony Brook UniversityStony BrookNew York
- Massachusetts Institute of TechnologyCambridgeMassachusetts
| | - Ann Lin
- Cold Spring Harbor LaboratoryCold Spring HarborNew York
- Stony Brook UniversityStony BrookNew York
| | - Vishruth Girish
- Cold Spring Harbor LaboratoryCold Spring HarborNew York
- Stony Brook UniversityStony BrookNew York
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Aareskjold E, Grindheim AK, Hollås H, Goris M, Lillehaug JR, Vedeler A. Two tales of Annexin A2 knock-down: One of compensatory effects by antisense RNA and another of a highly active hairpin ribozyme. Biochem Pharmacol 2019; 166:253-263. [PMID: 31158338 DOI: 10.1016/j.bcp.2019.05.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/29/2019] [Indexed: 11/26/2022]
Abstract
Besides altering its own expression during cell transformation, Annexin A2 is upregulated during the progression of many cancer types and also plays key roles during viral infection and multiplication. Consequently, there has been great interest in Annexin A2 as a potential drug target. The successful design of efficient in vivo delivery systems constitutes an obstacle in full exploitation of antisense and RNA-cleaving technologies for the knock-down of specific targets. Efficiency is dependent on the method of delivery and accessibility of the target. Here, hairpin ribozymes and an antisense RNA against rat annexin A2 mRNA were tested for their efficiencies in a T7-driven coupled transcription/translation system. The most efficient ribozyme and antisense RNA were subsequently inserted into a retroviral vector under the control of a tRNA promoter, in a cassette inserted between retroviral Long Terminal Repeats for stable insertion into host DNA. The Phoenix package system based on defective retroviruses was used for virus-mediated gene transfer into PC12 cells. Cells infected with the ribozyme-containing particles died shortly after infection. However, the same ribozyme showed a very high catalytic effect in vitro in cell lysates, explained by its loose hinge helix 2 region. This principle can be transferred to other ribozymes, such as those designed to cleave the guide RNA in the CRISPR/Cas9 technology, as well as to target specific viral RNAs. Interestingly, efficient down-regulation of the expression of Annexin A2 by the antisense RNA resulted in up-regulation of Annexin A7 as a compensatory effect after several cell passages. Indeed, compensatory effects have previously been observed during gene knock-out, but not during knock-down of protein expression. This highlights the problems in interpreting the phenotypic effects of knocking down the expression of a protein. In addition, these data are highly relevant when considering the effects of the CRISPR/Cas9 approach.
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Affiliation(s)
- Elin Aareskjold
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Ann Kari Grindheim
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Hanne Hollås
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Marianne Goris
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Johan R Lillehaug
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
| | - Anni Vedeler
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
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Esposito R, Bosch N, Lanzós A, Polidori T, Pulido-Quetglas C, Johnson R. Hacking the Cancer Genome: Profiling Therapeutically Actionable Long Non-coding RNAs Using CRISPR-Cas9 Screening. Cancer Cell 2019; 35:545-557. [PMID: 30827888 DOI: 10.1016/j.ccell.2019.01.019] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/20/2018] [Accepted: 01/28/2019] [Indexed: 12/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) represent a huge reservoir of potential cancer targets. Such "onco-lncRNAs" have resisted traditional RNAi methods, but CRISPR-Cas9 genome editing now promises functional screens at high throughput and low cost. The unique biology of lncRNAs demands screening strategies distinct from protein-coding genes. The first such screens have identified hundreds of onco-lncRNAs promoting cell proliferation and drug resistance. Ongoing developments will further improve screen performance and translational relevance. This Review aims to highlight the potential of CRISPR screening technology for discovering new onco-lncRNAs, and to guide molecular oncologists wishing to apply it to their cancer of interest.
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Affiliation(s)
- Roberta Esposito
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Núria Bosch
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andrés Lanzós
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Taisia Polidori
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Carlos Pulido-Quetglas
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland.
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Casden N, Behar O. An approach for accelerated isolation of genetically manipulated cell clones with reduced clonal variability. J Cell Sci 2019; 132:jcs.217661. [PMID: 30796102 DOI: 10.1242/jcs.217661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 01/18/2019] [Indexed: 11/20/2022] Open
Abstract
Genomic editing methods, such as the CRISPR/Cas9 system, are routinely used to study gene function in somatic cells. Owing to the heterogeneity of mutations, it is necessary to purify cell clones grown from high dilution to the point of colony formation, which can be a time-consuming process. Here, we tested a modified approach in which we seeded cells at high dilution, together with non-edited carrier cells. As a comparison, cells were also grown at high dilution with conditioned medium from a high-density culture. When using carrier cells or conditioned medium, the formation of cell colonies is accelerated. Additionally, clones grown with carrier cells are more similar to the parental lines in terms of their tumorigenic properties. Surprisingly, key signaling cascades are highly divergent between clones isolated from low-density cultures, even with conditioned medium, in contrast to clones isolated with carrier cells. Thus, our study uncovers a significant limitation using the common approach of isolating cell clones following genetic modifications and suggests an alternative method that mitigates the problem of heterogeneity of gene expression between clones.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Natania Casden
- Department of Developmental Biology and Cancer Research, The Hebrew University, P.O. Box 12271, Ein Kerem, Jerusalem 91120, Israel.,The Institute for Medical Research, Faculty of Medicine, The Hebrew University, P.O. Box 12271, Ein Kerem, Jerusalem 91120, Israel
| | - Oded Behar
- Department of Developmental Biology and Cancer Research, The Hebrew University, P.O. Box 12271, Ein Kerem, Jerusalem 91120, Israel .,The Institute for Medical Research, Faculty of Medicine, The Hebrew University, P.O. Box 12271, Ein Kerem, Jerusalem 91120, Israel
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