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Yuan Q, Lv N, Chen Q, Shen S, Wang Y, Tong J. Application of single cell sequencing technology in ovarian cancer research (review). Funct Integr Genomics 2024; 24:144. [PMID: 39196391 PMCID: PMC11358195 DOI: 10.1007/s10142-024-01432-w] [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: 06/16/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 08/29/2024]
Abstract
Ovarian cancer is a malignant tumor of ovary. It has the characteristics of difficult early diagnosis, poor late curative effect and high recurrence rate. It is the biggest disease that seriously threatens women's health. Single cell sequencing technology refers to sequencing the genetic information carried by it at the single cell level to obtain the gene sequence, transcript, protein and epigenetic expression profile information of a certain cell type and conduct integrated analysis. It has unique advantages in the study of tumor occurrence and evolution, and can provide new methods for the study of ovarian cancer. This paper reviews the single cell sequencing technology and its application in ovarian cancer.
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Affiliation(s)
- Qiqolei Yuan
- Department of The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
- Department of Obstetrics and Gynecology, Affiliated Hangzhou First People's Hospital, Xihu University, Hangzhou, 310006, Zhejiang, P.R. China
| | - Nengyuan Lv
- Department of Obstetrics and Gynecology, Shengzhou People's Hospital (The First Affiliated Hospital of Zhejiang University Shengzhou Branch), No. 666 Dangui Road, Shengzhou, 312400, Zhejiang, China
| | - Qianying Chen
- Department of Obstetrics and Gynecology, Affiliated Hangzhou First People's Hospital, Xihu University, Hangzhou, 310006, Zhejiang, P.R. China
| | - Siyi Shen
- Community Health Service Center, Donghu Street, Linping District, Hangzhou, 311103, Zhejiang, China
| | - Yahui Wang
- Department of Obstetrics and Gynecology, Affiliated Hangzhou First People's Hospital, Xihu University, Hangzhou, 310006, Zhejiang, P.R. China
| | - Jinyi Tong
- Department of The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China.
- Department of Obstetrics and Gynecology, Affiliated Hangzhou First People's Hospital, Xihu University, Hangzhou, 310006, Zhejiang, P.R. China.
- Department of Obstetrics and Gynecology, Affiliated Hangzhou First People's Hospital, Xihu University of Medicine, 261 Huansha Road, Shangcheng, Hangzhou, 310006, Zhejiang, P.R. China.
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2
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Lin L, Tao J, Meng Y, Gan Y, He X, Li S, Zhang J, Gao F, Xin D, Wang L, Fan Y, Chen B, Lu Z, Xu Y. Genome-wide CRISPR screening identifies critical role of phosphatase and tensin homologous ( PTEN) in sensitivity of acute myeloid leukemia to chemotherapy. J Zhejiang Univ Sci B 2024; 25:700-710. [PMID: 39155782 PMCID: PMC11337085 DOI: 10.1631/jzus.b2300555] [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: 08/03/2023] [Accepted: 10/15/2023] [Indexed: 08/20/2024]
Abstract
Although significant progress has been made in the development of novel targeted drugs for the treatment of acute myeloid leukemia (AML) in recent years, chemotherapy still remains the mainstay of treatment and the overall survival is poor in most patients. Here, we demonstrated the antileukemia activity of a novel small molecular compound NL101, which is formed through the modification on bendamustine with a suberanilohydroxamic acid (SAHA) radical. NL101 suppresses the proliferation of myeloid malignancy cells and primary AML cells. It induces DNA damage and caspase 3-mediated apoptosis. A genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) library screen revealed that phosphatase and tensin homologous (PTEN) gene is critical for the regulation of cell survival upon NL101 treatment. The knockout or inhibition of PTEN significantly reduced NL101-induced apoptosis in AML and myelodysplastic syndrome (MDS) cells, accompanied by the activation of protein kinase B (AKT) signaling pathway. The inhibition of mammalian target of rapamycin (mTOR) by rapamycin enhanced the sensitivity of AML cells to NL101-induced cell death. These findings uncover PTEN protein expression as a major determinant of chemosensitivity to NL101 and provide a novel strategy to treat AML with the combination of NL101 and rapamycin.
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Affiliation(s)
- Liming Lin
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital and Institute of Translational Medicine, Cancer Center, Zhejiang University School of Medicine, Hangzhou 310029, China
| | - Jingjing Tao
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital and Institute of Translational Medicine, Cancer Center, Zhejiang University School of Medicine, Hangzhou 310029, China
| | - Ying Meng
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital and Institute of Translational Medicine, Cancer Center, Zhejiang University School of Medicine, Hangzhou 310029, China
| | - Yichao Gan
- Institute of Genetics, Zhejiang University, Hangzhou 310058, China
| | - Xin He
- Division of Hematopoietic Stem Cell & Leukemia Research, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Shu Li
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jiawei Zhang
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Feiqiong Gao
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Dijia Xin
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Luyao Wang
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Yili Fan
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Boxiao Chen
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Zhimin Lu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital and Institute of Translational Medicine, Cancer Center, Zhejiang University School of Medicine, Hangzhou 310029, China.
| | - Yang Xu
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China. ,
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3
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Allen B, Savoy L, Ryabinin P, Bottomly D, Chen R, Goff B, Wang A, McWheeny SK, Zhang H. Upregulation of HOXA3 by isoform-specific Wilms tumour 1 drives chemotherapy resistance in acute myeloid leukaemia. Br J Haematol 2024; 205:207-219. [PMID: 38867543 PMCID: PMC11448753 DOI: 10.1111/bjh.19563] [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: 03/04/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024]
Abstract
Upregulation of the Wilms' tumour 1 (WT1) gene is common in acute myeloid leukaemia (AML) and is associated with poor prognosis. WT1 generates 12 primary transcripts through different translation initiation sites and alternative splicing. The short WT1 transcripts express abundantly in primary leukaemia samples. We observed that overexpression of short WT1 transcripts lacking exon 5 with and without the KTS motif (sWT1+/- and sWT1-/-) led to reduced cell growth. However, only sWT1+/- overexpression resulted in decreased CD71 expression, G1 arrest, and cytarabine resistance. Primary AML patient cells with low CD71 expression exhibit resistance to cytarabine, suggesting that CD71 may serve as a potential biomarker for chemotherapy. RNAseq differential expressed gene analysis identified two transcription factors, HOXA3 and GATA2, that are specifically upregulated in sWT1+/- cells, whereas CDKN1A is upregulated in sWT1-/- cells. Overexpression of either HOXA3 or GATA2 reproduced the effects of sWT1+/-, including decreased cell growth, G1 arrest, reduced CD71 expression and cytarabine resistance. HOXA3 expression correlates with chemotherapy response and overall survival in NPM1 mutation-negative leukaemia specimens. Overexpression of HOXA3 leads to drug resistance against a broad spectrum of chemotherapeutic agents. Our results suggest that WT1 regulates cell proliferation and drug sensitivity in an isoform-specific manner.
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MESH Headings
- Humans
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Antigens, CD/biosynthesis
- Cell Line, Tumor
- Cytarabine/pharmacology
- Cytarabine/therapeutic use
- Drug Resistance, Neoplasm/genetics
- Gene Expression Regulation, Leukemic/drug effects
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Nucleophosmin
- Protein Isoforms
- Receptors, Transferrin
- Up-Regulation
- WT1 Proteins/genetics
- WT1 Proteins/metabolism
- WT1 Proteins/biosynthesis
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Affiliation(s)
- Basil Allen
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Lindsey Savoy
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Peter Ryabinin
- Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Daniel Bottomly
- Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Reid Chen
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Bonnie Goff
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Anthony Wang
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Shannon K McWheeny
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | - Haijiao Zhang
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
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4
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Quintero-Ruiz N, Oliveira WDL, Esteca MV, Granato DC, Simabuco FM. Uncovering the bookshelves of CRISPR-based libraries: Advances and applications in cancer studies. Crit Rev Oncol Hematol 2024; 196:104287. [PMID: 38342473 DOI: 10.1016/j.critrevonc.2024.104287] [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: 12/01/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/13/2024] Open
Abstract
The advent of CRISPR/Cas9 technology has revolutionized the genome editing field. CRISPR-based libraries have become powerful tools for high-throughput functional genomics and genetic screening. CRISPR-based libraries can represent a powerful approach to uncovering genes related to chemoresistance and therapy efficacy and to studying cancer cells' fitness. In this review, we conducted an extensive literature search and summarized multiple studies that utilized these libraries in both in vitro and in vivo research, emphasizing their key findings. We provide an overview of the design, construction, and applications of CRISPR-based libraries in different cancer-focused studies and discuss the different types of CRISPR-based libraries. We finally point out the challenges associated with library design, including guide RNA selection, off-target effects, and library complexity. This review provides an overview of the work conducted with CRISPR libraries in the search for new targets that could potentially assist in cancer therapy by contributing to functional approaches.
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Affiliation(s)
- Nathalia Quintero-Ruiz
- Multidisciplinary Laboratory of Food and Health (LabMAS), School of Applied Sciences (FCA), University of Campinas (UNICAMP), Limeira, SP 13484-350, Brazil
| | - Wesley de Lima Oliveira
- Multidisciplinary Laboratory of Food and Health (LabMAS), School of Applied Sciences (FCA), University of Campinas (UNICAMP), Limeira, SP 13484-350, Brazil; Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa Em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Marcos Vinicius Esteca
- Multidisciplinary Laboratory of Food and Health (LabMAS), School of Applied Sciences (FCA), University of Campinas (UNICAMP), Limeira, SP 13484-350, Brazil
| | - Daniela Campos Granato
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa Em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Fernando Moreira Simabuco
- Multidisciplinary Laboratory of Food and Health (LabMAS), School of Applied Sciences (FCA), University of Campinas (UNICAMP), Limeira, SP 13484-350, Brazil; Department of Biochemistry, Federal University of São Paulo, São Paulo, SP 04044-020, Brazil.
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5
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Sahu S, Poplawska M, Lim SH, Dutta D. CRISPR-based precision medicine for hematologic disorders: Advancements, challenges, and prospects. Life Sci 2023; 333:122165. [PMID: 37832631 DOI: 10.1016/j.lfs.2023.122165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023]
Abstract
The development of programmable nucleases to introduce defined alterations in genomic sequences has been a powerful tool for precision medicine. While several nucleases such as zinc-finger nucleases (ZFN), transcriptor activator-like effector nucleases (TALEN), and meganucleases have been explored, the advent of CRISPR/Cas9 technology has revolutionized the field of genome engineering. In addition to disease modeling, the CRISPR/Cas9 technology has contributed to safer and more effective treatment strategies for hematologic diseases and personalized T-cell-based therapies. Here we discuss the applications of the CRISPR technology in the treatment of hematologic diseases, their efficacy, and ongoing clinical trials. We examine the obstacles to their successful use and the approaches investigated to overcome these challenges. Finally, we provide our perspectives to improve this genome editing tool for targeted therapies.
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Affiliation(s)
- Sounak Sahu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, 1050 Boyles Street, Building 560, Room 32-04, Frederick, MD 21702, USA.
| | - Maria Poplawska
- Department of Medicine (Division of Hematology and Oncology), State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA
| | - Seah H Lim
- Department of Medicine (Division of Hematology and Oncology), State University of New York Upstate Medical University, 750 E Adams, Syracuse, NY 13210, USA
| | - Dibyendu Dutta
- Department of Medicine (Division of Hematology and Oncology), State University of New York Upstate Medical University, 750 E Adams, Syracuse, NY 13210, USA.
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6
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Bansal D, Davidson A, Supriyadi E, Njuguna F, Ribeiro RC, Kaspers GJL. SIOP PODC adapted risk stratification and treatment guidelines: Recommendations for acute myeloid leukemia in resource-limited settings. Pediatr Blood Cancer 2023; 70:e28087. [PMID: 31774234 DOI: 10.1002/pbc.28087] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 10/21/2019] [Accepted: 10/30/2019] [Indexed: 01/09/2023]
Abstract
In low- and middle-income countries (LMICs), limited resources, suboptimal risk stratification, and disproportionate patient-to-infrastructure ratio result in low survival of patients with acute myeloid leukemia (AML). A high incidence of relapse, inherent to the biology, renders management arduous. The challenge of treating AML in LMICs is of balancing the intensity of myelosuppressive chemotherapy, which appears necessary for cure, with available supportive care, which influences treatment-related mortality. The recommendations outlined in this paper are based on published evidence and expert opinion. The principle of this adapted protocol is to tailor treatment to available resources, reduce preventable toxic death, and direct limited resources toward those children who are most likely to be cured.
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Affiliation(s)
- Deepak Bansal
- Department of Pediatrics, Hematology-Oncology Unit, Advanced Pediatrics Center, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Alan Davidson
- Haematology-Oncology Service, Red Cross Children's Hospital, Cape Town, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Eddy Supriyadi
- Pediatric Hematology-Oncology Division, Department of Pediatrics, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Festus Njuguna
- Department of Child Health and Paediatrics, Moi University, Eldoret, Kenya
| | - Raul C Ribeiro
- St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Gertjan J L Kaspers
- Department of Pediatric Oncology, Emma Children's Hospital, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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7
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Alyateem G, Wade HM, Bickert AA, Lipsey CC, Mondal P, Smith MD, Labib RM, Mock BA, Robey RW, Gottesman MM. Use of CRISPR-based screens to identify mechanisms of chemotherapy resistance. Cancer Gene Ther 2023; 30:1043-1050. [PMID: 37029320 PMCID: PMC10722205 DOI: 10.1038/s41417-023-00608-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 04/09/2023]
Abstract
Despite the development of new classes of targeted anti-cancer drugs, the curative treatment of metastatic solid tumors remains out of reach owing to the development of resistance to current chemotherapeutics. Although many mechanisms of drug resistance have been described, there is still a general lack of understanding of the many means by which cancer cells elude otherwise effective chemotherapy. The traditional strategy of isolating resistant clones in vitro, defining their mechanism of resistance, and testing to see whether these mechanisms play a role in clinical drug resistance is time-consuming and in many cases falls short of providing clinically relevant information. In this review, we summarize the use of CRISPR technology, including the promise and pitfalls, to generate libraries of cancer cells carrying sgRNAs that define novel mechanisms of resistance. The existing strategies using CRISPR knockout, activation, and inhibition screens, and combinations of these approaches are described. In addition, specialized approaches to identify more than one gene that may be contributing to resistance, as occurs in synthetic lethality, are described. Although these CRISPR-based approaches to cataloguing drug resistance genes in cancer cells are just beginning to be utilized, appropriately used they promise to accelerate understanding of drug resistance in cancer.
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Affiliation(s)
- George Alyateem
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Heidi M Wade
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Aaron A Bickert
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Crystal C Lipsey
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Priya Mondal
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - MacKinzie D Smith
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rania M Labib
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Beverly A Mock
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert W Robey
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael M Gottesman
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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8
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Rodríguez-Macías G, Briz O, Cives-Losada C, Chillón MC, Martínez-Laperche C, Martínez-Arranz I, Buño I, González-Díaz M, Díez-Martín JL, Marin JJG, Macias RIR. Role of Intracellular Drug Disposition in the Response of Acute Myeloid Leukemia to Cytarabine and Idarubicin Induction Chemotherapy. Cancers (Basel) 2023; 15:3145. [PMID: 37370755 DOI: 10.3390/cancers15123145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Despite its often low efficacy and high toxicity, the standard treatment for acute myeloid leukemia (AML) is induction chemotherapy with cytarabine and idarubicin. Here, we have investigated the role of transporters and drug-metabolizing enzymes in this poor outcome. The expression levels (RT-qPCR) of potentially responsible genes in blasts collected at diagnosis were related to the subsequent response to two-cycle induction chemotherapy. The high expression of uptake carriers (ENT2), export ATP-binding cassette (ABC) pumps (MDR1), and enzymes (DCK, 5-NT, and CDA) in the blasts was associated with a lower response. Moreover, the sensitivity to cytarabine in AML cell lines was associated with ENT2 expression, whereas the expression of ABC pumps and enzymes was reduced. No ability of any AML cell line to export idarubicin through the ABC pumps, MDR1 and MRP, was found. The exposure of AML cells to cytarabine or idarubicin upregulated the detoxifying enzymes (5-NT and DCK). In AML patients, 5-NT and DCK expression was associated with the lack of response to induction chemotherapy (high sensitivity and specificity). In conclusion, in the blasts of AML patients, the reduction of the intracellular concentration of the active metabolite of cytarabine, mainly due to the increased expression of inactivating enzymes, can determine the response to induction chemotherapy.
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Affiliation(s)
- Gabriela Rodríguez-Macías
- Experimental Hepatology and Drug Targeting (HEVEPHARM) Group, Biomedical Research Institute of Salamanca (IBSAL), University of Salamanca, 37007 Salamanca, Spain
- Department of Hematology, Gregorio Marañón General University Hospital, 28007 Madrid, Spain
| | - Oscar Briz
- Experimental Hepatology and Drug Targeting (HEVEPHARM) Group, Biomedical Research Institute of Salamanca (IBSAL), University of Salamanca, 37007 Salamanca, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, 28029 Madrid, Spain
| | - Candela Cives-Losada
- Experimental Hepatology and Drug Targeting (HEVEPHARM) Group, Biomedical Research Institute of Salamanca (IBSAL), University of Salamanca, 37007 Salamanca, Spain
| | - María C Chillón
- Hematology, Biomedical Research Institute of Salamanca, Salamanca University Hospital, 37007 Salamanca, Spain
- CIBER in Oncology (CIBER-ONC), Carlos III National Institute of Health, 28029 Madrid, Spain
| | - Carolina Martínez-Laperche
- Department of Hematology, Gregorio Marañón General University Hospital, 28007 Madrid, Spain
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain
| | | | - Ismael Buño
- Department of Hematology, Gregorio Marañón General University Hospital, 28007 Madrid, Spain
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain
- Department of Cell Biology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - Marcos González-Díaz
- Hematology, Biomedical Research Institute of Salamanca, Salamanca University Hospital, 37007 Salamanca, Spain
- CIBER in Oncology (CIBER-ONC), Carlos III National Institute of Health, 28029 Madrid, Spain
| | - José L Díez-Martín
- Department of Hematology, Gregorio Marañón General University Hospital, 28007 Madrid, Spain
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain
- Department of Medicine, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - Jose J G Marin
- Experimental Hepatology and Drug Targeting (HEVEPHARM) Group, Biomedical Research Institute of Salamanca (IBSAL), University of Salamanca, 37007 Salamanca, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, 28029 Madrid, Spain
| | - Rocio I R Macias
- Experimental Hepatology and Drug Targeting (HEVEPHARM) Group, Biomedical Research Institute of Salamanca (IBSAL), University of Salamanca, 37007 Salamanca, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, 28029 Madrid, Spain
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9
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Sugita K, Onishi I, Nakayama R, Ishibashi S, Ikeda M, Inoue M, Narita R, Oshima S, Shimizu K, Saito S, Sato S, Moriarity BS, Yamamoto K, Largaespada DA, Kitagawa M, Kurata M. Indirect CRISPR screening with photoconversion revealed key factors of drug resistance with cell-cell interactions. Commun Biol 2023; 6:582. [PMID: 37264057 PMCID: PMC10235018 DOI: 10.1038/s42003-023-04941-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/15/2023] [Indexed: 06/03/2023] Open
Abstract
Comprehensive screenings to clarify indirect cell-cell interactions, such as those in the tumor microenvironment, especially comprehensive assessments of supporting cells' effects, are challenging. Therefore, in this study, indirect CRISPR screening for drug resistance with cell-cell interactions was invented. The photoconvertible fluorescent protein Dendra2 was inducted to supporting cells and explored the drug resistance responsible factors of supporting cells with CRISPR screenings. Random mutated supporting cells co-cultured with leukemic cells induced drug resistance with cell-cell interactions. Supporting cells responsible for drug resistance were isolated with green-to-red photoconversion, and 39 candidate genes were identified. Knocking out C9orf89, MAGI2, MLPH, or RHBDD2 in supporting cells reduced the ratio of apoptosis of cancer cells. In addition, the low expression of RHBDD2 in supporting cells, specifically fibroblasts, of clinical pancreatic cancer showed a shortened prognosis, and a negative correlation with CXCL12 was observed. Indirect CRISPR screening was established to isolate the responsible elements of cell-cell interactions. This screening method could reveal unknown mechanisms in all kinds of cell-cell interactions by revealing live phenotype-inducible cells, and it could be a platform for discovering new targets of drugs for conventional chemotherapies.
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Affiliation(s)
- Keisuke Sugita
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Iichiroh Onishi
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Ran Nakayama
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Sachiko Ishibashi
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Masumi Ikeda
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Miori Inoue
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Rina Narita
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Shiori Oshima
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kaho Shimizu
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Shinichiro Saito
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Shingo Sato
- Center for Innovative Cancer Treatment, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | | | - Kouhei Yamamoto
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | | | - Masanobu Kitagawa
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Morito Kurata
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
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10
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Wang H, Zhou J, Ma X, Jiao C, Chen E, Wu Z, Zhang Y, Pan M, Cui J, Luan C, Ge J. Dexamethasone enhances venetoclax-induced apoptosis in acute myeloid leukemia cells. Med Oncol 2023; 40:193. [PMID: 37261571 DOI: 10.1007/s12032-023-02056-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
Acute myeloid leukemia (AML) therapies have been significantly improved by the development of medicines that can target BCL-2. On the other hand, non-recurrent alterations in oncogenic pathways and gene expression patterns have already been linked to therapeutic resistance to venetoclax therapy. Bone marrow mesenchymal stromal cells (BM-MSCs) support leukemic cells in preventing chemotherapy-induced apoptosis by mitochondrial transfer in leukemic microenvironment. In this study, we investigated the enhancement of the antitumor effect of BCL-2 inhibitor venetoclax by dexamethasone. In particular, dexamethasone had no significant effect on the viability of AML cells, but dexamethasone combined with venetoclax could significantly increase the apoptosis of AML cells induced by venetoclax. When AML cells were co-cultured with BM-MSCs, dexamethasone combined with venetoclax showed additional anti-tumor effect compared to venetoclax alone. Venetoclax increased reactive oxygen species level in co-cultured AML cells, contributed to transfer more mitochondria from BM-MSCs to AML cells and protect AML cells from apoptosis. Dexamethasone combined with venetoclax induced more apoptosis, but dexamethasone reduced the venetoclax-induced reactive oxygen species level in AML cells and reduced the transfer of mitochondria from BM-MSCs to AML cells. This may lead to a diminished protective effect of BM-MSCs on AML cells. Together, our findings indicated that venetoclax in combination with dexamethasone could be a promising therapy in AML.
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Affiliation(s)
- Haixia Wang
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Junjie Zhou
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Xiaoyu Ma
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Changqing Jiao
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Enbo Chen
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Zhonghui Wu
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Yan Zhang
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Mengya Pan
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Jianling Cui
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Chengxin Luan
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Jian Ge
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
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11
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Yang X, Zhang B. A review on CRISPR/Cas: a versatile tool for cancer screening, diagnosis, and clinic treatment. Funct Integr Genomics 2023; 23:182. [PMID: 37231285 DOI: 10.1007/s10142-023-01117-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
Cancer is one of the leading causes of death worldwide and it has the trend of increase incidence. However, in the past decades, as quickly developed new technologies and modified old techniques for cancer screening, diagnosis, and treatment, the cancer-caused mortality rates dropped quickly, and the survival times of cancer patients are enhanced. However, the current death rate is still about 50% and the survival patients always suffer from the side effect of current cancer treatments. Recently developed Nobel Prize-winning CRISPR/Cas technology provides new hope on cancer screening, early diagnosis, and clinic treatment as well as new drug development. Currently, four major CRISPR/Cas9-derived genome editors, CRISPR/Cas9 nucleotide sequence editor, CRISPR/Cas base editor (BE), CRISPR prime editor (PE), and CRISPR interference (CRISPRi) (including both CRISPRa and CRISPRr), were well developed and used to various research and applications, including cancer biology study and cancer screening, diagnosis, and treatment. Additionally, CRISPR/Cas12 and CRISPR/Cas13 genome editors were also widely used in cancer-related basic and applied research as well as treatment. Cancer-associated SNPs and genetic mutations as well as both oncogenes and tumor suppressor genes are perfect targets for CRISPR/Cas-based gene therapy for cancer treatment. CRISPR/Cas is also employed to modify and generate new Chimeric antigen receptor (CAR) T-cells for improving its safety, efficiency, and longer-time last for treating various cancers. Currently, there are many clinic trails of CRISPR-based gene therapy for cancer treatments. Although all CRISPR/Cas-derived genome and epigenome tools are promising methods for cancer biology study and treatment, the efficiency and long term-safety are still the major concerns for CRISPR-based gene therapy. Developing new CRISPR/Cas delivery methods and reducing the potential side effects, including off-target impacts, will enhance CRISPR/Cas application in cancer-related research, diagnosis, and therapeutical treatment.
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Affiliation(s)
- Xianguang Yang
- College of Life Science, Henan Normal University, Xinxiang, 453007, Henan, China.
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
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12
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Chen JZ, Wang LN, Luo XQ, Tang YL. The genomic landscape of sensitivity to arsenic trioxide uncovered by genome-wide CRISPR-Cas9 screening. Front Oncol 2023; 13:1178686. [PMID: 37251921 PMCID: PMC10214836 DOI: 10.3389/fonc.2023.1178686] [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: 03/03/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction Arsenic trioxide (ATO) is a promising anticancer drug for hematological malignancy. Given the dramatic efficacy of acute promyelocytic leukemia (APL), ATO has been utilized in other types of cancers, including solid tumors. Unfortunately, the results were not comparable with the effects on APL, and the resistance mechanism has not been clarified yet. This study intends to identify relevant genes and pathways affecting ATO drug sensitivity through genome-wide CRISPR-Cas9 knockdown screening to provide a panoramic view for further study of ATO targets and improved clinical outcomes. Methods A genome-wide CRISPR-Cas9 knockdown screening system was constructed for ATO screening. The screening results were processed with MAGeCK, and the results were subjected to pathway enrichment analysis using WebGestalt and KOBAS. We also performed protein-protein interaction (PPI) network analysis using String and Cytoscape, followed by expression profiling and survival curve analysis of critical genes. Virtual screening was used to recognize drugs that may interact with the hub gene. Results We applied enrichment analysis and identified vital ATO-related pathways such as metabolism, chemokines and cytokines production and signaling, and immune system responses. In addition, we identified KEAP1 as the top gene relating to ATO resistance. We found that KEAP1 expression was higher in the pan-cancer, including ALL, than in normal tissue. Patients with acute myeloid leukemia (AML) with higher KEAP1 expression had worse overall survival (OS). A virtual screen showed that etoposide and eltrombopag could bind to KEAP1 and potentially interact with ATO. Discussion ATO is a multi-target anticancer drug, and the key pathways regulating its sensitivity include oxidative stress, metabolism, chemokines and cytokines, and the immune system. KEAP1 is the most critical gene regulating ATO drug sensitivity, which is related to AML prognosis and may bind to some clinical drugs leading to an interaction with ATO. These integrated results provided new insights into the pharmacological mechanism of ATO and potentiate for further applications in cancer treatments.
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Affiliation(s)
- Jun-Zhu Chen
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Li-Na Wang
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xue-Qun Luo
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yan-Lai Tang
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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13
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Ling VY, Straube J, Godfrey W, Haldar R, Janardhanan Y, Cooper L, Bruedigam C, Cooper E, Tavakoli Shirazi P, Jacquelin S, Tey SK, Baell J, Huang F, Jin J, Zhao Y, Bullinger L, Bywater MJ, Lane SW. Targeting cell cycle and apoptosis to overcome chemotherapy resistance in acute myeloid leukemia. Leukemia 2023; 37:143-153. [PMID: 36400926 DOI: 10.1038/s41375-022-01755-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 10/21/2022] [Accepted: 10/31/2022] [Indexed: 11/21/2022]
Abstract
Chemotherapy-resistant acute myeloid leukemia (AML), frequently driven by clonal evolution, has a dismal prognosis. A genome-wide CRISPR knockout screen investigating resistance to doxorubicin and cytarabine (Dox/AraC) in human AML cell lines identified gene knockouts involving AraC metabolism and genes that regulate cell cycle arrest (cyclin dependent kinase inhibitor 2A (CDKN2A), checkpoint kinase 2 (CHEK2) and TP53) as contributing to resistance. In human AML cohorts, reduced expression of CDKN2A conferred inferior overall survival and CDKN2A downregulation occurred at relapse in paired diagnosis-relapse samples, validating its clinical relevance. Therapeutically targeting the G1S cell cycle restriction point (with CDK4/6 inhibitor, palbociclib and KAT6A inhibitor, WM-1119, to upregulate CDKN2A) synergized with chemotherapy. Additionally, direct promotion of apoptosis with venetoclax, showed substantial synergy with chemotherapy, overcoming resistance mediated by impaired cell cycle arrest. Altogether, we identify defective cell cycle arrest as a clinically relevant contributor to chemoresistance and identify rationally designed therapeutic combinations that enhance response in AML, potentially circumventing chemoresistance.
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Affiliation(s)
- Victoria Y Ling
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Jasmin Straube
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - William Godfrey
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Rohit Haldar
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Leanne Cooper
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Claudia Bruedigam
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Emily Cooper
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | | | - Siok-Keen Tey
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Jonathan Baell
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, People's Republic of China
| | - Fei Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, People's Republic of China
| | - Jianwen Jin
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Yichao Zhao
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Lars Bullinger
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Megan J Bywater
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.
| | - Steven W Lane
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.
- Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia.
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14
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Chen TC, Minea RO, Swenson S, Yang Z, Thein TZ, Schönthal AH. NEO212, a Perillyl Alcohol-Temozolomide Conjugate, Triggers Macrophage Differentiation of Acute Myeloid Leukemia Cells and Blocks Their Tumorigenicity. Cancers (Basel) 2022; 14:6065. [PMID: 36551551 PMCID: PMC9776529 DOI: 10.3390/cancers14246065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
Many patients with acute myeloid leukemia (AML) are still dying from this disease. In the past, the alkylating agent temozolomide (TMZ) has been investigated for AML and found to be partially effective; however, the presence of O6-methylguanine DNA methyltransferase (MGMT; a DNA repair enzyme) in tumor cells confers profound treatment resistance against TMZ. We are developing a novel anticancer compound, called NEO212, where TMZ was covalently conjugated to perillyl alcohol (a naturally occurring monoterpene). NEO212 has revealed robust therapeutic activity in a variety of preclinical cancer models, including AML. In the current study, we investigated its impact on a panel of human AML cell lines and found that it exerted cytotoxic potency even against MGMT-positive cells that were highly resistant to TMZ. Furthermore, NEO212 strongly stimulated the expression of a large number of macrophage-associated marker genes, including CD11b/ITGAM. This latter effect could not be mimicked when cells were treated with TMZ or an equimolar mix of individual agents, TMZ plus perillyl alcohol. The superior cytotoxic impact of NEO212 appeared to involve down-regulation of MGMT protein levels. In a mouse model implanted with TMZ-resistant, MGMT-positive AML cells, two 5-day cycles of 25 mg/kg NEO212 achieved an apparent cure, as mice survived >300 days without any signs of disease. In parallel toxicity studies with rats, a 5-day cycle of 200 mg/kg NEO212 was well tolerated by these animals, whereas animals that were given 200 mg/kg TMZ all died due to severe leukopenia. Together, our results show that NEO212 exerts pleiotropic effects on AML cells that include differentiation, proliferation arrest, and eventual cell death. In vivo, NEO212 was well tolerated even at dosages that far exceed the therapeutic need, indicating a large therapeutic window. These results present NEO212 as an agent that should be considered for development as a therapeutic agent for AML.
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Affiliation(s)
- Thomas C. Chen
- Department of Neurosurgery, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Radu O. Minea
- Department of Neurosurgery, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Steve Swenson
- Department of Neurosurgery, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90089, USA
| | - Zhuoyue Yang
- Department of Molecular Microbiology & Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Thu Zan Thein
- Department of Neurosurgery, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90089, USA
| | - Axel H. Schönthal
- Department of Molecular Microbiology & Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
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15
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Zhao J, Tang Z, Selvaraju M, Johnson KA, Douglas JT, Gao PF, Petrassi HM, Wang MZ, Wang J. Cellular Target Deconvolution of Small Molecules Using a Selection-Based Genetic Screening Platform. ACS CENTRAL SCIENCE 2022; 8:1424-1434. [PMID: 36313155 PMCID: PMC9615120 DOI: 10.1021/acscentsci.2c00609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Indexed: 05/04/2023]
Abstract
Small-molecule drug target identification is an essential and often rate-limiting step in phenotypic drug discovery and remains a major challenge. Here, we report a novel platform for target identification of activators of signaling pathways by leveraging the power of a clustered regularly interspaced short palindromic repeats (CRISPR) knockout library. This platform links the expression of a suicide gene to the small-molecule-activated signaling pathway to create a selection system. With this system, loss-of-function screening using a CRISPR single-guide (sg) RNA library positively enriches cells in which the target has been knocked out. The identities of the drug targets and other essential genes required for the activity of small molecules of interest are then uncovered by sequencing. We tested this platform on BDW568, a newly discovered type-I interferon signaling activator, and identified stimulator of interferon genes (STING) as its target and carboxylesterase 1 (CES1) to be a key metabolizing enzyme required to activate BDW568 for target engagement. The platform we present here can be a general method applicable for target identification for a wide range of small molecules that activate different signaling pathways.
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Affiliation(s)
- Junxing Zhao
- Department
of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Zhichao Tang
- Department
of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Manikandan Selvaraju
- Department
of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Kristen A. Johnson
- Calibr,
Scripps Research Institute, La Jolla, California 92037, United States
| | - Justin T. Douglas
- Nuclear
Magnetic Resonance Laboratory, University
of Kansas, Lawrence, Kansas 66047, United States
| | - Philip F. Gao
- Protein
Production Group, University of Kansas, Lawrence, Kansas 66047, United States
| | - H. Michael Petrassi
- Calibr,
Scripps Research Institute, La Jolla, California 92037, United States
| | - Michael Zhuo Wang
- Department
of Pharmaceutical Chemistry, University
of Kansas, Lawrence, Kansas 66047, United States
| | - Jingxin Wang
- Department
of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
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16
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Identification of the Factor That Leads Human Mesenchymal Stem Cell Lines into Decellularized Bone. Bioengineering (Basel) 2022; 9:bioengineering9100490. [PMID: 36290460 PMCID: PMC9598111 DOI: 10.3390/bioengineering9100490] [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: 07/28/2022] [Revised: 09/14/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Hematopoiesis is maintained by the interaction of hematopoietic stem cells (HSCs) and bone marrow mesenchymal stem cells (MSCs) in bone marrow microenvironments, called niches. Certain genetic mutations in MSCs, not HSCs, provoke some hematopoietic neoplasms, such as myelodysplastic syndrome. An in vivo bone marrow niche model using human MSC cell lines with specific genetic mutations and bone scaffolds is necessary to elucidate these interactions and the disease onset. We focused on decellularized bone (DCB) as a useful bone scaffold and attempted to induce human MSCs (UE7T-9 cells) into the DCB. Using the CRISPR activation library, we identified SHC4 upregulation as a candidate factor, with the SHC4 overexpression in UE7T-9 cells activating their migratory ability and upregulating genes to promote hematopoietic cell migration. This is the first study to apply the CRISPR library to engraft cells into decellularized biomaterials. SHC4 overexpression is essential for engrafting UE7T-9 cells into DCB, and it might be the first step toward creating an in vivo human–mouse hybrid bone marrow niche model.
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17
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Ancos-Pintado R, Bragado-García I, Morales ML, García-Vicente R, Arroyo-Barea A, Rodríguez-García A, Martínez-López J, Linares M, Hernández-Sánchez M. High-Throughput CRISPR Screening in Hematological Neoplasms. Cancers (Basel) 2022; 14:3612. [PMID: 35892871 PMCID: PMC9329962 DOI: 10.3390/cancers14153612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
CRISPR is becoming an indispensable tool in biological research, revolutionizing diverse fields of medical research and biotechnology. In the last few years, several CRISPR-based genome-targeting tools have been translated for the study of hematological neoplasms. However, there is a lack of reviews focused on the wide uses of this technology in hematology. Therefore, in this review, we summarize the main CRISPR-based approaches of high throughput screenings applied to this field. Here we explain several libraries and algorithms for analysis of CRISPR screens used in hematology, accompanied by the most relevant databases. Moreover, we focus on (1) the identification of novel modulator genes of drug resistance and efficacy, which could anticipate relapses in patients and (2) new therapeutic targets and synthetic lethal interactions. We also discuss the approaches to uncover novel biomarkers of malignant transformations and immune evasion mechanisms. We explain the current literature in the most common lymphoid and myeloid neoplasms using this tool. Then, we conclude with future directions, highlighting the importance of further gene candidate validation and the integration and harmonization of the data from CRISPR screening approaches.
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Affiliation(s)
- Raquel Ancos-Pintado
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - Irene Bragado-García
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - María Luz Morales
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Roberto García-Vicente
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Andrés Arroyo-Barea
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - Alba Rodríguez-García
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Joaquín Martínez-López
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Medicine, Medicine School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain
| | - María Linares
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - María Hernández-Sánchez
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
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18
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Prajapati SC, Dunham N, Fan H, Garrett-Bakelman FE. Validation of CRISPR targeting for proliferation and cytarabine resistance control genes in the acute myeloid leukemia cell line MOLM-13. Biotechniques 2022; 72:81-84. [PMID: 35119307 PMCID: PMC9413368 DOI: 10.2144/btn-2021-0089] [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] [Indexed: 11/23/2022] Open
Abstract
Acute myeloid leukemia patients with FMS-like tyrosine kinase 3–internal tandem duplications and mixed lineage leukemia–protein AF9 fusion proteins suffer from poor clinical outcomes. The MOLM-13 acute myeloid leukemia cell line harbors both of these abnormalities and is used in CRISPR experiments to identify disease drivers. However, experimental observations may be biased or inconclusive in the absence of experimentally validated positive control genes. We validated sgRNAs for knockdown of TP53 for cell proliferation and for DCK knockdown and CDA upregulation for cytarabine resistance control genes in MOLM-13 cells. We have provided a detailed CRISPR protocol applicable to both gene knockdown or activation experiments and downstream leukemic phenotype analyses. Inclusion of these controls in CRISPR experiments will enhance the capacity to identify novel myeloid leukemia drivers in MOLM-13 cells. CRISPR-Cas9 knockdown and upregulation approaches were used for changing the expression of control genes TP53, DCK, and CDA in the acute myeloid leukemia cell line MOLM-13. Lentivirus transduced cells were selected (sorted for green fluorescent protein positive cells or selected by antibiotic treatment), and knockdown or upregulation of genes in the stable cells was confirmed by real-time quantitative PCR and western blot analyses. EdU incorporation assay was used to measure cell proliferation. Colorimetric proliferation/survival assay and flow cytometric cell counting were used to measure cell growth and survival. Results from the experimental and control groups were compared using Student's t-test.
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Affiliation(s)
- Subhash C Prajapati
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Nicholas Dunham
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Hao Fan
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Francine E Garrett-Bakelman
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.,Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.,University of Virginia Cancer Center, Charlottesville, VA 22903, USA
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19
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XU L, SONG JD. Crocin reversed the antitumor effects through up-regulation of MicroRNA-181a in cervical cancer cells. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.09422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Lina XU
- The Affiliated Hospital of Inner Mongolia Medical University, China
| | - Jian-Dong SONG
- The Affiliated Hospital of Inner Mongolia Medical University, China
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20
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Yoshida-Sakai N, Watanabe T, Yamamoto Y, Ureshino H, Kamachi K, Kurahashi Y, Fukuda-Kurahashi Y, Kimura S. Adult T-cell leukemia-lymphoma acquires resistance to DNA demethylating agents through dysregulation of enzymes involved in pyrimidine metabolism. Int J Cancer 2021; 150:1184-1197. [PMID: 34913485 PMCID: PMC9303000 DOI: 10.1002/ijc.33901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 01/05/2023]
Abstract
Adult T-cell leukemia-lymphoma (ATL) is an aggressive neoplasm derived from T-cells transformed by human T-cell lymphotropic virus-1 (HTLV-1). Recently, we reported that regional DNA hypermethylation in HTLV-1-infected T-cells reflects the disease status of ATL and the anti-ATL effects of DNA demethylating agents, including azacitidine (AZA), decitabine (DAC) and a new DAC prodrug, OR-2100 (OR21), which we developed. Here, to better understand the mechanisms underlying drug resistance, we generated AZA-, DAC- and OR21-resistant (AZA-R, DAC-R and OR21-R, respectively) cells from the ATL cell line TL-Om1 and the HTLV-1-infected cell line MT-2 via long-term drug exposure. The efficacy of OR21 was almost the same as that of DAC, indicating that the pharmacodynamics of OR21 were due to release of DAC from OR21. Resistant cells did not show cellular responses observed in parental cells induced by treatment with drugs, including growth suppression, depletion of DNA methyltransferase DNMT1 and DNA hypomethylation. We also found that reduced expression of deoxycytidine kinase (DCK) correlated with lower susceptibility to DAC/OR21 and that reduced expression of uridine cytidine kinase2 (UCK2) correlated with reduced susceptibility to AZA. DCK and UCK2 catalyze phosphorylation of DAC and AZA, respectively; reconstitution of expression reversed the resistant phenotypes. A large homozygous deletion in DCK and a homozygous splice donor site mutation in UCK2 were identified in DAC-R TL-Om1 and AZA-R TL-Om1, respectively. Both genomic mutations might lead to loss of protein expression. Thus, inactivation of UCK2 and DCK might be a putative cause of phenotypes that are resistant to AZA and DAC/OR21, respectively.
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Affiliation(s)
- Nao Yoshida-Sakai
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan.,Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Tatsuro Watanabe
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuta Yamamoto
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Hiroshi Ureshino
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan.,Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Kazuharu Kamachi
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan.,Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuki Kurahashi
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan.,Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan.,OHARA Pharmaceutical Co, Ltd, Tokyo, Japan
| | - Yuki Fukuda-Kurahashi
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan.,OHARA Pharmaceutical Co, Ltd, Tokyo, Japan
| | - Shinya Kimura
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan.,Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
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21
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Schönthal AH, Swenson S, Minea RO, Kim HN, Cho H, Mohseni N, Kim YM, Chen TC. Potentially Curative Therapeutic Activity of NEO212, a Perillyl Alcohol-Temozolomide Conjugate, in Preclinical Cytarabine-Resistant Models of Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13143385. [PMID: 34298603 PMCID: PMC8305595 DOI: 10.3390/cancers13143385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/01/2021] [Accepted: 07/04/2021] [Indexed: 12/29/2022] Open
Abstract
Simple Summary Many patients are still dying from acute myeloid leukemia (AML). Initial treatment of this blood-borne cancer consists of chemotherapy, usually with the agent cytarabine (AraC). However, the cancer cells can become drug resistant and unresponsive to AraC, which complicates further treatment and worsens prognosis. More effective treatments are needed. We are developing a novel anticancer compound called NEO212. We investigated its AML-therapeutic potential with the use of AraC-resistant AML cells grown in culture and in mice implanted with such AML cells. We found that NEO212 effectively killed AML cells in culture. The majority of AML mice that received NEO212 treatment survived and thrived without signs of tumor recurrence. At the same time, NEO212 treatment did not result in any detectable side effects, showing that this drug was very well tolerated by these animals. We deem it worthwhile to further develop NEO212 toward its evaluation in AML patients, in particular in those where initial therapy with AraC has failed. Abstract Despite progress in the treatment of acute myeloid leukemia (AML), the clinical outcome remains suboptimal and many patients are still dying from this disease. First-line treatment consists of chemotherapy, which typically includes cytarabine (AraC), either alone or in combination with anthracyclines, but drug resistance can develop and significantly worsen prognosis. Better treatments are needed. We are developing a novel anticancer compound, NEO212, that was created by covalent conjugation of two different molecules with already established anticancer activity, the alkylating agent temozolomide (TMZ) and the natural monoterpene perillyl alcohol (POH). We investigated the anticancer activity of NEO212 in several in vitro and in vivo models of AML. Human HL60 and U937 AML cell lines, as well as different AraC-resistant AML cell lines, were treated with NEO212 and effects on cell proliferation, cell cycle, and cell death were investigated. Mice with implanted AraC-sensitive or AraC-resistant AML cells were dosed with oral NEO212, and animal survival was monitored. Our in vitro experiments show that treatment of cells with NEO212 results in growth inhibition via potent G2 arrest, which is followed by apoptotic cell death. Intriguingly, NEO212 was equally potent in highly AraC-resistant cells. In vivo, NEO212 treatment strikingly extended survival of AML mice and the majority of treated mice continued to thrive and survive without any signs of illness. At the same time, we were unable to detect toxic side effects of NEO212 treatment. All in all, the absence of side effects, combined with striking therapeutic activity even in an AraC-resistant context, suggests that NEO212 should be developed further toward clinical testing.
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Affiliation(s)
- Axel H. Schönthal
- Department of Molecular Microbiology & Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA;
- Correspondence: (A.H.S.); (T.C.C.); Tel.: +1-323-442-1730 (A.H.S.); +1-323-409-7422 (T.C.C.); Fax: +1-323-442-1721 (A.H.S.); +1-323-226-7833 (T.C.C.)
| | - Steve Swenson
- Department of Neurosurgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA; (S.S.); (R.O.M.); (H.C.)
| | - Radu O. Minea
- Department of Neurosurgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA; (S.S.); (R.O.M.); (H.C.)
| | - Hye Na Kim
- Department Pediatrics, Division of Hematology, Oncology, Blood and Bone Marrow Transplantation, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, USA; (H.N.K.); (Y.-M.K.)
| | - Heeyeon Cho
- Department of Neurosurgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA; (S.S.); (R.O.M.); (H.C.)
| | - Nazleen Mohseni
- Department of Molecular Microbiology & Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA;
| | - Yong-Mi Kim
- Department Pediatrics, Division of Hematology, Oncology, Blood and Bone Marrow Transplantation, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, USA; (H.N.K.); (Y.-M.K.)
| | - Thomas C. Chen
- Department of Neurosurgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA; (S.S.); (R.O.M.); (H.C.)
- Correspondence: (A.H.S.); (T.C.C.); Tel.: +1-323-442-1730 (A.H.S.); +1-323-409-7422 (T.C.C.); Fax: +1-323-442-1721 (A.H.S.); +1-323-226-7833 (T.C.C.)
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22
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Soares F, Chen B, Lee JB, Ahmed M, Ly D, Tin E, Kang H, Zeng Y, Akhtar N, Minden MD, He HH, Zhang L. CRISPR screen identifies genes that sensitize AML cells to double-negative T-cell therapy. Blood 2021; 137:2171-2181. [PMID: 33270841 DOI: 10.1182/blood.2019004108] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Acute myeloid leukemia (AML) remains a devastating disease in need of new therapies to improve patient survival. Targeted adoptive T-cell therapies have achieved impressive clinical outcomes in some B-cell leukemias and lymphomas but not in AML. Double-negative T cells (DNTs) effectively kill blast cells from the majority of AML patients and are now being tested in clinical trials. However, AML blasts obtained from ∼30% of patients show resistance to DNT-mediated cytotoxicity; the markers or mechanisms underlying this resistance have not been elucidated. Here, we used a targeted clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) screen to identify genes that cause susceptibility of AML cells to DNT therapy. Inactivation of the Spt-Ada-Gcn5-acetyltransferase (SAGA) deubiquitinating complex components sensitized AML cells to DNT-mediated cytotoxicity. In contrast, CD64 inactivation resulted in resistance to DNT-mediated cytotoxicity. Importantly, the level of CD64 expression correlated strongly with the sensitivity of AML cells to DNT treatment. Furthermore, the ectopic expression of CD64 overcame AML resistance to DNTs in vitro and in vivo. Altogether, our data demonstrate the utility of CRISPR/Cas9 screens to uncover mechanisms underlying the sensitivity to DNT therapy and suggest CD64 as a predictive marker for response in AML patients.
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Affiliation(s)
| | - Branson Chen
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada; and
- Department of Laboratory Medicine and Pathobiology
| | - Jong Bok Lee
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada; and
- Department of Immunology, and
| | | | - Dalam Ly
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada; and
- Department of Immunology, and
| | - Enoch Tin
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada; and
- Department of Immunology, and
| | - Hyeonjeong Kang
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada; and
- Department of Laboratory Medicine and Pathobiology
| | | | | | | | - Housheng Hansen He
- Princess Margaret Cancer Centre and
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Li Zhang
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada; and
- Department of Laboratory Medicine and Pathobiology
- Department of Immunology, and
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23
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He C, Han S, Chang Y, Wu M, Zhao Y, Chen C, Chu X. CRISPR screen in cancer: status quo and future perspectives. Am J Cancer Res 2021; 11:1031-1050. [PMID: 33948344 PMCID: PMC8085856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) system offers a powerful platform for genome manipulation, including protein-coding genes, noncoding RNAs and regulatory elements. The development of CRISPR screen enables high-throughput interrogation of gene functions in diverse tumor biologies, such as tumor growth, metastasis, synthetic lethal interactions, therapeutic resistance and immunotherapy response, which are mostly performed in vitro or in transplant models. Recently, direct in vivo CRISPR screens have been developed to identify drivers of tumorigenesis in native microenvironment. Key parameters of CRISPR screen are constantly being optimized to achieve higher targeting efficiency and lower off-target effect. Here, we review the recent advances of CRISPR screen in cancer studies both in vitro and in vivo, with a particular focus on identifying cancer immunotherapy targets, and propose optimizing strategies and future perspectives for CRISPR screen.
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Affiliation(s)
- Chenglong He
- Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical UniversityNanjing 210002, China
| | - Siqi Han
- Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical UniversityNanjing 210002, China
| | - Yue Chang
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing UniversityNanjing 210002, China
| | - Meijuan Wu
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing UniversityNanjing 210002, China
| | - Yulu Zhao
- Department of Medical Oncology, Jinling Hospital, Nanjing Medical UniversityNanjing 210002, China
| | - Cheng Chen
- Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical UniversityNanjing 210002, China
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing UniversityNanjing 210002, China
| | - Xiaoyuan Chu
- Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical UniversityNanjing 210002, China
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing UniversityNanjing 210002, China
- Department of Medical Oncology, Jinling Hospital, Nanjing Medical UniversityNanjing 210002, China
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24
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Récher C. Clinical Implications of Inflammation in Acute Myeloid Leukemia. Front Oncol 2021; 11:623952. [PMID: 33692956 PMCID: PMC7937902 DOI: 10.3389/fonc.2021.623952] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Recent advances in the description of the tumor microenvironment of acute myeloid leukemia, including the comprehensive analysis of the leukemic stem cell niche and clonal evolution, indicate that inflammation may play a major role in many aspects of acute myeloid leukemia (AML) such as disease progression, chemoresistance, and myelosuppression. Studies on the mechanisms of resistance to chemotherapy or tyrosine kinase inhibitors along with high-throughput drug screening have underpinned the potential role of glucocorticoids in this disease classically described as steroid-resistant in contrast to acute lymphoblastic leukemia. Moreover, some mutated oncogenes such as RUNX1, NPM1, or SRSF2 transcriptionally modulate cell state in a manner that primes leukemic cells for glucocorticoid sensitivity. In clinical practice, inflammatory markers such as serum ferritin or IL-6 have a strong prognostic impact and may directly affect disease progression, whereas interesting preliminary data suggested that dexamethasone may improve the outcome for AML patients with a high white blood cell count, which paves the way to develop prospective clinical trials that evaluate the role of glucocorticoids in AML.
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Affiliation(s)
- Christian Récher
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Université Toulouse III Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
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25
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Kerek EM, Cromwell CR, Hubbard BP. Identification of Drug Resistance Genes Using a Pooled Lentiviral CRISPR/Cas9 Screening Approach. Methods Mol Biol 2021; 2381:227-242. [PMID: 34590280 DOI: 10.1007/978-1-0716-1740-3_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In addition to advancing the development of gene-editing therapeutics, CRISPR/Cas9 is transforming how functional genetic studies are carried out in the lab. By increasing the ease with which genetic information can be inserted, deleted, or edited in cell and organism models, it facilitates genotype-phenotype analysis. Moreover, CRISPR/Cas9 has revolutionized the speed at which new genes underlying a particular phenotype can be identified through its application in genomic screens. Arrayed high-throughput and pooled lentiviral-based CRISPR/Cas9 screens have now been used in a wide variety of contexts, including the identification of essential genes, genes involved in cancer metastasis and tumor growth, and even genes involved in viral response. This technology has also been successfully used to identify drug targets and drug resistance mechanisms. Here, we provide a detailed protocol for performing a genome-wide pooled lentiviral CRISPR/Cas9 knockout screen to identify genetic modulators of a small-molecule drug. While we exemplify how to identify genes involved in resistance to a cytotoxic histone deacetylase inhibitor, Trichostatin A (TSA), the workflow we present can easily be adapted to different types of selections and other types of exogenous ligands or drugs.
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Affiliation(s)
- Evan M Kerek
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
| | | | - Basil P Hubbard
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada.
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26
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Yamamoto A, Kurata M, Yamamoto K, Nogawa D, Inoue M, Ishibashi S, Ikeda M, Miyasaka N, Kitagawa M. High amplification of PVT1 and MYC predict favorable prognosis in early ovarian carcinoma. Pathol Res Pract 2020; 216:153175. [PMID: 32841774 DOI: 10.1016/j.prp.2020.153175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 08/07/2020] [Accepted: 08/09/2020] [Indexed: 10/23/2022]
Abstract
INTRODUCTION The objective of this study was to evaluate the status of MYC and PVT1, which are frequently amplified in malignant tumors, and to assess their biological features according to histological subtypes in early-stage epithelial ovarian cancer (EOC). METHODS Formalin-fixed and paraffin-embedded (FFPE) samples of 64 EOC tissues in International Federation of Gynecology and Obstetrics stages I-II and 20 normal ovarian tissues were analyzed for copy number and mRNA expression of MYC and PVT1 by qPCR and for MYC protein expression by immunohistochemistry. MYC protein expression was assessed by western blotting in a PVT1 siRNA-transfected ovarian cancer cell line. MYC and PVT1 was assessed as a prognostic factor using Kaplan-Meier analysis. The median follow-up period was 49.9 months and 17 cases in 64 of EOC recurred during follow-up. RESULTS Copy number variations showed significantly higher MYC and PVT1 in EOC than in normal ovaries. The copy number of PVT1 was significantly higher in serous carcinoma than in the other histological types. The mRNA of MYC and PVT1 was also higher in cancer tissues and showed a strong correlation in all histological subtypes. Immunohistochemistry revealed a positive association between the phosphorylated MYC (pMYC) index and high expression of proliferation markers, such as Ki-67 index, and a negative correlation between pMYC protein and the PVT1 copy number. Knockdown of PVT1 in ovarian cancer cell lines resulted in upregulation of MYC protein and pMYC. Kaplan-Meier survival analysis showed that low copy numbers of both MYC and PVT1 were associated with a statistically significantly poor prognosis. CONCLUSION Expression of pMYC and the Ki-67 index were affected by the PVT1 copy number but not mRNA. A high PVT1 copy number in FFPE samples might suggest favorable prognosis in early ovarian cancers.
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Affiliation(s)
- Akiko Yamamoto
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan
| | - Morito Kurata
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan.
| | - Kohei Yamamoto
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan
| | - Daichi Nogawa
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan
| | - Miori Inoue
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan
| | - Sachiko Ishibashi
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan
| | - Masumi Ikeda
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan
| | - Naoyuki Miyasaka
- Department of Obstetrics and Gynecology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan
| | - Masanobu Kitagawa
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan
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Liu Q, Garcia M, Wang S, Chen CW. Therapeutic Target Discovery Using High-Throughput Genetic Screens in Acute Myeloid Leukemia. Cells 2020; 9:cells9081888. [PMID: 32806592 PMCID: PMC7465943 DOI: 10.3390/cells9081888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 12/20/2022] Open
Abstract
The development of high-throughput gene manipulating tools such as short hairpin RNA (shRNA) and CRISPR/Cas9 libraries has enabled robust characterization of novel functional genes contributing to the pathological states of the diseases. In acute myeloid leukemia (AML), these genetic screen approaches have been used to identify effector genes with previously unknown roles in AML. These AML-related genes centralize alongside the cellular pathways mediating epigenetics, signaling transduction, transcriptional regulation, and energy metabolism. The shRNA/CRISPR genetic screens also realized an array of candidate genes amenable to pharmaceutical targeting. This review aims to summarize genes, mechanisms, and potential therapeutic strategies found via high-throughput genetic screens in AML. We also discuss the potential of these findings to instruct novel AML therapies for combating drug resistance in this genetically heterogeneous disease.
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Affiliation(s)
- Qiao Liu
- Fujian Provincial Key Laboratory on Hematology, Department of Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou 350108, China; (Q.L.); (S.W.)
- Union Clinical Medical College, Fujian Medical University, Fuzhou 350108, China
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA;
| | - Michelle Garcia
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA;
- Pomona College, Claremont, CA 91711, USA
| | - Shaoyuan Wang
- Fujian Provincial Key Laboratory on Hematology, Department of Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou 350108, China; (Q.L.); (S.W.)
- Union Clinical Medical College, Fujian Medical University, Fuzhou 350108, China
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA;
- Correspondence:
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Zhang F, Liu R, Liu C, Zhang H, Lu Y. Nanos3, a cancer-germline gene, promotes cell proliferation, migration, chemoresistance, and invasion of human glioblastoma. Cancer Cell Int 2020; 20:197. [PMID: 32508533 PMCID: PMC7249350 DOI: 10.1186/s12935-020-01272-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/16/2020] [Indexed: 12/15/2022] Open
Abstract
Background Radiotherapy, chemotherapy, and surgery have made crucial strides in glioblastoma treatment, yet they often fail; thus, new treatment and new detection methods are needed. Aberrant expression of Nanos3 has been functionally associated with various cancers. Here, we sought to identify the clinical significance and potential mechanisms of Nanos3 in human glioblastoma. Methods Nanos3 expression was studied in nude mouse glioblastoma tissues and glioblastoma cell lines by immunohistochemistry, Western blot, and RT-PCR. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 gene editing assay was performed to generate the Nanos3 knockdown glioblastoma cell lines. The effects of Nanos3 on glioblastoma cells proliferation, migration, invasion, chemoresistance, germ cell characteristics, and tumor formation were analyzed by CCK8, transwell, cell survival experiments and alkaline phosphatase staining in vitro and in nude mouse models in vivo. Correlation between the expression of stemness proteins and the expression of Nanos3 was evaluated by Western blot. Results We found that Nanos3 was strongly expressed in both glioblastoma cell lines and tissues. Western blot and sequencing assays showed that the Nanos3 knockdown glioblastoma cell lines were established successfully, and we discovered that Nanos3 deletion reduced the proliferation, migration, and invasion of glioblastoma cells in vitro (P < 0.05). Nanos3 knockdown enhanced the sensitivity of glioblastoma cells to doxorubicin (DOX) and temozolomide (TMZ) (P < 0.05), and Nanos3+/- glioblastoma cell lines did not show the characteristics of the germline cells. In addition, Nanos3 deletion inhibited subcutaneous xenograft tumor growth in vivo (P < 0.001). Moreover, the oncogenesis germline protein levels of CD133, Oct4, Ki67, and Dazl decreased significantly in glioblastoma cells following Nanos3 knockdown. Conclusions Both in vitro and in vivo assays suggest that Nanos3, which is a cancer-germline gene, initiates the tumorigenesis of glioblastoma via acquiring the oncogenesis germline traits. These data demonstrate that ectopic germline traits are necessary for glioblastoma growth.
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Affiliation(s)
- Fengyu Zhang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, 12 Wulumuqi Road, Jing-an District, Shanghai, 200040 China
| | - Ruilai Liu
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, 12 Wulumuqi Road, Jing-an District, Shanghai, 200040 China
| | - Cheng Liu
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, 12 Wulumuqi Road, Jing-an District, Shanghai, 200040 China
| | - Haishi Zhang
- Department of Neurosurgery, Huashan Hospital, Fudan University, 12 Wulumuqi Road, Jing-an District, Shanghai, 200040 China
| | - Yuan Lu
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, 12 Wulumuqi Road, Jing-an District, Shanghai, 200040 China
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29
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Yamamoto A, Kurata M, Onishi I, Sugita K, Matsumura M, Ishibashi S, Ikeda M, Yamamoto K, Kitagawa M. CRISPR screening identifies M1AP as a new MYC regulator with a promoter-reporter system. PeerJ 2020; 8:e9046. [PMID: 32411526 PMCID: PMC7210806 DOI: 10.7717/peerj.9046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/02/2020] [Indexed: 12/26/2022] Open
Abstract
Background MYC is one of the proto-oncogenes contributing to tumorigenesis in many human cancers. Although the mechanism of MYC regulation is still not fully understood, learning about the comprehensive mechanism controlling the transcriptional activity of MYC will lead to therapeutic targets. The CRISPR/Cas9 library system is a simple and powerful screening technique. This study aims to identify new transcriptional upstream activators of MYC using the CRISPR activation library with new promoter-reporter systems. Methods and Results The MYC promoter-reporter system was developed with a photoconvertible fluorescent protein, Dendra2, and named “pMYC-promoter-Dendra2.” This MYC promoter-reporter system was designed to harbor a proximal MYC promoter at (3.1 kb). Both the CRISPR activation library and pMYC-promoter-Dendra2 were induced to HEK 293T cells, and Dendra2-positive cells, that are supposed that MYC should be upregulated, were collected individually by a cell sorter. Among the 169 cells collected, 12 clones were successfully established. Then, pMYC-promoter-Dendra2 was transfected again into these 12 clones, and two of 12 clones showed Dendra2 positivity. In this procedure, the cells with non-specific autofluorescence were correctly distinguished by utilizing the photoswitchable character of Dendra2. Using extracted genomic DNA of these two Dendra2 positive clones, polymerase chain reaction (PCR) was performed to amplify the guide RNA (gRNA) containing region, which was introduced by the CRISPR activation library. Eventually, PLEKHO2, MICU, MBTPS1, and M1AP were identified, and these gRNAs were transfected individually into HEK 293T cells again using the CRISPR activation system. Only M1AP gRNA transfected cells showed Dendra2-positive fluorescence. Then, the overexpression vector for M1AP with a doxycycline-inducible vector confirmed that M1AP induced high MYC expression by real-time quantitative PCR and western blot. Furthermore, the dual-luciferase assay showed a significant increase of promoter activity, and MYC mRNA was higher in M1AP- overexpressing cells. M1AP is highly expressed in several cancers, though, a positive correlation between M1AP and MYC was observed only in human acute myeloid leukemia. Conclusion The present study confirmed that the experimental method using the CRISPR library technology functions effectively for the identification of molecules that activate endogenous MYC. This method will help elucidate the regulatory mechanism of MYC expression, as well as supporting further drug research against malignant tumors.
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Affiliation(s)
- Akiko Yamamoto
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Morito Kurata
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Iichiroh Onishi
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keisuke Sugita
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Miwa Matsumura
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sachiko Ishibashi
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masumi Ikeda
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kouhei Yamamoto
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masanobu Kitagawa
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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Cai J, Chen J, Wu T, Cheng Z, Tian Y, Pu C, Shi W, Suo X, Wu X, Zhang K. Genome-scale CRISPR activation screening identifies a role of LRP8 in Sorafenib resistance in Hepatocellular carcinoma. Biochem Biophys Res Commun 2020; 526:1170-1176. [PMID: 32312520 DOI: 10.1016/j.bbrc.2020.04.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/10/2020] [Indexed: 12/21/2022]
Abstract
Sorafenib may provide survival benefits for patients with advanced hepatocellular carcinoma. However, tumor cells can display primary or secondary resistance to Sorafenib. To identify genes capable of conveying Sorafenib resistance, we performed a genome-wide CRISPR transcriptional activation library (SAM) in human Huh7 cells. We identified that a group of sgRNAs were significantly enriched in Sorafenib resistant Huh7 cells, which indicated that these sgRNAs up-regulated their target genes and induced resistance. We finally identified LRP8 as a key gene that can drive HCC cell to acquire sorafenib resistance. All three sgRNAs targeting LRP8 were identified in Sorafenib resistant Huh7 cells with high copy. We also showed that sorafenib-acquired resistant Huh7 cells have much higher LRP8 expression level than parental Huh7 cells. We proved that overexpression of LRP8 in HCC cell lines activated β-catenin and significantly promoted its resistance to Sorafenib. We further showed that overexpression of LRP8 reduced the apoptosis level of HCC cell lines. To summary, genome-scale CRISPR activation screening identifies a role of LRP8 in Sorafenib resistance in Hepatocellular carcinoma.
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Affiliation(s)
- Jun Cai
- Department of Hepatobiliary Surgery, Peking University International Hospital, Beijing 102206, China
| | - Jianfei Chen
- Department of Hepatobiliary Surgery, Peking University International Hospital, Beijing 102206, China
| | - Tiantian Wu
- Department of Hepatobiliary Surgery, Peking University International Hospital, Beijing 102206, China
| | - Zhilei Cheng
- Department of Hepatobiliary Surgery, Peking University International Hospital, Beijing 102206, China
| | - Yuanhu Tian
- Department of Hepatobiliary Surgery, Peking University International Hospital, Beijing 102206, China
| | - Changsheng Pu
- Department of Hepatobiliary Surgery, Peking University International Hospital, Beijing 102206, China
| | - Wenzai Shi
- Department of Hepatobiliary Surgery, Peking University International Hospital, Beijing 102206, China
| | - Xiaopeng Suo
- Department of Hepatobiliary Surgery, Peking University International Hospital, Beijing 102206, China
| | - Xianjia Wu
- Department of Hepatobiliary Surgery, Peking University International Hospital, Beijing 102206, China
| | - Keming Zhang
- Department of Hepatobiliary Surgery, Peking University International Hospital, Beijing 102206, China.
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Sato M. Phenotypic screening using large-scale genomic libraries to identify drug targets for the treatment of cancer. Oncol Lett 2020; 19:3617-3626. [PMID: 32391087 PMCID: PMC7204489 DOI: 10.3892/ol.2020.11512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/04/2020] [Indexed: 02/06/2023] Open
Abstract
During malignant progression to overt cancer cells, normal cells accumulate multiple genetic and non-genetic changes, which result in the acquisition of various oncogenic properties, such as uncontrolled proliferation, drug resistance, invasiveness, anoikis-resistance, the ability to bypass oncogene-induced senescence and cancer stemness. To identify potential novel drug targets contributing to these malignant phenotypes, researchers have performed large-scale genomic screening using various in vitro and in vivo screening models and identified numerous promising cancer drug target genes. However, there are issues with these identified genes, such as low reproducibility between different datasets. In the present study, the recent advances in the functional screening for identification of cancer drug target genes are summarized, and current issues and future perspectives are discussed.
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Affiliation(s)
- Mitsuo Sato
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi 461-8673, Japan
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Simonneau C, Yang J, Kong X, Kilker R, Edelstein L, Fortina P, Londin E, Horowitz A. Validation of a Miniaturized Permeability Assay Compatible with CRISPR-Mediated Genome-Wide Screen. Sci Rep 2019; 9:14238. [PMID: 31578372 PMCID: PMC6775082 DOI: 10.1038/s41598-019-50588-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 09/11/2019] [Indexed: 12/28/2022] Open
Abstract
The impermeability of the luminal endothelial cell monolayer is crucial for the normal performance of the vascular and lymphatic systems. A key to this function is the integrity of the monolayer's intercellular junctions. The known repertoire of junction-regulating genes is incomplete. Current permeability assays are incompatible with high-throughput genome-wide screens that could identify these genes. To overcome these limitations, we designed a new permeability assay that consists of cell monolayers grown on ~150 μm microcarriers (MCs). Each MC functions as a miniature individual assay of permeability (MAP). We demonstrate that false-positive results can be minimized, and that MAP sensitivity to thrombin-induced increase in monolayer permeability is similar to the sensitivity of impedance measurement. We validated the assay by showing that the expression of single guide RNAs (sgRNAs) that target genes encoding known thrombin signaling proteins blocks effectively thrombin-induced junction disassembly, and that MAPs carrying such cells can be separated effectively by fluorescence-assisted sorting from those that carry cells expressing non-targeting sgRNAs. These results indicate that MAPs are suitable for high-throughput experimentation and for genome-wide screens for genes that mediate the disruptive effect of thrombin on endothelial cell junctions.
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Affiliation(s)
- Claire Simonneau
- Cardeza Center for Hematology Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
- Roche Innovation Center Basel, Zürich, Switzerland
| | - Junning Yang
- Cardeza Center for Hematology Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Xianguo Kong
- Cardeza Center for Hematology Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Robert Kilker
- Cardeza Center for Hematology Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Leonard Edelstein
- Cardeza Center for Hematology Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Paolo Fortina
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
- Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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Zhao WS, Yan WP, Chen DB, Dai L, Yang YB, Kang XZ, Fu H, Chen P, Deng KJ, Wang XY, Xie XW, Chen HS, Chen KN. Genome-scale CRISPR activation screening identifies a role of ELAVL2-CDKN1A axis in paclitaxel resistance in esophageal squamous cell carcinoma. Am J Cancer Res 2019; 9:1183-1200. [PMID: 31285951 PMCID: PMC6610048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/07/2019] [Indexed: 06/09/2023] Open
Abstract
Neoadjuvant chemotherapy (NAC) may provide survival benefits for patients with advanced esophageal squamous cell carcinoma. However, tumor cells can display primary or secondary resistance to paclitaxel (PTX), a primary component of induction chemotherapy regimen. To identify genes capable of conveying PTX resistance, we performed a genome-wide CRISPR transcriptional activation library in human KYSE-180 cells. High throughput next generation sequencing was further applied to establish the phenotype-to-genotype relationship. Our highest-ranking hits are CDKN1A, TSPAN4, ELAVL2, JUNB and PAAF1. We generated evidence that esophageal tumors with high CDKN1A, ELAVL2 and TSPAN4 levels, quantified using qRT-PCR and Western blot assays, showed poorer chemotherapy response. Higher expression levels of TSPAN4 and ELAVL2 protein are independent risk factors for poor chemotherapy response in ESCC patients. We then found that overexpression of CDKN1A, ELAVL2 or TSPAN4 in ESCC cell lines significantly promoted the resistance to PTX by inhibiting cell apoptosis. Interestingly, ESCC cells overexpressed CDKN1A, ELAVL2 or TSPAN4 also acquired resistance to cisplatin (DDP). This phenomenon may be explained by cross-resistance of chemotherapy. We additionally found an association between ELAVL2 and CDKN1A, which may be regarded as the upstream and downstream factors that synergistically involved in the regulation of chemo-resistance in ESCC. Therefore, our study demonstrated that the genome-wide CRISPR activation library is a powerful strategy for the discovery of chemo-resistant genes critical for ESCC and we reported the first evidence that the ELAVL2-CDKN1A axis may be an important mechanism involved in chemo-resistance in ESCC.
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Affiliation(s)
- Wen-Si Zhao
- Department of Thoracic Surgery I, Peking University Cancer Hospital and InstituteBeijing 100142, China
| | - Wan-Pu Yan
- Department of Thoracic Surgery I, Peking University Cancer Hospital and InstituteBeijing 100142, China
| | - Dong-Bo Chen
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver DiseaseBeijing 100044, China
| | - Liang Dai
- Department of Thoracic Surgery I, Peking University Cancer Hospital and InstituteBeijing 100142, China
| | - Yong-Bo Yang
- Department of Thoracic Surgery I, Peking University Cancer Hospital and InstituteBeijing 100142, China
| | - Xiao-Zheng Kang
- Department of Thoracic Surgery I, Peking University Cancer Hospital and InstituteBeijing 100142, China
| | - Hao Fu
- Department of Thoracic Surgery I, Peking University Cancer Hospital and InstituteBeijing 100142, China
| | - Pu Chen
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver DiseaseBeijing 100044, China
| | - Kang-Jian Deng
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver DiseaseBeijing 100044, China
| | - Xue-Yan Wang
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver DiseaseBeijing 100044, China
| | - Xing-Wang Xie
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver DiseaseBeijing 100044, China
| | - Hong-Song Chen
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver DiseaseBeijing 100044, China
| | - Ke-Neng Chen
- Department of Thoracic Surgery I, Peking University Cancer Hospital and InstituteBeijing 100142, China
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Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute. Nat Protoc 2019; 14:756-780. [PMID: 30710114 PMCID: PMC6862721 DOI: 10.1038/s41596-018-0113-7] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 12/07/2018] [Indexed: 12/25/2022]
Abstract
Genome-wide screening using CRISPR coupled with nuclease Cas9 (CRISPR-Cas9) is a powerful technology for the systematic evaluation of gene function. Statistically principled analysis is needed for the accurate identification of gene hits and associated pathways. Here, we describe how to perform computational analysis of CRISPR screens using the MAGeCKFlute pipeline. MAGeCKFlute combines the MAGeCK and MAGeCK-VISPR algorithms and incorporates additional downstream analysis functionalities. MAGeCKFlute is distinguished from other currently available tools by its comprehensive pipeline, which contains a series of functions for analyzing CRISPR screen data. This protocol explains how to use MAGeCKFlute to perform quality control (QC), normalization, batch effect removal, copy-number bias correction, gene hit identification and downstream functional enrichment analysis for CRISPR screens. We also describe gene identification and data analysis in CRISPR screens involving drug treatment. Completing the entire MAGeCKFlute pipeline requires ~3 h on a desktop computer running Linux or Mac OS with R support.
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Yan Y, Su W, Zeng S, Qian L, Chen X, Wei J, Chen N, Gong Z, Xu Z. Effect and Mechanism of Tanshinone I on the Radiosensitivity of Lung Cancer Cells. Mol Pharm 2018; 15:4843-4853. [PMID: 30216081 DOI: 10.1021/acs.molpharmaceut.8b00489] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Resistance to radiotherapy is one of the main obstacles to improving cancer prognoses. To effectively destroy cancer cells, novel radiation sensitizers are needed. Recently, several natural products have been shown to exhibit promising tumor-killing properties. However, little is known about the specific mechanisms of these natural compounds on cancer treatment. In this study, after screening a high-throughput natural product library, we identified tanshinone I (Tan I) as a potential radiation sensitizer in lung cancer cells. METHODS Lung cancer radioresistant cell lines, H358-IR and H157-IR, were first established to confirm the radioresistant phenotypes. After that, a natural product library was used to screen the potential radiation sensitizer. We further examined the inhibition functions of Tan I on radioresistant cancer cells via a series of experiments. RESULTS Tan I significantly inhibited cell proliferation and clone formation, consequently enhancing radiosensitivity in radioresistant lung cancer cells, H358-IR and H157-IR. Stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative proteomics indicated that Tan I downregulates expression of pro-oncogenic protein phosphoribosyl pyrophosphate aminotransferase (PPAT) in both H358-IR and H157-IR cells. Further analysis of molecular docking showed that Tan I is well-docked into the active pocket of the structure of PPAT, serving as a potential PPAT inhibitor. CONCLUSIONS Taken together, these findings suggest that inhibition of the tumor promoter PPAT by Tan I exerts marked inhibitory effects on radioresistant lung cancer cells, improving radiation efficacy.
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Cao J, Wei J, Yang P, Zhang T, Chen Z, He F, Wei F, Chen H, Hu H, Zhong J, Yang Z, Cai W, Li W, Wang Q. Genome-scale CRISPR-Cas9 knockout screening in gastrointestinal stromal tumor with Imatinib resistance. Mol Cancer 2018; 17:121. [PMID: 30103756 PMCID: PMC6090611 DOI: 10.1186/s12943-018-0865-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 07/25/2018] [Indexed: 11/18/2022] Open
Abstract
Genome-scale CRISPR-Cas9 Knockout Screening was applied to investigate novel targets in imatinib-resistant gastrointestinal stromal tumor (GIST). 20 genes and 2 miRNAs have been selected by total reads of sgRNA and sgRNA diversity, which has been further validated in imatinib-resistant GIST cells by CCK8 and qPCR analysis. Our study has finally revealed 9 genes (DBP, NR3C1, TCF12, TP53, ZNF12, SOCS6, ZFP36, ACYP1, and DRD1) involved in imatinib-resistant GIST-T1 cells. TP53 and SOCS6 may be the most promising candidate genes for imatinib-resistance due to the possible signaling pathway, such as apoptosis pathway and Wnt signaling pathway, JAK-STAT signaling pathway. It is necessary to perform more studies to discover novel targets in imatinib-resistant GIST, including DBP, NR3C1, TCF12, ZNF12, ZFP36, ACYP1 and DRD1.
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Affiliation(s)
- Jie Cao
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China.
| | - Jianchang Wei
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Ping Yang
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Tong Zhang
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Zhuanpeng Chen
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Feng He
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Fang Wei
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Huacui Chen
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - He Hu
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Junbin Zhong
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Zhi Yang
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Wensong Cai
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Wanglin Li
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China.
| | - Qiang Wang
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China.
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Tsesmetzis N, Paulin CBJ, Rudd SG, Herold N. Nucleobase and Nucleoside Analogues: Resistance and Re-Sensitisation at the Level of Pharmacokinetics, Pharmacodynamics and Metabolism. Cancers (Basel) 2018; 10:cancers10070240. [PMID: 30041457 PMCID: PMC6071274 DOI: 10.3390/cancers10070240] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 02/07/2023] Open
Abstract
Antimetabolites, in particular nucleobase and nucleoside analogues, are cytotoxic drugs that, starting from the small field of paediatric oncology, in combination with other chemotherapeutics, have revolutionised clinical oncology and transformed cancer into a curable disease. However, even though combination chemotherapy, together with radiation, surgery and immunotherapy, can nowadays cure almost all types of cancer, we still fail to achieve this for a substantial proportion of patients. The understanding of differences in metabolism, pharmacokinetics, pharmacodynamics, and tumour biology between patients that can be cured and patients that cannot, builds the scientific basis for rational therapy improvements. Here, we summarise current knowledge of how tumour-specific and patient-specific factors can dictate resistance to nucleobase/nucleoside analogues, and which strategies of re-sensitisation exist. We revisit well-established hurdles to treatment efficacy, like the blood-brain barrier and reduced deoxycytidine kinase activity, but will also discuss the role of novel resistance factors, such as SAMHD1. A comprehensive appreciation of the complex mechanisms that underpin the failure of chemotherapy will hopefully inform future strategies of personalised medicine.
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Affiliation(s)
- Nikolaos Tsesmetzis
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden.
| | - Cynthia B J Paulin
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden.
| | - Sean G Rudd
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden.
| | - Nikolas Herold
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden.
- Paediatric Oncology, Theme of Children's and Women's Health, Karolinska University Hospital Solna, 171 76 Stockholm, Sweden.
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Kurata JS, Lin RJ. MicroRNA-focused CRISPR-Cas9 library screen reveals fitness-associated miRNAs. RNA (NEW YORK, N.Y.) 2018; 24:966-981. [PMID: 29720387 PMCID: PMC6004052 DOI: 10.1261/rna.066282.118] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
MicroRNAs (miRNAs) are post-transcriptional gene regulators that play important roles in the control of cell fitness, differentiation, and development. The CRISPR-Cas9 gene-editing system is composed of the Cas9 nuclease in complex with a single guide RNA (sgRNA) and directs DNA cleavage at a predetermined site. Several CRISPR-Cas9 libraries have been constructed for genome-scale knockout screens of protein function; however, few libraries have included miRNA genes. Here we constructed a miRNA-focused CRISPR-Cas9 library that targets 1594 (85%) annotated human miRNA stem-loops. The sgRNAs in our LX-miR library are designed to have high on-target and low off-target activity, and each miRNA is targeted by four to five sgRNAs. We used this sgRNA library to screen for miRNAs that affect cell fitness of HeLa or NCI-N87 cells by monitoring the change in frequency of each sgRNA over time. By considering the expression in the tested cells and the dysregulation of the miRNAs in cancer specimens, we identified five HeLa pro-fitness and cervical cancer up-regulated miRNAs (miR-31-5p, miR-92b-3p, miR-146b-5p, miR-151a-3p, and miR-194-5p). Similarly, we identified six NCI-N87 pro-fitness and gastric cancer up-regulated miRNAs (miR-95-3p, miR-181a-5p, miR-188-5p, miR-196b-5p, miR-584-5p, and miR-1304-3p), as well as three anti-fitness and down-regulated miRNAs (let-7a-3p, miR-100-5p, and miR-149-5p). Some of those miRNAs are known to be oncogenic or tumor-suppressive, but others are novel. Taken together, the LX-miR library is useful for genome-wide unbiased screening to identify miRNAs important for cellular fitness and likely to be useful for other functional screens.
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Affiliation(s)
- Jessica S Kurata
- Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
- Irell and Manella Graduate School of Biological Sciences of the City of Hope, Duarte, California 91010, USA
| | - Ren-Jang Lin
- Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
- Irell and Manella Graduate School of Biological Sciences of the City of Hope, Duarte, California 91010, USA
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Kweon J, Kim DE, Jang AH, Kim Y. CRISPR/Cas-based customization of pooled CRISPR libraries. PLoS One 2018; 13:e0199473. [PMID: 29924860 PMCID: PMC6010251 DOI: 10.1371/journal.pone.0199473] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/07/2018] [Indexed: 12/21/2022] Open
Abstract
Pooled CRISPR libraries are widely used in high-throughput screening to study various biological processes. Various pooled CRISPR libraries have been shared for CRISPR screens and useful tools have been developed to construct researcher’s own libraries, however, many researchers are struggling to create their own pooled CRISPR libraries: it is a time-consuming, labor-intensive, and expensive process. In this study, we develop a simple method to customize conventional pooled CRISPR libraries using the CRISPR/Cas9 system. We show that conventional pooled CRISPR libraries can be modified by eliminating gRNAs that target positive genes, enabling the identification of unknown target genes in CRISPR screening. CRISPR/Cas9 system can be applied as a precise tool for customizing conventional pooled CRISPR libraries and will broaden the scope of high-throughput screening technology.
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Affiliation(s)
- Jiyeon Kweon
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Da-eun Kim
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, Republic of Korea
| | - An-Hee Jang
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yongsub Kim
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
- * E-mail:
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Guo X, Chitale P, Sanjana NE. Target Discovery for Precision Medicine Using High-Throughput Genome Engineering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1016:123-145. [PMID: 29130157 DOI: 10.1007/978-3-319-63904-8_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the past few years, programmable RNA-guided nucleases such as the CRISPR/Cas9 system have ushered in a new era of precision genome editing in diverse model systems and in human cells. Functional screens using large libraries of RNA guides can interrogate a large hypothesis space to pinpoint particular genes and genetic elements involved in fundamental biological processes and disease-relevant phenotypes. Here, we review recent high-throughput CRISPR screens (e.g. loss-of-function, gain-of-function, and targeting noncoding elements) and highlight their potential for uncovering novel therapeutic targets, such as those involved in cancer resistance to small molecular drugs and immunotherapies, tumor evolution, infectious disease, inborn genetic disorders, and other therapeutic challenges.
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Affiliation(s)
- Xinyi Guo
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
- Department of Biology, New York University, New York, NY, 10003, USA
| | - Poonam Chitale
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
- Department of Biology, New York University, New York, NY, 10003, USA
| | - Neville E Sanjana
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.
- Department of Biology, New York University, New York, NY, 10003, USA.
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41
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Zhang C, Quan R, Wang J. Development and application of CRISPR/Cas9 technologies in genomic editing. Hum Mol Genet 2018; 27:R79-R88. [DOI: 10.1093/hmg/ddy120] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 04/03/2018] [Indexed: 12/13/2022] Open
Affiliation(s)
- Cui Zhang
- Institute of Cell and Development Biology, College of Life Sciences, Zijingang Campus, Zhejiang University, Hangzhou, Zhejiang, P.R. China
| | - Renfu Quan
- Institute of Orthopedics, Xiaoshan Traditional Chinese Medical Hospital, Hangzhou, Zhejiang, China
| | - Jinfu Wang
- Institute of Cell and Development Biology, College of Life Sciences, Zijingang Campus, Zhejiang University, Hangzhou, Zhejiang, P.R. China
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42
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Bertoli S, Picard M, Bérard E, Griessinger E, Larrue C, Mouchel PL, Vergez F, Tavitian S, Yon E, Ruiz J, Delabesse E, Luquet I, Linares LK, Saland E, Carroll M, Danet-Desnoyers G, Sarry A, Huguet F, Sarry JE, Récher C. Dexamethasone in hyperleukocytic acute myeloid leukemia. Haematologica 2018. [PMID: 29519869 PMCID: PMC6058767 DOI: 10.3324/haematol.2017.184267] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Patients with acute myeloid leukemia and a high white blood cell count are at increased risk of early death and relapse. Because mediators of inflammation contribute to leukostasis and chemoresistance, dexamethasone added to chemotherapy could improve outcomes. This retrospective study evaluated the impact of adding or not adding dexamethasone to chemotherapy in a cohort of 160 patients with at least 50×109 white blood cells. In silico studies, primary samples, leukemic cell lines, and xenograft mouse models were used to explore the antileukemic activity of dexamethasone. There was no difference with respect to induction death rate, response, and infections between the 60 patients in the dexamethasone group and the 100 patients in the no dexamethasone group. Multivariate analysis showed that dexamethasone was significantly associated with improved relapse incidence (adjusted sub-HR: 0.30; 95% CI: 0.14–0.62; P=0.001), disease-free survival (adjusted HR: 0.50; 95% CI: 0.29–0.84; P=0.010), event-free survival (adjusted HR: 0.35; 95% CI: 0.21–0.58; P<0.001), and overall survival (adjusted HR: 0.41; 95% CI: 0.22–0.79; P=0.007). In a co-culture system, dexamethasone reduced the frequency of leukemic long-term culture initiating cells by 38% and enhanced the cytotoxicity of doxorubicin and cytarabine. In a patient-derived xenograft model treated with cytarabine, chemoresistant cells were enriched in genes of the inflammatory response modulated by dexamethasone. Dexamethasone also demonstrated antileukemic activity in NPM1-mutated samples. Dexamethasone may improve the outcome of acute myeloid leukemia patients receiving intensive chemotherapy. This effect could be due to the modulation of inflammatory chemoresistance pathways and to a specific activity in acute myeloid leukemia with NPM1 mutation.
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Affiliation(s)
- Sarah Bertoli
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, France.,Université Toulouse III Paul Sabatier, France.,Cancer Research Center of Toulouse, UMR1037-INSERM, ERL5294 CNRS, France
| | - Muriel Picard
- Service de Réanimation Polyvalente, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, France
| | - Emilie Bérard
- Service d'Epidémiologie, Centre Hospitalier Universitaire de Toulouse, France.,UMR 1027, INSERM-Université de Toulouse III, France
| | - Emmanuel Griessinger
- Université Côte d'Azur, INSERM U1065, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Clément Larrue
- Cancer Research Center of Toulouse, UMR1037-INSERM, ERL5294 CNRS, France
| | - Pierre Luc Mouchel
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, France.,Cancer Research Center of Toulouse, UMR1037-INSERM, ERL5294 CNRS, France
| | - François Vergez
- Université Toulouse III Paul Sabatier, France.,Cancer Research Center of Toulouse, UMR1037-INSERM, ERL5294 CNRS, France.,Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, France
| | - Suzanne Tavitian
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, France
| | - Edwige Yon
- Service d'Epidémiologie, Centre Hospitalier Universitaire de Toulouse, France
| | - Jean Ruiz
- Service de Réanimation Polyvalente, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, France
| | - Eric Delabesse
- Université Toulouse III Paul Sabatier, France.,Cancer Research Center of Toulouse, UMR1037-INSERM, ERL5294 CNRS, France.,Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, France
| | - Isabelle Luquet
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, France
| | - Laetitia Karine Linares
- IRCM, Institut de Recherche en Cancérologie de Montpellier-INSERM, U1194, France.,Université Montpellier, F-34298, France.,Institut Régional du Cancer Montpellier, France
| | - Estelle Saland
- Cancer Research Center of Toulouse, UMR1037-INSERM, ERL5294 CNRS, France
| | - Martin Carroll
- Stem Cell and Xenograft Core, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Gwenn Danet-Desnoyers
- Stem Cell and Xenograft Core, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Audrey Sarry
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, France
| | - Françoise Huguet
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, France
| | | | - Christian Récher
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, France .,Université Toulouse III Paul Sabatier, France.,Cancer Research Center of Toulouse, UMR1037-INSERM, ERL5294 CNRS, France
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43
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Affiliation(s)
- Andrea Ventura
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lukas E. Dow
- Department of Medicine, Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY 10021, USA
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44
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New tools for old drugs: Functional genetic screens to optimize current chemotherapy. Drug Resist Updat 2018; 36:30-46. [PMID: 29499836 PMCID: PMC5844649 DOI: 10.1016/j.drup.2018.01.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/29/2017] [Accepted: 01/06/2018] [Indexed: 12/26/2022]
Abstract
Despite substantial advances in the treatment of various cancers, many patients still receive anti-cancer therapies that hardly eradicate tumor cells but inflict considerable side effects. To provide the best treatment regimen for an individual patient, a major goal in molecular oncology is to identify predictive markers for a personalized therapeutic strategy. Regarding novel targeted anti-cancer therapies, there are usually good markers available. Unfortunately, however, targeted therapies alone often result in rather short remissions and little cytotoxic effect on the cancer cells. Therefore, classical chemotherapy with frequent long remissions, cures, and a clear effect on cancer cell eradication remains a corner stone in current anti-cancer therapy. Reliable biomarkers which predict the response of tumors to classical chemotherapy are rare, in contrast to the situation for targeted therapy. For the bulk of cytotoxic therapeutic agents, including DNA-damaging drugs, drugs targeting microtubules or antimetabolites, there are still no reliable biomarkers used in the clinic to predict tumor response. To make progress in this direction, meticulous studies of classical chemotherapeutic drug action and resistance mechanisms are required. For this purpose, novel functional screening technologies have emerged as successful technologies to study chemotherapeutic drug response in a variety of models. They allow a systematic analysis of genetic contributions to a drug-responsive or −sensitive phenotype and facilitate a better understanding of the mode of action of these drugs. These functional genomic approaches are not only useful for the development of novel targeted anti-cancer drugs but may also guide the use of classical chemotherapeutic drugs by deciphering novel mechanisms influencing a tumor’s drug response. Moreover, due to the advances of 3D organoid cultures from patient tumors and in vivo screens in mice, these genetic screens can be applied using conditions that are more representative of the clinical setting. Patient-derived 3D organoid lines furthermore allow the characterization of the “essentialome”, the specific set of genes required for survival of these cells, of an individual tumor, which could be monitored over the course of treatment and help understanding how drug resistance evolves in clinical tumors. Thus, we expect that these functional screens will enable the discovery of novel cancer-specific vulnerabilities, and through clinical validation, move the field of predictive biomarkers forward. This review focuses on novel advanced techniques to decipher the interplay between genetic alterations and drug response.
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45
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Bertoli S, Tavitian S, Huynh A, Borel C, Guenounou S, Luquet I, Delabesse E, Sarry A, Laurent G, Attal M, Huguet F, Bérard E, Récher C. Improved outcome for AML patients over the years 2000-2014. Blood Cancer J 2017; 7:635. [PMID: 29184070 PMCID: PMC5802565 DOI: 10.1038/s41408-017-0011-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/12/2017] [Accepted: 09/15/2017] [Indexed: 12/15/2022] Open
Abstract
Few recent studies from registries have reported an improvement in overall survival of younger patients with acute myeloid leukemia (AML). However, reasons for this improvement are not defined. We analyzed the therapeutic course and outcome of 976 patients treated by intensive chemotherapy between 2000 and 2014. The number of patients receiving allogeneic stem cell transplantation in first or second response significantly increased over time whereas autologous transplantation was progressively abandoned. In the 513 younger patients, there were no differences in first complete response, induction failure, incidence of relapse, or non-relapse mortality over time. The period of time was significantly associated with a better overall survival especially in 2010–2014. The 2010–2014 period effect was still significant in multivariate analysis and was independent of allogeneic stem cell transplantation. In the 463 older patients, there was a significant interaction between the period and leukocytosis in multivariate analysis meaning that the 2010–2014 period had only an impact in patients with white blood cell count >50 giga/L for response and overall survival. Progresses have been made in each phase of the therapeutic course of younger AML patients resulting in survival improvement. In older patients, the outcome of hyperleukocytic patients has significantly improved in 2010–2014.
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Affiliation(s)
- Sarah Bertoli
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Cancer Research Center of Toulouse, UMR1037-INSERM, ERL5294 CNRS, Toulouse, France
| | - Suzanne Tavitian
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Anne Huynh
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Cécile Borel
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Sarah Guenounou
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Isabelle Luquet
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Eric Delabesse
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Audrey Sarry
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Guy Laurent
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France
| | - Michel Attal
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France
| | - Françoise Huguet
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Emilie Bérard
- Service d'Epidémiologie, Centre Hospitalier Universitaire de Toulouse, Toulouse, France.,UMR 1027, INSERM-Université de Toulouse III, Toulouse, France
| | - Christian Récher
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France. .,Université Toulouse III Paul Sabatier, Toulouse, France. .,Cancer Research Center of Toulouse, UMR1037-INSERM, ERL5294 CNRS, Toulouse, France.
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46
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Kurata M, Yamamoto K, Moriarity BS, Kitagawa M, Largaespada DA. CRISPR/Cas9 library screening for drug target discovery. J Hum Genet 2017; 63:179-186. [DOI: 10.1038/s10038-017-0376-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 12/26/2022]
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47
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Irwin CR, Hitt MM, Evans DH. Targeting Nucleotide Biosynthesis: A Strategy for Improving the Oncolytic Potential of DNA Viruses. Front Oncol 2017; 7:229. [PMID: 29018771 PMCID: PMC5622948 DOI: 10.3389/fonc.2017.00229] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/07/2017] [Indexed: 12/14/2022] Open
Abstract
The rapid growth of tumors depends upon elevated levels of dNTPs, and while dNTP concentrations are tightly regulated in normal cells, this control is often lost in transformed cells. This feature of cancer cells has been used to advantage to develop oncolytic DNA viruses. DNA viruses employ many different mechanisms to increase dNTP levels in infected cells, because the low concentration of dNTPs found in non-cycling cells can inhibit virus replication. By disrupting the virus-encoded gene(s) that normally promote dNTP biosynthesis, one can assemble oncolytic versions of these agents that replicate selectively in cancer cells. This review covers the pathways involved in dNTP production, how they are dysregulated in cancer cells, and the various approaches that have been used to exploit this biology to improve the tumor specificity of oncolytic viruses. In particular, we compare and contrast the ways that the different types of oncolytic virus candidates can directly modulate these processes. We limit our review to the large DNA viruses that naturally encode homologs of the cellular enzymes that catalyze dNTP biogenesis. Lastly, we consider how this knowledge might guide future development of oncolytic viruses.
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Affiliation(s)
- Chad R Irwin
- Faculty of Medicine and Dentistry, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada.,Faculty of Medicine and Dentistry, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Mary M Hitt
- Faculty of Medicine and Dentistry, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada.,Faculty of Medicine and Dentistry, Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - David H Evans
- Faculty of Medicine and Dentistry, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada.,Faculty of Medicine and Dentistry, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
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48
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Shang W, Wang F, Fan G, Wang H. Key elements for designing and performing a CRISPR/Cas9-based genetic screen. J Genet Genomics 2017; 44:439-449. [PMID: 28967615 DOI: 10.1016/j.jgg.2017.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/09/2017] [Accepted: 09/04/2017] [Indexed: 12/26/2022]
Abstract
Reverse genetic screens are invaluable for uncovering gene functions, but are traditionally hampered by some technical limitations. Over the past few years, since the advent of the revolutionary CRISPR/Cas9 technology, its power in genome editing has been harnessed to overcome the traditional limitations in reverse genetic screens, with successes in various biological contexts. Here, we outline these CRISPR/Cas9-based screens, provide guidance on the design of effective screens and discuss the potential future directions of development of this field.
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Affiliation(s)
- Wanjing Shang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaofeng Fan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Haopeng Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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