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Mallikarjuna T, Thummadi NB, Vindal V, Manimaran P. Prioritizing cervical cancer candidate genes using chaos game and fractal-based time series approach. Theory Biosci 2024:10.1007/s12064-024-00418-3. [PMID: 38807013 DOI: 10.1007/s12064-024-00418-3] [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: 08/17/2023] [Accepted: 05/14/2024] [Indexed: 05/30/2024]
Abstract
Cervical cancer is one of the most severe threats to women worldwide and holds fourth rank in lethality. It is estimated that 604, 127 cervical cancer cases have been reported in 2020 globally. With advancements in high throughput technologies and bioinformatics, several cervical candidate genes have been proposed for better therapeutic strategies. In this paper, we intend to prioritize the candidate genes that are involved in cervical cancer progression through a fractal time series-based cross-correlations approach. we apply the chaos game representation theory combining a two-dimensional multifractal detrended cross-correlations approach among the known and candidate genes involved in cervical cancer progression to prioritize the candidate genes. We obtained 16 candidate genes that showed cross-correlation with known cancer genes. Functional enrichment analysis of the candidate genes shows that they involve GO terms: biological processes, cell-cell junction assembly, cell-cell junction organization, regulation of cell shape, cortical actin cytoskeleton organization, and actomyosin structure organization. KEGG pathway analysis revealed genes' role in Rap1 signaling pathway, ErbB signaling pathway, MAPK signaling pathway, PI3K-Akt signaling pathway, mTOR signaling pathway, Acute myeloid leukemia, chronic myeloid leukemia, Breast cancer, Thyroid cancer, Bladder cancer, and Gastric cancer. Further, we performed survival analysis and prioritized six genes CDH2, PAIP1, BRAF, EPB41L3, OSMR, and RUNX1 as potential candidate genes for cervical cancer that has a crucial role in tumor progression. We found that our study through this integrative approach an efficient tool and paved a new way to prioritize the candidate genes and these genes could be evaluated experimentally for potential validation. We suggest this may be useful in analyzing the nucleotide sequences and protein sequences for clustering, classification, class affiliation, etc.
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Affiliation(s)
- T Mallikarjuna
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - N B Thummadi
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Vaibhav Vindal
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - P Manimaran
- School of Physics, University of Hyderabad, Gachibowli, Hyderabad, Telangana, 500046, India.
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2
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Ong SY, Wang L. Leveraging genomics, transcriptomics and epigenomics to understand chemoimmunotherapy resistance in chronic lymphocytic leukemia. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2024; 7:7. [PMID: 38434768 PMCID: PMC10905154 DOI: 10.20517/cdr.2023.98] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Patients with chronic lymphocytic leukemia (CLL) have differing clinical outcomes. Recent advances integrating multi-omic data have uncovered molecular subtypes in CLL with different prognostic implications and may allow better prediction of therapy response. While finite-duration chemoimmunotherapy (CIT) has enabled deep responses and prolonged duration of responses in the past, the advent of novel targeted therapy for the treatment of CLL has dramatically changed the therapeutic landscape. In this review, we discuss the latest genomic, transcriptomic, and epigenetic alterations regarded as major drivers of resistance to CIT in CLL. Further advances in genomic medicine will allow for better prediction of response to therapy and provide the basis for rational selection of therapy for long-term remissions with minimal toxicity.
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Affiliation(s)
- Shin Yeu Ong
- Department of Hematology/Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010, USA
- Department of Hematology, Singapore General Hospital, Singapore 169608, Singapore
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
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3
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Schmid VK, Hobeika E. B cell receptor signaling and associated pathways in the pathogenesis of chronic lymphocytic leukemia. Front Oncol 2024; 14:1339620. [PMID: 38469232 PMCID: PMC10926848 DOI: 10.3389/fonc.2024.1339620] [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: 11/16/2023] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
B cell antigen receptor (BCR) signaling is a key driver of growth and survival in both normal and malignant B cells. Several lines of evidence support an important pathogenic role of the BCR in chronic lymphocytic leukemia (CLL). The significant improvement of CLL patients' survival with the use of various BCR pathway targeting inhibitors, supports a crucial involvement of BCR signaling in the pathogenesis of CLL. Although the treatment landscape of CLL has significantly evolved in recent years, no agent has clearly demonstrated efficacy in patients with treatment-refractory CLL in the long run. To identify new drug targets and mechanisms of drug action in neoplastic B cells, a detailed understanding of the molecular mechanisms of leukemic transformation as well as CLL cell survival is required. In the last decades, studies of genetically modified CLL mouse models in line with CLL patient studies provided a variety of exciting data about BCR and BCR-associated kinases in their role in CLL pathogenesis as well as disease progression. BCR surface expression was identified as a particularly important factor regulating CLL cell survival. Also, BCR-associated kinases were shown to provide a crosstalk of the CLL cells with their tumor microenvironment, which highlights the significance of the cells' milieu in the assessment of disease progression and treatment. In this review, we summarize the major findings of recent CLL mouse as well as patient studies in regard to the BCR signalosome and discuss its relevance in the clinics.
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Affiliation(s)
| | - Elias Hobeika
- Institute of Immunology, Ulm University, Ulm, Germany
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4
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Ecker V, Brandmeier L, Stumpf M, Giansanti P, Moreira AV, Pfeuffer L, Fens MHAM, Lu J, Kuster B, Engleitner T, Heidegger S, Rad R, Ringshausen I, Zenz T, Wendtner CM, Müschen M, Jellusova J, Ruland J, Buchner M. Negative feedback regulation of MAPK signaling is an important driver of chronic lymphocytic leukemia progression. Cell Rep 2023; 42:113017. [PMID: 37792532 DOI: 10.1016/j.celrep.2023.113017] [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: 03/13/2023] [Revised: 06/08/2023] [Accepted: 08/06/2023] [Indexed: 10/06/2023] Open
Abstract
Despite available targeted treatments for the disease, drug-resistant chronic lymphocytic leukemia (CLL) poses a clinical challenge. The objective of this study is to examine whether the dual-specific phosphatases DUSP1 and DUSP6 are required to negatively regulate mitogen-activated protein kinases (MAPKs) and thus counterbalance excessive MAPK activity. We show that high expression of DUSP6 in CLL correlates with poor clinical prognosis. Importantly, genetic deletion of the inhibitory phosphatase DUSP1 or DUSP6 and blocking DUSP1/6 function using a small-molecule inhibitor reduces CLL cell survival in vitro and in vivo. Using global phospho-proteome approaches, we observe acute activation of MAPK signaling by DUSP1/6 inhibition. This promotes accumulation of mitochondrial reactive oxygen species and, thereby, DNA damage and apoptotic cell death in CLL cells. Finally, we observe that DUSP1/6 inhibition is particularly effective against treatment-resistant CLL and therefore suggest transient DUSP1/6 inhibition as a promising treatment concept to eliminate drug-resistant CLL cells.
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Affiliation(s)
- Veronika Ecker
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany
| | - Lisa Brandmeier
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany
| | - Martina Stumpf
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany
| | - Piero Giansanti
- TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany; Bavarian Center for Biomolecular Mass Spectrometry at the University hospital rechts der Isar (BayBioMS@MRI), Technical University of Munich, Munich, Germany
| | - Aida Varela Moreira
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lisa Pfeuffer
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany
| | - Marcel H A M Fens
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Junyan Lu
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany; Bavarian Center for Biomolecular Mass Spectrometry at the University hospital rechts der Isar (BayBioMS@MRI), Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), Munich Partner Site, Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Engleitner
- TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany; Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Simon Heidegger
- TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany; Department of Medicine III, School of Medicine, Technical University of Munich, Munich, Germany
| | - Roland Rad
- TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany; German Cancer Consortium (DKTK), Munich Partner Site, Munich, Germany; Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Ingo Ringshausen
- Wellcome Trust/MRC Cambridge Stem Cell Institute and Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AH, UK
| | - Thorsten Zenz
- Department of Medical Oncology and Hematology, University Hospital and University of Zurich, 8091 Zurich, Switzerland
| | - Clemens-Martin Wendtner
- Munich Clinic Schwabing, Academic Teaching Hospital, Ludwig-Maximilian University (LMU), Munich, Germany
| | - Markus Müschen
- Center of Molecular and Cellular Oncology, Yale School of Medicine, 300 George Street, New Haven, CT 06520, USA
| | - Julia Jellusova
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany
| | - Jürgen Ruland
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany; German Cancer Consortium (DKTK), Munich Partner Site, Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Maike Buchner
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany.
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5
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da Silva JCL, Saldanha-Araujo F, de Melo RCB, Vicari HP, Silva-Carvalho AE, Rego EM, Buccheri V, Machado-Neto JA. Ezrin is highly expressed and a druggable target in chronic lymphocytic leukemia. Life Sci 2022; 311:121146. [DOI: 10.1016/j.lfs.2022.121146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/17/2022] [Accepted: 10/29/2022] [Indexed: 11/06/2022]
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6
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Yu Z, Su H, Chen J, Hu G. Deciphering Conformational Changes of the GDP-Bound NRAS Induced by Mutations G13D, Q61R, and C118S through Gaussian Accelerated Molecular Dynamic Simulations. Molecules 2022; 27:molecules27175596. [PMID: 36080363 PMCID: PMC9457619 DOI: 10.3390/molecules27175596] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022] Open
Abstract
The conformational changes in switch domains significantly affect the activity of NRAS. Gaussian-accelerated molecular dynamics (GaMD) simulations of three separate replicas were performed to decipher the effects of G13D, Q16R, and C118S on the conformational transformation of the GDP-bound NRAS. The analyses of root-mean-square fluctuations and dynamics cross-correlation maps indicated that the structural flexibility and motion modes of the switch domains involved in the binding of NRAS to effectors are highly altered by the G13D, Q61R, and C118Smutations. The free energy landscapes (FELs) suggested that mutations induce more energetic states in NRAS than the GDP-bound WT NRAS and lead to high disorder in the switch domains. The FELs also indicated that the different numbers of sodium ions entering the GDP binding regions compensate for the changes in electrostatic environments caused by mutations, especially for G13D. The GDP–residue interactions revealed that the disorder in the switch domains was attributable to the unstable hydrogen bonds between GDP and two residues, V29 and D30. This work is expected to provide information on the energetic basis and dynamics of conformational changes in switch domains that can aid in deeply understanding the target roles of NRAS in anticancer treatment.
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Affiliation(s)
- Zhiping Yu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Hongyi Su
- Laoling People's Hospital, Dezhou 253600, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
- Laoling People's Hospital, Dezhou 253600, China
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7
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Pérez‐Carretero C, Hernández‐Sánchez M, González T, Quijada‐Álamo M, Martín‐Izquierdo M, Santos‐Mínguez S, Miguel‐García C, Vidal M, García‐De‐Coca A, Galende J, Pardal E, Aguilar C, Vargas‐Pabón M, Dávila J, Gascón‐Y‐Marín I, Hernández‐Rivas J, Benito R, Hernández‐Rivas J, Rodríguez‐Vicente A. TRAF3 alterations are frequent in del-3'IGH chronic lymphocytic leukemia patients and define a specific subgroup with adverse clinical features. Am J Hematol 2022; 97:903-914. [PMID: 35472012 DOI: 10.1002/ajh.26578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/11/2022] [Accepted: 04/17/2022] [Indexed: 11/08/2022]
Abstract
Interstitial 14q32 deletions involving IGH gene are infrequent events in chronic lymphocytic leukemia (CLL), affecting less than 5% of patients. To date, little is known about their clinical impact and molecular underpinnings, and its mutational landscape is currently unknown. In this work, a total of 871 CLLs were tested for the IGH break-apart probe, and 54 (6.2%) had a 300 kb deletion of 3'IGH (del-3'IGH CLLs), which contributed to a shorter time to first treatment (TFT). The mutational analysis by next-generation sequencing of 317 untreated CLLs (54 del-3'IGH and 263 as the control group) showed high mutational frequencies of NOTCH1 (30%), ATM (20%), genes involved in the RAS signaling pathway (BRAF, KRAS, NRAS, and MAP2K1) (15%), and TRAF3 (13%) within del-3'IGH CLLs. Notably, the incidence of TRAF3 mutations was significantly higher in del-3'IGH CLLs than in the control group (p < .001). Copy number analysis also revealed that TRAF3 loss was highly enriched in CLLs with 14q deletion (p < .001), indicating a complete biallelic inactivation of this gene through deletion and mutation. Interestingly, the presence of mutations in the aforementioned genes negatively refined the prognosis of del-3'IGH CLLs in terms of overall survival (NOTCH1, ATM, and RAS signaling pathway genes) and TFT (TRAF3). Furthermore, TRAF3 biallelic inactivation constituted an independent risk factor for TFT in the entire CLL cohort. Altogether, our work demonstrates the distinct genetic landscape of del-3'IGH CLL with multiple molecular pathways affected, characterized by a TRAF3 biallelic inactivation that contributes to a marked poor outcome in this subgroup of patients.
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Affiliation(s)
- Claudia Pérez‐Carretero
- Universidad de Salamanca, IBSAL, IBMCC‐ Centro de Investigación del Cáncer (USAL‐CSIC) Salamanca Spain
- Servicio de Hematología Hospital Universitario de Salamanca Salamanca Spain
| | - María Hernández‐Sánchez
- Universidad de Salamanca, IBSAL, IBMCC‐ Centro de Investigación del Cáncer (USAL‐CSIC) Salamanca Spain
- Servicio de Hematología Hospital Universitario de Salamanca Salamanca Spain
| | - Teresa González
- Universidad de Salamanca, IBSAL, IBMCC‐ Centro de Investigación del Cáncer (USAL‐CSIC) Salamanca Spain
- Servicio de Hematología Hospital Universitario de Salamanca Salamanca Spain
| | - Miguel Quijada‐Álamo
- Universidad de Salamanca, IBSAL, IBMCC‐ Centro de Investigación del Cáncer (USAL‐CSIC) Salamanca Spain
- Servicio de Hematología Hospital Universitario de Salamanca Salamanca Spain
| | - Marta Martín‐Izquierdo
- Universidad de Salamanca, IBSAL, IBMCC‐ Centro de Investigación del Cáncer (USAL‐CSIC) Salamanca Spain
- Servicio de Hematología Hospital Universitario de Salamanca Salamanca Spain
| | - Sandra Santos‐Mínguez
- Universidad de Salamanca, IBSAL, IBMCC‐ Centro de Investigación del Cáncer (USAL‐CSIC) Salamanca Spain
- Servicio de Hematología Hospital Universitario de Salamanca Salamanca Spain
| | - Cristina Miguel‐García
- Universidad de Salamanca, IBSAL, IBMCC‐ Centro de Investigación del Cáncer (USAL‐CSIC) Salamanca Spain
- Servicio de Hematología Hospital Universitario de Salamanca Salamanca Spain
| | | | | | | | - Emilia Pardal
- Servicio de Hematología Hospital Virgen del Puerto Plasencia Spain
| | - Carlos Aguilar
- Servicio de Hematología, Complejo Hospitalario de Soria Soria Spain
| | | | - Julio Dávila
- Servicio de Hematología Hospital Nuestra Señora de Sonsoles Ávila Spain
| | - Isabel Gascón‐Y‐Marín
- Servicio de Hematología, Hospital Universitario Infanta Leonor Universidad Complutense Madrid Spain
| | | | - Rocío Benito
- Universidad de Salamanca, IBSAL, IBMCC‐ Centro de Investigación del Cáncer (USAL‐CSIC) Salamanca Spain
- Servicio de Hematología Hospital Universitario de Salamanca Salamanca Spain
| | - Jesús‐María Hernández‐Rivas
- Universidad de Salamanca, IBSAL, IBMCC‐ Centro de Investigación del Cáncer (USAL‐CSIC) Salamanca Spain
- Servicio de Hematología Hospital Universitario de Salamanca Salamanca Spain
| | - Ana‐Eugenia Rodríguez‐Vicente
- Universidad de Salamanca, IBSAL, IBMCC‐ Centro de Investigación del Cáncer (USAL‐CSIC) Salamanca Spain
- Servicio de Hematología Hospital Universitario de Salamanca Salamanca Spain
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Yim J, Koh J, Kim S, Song SG, Bae JM, Yun H, Sung JY, Kim TM, Park SH, Jeon YK. Clinicopathologic and Genetic Features of Primary T-cell Lymphomas of the Central Nervous System: An Analysis of 11 Cases Using Targeted Gene Sequencing. Am J Surg Pathol 2022; 46:486-497. [PMID: 34980830 PMCID: PMC8923358 DOI: 10.1097/pas.0000000000001859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Primary central nervous system lymphoma (PCNSL) of peripheral T-cell lineage (T-PCNSL) is rare, and its genetic and clinicopathologic features remain unclear. Here, we present 11 cases of T-PCNSL in immunocompetent individuals from a single institute, focusing on their genetic alterations. Seven cases were subject to targeted panel sequencing covering 120 lymphoma-related genes. Nine of the eleven cases were classified as peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS), of which one was of γδT-cell lineage. There was one case of anaplastic lymphoma kinase-positive anaplastic large cell lymphoma and another of extranodal natural killer (NK)/T-cell lymphoma (ENKTL) of αβT-cell lineage. The male to female ratio was 7 : 4 and the age ranged from 3 to 75 years (median, 61 y). Most patients presented with neurological deficits (n=10) and showed multifocal lesions (n=9) and deep brain structure involvement (n=9). Tumor cells were mostly small-to-medium, and T-cell monoclonality was detected in all nine evaluated cases. PTCL-NOS was CD4-positive (n=4), CD8-positive (n=3), mixed CD4-positive and CD8-positive (n=1), or CD4/CD8-double-negative (n=1, γδT-cell type). Cytotoxic molecule expression was observed in 4 (67%) of the 6 evaluated cases. Pathogenic alterations were found in 4 patients: one PTCL-NOS case had a frameshift mutation in KMT2C, another PTCL-NOS case harbored a truncating mutation in TET2, and another (γδT-cell-PTCL-NOS) harbored NRAS G12S and JAK3 M511I mutations, and homozygous deletions of CDKN2A and CDKN2B. The ENKTL (αβT-cell lineage) case harbored mutations in genes ARID1B, FAS, TP53, BCOR, KMT2C, POT1, and PRDM1. In conclusion, most of the T-PCNSL were PTCL-NOS, but sporadic cases of other subtypes including γδT-cell lymphoma, anaplastic lymphoma kinase-positive anaplastic large cell lymphoma, and ENKTL were also encountered. Immunophenotypic analysis, clonality test, and targeted gene sequencing along with clinicoradiologic evaluation, may be helpful for establishing the diagnosis of T-PCNSL. Moreover, this study demonstrates genetic alterations with potential diagnostic and therapeutic utility in T-PCNSL.
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MESH Headings
- Adolescent
- Adult
- Aged
- Anaplastic Lymphoma Kinase/metabolism
- Central Nervous System Neoplasms/genetics
- Central Nervous System Neoplasms/metabolism
- Central Nervous System Neoplasms/pathology
- Child
- Child, Preschool
- Female
- Humans
- Lymphoma, Extranodal NK-T-Cell/genetics
- Lymphoma, Extranodal NK-T-Cell/metabolism
- Lymphoma, Extranodal NK-T-Cell/pathology
- Lymphoma, Large-Cell, Anaplastic/genetics
- Lymphoma, Large-Cell, Anaplastic/metabolism
- Lymphoma, Large-Cell, Anaplastic/pathology
- Lymphoma, T-Cell, Peripheral/genetics
- Lymphoma, T-Cell, Peripheral/metabolism
- Lymphoma, T-Cell, Peripheral/pathology
- Male
- Middle Aged
- Young Adult
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Affiliation(s)
| | - Jiwon Koh
- Department of Pathology
- Center for Precision Medicine, Seoul National University Hospital
| | - Sehui Kim
- Department of Pathology
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine
| | | | - Jeong Mo Bae
- Department of Pathology
- Center for Precision Medicine, Seoul National University Hospital
| | - Hongseok Yun
- Center for Precision Medicine, Seoul National University Hospital
| | - Ji-Youn Sung
- Department of Pathology, Kyung Hee University School of Medicine
| | - Tae Min Kim
- Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | | | - Yoon Kyung Jeon
- Department of Pathology
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
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9
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Oscier D, Stamatopoulos K, Mirandari A, Strefford J. The Genomics of Hairy Cell Leukaemia and Splenic Diffuse Red Pulp Lymphoma. Cancers (Basel) 2022; 14:697. [PMID: 35158965 PMCID: PMC8833447 DOI: 10.3390/cancers14030697] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/12/2022] Open
Abstract
Classical hairy cell leukaemia (HCLc), its variant form (HCLv), and splenic diffuse red pulp lymphoma (SDRPL) constitute a subset of relatively indolent B cell tumours, with low incidence rates of high-grade transformations, which primarily involve the spleen and bone marrow and are usually associated with circulating tumour cells characterised by villous or irregular cytoplasmic borders. The primary aim of this review is to summarise their cytogenetic, genomic, immunogenetic, and epigenetic features, with a particular focus on the clonal BRAFV600E mutation, present in most cases currently diagnosed with HCLc. We then reflect on their cell of origin and pathogenesis as well as present the clinical implications of improved biological understanding, extending from diagnosis to prognosis assessment and therapy response.
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Affiliation(s)
- David Oscier
- Department of Haematology, Royal Bournemouth and Christchurch NHS Trust, Bournemouth BH7 7DW, UK
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology-Hellas, 57001 Thessaloniki, Greece;
| | - Amatta Mirandari
- Cancer Genomics Group, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK; (A.M.); (J.S.)
| | - Jonathan Strefford
- Cancer Genomics Group, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK; (A.M.); (J.S.)
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10
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Vendramini E, Bomben R, Pozzo F, Bittolo T, Tissino E, Gattei V, Zucchetto A. KRAS and RAS-MAPK Pathway Deregulation in Mature B Cell Lymphoproliferative Disorders. Cancers (Basel) 2022; 14:cancers14030666. [PMID: 35158933 PMCID: PMC8833570 DOI: 10.3390/cancers14030666] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
KRAS mutations account for the most frequent mutations in human cancers, and are generally correlated with disease aggressiveness, poor prognosis, and poor response to therapies. KRAS is required for adult hematopoiesis and plays a key role in B cell development and mature B cell proliferation and survival, proved to be critical for B cell receptor-induced ERK pathway activation. In mature B cell neoplasms, commonly seen in adults, KRAS and RAS-MAPK pathway aberrations occur in a relevant fraction of patients, reaching high recurrence in some specific subtypes like multiple myeloma and hairy cell leukemia. As inhibitors targeting the RAS-MAPK pathway are being developed and improved, it is of outmost importance to precisely identify all subgroups of patients that could potentially benefit from their use. Herein, we review the role of KRAS and RAS-MAPK signaling in malignant hematopoiesis, focusing on mature B cell lymphoproliferative disorders. We discuss KRAS and RAS-MAPK pathway aberrations describing type, incidence, mutual exclusion with other genetic abnormalities, and association with prognosis. We review the current therapeutic strategies applied in mature B cell neoplasms to counteract RAS-MAPK signaling in pre-clinical and clinical studies, including most promising combination therapies. We finally present an overview of genetically engineered mouse models bearing KRAS and RAS-MAPK pathway aberrations in the hematopoietic compartment, which are valuable tools in the understanding of cancer biology and etiology.
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11
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Kolijn PM, Muggen AF, Ljungström V, Agathangelidis A, Wolvers-Tettero ILM, Beverloo HB, Pál K, Hengeveld PJ, Darzentas N, Hendriks RW, van Dongen JJM, Rosenquist R, Langerak AW. Consistent B Cell Receptor Immunoglobulin Features Between Siblings in Familial Chronic Lymphocytic Leukemia. Front Oncol 2021; 11:740083. [PMID: 34513715 PMCID: PMC8427434 DOI: 10.3389/fonc.2021.740083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
Key processes in the onset and evolution of chronic lymphocytic leukemia (CLL) are thought to include chronic (antigenic) activation of mature B cells through the B cell receptor (BcR), signals from the microenvironment, and acquisition of genetic alterations. Here we describe three families in which two or more siblings were affected by CLL. We investigated whether there are immunogenetic similarities in the leukemia-specific immunoglobulin heavy (IGH) and light (IGL/IGK) chain gene rearrangements of the siblings in each family. Furthermore, we performed array analysis to study if similarities in CLL-associated chromosomal aberrations are present within each family and screened for somatic mutations using paired tumor/normal whole-genome sequencing (WGS). In two families a consistent IGHV gene mutational status (one IGHV-unmutated, one IGHV-mutated) was observed. Intriguingly, the third family with four affected siblings was characterized by usage of the lambda IGLV3-21 gene, with the hallmark R110 mutation of the recently described clinically aggressive IGLV3-21R110 subset. In this family, the CLL-specific rearrangements in two siblings could be assigned to either stereotyped subset #2 or the immunogenetically related subset #169, both of which belong to the broader IGLV3-21R110 subgroup. Consistent patterns of cytogenetic aberrations were encountered in all three families. Furthermore, the CLL clones carried somatic mutations previously associated with IGHV mutational status, cytogenetic aberrations and stereotyped subsets, respectively. From these findings, we conclude that similarities in immunogenetic characteristics in familial CLL, in combination with genetic aberrations acquired, point towards shared underlying mechanisms behind CLL development within each family.
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Affiliation(s)
- P Martijn Kolijn
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Alice F Muggen
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Ingrid L M Wolvers-Tettero
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - H Berna Beverloo
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Karol Pál
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Paul J Hengeveld
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Nikos Darzentas
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | | | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden
| | - Anton W Langerak
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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12
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Thummadi NB, T M, Vindal V, P M. Prioritizing the candidate genes related to cervical cancer using the moment of inertia tensor. Proteins 2021; 90:363-371. [PMID: 34468998 DOI: 10.1002/prot.26226] [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: 06/14/2021] [Revised: 08/07/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022]
Abstract
It is well known that cervical cancer poses the fourth most malignancy threat to women worldwide among all cancer types. There is a tremendous improvement in realizing the underlying molecular associations in cervical cancer. Several studies reported pieces of evidence for the involvement of various genes in the disease progression. However, with the ever-evolving bioinformatics tools, there has been an upsurge in predicting numerous genes responsible for cervical cancer progression and making it highly complex to target the genes for further evaluation. In this article, we prioritized the candidate genes based on the sequence similarity analysis with known cancer genes. For this purpose, we used the concept of the moment of inertia tensor, which reveals the similarities between the protein sequences more efficiently. Tensor for moment of inertia explores the similarity of the protein sequences based on the physicochemical properties of amino acids. From our analysis, we obtained 14 candidate cervical cancer genes, which are highly similar to known cervical cancer genes. Further, we analyzed the GO terms and prioritized these genes based on the number of hits with biological process, molecular functions, and their involvement in KEGG pathways. We also discussed the evidence-based involvement of the prioritized genes in other cancers and listed the available drugs for those genes.
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Affiliation(s)
- Neelesh Babu Thummadi
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
| | - Mallikarjuna T
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
| | - Vaibhav Vindal
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
| | - Manimaran P
- School of Physics, University of Hyderabad, Gachibowli, Hyderabad, India
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13
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Else M, Blakemore SJ, Strefford JC, Catovsky D. The association between deaths from infection and mutations of the BRAF, FBXW7, NRAS and XPO1 genes: a report from the LRF CLL4 trial. Leukemia 2021; 35:2563-2569. [PMID: 33580200 PMCID: PMC7880018 DOI: 10.1038/s41375-021-01165-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/12/2021] [Accepted: 01/26/2021] [Indexed: 11/22/2022]
Abstract
Causes of death, in particular deaths due to infection, have not been widely studied in randomised trials in chronic lymphocytic leukaemia. With long-term follow-up (median 13 years) we examined the cause of death in 600/777 patients in the LRF CLL4 trial. Blood samples, taken at randomisation from 499 patients, were available for identifying gene mutations. Infection was a cause of death in 258 patients (43%). Patients dying of infection were more likely than those who died of other causes to have received ≥2 lines of treatment (194/258 [75%] versus 231/342 [68%], P = 0.04) and to have died in the winter months (149/258 [58%] versus 166/342 [49%], P = 0.03), respectively. In patients with mutation data, the factors significantly associated with death from infection versus all other deaths were 11q deletion (47/162 [29%] versus 40/209 [19%], P = 0.03) and mutations of the BRAF, FBXW7, NRAS and XPO1 genes. Death was caused by an infection in 46/67 assessable patients (69%) who had a mutation of one or more of these four genes versus only 129/333 patients (39%) without any of these mutations (odds ratio: 3.46 [95% CI 1.98-6.07] P < 0.0001). Careful management of infection risk, including prophylaxis against infection, may be important in patients who carry these mutations.
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Affiliation(s)
- Monica Else
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Stuart J Blakemore
- Cancer Genomics, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Jonathan C Strefford
- Cancer Genomics, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Daniel Catovsky
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
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14
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López-Oreja I, Playa-Albinyana H, Arenas F, López-Guerra M, Colomer D. Challenges with Approved Targeted Therapies against Recurrent Mutations in CLL: A Place for New Actionable Targets. Cancers (Basel) 2021; 13:3150. [PMID: 34202439 PMCID: PMC8269088 DOI: 10.3390/cancers13133150] [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: 05/05/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 12/17/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by a high degree of genetic variability and interpatient heterogeneity. In the last decade, novel alterations have been described. Some of them impact on the prognosis and evolution of patients. The approval of BTK inhibitors, PI3K inhibitors and Bcl-2 inhibitors has drastically changed the treatment of patients with CLL. The effect of these new targeted therapies has been widely analyzed in TP53-mutated cases, but few data exist about the response of patients carrying other recurrent mutations. In this review, we describe the biological pathways recurrently altered in CLL that might have an impact on the response to these new therapies together with the possibility to use new actionable targets to optimize treatment responses.
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Affiliation(s)
- Irene López-Oreja
- Experimental Therapies in Lymphoid Neoplasms, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (I.L.-O.); (H.P.-A.); (F.A.); (M.L.-G.)
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), 28029 Madrid, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08005 Barcelona, Spain
| | - Heribert Playa-Albinyana
- Experimental Therapies in Lymphoid Neoplasms, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (I.L.-O.); (H.P.-A.); (F.A.); (M.L.-G.)
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), 28029 Madrid, Spain
| | - Fabián Arenas
- Experimental Therapies in Lymphoid Neoplasms, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (I.L.-O.); (H.P.-A.); (F.A.); (M.L.-G.)
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), 28029 Madrid, Spain
| | - Mónica López-Guerra
- Experimental Therapies in Lymphoid Neoplasms, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (I.L.-O.); (H.P.-A.); (F.A.); (M.L.-G.)
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), 28029 Madrid, Spain
- Hematopathology Section, Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain
| | - Dolors Colomer
- Experimental Therapies in Lymphoid Neoplasms, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (I.L.-O.); (H.P.-A.); (F.A.); (M.L.-G.)
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), 28029 Madrid, Spain
- Hematopathology Section, Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain
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15
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Sarkar MK, Kar A, Jayaraman A, Kar Mahapatra S, Vadivel V. Vitexin isolated from Prosopis cineraria leaves induce apoptosis in K-562 leukemia cells via inhibition of the BCR-ABL-Ras-Raf pathway. J Pharm Pharmacol 2021; 74:103-111. [PMID: 34109977 DOI: 10.1093/jpp/rgab085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/14/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Leukemia is one of the severe cancer types all around the globe. Even though some chemotherapeutic drugs are available for treating leukemia, they have various side effects. As an alternative approach, herbal drugs are focused on current research to overcome leukemia. The present work was conducted to investigate the antileukemic mechanism of active phytochemical vitexin, which was isolated from ethno-medicine (Prosopis cineraria leaf) used by traditional healers of West Bengal, India. METHODS Antiproliferative mechanisms of selected phyto-compound against K-562 cells were evaluated using cellular uptake, morphological changes, DNA fragmentation, mitochondrial membrane potential and signaling pathways analysis. KEY FINDINGS Vitexin exhibited cytotoxicity by reducing mitochondrial membrane potential (32.40%) and causing DNA fragmentation (84.15%). The western blotting study indicated inhibition of cell survival proteins (BCR, ABL, H-RAS, N-RAS, K-RAS and RAF) and expression of apoptotic proteins (p38, BAX and caspase-9) in leukemia cells upon treatment with vitexin. CONCLUSIONS Based on the results, presently investigated phyto-compound vitexin could be considered for developing safe and natural drugs to treat leukemia after conducting suitable preclinical and clinical trials.
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Affiliation(s)
- Monaj Kumar Sarkar
- Chemical Biology Lab (ASK-II-409), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Thanjavur, India
| | - Amrita Kar
- Medicinal Chemistry and Immunology Lab (ASK-II-406), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Thanjavur, India
| | - Adithyan Jayaraman
- Medicinal Chemistry and Immunology Lab (ASK-II-406), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Thanjavur, India
| | - Santanu Kar Mahapatra
- Medicinal Chemistry and Immunology Lab (ASK-II-406), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Thanjavur, India
| | - Vellingiri Vadivel
- Chemical Biology Lab (ASK-II-409), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Thanjavur, India
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16
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Reid JC, Golubeva D, Boyd AL, Hollands CG, Henly C, Orlando L, Leber A, Hébert J, Morabito F, Cutrona G, Agnelli L, Gentile M, Ferrarini M, Neri A, Leber B, Bhatia M. Human pluripotent stem cells identify molecular targets of trisomy 12 in chronic lymphocytic leukemia patients. Cell Rep 2021; 34:108845. [PMID: 33730576 DOI: 10.1016/j.celrep.2021.108845] [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: 06/11/2020] [Revised: 01/13/2021] [Accepted: 02/17/2021] [Indexed: 10/21/2022] Open
Abstract
Identifying precise targets of individual cancers remains challenging. Chronic lymphocytic leukemia (CLL) represents the most common adult hematologic malignancy, and trisomy 12 (tri12) represents a quarter of CLL patients. We report that tri12 human pluripotent stem cells (hPSCs) allow for the identification of gene networks and targets specific to tri12, which are controlled by comparative normal PSCs. Identified targets are upregulated in tri12 leukemic cells from a cohort of 159 patients with monoclonal B cell lymphocytosis and CLL. tri12 signaling patterns significantly influence progression-free survival. Actionable targets are identified using high-content drug testing and functionally validated in an additional 44 CLL patient samples. Using xenograft models, interleukin-1 receptor-associated kinase 4 (IRAK4) inhibitor is potent and selective against human tri12 CLL versus healthy patient-derived xenografts. Our study uses hPSCs to uncover targets from genetic aberrations and apply them to cancer. These findings provide immediate translational potential as biomarkers and targets for therapeutic intervention.
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Affiliation(s)
- Jennifer C Reid
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Diana Golubeva
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Allison L Boyd
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Cameron G Hollands
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Charisa Henly
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Luca Orlando
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Andrew Leber
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Josée Hébert
- Department of Medicine, Université de Montréal, Montreal, QC, Canada; Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada
| | - Fortunato Morabito
- Department of Onco-Hematology, Biotechnology Research Unit, AO of Cosenza, Cosenza, Italy; Hematology and Bone Marrow Transplant Unit, Augusta Victoria Hospital, Jerusalem, Israel
| | - Giovanna Cutrona
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Luca Agnelli
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy; Department of Onco-Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy; Pathobiology Unit 2, IRCCS National Cancer Institute, Milan, Italy
| | - Massimo Gentile
- Department of Onco-Hematology, Biotechnology Research Unit, AO of Cosenza, Cosenza, Italy
| | - Manlio Ferrarini
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Antonino Neri
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy; Department of Onco-Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Brian Leber
- Department of Medicine, McMaster University, Juravinski Hospital, Hamilton, ON, Canada
| | - Mickie Bhatia
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
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17
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Targeting KRAS in Cancer: Promising Therapeutic Strategies. Cancers (Basel) 2021; 13:cancers13061204. [PMID: 33801965 PMCID: PMC7999304 DOI: 10.3390/cancers13061204] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/05/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Since the Kirsten rat sarcoma viral oncogene homolog (KRAS) is mutated in about 25% of all human cancers and is at the center of pathways involved in tumorigenesis, it is necessary to compile and highlight the novel therapeutic strategies behind targeting this oncoprotein in cancer. Over the years, many have studied various methods to directly target KRAS with no success. Fortunately, there has been more success in targeting other proteins along the RAS pathway to yield a therapeutic response. However, some recent findings show promising results indicating that we are one step closer to developing an effective inhibitor that directly targets KRAS. The review presented here summarizes these recent findings and emphasizes the need to continue the search for the most optimal KRAS inhibitor that can be used to treat and potentially even cure certain tumor types. Abstract The Kirsten rat sarcoma viral oncogene homolog (KRAS) is mutated in approximately 25% of all human cancers and is known to be a major player promoting and maintaining tumorigenesis through the RAS/MAPK pathway. Over the years, a large number of studies have identified strategies at different regulatory levels to tackle this ‘difficult-to-target’ oncoprotein. Yet, the most ideal strategy to overcome KRAS and its downstream effects has yet to be uncovered. This review summarizes the role of KRAS activating mutations in multiple cancer types as well as the key findings for potential strategies inhibiting its oncogenic behavior. A comprehensive analysis of the different pathways and mechanisms associated with KRAS activity in tumors will ultimately pave the way for promising future work that will identify optimum therapeutic strategies.
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18
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Uprety D, Adjei AA. KRAS: From undruggable to a druggable Cancer Target. Cancer Treat Rev 2020; 89:102070. [DOI: 10.1016/j.ctrv.2020.102070] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 02/07/2023]
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19
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Biernacki MA, Bleakley M. Neoantigens in Hematologic Malignancies. Front Immunol 2020; 11:121. [PMID: 32117272 PMCID: PMC7033457 DOI: 10.3389/fimmu.2020.00121] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/16/2020] [Indexed: 12/18/2022] Open
Abstract
T cell cancer neoantigens are created from peptides derived from cancer-specific aberrant proteins, such as mutated and fusion proteins, presented in complex with human leukocyte antigens on the cancer cell surface. Because expression of the aberrant target protein is exclusive to malignant cells, immunotherapy directed against neoantigens should avoid “on-target, off-tumor” toxicity. The efficacy of neoantigen vaccines in melanoma and glioblastoma and of adoptive transfer of neoantigen-specific T cells in epithelial tumors indicates that neoantigens are valid therapeutic targets. Improvements in sequencing technology and innovations in antigen discovery approaches have facilitated the identification of neoantigens. In comparison to many solid tumors, hematologic malignancies have few mutations and thus fewer potential neoantigens. Despite this, neoantigens have been identified in a wide variety of hematologic malignancies. These include mutated nucleophosmin1 and PML-RARA in acute myeloid leukemia, ETV6-RUNX1 fusions and other mutated proteins in acute lymphoblastic leukemia, BCR-ABL1 fusions in chronic myeloid leukemia, driver mutations in myeloproliferative neoplasms, immunoglobulins in lymphomas, and proteins derived from patient-specific mutations in chronic lymphoid leukemias. We will review advances in the field of neoantigen discovery, describe the spectrum of identified neoantigens in hematologic malignancies, and discuss the potential of these neoantigens for clinical translation.
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Affiliation(s)
- Melinda A Biernacki
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Medicine, University of Washington, Seattle, WA, United States
| | - Marie Bleakley
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States
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20
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Wang F, Liu T, Wang L, Gu Z, Yang N, Luo L, Zhu C, Li M, Liu D, Gao C. Unmanipulated haploidentical peripheral blood stem cell transplantation for patients with Philadelphia-negative acute lymphoblastic leukaemia in first complete remission. Leuk Lymphoma 2019; 61:118-127. [PMID: 31519118 DOI: 10.1080/10428194.2019.1660965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Haploidentical peripheral blood stem cell transplantation (Haplo-PBSCT) is a promising treatment option for patients with Ph-negative acute lymphoblastic leukemia (ALL). In this study, we retrospectively analyzed data from Ph-negative ALL patients who underwent haplo-PBSCT during their first complete remission (CR1), and compared the long-term outcomes between the standard-risk and high-risk patients. The 3-year probability of relapse was 7.6% and 16.7% for the standard- and high-risk group (p = .274). The 3-year probability of disease-free survival (DFS) and overall survival (OS) for the standard-risk versus high-risk groups were 84.6% versus 50% (p = .0063) and 92.3% versus 61.1% (p = .046), respectively. Univariate analysis showed that a diagnosis of high risk with fusion/mutation genes were associated with worse outcomes, which was confirmed by multivariate analysis (p = .016). In summary, haplo-PBSCT may be a promising alternative for patients with Ph-negative ALL in CR1, although the fusion/mutation genes in high-risk patients may relatively impair the long-term efficacy compared with standard-risk patients.
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Affiliation(s)
- Feiyan Wang
- Medical School, Nankai University, Tianjin, China.,Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Tong Liu
- Inpatient Department, 66242 Army Hospital, Xilin Gol, China
| | - Li Wang
- Department of Hematology and Oncology, Chinese PLA 401 Hospital, Qingdao, China
| | - Zhenyang Gu
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Nan Yang
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Lan Luo
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Chengying Zhu
- Medical School, Nankai University, Tianjin, China.,Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Meng Li
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Daihong Liu
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Chunji Gao
- Medical School, Nankai University, Tianjin, China.,Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
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