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Lang F, Cornwell JA, Kaur K, Elmogazy O, Zhang W, Zhang M, Song H, Sun Z, Wu X, Aladjem MI, Aregger M, Cappell SD, Yang C. Abrogation of the G2/M checkpoint as a chemosensitization approach for alkylating agents. Neuro Oncol 2024; 26:1083-1096. [PMID: 38134889 PMCID: PMC11145461 DOI: 10.1093/neuonc/noad252] [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: 08/17/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND The cell cycle is tightly regulated by checkpoints, which play a vital role in controlling its progression and timing. Cancer cells exploit the G2/M checkpoint, which serves as a resistance mechanism against genotoxic anticancer treatments, allowing for DNA repair prior to cell division. Manipulating cell cycle timing has emerged as a potential strategy to augment the effectiveness of DNA damage-based therapies. METHODS In this study, we conducted a forward genome-wide CRISPR/Cas9 screening with repeated exposure to the alkylating agent temozolomide (TMZ) to investigate the mechanisms underlying tumor cell survival under genotoxic stress. RESULTS Our findings revealed that canonical DNA repair pathways, including the Ataxia-telangiectasia mutated (ATM)/Fanconi and mismatch repair, determine cell fate under genotoxic stress. Notably, we identified the critical role of PKMYT1, in ensuring cell survival. Depletion of PKMYT1 led to overwhelming TMZ-induced cytotoxicity in cancer cells. Isobologram analysis demonstrated potent drug synergy between alkylating agents and a Myt1 kinase inhibitor, RP-6306. Mechanistically, inhibiting Myt1 forced G2/M-arrested cells into an unscheduled transition to the mitotic phase without complete resolution of DNA damage. This forced entry into mitosis, along with persistent DNA damage, resulted in severe mitotic abnormalities. Ultimately, these aberrations led to mitotic exit with substantial apoptosis. Preclinical animal studies demonstrated that the combination regimen involving TMZ and RP-6306 prolonged the overall survival of glioma-bearing mice. CONCLUSIONS Collectively, our findings highlight the potential of targeting cell cycle timing through Myt1 inhibition as an effective strategy to enhance the efficacy of current standard cancer therapies, potentially leading to improved disease outcomes.
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Affiliation(s)
- Fengchao Lang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - James A Cornwell
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Karambir Kaur
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Omar Elmogazy
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Wei Zhang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Meili Zhang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Hua Song
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Zhonghe Sun
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Xiaolin Wu
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Michael Aregger
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Steven D Cappell
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Chunzhang Yang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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2
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Hoellerbauer P, Kufeld M, Arora S, Mitchell K, Girard E, Herman J, Olson J, Paddison P. FBXO42 activity is required to prevent mitotic arrest, spindle assembly checkpoint activation and lethality in glioblastoma and other cancers. NAR Cancer 2024; 6:zcae021. [PMID: 38774470 PMCID: PMC11106029 DOI: 10.1093/narcan/zcae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/23/2024] [Accepted: 05/15/2024] [Indexed: 05/24/2024] Open
Abstract
Glioblastoma (GBM) is the most common and aggressive brain tumor in adults. To identify genes differentially required for the viability of GBM stem-like cells (GSCs), we performed functional genomic lethality screens comparing GSCs and control human neural stem cells. Among top-scoring hits in a subset of GBM cells was the F-box-containing gene FBXO42, which was also predicted to be essential in ∼15% of cell lines derived from a broad range of cancers. Mechanistic studies revealed that, in sensitive cells, FBXO42 activity prevents chromosome alignment defects, mitotic cell cycle arrest and cell death. The cell cycle arrest, but not the cell death, triggered by FBXO42 inactivation could be suppressed by brief exposure to a chemical inhibitor of Mps1, a key spindle assembly checkpoint (SAC) kinase. FBXO42's cancer-essential function requires its F-box and Kelch domains, which are necessary for FBXO42's substrate recognition and targeting by SCF (SKP1-CUL1-F-box protein) ubiquitin ligase complex. However, none of FBXO42's previously proposed targets, including ING4, p53 and RBPJ, were responsible for the observed phenotypes. Instead, our results suggest that FBOX42 alters the activity of one or more proteins that perturb chromosome-microtubule dynamics in cancer cells, which in turn leads to induction of the SAC and cell death.
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Affiliation(s)
- Pia Hoellerbauer
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109 USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, 98109 USA
| | - Megan Kufeld
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109 USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109 USA
| | - Kelly Mitchell
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109 USA
| | - Emily J Girard
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109 USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA, 98101 USA
| | - Jacob A Herman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109 USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109 USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA, 98101 USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109 USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, 98109 USA
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3
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Fang Y, Li X, Tian R. Unlocking Glioblastoma Vulnerabilities with CRISPR-Based Genetic Screening. Int J Mol Sci 2024; 25:5702. [PMID: 38891890 PMCID: PMC11171782 DOI: 10.3390/ijms25115702] [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: 03/31/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Glioblastoma (GBM) is the most common malignant brain tumor in adults. Despite advancements in treatment, the prognosis for patients with GBM remains poor due to its aggressive nature and resistance to therapy. CRISPR-based genetic screening has emerged as a powerful tool for identifying genes crucial for tumor progression and treatment resistance, offering promising targets for tumor therapy. In this review, we provide an overview of the recent advancements in CRISPR-based genetic screening approaches and their applications in GBM. We highlight how these approaches have been used to uncover the genetic determinants of GBM progression and responsiveness to various therapies. Furthermore, we discuss the ongoing challenges and future directions of CRISPR-based screening methods in advancing GBM research.
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Affiliation(s)
- Yitong Fang
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.F.); (X.L.)
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xing Li
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.F.); (X.L.)
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruilin Tian
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.F.); (X.L.)
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, China
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4
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Wang S, Xiong Y, Luo Y, Shen Y, Zhang F, Lan H, Pang Y, Wang X, Li X, Zheng X, Lu X, Liu X, Cheng Y, Wu T, Dong Y, Lu Y, Cui J, Jia X, Yang S, Wang L, Wang Y. Genome-wide CRISPR screens identify PKMYT1 as a therapeutic target in pancreatic ductal adenocarcinoma. EMBO Mol Med 2024; 16:1115-1142. [PMID: 38570712 PMCID: PMC11099189 DOI: 10.1038/s44321-024-00060-y] [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: 10/25/2023] [Revised: 03/10/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with an overall 5-year survival rate of <12% due to the lack of effective treatments. Novel treatment strategies are urgently needed. Here, PKMYT1 is identified through genome-wide CRISPR screens as a non-mutant, genetic vulnerability of PDAC. Higher PKMYT1 expression levels indicate poor prognosis in PDAC patients. PKMYT1 ablation inhibits tumor growth and proliferation in vitro and in vivo by regulating cell cycle progression and inducing apoptosis. Moreover, pharmacological inhibition of PKMYT1 shows efficacy in multiple PDAC cell models and effectively induces tumor regression without overt toxicity in PDAC cell line-derived xenograft and in more clinically relevant patient-derived xenograft models. Mechanistically, in addition to its canonical function of phosphorylating CDK1, PKMYT1 functions as an oncogene to promote PDAC tumorigenesis by regulating PLK1 expression and phosphorylation. Finally, TP53 function and PRKDC activation are shown to modulate the sensitivity to PKMYT1 inhibition. These results define PKMYT1 dependency in PDAC and identify potential therapeutic strategies for clinical translation.
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Affiliation(s)
- Simin Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yangjie Xiong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yuxiang Luo
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yanying Shen
- Department of Pathology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Fengrui Zhang
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, 200011, Shanghai, China
| | - Haoqi Lan
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yuzhi Pang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xiaofang Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xiaoqi Li
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Xufen Zheng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xiaojing Lu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xiaoxiao Liu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yumei Cheng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Tanwen Wu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yue Dong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yuan Lu
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, 200011, Shanghai, China
| | - Jiujie Cui
- Department of Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Xiaona Jia
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Sheng Yang
- Department of Oncology, Fujian Medical University Union Hospital, 350001, Fuzhou, Fujian, China
| | - Liwei Wang
- Department of Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Yuexiang Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China.
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5
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Nuechterlein N, Shelbourn A, Szulzewsky F, Arora S, Casad M, Pattwell S, Merino-Galan L, Sulman E, Arowa S, Alvinez N, Jung M, Brown D, Tang K, Jackson S, Stoica S, Chittaboina P, Banasavadi-Siddegowda YK, Wirsching HG, Stella N, Shapiro L, Paddison P, Patel AP, Gilbert MR, Abdullaev Z, Aldape K, Pratt D, Holland EC, Cimino PJ. Haploinsufficiency of phosphodiesterase 10A activates PI3K/AKT signaling independent of PTEN to induce an aggressive glioma phenotype. Genes Dev 2024; 38:273-288. [PMID: 38589034 PMCID: PMC11065166 DOI: 10.1101/gad.351350.123] [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: 11/10/2023] [Accepted: 03/27/2024] [Indexed: 04/10/2024]
Abstract
Glioblastoma is universally fatal and characterized by frequent chromosomal copy number alterations harboring oncogenes and tumor suppressors. In this study, we analyzed exome-wide human glioblastoma copy number data and found that cytoband 6q27 is an independent poor prognostic marker in multiple data sets. We then combined CRISPR-Cas9 data, human spatial transcriptomic data, and human and mouse RNA sequencing data to nominate PDE10A as a potential haploinsufficient tumor suppressor in the 6q27 region. Mouse glioblastoma modeling using the RCAS/tv-a system confirmed that Pde10a suppression induced an aggressive glioma phenotype in vivo and resistance to temozolomide and radiation therapy in vitro. Cell culture analysis showed that decreased Pde10a expression led to increased PI3K/AKT signaling in a Pten-independent manner, a response blocked by selective PI3K inhibitors. Single-nucleus RNA sequencing from our mouse gliomas in vivo, in combination with cell culture validation, further showed that Pde10a suppression was associated with a proneural-to-mesenchymal transition that exhibited increased cell adhesion and decreased cell migration. Our results indicate that glioblastoma patients harboring PDE10A loss have worse outcomes and potentially increased sensitivity to PI3K inhibition.
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Affiliation(s)
- Nicholas Nuechterlein
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Allison Shelbourn
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Michelle Casad
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Siobhan Pattwell
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington 98145, USA
| | - Leyre Merino-Galan
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington 98145, USA
| | - Erik Sulman
- Department of Radiation Oncology, New York University Grossman School of Medicine, New York, New York 11220, USA
| | - Sumaita Arowa
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Neriah Alvinez
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Miyeon Jung
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Desmond Brown
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Kayen Tang
- Developmental Therapeutics and Pharmacology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Sadhana Jackson
- Developmental Therapeutics and Pharmacology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Stefan Stoica
- Neurosurgery Unit for Pituitary and Inheritable Diseases, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Prashant Chittaboina
- Neurosurgery Unit for Pituitary and Inheritable Diseases, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Yeshavanth K Banasavadi-Siddegowda
- Molecular and Therapeutics Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Hans-Georg Wirsching
- Department of Neurology, University Hospital, University of Zurich, Zurich 8091, Switzerland
| | - Nephi Stella
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Linda Shapiro
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Patrick Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Anoop P Patel
- Department of Neurosurgery, Preston Robert Tisch Brain Tumor Center, Duke University, Durham, North Carolina 27710, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Patrick J Cimino
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA;
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6
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Turkarslan S, He Y, Hothi P, Murie C, Nicolas A, Kannan K, Park JH, Pan M, Awawda A, Cole ZD, Shapiro MA, Stuhlmiller TJ, Lee H, Patel AP, Cobbs C, Baliga NS. An atlas of causal and mechanistic drivers of interpatient heterogeneity in glioma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.05.24305380. [PMID: 38633778 PMCID: PMC11023657 DOI: 10.1101/2024.04.05.24305380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Grade IV glioma, formerly known as glioblastoma multiforme (GBM) is the most aggressive and lethal type of brain tumor, and its treatment remains challenging in part due to extensive interpatient heterogeneity in disease driving mechanisms and lack of prognostic and predictive biomarkers. Using mechanistic inference of node-edge relationship (MINER), we have analyzed multiomics profiles from 516 patients and constructed an atlas of causal and mechanistic drivers of interpatient heterogeneity in GBM (gbmMINER). The atlas has delineated how 30 driver mutations act in a combinatorial scheme to causally influence a network of regulators (306 transcription factors and 73 miRNAs) of 179 transcriptional "programs", influencing disease progression in patients across 23 disease states. Through extensive testing on independent patient cohorts, we share evidence that a machine learning model trained on activity profiles of programs within gbmMINER significantly augments risk stratification, identifying patients who are super-responders to standard of care and those that would benefit from 2 nd line treatments. In addition to providing mechanistic hypotheses regarding disease prognosis, the activity of programs containing targets of 2 nd line treatments accurately predicted efficacy of 28 drugs in killing glioma stem-like cells from 43 patients. Our findings demonstrate that interpatient heterogeneity manifests from differential activities of transcriptional programs, providing actionable strategies for mechanistically characterizing GBM from a systems perspective and developing better prognostic and predictive biomarkers for personalized medicine.
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7
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Qi X, Li G, Liu J, Mou L, Zhang Y, Guo S, Chen X, Li W. Structural and energetic insights into the selective inhibition of PKMYT1 against WEE1. J Biomol Struct Dyn 2024; 42:3010-3018. [PMID: 37345529 DOI: 10.1080/07391102.2023.2225106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/30/2023] [Indexed: 06/23/2023]
Abstract
Protein kinase, membrane-associated tyrosine/threonine 1 (PKMYT1), a member of the WEE family and responsible for the regulation of CDK1 phosphorylation, has been considered a promising therapeutic target for cancer therapy. However, the highly structural conservation of the ATP-binding sites of the WEE family poses a challenge to the design of selective inhibitors for PKMYT1. Here, molecular docking, multiple microsecond-length molecular dynamics (MD) simulations and end-point free energy calculations were performed to uncover the molecular mechanism of the binding selectivity of RP-6306 toward PKMYT1 over its highly homologous kinase WEE1. The binding specificity of RP-6306 reported in previous experimental bioassays was clarified by MD simulations and binding free energy calculations. Further, the binding free energy prediction indicated that the binding selectivity of RP-6306 largely derived from the difference in the protein-ligand electrostatic interactions. The per-residue free energy decomposition suggested that the non-conserved gatekeeper residue in the hinge domain of PKMYT1/WEE1, Thr187/Asn376, is the critical factor responsible for the binding selectivity of RP-6306 toward PKMYT1. In addition, a water-mediated hydrogen bond was formed between RP-6306 and Gly191 at the hinge domain in the PKMYT1/RP-6306 complex, which was absent in the WEE1/RP-6306 complex. This study is expected to offer useful information for the design of more potent and selective PKMYT1 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xuesen Qi
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Guozhen Li
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Jiahai Liu
- Department of Gastrointestinal and Anal Diseases Surgery, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Linkai Mou
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Yusheng Zhang
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Shilin Guo
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Xiangyu Chen
- School of Medical Laboratory, Weifang Medical University, Weifang, Shandong, China
| | - Wenxing Li
- Pathology Department, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
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8
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Wu X, Yuan H, Wu Q, Gao Y, Duan T, Yang K, Huang T, Wang S, Yuan F, Lee D, Taori S, Plute T, Heissel S, Alwaseem H, Isay-Del Viscio M, Molina H, Agnihotri S, Hsu DJ, Zhang N, Rich JN. Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming. NATURE CANCER 2024:10.1038/s43018-024-00748-7. [PMID: 38519786 DOI: 10.1038/s43018-024-00748-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 02/23/2024] [Indexed: 03/25/2024]
Abstract
Cancers commonly reprogram translation and metabolism, but little is known about how these two features coordinate in cancer stem cells. Here we show that glioblastoma stem cells (GSCs) display elevated protein translation. To dissect underlying mechanisms, we performed a CRISPR screen and identified YRDC as the top essential transfer RNA (tRNA) modification enzyme in GSCs. YRDC catalyzes the formation of N6-threonylcarbamoyladenosine (t6A) on ANN-decoding tRNA species (A denotes adenosine, and N denotes any nucleotide). Targeting YRDC reduced t6A formation, suppressed global translation and inhibited tumor growth both in vitro and in vivo. Threonine is an essential substrate of YRDC. Threonine accumulated in GSCs, which facilitated t6A formation through YRDC and shifted the proteome to support mitosis-related genes with ANN codon bias. Dietary threonine restriction (TR) reduced tumor t6A formation, slowed xenograft growth and augmented anti-tumor efficacy of chemotherapy and anti-mitotic therapy, providing a molecular basis for a dietary intervention in cancer treatment.
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Affiliation(s)
- Xujia Wu
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Neurosurgery, the First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangdong Translational Medicine Innovation Platform, Guangzhou, China
| | - Huairui Yuan
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Qiulian Wu
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Yixin Gao
- Department of Neurosurgery, the First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangdong Translational Medicine Innovation Platform, Guangzhou, China
| | - Tingting Duan
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Tengfei Huang
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Shuai Wang
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Fanen Yuan
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Derrick Lee
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Suchet Taori
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Tritan Plute
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Søren Heissel
- Proteomics Resource Center, the Rockefeller University, New York, NY, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, the Rockefeller University, New York, NY, USA
| | | | - Henrik Molina
- Proteomics Resource Center, the Rockefeller University, New York, NY, USA
| | - Sameer Agnihotri
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Dennis J Hsu
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nu Zhang
- Department of Neurosurgery, the First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangdong Translational Medicine Innovation Platform, Guangzhou, China.
| | - Jeremy N Rich
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA.
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9
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McFaline-Figueroa JL, Srivatsan S, Hill AJ, Gasperini M, Jackson DL, Saunders L, Domcke S, Regalado SG, Lazarchuck P, Alvarez S, Monnat RJ, Shendure J, Trapnell C. Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy. CELL GENOMICS 2024; 4:100487. [PMID: 38278156 PMCID: PMC10879025 DOI: 10.1016/j.xgen.2023.100487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 09/26/2023] [Accepted: 12/15/2023] [Indexed: 01/28/2024]
Abstract
Chemical genetic screens are a powerful tool for exploring how cancer cells' response to drugs is shaped by their mutations, yet they lack a molecular view of the contribution of individual genes to the response to exposure. Here, we present sci-Plex-Gene-by-Environment (sci-Plex-GxE), a platform for combined single-cell genetic and chemical screening at scale. We highlight the advantages of large-scale, unbiased screening by defining the contribution of each of 522 human kinases to the response of glioblastoma to different drugs designed to abrogate signaling from the receptor tyrosine kinase pathway. In total, we probed 14,121 gene-by-environment combinations across 1,052,205 single-cell transcriptomes. We identify an expression signature characteristic of compensatory adaptive signaling regulated in a MEK/MAPK-dependent manner. Further analyses aimed at preventing adaptation revealed promising combination therapies, including dual MEK and CDC7/CDK9 or nuclear factor κB (NF-κB) inhibitors, as potent means of preventing transcriptional adaptation of glioblastoma to targeted therapy.
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Affiliation(s)
- José L McFaline-Figueroa
- Department of Biomedical Engineering, Columbia University, New York, NY, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Andrew J Hill
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Molly Gasperini
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Dana L Jackson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Lauren Saunders
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Silvia Domcke
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Samuel G Regalado
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Paul Lazarchuck
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Sarai Alvarez
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Raymond J Monnat
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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10
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Chen K, Zhang J, Meng L, Kong L, Lu M, Wang Z, Wang W. The epigenetic downregulation of LncGHRLOS mediated by RNA m6A methylase ZCCHC4 promotes colorectal cancer tumorigenesis. J Exp Clin Cancer Res 2024; 43:44. [PMID: 38326863 PMCID: PMC10848513 DOI: 10.1186/s13046-024-02965-5] [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: 08/19/2023] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND m6A modification is currently recognized as a major driver of RNA function that maintains cancer cell homeostasis. Long non-coding (Lnc) RNAs control cell proliferation and play an important role in the occurrence and progression of colorectal cancer (CRC). ZCCHC4 is a newly discovered m6A methyltransferase whose role and mechanism in tumors have not yet been elucidated. METHODS The EpiQuik m6A RNA methylation kit was used to detect the level of total RNA m6A in six types of digestive tract tumors. The Kaplan-Meier method and receiver operating characteristic curve were used to evaluate the prognostic and diagnostic value of the newly discovered m6A methyltransferase, ZCCHC4, in CRC. The effects on CRC growth in vitro and in vivo were studied using gain- and loss-of-function experiments. The epigenetic mechanisms underlying ZCCHC4 upregulation in CRC were studied using RIP, MeRIP-seq, RNA pull-down, and animal experiments. RESULTS We reported that the ZCCHC4-LncRNAGHRLOS-KDM5D axis regulates the growth of CRC in vitro and in vivo. We found that ZCCHC4 was upregulated in primary CRC samples and could predict adverse clinical outcomes in patients with CRC. Mechanistically, ZCCHC4 downregulated LncRNAGHRLOS to promote CRC tumorigenesis. As a downstream molecule of LncRNAGHRLOS, KDM5D directly controls CRC cell proliferation, migration, and invasion. CONCLUSION This study suggests that the ZCCHC4 axis contributes to the tumorigenesis and progression of CRC and that ZCCHC4 may be a potential biomarker for this malignancy.
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Affiliation(s)
- Ke Chen
- Vascular Surgery Department, Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing, China
| | - Jingcheng Zhang
- Department of Surgery, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Lei Meng
- General Surgery Department, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lingshang Kong
- General Surgery Department, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ming Lu
- General Surgery Department, Anhui Provincial Hospital, Hefei, China
| | - Zhengguang Wang
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, Hefei, China.
| | - Wenbin Wang
- General Surgery Department, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.
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11
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Khamidullina AI, Abramenko YE, Bruter AV, Tatarskiy VV. Key Proteins of Replication Stress Response and Cell Cycle Control as Cancer Therapy Targets. Int J Mol Sci 2024; 25:1263. [PMID: 38279263 PMCID: PMC10816012 DOI: 10.3390/ijms25021263] [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: 12/07/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
Replication stress (RS) is a characteristic state of cancer cells as they tend to exchange precision of replication for fast proliferation and increased genomic instability. To overcome the consequences of improper replication control, malignant cells frequently inactivate parts of their DNA damage response (DDR) pathways (the ATM-CHK2-p53 pathway), while relying on other pathways which help to maintain replication fork stability (ATR-CHK1). This creates a dependency on the remaining DDR pathways, vulnerability to further destabilization of replication and synthetic lethality of DDR inhibitors with common oncogenic alterations such as mutations of TP53, RB1, ATM, amplifications of MYC, CCNE1 and others. The response to RS is normally limited by coordination of cell cycle, transcription and replication. Inhibition of WEE1 and PKMYT1 kinases, which prevent unscheduled mitosis entry, leads to fragility of under-replicated sites. Recent evidence also shows that inhibition of Cyclin-dependent kinases (CDKs), such as CDK4/6, CDK2, CDK8/19 and CDK12/13 can contribute to RS through disruption of DNA repair and replication control. Here, we review the main causes of RS in cancers as well as main therapeutic targets-ATR, CHK1, PARP and their inhibitors.
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Affiliation(s)
- Alvina I. Khamidullina
- Laboratory of Molecular Oncobiology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia; (A.I.K.); (Y.E.A.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
| | - Yaroslav E. Abramenko
- Laboratory of Molecular Oncobiology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia; (A.I.K.); (Y.E.A.)
| | - Alexandra V. Bruter
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
| | - Victor V. Tatarskiy
- Laboratory of Molecular Oncobiology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia; (A.I.K.); (Y.E.A.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
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12
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Tepeli YI, Seale C, Gonçalves JP. ELISL: early-late integrated synthetic lethality prediction in cancer. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btad764. [PMID: 38113447 DOI: 10.1093/bioinformatics/btad764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/06/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023]
Abstract
MOTIVATION Anti-cancer therapies based on synthetic lethality (SL) exploit tumour vulnerabilities for treatment with reduced side effects, by targeting a gene that is jointly essential with another whose function is lost. Computational prediction is key to expedite SL screening, yet existing methods are vulnerable to prevalent selection bias in SL data and reliant on cancer or tissue type-specific omics, which can be scarce. Notably, sequence similarity remains underexplored as a proxy for related gene function and joint essentiality. RESULTS We propose ELISL, Early-Late Integrated SL prediction with forest ensembles, using context-free protein sequence embeddings and context-specific omics from cell lines and tissue. Across eight cancer types, ELISL showed superior robustness to selection bias and recovery of known SL genes, as well as promising cross-cancer predictions. Co-occurring mutations in a BRCA gene and ELISL-predicted pairs from the HH, FGF, WNT, or NEIL gene families were associated with longer patient survival times, revealing therapeutic potential. AVAILABILITY AND IMPLEMENTATION Data: 10.6084/m9.figshare.23607558 & Code: github.com/joanagoncalveslab/ELISL.
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Affiliation(s)
- Yasin I Tepeli
- Pattern Recognition & Bioinformatics, Department of Intelligent Systems, Faculty EEMCS, Delft University of Technology, Delft, The Netherlands
| | - Colm Seale
- Pattern Recognition & Bioinformatics, Department of Intelligent Systems, Faculty EEMCS, Delft University of Technology, Delft, The Netherlands
- Holland Proton Therapy Center (HollandPTC), Delft, The Netherlands
| | - Joana P Gonçalves
- Pattern Recognition & Bioinformatics, Department of Intelligent Systems, Faculty EEMCS, Delft University of Technology, Delft, The Netherlands
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13
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Sokhi S, Lewis CW, Bukhari AB, Hadfield J, Xiao EJ, Fung J, Yoon YJ, Hsu WH, Gamper AM, Chan GK. Myt1 overexpression mediates resistance to cell cycle and DNA damage checkpoint kinase inhibitors. Front Cell Dev Biol 2023; 11:1270542. [PMID: 38020882 PMCID: PMC10652759 DOI: 10.3389/fcell.2023.1270542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Cell cycle checkpoint kinases serve as important therapeutic targets for various cancers. When they are inhibited by small molecules, checkpoint abrogation can induce cell death or further sensitize cancer cells to other genotoxic therapies. Particularly aberrant Cdk1 activation at the G2/M checkpoint by kinase inhibitors causing unscheduled mitotic entry and mitotic arrest was found to lead to DNA damage and cell death selectively in cancer cells. Promising drugs inhibiting kinases like Wee1 (Adavosertib), Wee1+Myt1 (PD166285), ATR (AZD6738) and Chk1 (UCN-01) have been developed, but clinical data has shown variable efficacy for them with poorly understood mechanisms of resistance. Our lab recently identified Myt1 as a predictive biomarker of acquired resistance to the Wee1 kinase inhibitor, Adavosertib. Here, we investigate the role of Myt1 overexpression in promoting resistance to inhibitors (PD166285, UCN-01 and AZD6738) of other kinases regulating cell cycle progression. We demonstrate that Myt1 confers resistance by compensating Cdk1 inhibition in the presence of these different kinase inhibitors. Myt1 overexpression leads to reduced premature mitotic entry and decreased length of mitosis eventually leading to increased survival rates in Adavosertib treated cells. Elevated Myt1 levels also conferred resistance to inhibitors of ATR or Chk1 inhibitor. Our data supports that Myt1 overexpression is a common mechanism by which cancer cells can acquire resistance to a variety of drugs entering the clinic that aim to induce mitotic catastrophe by abrogating the G2/M checkpoint.
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Affiliation(s)
- Sargun Sokhi
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
- Experimental Oncology, Cross Cancer Institute, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Cody W. Lewis
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
- Experimental Oncology, Cross Cancer Institute, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Amirali B. Bukhari
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
- Experimental Oncology, Cross Cancer Institute, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Joanne Hadfield
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
- Experimental Oncology, Cross Cancer Institute, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Edric J. Xiao
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
- Experimental Oncology, Cross Cancer Institute, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Jeremy Fung
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
- Experimental Oncology, Cross Cancer Institute, Edmonton, AB, Canada
| | - Yea Jin Yoon
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
- Experimental Oncology, Cross Cancer Institute, Edmonton, AB, Canada
| | - Wen-Hsin Hsu
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
- Experimental Oncology, Cross Cancer Institute, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Armin M. Gamper
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
- Experimental Oncology, Cross Cancer Institute, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Gordon K. Chan
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
- Experimental Oncology, Cross Cancer Institute, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
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14
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Zeng J, Zeng XX. Systems Medicine for Precise Targeting of Glioblastoma. Mol Biotechnol 2023; 65:1565-1584. [PMID: 36859639 PMCID: PMC9977103 DOI: 10.1007/s12033-023-00699-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/14/2023] [Indexed: 03/03/2023]
Abstract
Glioblastoma (GBM) is a malignant cancer that is fatal even after standard therapy and the effects of current available therapeutics are not promising due its complex and evolving epigenetic and genetic profile. The mysteries that lead to GBM intratumoral heterogeneity and subtype transitions are not entirely clear. Systems medicine is an approach to view the patient in a whole picture integrating systems biology and synthetic biology along with computational techniques. Since the GBM oncogenesis involves genetic mutations, various therapies including gene therapeutics based on CRISPR-Cas technique, MicroRNAs, and implanted synthetic cells endowed with synthetic circuits against GBM with neural stem cells and mesenchymal stem cells acting as potential vehicles carrying therapeutics via the intranasal route, avoiding the risks of invasive methods in order to reach the GBM cells in the brain are discussed and proposed in this review. Systems medicine approach is a rather novel strategy, and since the GBM of a patient is complex and unique, thus to devise an individualized treatment strategy to tailor personalized multimodal treatments for the individual patient taking into account the phenotype of the GBM, the unique body health profile of the patient and individual responses according to the systems medicine concept might show potential to achieve optimum effects.
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Affiliation(s)
- Jie Zeng
- Benjoe Institute of Systems Bio-Engineering, High Technology Park, Xinbei District, Changzhou, 213022 Jiangsu People’s Republic of China
| | - Xiao Xue Zeng
- Department of Health Management, Centre of General Practice, The Seventh Affiliated Hospital, Southern Medical University, No. 28, Desheng Road Section, Liguan Road, Lishui Town, Nanhai District, Foshan, 528000 Guangdong People’s Republic of China
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15
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Benada J, Bulanova D, Azzoni V, Petrosius V, Ghazanfar S, Wennerberg K, Sørensen C. Synthetic lethal interaction between WEE1 and PKMYT1 is a target for multiple low-dose treatment of high-grade serous ovarian carcinoma. NAR Cancer 2023; 5:zcad029. [PMID: 37325550 PMCID: PMC10262308 DOI: 10.1093/narcan/zcad029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/24/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
Ovarian cancer is driven by genetic alterations that necessitate protective DNA damage and replication stress responses through cell cycle control and genome maintenance. This creates specific vulnerabilities that may be exploited therapeutically. WEE1 kinase is a key cell cycle control kinase, and it has emerged as a promising cancer therapy target. However, adverse effects have limited its clinical progress, especially when tested in combination with chemotherapies. A strong genetic interaction between WEE1 and PKMYT1 led us to hypothesize that a multiple low-dose approach utilizing joint WEE1 and PKMYT1 inhibition would allow exploitation of the synthetic lethality. We found that the combination of WEE1 and PKMYT1 inhibition exhibited synergistic effects in eradicating ovarian cancer cells and organoid models at a low dose. The WEE1 and PKMYT1 inhibition synergistically promoted CDK activation. Furthermore, the combined treatment exacerbated DNA replication stress and replication catastrophe, leading to increase of the genomic instability and inflammatory STAT1 signalling activation. These findings suggest a new multiple low-dose approach to harness the potency of WEE1 inhibition through the synthetic lethal interaction with PKMYT1 that may contribute to the development of new treatments for ovarian cancer.
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Affiliation(s)
- Jan Benada
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Daria Bulanova
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Violette Azzoni
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Valdemaras Petrosius
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kgs Lyngby, Denmark
| | - Saba Ghazanfar
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Krister Wennerberg
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Claus Storgaard Sørensen
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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16
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Ariey-Bonnet J, Berges R, Montero MP, Mouysset B, Piris P, Muller K, Pinna G, Failes TW, Arndt GM, Morando P, Baeza-Kallee N, Colin C, Chinot O, Braguer D, Morelli X, André N, Carré M, Tabouret E, Figarella-Branger D, Le Grand M, Pasquier E. Combination drug screen targeting glioblastoma core vulnerabilities reveals pharmacological synergisms. EBioMedicine 2023; 95:104752. [PMID: 37572644 PMCID: PMC10433015 DOI: 10.1016/j.ebiom.2023.104752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/14/2023] Open
Abstract
BACKGROUND Pharmacological synergisms are an attractive anticancer strategy. However, with more than 5000 approved-drugs and compounds in clinical development, identifying synergistic treatments represents a major challenge. METHODS High-throughput screening was combined with target deconvolution and functional genomics to reveal targetable vulnerabilities in glioblastoma. The role of the top gene hit was investigated by RNA interference, transcriptomics and immunohistochemistry in glioblastoma patient samples. Drug combination screen using a custom-made library of 88 compounds in association with six inhibitors of the identified glioblastoma vulnerabilities was performed to unveil pharmacological synergisms. Glioblastoma 3D spheroid, organotypic ex vivo and syngeneic orthotopic mouse models were used to validate synergistic treatments. FINDINGS Nine targetable vulnerabilities were identified in glioblastoma and the top gene hit RRM1 was validated as an independent prognostic factor. The associations of CHK1/MEK and AURKA/BET inhibitors were identified as the most potent amongst 528 tested pairwise drug combinations and their efficacy was validated in 3D spheroid models. The high synergism of AURKA/BET dual inhibition was confirmed in ex vivo and in vivo glioblastoma models, without detectable toxicity. INTERPRETATION Our work provides strong pre-clinical evidence of the efficacy of AURKA/BET inhibitor combination in glioblastoma and opens new therapeutic avenues for this unmet medical need. Besides, we established the proof-of-concept of a stepwise approach aiming at exploiting drug poly-pharmacology to unveil druggable cancer vulnerabilities and to fast-track the identification of synergistic combinations against refractory cancers. FUNDING This study was funded by institutional grants and charities.
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Affiliation(s)
- Jérémy Ariey-Bonnet
- Aix Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Marseille, France
| | - Raphael Berges
- Aix Marseille Université, CNRS, UMR 7051, INP, Inst Neurophysiopathol, Marseille, France
| | - Marie-Pierre Montero
- Aix Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Marseille, France
| | - Baptiste Mouysset
- Aix Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Marseille, France
| | - Patricia Piris
- Aix Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Marseille, France
| | - Kevin Muller
- Aix Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Marseille, France
| | - Guillaume Pinna
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette F-91198, France
| | - Tim W Failes
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2052, Australia; ACRF Drug Discovery Centre for Childhood Cancer, Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Greg M Arndt
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2052, Australia; ACRF Drug Discovery Centre for Childhood Cancer, Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Philippe Morando
- Aix Marseille Université, CNRS, UMR 7051, INP, Inst Neurophysiopathol, Marseille, France
| | - Nathalie Baeza-Kallee
- Aix Marseille Université, CNRS, UMR 7051, INP, Inst Neurophysiopathol, Marseille, France
| | - Carole Colin
- Aix Marseille Université, CNRS, UMR 7051, INP, Inst Neurophysiopathol, Marseille, France
| | - Olivier Chinot
- Aix-Marseille University, Assistance Publique-Hopitaux de Marseille, Centre Hospitalo-Universitaire Timone, Service de Neuro-Oncologie, Marseille, France
| | - Diane Braguer
- Aix Marseille Université, CNRS, UMR 7051, INP, Inst Neurophysiopathol, Marseille, France
| | - Xavier Morelli
- Aix Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Marseille, France
| | - Nicolas André
- Aix Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Marseille, France; Pediatric Oncology and Hematology Department, Hôpital pour Enfant de La Timone, AP-HM, Marseille, France; Metronomics Global Health Initiative, Marseille 13385, France
| | - Manon Carré
- Aix Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Marseille, France
| | - Emeline Tabouret
- Aix Marseille Université, CNRS, UMR 7051, INP, Inst Neurophysiopathol, Marseille, France; Aix-Marseille University, Assistance Publique-Hopitaux de Marseille, Centre Hospitalo-Universitaire Timone, Service de Neuro-Oncologie, Marseille, France
| | | | - Marion Le Grand
- Aix Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Marseille, France.
| | - Eddy Pasquier
- Aix Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Marseille, France; Metronomics Global Health Initiative, Marseille 13385, France.
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17
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McFaline-Figueroa JL, Srivatsan S, Hill AJ, Gasperini M, Jackson DL, Saunders L, Domcke S, Regalado SG, Lazarchuck P, Alvarez S, Monnat RJ, Shendure J, Trapnell C. Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.10.531983. [PMID: 37398090 PMCID: PMC10312454 DOI: 10.1101/2023.03.10.531983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Chemical genetic screens are a powerful tool for exploring how cancer cells' response to drugs is shaped by their mutations, yet they lack a molecular view of the contribution of individual genes to the response to exposure. Here, we present sci-Plex-Gene-by-Environment (sci-Plex-GxE), a platform for combined single-cell genetic and chemical screening at scale. We highlight the advantages of large-scale, unbiased screening by defining the contribution of each of 522 human kinases to the response of glioblastoma to different drugs designed to abrogate signaling from the receptor tyrosine kinase pathway. In total, we probed 14,121 gene-by-environment combinations across 1,052,205 single-cell transcriptomes. We identify an expression signature characteristic of compensatory adaptive signaling regulated in a MEK/MAPK-dependent manner. Further analyses aimed at preventing adaptation revealed promising combination therapies, including dual MEK and CDC7/CDK9 or NF-kB inhibitors, as potent means of preventing transcriptional adaptation of glioblastoma to targeted therapy.
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Affiliation(s)
- José L. McFaline-Figueroa
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Andrew J. Hill
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Molly Gasperini
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Dana L. Jackson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Lauren Saunders
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Silvia Domcke
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Samuel G. Regalado
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Paul Lazarchuck
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Sarai Alvarez
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Raymond J. Monnat
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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18
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Kalamakis G, Platt RJ. CRISPR for neuroscientists. Neuron 2023:S0896-6273(23)00306-9. [PMID: 37201524 DOI: 10.1016/j.neuron.2023.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/14/2023] [Accepted: 04/18/2023] [Indexed: 05/20/2023]
Abstract
Genome engineering technologies provide an entry point into understanding and controlling the function of genetic elements in health and disease. The discovery and development of the microbial defense system CRISPR-Cas yielded a treasure trove of genome engineering technologies and revolutionized the biomedical sciences. Comprising diverse RNA-guided enzymes and effector proteins that evolved or were engineered to manipulate nucleic acids and cellular processes, the CRISPR toolbox provides precise control over biology. Virtually all biological systems are amenable to genome engineering-from cancer cells to the brains of model organisms to human patients-galvanizing research and innovation and giving rise to fundamental insights into health and powerful strategies for detecting and correcting disease. In the field of neuroscience, these tools are being leveraged across a wide range of applications, including engineering traditional and non-traditional transgenic animal models, modeling disease, testing genomic therapies, unbiased screening, programming cell states, and recording cellular lineages and other biological processes. In this primer, we describe the development and applications of CRISPR technologies while highlighting outstanding limitations and opportunities.
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Affiliation(s)
- Georgios Kalamakis
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Department of Chemistry, University of Basel, Petersplatz 1, 4003 Basel, Switzerland; NCCR MSE, Mattenstrasse 24a, 4058 Basel, Switzerland; Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland.
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19
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Petrosyan E, Fares J, Fernandez LG, Yeeravalli R, Dmello C, Duffy JT, Zhang P, Lee-Chang C, Miska J, Ahmed AU, Sonabend AM, Balyasnikova IV, Heimberger AB, Lesniak MS. Endoplasmic Reticulum Stress in the Brain Tumor Immune Microenvironment. Mol Cancer Res 2023; 21:389-396. [PMID: 36652630 PMCID: PMC10159901 DOI: 10.1158/1541-7786.mcr-22-0920] [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: 11/16/2022] [Revised: 01/05/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023]
Abstract
Immunotherapy has emerged as a powerful strategy for halting cancer progression. However, primary malignancies affecting the brain have been exempt to this success. Indeed, brain tumors continue to portend severe morbidity and remain a globally lethal disease. Extensive efforts have been directed at understanding how tumor cells survive and propagate within the unique microenvironment of the central nervous system (CNS). Cancer genetic aberrations and metabolic abnormalities provoke a state of persistent endoplasmic reticulum (ER) stress that in turn promotes tumor growth, invasion, therapeutic resistance, and the dynamic reprogramming of the infiltrating immune cells. Consequently, targeting ER stress is a potential therapeutic approach. In this work, we provide an overview of how ER stress response is advantageous to brain tumor development, discuss the significance of ER stress in governing antitumor immunity, and put forth therapeutic strategies of regulating ER stress to augment the effect of immunotherapy for primary CNS tumors.
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Affiliation(s)
- Edgar Petrosyan
- Department of Neurological Surgery
- Northwestern Medicine Malnati Brain Tumor Institute, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Jawad Fares
- Department of Neurological Surgery
- Northwestern Medicine Malnati Brain Tumor Institute, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Luis G. Fernandez
- Department of Neurological Surgery
- Northwestern Medicine Malnati Brain Tumor Institute, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Ragini Yeeravalli
- Department of Neurological Surgery
- Northwestern Medicine Malnati Brain Tumor Institute, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Crismita Dmello
- Department of Neurological Surgery
- Northwestern Medicine Malnati Brain Tumor Institute, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Joseph T. Duffy
- Department of Neurological Surgery
- Northwestern Medicine Malnati Brain Tumor Institute, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Peng Zhang
- Department of Neurological Surgery
- Northwestern Medicine Malnati Brain Tumor Institute, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Catalina Lee-Chang
- Department of Neurological Surgery
- Northwestern Medicine Malnati Brain Tumor Institute, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Jason Miska
- Department of Neurological Surgery
- Northwestern Medicine Malnati Brain Tumor Institute, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Atique U. Ahmed
- Department of Neurological Surgery
- Northwestern Medicine Malnati Brain Tumor Institute, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Adam M. Sonabend
- Department of Neurological Surgery
- Northwestern Medicine Malnati Brain Tumor Institute, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Irina V. Balyasnikova
- Department of Neurological Surgery
- Northwestern Medicine Malnati Brain Tumor Institute, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Amy B. Heimberger
- Department of Neurological Surgery
- Northwestern Medicine Malnati Brain Tumor Institute, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Maciej S. Lesniak
- Department of Neurological Surgery
- Northwestern Medicine Malnati Brain Tumor Institute, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
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20
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Advanced Bioinformatics Analysis and Genetic Technologies for Targeting Autophagy in Glioblastoma Multiforme. Cells 2023; 12:cells12060897. [PMID: 36980238 PMCID: PMC10047676 DOI: 10.3390/cells12060897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
As the most malignant primary brain tumor in adults, a diagnosis of glioblastoma multiforme (GBM) continues to carry a poor prognosis. GBM is characterized by cytoprotective homeostatic processes such as the activation of autophagy, capability to confer therapeutic resistance, evasion of apoptosis, and survival strategy even in the hypoxic and nutrient-deprived tumor microenvironment. The current gold standard of therapy, which involves radiotherapy and concomitant and adjuvant chemotherapy with temozolomide (TMZ), has been a game-changer for patients with GBM, relatively improving both overall survival (OS) and progression-free survival (PFS); however, TMZ is now well-known to upregulate undesirable cytoprotective autophagy, limiting its therapeutic efficacy for induction of apoptosis in GBM cells. The identification of targets utilizing bioinformatics-driven approaches, advancement of modern molecular biology technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)—CRISPR-associated protein (Cas9) or CRISPR-Cas9 genome editing, and usage of microRNA (miRNA)-mediated regulation of gene expression led to the selection of many novel targets for new therapeutic development and the creation of promising combination therapies. This review explores the current state of advanced bioinformatics analysis and genetic technologies and their utilization for synergistic combination with TMZ in the context of inhibition of autophagy for controlling the growth of GBM.
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21
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Pöhlking C, Beier S, Formanski JP, Friese M, Schreiber M, Schwalbe B. Isolation of Cells from Glioblastoma Multiforme Grade 4 Tumors for Infection with Zika Virus prME and ME Pseudotyped HIV-1. Int J Mol Sci 2023; 24:ijms24054467. [PMID: 36901897 PMCID: PMC10002608 DOI: 10.3390/ijms24054467] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/01/2023] [Accepted: 02/21/2023] [Indexed: 03/12/2023] Open
Abstract
This study aimed to isolate cells from grade 4 glioblastoma multiforme tumors for infection experiments with Zika virus (ZIKV) prME or ME enveloped HIV-1 pseudotypes. The cells obtained from tumor tissue were successfully cultured in human cerebrospinal fluid (hCSF) or a mixture of hCSF/DMEM in cell culture flasks with polar and hydrophilic surfaces. The isolated tumor cells as well as the U87, U138, and U343 cells tested positive for ZIKV receptors Axl and Integrin αvβ5. Pseudotype entry was detected by the expression of firefly luciferase or green fluorescent protein (gfp). In prME and ME pseudotype infections, luciferase expression in U-cell lines was 2.5 to 3.5 logarithms above the background, but still two logarithms lower than in the VSV-G pseudotype control. Infection of single cells was successfully detected in U-cell lines and isolated tumor cells by gfp detection. Even though prME and ME pseudotypes had low infection rates, pseudotypes with ZIKV envelopes are promising candidates for the treatment of glioblastoma.
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Affiliation(s)
- Celine Pöhlking
- Department of Virology, LG-Schreiber, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Sebastian Beier
- Department of Virology, LG-Schreiber, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Jan Patrick Formanski
- Department of Virology, LG-Schreiber, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Michael Friese
- Department of Pathology and Neuropathology, Asklepios Kliniken Hamburg GmbH, Asklepios Klinik Nord, Standort Heidberg, 22417 Hamburg, Germany
| | - Michael Schreiber
- Department of Virology, LG-Schreiber, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
- Correspondence:
| | - Birco Schwalbe
- Department of Neurosurgery, Asklepios Kliniken Hamburg GmbH, Asklepios Klinik Nord, Standort Heidberg, 22417 Hamburg, Germany
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22
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Mitchell K, Sprowls SA, Arora S, Shakya S, Silver DJ, Goins CM, Wallace L, Roversi G, Schafer RE, Kay K, Miller TE, Lauko A, Bassett J, Kashyap A, D'Amato Kass J, Mulkearns-Hubert EE, Johnson S, Alvarado J, Rich JN, Holland EC, Paddison PJ, Patel AP, Stauffer SR, Hubert CG, Lathia JD. WDR5 represents a therapeutically exploitable target for cancer stem cells in glioblastoma. Genes Dev 2023; 37:86-102. [PMID: 36732025 PMCID: PMC10069451 DOI: 10.1101/gad.349803.122] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023]
Abstract
Glioblastomas (GBMs) are heterogeneous, treatment-resistant tumors driven by populations of cancer stem cells (CSCs). However, few molecular mechanisms critical for CSC population maintenance have been exploited for therapeutic development. We developed a spatially resolved loss-of-function screen in GBM patient-derived organoids to identify essential epigenetic regulators in the SOX2-enriched, therapy-resistant niche and identified WDR5 as indispensable for this population. WDR5 is a component of the WRAD complex, which promotes SET1 family-mediated Lys4 methylation of histone H3 (H3K4me), associated with positive regulation of transcription. In GBM CSCs, WDR5 inhibitors blocked WRAD complex assembly and reduced H3K4 trimethylation and expression of genes involved in CSC-relevant oncogenic pathways. H3K4me3 peaks lost with WDR5 inhibitor treatment occurred disproportionally on POU transcription factor motifs, including the POU5F1(OCT4)::SOX2 motif. Use of a SOX2/OCT4 reporter demonstrated that WDR5 inhibitor treatment diminished cells with high reporter activity. Furthermore, WDR5 inhibitor treatment and WDR5 knockdown altered the stem cell state, disrupting CSC in vitro growth and self-renewal, as well as in vivo tumor growth. These findings highlight the role of WDR5 and the WRAD complex in maintaining the CSC state and provide a rationale for therapeutic development of WDR5 inhibitors for GBM and other advanced cancers.
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Affiliation(s)
- Kelly Mitchell
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
| | - Samuel A Sprowls
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Sajina Shakya
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Daniel J Silver
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Christopher M Goins
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA;
| | - Lisa Wallace
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Gustavo Roversi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Rachel E Schafer
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Kristen Kay
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Tyler E Miller
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Adam Lauko
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Medical Scientist Training Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - John Bassett
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Anjali Kashyap
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Jonathan D'Amato Kass
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Erin E Mulkearns-Hubert
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Sadie Johnson
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Joseph Alvarado
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Jeremy N Rich
- University of Pittsburgh Medical Center Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Anoop P Patel
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
- Department of Neurological Surgery, University of Washington, Seattle, Washington 98195, USA
| | - Shaun R Stauffer
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Christopher G Hubert
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Justin D Lathia
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA;
- Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio 44106, USA
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23
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Wang S, Liu X, Zhou T, Li J, Lin Y, Zhou A, Huang J, Zhao J, Cai J, Cai X, Huang Y, Li X. PKMYT1 inhibits lung adenocarcinoma progression by abrogating AKT1 activity. Cell Oncol (Dordr) 2023; 46:195-209. [PMID: 36350496 DOI: 10.1007/s13402-022-00744-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2022] [Indexed: 11/11/2022] Open
Abstract
PURPOSE AKT hyperactivation drives malignant phenotypes in lung cancer via promoting tumor cell proliferation and survival. However, the relationship between dysregulation of cell cycle progression and AKT1 kinase activity is still not clear. METHODS Following the expression level of PKMYT1 in lung cancer, we performed cell proliferation, migration, invasion, and xenograft assays to determine the function of PKMYT1. We used RNA-seq to explore the anti-tumor mechanism of PKMYT1 and examined the effect of PKMYT1 on AKT1 activity. RESULTS In this study, we report that PKMYT1 is downregulated in lung adenocarcinoma (LUAD) tissues and its low expression predicts a poor prognosis in LUAD patients. PKMYT1 exerts potent tumor-suppressive functions in LUAD cells by inhibiting AKT1 activation and thereby repressing cell cycle progression, which depends on its tyrosine and threonine protein kinase activity. Interestingly, PKMYT1 could directly bind AKT1 to abrogate AKT1 activation. Moreover, silencing AKT1 and inhibitors targeting the AKT pathway effectively reverse the promoting effects of PKMYT1 knockdown on proliferation, migration and invasion of LUAD cells. CONCLUSION This work reveals the anti-tumor effect of PKMYT1 in LUAD and provides evidence to clarify the dual roles of PKMYT1 in tumor progression. Moreover, our findings broaden the current understandings on AKT1 activation and identify PKMYT1 as a potential negative regulator of AKT1 kinase activity, providing further insights into targeting the AKT pathway in LUAD.
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Affiliation(s)
- Shuang Wang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Ximeng Liu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Ting Zhou
- Department of Immunology, Sun Yat-Sen University Zhongshan School of Medicine, Guangzhou, 510080, China
| | - Jinling Li
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Ying Lin
- Department of Immunology, Sun Yat-Sen University Zhongshan School of Medicine, Guangzhou, 510080, China
| | - Anni Zhou
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jiamin Huang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jingjing Zhao
- Department of Cardiac Surgery Center, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, China
| | - Junchao Cai
- Department of Immunology, Sun Yat-Sen University Zhongshan School of Medicine, Guangzhou, 510080, China
| | - Xiuyu Cai
- Department of General Internal Medicine, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Yongbo Huang
- State Key Laboratory of Respiratory Diseases and Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510060, China.
| | - Xu Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China.
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24
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Du XJ, Yang XR, Wang QC, Lin GL, Li PF, Zhang WF. Identification and validation of a five-gene prognostic signature based on bioinformatics analyses in breast cancer. Heliyon 2023; 9:e13185. [PMID: 36747547 PMCID: PMC9898304 DOI: 10.1016/j.heliyon.2023.e13185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 01/28/2023] Open
Abstract
Background This study aimed to identify prognostic signatures to predict the prognosis of breast cancer (BRCA) patients based on a series of comprehensive analyses of gene expression data. Methods The RNA-sequencing expression data and corresponding BRCA patient clinical data were collected from the Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) datasets. Firstly, the differently expressed genes (DEGs) related to prognosis between tumor tissues and normal tissues were ascertained by performing R package "limma". Secondly, the DEGs were used to construct a polygenic risk scoring model by the weighted gene co-expression network analysis (WGCNA) and the least absolute shrinkage and selection operator Cox regression (Lasso-cox) analysis method. Thirdly, survival analysis was performed to investigate the risk score values in the TCGA cohort. And the enrichment analysis, immune cell infiltration levels analysis, and protein-protein internet (PPI) analysis were performed. Simultaneously, the GEO cohort was used to validate the model. Lastly, we constructed a nomogram to explore the influence of polygenic risk score and other clinical factors on the survival probability of patients with BRCA. Results A total of 1000 DEGs including 396 upregulated genes and 604 downregulated genes were identified from the TCGA-BRCA dataset. We obtained 5 prognosis-related genes, as the key biomarkers by Lasso-cox analysis (FBXL19, HAGHL, PHKG2, PKMYT1, and TXNDC17), all of which were significantly upregulated in breast tumors. The prognostic prediction of the 5 genes model was great in training and validation cohorts. Moreover, the high-risk group had a poorer prognosis. The Cox regression analysis showed that the comprehensive risk score for 5 genes was an independent prognosis factor. Conclusion The 5 genes risk model constructed in this study had an independent predictive ability to distinguish patients with a high risk of death from those with a low-risk score, and it can be used as a practical and reliable prognostic tool for BRCA.
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Affiliation(s)
- Xin-jie Du
- Department of Thyroid and Breast Surgery, LongYan First Hospital, Longyan, 364000, Fujian, China
| | - Xian-rong Yang
- Department of Thyroid and Breast Surgery, LongYan First Hospital, Longyan, 364000, Fujian, China
| | - Qi-cai Wang
- Department of Thyroid and Breast Surgery, LongYan First Hospital, Longyan, 364000, Fujian, China
| | - Guo-liang Lin
- Department of Thyroid and Breast Surgery, LongYan First Hospital, Longyan, 364000, Fujian, China
| | - Peng-fei Li
- Department of Thyroid and Breast Surgery, LongYan First Hospital, Longyan, 364000, Fujian, China
| | - Wei-feng Zhang
- Department of General Surgery, Linhai Hospital of Traditional Chinese Medicine, Linhai, 317000, Zhejiang, China,Corresponding author.
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25
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Johanssen T, McVeigh L, Erridge S, Higgins G, Straehla J, Frame M, Aittokallio T, Carragher NO, Ebner D. Glioblastoma and the search for non-hypothesis driven combination therapeutics in academia. Front Oncol 2023; 12:1075559. [PMID: 36733367 PMCID: PMC9886867 DOI: 10.3389/fonc.2022.1075559] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
Glioblastoma (GBM) remains a cancer of high unmet clinical need. Current standard of care for GBM, consisting of maximal surgical resection, followed by ionisation radiation (IR) plus concomitant and adjuvant temozolomide (TMZ), provides less than 15-month survival benefit. Efforts by conventional drug discovery to improve overall survival have failed to overcome challenges presented by inherent tumor heterogeneity, therapeutic resistance attributed to GBM stem cells, and tumor niches supporting self-renewal. In this review we describe the steps academic researchers are taking to address these limitations in high throughput screening programs to identify novel GBM combinatorial targets. We detail how they are implementing more physiologically relevant phenotypic assays which better recapitulate key areas of disease biology coupled with more focussed libraries of small compounds, such as drug repurposing, target discovery, pharmacologically active and novel, more comprehensive anti-cancer target-annotated compound libraries. Herein, we discuss the rationale for current GBM combination trials and the need for more systematic and transparent strategies for identification, validation and prioritisation of combinations that lead to clinical trials. Finally, we make specific recommendations to the preclinical, small compound screening paradigm that could increase the likelihood of identifying tractable, combinatorial, small molecule inhibitors and better drug targets specific to GBM.
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Affiliation(s)
- Timothy Johanssen
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Laura McVeigh
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Sara Erridge
- Edinburgh Cancer Centre, Western General Hospital, Edinburgh, United Kingdom
| | - Geoffrey Higgins
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Joelle Straehla
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA, United States
| | - Margaret Frame
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Institute for Cancer Research, Department of Cancer Genetics, Oslo University Hospital, Oslo, Norway
- Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Neil O. Carragher
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel Ebner
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
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26
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Li J, Lu J, Xu M, Yang S, Yu T, Zheng C, Huang X, Pan Y, Chen Y, Long J, Zhang C, Huang H, Dai Q, Li B, Wang W, Yao S, Pan C. ODF2L acts as a synthetic lethal partner with WEE1 inhibition in epithelial ovarian cancer models. J Clin Invest 2023; 133:161544. [PMID: 36378528 PMCID: PMC9843051 DOI: 10.1172/jci161544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
WEE1 has emerged as an attractive target in epithelial ovarian cancer (EOC), but how EOC cells may alter their sensitivity to WEE1 inhibition remains unclear. Here, through a cell cycle machinery-related gene RNAi screen, we found that targeting outer dense fiber of sperm tails 2-like (ODF2L) was a synthetic lethal partner with WEE1 kinase inhibition in EOC cells. Knockdown of ODF2L robustly sensitized cells to treatment with the WEE1 inhibitor AZD1775 in EOC cell lines in vitro as well as in xenografts in vivo. Mechanistically, the increased sensitivity to WEE1 inhibition upon ODF2L loss was accompanied by accumulated DNA damage. ODF2L licensed the recruitment of PKMYT1, a functionally redundant kinase of WEE1, to the CDK1-cyclin B complex and thus restricted the activity of CDK1 when WEE1 was inhibited. Clinically, upregulation of ODF2L correlated with CDK1 activity, DNA damage levels, and sensitivity to WEE1 inhibition in patient-derived EOC cells. Moreover, ODF2L levels predicted the response to WEE1 inhibition in an EOC patient-derived xenograft model. Combination treatment with tumor-targeted lipid nanoparticles that packaged ODF2L siRNA and AZD1775 led to the synergistic attenuation of tumor growth in the ID8 ovarian cancer syngeneic mouse model. These data suggest that WEE1 inhibition is a promising precision therapeutic strategy for EOC cells expressing low levels of ODF2L.
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Affiliation(s)
- Jie Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital
| | - Jingyi Lu
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, and
| | - Manman Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital
| | - Shiyu Yang
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, and
| | - Tiantian Yu
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, and
| | - Cuimiao Zheng
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xi Huang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuwen Pan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital
| | - Yangyang Chen
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Junming Long
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chunyu Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital
| | - Hua Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital
| | - Qingyuan Dai
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Bo Li
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, and,Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wei Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital
| | - Shuzhong Yao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital
| | - Chaoyun Pan
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, and,Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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27
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Hoellerbauer P, Biery MC, Arora S, Rao Y, Girard EJ, Mitchell K, Dighe P, Kufeld M, Kuppers DA, Herman JA, Holland EC, Soroceanu L, Vitanza NA, Olson JM, Pritchard JR, Paddison PJ. Functional genomic analysis of adult and pediatric brain tumor isolates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522885. [PMID: 36711964 PMCID: PMC9881972 DOI: 10.1101/2023.01.05.522885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background Adult and pediatric tumors display stark differences in their mutation spectra and chromosome alterations. Here, we attempted to identify common and unique gene dependencies and their associated biomarkers among adult and pediatric tumor isolates using functional genetic lethal screens and computational modeling. Methods We performed CRISRP-Cas9 lethality screens in two adult glioblastoma (GBM) tumor isolates and five pediatric brain tumor isolates representing atypical teratoid rhabdoid tumors (ATRT), diffuse intrinsic pontine glioma, GBM, and medulloblastoma. We then integrated the screen results with machine learning-based gene-dependency models generated from data from >900 cancer cell lines. Results We found that >50% of candidate dependencies of 280 identified were shared between adult GBM tumors and individual pediatric tumor isolates. 68% of screen hits were found as nodes in our network models, along with shared and tumor-specific predictors of gene dependencies. We investigated network predictors associated with ADAR, EFR3A, FGFR1 (pediatric-specific), and SMARCC2 (ATRT-specific) gene dependency among our tumor isolates. Conclusions The results suggest that, despite harboring disparate genomic signatures, adult and pediatric tumor isolates share a preponderance of genetic dependences. Further, combining data from primary brain tumor lethality screens with large cancer cell line datasets produced valuable insights into biomarkers of gene dependency, even for rare cancers. Importance of the Study Our results demonstrate that large cancer cell lines data sets can be computationally mined to identify known and novel gene dependency relationships in adult and pediatric human brain tumor isolates. Gene dependency networks and lethality screen results represent a key resource for neuro-oncology and cancer research communities. We also highlight some of the challenges and limitations of this approach.
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Affiliation(s)
- Pia Hoellerbauer
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA USA
| | - Matt C Biery
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Yiyun Rao
- Huck Institute for the Life Sciences, Pennsylvania State University, State College, PA, USA
| | - Emily J Girard
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Kelly Mitchell
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Pratiksha Dighe
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
| | - Megan Kufeld
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Daniel A Kuppers
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Jacob A Herman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Liliana Soroceanu
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
| | - Nicholas A Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Justin R Pritchard
- Huck Institute for the Life Sciences, Pennsylvania State University, State College, PA, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA USA
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28
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Liu M, Zhang Y, Zhang A, Deng Y, Gao X, Wang J, Wang Y, Wang S, Liu J, Chen S, Yao W, Liu X. Compound K is a potential clinical anticancer agent in prostate cancer by arresting cell cycle. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 109:154584. [PMID: 36610114 DOI: 10.1016/j.phymed.2022.154584] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/25/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Ginsenosides, phenolic compounds, and polysaccharides are the bioactive constituents of Panax ginseng Meyer. Compound K (CK) is a secondary ginsenoside with better bioavailability. It is also a promising anticancer agent. PURPOSE We aimed to evaluate the effect of CK on prostate cancer (PCa) and its potential mechanisms. STUDY DESIGN The proliferation, migration and cell cycle of PCa cells after CK treatment were assessed in various PCa cell lines. Docetaxel was used as a positive control drug. Unlike other published studies, the potential mechanisms of CK (50 μM) were investigated by an unbiased global transcriptome sequencing in the current study. METHODS Key CK related genes (CRGs) with prognostic significance were identified and verified by bioinformatic methods using data from the TCGA dataset and GSE21034 dataset. The role of CDK1 in the effect of CK treatment on PCa cells was investigated by overexpression of CDK1. RESULTS CK inhibited the proliferation and migration of PCa cells at concentrations (less than 25 μM) without obvious cytotoxicity. Five key CRGs with prognostic significance were identified, including CCNA2, CCNB2, CCNE2, CDK1, and PKMYT1, which are involved in cell cycle pathways. CK inhibited the expression of these 5 genes and the cell cycle of PCa cells. According to the results of bioinformatic analysis, the expression of the five key CRGs was strongly associated with poor prognosis and advanced pathological stage and grade of PCa. In addition, CK could restore androgen sensitivity in castration-resistant PCa cells, probably by inhibiting the expression of CDK1. After CDK1 overexpression, the inhibition of proliferation and migration of PCa cells by CK was decreased. The inhibition on the phosphorylation of AKT by CK was also reduced. CONCLUSION CK can inhibit PCa cells, and the mechanisms may be associated with the inhibition of cell cycle pathways through CDK1. CK is also a potential clinical anticancer agent for treating PCa.
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Affiliation(s)
- Man Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yucong Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - An Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yuxuan Deng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xintao Gao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jiaxin Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yi Wang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang, China
| | - Shaogang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shaoyong Chen
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Weimin Yao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaming Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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29
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Gwynne WD, Suk Y, Custers S, Mikolajewicz N, Chan JK, Zador Z, Chafe SC, Zhai K, Escudero L, Zhang C, Zaslaver O, Chokshi C, Shaikh MV, Bakhshinyan D, Burns I, Chaudhry I, Nachmani O, Mobilio D, Maich WT, Mero P, Brown KR, Quaile AT, Venugopal C, Moffat J, Montenegro-Burke JR, Singh SK. Cancer-selective metabolic vulnerabilities in MYC-amplified medulloblastoma. Cancer Cell 2022; 40:1488-1502.e7. [PMID: 36368321 DOI: 10.1016/j.ccell.2022.10.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/09/2022] [Accepted: 10/06/2022] [Indexed: 11/12/2022]
Abstract
MYC-driven medulloblastoma (MB) is an aggressive pediatric brain tumor characterized by therapy resistance and disease recurrence. Here, we integrated data from unbiased genetic screening and metabolomic profiling to identify multiple cancer-selective metabolic vulnerabilities in MYC-driven MB tumor cells, which are amenable to therapeutic targeting. Among these targets, dihydroorotate dehydrogenase (DHODH), an enzyme that catalyzes de novo pyrimidine biosynthesis, emerged as a favorable candidate for therapeutic targeting. Mechanistically, DHODH inhibition acts on target, leading to uridine metabolite scarcity and hyperlipidemia, accompanied by reduced protein O-GlcNAcylation and c-Myc degradation. Pyrimidine starvation evokes a metabolic stress response that leads to cell-cycle arrest and apoptosis. We further show that an orally available small-molecule DHODH inhibitor demonstrates potent mono-therapeutic efficacy against patient-derived MB xenografts in vivo. The reprogramming of pyrimidine metabolism in MYC-driven medulloblastoma represents an unappreciated therapeutic strategy and a potential new class of treatments with stronger cancer selectivity and fewer neurotoxic sequelae.
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Affiliation(s)
- William D Gwynne
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Yujin Suk
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Michael G DeGroote School of Medicine, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Stefan Custers
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Nicholas Mikolajewicz
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
| | - Jeremy K Chan
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zsolt Zador
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Shawn C Chafe
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Kui Zhai
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Laura Escudero
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Cunjie Zhang
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Olga Zaslaver
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Chirayu Chokshi
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Muhammad Vaseem Shaikh
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - David Bakhshinyan
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Ian Burns
- Michael G DeGroote School of Medicine, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Iqra Chaudhry
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Omri Nachmani
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
| | - Daniel Mobilio
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - William T Maich
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Patricia Mero
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kevin R Brown
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
| | - Andrew T Quaile
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Chitra Venugopal
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Jason Moffat
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Institute for Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - J Rafael Montenegro-Burke
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Sheila K Singh
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada.
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30
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Kameda-Smith MM, Zhu H, Luo EC, Suk Y, Xella A, Yee B, Chokshi C, Xing S, Tan F, Fox RG, Adile AA, Bakhshinyan D, Brown K, Gwynne WD, Subapanditha M, Miletic P, Picard D, Burns I, Moffat J, Paruch K, Fleming A, Hope K, Provias JP, Remke M, Lu Y, Reya T, Venugopal C, Reimand J, Wechsler-Reya RJ, Yeo GW, Singh SK. Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma. Nat Commun 2022; 13:7506. [PMID: 36473869 PMCID: PMC9726987 DOI: 10.1038/s41467-022-35118-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/18/2022] [Indexed: 12/12/2022] Open
Abstract
Pediatric medulloblastoma (MB) is the most common solid malignant brain neoplasm, with Group 3 (G3) MB representing the most aggressive subgroup. MYC amplification is an independent poor prognostic factor in G3 MB, however, therapeutic targeting of the MYC pathway remains limited and alternative therapies for G3 MB are urgently needed. Here we show that the RNA-binding protein, Musashi-1 (MSI1) is an essential mediator of G3 MB in both MYC-overexpressing mouse models and patient-derived xenografts. MSI1 inhibition abrogates tumor initiation and significantly prolongs survival in both models. We identify binding targets of MSI1 in normal neural and G3 MB stem cells and then cross referenced these data with unbiased large-scale screens at the transcriptomic, translatomic and proteomic levels to systematically dissect its functional role. Comparative integrative multi-omic analyses of these large datasets reveal cancer-selective MSI1-bound targets sharing multiple MYC associated pathways, providing a valuable resource for context-specific therapeutic targeting of G3 MB.
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Affiliation(s)
- Michelle M. Kameda-Smith
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Surgery, Faculty of Health Sciences, McMaster University, Hamilton, ON Canada
| | - Helen Zhu
- grid.419890.d0000 0004 0626 690XComputational Biology Program, Ontario Institute for Cancer Research, Toronto, Canada ,grid.17063.330000 0001 2157 2938Department of Medical Biophysics, University of Toronto, Toronto, Canada ,grid.231844.80000 0004 0474 0428University Health Network, Toronto, ON Canada ,grid.494618.6Vector Institute Toronto, Toronto, ON Canada
| | - En-Ching Luo
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Stem Cell Program, University of California San Diego, La Jolla, CA USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, CA USA
| | - Yujin Suk
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Michael G DeGroote School of Medicine, McMaster University, Hamilton, Canada
| | - Agata Xella
- grid.479509.60000 0001 0163 8573Tumor Initiation and Maintenance Program, National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA USA
| | - Brian Yee
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Stem Cell Program, University of California San Diego, La Jolla, CA USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, CA USA
| | - Chirayu Chokshi
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - Sansi Xing
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - Frederick Tan
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Stem Cell Program, University of California San Diego, La Jolla, CA USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, CA USA
| | - Raymond G. Fox
- grid.266100.30000 0001 2107 4242Departments of Pharmacology and Medicine, University of California San Diego School of Medicine, Sanford Consortium for Regenerative Medicine, La Jolla, CA USA
| | - Ashley A. Adile
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - David Bakhshinyan
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - Kevin Brown
- grid.17063.330000 0001 2157 2938Donnelly Centre, Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - William D. Gwynne
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - Minomi Subapanditha
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada
| | - Petar Miletic
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - Daniel Picard
- grid.14778.3d0000 0000 8922 7789Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Ian Burns
- grid.25073.330000 0004 1936 8227Michael G DeGroote School of Medicine, McMaster University, Hamilton, Canada
| | - Jason Moffat
- grid.17063.330000 0001 2157 2938Donnelly Centre, Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Kamil Paruch
- grid.10267.320000 0001 2194 0956Department of Chemistry, CZ Openscreen, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ,grid.483343.bInternational Clinical Research Center, St. Anne’s University Hospital in Brno, 602 00 Brno, Czech Republic
| | - Adam Fleming
- grid.25073.330000 0004 1936 8227McMaster University, Departments of Pediatrics, Hematology and Oncology Division, Hamilton, Canada
| | - Kristin Hope
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - John P. Provias
- grid.25073.330000 0004 1936 8227McMaster University, Departments of Neuropathology, Hamilton, Canada
| | - Marc Remke
- grid.14778.3d0000 0000 8922 7789Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Yu Lu
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - Tannishtha Reya
- grid.266100.30000 0001 2107 4242Departments of Pharmacology and Medicine, University of California San Diego School of Medicine, Sanford Consortium for Regenerative Medicine, La Jolla, CA USA ,grid.239585.00000 0001 2285 2675Present Address: Herbert Irving Comprehensive Cancer Center, Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY USA
| | - Chitra Venugopal
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Surgery, Faculty of Health Sciences, McMaster University, Hamilton, ON Canada
| | - Jüri Reimand
- grid.419890.d0000 0004 0626 690XComputational Biology Program, Ontario Institute for Cancer Research, Toronto, Canada ,grid.17063.330000 0001 2157 2938Department of Medical Biophysics, University of Toronto, Toronto, Canada ,grid.17063.330000 0001 2157 2938Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Robert J. Wechsler-Reya
- grid.479509.60000 0001 0163 8573Tumor Initiation and Maintenance Program, National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA USA ,grid.239585.00000 0001 2285 2675Present Address: Herbert Irving Comprehensive Cancer Center, Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY USA
| | - Gene W. Yeo
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Stem Cell Program, University of California San Diego, La Jolla, CA USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, CA USA
| | - Sheila K. Singh
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Surgery, Faculty of Health Sciences, McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227McMaster University, Department of Pediatrics, Hamilton, Canada
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Hyper-active RAS/MAPK introduces cancer-specific mitotic vulnerabilities. Proc Natl Acad Sci U S A 2022; 119:e2208255119. [PMID: 36191188 PMCID: PMC9565228 DOI: 10.1073/pnas.2208255119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Aneuploidy, the incorrect number of whole chromosomes, is a common feature of tumors that contributes to their initiation and evolution. Preventing aneuploidy requires properly functioning kinetochores, which are large protein complexes assembled on centromeric DNA that link mitotic chromosomes to dynamic spindle microtubules and facilitate chromosome segregation. The kinetochore leverages at least two mechanisms to prevent aneuploidy: error correction and the spindle assembly checkpoint (SAC). BubR1, a factor involved in both processes, was identified as a cancer dependency and therapeutic target in multiple tumor types; however, it remains unclear what specific oncogenic pressures drive this enhanced dependency on BubR1 and whether it arises from BubR1's regulation of the SAC or error-correction pathways. Here, we use a genetically controlled transformation model and glioblastoma tumor isolates to show that constitutive signaling by RAS or MAPK is necessary for cancer-specific BubR1 vulnerability. The MAPK pathway enzymatically hyperstimulates a network of kinetochore kinases that compromises chromosome segregation, rendering cells more dependent on two BubR1 activities: counteracting excessive kinetochore-microtubule turnover for error correction and maintaining the SAC. This work expands our understanding of how chromosome segregation adapts to different cellular states and reveals an oncogenic trigger of a cancer-specific defect.
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CRISPR screening in cancer stem cells. Essays Biochem 2022; 66:305-318. [PMID: 35713228 DOI: 10.1042/ebc20220009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 12/14/2022]
Abstract
Cancer stem cells (CSCs) are a subpopulation of tumor cells with self-renewal ability. Increasing evidence points to the critical roles of CSCs in tumorigenesis, metastasis, therapy resistance, and cancer relapse. As such, the elimination of CSCs improves cancer treatment outcomes. However, challenges remain due to limited understanding of the molecular mechanisms governing self-renewal and survival of CSCs. Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 screening has been increasingly used to identify genetic determinants in cancers. In this primer, we discuss the progress made and emerging opportunities of coupling advanced CRISPR screening systems with CSC models to reveal the understudied vulnerabilities of CSCs.
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Jiang W, Xie N, Xu C. Characterization of a prognostic model for lung squamous cell carcinoma based on eight stemness index-related genes. BMC Pulm Med 2022; 22:224. [PMID: 35676660 PMCID: PMC9178800 DOI: 10.1186/s12890-022-02011-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/11/2022] [Indexed: 11/17/2022] Open
Abstract
Background Cancer stem cells (CSCs) are implicated in cancer progression, chemoresistance, and poor prognosis; thus, they may be promising therapeutic targets. In this study, we aimed to investigate the prognostic application of differentially expressed CSC-related genes in lung squamous cell carcinoma (LUSC). Methods The mRNA stemness index (mRNAsi)-related differentially expressed genes (DEGs) in tumors were identified and further categorized by LASSO Cox regression analysis and 1,000-fold cross-validation, followed by the construction of a prognostic score model for risk stratification. The fractions of tumor-infiltrating immune cells and immune checkpoint genes were analyzed in different risk groups. Results We found 404 mRNAsi-related DEGs in LUSC, 77 of which were significantly associated with overall survival. An eight-gene prognostic signature (PPP1R27, TLX2, ANKLE1, TIGD3, AMH, KCNK3, FLRT3, and PPBP) was identified and used to construct a risk score model. The TCGA set was dichotomized into two risk groups that differed significantly (p = 0.00057) in terms of overall survival time (1, 3, 5-year AUC = 0.830, 0.749, and 0.749, respectively). The model performed well in two independent GEO datasets (p = 0.029, 0.033; 1-year AUC = 0747, 0.783; 3-year AUC = 0.746, 0.737; 5-year AUC = 0.706, 0.723). Low-risk patients had markedly increased numbers of CD8+ T cells and M1 macrophages and downregulated immune checkpoint genes compared to the corresponding values in high-risk patients (p < 0.05). Conclusion A stemness-related prognostic model based on eight prognostic genes in LUSC was developed and validated. The results of this study would have prognostic and therapeutic implications. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-022-02011-0.
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Affiliation(s)
- Wenfa Jiang
- Thoracic Surgery Department, Ganzhou People's Hospital, 16 MeiGuan Ave, Zhanggong, 341000, Ganzhou, China
| | - Ning Xie
- Thoracic Surgery Department, Ganzhou People's Hospital, 16 MeiGuan Ave, Zhanggong, 341000, Ganzhou, China
| | - Chenyang Xu
- Thoracic Surgery Department, Ganzhou People's Hospital, 16 MeiGuan Ave, Zhanggong, 341000, Ganzhou, China.
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Li X, Xiong K, Bi D, Zhao C. A Novel CRISPR/Cas9 Screening Potential Index for Prognostic and Immunological Prediction in Low-Grade Glioma. Front Genet 2022; 13:839884. [PMID: 35586564 PMCID: PMC9109250 DOI: 10.3389/fgene.2022.839884] [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: 12/26/2021] [Accepted: 03/18/2022] [Indexed: 12/05/2022] Open
Abstract
Glioma is a malignancy with the highest mortality in central nervous system disorders. Here, we implemented the computational tools based on CRISPR/Cas9 to predict the clinical outcomes and biological characteristics of low-grade glioma (LGG). The transcriptional expression profiles and clinical phenotypes of LGG patients were retrieved from The Cancer Genome Atlas and Chinese Glioma Genome Atlas. The CERES algorithm was used to screen for LGG-lethal genes. Cox regression and random survival forest were adopted for survival-related gene selection. Nonnegative matrix factorization distinguished patients into different clusters. Single-sample gene set enrichment analysis was employed to create a novel CRISPR/Cas9 screening potential index (CCSPI), and patients were stratified into low- and high-CCSPI groups. Survival analysis, area under the curve values (AUCs), nomogram, and tumor microenvironment exploration were included for the model validation. A total of 20 essential genes in LGG were used to classify patients into two clusters and construct the CCSPI system. High-CCSPI patients were associated with a worse prognosis of both training and validation set (p < 0.0001) and higher immune fractions than low-CCSPI individuals. The CCSPI system had a promising performance with 1-, 3-, and 5-year AUCs of 0.816, 0.779, 0.724, respectively, and the C-index of the nomogram model reached 0.743 (95% CI = 0.725–0.760). Immune-infiltrating cells and immune checkpoints such as PD-1/PD-L1 and POLD3 were positively associated with CCSPI. In conclusion, the CCSPI had prognostic value in LGG, and the model will deepen our cognition of the interaction between the CNS and immune system in different LGG subtypes.
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Affiliation(s)
- Xiangpan Li
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Kewei Xiong
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China.,School of Mathematics and Statistics, Central China Normal University, Wuhan, China
| | - Dong Bi
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chen Zhao
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
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Pi Y, Fang C, Su Z. Protein phosphorylation: A potential target in glioma development. IBRAIN 2022; 8:176-189. [PMID: 37786890 PMCID: PMC10529010 DOI: 10.1002/ibra.12038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 04/09/2022] [Accepted: 04/24/2022] [Indexed: 10/04/2023]
Abstract
Glioma is one of the most common primary brain tumors, and mortality due to this disease is second only to cardiovascular and cerebrovascular diseases. In traditional surgery, it is difficult to eradicate glioma; often recurrence increases its malignant degree, leading to a large number of patients killed by this disease. It is one of the most important subjects to study its pathogenesis and explore effective treatment methods. Research on glioma mechanisms mainly focuses on the effect of DNA methylation in epigenetics. Although there are many studies on protein phosphorylation, there is no overall regulatory mechanism. Protein phosphorylation regulates a variety of cell functions, such as cell growth, division and differentiation, and apoptosis. As a consequence, protein phosphorylation plays a leading part in various activities of glioma, and can also be used as a target to regulate the development of glioma. This review is aimed at studying the effect of protein phosphorylation on glioma, understanding the pathological mechanism, and an in-depth analysis of it. The following is a discussion on glioma growth, migration and invasion, resistance and death in phosphorylation, and the possibility of treating glioma by phosphorylation.
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Affiliation(s)
- Yu Pi
- Department of AnesthesiologySouthwest Medical UniversityLuzhouSichuanChina
| | - Chang‐Le Fang
- Department of AnesthesiologySouthwest Medical UniversityLuzhouSichuanChina
| | - Zhang‐Yu Su
- Department of AnesthesiologySouthwest Medical UniversityLuzhouSichuanChina
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R132H IDH1 sensitizes glioma to the antiproliferative and cytotoxic effects of BET inhibition. J Cancer Res Clin Oncol 2022; 148:2275-2285. [PMID: 35467128 PMCID: PMC9349147 DOI: 10.1007/s00432-022-04018-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: 02/10/2022] [Accepted: 04/04/2022] [Indexed: 11/27/2022]
Abstract
Introduction Mutations in isocitrate dehydrogenase 1/2 (IDHmut) identify a subset of gliomas that exhibit epigenetic dysregulation via aberrant DNA methylation. These tumors are ultimately fatal and lack effective therapeutic strategies. Considering the epigenetic dysregulation of IDHmut gliomas, we hypothesized that epigenetic-targeting drugs may yield therapeutic benefits in gliomas bearing IDHmut. One set of targets includes the bromodomain and extraterminal (BET) family of transcriptional coactivators. Methods We used TCGA data from glioma patients to determine whether BET proteins affect patient survival differently based on IDH status. Follow-up experiments using a set of IDH wildtype/mutant glioma cultures, as well as an IDH wildtype glioblastoma cell line expressing exogenous R132H IDH1, focused on cell health assays to investigate whether IDHmut was associated with increased sensitivity to the BET inhibitor JQ1. Immunoblots were used to evaluate the molecular response to JQ1 in these cultures. Results We identified that high BRD4 expression associated with decreased survival only in IDHmut glioma patients. Cell viability analysis showed that IDHmut sensitized glioma cells to delayed cytotoxicity (10 days) in response to JQ1. Early effects of JQ1 (3 days) were primarily antiproliferative, with IDHmut glioma exhibiting a modest increase in sensitivity. Finally, exogenous R132H IDH1 expression in a resistant IDH wildtype cell line recapitulated the JQ1-mediated delayed cytotoxicity seen in our endogenous IDHmut glioma cells. Conclusion Overall, these data suggest that BRD4 enhances malignancy primarily in gliomas bearing IDHmut and is associated with greater sensitivity to BET inhibition. The finding that BET inhibition primarily exhibits delayed cytotoxicity may be overlooked in conventional short endpoint dose–response assays. Follow-up mechanistic and animal studies will help address the translational potential of these findings. Supplementary Information The online version contains supplementary material available at 10.1007/s00432-022-04018-w.
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Beiriger J, Habib A, Jovanovich N, Kodavali CV, Edwards L, Amankulor N, Zinn PO. The Subventricular Zone in Glioblastoma: Genesis, Maintenance, and Modeling. Front Oncol 2022; 12:790976. [PMID: 35359410 PMCID: PMC8960165 DOI: 10.3389/fonc.2022.790976] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/07/2022] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma (GBM) is a malignant tumor with a median survival rate of 15-16 months with standard care; however, cases of successful treatment offer hope that an enhanced understanding of the pathology will improve the prognosis. The cell of origin in GBM remains controversial. Recent evidence has implicated stem cells as cells of origin in many cancers. Neural stem/precursor cells (NSCs) are being evaluated as potential initiators of GBM tumorigenesis. The NSCs in the subventricular zone (SVZ) have demonstrated similar molecular profiles and share several distinctive characteristics to proliferative glioblastoma stem cells (GSCs) in GBM. Genomic and proteomic studies comparing the SVZ and GBM support the hypothesis that the tumor cells and SVZ cells are related. Animal models corroborate this connection, demonstrating migratory patterns from the SVZ to the tumor. Along with laboratory and animal research, clinical studies have demonstrated improved progression-free survival in patients with GBM after radiation to the ipsilateral SVZ. Additionally, key genetic mutations in GBM for the most part carry regulatory roles in the SVZ as well. An exciting avenue towards SVZ modeling and determining its role in gliomagenesis in the human context is human brain organoids. Here we comprehensively discuss and review the role of the SVZ in GBM genesis, maintenance, and modeling.
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Affiliation(s)
- Jamison Beiriger
- Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, PA, United States.,Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh PA, United States
| | - Ahmed Habib
- Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, PA, United States.,Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh PA, United States
| | - Nicolina Jovanovich
- Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, PA, United States.,Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh PA, United States
| | - Chowdari V Kodavali
- Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, PA, United States.,Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh PA, United States
| | - Lincoln Edwards
- Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, PA, United States.,Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh PA, United States
| | - Nduka Amankulor
- Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, PA, United States.,Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh PA, United States
| | - Pascal O Zinn
- Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, PA, United States.,Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh PA, United States
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Herman JA, Arora S, Carter L, Zhu J, Biggins S, Paddison PJ. Functional dissection of human mitotic genes using CRISPR-Cas9 tiling screens. Genes Dev 2022; 36:495-510. [PMID: 35483740 PMCID: PMC9067404 DOI: 10.1101/gad.349319.121] [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: 12/16/2021] [Accepted: 04/12/2022] [Indexed: 12/03/2022]
Abstract
In this Resource/Methodology, Herman et al. developed a method that leverages CRISPR–Cas9-induced mutations across protein-coding genes for the a priori identification of functional regions at the sequence level. As a test case, they applied this method to 48 human mitotic genes, revealing hundreds of regions required for cell proliferation, including domains that were experimentally characterized, ones that were predicted based on homology, and novel ones. The identity of human protein-coding genes is well known, yet our in-depth knowledge of their molecular functions and domain architecture remains limited by shortcomings in homology-based predictions and experimental approaches focused on whole-gene depletion. To bridge this knowledge gap, we developed a method that leverages CRISPR–Cas9-induced mutations across protein-coding genes for the a priori identification of functional regions at the sequence level. As a test case, we applied this method to 48 human mitotic genes, revealing hundreds of regions required for cell proliferation, including domains that were experimentally characterized, ones that were predicted based on homology, and novel ones. We validated screen outcomes for 15 regions, including amino acids 387–402 of Mad1, which were previously uncharacterized but contribute to Mad1 kinetochore localization and chromosome segregation fidelity. Altogether, we demonstrate that CRISPR–Cas9-based tiling mutagenesis identifies key functional domains in protein-coding genes de novo, which elucidates separation of function mutants and allows functional annotation across the human proteome.
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Affiliation(s)
- Jacob A Herman
- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Lucas Carter
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Sue Biggins
- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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Codrici E, Popescu ID, Tanase C, Enciu AM. Friends with Benefits: Chemokines, Glioblastoma-Associated Microglia/Macrophages, and Tumor Microenvironment. Int J Mol Sci 2022; 23:ijms23052509. [PMID: 35269652 PMCID: PMC8910233 DOI: 10.3390/ijms23052509] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 12/19/2022] Open
Abstract
Glioma is the most common primary intracranial tumor and has the greatest prevalence of all brain tumors. Treatment resistance and tumor recurrence in GBM are mostly explained by considerable alterations within the tumor microenvironment, as well as extraordinary cellular and molecular heterogeneity. Soluble factors, extracellular matrix components, tissue-resident cell types, resident or newly recruited immune cells together make up the GBM microenvironment. Regardless of many immune cells, a profound state of tumor immunosuppression is supported and developed, posing a considerable hurdle to cancer cells' immune-mediated destruction. Several studies have suggested that various GBM subtypes present different modifications in their microenvironment, although the importance of the microenvironment in treatment response has yet to be determined. Understanding the microenvironment and how it changes after therapies is critical because it can influence the remaining invasive GSCs and lead to recurrence. This review article sheds light on the various components of the GBM microenvironment and their roles in tumoral development, as well as immune-related biological processes that support the interconnection/interrelationship between different cell types. Also, we summarize the current understanding of the modulation of soluble factors and highlight the dysregulated inflammatory chemokine/specific receptors cascades/networks and their significance in tumorigenesis, cancer-related inflammation, and metastasis.
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Affiliation(s)
- Elena Codrici
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania;
- Correspondence: (E.C.); (I.-D.P.); (A.-M.E.)
| | - Ionela-Daniela Popescu
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania;
- Correspondence: (E.C.); (I.-D.P.); (A.-M.E.)
| | - Cristiana Tanase
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania;
- Department of Clinical Biochemistry, Faculty of Medicine, Titu Maiorescu University, 031593 Bucharest, Romania
| | - Ana-Maria Enciu
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania;
- Department of Cell Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Correspondence: (E.C.); (I.-D.P.); (A.-M.E.)
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40
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Significance of a PTEN Mutational Status-Associated Gene Signature in the Progression and Prognosis of Endometrial Carcinoma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:5130648. [PMID: 35251475 PMCID: PMC8890874 DOI: 10.1155/2022/5130648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/10/2021] [Accepted: 01/11/2022] [Indexed: 11/29/2022]
Abstract
Background PTEN mutations have been reported to be involved in the development and prognosis of endometrial carcinoma (EC). However, a prognostic gene signature associated with PTEN mutational status has not yet been developed. In this study, we generated a PTEN mutation-associated prognostic gene signature for EC. Methods We obtained the single-nucleotide variation and transcriptomic profiling data from The Cancer Genome Atlas database as training data and implemented the least absolute shrinkage and selection operator (LASSO) Cox regression algorithm to establish a PTEN mutation-associated prognostic gene signature. The overall survival rates of the high-risk and low-risk groups were determined with the Kaplan-Meier (K-M) method, and the accuracy of risk score prediction was tested by using the receiver operating characteristic (ROC) curve. Results The K-M curves revealed that the EC patients with PTEN mutations augured favorable survival outcomes. Differential expression analysis between the EC patients with PTEN mutation and wild-type PTEN identified 224 differentially expressed genes (DEGs). Eighty-four DEGs that manifested prognostic value were fitted into the LASSO-Cox analysis, and a PTEN gene signature with seven mutation-associated prognostic genes that showed robust prognostic ability was constructed; this signature was then successfully validated in the other two datasets from the cBioPortal database as well as with 60 clinical specimens. Furthermore, the PTEN mutation-associated prognostic gene signature proved to be an independent prognostic predictor of EC. Remarkably, the EC patients in the high-risk group were characterized by higher tumor stages and grades as well as lower tumor mutation burden with respect to EC, with a poor survival outcome. Collectively, the PTEN mutation-associated prognostic gene signature that we developed could now be used as a favorable prognostic biomarker for EC. Conclusion In summary, we developed and validated a prognostic predictor for EC associated with PTEN mutational status that may be used as a favorable prognostic biomarker and therapeutic target for EC.
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41
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Lin K, Shen SH, Lu F, Zheng P, Wu S, Liao J, Jiang X, Zeng G, Wei D. CRISPR screening of E3 ubiquitin ligases reveals Ring Finger Protein 185 as a novel tumor suppressor in glioblastoma repressed by promoter hypermethylation and miR-587. J Transl Med 2022; 20:96. [PMID: 35183197 PMCID: PMC8858481 DOI: 10.1186/s12967-022-03284-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 01/30/2022] [Indexed: 11/10/2022] Open
Abstract
Glioblastoma (GBM) is the most common and aggressive malignant primary brain tumor. E3 ligases play important functions in glioma pathogenesis. CRISPR system offers a powerful platform for genome manipulation, while the screen of E3 ligases in GBM still remains to be explored. Here, we first constructed an E3 ligase small guide RNA (sgRNAs) library for glioma cells growth screening. After four passages, 299 significantly enriched or lost genes (SELGs) were compared with the initial state. Then the clinical significance of SELGs were validated and analyzed with TCGA glioblastoma and CGGA datasets. As RNF185 showed lost signal, decreased expression and favorable prognostic significance, we chose RNF185 for functional analysis. In vitro overexpressed cellular phenotype showed that RNF185 was a tumor suppressor in two glioma cell lines. Finally, the molecular mechanism of decreased RNF185 expression was investigated and increased miR-587 expression and DNA hypermethylation was evaluated. This study would provide a link between the molecular basis and glioblastoma pathogenesis, and a novel perspective for glioblastoma treatment.
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42
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Bukhari AB, Chan GK, Gamper AM. Targeting the DNA Damage Response for Cancer Therapy by Inhibiting the Kinase Wee1. Front Oncol 2022; 12:828684. [PMID: 35251998 PMCID: PMC8891215 DOI: 10.3389/fonc.2022.828684] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/21/2022] [Indexed: 12/15/2022] Open
Abstract
Cancer cells typically heavily rely on the G2/M checkpoint to survive endogenous and exogenous DNA damage, such as genotoxic stress due to genome instability or radiation and chemotherapy. The key regulator of the G2/M checkpoint, the cyclin-dependent kinase 1 (CDK1), is tightly controlled, including by its phosphorylation state. This posttranslational modification, which is determined by the opposing activities of the phosphatase cdc25 and the kinase Wee1, allows for a more rapid response to cellular stress than via the synthesis or degradation of modulatory interacting proteins, such as p21 or cyclin B. Reducing Wee1 activity results in ectopic activation of CDK1 activity and drives premature entry into mitosis with unrepaired or under-replicated DNA and causing mitotic catastrophe. Here, we review efforts to use small molecule inhibitors of Wee1 for therapeutic purposes, including strategies to combine Wee1 inhibition with genotoxic agents, such as radiation therapy or drugs inducing replication stress, or inhibitors of pathways that show synthetic lethality with Wee1. Furthermore, it become increasingly clear that Wee1 inhibition can also modulate therapeutic immune responses. We will discuss the mechanisms underlying combination treatments identifying both cell intrinsic and systemic anti-tumor activities.
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Hu Y, Gong C, Li Z, Liu J, Chen Y, Huang Y, Luo Q, Wang S, Hou Y, Yang S, Xiao Y. Demethylase ALKBH5 suppresses invasion of gastric cancer via PKMYT1 m6A modification. Mol Cancer 2022; 21:34. [PMID: 35114989 PMCID: PMC8812266 DOI: 10.1186/s12943-022-01522-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 01/24/2022] [Indexed: 12/26/2022] Open
Abstract
Background Gastric cancer (GC) is one of the most pernicious tumors that seriously harm human healthcare. GC metastasis is one of the prime cause of failed cancer treatment, but correlation between N6-methyladenosine (m6A) and GC metastasis was less reported. Methods Methylated RNA immunoprecipitation sequencing (MeRIP-seq) of GC tissues was conducted. Quantitative real-time PCR (qRT-PCR), western blotting and immunohistochemistry (IHC) were taken to determine the expression of ALKBH5 in GC tissues and cell lines. RNA-seq together with MeRIP-qRT-PCR was used to screen the target gene of ALKBH5. RNA pulldown, mass spectrometry and RNA immunoprecipitation (RIP) were used to search the “reader” protein of target gene. The mechanism was also validated via a tail vein injection method for lung metastasis model. Results Decreased expression of ALKBH5 was detected in GC samples, and it was correlated with clinical tumor distal metastasis and lymph node metastasis. ALKBH5 interference promoted metastasis of GC cells and this effect was closely related to the demethylase activity of ALKBH5. PKMYT1, as a downstream target of ALKBH5, promoted invasion and migration in GC. Caused by ALKBH5 knockdown or its demethylase activity mutation, upregulated expression of PKMYT1 indicated that ALKBH5 modulates expression of PKMYT1 in an m6A-dependent manner. IGF2BP3 helped stabilize the mRNA stability of PKMYT1 via its m6A modification site. Conclusions This study established an ALKBH5-PKMYT1-IGF2BP3 regulation system in metastasis, representing a new therapeutic target for GC metastasis. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-022-01522-y.
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Affiliation(s)
- Yiyang Hu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Chunli Gong
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Zhibin Li
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Jiao Liu
- Department of Endoscope, General Hospital of Northern Theater Command, Shenyang, Liaoning, 110016, China
| | - Yang Chen
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Yu Huang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Qiang Luo
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Sumin Wang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Yu Hou
- Department of Hematology, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China. .,Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, China.
| | - Shiming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China.
| | - Yufeng Xiao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China.
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miR-138-5p Inhibits the Growth and Invasion of Glioma Cells by Regulating WEE1. Anal Cell Pathol (Amst) 2022; 2022:7809882. [PMID: 35127343 PMCID: PMC8816588 DOI: 10.1155/2022/7809882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 11/15/2021] [Accepted: 01/03/2022] [Indexed: 11/17/2022] Open
Abstract
Background. Accumulating evidence has demonstrated the role of differentially expressed miRNAs in glioma progression. Our previous bioinformatics analyses revealed a role of miR-138-5p in glioma. miR-138-5p was decreased in various tumors, and He et al. found that miR-138-5p had an inhibitory effect on glioma cells in 2021. However, the role of miR-138-5p in the development of glioma and the underlying mechanism is unknown. In this study, we explored whether miR-138-5p affects the biology of glioma by regulating WEE1 expression. Methods. miR-138-5p and WEE1 G2 checkpoint kinase (WEE1) RNA and protein expression levels in glioma tissues were detected with qRT-PCR and western blotting, respectively. The effects of miR-138-5p and WEE1 on glioma cell migration and invasion were investigated using Transwell assays. CCK-8 assay was used to measure the effects of miR-138-5p and WEE1 on glioma cell proliferation. The mortality of glioma cells transfected with miR-138-5p and WEE1 was measured with flow cytometry. The relationship between miR-138-5p and WEE1 was explored using a luciferase reporter analysis. Results. Functional studies indicated that overexpression of miR-138-5p suppressed cell proliferation, migration, and invasion and promoted death in glioma cell lines. WEE1 was identified as a target of miR-138-5p, and overexpression of miR-138-5p significantly suppressed the levels of WEE1. Moreover, reintroduction of WEE1 partially abrogated miR-138-5p-induced suppression of motility and invasion in glioma cells. Conclusion. The low expression of miR-138-5p in glioma suggests a tumor suppressor role for this miRNA. miR-138-5p suppresses glioma progression by regulating WEE1. These data provide new insights into the molecular mechanism of glioma.
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Xie XP, Laks DR, Sun D, Ganbold M, Wang Z, Pedraza AM, Bale T, Tabar V, Brennan C, Zhou X, Parada LF. Quiescent human glioblastoma cancer stem cells drive tumor initiation, expansion, and recurrence following chemotherapy. Dev Cell 2022; 57:32-46.e8. [PMID: 35016005 PMCID: PMC8820651 DOI: 10.1016/j.devcel.2021.12.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/01/2021] [Accepted: 12/03/2021] [Indexed: 01/12/2023]
Abstract
We test the hypothesis that glioblastoma harbors quiescent cancer stem cells that evade anti-proliferative therapies. Functional characterization of spontaneous glioblastomas from genetically engineered mice reveals essential quiescent stem-like cells that can be directly isolated from tumors. A derived quiescent cancer-stem-cell-specific gene expression signature is enriched in pre-formed patient GBM xenograft single-cell clusters that lack proliferative gene expression. A refined human 118-gene signature is preserved in quiescent single-cell populations from primary and recurrent human glioblastomas. The F3 cell-surface receptor mRNA, expressed in the conserved signature, identifies quiescent tumor cells by antibody immunohistochemistry. F3-antibody-sorted glioblastoma cells exhibit stem cell gene expression, enhance self-renewal in culture, drive tumor initiation and serial transplantation, and reconstitute tumor heterogeneity. Upon chemotherapy, the spared cancer stem cell pool becomes activated and accelerates transition to proliferation. These results help explain conventional treatment failure and lay a conceptual framework for alternative therapies.
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Affiliation(s)
- Xuanhua P. Xie
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,These authors contributed equally,Correspondence: ,
| | - Dan R. Laks
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,These authors contributed equally,Present address: Voyager Therapeutics, Cambridge, MA 02139, USA
| | - Daochun Sun
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Present address: Medical College of Wisconsin, Wauwatosa, WI 53226, USA
| | - Mungunsarnai Ganbold
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Zilai Wang
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Present address: Chicago Biosolutions, Inc, Chicago, IL 60612, USA
| | - Alicia M. Pedraza
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Tejus Bale
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Viviane Tabar
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Cameron Brennan
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Xiuping Zhou
- Institute of Nervous System Diseases, Xuzhou Medical University, Jiangsu 221002, PR China
| | - Luis F. Parada
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Lead Contact,Correspondence: ,
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Luo J, Junaid M, Hamid N, Duan JJ, Yang X, Pei DS. Current understanding of gliomagenesis: from model to mechanism. Int J Med Sci 2022; 19:2071-2079. [PMID: 36483593 PMCID: PMC9724244 DOI: 10.7150/ijms.77287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/03/2022] [Indexed: 11/24/2022] Open
Abstract
Glioma, a kind of central nervous system (CNS) tumor, is hard to cure and accounts for 32% of all CNS tumors. Establishing a stable glioma model is critically important to investigate the underlying molecular mechanisms involved in tumorigenesis and tumor progression. Various core signaling pathways have been identified in gliomagenesis, such as RTK/RAS/PI3K, TP53, and RB1. Traditional methods of establishing glioma animal models have included chemical induction, xenotransplantation, and genetic modifications (RCAS/t-va system, Cre-loxP, and TALENs). Recently, CRISPR/Cas9 has emerged as an efficient gene editing tool with high germline transmission and has extended the scope of stable and efficient glioma models that can be generated. Therefore, this review will highlight the documented evidence about the molecular characteristics, critical genetic markers, and signaling pathways responsible for gliomagenesis and progression. Moreover, methods of establishing glioma models using gene editing techniques and therapeutic aspects will be discussed. Finally, the prospect of applying gene editing in glioma by using CRISPR/Cas9 strategy and future research directions to establish a stable glioma model are also included in this review. In-depth knowledge of glioma signaling pathways and use of CRISPR/Cas9 can greatly assist in the development of a stable, efficient, and spontaneous glioma model, which can ultimately improve the effectiveness of therapeutic responses and cure glioma patients.
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Affiliation(s)
- Juanjuan Luo
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, China
| | - Muhammad Junaid
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Naima Hamid
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin-Jing Duan
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China
| | - Xiaojun Yang
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, China
- ✉ Corresponding authors: De-Sheng Pei, E-mail: ; Xiaojun Yang, E-mail:
| | - De-Sheng Pei
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China
- ✉ Corresponding authors: De-Sheng Pei, E-mail: ; Xiaojun Yang, E-mail:
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47
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He Y, Jiang X, Duan L, Xiong Q, Yuan Y, Liu P, Jiang L, Shen Q, Zhao S, Yang C, Chen Y. LncRNA PKMYT1AR promotes cancer stem cell maintenance in non-small cell lung cancer via activating Wnt signaling pathway. Mol Cancer 2021; 20:156. [PMID: 34856993 PMCID: PMC8638142 DOI: 10.1186/s12943-021-01469-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/22/2021] [Indexed: 11/23/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) is the most common type of human lung cancers, which has diverse pathological features. Although many signaling pathways and therapeutic targets have been defined to play important roles in NSCLC, limiting efficacies have been achieved. Methods Bioinformatics methods were used to identify differential long non-coding RNA expression in NSCLC. Real-time RT-PCR experiments were used to examine the expression pattern of lncRNA PKMYT1AR, miR-485-5p. Both in vitro and in vivo functional assays were performed to investigate the functional role of PKMYT1AR/miR-485-5p/PKMYT1 axis on regulating cell proliferation, migration and tumor growth. Dual luciferase reporter assay, fluorescent in situ hybridization (FISH), immunoblot, co-immunoprecipitation experiments were used to verify the molecular mechanism. Result Here, we identify a human-specific long non-coding RNA (lncRNA, ENST00000595422), termed PKMYT1AR (PKMYT1 associated lncRNA), that is induced in NSCLC by Yin Yang 1 (YY1) factor, especially in cancerous cell lines (H358, H1975, H1299, H1650, A549 and SPC-A1) compared to that in normal human bronchial epithelium cell line (BEAS-2B). We show that PKMYT1AR high expression correlates with worse clinical outcome, and knockdown of PKMYT1AR inhibits tumor cell proliferation, migration and xenograft tumor formation abilities. Bioinformatic analysis and a luciferase assay demonstrate that PKMYT1AR directly interacts with miR-485-5p to attenuate the inhibitory role on its downstream oncogenic factor PKMYT1 (the protein kinase, membrane-associated tyrosine/threonine 1) in NSCLC. Furthermore, we uncover that miR-485-5p is downregulated in both cancerous cell lines and peripheral blood serum isolated from NSCLC patients compared to reciprocal control groups. Consistently, forced expression of miR-485-5p inhibits the proliferation and migration abilities of tumor cells. Moreover, we provide evidence showing that PKMYT1AR targeting antisense oligonucleotide (ASO) dramatically inhibit tumor growth in vivo. Mechanistic study shows that PKMYT1AR/ miR-485-5p /PKMYT1 axis promotes cancer stem cells (CSCs) maintenance in NSCLC via inhibiting β-TrCP1 mediated ubiquitin degradation of β-catenin proteins, which in turn causes enhanced tumorigenesis. Conclusions Our findings reveal the critical role of PKMYT1AR/miR-485-5p /PKMYT1 axis during NSCLC progression, which could be used as novel therapeutic targets in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-021-01469-6.
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Affiliation(s)
- Yaomei He
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiulin Jiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lincan Duan
- Department of Thoracic Surgery, the Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, Yunnan, China
| | - Qiuxia Xiong
- Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
| | - Yixiao Yuan
- Department of Thoracic Surgery, the Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, Yunnan, China
| | - Peishen Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liping Jiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, Yunnan, China
| | - Qiushuo Shen
- Department of Thoracic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Song Zhao
- Department of Thoracic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Cuiping Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, Yunnan, China.
| | - Yongbin Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, Yunnan, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
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Onishi I, Yamamoto K, Kinowaki Y, Kitagawa M, Kurata M. To Discover the Efficient and Novel Drug Targets in Human Cancers Using CRISPR/Cas Screening and Databases. Int J Mol Sci 2021; 22:12322. [PMID: 34830205 PMCID: PMC8622676 DOI: 10.3390/ijms222212322] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas has emerged as an excelle nt gene-editing technology and is used worldwide for research. The CRISPR library is an ideal tool for identifying essential genes and synthetic lethality targeted for cancer therapies in human cancers. Synthetic lethality is defined as multiple genetic abnormalities that, when present individually, do not affect function or survival, but when present together, are lethal. Recently, many CRISPR libraries are available, and the latest libraries are more accurate and can be applied to few cells. However, it is easier to efficiently search for cancer targets with their own screenings by effectively using databases of CRISPR screenings, such as Depmap portal, PICKLES (Pooled In-Vitro CRISPR Knockout Library Essentiality Screens), iCSDB, Project Score database, and CRISP-view. This review will suggest recent optimal CRISPR libraries and effective databases for Novel Approaches in the Discovery and Design of Targeted Therapies.
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Affiliation(s)
- Iichiroh Onishi
- Department of Comprehensive Pathology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; (K.Y.); (Y.K.); (M.K.)
| | | | | | | | - Morito Kurata
- Department of Comprehensive Pathology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; (K.Y.); (Y.K.); (M.K.)
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49
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Kim DV, Kulishova LM, Torgasheva NA, Melentyev VS, Dianov GL, Medvedev SP, Zakian SM, Zharkov DO. Mild phenotype of knockouts of the major apurinic/apyrimidinic endonuclease APEX1 in a non-cancer human cell line. PLoS One 2021; 16:e0257473. [PMID: 34529719 PMCID: PMC8445474 DOI: 10.1371/journal.pone.0257473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/01/2021] [Indexed: 12/26/2022] Open
Abstract
The major human apurinic/apyrimidinic (AP) site endonuclease, APEX1, is a central player in the base excision DNA repair (BER) pathway and has a role in the regulation of DNA binding by transcription factors. In vertebrates, APEX1 knockouts are embryonic lethal, and only a handful of knockout cell lines are known. To facilitate studies of multiple functions of this protein in human cells, we have used the CRISPR/Cas9 system to knock out the APEX1 gene in a widely used non-cancer hypotriploid HEK 293FT cell line. Two stable knockout lines were obtained, one carrying two single-base deletion alleles and one single-base insertion allele in exon 3, another homozygous in the single-base insertion allele. Both mutations cause a frameshift that leads to premature translation termination before the start of the protein's catalytic domain. Both cell lines totally lacked the APEX1 protein and AP site-cleaving activity, and showed significantly lower levels of the APEX1 transcript. The APEX1-null cells were unable to support BER on uracil- or AP site-containing substrates. Phenotypically, they showed a moderately increased sensitivity to methyl methanesulfonate (MMS; ~2-fold lower EC50 compared with wild-type cells), and their background level of natural AP sites detected by the aldehyde-reactive probe was elevated ~1.5-2-fold. However, the knockout lines retained a nearly wild-type sensitivity to oxidizing agents hydrogen peroxide and potassium bromate. Interestingly, despite the increased MMS cytotoxicity, we observed no additional increase in AP sites in knockout cells upon MMS treatment, which could indicate their conversion into more toxic products in the absence of repair. Overall, the relatively mild cell phenotype in the absence of APEX1-dependent BER suggests that mammalian cells possess mechanisms of tolerance or alternative repair of AP sites. The knockout derivatives of the extensively characterized HEK 293FT cell line may provide a valuable tool for studies of APEX1 in DNA repair and beyond.
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Affiliation(s)
- Daria V. Kim
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Liliya M. Kulishova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | | | - Vasily S. Melentyev
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- SB RAS Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Grigory L. Dianov
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- SB RAS Institute of Cytology and Genetics, Novosibirsk, Russia
- Department of Oncology, MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | | | - Suren M. Zakian
- SB RAS Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
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50
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Lo Cascio C, McNamara JB, Melendez EL, Lewis EM, Dufault ME, Sanai N, Plaisier CL, Mehta S. Nonredundant, isoform-specific roles of HDAC1 in glioma stem cells. JCI Insight 2021; 6:e149232. [PMID: 34494550 PMCID: PMC8492336 DOI: 10.1172/jci.insight.149232] [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: 03/03/2021] [Accepted: 07/22/2021] [Indexed: 01/02/2023] Open
Abstract
Glioblastoma (GBM) is characterized by an aberrant yet druggable epigenetic landscape. One major family of epigenetic regulators, the histone deacetylases (HDACs), are considered promising therapeutic targets for GBM due to their repressive influences on transcription. Although HDACs share redundant functions and common substrates, the unique isoform-specific roles of different HDACs in GBM remain unclear. In neural stem cells, HDAC2 is the indispensable deacetylase to ensure normal brain development and survival in the absence of HDAC1. Surprisingly, we find that HDAC1 is the essential class I deacetylase in glioma stem cells, and its loss is not compensated for by HDAC2. Using cell-based and biochemical assays, transcriptomic analyses, and patient-derived xenograft models, we find that knockdown of HDAC1 alone has profound effects on the glioma stem cell phenotype in a p53-dependent manner. We demonstrate marked suppression in tumor growth upon targeting of HDAC1 and identify compensatory pathways that provide insights into combination therapies for GBM. Our study highlights the importance of HDAC1 in GBM and the need to develop isoform-specific drugs.
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Affiliation(s)
- Costanza Lo Cascio
- Ivy Brain Tumor Center, Barrow Neurological Institute, Phoenix, Arizona, USA.,Interdisciplinary Graduate Program in Neuroscience, School of Life Sciences, and
| | - James B McNamara
- Ivy Brain Tumor Center, Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Ernesto L Melendez
- Ivy Brain Tumor Center, Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Erika M Lewis
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona, USA
| | - Matthew E Dufault
- Ivy Brain Tumor Center, Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Nader Sanai
- Ivy Brain Tumor Center, Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Christopher L Plaisier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona, USA
| | - Shwetal Mehta
- Ivy Brain Tumor Center, Barrow Neurological Institute, Phoenix, Arizona, USA
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