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Assis AJB, Santana BLDO, Gualberto ACM, Pittella-Silva F. Therapeutic applications of CRISPR/Cas9 mediated targeted gene editing in acute lymphoblastic leukemia: current perspectives, future challenges, and clinical implications. Front Pharmacol 2023; 14:1322937. [PMID: 38130408 PMCID: PMC10733529 DOI: 10.3389/fphar.2023.1322937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Acute Lymphoblastic Leukemia (ALL) is the predominant hematological malignancy in pediatric populations, originating from B- or T-cell precursors within the bone marrow. The disease exhibits a high degree of heterogeneity, both at the molecular level and in terms of clinical presentation. A complex interplay between inherited and acquired genetic alterations contributes to disease pathogenesis, often resulting in the disruption of cellular functions integral to the leukemogenic process. The advent of CRISPR/Cas9 as a gene editing tool has revolutionized biological research, underscoring its potential to modify specific genomic loci implicated in cancer. Enhanced understanding of molecular alterations in ALL has facilitated significant advancements in therapeutic strategies. In this review, we scrutinize the application of CRISPR/Cas9 as a tool for identifying genetic targets to improve therapy, circumvent drug resistance, and facilitate CAR-T cell-based immunotherapy. Additionally, we discuss the challenges and future prospects of CRISPR/Cas9 applications in ALL.
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Affiliation(s)
| | | | | | - Fabio Pittella-Silva
- Laboratory of Molecular Pathology of Cancer, Faculty of Health Sciences and Medicine, University of Brasília, Brasília, Brazil
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2
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Sharma G, Tran TM, Bansal I, Beg MS, Bhardwaj R, Bassi J, Tan Y, Jaiswal AK, Tso C, Jain A, Singh J, Chattopadhyay P, Singh A, Chopra A, Bakhshi S, Casero D, Rao DS, Palanichamy JK. RNA binding protein IGF2BP1 synergizes with ETV6-RUNX1 to drive oncogenic signaling in B-cell Acute Lymphoblastic Leukemia. J Exp Clin Cancer Res 2023; 42:231. [PMID: 37670323 PMCID: PMC10478443 DOI: 10.1186/s13046-023-02810-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 08/27/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Acute lymphoblastic leukemia (ALL) is the most common pediatric hematological malignancy, with ETV6::RUNX1 being the most prevalent translocation whose exact pathogenesis remains unclear. IGF2BP1 (Insulin-like Growth Factor 2 Binding Protein 1) is an oncofetal RNA binding protein seen to be specifically overexpressed in ETV6::RUNX1 positive B-ALL. In this study, we have studied the mechanistic role of IGF2BP1 in leukemogenesis and its synergism with the ETV6::RUNX1 fusion protein. METHODS Gene expression was analyzed from patient bone marrow RNA using Real Time RT-qPCR. Knockout cell lines were created using CRISPR-Cas9 based lentiviral vectors. RNA-Seq and RNA Immunoprecipitation sequencing (RIP-Seq) after IGF2BP1 pulldown were performed using the Illumina platform. Mouse experiments were done by retroviral overexpression of donor HSCs followed by lethal irradiation of recipients using a bone marrow transplant model. RESULTS We observed specific overexpression of IGF2BP1 in ETV6::RUNX1 positive patients in an Indian cohort of pediatric ALL (n=167) with a positive correlation with prednisolone resistance. IGF2BP1 expression was essential for tumor cell survival in multiple ETV6::RUNX1 positive B-ALL cell lines. Integrated analysis of transcriptome sequencing after IGF2BP1 knockout and RIP-Seq after IGF2BP1 pulldown in Reh cell line revealed that IGF2BP1 targets encompass multiple pro-oncogenic signalling pathways including TNFα/NFκB and PI3K-Akt pathways. These pathways were also dysregulated in primary ETV6::RUNX1 positive B-ALL patient samples from our center as well as in public B-ALL patient datasets. IGF2BP1 showed binding and stabilization of the ETV6::RUNX1 fusion transcript itself. This positive feedback loop led to constitutive dysregulation of several oncogenic pathways. Enforced co-expression of ETV6::RUNX1 and IGF2BP1 in mouse bone marrow resulted in marrow hypercellularity which was characterized by multi-lineage progenitor expansion and strong Ki67 positivity. This pre-leukemic phenotype confirmed their synergism in-vivo. Clonal expansion of cells overexpressing both ETV6::RUNX1 and IGF2BP1 was clearly observed. These mice also developed splenomegaly indicating extramedullary hematopoiesis. CONCLUSION Our data suggest a combined impact of the ETV6::RUNX1 fusion protein and RNA binding protein, IGF2BP1 in activating multiple oncogenic pathways in B-ALL which makes IGF2BP1 and these pathways as attractive therapeutic targets and biomarkers.
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Affiliation(s)
- Gunjan Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Tiffany M Tran
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Ishu Bansal
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Mohammad Sabique Beg
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Ruchi Bhardwaj
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Jaspal Bassi
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Yuande Tan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Amit Kumar Jaiswal
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Christine Tso
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Ayushi Jain
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Jay Singh
- Department of Laboratory Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Parthaprasad Chattopadhyay
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Archna Singh
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Anita Chopra
- Department of Laboratory Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Sameer Bakhshi
- Department of Medical Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - David Casero
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dinesh S Rao
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Jayanth Kumar Palanichamy
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India.
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Pillsbury CE, Dougan J, Rabe JL, Fonseca JA, Zhou C, Evans AN, Abukharma H, Ichoku O, Gonzalez-Flamenco G, Park SI, Aljudi A, DeRyckere D, Castellino SM, Rafiq S, Langermann S, Liu LN, Henry CJ, Porter CC. Siglec-15 Promotes Evasion of Adaptive Immunity in B-cell Acute Lymphoblastic Leukemia. CANCER RESEARCH COMMUNICATIONS 2023; 3:1248-1259. [PMID: 37465593 PMCID: PMC10351425 DOI: 10.1158/2767-9764.crc-23-0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/28/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023]
Abstract
Siglec-15 (Sig15) has been implicated as an immune checkpoint expressed in solid tumor-infiltrating macrophages and is being targeted in clinical trials with mAbs to normalize the tumor immune microenvironment and stimulate antitumor immunity. However, the role of Sig15 in hematologic malignancies remains undefined. Sig15 mRNA and protein expression levels in hematologic malignancies were determined from publicly available databases, cell lines, and primary patient samples. Human B-cell acute lymphoblastic leukemia (B-ALL) cell lines were used to identify signaling pathways involved in the regulation of Sig15 expression. Secreted/soluble Sig15 and cytokine levels were measured from the plasma of children with leukemia and healthy controls. Knockdown and knockout of Siglec15 in a murine model of B-ALL was used to evaluate the effect of leukemia-derived Sig15 on the immune response to leukemia. We observed pathologic overexpression of Sig15 in a variety of hematologic malignancies, including primary B-ALL samples. This overexpression was driven by NFκB activation, which also increased the surface localization of Sig15. Secreted/soluble Sig15 was found to circulate at elevated levels in the plasma of children with B-ALL and correlated with an immune-suppressive cytokine milieu. Genetic inhibition of Sig15 in murine B-ALL promoted clearance of the leukemia by the immune system and a marked reversal of the immune-privileged leukemia bone marrow niche, including expanded early effector CD8+ T cells and reduction of immunosuppressive cytokines. Thus, Sig15 is a novel, potent immunosuppressive molecule active in leukemia that may be targeted therapeutically to activate T lymphocytes against leukemia cells. Significance We demonstrate that Sig15 is overexpressed in hematologic malignancies driven by NFκB, is required for immune evasion in a mouse model of leukemia, and, for the first time, that it circulates at high levels in the plasma of children with leukemia.
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Affiliation(s)
- Claire E. Pillsbury
- Cancer Biology Program, Laney Graduate School, Emory University, Atlanta, Georgia
| | - Jodi Dougan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Jennifer L. Rabe
- Molecular Biology Program, University of Colorado Denver, Aurora, Colorado
| | - Jairo A. Fonseca
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Chengjing Zhou
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Alyssa N. Evans
- Winship Cancer Institute, Emory University, Atlanta, Georgia
| | | | | | | | - Sunita I. Park
- Clinical Laboratory, Children's Healthcare of Atlanta, Atlanta, Georgia
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia
| | - Ahmed Aljudi
- Clinical Laboratory, Children's Healthcare of Atlanta, Atlanta, Georgia
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia
| | - Deborah DeRyckere
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
- Winship Cancer Institute, Emory University, Atlanta, Georgia
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Sharon M. Castellino
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
- Winship Cancer Institute, Emory University, Atlanta, Georgia
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Sarwish Rafiq
- Winship Cancer Institute, Emory University, Atlanta, Georgia
| | | | | | - Curtis J. Henry
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
- Winship Cancer Institute, Emory University, Atlanta, Georgia
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Christopher C. Porter
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
- Winship Cancer Institute, Emory University, Atlanta, Georgia
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia
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Renosi F, Callanan M, Lefebvre C. Genetics and Epigenetics in Neoplasms with Plasmacytoid Dendritic Cells. Cancers (Basel) 2022; 14:cancers14174132. [PMID: 36077669 PMCID: PMC9454802 DOI: 10.3390/cancers14174132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Differential diagnosis between Blastic pDC Neoplasm (BPDCN) and Acute Myeloid Leukemia with pDC expansion (pDC-AML) is particularly challenging, and genomic features can help in diagnosis. This review aims at clarifying recent data on genomics features because the past five years have generated a large amount of original data regarding pDC neoplasms. The genetic landscape of BPDCN is now well-defined, with important updates concerning MYC/MYC rearrangements, but also epigenetic defects and novel concepts in oncogenic and immune pathways. Concerning pDC-AML, they now appear to exhibit an original mutation landscape, especially with RUNX1 mutations, which is of interest for diagnostic criteria and for therapeutic purposes. We highlight here these two different profiles, which contribute to differential diagnosis between BPDCN and pDC-AML. This point is particularly important for the study of different therapeutic strategies between BPDCN and AML. Abstract Plasmacytoid Dendritic Cells (pDC) are type I interferon (IFN)-producing cells that play a key role in immune responses. Two major types of neoplastic counterparts for pDC are now discriminated: Blastic pDC Neoplasm (BPDCN) and Mature pDC Proliferation (MPDCP), associated with myeloid neoplasm. Two types of MPDCP are now better described: Chronic MyeloMonocytic Leukemia with pDC expansion (pDC-CMML) and Acute Myeloid Leukemia with pDC expansion (pDC-AML). Differential diagnosis between pDC-AML and BPDCN is particularly challenging, and genomic features can help for diagnosis. Here, we systematically review the cytogenetic, molecular, and transcriptional characteristics of BPDCN and pDC-AML. BPDCN are characterized by frequent complex karyotypes with recurrent MYB/MYC rearrangements as well as recurrent deletions involving ETV6, IKZF1, RB1, and TP53 loci. Epigenetic and splicing pathways are also particularly mutated, while original processes are dysregulated, such as NF-kB, TCF4, BCL2, and IFN pathways; neutrophil-specific receptors; and cholinergic signaling. In contrast, cytogenetic abnormalities are limited in pDC-AML and are quite similar to other AML. Interestingly, RUNX1 is the most frequently mutated gene (70% of cases). These typical genomic features are of potential interest for diagnosis, and also from a prognostic or therapeutic perspective.
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Affiliation(s)
- Florian Renosi
- INSERM, EFS BFC, UMR1098 RIGHT, University of Bourgogne Franche-Comté, F-25000 Besancon, France
- Laboratoire d’Hématologie et d’Immunologie Régional, Etablissement Français du Sang Bourgogne Franche-Comté, F-25000 Besancon, France
- Correspondence:
| | - Mary Callanan
- INSERM 1231 and 1209, University of Bourgogne-Franche Comté, F-21000 Dijon, France
- Service d’Oncologie Génétique, CHU Dijon Bourgogne, F-21000 Dijon, France
| | - Christine Lefebvre
- INSERM 1209 and CNRS UMR 5309, Université Grenoble-Alpes, F-38000 Grenoble, France
- Laboratoire de Génétique des hémopathies, Institut de Biologie et de Pathologie, CHU Grenoble Alpes, F-38000 Grenoble, France
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Maimaitiyiming Y, Ye L, Yang T, Yu W, Naranmandura H. Linear and Circular Long Non-Coding RNAs in Acute Lymphoblastic Leukemia: From Pathogenesis to Classification and Treatment. Int J Mol Sci 2022; 23:ijms23084442. [PMID: 35457264 PMCID: PMC9033105 DOI: 10.3390/ijms23084442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 02/07/2023] Open
Abstract
The coding regions account for only a small part of the human genome, and the remaining vast majority of the regions generate large amounts of non-coding RNAs. Although non-coding RNAs do not code for any protein, they are suggested to work as either tumor suppressers or oncogenes through modulating the expression of genes and functions of proteins at transcriptional, posttranscriptional and post-translational levels. Acute Lymphoblastic Leukemia (ALL) originates from malignant transformed B/T-precursor-stage lymphoid progenitors in the bone marrow (BM). The pathogenesis of ALL is closely associated with aberrant genetic alterations that block lymphoid differentiation and drive abnormal cell proliferation as well as survival. While treatment of pediatric ALL represents a major success story in chemotherapy-based elimination of a malignancy, adult ALL remains a devastating disease with relatively poor prognosis. Thus, novel aspects in the pathogenesis and progression of ALL, especially in the adult population, need to be further explored. Accumulating evidence indicated that genetic changes alone are rarely sufficient for development of ALL. Recent advances in cytogenic and sequencing technologies revealed epigenetic alterations including that of non-coding RNAs as cooperating events in ALL etiology and progression. While the role of micro RNAs in ALL has been extensively reviewed, less attention, relatively, has been paid to other non-coding RNAs. Herein, we review the involvement of linear and circular long non-coding RNAs in the etiology, maintenance, and progression of ALL, highlighting the contribution of these non-coding RNAs in ALL classification and diagnosis, risk stratification as well as treatment.
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Affiliation(s)
- Yasen Maimaitiyiming
- The Affiliated Sir Run Run Shaw Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (Y.M.); (L.Y.); (T.Y.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou 310058, China
| | - Linyan Ye
- The Affiliated Sir Run Run Shaw Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (Y.M.); (L.Y.); (T.Y.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Tao Yang
- The Affiliated Sir Run Run Shaw Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (Y.M.); (L.Y.); (T.Y.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Wenjuan Yu
- Department of Hematology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Correspondence: (W.Y.); (H.N.)
| | - Hua Naranmandura
- The Affiliated Sir Run Run Shaw Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (Y.M.); (L.Y.); (T.Y.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
- Department of Hematology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
- Correspondence: (W.Y.); (H.N.)
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Lin TC. RUNX1 and cancer. Biochim Biophys Acta Rev Cancer 2022; 1877:188715. [DOI: 10.1016/j.bbcan.2022.188715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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Fang F, Jia R, Liu C, Zhao H, Sun W. Genetic analysis and clinical significance of a rare t(1;12)(q21;p13) in a patient with high-risk myelodysplastic syndrome. Mol Genet Genomic Med 2022; 10:e1893. [PMID: 35192745 PMCID: PMC9000942 DOI: 10.1002/mgg3.1893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 01/07/2022] [Accepted: 01/25/2022] [Indexed: 11/24/2022] Open
Abstract
To explore the genetic and clinical features of a rare t(1;12)(q21;p13) in a patient with myelodysplastic syndrome (MDS). A 53‐year‐old male was diagnosed as high‐risk MDS, and died in a short period. A complete cytogenetic analysis of bone marrow by conventional G‐banding karyotyping was performed at the time of initial evaluation. On the basis of chromosome karyotype, interphase and metaphase fluorescence in‐situ hybridization (FISH) were carried out to further confirm the abnormal karyotypes. Reverse‐transcription polymerase chain reaction (RT‐PCR) was performed to determine ETV6/ARNT fusion gene status. G‐banding revealed karyotype 47, XY, +8, der(12) t(1;12)(q21;p13). FISH with the centromere 8 probe verified the trisomy 8, and the ETV 6 break‐apart probe suggested heterozygous loss of ETV6 allele located in short arm of chromosome 12. Subsequently, the painting probe of whole chromosome 12 further confirmed the part break of short arm of chromosome 12, and the 1q21/1p36 probe yielded three signals of 1q21 and two signals of 1p36. The results of FISH were in accordance with the karyotype completely. No ETV6/ARNT fusion gene was detected by PCR. T(1;12)(q21;p13) is a rare abnormal karyotype, and the limited reports cannot supply definite clinical significance. Rapid deterioration of our case suggests this translocation of chromosome might have a poor effect on the survival of MDS.
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Affiliation(s)
- Fang Fang
- Department of Hematology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Ru Jia
- Department of Hematology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Congyan Liu
- Department of Hematology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Hong Zhao
- Department of Hematology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Wanling Sun
- Department of Hematology, Xuanwu Hospital, Capital Medical University, Beijing, China
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Solayappan M, Azlan A, Khor KZ, Yik MY, Khan M, Yusoff NM, Moses EJ. Utilization of CRISPR-Mediated Tools for Studying Functional Genomics in Hematological Malignancies: An Overview on the Current Perspectives, Challenges, and Clinical Implications. Front Genet 2022; 12:767298. [PMID: 35154242 PMCID: PMC8834884 DOI: 10.3389/fgene.2021.767298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/17/2021] [Indexed: 11/26/2022] Open
Abstract
Hematological malignancies (HM) are a group of neoplastic diseases that are usually heterogenous in nature due to the complex underlying genetic aberrations in which collaborating mutations enable cells to evade checkpoints that normally safeguard it against DNA damage and other disruptions of healthy cell growth. Research regarding chromosomal structural rearrangements and alterations, gene mutations, and functionality are currently being carried out to understand the genomics of these abnormalities. It is also becoming more evident that cross talk between the functional changes in transcription and proteins gives the characteristics of the disease although specific mutations may induce unique phenotypes. Functional genomics is vital in this aspect as it measures the complete genetic change in cancerous cells and seeks to integrate the dynamic changes in these networks to elucidate various cancer phenotypes. The advent of CRISPR technology has indeed provided a superfluity of benefits to mankind, as this versatile technology enables DNA editing in the genome. The CRISPR-Cas9 system is a precise genome editing tool, and it has revolutionized methodologies in the field of hematology. Currently, there are various CRISPR systems that are used to perform robust site-specific gene editing to study HM. Furthermore, experimental approaches that are based on CRISPR technology have created promising tools for developing effective hematological therapeutics. Therefore, this review will focus on diverse applications of CRISPR-based gene-editing tools in HM and its potential future trajectory. Collectively, this review will demonstrate the key roles of different CRISPR systems that are being used in HM, and the literature will be a representation of a critical step toward further understanding the biology of HM and the development of potential therapeutic approaches.
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Affiliation(s)
- Maheswaran Solayappan
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong, Malaysia
| | - Adam Azlan
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
- *Correspondence: Emmanuel Jairaj Moses,
| | - Kang Zi Khor
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Mot Yee Yik
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Matiullah Khan
- Department of Pathology, Faculty of Medicine, AIMST University, Bedong, Malaysia
| | - Narazah Mohd Yusoff
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Emmanuel Jairaj Moses
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
- *Correspondence: Emmanuel Jairaj Moses,
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Ahmadi SE, Rahimi S, Zarandi B, Chegeni R, Safa M. MYC: a multipurpose oncogene with prognostic and therapeutic implications in blood malignancies. J Hematol Oncol 2021; 14:121. [PMID: 34372899 PMCID: PMC8351444 DOI: 10.1186/s13045-021-01111-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/12/2021] [Indexed: 12/17/2022] Open
Abstract
MYC oncogene is a transcription factor with a wide array of functions affecting cellular activities such as cell cycle, apoptosis, DNA damage response, and hematopoiesis. Due to the multi-functionality of MYC, its expression is regulated at multiple levels. Deregulation of this oncogene can give rise to a variety of cancers. In this review, MYC regulation and the mechanisms by which MYC adjusts cellular functions and its implication in hematologic malignancies are summarized. Further, we also discuss potential inhibitors of MYC that could be beneficial for treating hematologic malignancies.
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Affiliation(s)
- Seyed Esmaeil Ahmadi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Rahimi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Bahman Zarandi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rouzbeh Chegeni
- Medical Laboratory Sciences Program, College of Health and Human Sciences, Northern Illinois University, DeKalb, IL, USA.
| | - Majid Safa
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran.
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.
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Björk C, Subramanian N, Liu J, Acosta JR, Tavira B, Eriksson AB, Arner P, Laurencikiene J. An RNAi Screening of Clinically Relevant Transcription Factors Regulating Human Adipogenesis and Adipocyte Metabolism. Endocrinology 2021; 162:6272286. [PMID: 33963396 PMCID: PMC8197287 DOI: 10.1210/endocr/bqab096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 12/13/2022]
Abstract
CONTEXT Healthy hyperplasic (many but smaller fat cells) white adipose tissue (WAT) expansion is mediated by recruitment, proliferation and/or differentiation of new fat cells. This process (adipogenesis) is controlled by transcriptional programs that have been mostly identified in rodents. OBJECTIVE A systemic investigation of adipogenic human transcription factors (TFs) that are relevant for metabolic conditions has not been revealed previously. METHODS TFs regulated in WAT by obesity, adipose morphology, cancer cachexia, and insulin resistance were selected from microarrays. Their role in differentiation of human adipose tissue-derived stem cells (hASC) was investigated by RNA interference (RNAi) screen. Lipid accumulation, cell number, and lipolysis were measured for all screened factors (148 TFs). RNA (RNAseq), protein (Western blot) expression, insulin, and catecholamine responsiveness were examined in hASC following siRNA treatment of selected target TFs. RESULTS Analysis of TFs regulated by metabolic conditions in human WAT revealed that many of them belong to adipogenesis-regulating pathways. The RNAi screen identified 39 genes that affected fat cell differentiation in vitro, where 11 genes were novel. Of the latter JARID2 stood out as being necessary for formation of healthy fat cell metabolic phenotype by regulating expression of multiple fat cell phenotype-specific genes. CONCLUSION This comprehensive RNAi screening in hASC suggests that a large proportion of WAT TFs that are impacted by metabolic conditions might be important for hyperplastic adipose tissue expansion. The screen also identified JARID2 as a novel TF essential for the development of functional adipocytes.
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Affiliation(s)
- Christel Björk
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, SE-14186, Sweden
| | - Narmadha Subramanian
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, SE-14186, Sweden
| | - Jianping Liu
- Karolinska High Throughput Center, Department of Medical Biochemistry and Biophysics (MBB), Division of Functional Genomics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Juan Ramon Acosta
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, SE-14186, Sweden
| | - Beatriz Tavira
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, SE-14186, Sweden
| | - Anders B Eriksson
- Karolinska High Throughput Center, Department of Medical Biochemistry and Biophysics (MBB), Division of Functional Genomics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Peter Arner
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, SE-14186, Sweden
| | - Jurga Laurencikiene
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, SE-14186, Sweden
- Correspondence: Jurga Laurencikiene, PhD, Karolinska Institutet, Lipid laboratory, Dept. of Medicine Huddinge (MedH), NEO, Hälsovägen 9/Blickagången 16, 14183 Huddinge, Sweden.
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Comprehensive Custom NGS Panel Validation for the Improvement of the Stratification of B-Acute Lymphoblastic Leukemia Patients. J Pers Med 2020; 10:jpm10030137. [PMID: 32967112 PMCID: PMC7565730 DOI: 10.3390/jpm10030137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/13/2020] [Accepted: 09/19/2020] [Indexed: 01/06/2023] Open
Abstract
Background: B-acute lymphoblastic leukemia (B-ALL) is a hematological neoplasm of the stem lymphoid cell of the B lineage, characterized by the presence of genetic alterations closely related to the course of the disease. The number of alterations identified in these patients grows as studies of the disease progress, but in clinical practice, the conventional techniques frequently used are only capable of detecting the most common alterations. However, techniques, such as next-generation sequencing (NGS), are being implemented to detect a wide spectrum of new alterations that also include point mutations. Methods: In this study, we designed and validated a comprehensive custom NGS panel to detect the main genetic alterations present in the disease in a single step. For this purpose, 75 B-ALL diagnosis samples from patients previously characterized by standard-of-care diagnostic techniques were sequenced. Results: The use of the custom NGS panel allowed the correct detection of the main genetic alterations present in B-ALL patients, including the presence of an aneuploid clone in 14 of the samples and some of the recurrent fusion genes in 35 of the samples. The panel was also able to successfully detect a number of secondary alterations, such as single nucleotide variants (SNVs) and copy number variations (CNVs) in 66 and 46 of the samples analyzed, respectively, allowing for further refinement of the stratification of patients. The custom NGS panel could also detect alterations with a high level of sensitivity and reproducibility when the findings obtained by NGS were compared with those obtained from other conventional techniques. Conclusions: The use of this custom NGS panel allows us to quickly and efficiently detect the main genetic alterations present in B-ALL patients in a single assay (SNVs and insertions/deletions (INDELs), recurrent fusion genes, CNVs, aneuploidies, and single nucleotide polymorphisms (SNPs) associated with pharmacogenetics). The application of this panel would thus allow us to speed up and simplify the molecular diagnosis of patients, helping patient stratification and management.
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Biswas A, Rajesh Y, Mitra P, Mandal M. ETV6 gene aberrations in non-haematological malignancies: A review highlighting ETV6 associated fusion genes in solid tumors. Biochim Biophys Acta Rev Cancer 2020; 1874:188389. [PMID: 32659251 DOI: 10.1016/j.bbcan.2020.188389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/23/2020] [Accepted: 07/01/2020] [Indexed: 10/23/2022]
Abstract
ETV6 (translocation-Ets-leukemia virus) gene is a transcriptional repressor mainly involved in haematopoiesis and maintenance of vascular networks and has developed to be a major oncogene with the potential ability of forming fusion partners with many other genes with carcinogenic consequences. ETV6 fusions function primarily by constitutive activation of kinase activity of the fusion partners, modifications in the normal functions of ETV6 transcription factor, loss of function of ETV6 or the partner gene and activation of a proto-oncogene near the site of translocation. The role of ETV6 fusion gene in tumorigenesis has been well-documented and more variedly found in haematological malignancies. However, the role of the ETV6 oncogene in solid tumors has also risen to prominence due to an increasing number of cases being reported with this malignancy. Since, solid tumors can be well-targeted, the diagnosis of this genre of tumors based on ETV6 malignancy is of crucial importance for treatment. This review highlights the important ETV6 associated fusions in solid tumors along with critical insights as to existing and novel means of targeting it. A consolidation of novel therapies such as immune, gene, RNAi, stem cell therapy and protein degradation hitherto unused in the case of ETV6 solid tumor malignancies may open further therapeutic avenues.
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Affiliation(s)
- Angana Biswas
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Yetirajam Rajesh
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Mahitosh Mandal
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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