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van Outersterp I, Tasian SK, Reichert CEJ, Boeree A, de Groot-Kruseman HA, Escherich G, Boer JM, den Boer ML. Tyrosine kinase inhibitor response of ABL-class acute lymphoblastic leukemia: the role of kinase type and SH3 domain. Blood 2024; 143:2178-2189. [PMID: 38394665 DOI: 10.1182/blood.2023023120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/10/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
ABSTRACT Acute lymphoblastic leukemia (ALL) with fusions of ABL-class tyrosine kinase genes other than BCR::ABL1 occurs in ∼3% of children with ALL. The tyrosine kinase genes involved in this BCR::ABL1-like (Ph-like) subtype include ABL1, PDGFRB, ABL2, and CSF1R, each of which has up to 10 described partner genes. ABL-class ALL resembles BCR::ABL1-positive ALL with a similar gene expression profile, poor response to chemotherapy, and sensitivity to tyrosine kinase inhibitors (TKIs). There is a lack of comprehensive data regarding TKI sensitivity in the heterogeneous group of ABL-class ALL. We observed variability in TKI sensitivity within and among each ABL-class tyrosine kinase gene subgroup. We showed that ALL samples with fusions for any of the 4 tyrosine kinase genes were relatively sensitive to imatinib. In contrast, the PDGFRB-fused ALL samples were less sensitive to dasatinib and bosutinib. Variation in ex vivo TKI response within the subset of samples with the same ABL-class tyrosine kinase gene was not associated with the ALL immunophenotype, 5' fusion partner, presence or absence of Src-homology-2/3 domains, or deletions of IKZF1, PAX5, or CDKN2A/B. In conclusion, the tyrosine kinase gene involved in ABL-class ALL is the main determinant of TKI sensitivity and relevant for specific TKI selection.
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Affiliation(s)
| | - Sarah K Tasian
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Aurélie Boeree
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Gabriele Escherich
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Judith M Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Monique L den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Oncology and Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
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2
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Huang Z, Zhang L, Gong X, Li J, Deng S, Cai Z, Tang B, Huang K, Li X, Zhao W, Xu Y, Xuan L, Liu Q, Wang Y, Chen S, Zhou H. An integrated classification of tumor suppressor IKZF1 inactivation and oncogenic activation in Philadelphia chromosome-like acute lymphoblastic leukemia. Hemasphere 2024; 8:e82. [PMID: 38774654 PMCID: PMC11106797 DOI: 10.1002/hem3.82] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/14/2024] [Accepted: 04/11/2024] [Indexed: 05/24/2024] Open
Abstract
Philadelphia chromosome (Ph)-like acute lymphoblastic leukemia (ALL) is recognized for its genetic and clinical diversity. In this study, we identified a novel high-risk subset of Ph-like ALL, characterized by the activation of oncogenic signaling and the inactivation of the tumor suppressor gene IKZF1, resulting in a dismal outcome. The association between cytogenetic aberrations and clinical features was assessed on a cohort of 191 patients with Ph-like ALL. Our findings revealed that patients with inactivation of IKZF1 combined with activation of oncogenic signaling (CRLF2/EPOR/JAK2 rearrangements or p-CRKL/p-STAT5 high expression) had the worst outcome (3-year overall survival [OS] of 28.8% vs. 80.1% for others, p < 0.001; 2-year event-free survival [EFS] of 6.5% vs. 57.0% for others, p < 0.001). Multivariable analysis demonstrated that this high-risk feature was an independent inferior prognostic factor (adjusted hazard ratio for OS = 4.55, 95% confidence interval [CI]: 2.35-8.81, p < 0.001; adjusted hazard ratio for EFS = 3.27, 95% CI: 1.99-5.39, p < 0.001). Allogeneic hematopoietic stem cell transplantation was associated with improved prognoses in patients within the high-risk subgroup. In conclusion, this study identified a clinically distinct entity that possesses effective prognostic features and provides potential guidance for refining risk stratification in Ph-like ALL.
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Affiliation(s)
- Zicong Huang
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
- Guangdong Provincial Clinical Research Center for Hematologic Diseases, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
- Department of HematologyGanzhou People's Hospital (Nanfang Hospital Ganzhou Hospital)GanzhouChina
| | - Ling Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of HematologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Xiaoyuan Gong
- State Key Laboratory of Experimental HematologyInstitute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Jia Li
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
- Guangdong Provincial Clinical Research Center for Hematologic Diseases, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Shiyu Deng
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
- Guangdong Provincial Clinical Research Center for Hematologic Diseases, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Zihong Cai
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
- Guangdong Provincial Clinical Research Center for Hematologic Diseases, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Bingqing Tang
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
- Guangdong Provincial Clinical Research Center for Hematologic Diseases, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Kangyu Huang
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
- Guangdong Provincial Clinical Research Center for Hematologic Diseases, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Xin Li
- Department of Hematology, The Third Xiangya HospitalCentral South UniversityChangshaChina
| | - Weihua Zhao
- Department of HematologyThe First Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Yang Xu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of HematologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Li Xuan
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
- Guangdong Provincial Clinical Research Center for Hematologic Diseases, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Qifa Liu
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
- Guangdong Provincial Clinical Research Center for Hematologic Diseases, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Ying Wang
- State Key Laboratory of Experimental HematologyInstitute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Suning Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of HematologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Hongsheng Zhou
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
- Guangdong Provincial Clinical Research Center for Hematologic Diseases, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
- Department of HematologyGanzhou People's Hospital (Nanfang Hospital Ganzhou Hospital)GanzhouChina
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3
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Podgorica M, Drivet E, Viken JK, Richman A, Vestbøstad J, Szodoray P, Kvam AK, Wik HS, Tjønnfjord GE, Munthe LA, Frietze S, Schjerven H. Transcriptome analysis of primary adult B-cell lineage acute lymphoblastic leukemia identifies pathogenic variants and gene fusions, and predicts subtypes for in depth molecular diagnosis. Eur J Haematol 2024; 112:731-742. [PMID: 38192186 PMCID: PMC10990798 DOI: 10.1111/ejh.14164] [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: 07/25/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND B-cell acute lymphoblastic leukemia (B-ALL) is classified into subgroups based on known driver oncogenes and molecular lesions, including translocations and recurrent mutations. However, the current diagnostic tests do not identify subtypes or oncogenic lesions for all B-ALL samples, creating a heterogeneous B-ALL group of unknown subtypes. METHODS We sorted primary adult B-ALL cells and performed transcriptome analysis by bulk RNA sequencing (RNA-seq). RESULTS Transcriptomic analysis of an adult B-ALL cohort allowed the classification of four patient samples with subtypes that were not previously revealed by standard gene panels. The leukemia of two patients were of the DUX4 subtype and two were CRLF2+ Ph-like B-ALL. Furthermore, single nucleotide variant analysis detected the oncogenic NRAS-G12D, KRAS-G12D, and KRAS-G13D mutations in three of the patient samples, presenting targetable mutations. Additional oncogenic variants and gene fusions were uncovered, as well as multiple variants in the PDE4DIP gene across five of the patient samples. CONCLUSION We demonstrate that RNA-seq is an effective tool for precision medicine in B-ALL by providing comprehensive molecular profiling of leukemia cells, identifying subtype and oncogenic lesions, and stratifying patients for appropriate therapy.
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Affiliation(s)
- Mirjam Podgorica
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Elsa Drivet
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jonas Krag Viken
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Laboratory Medicine, University of California San Francisco, CA, USA
| | - Alyssa Richman
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, USA
| | - Johanne Vestbøstad
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Peter Szodoray
- B Cell Receptor Signaling Group (BCRSG), Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Ann Kristin Kvam
- Department of Haematology, Oslo University Hospital, Oslo, Norway
| | | | - Geir E. Tjønnfjord
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Haematology, Oslo University Hospital, Oslo, Norway
| | - Ludvig A. Munthe
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, USA
| | - Hilde Schjerven
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Laboratory Medicine, University of California San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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4
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Jiménez C, Garrote-de-Barros A, López-Portugués C, Hernández-Sánchez M, Díez P. Characterization of Human B Cell Hematological Malignancies Using Protein-Based Approaches. Int J Mol Sci 2024; 25:4644. [PMID: 38731863 PMCID: PMC11083628 DOI: 10.3390/ijms25094644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
The maturation of B cells is a complex, multi-step process. During B cell differentiation, errors can occur, leading to the emergence of aberrant versions of B cells that, finally, constitute a malignant tumor. These B cell malignancies are classified into three main groups: leukemias, myelomas, and lymphomas, the latter being the most heterogeneous type. Since their discovery, multiple biological studies have been performed to characterize these diseases, aiming to define their specific features and determine potential biomarkers for diagnosis, stratification, and prognosis. The rise of advanced -omics approaches has significantly contributed to this end. Notably, proteomics strategies appear as promising tools to comprehensively profile the final molecular effector of these cells. In this narrative review, we first introduce the main B cell malignancies together with the most relevant proteomics approaches. Then, we describe the core studies conducted in the field and their main findings and, finally, we evaluate the advantages and drawbacks of flow cytometry, mass cytometry, and mass spectrometry for the profiling of human B cell disorders.
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Affiliation(s)
- Cristina Jiménez
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain;
| | - Alba Garrote-de-Barros
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.G.-d.-B.); (M.H.-S.)
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, 28029 Madrid, Spain
| | - Carlos López-Portugués
- Department of Physical and Analytical Chemistry Chemistry, Faculty of Chemistry, University of Oviedo, 33006 Oviedo, Spain;
- Health Research Institute of the Principality of Asturias (ISPA), 33011 Oviedo, Spain
| | - María Hernández-Sánchez
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.G.-d.-B.); (M.H.-S.)
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, 28029 Madrid, Spain
| | - Paula Díez
- Department of Physical and Analytical Chemistry Chemistry, Faculty of Chemistry, University of Oviedo, 33006 Oviedo, Spain;
- Health Research Institute of the Principality of Asturias (ISPA), 33011 Oviedo, Spain
- Department of Functional Biology, Faculty of Medicine and Health Science, University of Oviedo, 33006 Oviedo, Spain
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5
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van Outersterp I, Boer JM, van de Ven C, Reichert CEJ, Boeree A, Kruisinga B, de Groot-Kruseman HA, Escherich G, Sijs-Szabo A, Rijneveld AW, den Boer ML. Tyrosine kinase inhibitor resistance in de novo BCR::ABL1-positive BCP-ALL beyond kinase domain mutations. Blood Adv 2024; 8:1835-1845. [PMID: 38386975 PMCID: PMC11007435 DOI: 10.1182/bloodadvances.2023012162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
ABSTRACT A better understanding of ABL1 kinase domain mutation-independent causes of tyrosine kinase inhibitor (TKI) resistance is needed for BCR::ABL1-positive B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Although TKIs have dramatically improved outcomes, a subset of patients still experiences relapsed or refractory disease. We aimed to identify potential biomarkers of intrinsic TKI resistance at diagnosis in samples from 32 pediatric and 19 adult patients with BCR::ABL1-positive BCP-ALL. Reduced ex vivo imatinib sensitivity was observed in cells derived from newly diagnosed patients who relapsed after combined TKI and chemotherapy treatment compared with cells derived from patients who remained in continuous complete remission. We observed that ex vivo imatinib resistance was inversely correlated with the amount of (phosphorylated) BCR::ABL1/ABL1 protein present in samples that were taken at diagnosis without prior TKI exposure. This suggests an intrinsic cause of TKI resistance that is independent of functional BCR::ABL1 signaling. Simultaneous deletions of IKZF1 and CDKN2A/B and/or PAX5 (IKZF1plus), as well as deletions of PAX5 alone, were related to ex vivo imatinib resistance. In addition, somatic lesions involving ZEB2, SETD2, SH2B3, and CRLF2 were associated with reduced ex vivo imatinib sensitivity. Our data suggest that the poor prognostic value of IKZF1(plus) deletions is linked to intrinsic mechanisms of TKI resistance other than ABL1 kinase domain mutations in newly diagnosed pediatric and adult BCR::ABL1-positive BCP-ALL.
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Affiliation(s)
| | - Judith M. Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Cesca van de Ven
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Aurelie Boeree
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Brian Kruisinga
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Gabriele Escherich
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Aniko Sijs-Szabo
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Anita W. Rijneveld
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Monique L. den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Oncology and Hematology, Erasmus MC - Sophia Children's Hospital, Rotterdam, The Netherlands
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6
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Minnie SA, Waltner OG, Zhang P, Takahashi S, Nemychenkov NS, Ensbey KS, Schmidt CR, Legg SRW, Comstock M, Boiko JR, Nelson E, Bhise SS, Wilkens AB, Koyama M, Dhodapkar MV, Chesi M, Riddell SR, Green DJ, Spencer A, Furlan SN, Hill GR. TIM-3 + CD8 T cells with a terminally exhausted phenotype retain functional capacity in hematological malignancies. Sci Immunol 2024; 9:eadg1094. [PMID: 38640253 PMCID: PMC11093588 DOI: 10.1126/sciimmunol.adg1094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/27/2024] [Indexed: 04/21/2024]
Abstract
Chronic antigen stimulation is thought to generate dysfunctional CD8 T cells. Here, we identify a CD8 T cell subset in the bone marrow tumor microenvironment that, despite an apparent terminally exhausted phenotype (TPHEX), expressed granzymes, perforin, and IFN-γ. Concurrent gene expression and DNA accessibility revealed that genes encoding these functional proteins correlated with BATF expression and motif accessibility. IFN-γ+ TPHEX effectively killed myeloma with comparable efficacy to transitory effectors, and disease progression correlated with numerical deficits in IFN-γ+ TPHEX. We also observed IFN-γ+ TPHEX within CD19-targeted chimeric antigen receptor T cells, which killed CD19+ leukemia cells. An IFN-γ+ TPHEX gene signature was recapitulated in TEX cells from human cancers, including myeloma and lymphoma. Here, we characterize a TEX subset in hematological malignancies that paradoxically retains function and is distinct from dysfunctional TEX found in chronic viral infections. Thus, IFN-γ+ TPHEX represent a potential target for immunotherapy of blood cancers.
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Affiliation(s)
- Simone A. Minnie
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Olivia G. Waltner
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Ping Zhang
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Shuichiro Takahashi
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Nicole S. Nemychenkov
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Kathleen S. Ensbey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Christine R. Schmidt
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Samuel RW. Legg
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Melissa Comstock
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Julie R. Boiko
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Department of Pediatrics, University of Washington; WA, UNITED STATES
| | - Ethan Nelson
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Shruti S. Bhise
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Alec B. Wilkens
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Motoko Koyama
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Madhav V. Dhodapkar
- Department of Hematology/Medical Oncology, Atlanta, GA, UNITED STATES
- Winship Cancer Institute, Emory University, Atlanta, GA, UNITED STATES
| | - Marta Chesi
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, AZ, UNITED STATES
| | - Stanley R. Riddell
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Division of Medical Oncology, University of Washington; Seattle, WA, UNITED STATES
| | - Damian J. Green
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Division of Medical Oncology, University of Washington; Seattle, WA, UNITED STATES
| | - Andrew Spencer
- Australian Center for Blood Diseases, Monash University/The Alfred Hospital, Melbourne, VIC, AUSTRALIA
- Malignant Haematology and Stem Cell Transplantation, The Alfred Hospital, Melbourne, VIC, AUSTRALIA
- Department of Clinical Haematology, Monash University, Melbourne, VIC
| | - Scott N. Furlan
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Department of Pediatrics, University of Washington; WA, UNITED STATES
| | - Geoffrey R. Hill
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Division of Medical Oncology, University of Washington; Seattle, WA, UNITED STATES
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7
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Paolino J, Tsai HK, Harris MH, Pikman Y. IKZF1 Alterations and Therapeutic Targeting in B-Cell Acute Lymphoblastic Leukemia. Biomedicines 2024; 12:89. [PMID: 38255194 PMCID: PMC10813044 DOI: 10.3390/biomedicines12010089] [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: 11/21/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
IKZF1 encodes the transcription factor IKAROS, a zinc finger DNA-binding protein with a key role in lymphoid lineage development. IKAROS plays a critical role in the development of lineage-restricted mature lymphocytes. Deletions within IKZF1 in B-cell acute lymphoblastic leukemia (B-ALL) lead to a loss of normal IKAROS function, conferring leukemic stem cell properties, including self-renewal and subsequent uncontrolled growth. IKZF1 deletions are associated with treatment resistance and inferior outcomes. Early identification of IKZF1 deletions in B-ALL may inform the intensification of therapy and other potential treatment strategies to improve outcomes in this high-risk leukemia.
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Affiliation(s)
- Jonathan Paolino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Harrison K. Tsai
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA (M.H.H.)
| | - Marian H. Harris
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA (M.H.H.)
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
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8
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Pieters R, Mullighan CG, Hunger SP. Advancing Diagnostics and Therapy to Reach Universal Cure in Childhood ALL. J Clin Oncol 2023; 41:5579-5591. [PMID: 37820294 PMCID: PMC10730082 DOI: 10.1200/jco.23.01286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/24/2023] [Accepted: 08/10/2023] [Indexed: 10/13/2023] Open
Abstract
Systemic combination chemotherapy and intrathecal chemotherapy markedly increased the survival rate of children with ALL. In the past two decades, the use of minimal (measurable) residual disease (MRD) measurements early in therapy improved risk group stratification with subsequent treatment intensifications for patients at high risk of relapse, and enabled a reduction of treatment for low-risk patients. The recent development of more sensitive MRD technologies may further affect risk stratification. Molecular genetic profiling has led to the discovery of many new subtypes and their driver genetic alterations. This increased our understanding of the biological basis of ALL, improved risk classification, and enabled implementation of precision medicine. In the past decade, immunotherapies, including bispecific antibodies, antibody-drug conjugates, and cellular therapies directed against surface proteins, led to more effective and less toxic therapies, replacing intensive chemotherapy courses and allogeneic stem-cell transplantation in patients with relapsed and refractory ALL, and are now being tested in newly diagnosed patients. It has taken 50-60 years to increase the cure rate in childhood ALL from 0% to 90% by stepwise improvements in chemotherapy. This review provides an overview of how the developments over the past 10-15 years mentioned above have significantly changed the diagnostic and treatment approach in ALL, and discusses how the integrated use of molecular and immunotherapeutic insights will very likely direct efforts to cure those children with ALL who are not cured today, and improve the quality of life for survivors who should have decades of life ahead. Future efforts must focus on making effective, yet very expensive, new technologies and therapies available to children with ALL worldwide.
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Affiliation(s)
- Rob Pieters
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Charles G. Mullighan
- Department of Pathology and Hematological Malignancies Program, Comprehensive Cancer Center, St Jude Children's Research Hospital, Memphis, TN
| | - Stephen P. Hunger
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
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9
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Barnett KR, Mobley RJ, Diedrich JD, Bergeron BP, Bhattarai KR, Monovich AC, Narina S, Yang W, Crews KR, Manring CS, Jabbour E, Paietta E, Litzow MR, Kornblau SM, Stock W, Inaba H, Jeha S, Pui CH, Mullighan CG, Relling MV, Pruett-Miller SM, Ryan RJ, Yang JJ, Evans WE, Savic D. Epigenomic mapping reveals distinct B cell acute lymphoblastic leukemia chromatin architectures and regulators. CELL GENOMICS 2023; 3:100442. [PMID: 38116118 PMCID: PMC10726428 DOI: 10.1016/j.xgen.2023.100442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/30/2023] [Accepted: 10/20/2023] [Indexed: 12/21/2023]
Abstract
B cell lineage acute lymphoblastic leukemia (B-ALL) is composed of diverse molecular subtypes, and while transcriptional and DNA methylation profiling has been extensively examined, the chromatin landscape is not well characterized for many subtypes. We therefore mapped chromatin accessibility using ATAC-seq in primary B-ALL cells from 156 patients spanning ten molecular subtypes and present this dataset as a resource. Differential chromatin accessibility and transcription factor (TF) footprint profiling were employed and identified B-ALL cell of origin, TF-target gene interactions enriched in B-ALL, and key TFs associated with accessible chromatin sites preferentially active in B-ALL. We further identified over 20% of accessible chromatin sites exhibiting strong subtype enrichment and candidate TFs that maintain subtype-specific chromatin architectures. Over 9,000 genetic variants were uncovered, contributing to variability in chromatin accessibility among patient samples. Our data suggest that distinct chromatin architectures are driven by diverse TFs and inherited genetic variants that promote unique gene-regulatory networks.
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Affiliation(s)
- Kelly R. Barnett
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robert J. Mobley
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jonathan D. Diedrich
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Brennan P. Bergeron
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kashi Raj Bhattarai
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Alexander C. Monovich
- Department of Pathology, University of Michigan–Ann Arbor, Rogel Cancer Center, Ann Arbor, MI 48109, USA
| | - Shilpa Narina
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Wenjian Yang
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kristine R. Crews
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Christopher S. Manring
- Alliance Hematologic Malignancy Biorepository, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH 43210, USA
| | - Elias Jabbour
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Elisabeth Paietta
- Department of Oncology, Montefiore Medical Center, Bronx, NY 10467, USA
| | - Mark R. Litzow
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Steven M. Kornblau
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Wendy Stock
- University of Chicago Comprehensive Cancer Center, Chicago, IL 60637, USA
| | - Hiroto Inaba
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sima Jeha
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Charles G. Mullighan
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Mary V. Relling
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Russell J.H. Ryan
- Department of Pathology, University of Michigan–Ann Arbor, Rogel Cancer Center, Ann Arbor, MI 48109, USA
| | - Jun J. Yang
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - William E. Evans
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Daniel Savic
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38105, USA
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10
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Libura M, Karabin K, Tyrna P, Czyż A, Makuch-Łasica H, Jaźwiec B, Paluszewska M, Piątkowska-Jakubas B, Zawada M, Gniot M, Trubicka J, Szymańska M, Borg K, Więsik M, Czekalska S, Florek I, Król M, Paszkowska-Kowalewska M, Gil L, Kapelko-Słowik K, Patkowska E, Tomaszewska A, Mądry K, Machowicz R, Czerw T, Piekarska A, Dutka M, Kopińska A, Helbig G, Gromek T, Lewandowski K, Zacharczuk M, Pastwińska A, Wróbel T, Haus O, Basak G, Hołowiecki J, Juszczyński P, Lech-Marańda E, Giebel S, Jędrzejczak WW. Prognostic Impact of Copy Number Alterations' Profile and AID/RAG Signatures in Acute Lymphoblastic Leukemia (ALL) with BCR::ABL and without Recurrent Genetic Aberrations (NEG ALL) Treated with Intensive Chemotherapy. Cancers (Basel) 2023; 15:5431. [PMID: 38001691 PMCID: PMC10670434 DOI: 10.3390/cancers15225431] [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: 10/09/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Adult acute lymphoblastic leukemia (ALL) is associated with poor outcomes. ALL is initiated by primary aberrations, but secondary genetic lesions are necessary for overt ALL. In this study, we reassessed the value of primary and secondary aberrations in intensively treated ALL patients in relation to mutator enzyme expression. RT-PCR, genomic PCR, and sequencing were applied to evaluate primary aberrations, while qPCR was used to measure the expression of RAG and AID mutator enzymes in 166 adult ALL patients. Secondary copy number alterations (CNA) were studied in 94 cases by MLPA assay. Primary aberrations alone stratified 30% of the patients (27% high-risk, 3% low-risk cases). The remaining 70% intermediate-risk patients included BCR::ABL1pos subgroup and ALL lacking identified genetic markers (NEG ALL). We identified three CNA profiles: high-risk bad-CNA (CNAhigh/IKZF1pos), low-risk good-CNA (all other CNAs), and intermediate-risk CNAneg. Furthermore, based on RAG/AID expression, we report possible mechanisms underlying the CNA profiles associated with poor outcome: AID stratified outcome in CNAneg, which accompanied most likely a particular profile of single nucleotide variations, while RAG in CNApos increased the odds for CNAhigh/IKZF1pos development. Finally, we integrated primary genetic aberrations with CNA to propose a revised risk stratification code, which allowed us to stratify 75% of BCR::ABL1pos and NEG patients.
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Affiliation(s)
- Marta Libura
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (P.T.); (M.P.); (M.S.); (M.W.); (M.K.); (M.P.-K.); (A.T.); (K.M.); (G.B.); (W.W.J.)
| | - Karolina Karabin
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (P.T.); (M.P.); (M.S.); (M.W.); (M.K.); (M.P.-K.); (A.T.); (K.M.); (G.B.); (W.W.J.)
| | - Paweł Tyrna
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (P.T.); (M.P.); (M.S.); (M.W.); (M.K.); (M.P.-K.); (A.T.); (K.M.); (G.B.); (W.W.J.)
| | - Anna Czyż
- Department of Hematology, Blood Neoplasms and Bone Marrow Transplantation, Medical University of Wrocław, 50-137 Wrocław, Poland; (A.C.); (B.J.); (K.K.-S.); (M.Z.); (T.W.)
| | - Hanna Makuch-Łasica
- Institute of Hematology and Transfusion Medicine, 02-776 Warsaw, Poland; (H.M.-Ł.); (K.B.); (E.P.); (P.J.); (E.L.-M.)
| | - Bożena Jaźwiec
- Department of Hematology, Blood Neoplasms and Bone Marrow Transplantation, Medical University of Wrocław, 50-137 Wrocław, Poland; (A.C.); (B.J.); (K.K.-S.); (M.Z.); (T.W.)
| | - Monika Paluszewska
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (P.T.); (M.P.); (M.S.); (M.W.); (M.K.); (M.P.-K.); (A.T.); (K.M.); (G.B.); (W.W.J.)
| | - Beata Piątkowska-Jakubas
- Department of Hematology, Jagiellonian University Medical College, 31-008 Cracow, Poland; (B.P.-J.); (M.Z.); (S.C.); (I.F.)
| | - Magdalena Zawada
- Department of Hematology, Jagiellonian University Medical College, 31-008 Cracow, Poland; (B.P.-J.); (M.Z.); (S.C.); (I.F.)
| | - Michał Gniot
- Department of Hematology and Bone Marrow Transplantation, Poznań University of Medical Sciences, 61-701 Poznań, Poland; (M.G.); (L.G.); (K.L.)
| | - Joanna Trubicka
- Children’s Memorial Health Institute, 04-736 Warsaw, Poland;
| | - Magdalena Szymańska
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (P.T.); (M.P.); (M.S.); (M.W.); (M.K.); (M.P.-K.); (A.T.); (K.M.); (G.B.); (W.W.J.)
| | - Katarzyna Borg
- Institute of Hematology and Transfusion Medicine, 02-776 Warsaw, Poland; (H.M.-Ł.); (K.B.); (E.P.); (P.J.); (E.L.-M.)
| | - Marta Więsik
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (P.T.); (M.P.); (M.S.); (M.W.); (M.K.); (M.P.-K.); (A.T.); (K.M.); (G.B.); (W.W.J.)
| | - Sylwia Czekalska
- Department of Hematology, Jagiellonian University Medical College, 31-008 Cracow, Poland; (B.P.-J.); (M.Z.); (S.C.); (I.F.)
| | - Izabela Florek
- Department of Hematology, Jagiellonian University Medical College, 31-008 Cracow, Poland; (B.P.-J.); (M.Z.); (S.C.); (I.F.)
| | - Maria Król
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (P.T.); (M.P.); (M.S.); (M.W.); (M.K.); (M.P.-K.); (A.T.); (K.M.); (G.B.); (W.W.J.)
| | - Małgorzata Paszkowska-Kowalewska
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (P.T.); (M.P.); (M.S.); (M.W.); (M.K.); (M.P.-K.); (A.T.); (K.M.); (G.B.); (W.W.J.)
| | - Lidia Gil
- Department of Hematology and Bone Marrow Transplantation, Poznań University of Medical Sciences, 61-701 Poznań, Poland; (M.G.); (L.G.); (K.L.)
| | - Katarzyna Kapelko-Słowik
- Department of Hematology, Blood Neoplasms and Bone Marrow Transplantation, Medical University of Wrocław, 50-137 Wrocław, Poland; (A.C.); (B.J.); (K.K.-S.); (M.Z.); (T.W.)
| | - Elżbieta Patkowska
- Institute of Hematology and Transfusion Medicine, 02-776 Warsaw, Poland; (H.M.-Ł.); (K.B.); (E.P.); (P.J.); (E.L.-M.)
| | - Agnieszka Tomaszewska
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (P.T.); (M.P.); (M.S.); (M.W.); (M.K.); (M.P.-K.); (A.T.); (K.M.); (G.B.); (W.W.J.)
| | - Krzysztof Mądry
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (P.T.); (M.P.); (M.S.); (M.W.); (M.K.); (M.P.-K.); (A.T.); (K.M.); (G.B.); (W.W.J.)
| | - Rafał Machowicz
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (P.T.); (M.P.); (M.S.); (M.W.); (M.K.); (M.P.-K.); (A.T.); (K.M.); (G.B.); (W.W.J.)
| | - Tomasz Czerw
- Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (T.C.); (J.H.); (S.G.)
| | - Agnieszka Piekarska
- Department of Hematology and Transplantology, Medical University of Gdańsk, 80-214 Gdańsk, Poland; (A.P.); (M.D.)
| | - Magdalena Dutka
- Department of Hematology and Transplantology, Medical University of Gdańsk, 80-214 Gdańsk, Poland; (A.P.); (M.D.)
| | - Anna Kopińska
- Department of Hematology and Bone Marrow Transplantation, Medical University of Silesia, 40-032 Katowice, Poland; (A.K.); (G.H.)
| | - Grzegorz Helbig
- Department of Hematology and Bone Marrow Transplantation, Medical University of Silesia, 40-032 Katowice, Poland; (A.K.); (G.H.)
| | - Tomasz Gromek
- Department of Hematooncology and Bone Marrow Transplantation, Medical University of Lublin, 20-081 Lublin, Poland;
| | - Krzysztof Lewandowski
- Department of Hematology and Bone Marrow Transplantation, Poznań University of Medical Sciences, 61-701 Poznań, Poland; (M.G.); (L.G.); (K.L.)
| | - Marta Zacharczuk
- Department of Hematology, Blood Neoplasms and Bone Marrow Transplantation, Medical University of Wrocław, 50-137 Wrocław, Poland; (A.C.); (B.J.); (K.K.-S.); (M.Z.); (T.W.)
| | - Anna Pastwińska
- Department of Tumor Biology and Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland;
| | - Tomasz Wróbel
- Department of Hematology, Blood Neoplasms and Bone Marrow Transplantation, Medical University of Wrocław, 50-137 Wrocław, Poland; (A.C.); (B.J.); (K.K.-S.); (M.Z.); (T.W.)
| | - Olga Haus
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Toruń, Poland;
| | - Grzegorz Basak
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (P.T.); (M.P.); (M.S.); (M.W.); (M.K.); (M.P.-K.); (A.T.); (K.M.); (G.B.); (W.W.J.)
| | - Jerzy Hołowiecki
- Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (T.C.); (J.H.); (S.G.)
| | - Przemysław Juszczyński
- Institute of Hematology and Transfusion Medicine, 02-776 Warsaw, Poland; (H.M.-Ł.); (K.B.); (E.P.); (P.J.); (E.L.-M.)
| | - Ewa Lech-Marańda
- Institute of Hematology and Transfusion Medicine, 02-776 Warsaw, Poland; (H.M.-Ł.); (K.B.); (E.P.); (P.J.); (E.L.-M.)
| | - Sebastian Giebel
- Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (T.C.); (J.H.); (S.G.)
| | - Wiesław Wiktor Jędrzejczak
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (P.T.); (M.P.); (M.S.); (M.W.); (M.K.); (M.P.-K.); (A.T.); (K.M.); (G.B.); (W.W.J.)
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11
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Qiao X, Qi X, Xing P, Liu T, Hao H, Yang X, Jiang B, Cui M, Su X. Tandem Mass Tag-Based Proteomic Profiling Identifies Biomarkers in Drainage Fluid for Early Detection of Anastomotic Leakage after Rectal Cancer Resection. J Proteome Res 2023; 22:3559-3569. [PMID: 37793102 DOI: 10.1021/acs.jproteome.3c00394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Anastomotic leakage (AL), one of the most severe complications in rectal surgery, is often diagnosed late because of the low specificity of the clinical symptoms and limitations of current clinical investigations. Identification of patients with early AL remains challenging. Here, we explored the protein expression profiles of AL patients to provide potential biomarkers to identify AL in patients who undergo surgery for rectal cancer. We screened differentially expressed proteins (DEPs) in drainage fluid from AL and non-AL patients using a tandem mass tag method. A total of 248 DEPs, including 98 upregulated and 150 downregulated proteins, were identified between AL and non-AL groups. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses suggested that DEPs were enriched in neutrophil degranulation, bacterial infection, proteolysis, hemostasis, and complement and coagulation cascades. The results of enzyme-linked immunosorbent assay validated that the expression of the top three upregulated DEPs, AMY2A, RETN, and CELA3A, was significantly increased in the drainage fluid of AL patients, compared with that of non-AL patients (AMY2A, P = 0.001; RETN, P < 0.0001; and CELA3A, P = 0.023). Thus, our findings provide several potential biomarkers for the early diagnosis of AL after rectal cancer resection.
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Affiliation(s)
- Xiaowen Qiao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xinyu Qi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Pu Xing
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Tianqi Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Hao Hao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xinying Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Beihai Jiang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Ming Cui
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xiangqian Su
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
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12
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Koyama M, Hippe DS, Srinivasan S, Proll SC, Miltiadous O, Li N, Zhang P, Ensbey KS, Hoffman NG, Schmidt CR, Yeh AC, Minnie SA, Strenk SM, Fiedler TL, Hattangady N, Kowalsky J, Grady WM, Degli-Esposti MA, Varelias A, Clouston AD, van den Brink MRM, Dey N, Randolph TW, Markey KA, Fredricks DN, Hill GR. Intestinal microbiota controls graft-versus-host disease independent of donor-host genetic disparity. Immunity 2023; 56:1876-1893.e8. [PMID: 37480848 PMCID: PMC10530372 DOI: 10.1016/j.immuni.2023.06.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 04/11/2023] [Accepted: 06/28/2023] [Indexed: 07/24/2023]
Abstract
Acute graft-versus-host disease (aGVHD) remains a major limitation of allogeneic stem cell transplantation (SCT), and severe intestinal manifestation is the major cause of early mortality. Intestinal microbiota control MHC class II (MHC-II) expression by ileal intestinal epithelial cells (IECs) that promote GVHD. Here, we demonstrated that genetically identical mice of differing vendor origins had markedly different intestinal microbiota and ileal MHC-II expression, resulting in discordant GVHD severity. We utilized cohousing and antibiotic treatment to characterize the bacterial taxa positively and negatively associated with MHC-II expression. A large proportion of bacterial MHC-II inducers were vancomycin sensitive, and peri-transplant oral vancomycin administration attenuated CD4+ T cell-mediated GVHD. We identified a similar relationship between pre-transplant microbes, HLA class II expression, and both GVHD and mortality in a large clinical SCT cohort. These data highlight therapeutically tractable mechanisms by which pre-transplant microbial taxa contribute to GVHD independently of genetic disparity.
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Affiliation(s)
- Motoko Koyama
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA.
| | - Daniel S Hippe
- Clinical Research Division, FHCC, Seattle, WA 98109, USA
| | | | - Sean C Proll
- Vaccine and Infectious Disease Division, FHCC, Seattle, WA 98109, USA
| | - Oriana Miltiadous
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Naisi Li
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Ping Zhang
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Kathleen S Ensbey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Noah G Hoffman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Christine R Schmidt
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Albert C Yeh
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Simone A Minnie
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Susan M Strenk
- Vaccine and Infectious Disease Division, FHCC, Seattle, WA 98109, USA
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, FHCC, Seattle, WA 98109, USA
| | - Namita Hattangady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Jacob Kowalsky
- Vaccine and Infectious Disease Division, FHCC, Seattle, WA 98109, USA
| | - Willian M Grady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Mariapia A Degli-Esposti
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA 6009, Australia
| | - Antiopi Varelias
- Transplantation Immunology Laboratory, Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; Faculty of Medicine, University of Queensland, St Lucia, QLD 4067, Australia
| | - Andrew D Clouston
- Molecular and Cellular Pathology, University of Queensland, Brisbane, QLD 4006, Australia
| | - Marcel R M van den Brink
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Medical College, New York, NY 10065, USA; Department of Immunology, Sloan Kettering Institute, New York, NY 10065, USA
| | - Neelendu Dey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Timothy W Randolph
- Clinical Research Division, FHCC, Seattle, WA 98109, USA; Public Health Sciences Division, FHCC, WA 98109, USA
| | - Kate A Markey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Medical College, New York, NY 10065, USA
| | - David N Fredricks
- Vaccine and Infectious Disease Division, FHCC, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Geoffrey R Hill
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA.
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13
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Park CS, Yoshihara H, Gao Q, Qu C, Iacobucci I, Ghate PS, Connelly JP, Pruett-Miller SM, Wagner B, Robinson CG, Mishra A, Peng J, Yang L, Rankovic Z, Finkelstein D, Luger S, Litzow M, Paietta EM, Hebbar N, Velasquez MP, Mullighan CG. Stromal-induced epithelial-mesenchymal transition induces targetable drug resistance in acute lymphoblastic leukemia. Cell Rep 2023; 42:112804. [PMID: 37453060 PMCID: PMC10529385 DOI: 10.1016/j.celrep.2023.112804] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 04/05/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023] Open
Abstract
The bone marrow microenvironment (BME) drives drug resistance in acute lymphoblastic leukemia (ALL) through leukemic cell interactions with bone marrow (BM) niches, but the underlying mechanisms remain unclear. Here, we show that the interaction between ALL and mesenchymal stem cells (MSCs) through integrin β1 induces an epithelial-mesenchymal transition (EMT)-like program in MSC-adherent ALL cells, resulting in drug resistance and enhanced survival. Moreover, single-cell RNA sequencing analysis of ALL-MSC co-culture identifies a hybrid cluster of MSC-adherent ALL cells expressing both B-ALL and MSC signature genes, orchestrated by a WNT/β-catenin-mediated EMT-like program. Blockade of interaction between β-catenin and CREB binding protein impairs the survival and drug resistance of MSC-adherent ALL cells in vitro and results in a reduction in leukemic burden in vivo. Targeting of this WNT/β-catenin-mediated EMT-like program is a potential therapeutic approach to overcome cell extrinsically acquired drug resistance in ALL.
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Affiliation(s)
- Chun Shik Park
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hiroki Yoshihara
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Qingsong Gao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Pankaj S Ghate
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jon P Connelly
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ben Wagner
- Cell and Tissue Imaging Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Camenzind G Robinson
- Cell and Tissue Imaging Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ashutosh Mishra
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Selina Luger
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19106, USA
| | - Mark Litzow
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Nikhil Hebbar
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - M Paulina Velasquez
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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14
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Barnett KR, Mobley RJ, Diedrich JD, Bergeron BP, Bhattarai KR, Yang W, Crews KR, Manring CS, Jabbour E, Paietta E, Litzow MR, Kornblau SM, Stock W, Inaba H, Jeha S, Pui CH, Mullighan CG, Relling MV, Yang JJ, Evans WE, Savic D. Epigenomic mapping in B-cell acute lymphoblastic leukemia identifies transcriptional regulators and noncoding variants promoting distinct chromatin architectures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528493. [PMID: 36824825 PMCID: PMC9949063 DOI: 10.1101/2023.02.14.528493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
B-cell lineage acute lymphoblastic leukemia (B-ALL) is comprised of diverse molecular subtypes and while transcriptional and DNA methylation profiling of B-ALL subtypes has been extensively examined, the accompanying chromatin landscape is not well characterized for many subtypes. We therefore mapped chromatin accessibility using ATAC-seq for 10 B-ALL molecular subtypes in primary ALL cells from 154 patients. Comparisons with B-cell progenitors identified candidate B-ALL cell-of-origin and AP-1-associated cis-regulatory rewiring in B-ALL. Cis-regulatory rewiring promoted B-ALL-specific gene regulatory networks impacting oncogenic signaling pathways that perturb normal B-cell development. We also identified that over 20% of B-ALL accessible chromatin sites exhibit strong subtype enrichment, with transcription factor (TF) footprint profiling identifying candidate TFs that maintain subtype-specific chromatin architectures. Over 9000 inherited genetic variants were further uncovered that contribute to variability in chromatin accessibility among individual patient samples. Overall, our data suggest that distinct chromatin architectures are driven by diverse TFs and inherited genetic variants which promote unique gene regulatory networks that contribute to transcriptional differences among B-ALL subtypes.
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Affiliation(s)
- Kelly R. Barnett
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robert J. Mobley
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jonathan D. Diedrich
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Brennan P. Bergeron
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kashi Raj Bhattarai
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Wenjian Yang
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kristine R. Crews
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Christopher S. Manring
- Alliance Hematologic Malignancy Biorepository; Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH 43210, USA
| | - Elias Jabbour
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Elisabeth Paietta
- Department of Oncology, Montefiore Medical Center, Bronx, NY 10467, USA
| | - Mark R. Litzow
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Steven M. Kornblau
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Wendy Stock
- University of Chicago Comprehensive Cancer Center, Chicago, IL 60637, USA
| | - Hiroto Inaba
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sima Jeha
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Charles G. Mullighan
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Mary V. Relling
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jun J. Yang
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - William E. Evans
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Daniel Savic
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38105, USA
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15
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Xu Y, Yan J, Zhou C, Wu L, Wang H, Zhao J, Zhou M, Wang J, Zheng X, Zhang L, Jiang K, Zheng X, Miao Q, Wu S, Zou Z, Lian R, He Y, Chen R, Yang S, Li Y, Chen S, Lin G. Genomic characterisation of de novo EGFR copy number gain and its impact on the efficacy of first-line EGFR-tyrosine kinase inhibitors for EGFR mutated non-small cell lung cancer. Eur J Cancer 2023; 188:81-89. [PMID: 37201385 DOI: 10.1016/j.ejca.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) patients with epidermal growth factor receptor (EGFR) mutation generally respond well to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs). However, genomic characterisation of de novo EGFR copy number gain (CNG) and its impact on the efficacy of first-line EGFR-TKIs remains unclear. METHODS This multicenter, retrospective and real-world study included two cohorts that enroled EGFR mutant NSCLC patients. EGFR CNG was tested by next-generation sequencing of untreated tissue specimens. Cohort 1 detected the impact of EGFR CNG on first-line EGFR-TKIs treatment, and cohort 2 explored the genomic characterisation. RESULTS Cohort 1 enroled 355 patients from four cancer centres between January 2013 and March 2022. The patients were divided into three groups, included the EGFR non-CNG, EGFR CNG, and EGFR uncertain-CNG. No significant difference in progression-free survival (PFS) was found between the three groups (10.0 months vs. 10.8 months vs. 9.9 months, respectively, p = 0.384). Furthermore, the overall response rate was not statistically significant in the EGFR CNG group compared to the EGFR non-CNG or uncertain arm (70.3% vs. 63.2% vs. 54.5%, respectively, p = 0.154). Cohort 2 included 7876 NSCLC patients with 16.4% showing EGFR CNG. Gene mutations such as TP53, IKZF1, RAC1, MYC, MET, CDKN2A/B and alterations of the metabolic-related and ERK signalling pathway were significantly associated with patients with EGFR CNG compared to those without. CONCLUSIONS De novo EGFR CNG had no effect on the efficacy of first-line EGFR-TKI treatment in EGFR mutant NSCLC patients, and tumours with EGFR CNG had more complex genomic profiles than those without.
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Affiliation(s)
- Yiquan Xu
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Jingjing Yan
- Department of Respiratory and Critical Care Medicine, Hebei Petrochina Central Hospital, Langfang, China
| | - Chengzhi Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Lin Wu
- The Second Department of Thoracic Oncology, the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, China
| | - Haibo Wang
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Jun Zhao
- Department of Thoracic Medical Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Maolin Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jingyi Wang
- The Second Department of Thoracic Oncology, the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, China
| | - Xinlong Zheng
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Longfeng Zhang
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Kan Jiang
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Xiaobin Zheng
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Qian Miao
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Shiwen Wu
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Zihua Zou
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Rong Lian
- Beijing GenePlus Technology Co., Ltd., Beijing, China
| | - Yuange He
- Beijing GenePlus Technology Co., Ltd., Beijing, China
| | - Rongrong Chen
- Beijing GenePlus Technology Co., Ltd., Beijing, China
| | - Shanshan Yang
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Yujing Li
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Sihui Chen
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Gen Lin
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China.
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16
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Kim JC, Chan-Seng-Yue M, Ge S, Zeng AGX, Ng K, Gan OI, Garcia-Prat L, Flores-Figueroa E, Woo T, Zhang AXW, Arruda A, Chithambaram S, Dobson SM, Khoo A, Khan S, Ibrahimova N, George A, Tierens A, Hitzler J, Kislinger T, Dick JE, McPherson JD, Minden MD, Notta F. Transcriptomic classes of BCR-ABL1 lymphoblastic leukemia. Nat Genet 2023:10.1038/s41588-023-01429-4. [PMID: 37337105 DOI: 10.1038/s41588-023-01429-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 05/17/2023] [Indexed: 06/21/2023]
Abstract
In BCR-ABL1 lymphoblastic leukemia, treatment heterogeneity to tyrosine kinase inhibitors (TKIs), especially in the absence of kinase domain mutations in BCR-ABL1, is poorly understood. Through deep molecular profiling, we uncovered three transcriptomic subtypes of BCR-ABL1 lymphoblastic leukemia, each representing a maturation arrest at a stage of B-cell progenitor differentiation. An earlier arrest was associated with lineage promiscuity, treatment refractoriness and poor patient outcomes. A later arrest was associated with lineage fidelity, durable leukemia remissions and improved patient outcomes. Each maturation arrest was marked by specific genomic events that control different transition points in B-cell development. Interestingly, these events were absent in BCR-ABL1+ preleukemic stem cells isolated from patients regardless of subtype, which supports that transcriptomic phenotypes are determined downstream of the leukemia-initialing event. Overall, our data indicate that treatment response and TKI efficacy are unexpected outcomes of the differentiation stage at which this leukemia transforms.
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Affiliation(s)
- Jaeseung C Kim
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | | | - Sabrina Ge
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Karen Ng
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | | - Tristan Woo
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | | | - Andrea Arruda
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Shivapriya Chithambaram
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Amanda Khoo
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Ann George
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Anne Tierens
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Johann Hitzler
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John D McPherson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Mark D Minden
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Faiyaz Notta
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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17
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Modvig S, Jeyakumar J, Marquart HV, Christensen C. Integrins and the Metastasis-like Dissemination of Acute Lymphoblastic Leukemia to the Central Nervous System. Cancers (Basel) 2023; 15:cancers15092504. [PMID: 37173970 PMCID: PMC10177281 DOI: 10.3390/cancers15092504] [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: 03/31/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) disseminates with high prevalence to the central nervous system (CNS) in a process resembling aspects of the CNS surveillance of normal immune cells as well as aspects of brain metastasis from solid cancers. Importantly, inside the CNS, the ALL blasts are typically confined within the cerebrospinal fluid (CSF)-filled cavities of the subarachnoid space, which they use as a sanctuary protected from both chemotherapy and immune cells. At present, high cumulative doses of intrathecal chemotherapy are administered to patients, but this is associated with neurotoxicity and CNS relapse still occurs. Thus, it is imperative to identify markers and novel therapy targets specific to CNS ALL. Integrins represent a family of adhesion molecules involved in cell-cell and cell-matrix interactions, implicated in the adhesion and migration of metastatic cancer cells, normal immune cells, and leukemic blasts. The ability of integrins to also facilitate cell-adhesion mediated drug resistance, combined with recent discoveries of integrin-dependent routes of leukemic cells into the CNS, have sparked a renewed interest in integrins as markers and therapeutic targets in CNS leukemia. Here, we review the roles of integrins in CNS surveillance by normal lymphocytes, dissemination to the CNS by ALL cells, and brain metastasis from solid cancers. Furthermore, we discuss whether ALL dissemination to the CNS abides by known hallmarks of metastasis, and the potential roles of integrins in this context.
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Affiliation(s)
- Signe Modvig
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jenani Jeyakumar
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | - Hanne Vibeke Marquart
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Claus Christensen
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
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18
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Functional damaging germline variants in ETV6, IKZF1, PAX5 and RUNX1 predisposing to B-cell precursor acute lymphoblastic leukemia. Eur J Med Genet 2023; 66:104725. [PMID: 36764385 DOI: 10.1016/j.ejmg.2023.104725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/29/2022] [Accepted: 02/03/2023] [Indexed: 02/11/2023]
Abstract
Recent genome-wide studies have demonstrated that a significant proportion of children with cancer carry predisposing germline variants, with varying incidence according to cancer type. In general, there is a lower incidence of underlying germline predisposing variants among patients with B-cell acute lymphoblastic leukemia (B-ALL) compared to other types of cancer, but higher rates may be found in patients with specific leukemia subtypes. Two categories of ALL-predisposing variants have been described: common polymorphisms, conferring low-penetrance ALL susceptibility, and rare variants, conferring high-penetrance ALL susceptibility. Variants in genes encoding hematopoietic transcription factors are an example of the latter, and include ETV6, IKZF1, PAX5 and RUNX1. Here, we present an overview of the germline variants detected in patients with B-ALL in these four genes and a summary of functional studies analyzing the impacts of these variants upon protein function, and hence their effects with regard to leukemia predisposition. Furthermore, we review specific clinical characteristics of patients with B-ALL, including specific features of the patient or family history and associated somatic genetic characteristics, which are suggestive of underlying germline alterations in one of these genes. This review may be of assistance in the interpretation of patient genetic germline findings, made even more challenging by the absence of a suggestive family history or by an unknown familial cancer history. Despite a low incidence of underlying germline alterations in ETV6, IKZF1, PAX5 and RUNX1 in patients with B-ALL, identification of an underlying ALL predisposition syndrome is relevant to the clinical management of patients and their relatives, as the latter are also at risk of developing cancer.
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19
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Zhang X, Huang A, Liu L, Qin J, Wang C, Yang M, Lou Y, Wang L, Ni X, Hu X, Tang G, Zhang M, Cao S, Mao L, Qian J, Xu W, Wei J, Xu G, Meng H, Mai W, Yang C, Zhu H, Tong H, Yang J, Yu W, Wang J, Jin J. The clinical impact of IKZF1 mutation in acute myeloid leukemia. Exp Hematol Oncol 2023; 12:33. [PMID: 36997950 PMCID: PMC10061890 DOI: 10.1186/s40164-023-00398-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
AbstractGenetic heterogeneity poses a great challenge to the understanding and management of acute myeloid leukemia (AML). Knowledge of the IKZF1 mutation in AML specifically is extremely limited. In a previous work, we described the distribution pattern of IKZF1 mutation in AML, but its clinical impact has remained undefined due to the limited number of cases. Herein, we attempt to answer this question in one relatively large cohort covering 522 newly diagnosed AML patients. A total of 26 IKZF1 mutations were found in 20 AML patients (20/522, 3.83%). This condition has a young median age of onset of morbidity (P = 0.032). The baseline characteristics of IKZF1-mutated and wild-type patients were comparable. IKZF1 mutation showed significant co-occurrences with CEBPA (P < 0.001), SF3B1 (P < 0.001), and CSF3R (P = 0.005) mutations, and it was mutually exclusive with NPM1 mutation (P = 0.033). Although IKZF1-mutated AML was more preferably classified into the intermediate-risk group (P = 0.004), it showed one inferior complete remission rate (P = 0.032). AML with high burden of IKZF1 mutation (variant allele frequency > 0.20) showed relatively short overall survival period (P = 0.012), and it was an independent factor for the increased risk of death (hazard ratio, 6.101; 95% CI 2.278–16.335; P = 0.0003). In subgroup analysis, our results showed that IKZF1 mutation conferred poor therapeutic response and prognosis for SF3B1-mutated AML (P = 0.0017). We believe this work improves our knowledge of IKZF1 mutation.
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20
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Conserva MR, Redavid I, Anelli L, Zagaria A, Tarantini F, Cumbo C, Tota G, Parciante E, Coccaro N, Minervini CF, Minervini A, Specchia G, Musto P, Albano F. IKAROS in Acute Leukemia: A Positive Influencer or a Mean Hater? Int J Mol Sci 2023; 24:ijms24043282. [PMID: 36834692 PMCID: PMC9961161 DOI: 10.3390/ijms24043282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/31/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023] Open
Abstract
One key process that controls leukemogenesis is the regulation of oncogenic gene expression by transcription factors acting as tumor suppressors. Understanding this intricate mechanism is crucial to elucidating leukemia pathophysiology and discovering new targeted treatments. In this review, we make a brief overview of the physiological role of IKAROS and the molecular pathway that contributes to acute leukemia pathogenesis through IKZF1 gene lesions. IKAROS is a zinc finger transcription factor of the Krüppel family that acts as the main character during hematopoiesis and leukemogenesis. It can activate or repress tumor suppressors or oncogenes, regulating the survival and proliferation of leukemic cells. More than 70% of Ph+ and Ph-like cases of acute lymphoblastic leukemia exhibit IKZF1 gene variants, which are linked to worse treatment outcomes in both childhood and adult B-cell precursor acute lymphoblastic leukemia. In the last few years, much evidence supporting IKAROS involvement in myeloid differentiation has been reported, suggesting that loss of IKZF1 might also be a determinant of oncogenesis in acute myeloid leukemia. Considering the complicated "social" network that IKAROS manages in hematopoietic cells, we aim to focus on its involvement and the numerous alterations of molecular pathways it can support in acute leukemias.
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Affiliation(s)
- Maria Rosa Conserva
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Immacolata Redavid
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Luisa Anelli
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Antonella Zagaria
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Francesco Tarantini
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Cosimo Cumbo
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Giuseppina Tota
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Elisa Parciante
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Nicoletta Coccaro
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Crescenzio Francesco Minervini
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Angela Minervini
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Giorgina Specchia
- School of Medicine, University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Pellegrino Musto
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Francesco Albano
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
- Correspondence:
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21
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Matza Porges S, Shamriz O. Genetics of Immune Dysregulation and Cancer Predisposition: Two Sides of the Same Coin. Clin Exp Immunol 2022; 210:114-127. [PMID: 36165533 PMCID: PMC9750831 DOI: 10.1093/cei/uxac089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/17/2022] [Accepted: 09/23/2022] [Indexed: 01/25/2023] Open
Abstract
Approximately 10% of cancers have a hereditary predisposition. However, no genetic diagnosis is available in 60%-80% of familial cancers. In some of these families, immune dysregulation-mediated disease is frequent. The immune system plays a critical role in identifying and eliminating tumors; thus, dysregulation of the immune system can increase the risk of developing cancer. This review focuses on some of the genes involved in immune dysregulation the promote the risk for cancer. Genetic counseling for patients with cancer currently focuses on known genes that raise the risk of cancer. In missing hereditary familial cases, the history family of immune dysregulation should be recorded, and genes related to the immune system should be analyzed in relevant families. On the other hand, patients with immune disorders diagnosed with a pathogenic mutation in an immune regulatory gene may have an increased risk of cancer. Therefore, those patients need to be under surveillance for cancer. Gene panel and exome sequencing are currently standard methods for genetic diagnosis, providing an excellent opportunity to jointly test cancer and immune genes.
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Affiliation(s)
- Sigal Matza Porges
- Department of Human Genetics, Institute for Medical Research, the Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Biotechnology, Hadassah Academic College, Jerusalem, Israel
| | - Oded Shamriz
- Allergy and Clinical Immunology Unit, Department of Medicine, Hadassah Medical Organization, The Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, The Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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22
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Xu K, Li S, Pandey P, Kang AY, Morimoto LM, Mancuso N, Ma X, Metayer C, Wiemels JL, de Smith AJ. Investigating DNA methylation as a mediator of genetic risk in childhood acute lymphoblastic leukemia. Hum Mol Genet 2022; 31:3741-3756. [PMID: 35717575 PMCID: PMC9616572 DOI: 10.1093/hmg/ddac137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/28/2022] [Accepted: 06/13/2022] [Indexed: 11/14/2022] Open
Abstract
Genome-wide association studies have identified a growing number of single nucleotide polymorphisms (SNPs) associated with childhood acute lymphoblastic leukemia (ALL), yet the functional roles of most SNPs are unclear. Multiple lines of evidence suggest that epigenetic mechanisms may mediate the impact of heritable genetic variation on phenotypes. Here, we investigated whether DNA methylation mediates the effect of genetic risk loci for childhood ALL. We performed an epigenome-wide association study (EWAS) including 808 childhood ALL cases and 919 controls from California-based studies using neonatal blood DNA. For differentially methylated CpG positions (DMPs), we next conducted association analysis with 23 known ALL risk SNPs followed by causal mediation analyses addressing the significant SNP-DMP pairs. DNA methylation at CpG cg01139861, in the promoter region of IKZF1, mediated the effects of the intronic IKZF1 risk SNP rs78396808, with the average causal mediation effect (ACME) explaining ~30% of the total effect (ACME P = 0.0031). In analyses stratified by self-reported race/ethnicity, the mediation effect was only significant in Latinos, explaining ~41% of the total effect of rs78396808 on ALL risk (ACME P = 0.0037). Conditional analyses confirmed the presence of at least three independent genetic risk loci for childhood ALL at IKZF1, with rs78396808 unique to non-European populations. We also demonstrated that the most significant DMP in the EWAS, CpG cg13344587 at gene ARID5B (P = 8.61 × 10-10), was entirely confounded by the ARID5B ALL risk SNP rs7090445. Our findings provide new insights into the functional pathways of ALL risk SNPs and the DNA methylation differences associated with risk of childhood ALL.
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Affiliation(s)
- Keren Xu
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90033, USA
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90033, USA
| | - Priyatama Pandey
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90033, USA
| | - Alice Y Kang
- School of Public Health, University of California, Berkeley, Berkeley, CA 94704, USA
| | - Libby M Morimoto
- School of Public Health, University of California, Berkeley, Berkeley, CA 94704, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90033, USA
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, Berkeley, CA 94704, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90033, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90033, USA
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23
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Tang B, Cai Z, Wang Z, Lin D, He X, Li Q, Liang X, Huang K, Zhou X, Lin R, Xu N, Fan Z, Huang F, Sun J, Liu X, Liu Q, Zhou H. Allogeneic hematopoietic stem cell transplantation overcome the poor prognosis of patients with IKZF1plus CD20-a very high-risk subtype in B-cell acute lymphoblastic leukemia. Bone Marrow Transplant 2022; 57:1751-1757. [PMID: 36056210 DOI: 10.1038/s41409-022-01797-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/13/2022] [Accepted: 08/17/2022] [Indexed: 11/10/2022]
Abstract
Genetic deletions of IKZF1 (IKZF1del) and IKZF1del plus other mutations (IKZF1plus) have been identified in B-cell acute lymphoblastic leukemia (B-ALL) with a poor prognosis. Herein, we investigated the combination of IKZF1del and CD20 immunotypes in adult patients with B-ALL in the PDT-ALL-2016 cohort. This study cohort consisted of 161 patients with B-ALL with detailed information on IKZF1del and CD20 expression. The independent cohort included 196 patients from the TARGET dataset. IKZF1del was detected in 36.0% of patients with 3-year event-free survival (EFS) of 37.1 ± 6.7% and overall survival (OS) of 51.5 ± 7.3%, compared to IKZF1 wild-type (IKZF1wt) with an EFS 55.3 ± 5.1% (P = 0.011) and OS 74.4 ± 4.5% (P = 0.013), respectively. CD20-positive (CD20+) was associated with inferior EFS compared to the CD20-negative (CD20-) group (P = 0.020). Furthermore, IKZF1del coupled with CD20+, IKZF1del/CD20+, comprised 12.4% of patients with a 3-year EFS of 25.0 ± 9.7%, compared with IKZF1wt/CD20- (P ≤ 0.001) and IKZF1del/CD20- (P = 0.047) groups. Multivariable analyses demonstrated the independence of IKZF1del/CD20+, with the highest predicted hazard ratio for EFS and OS. Furthermore, the prognostic panel of IKZF1del/CD20+ was confirmed in the TARGET cohort. Notably, neither the IKZF1del, CD20+, or IKZF1del/CD20+ groups were identified to have poor outcomes in the cohort of allogeneic hematopoietic stem cell transplantation (n = 81).Collectively, our data define IKZF1del/CD20+ as a very high-risk subtype in B-ALL, and allo-HSCT could abrogate the poor outcome of both IKZF1del and IKZF1del/CD20+ subsets.
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Affiliation(s)
- Bingqing Tang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Hematology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Zihong Cai
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhixiang Wang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dainan Lin
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Hematology, Guangzhou Twelfth People's Hospital, Guangzhou, China
| | - Xianjun He
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Hematology, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Qiuli Li
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Hematology, the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xiaojie Liang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kangyu Huang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xuan Zhou
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ren Lin
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Na Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhiping Fan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fen Huang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jing Sun
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoli Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Hongsheng Zhou
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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24
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Nuclear Vav3 is required for polycomb repression complex-1 activity in B-cell lymphoblastic leukemogenesis. Nat Commun 2022; 13:3056. [PMID: 35650206 PMCID: PMC9160250 DOI: 10.1038/s41467-022-30651-7] [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: 04/14/2021] [Accepted: 05/10/2022] [Indexed: 12/23/2022] Open
Abstract
Acute B-cell lymphoblastic leukemia (B-ALL) results from oligo-clonal evolution of B-cell progenitors endowed with initiating and propagating leukemia properties. The activation of both the Rac guanine nucleotide exchange factor (Rac GEF) Vav3 and Rac GTPases is required for leukemogenesis mediated by the oncogenic fusion protein BCR-ABL. Vav3 expression becomes predominantly nuclear upon expression of BCR-ABL signature. In the nucleus, Vav3 interacts with BCR-ABL, Rac, and the polycomb repression complex (PRC) proteins Bmi1, Ring1b and Ezh2. The GEF activity of Vav3 is required for the proliferation, Bmi1-dependent B-cell progenitor self-renewal, nuclear Rac activation, protein interaction with Bmi1, mono-ubiquitination of H2A(K119) (H2AK119Ub) and repression of PRC-1 (PRC1) downstream target loci, of leukemic B-cell progenitors. Vav3 deficiency results in de-repression of negative regulators of cell proliferation and repression of oncogenic transcriptional factors. Mechanistically, we show that Vav3 prevents the Phlpp2-sensitive and Akt (S473)-dependent phosphorylation of Bmi1 on the regulatory residue S314 that, in turn, promotes the transcriptional factor reprogramming of leukemic B-cell progenitors. These results highlight the importance of non-canonical nuclear Rho GTPase signaling in leukemogenesis. Ph+ and Ph-like B-ALL remain poor prognosis leukemias. VAV3, a guanine nucleotide exchange factor, is activated and overexpressed in these leukemias. Here the authors reveal that leukemic VAV3 is predominantly nuclear. Nuclear VAV3, through its guanine nucleotide exchange factor and its effector nuclear RAC2, controls the repressive transcriptional activity of the polycomb repression complex-1 via nuclear AKT/PHLPP2 regulated BMI1.
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25
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Modvig S, Wernersson R, Øbro NF, Olsen LR, Christensen C, Rosthøj S, Degn M, Jürgensen GW, Madsen HO, Albertsen BK, Wehner PS, Rosthøj S, Lilljebjörn H, Fioretos T, Schmiegelow K, Marquart HV. High CD34 surface expression in BCP-ALL predicts poor induction therapy response and is associated with altered expression of genes related to cell migration and adhesion. Mol Oncol 2022; 16:2015-2030. [PMID: 35271751 PMCID: PMC9120905 DOI: 10.1002/1878-0261.13207] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 02/01/2022] [Accepted: 03/07/2022] [Indexed: 11/25/2022] Open
Abstract
Minimal residual disease (MRD) constitutes the most important prognostic factor in B‐cell precursor acute lymphoblastic leukemia (BCP‐ALL). Flow cytometry is widely used in MRD assessment, yet little is known regarding the effect of different immunophenotypic subsets on outcome. In this study of 200 BCP‐ALL patients, we found that a CD34‐positive, CD38 dim‐positive, nTdT dim‐positive immunophenotype on the leukemic blasts was associated with poor induction therapy response and predicted an MRD level at the end of induction therapy (EOI) of ≥ 0.001. CD34 expression was strongly and positively associated with EOI MRD, whereas CD34‐negative patients had a low relapse risk. Further, CD34 expression increased from diagnosis to relapse. CD34 is a stemness‐associated cell‐surface molecule, possibly involved in cell adhesion/migration or survival. Accordingly, genes associated with stemness were overrepresented among the most upregulated genes in CD34‐positive leukemias, and protein–protein interaction networks showed an overrepresentation of genes associated with cell migration, cell adhesion, and negative regulation of apoptosis. The present work is the first to demonstrate a CD34‐negative immunophenotype as a good prognostic factor in ALL, whereas high CD34 expression is associated with poor therapy response and an altered gene expression profile reminiscent of migrating cancer stem‐like cells.
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Affiliation(s)
- Signe Modvig
- Dept. of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Rasmus Wernersson
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.,Intomics A/S, Lyngby, Denmark
| | - Nina Friesgaard Øbro
- Dept. of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Lars Rønn Olsen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Claus Christensen
- Dept. of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Susanne Rosthøj
- Section of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - Matilda Degn
- Dept. of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet
| | - Gitte Wullf Jürgensen
- Dept. of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Hans O Madsen
- Dept. of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Birgitte Klug Albertsen
- Dept. of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Peder Skov Wehner
- H.C. Andersen Children's Hospital, Odense University Hospital, Odense, Denmark
| | - Steen Rosthøj
- Department of Pediatrics and Adolescent Medicine, Aalborg University Hospital, Aalborg, Denmark
| | - Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Kjeld Schmiegelow
- Dept. of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Dept. of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Faculty of Medicine, Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Hanne Vibeke Marquart
- Dept. of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
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26
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Braun M, Pastorczak A, Sedek L, Taha J, Madzio J, Jatczak-Pawlik I, Wypyszczak K, Matysiak M, Derwich K, Lejman M, Kazanowska B, Szczepanski T, Kowalczyk JR, Mlynarski W. Prognostic significance of IKZF1 deletions and IKZF1 plus profile in children with B-cell precursor acute lymphoblastic leukemia treated according to the ALL-IC BFM 2009 protocol. Hematol Oncol 2022; 40:430-441. [PMID: 35118711 DOI: 10.1002/hon.2973] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 11/07/2022]
Abstract
The strongest predictors of outcome in pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) are minimal residual disease (MRD) and specific molecular abnormalities. One unfavorable prognostic factor is the presence of IKZF1 gene aberrations, particularly when co-occurring with high MRD level at the end of induction treatment. The present study determines the predictive value of a recently-defined IKZF1-plus (IKZF1plus ) microdeletion profile in 373 children with BCP-ALL treated according to the ALL-IC BFM 2009 protocol. IKZF1-wild type (IKZF1wt ) patients demonstrated lower leukemic burden parameters than those carrying IKZF1 deletion (IKZF1del [n=26, 7.0%]) or IKZF1plus pattern (n=34, 9.1%): i) median blast percentage at diagnosis (78.0% vs. 86.9% vs. 86.0%; p=0.021); ii) median MRD level at day 15 of induction protocol (0.3% vs. 2.1% vs. 0.8%; p=0.011); iii) poor steroid response (7.6% vs. 26.5% vs. 12.5%; p=0.010). MRD level at day 33 (MRD33) exceeding 10-4 was more frequently observed in both the IKZF1del and IKZF1plus subgroups than in IKZF1wt patients (n=9 [36.0%] vs. n=13 [41.9%] vs. n=70 [24.0%], p=0.051). IKZF1plus individuals showed a tendency for a lower MRD reduction between day 15 and 33 compared to IKZF1del patients (p=0.124). IKZF1del and IKZF1plus patients showed decreased relapse-free survival (HR [95%CI] for IKZF1wt as reference=2.72 [1.21-6.11] and 2.00 [0.87-4.49], respectively, p=0.023). Both genetic markers including IKZF1del and IKZF1plus microdeletion profile provide additional predictive value of treatment outcome in childhood BCP-ALL and may contribute to more efficient patient stratification; the same is true in MRD guided protocols, which are based on flow cytometric measurements on day 15 of induction protocol. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Marcin Braun
- Department of Pathology, Chair of Oncology, Medical University of Lodz, Poland.,Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Poland
| | - Agata Pastorczak
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Poland
| | - Lukasz Sedek
- Department of Pediatric Hematology and Oncology, Medical University of Silesia, Zabrze, Poland
| | - Joanna Taha
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Poland
| | - Joanna Madzio
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Poland
| | | | - Kamila Wypyszczak
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Poland
| | - Michał Matysiak
- Department of Pediatric Hematology and Oncology, Medical University of Warsaw, Poland
| | - Katarzyna Derwich
- Department of Pediatric Hematology, Oncology and Transplantology, University of Medical Sciences, Poznan, Poland
| | - Monika Lejman
- Laboratory of Genetic Diagnostics, Medical University of Lublin, Poland
| | - Bernarda Kazanowska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Wroclaw, Poland
| | - Tomasz Szczepanski
- Department of Pediatric Hematology and Oncology, Medical University of Silesia, Zabrze, Poland
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology and Oncology, Medical University of Lublin, Poland
| | - Wojciech Mlynarski
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Poland
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27
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Hasan MDM, Rashid MU, Suman SP, Perreault H, Paliwal J, Rodas-González A. Tandem Mass Tag Labeling-Based Analysis to Characterize Muscle-Specific Proteome Changes during Postmortem Aging of Bison Longissimus Lumborum and Psoas Major Muscles. MEAT AND MUSCLE BIOLOGY 2021. [DOI: 10.22175/mmb.13055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The objective of the study was to examine the variations in sarcoplasmic proteomes of bison longissimus lumborum (LL) and psoas major (PM) muscles during postmortem aging utilizing tandem mass tag (TMT) isobaric labeling coupled with liquid chromatography mass-spectrometry (LC-MS/MS) for the categorization of muscles with muscle-specific inherent color stability. A total of 576 proteins were identified (P < 0.05) in both bison LL and PM muscles, where 97 proteins were identified as differentially abundant (fold change > 1.5, P < 0.05) from the three comparisons between muscles during postmortem aging periods (PM vs LL at 2 d, 7 d and 14 d). Among those proteins, the most important protein groups based on functions are related to electron transport chain (ETC) or oxidative phosphorylation, tricarboxylic acid cycle (TCA), ATP transport, carbohydrate metabolism, fatty acid oxidation, chaperones, oxygen transport, muscle contraction, calcium signaling, and protein synthesis. In PM, most of the proteins from ETC, TCA cycle, fatty acid oxidation, ATP and oxygen transport, and muscle contraction were more abundant or exhibited increased expression during aging compared to LL. On the other hand, the proteins involved in carbohydrate metabolism, chaperone function and protein synthesis mostly exhibited decreased expression in PM muscle relative to LL. These results clearly demonstrate that the proteins associated with oxidative metabolism showed increased expression in PM muscles. This indicates that oxidative damage or subsequent color deterioration resulted in bison PM muscles being attacked by the reactive oxygen species produced during those metabolic process. In contrast, proteins involved in glycolysis and chaperone activity exhibited a decrease in expression in bison PM muscles, resulting decline in color stability compared with LL. Because glycolytic enzymes and chaperones maintain oxidative and/or color stability by producing reducing equivalents in glycolytic pathway and with the protein folding ability of chaperones, respectively in LL muscles.
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28
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Xia R, Cheng Y, Han X, Wei Y, Wei X. Ikaros Proteins in Tumor: Current Perspectives and New Developments. Front Mol Biosci 2021; 8:788440. [PMID: 34950704 PMCID: PMC8689071 DOI: 10.3389/fmolb.2021.788440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/09/2021] [Indexed: 02/05/2023] Open
Abstract
Ikaros is a zinc finger transcription factor (TF) of the Krüppel family member, which significantly regulates normal lymphopoiesis and tumorigenesis. Ikaros can directly initiate or suppress tumor suppressors or oncogenes, consequently regulating the survival and proliferation of cancer cells. Over recent decades, a series of studies have been devoted to exploring and clarifying the relationship between Ikaros and associated tumors. Therapeutic strategies targeting Ikaros have shown promising therapeutic effects in both pre-clinical and clinical trials. Nevertheless, the increasingly prominent problem of drug resistance targeted to Ikaros and its analog is gradually appearing in our field of vision. This article reviews the role of Ikaros in tumorigenesis, the mechanism of drug resistance, the progress of targeting Ikaros in both pre-clinical and clinical trials, and the potential use of associated therapy in cancer therapy.
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Affiliation(s)
- Ruolan Xia
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yuan Cheng
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xuejiao Han
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
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29
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Chang Y, Min J, Jarusiewicz JA, Actis M, Yu-Chen Bradford S, Mayasundari A, Yang L, Chepyala D, Alcock LJ, Roberts KG, Nithianantham S, Maxwell D, Rowland L, Larsen R, Seth A, Goto H, Imamura T, Akahane K, Hansen BS, Pruett-Miller SM, Paietta EM, Litzow MR, Qu C, Yang JJ, Fischer M, Rankovic Z, Mullighan CG. Degradation of Janus kinases in CRLF2-rearranged acute lymphoblastic leukemia. Blood 2021; 138:2313-2326. [PMID: 34110416 PMCID: PMC8662068 DOI: 10.1182/blood.2020006846] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 04/02/2021] [Indexed: 11/20/2022] Open
Abstract
CRLF2-rearranged (CRLF2r) acute lymphoblastic leukemia (ALL) accounts for more than half of Philadelphia chromosome-like (Ph-like) ALL and is associated with a poor outcome in children and adults. Overexpression of CRLF2 results in activation of Janus kinase (JAK)-STAT and parallel signaling pathways in experimental models, but existing small molecule inhibitors of JAKs show variable and limited efficacy. Here, we evaluated the efficacy of proteolysis-targeting chimeras (PROTACs) directed against JAKs. Solving the structure of type I JAK inhibitors ruxolitinib and baricitinib bound to the JAK2 tyrosine kinase domain enabled the rational design and optimization of a series of cereblon (CRBN)-directed JAK PROTACs utilizing derivatives of JAK inhibitors, linkers, and CRBN-specific molecular glues. The resulting JAK PROTACs were evaluated for target degradation, and activity was tested in a panel of leukemia/lymphoma cell lines and xenograft models of kinase-driven ALL. Multiple PROTACs were developed that degraded JAKs and potently killed CRLF2r cell lines, the most active of which also degraded the known CRBN neosubstrate GSPT1 and suppressed proliferation of CRLF2r ALL in vivo, e.g. compound 7 (SJ988497). Although dual JAK/GSPT1-degrading PROTACs were the most potent, the development and evaluation of multiple PROTACs in an extended panel of xenografts identified a potent JAK2-degrading, GSPT1-sparing PROTAC that demonstrated efficacy in the majority of kinase-driven xenografts that were otherwise unresponsive to type I JAK inhibitors, e.g. compound 8 (SJ1008030). Together, these data show the potential of JAK-directed protein degradation as a therapeutic approach in JAK-STAT-driven ALL and highlight the interplay of JAK and GSPT1 degradation activity in this context.
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Affiliation(s)
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics
| | | | | | | | | | - Lei Yang
- Department of Chemical Biology and Therapeutics
| | | | | | | | | | | | | | - Randolph Larsen
- Department of Pharmaceutical Sciences, and
- Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN
| | | | - Hiroaki Goto
- Division of Hemato-Oncology/Regenerative Medicine, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Toshihiko Imamura
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Koshi Akahane
- Department of Pediatrics, School of Medicine, University of Yamanashi, Chuo, Japan
| | - Baranda S Hansen
- Center for Advanced Genome Engineering, St Jude Children's Research Hospital, Memphis, TN
| | | | - Elisabeth M Paietta
- Cancer Center, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY
| | - Mark R Litzow
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN; and
| | | | - Jun J Yang
- Department of Pharmaceutical Sciences, and
- Hematological Malignancies Program, St Jude Children's Research Hospital, Memphis, TN
| | - Marcus Fischer
- Department of Chemical Biology and Therapeutics
- Department of Structural Biology
- Cancer Biology Program, and
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics
- Cancer Biology Program, and
| | - Charles G Mullighan
- Department of Pathology
- Hematological Malignancies Program, St Jude Children's Research Hospital, Memphis, TN
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30
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Tran TH, Tasian SK. Has Ph-like ALL Superseded Ph+ ALL as the Least Favorable Subtype? Best Pract Res Clin Haematol 2021; 34:101331. [PMID: 34865703 DOI: 10.1016/j.beha.2021.101331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is a subset of high-risk B-ALL associated with high relapse risk and inferior clinical outcomes across the pediatric-to-adult age spectrum. Ph-like ALL is characterized by frequent IKZF1 alterations and a kinase-activated gene expression profile similar to that of Philadelphia chromosome-positive (Ph+) ALL, yet lacks the canonical BCR-ABL1 rearrangement. Advances in high-throughput sequencing technologies during the past decade have unraveled the genomic landscape of Ph-like ALL, revealing a diverse array of kinase-activating translocations and mutations that may be amenable to targeted therapies that have set a remarkable precision medicine paradigm for patients with Ph + ALL. Collaborative scientific efforts to identify and characterise Ph-like ALL during the past decade has directly informed current precision medicine trials investigating the therapeutic potential of tyrosine kinase inhibitor-based therapies for children, adolescents, and adults with Ph-like ALL, although the most optimal treatment paradigm for this high-risk group of patients has yet to be established. Herein, we describe the epidemiology, clinical features, and biology of Ph-like ALL, highlight challenges in implementing pragmatic and cost-effective diagnostic algorithms in the clinic, and describe the milieu of treatment strategies under active investigation that strive to decrease relapse risk and improve long-term survival for patients with Ph-like ALL as has been successfully achieved for those with Ph + ALL.
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Affiliation(s)
- Thai Hoa Tran
- Division of Pediatric Hematology-Oncology, Charles-Bruneau Cancer Center, CHU Sainte-Justine, Montreal, QC, Canada; Department of Pediatrics, University of Montreal, Montreal, QC, Canada
| | - Sarah K Tasian
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics and Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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31
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Modeling IKZF1 lesions in B-ALL reveals distinct chemosensitivity patterns and potential therapeutic vulnerabilities. Blood Adv 2021; 5:3876-3890. [PMID: 34492683 DOI: 10.1182/bloodadvances.2020002408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 05/26/2021] [Indexed: 12/25/2022] Open
Abstract
IKAROS family zinc finger 1 (IKZF1) alterations represent a diverse group of genetic lesions that are associated with an increased risk of relapse in B-cell acute lymphoblastic leukemia. Due to the heterogeneity of concomitant lesions, it remains unclear how IKZF1 abnormalities directly affect cell function and therapy resistance, and whether their consideration as a prognostic indicator is valuable in improving outcome. CRISPR/Cas9 strategies were used to engineer multiple panels of isogeneic lymphoid leukemia cell lines with a spectrum of IKZF1 lesions to measure changes in chemosensitivity, gene expression, cell cycle, and in vivo engraftment that can be linked to loss of IKAROS protein. IKZF1 knockout and heterozygous null cells displayed relative resistance to a number of common therapies for B-cell acute lymphoblastic leukemia, including dexamethasone, asparaginase, and daunorubicin. Transcription profiling revealed a stem/myeloid cell-like phenotype and JAK/STAT upregulation after IKAROS loss. A CRISPR homology-directed repair strategy was also used to knock-in the dominant-negative IK6 isoform into the endogenous locus, and a similar drug resistance profile, with the exception of retained dexamethasone sensitivity, was observed. Interestingly, IKZF1 knockout and IK6 knock-in cells both have significantly increased sensitivity to cytarabine, likely owing to marked downregulation of SAMHD1 after IKZF1 knockout. Both types of IKZF1 lesions decreased the survival time of xenograft mice, with higher numbers of circulating blasts and increased organ infiltration. Given these findings, exact specification of IKZF1 status in patients may be a beneficial addition to risk stratification and could inform therapy.
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32
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Mangum DS, Meyer JA, Mason CC, Shams S, Maese LD, Gardiner JD, Downie JM, Pei D, Cheng C, Gleason A, Luo M, Pui CH, Aplenc R, Hunger SP, Loh M, Greaves M, Trede N, Raetz E, Frazer JK, Mullighan CG, Engel ME, Miles RR, Rabin KR, Schiffman JD. Association of Combined Focal 22q11.22 Deletion and IKZF1 Alterations With Outcomes in Childhood Acute Lymphoblastic Leukemia. JAMA Oncol 2021; 7:1521-1528. [PMID: 34410295 DOI: 10.1001/jamaoncol.2021.2723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Alterations in the IKZF1 gene drive B-cell acute lymphoblastic leukemia (B-ALL) but are not routinely used to stratify patients by risk because of inconsistent associations with outcomes. We describe a novel deletion in 22q11.22 that was consistently associated with very poor outcomes in patients with B-ALL with IKZF1 alterations. Objective To determine whether focal deletions within the λ variable chain region in chromosome 22q11.22 were associated with patients with B-ALL with IKZF1 alterations with the highest risk of relapse and/or death. Design, Setting, and Participants This cohort study included 1310 primarily high-risk pediatric patients with B-ALL who were taken from 6 independent clinical cohorts, consisting of 3 multicenter cohorts (AALL0232 [2004-2011], P9906 [2000-2003], and patients with Down syndrome who were pooled from national and international studies) and 3 single-institution cohorts (University of Utah [Salt Lake City], Children's Hospital of Philadelphia [Philadelphia, Pennsylvania], and St. Jude Children's Hospital [Memphis, Tennessee]). Data analysis began in 2011 using patients from the older studies first, and data analysis concluded in 2021. Exposures Focal 22q11.22 deletions. Main Outcomes and Measures Event-free and overall survival was investigated. The hypothesis that 22q11.22 deletions stratified the prognostic effect of IKZF1 alterations was formulated while investigating nearby deletions in VPREB1 in 2 initial cohorts (n = 270). Four additional cohorts were then obtained to further study this association (n = 1040). Results This study of 1310 patients with B-ALL (717 male [56.1%] and 562 female patients [43.9%]) found that focal 22q11.22 deletions are frequent (518 of 1310 [39.5%]) in B-ALL and inconsistent with physiologic V(D)J recombination. A total of 299 of 1310 patients with B-ALL had IKZF1 alterations. Among patients with IKZF1 alterations, more than half shared concomitant focal 22q11.22 deletions (159 of 299 [53.0%]). Patients with combined IKZF1 alterations and 22q11.22 deletions had worse outcomes compared with patients with IKZF1 alterations and wild-type 22q11.22 alleles in every cohort examined (combined cohorts: 5-year event-free survival rates, 43.3% vs 68.5%; hazard ratio [HR], 2.18; 95% CI, 1.54-3.07; P < .001; 5-year overall survival rates, 66.9% vs 83.9%; HR, 2.05; 95% CI, 1.32-3.21; P = .001). While 22q11.22 deletions were not prognostic in patients with wild-type IKZF1 , concomitant 22q11.22 deletions in patients with IKZF1 alterations stratified outcomes across additional risk groups, including patients who met the IKZF1plus criteria, and maintained independent significance in multivariate analysis for event-free survival (HR, 2.05; 95% CI, 1.27-3.29; P = .003) and overall survival (HR, 1.83; 95% CI, 1.01-3.34; P = .05). Conclusions and Relevance This cohort study suggests that 22q11.22 deletions identify patients with B-ALL and IKZF1 alterations who have very poor outcomes and may offer a new genetic biomarker to further refine B-ALL risk stratification and treatment strategies.
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Affiliation(s)
- David Spencer Mangum
- Nemours/Alfred I. DuPont Hospital for Children, Division of Pediatric Hematology/Oncology, Wilmington, Delaware
| | - Julia A Meyer
- Division of Pediatric Hematology & Oncology, Department of Pediatrics, University of Utah, Salt Lake City.,Division of Pediatric Hematology and Oncology, University of California, San Francisco
| | - Clinton C Mason
- Division of Pediatric Hematology & Oncology, Department of Pediatrics, University of Utah, Salt Lake City
| | | | - Luke D Maese
- Division of Pediatric Hematology & Oncology, Department of Pediatrics, University of Utah, Salt Lake City
| | - Jamie D Gardiner
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City
| | | | - Deqing Pei
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Cheng Cheng
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Adam Gleason
- Department of Pathology & Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Minjie Luo
- Department of Pathology & Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ching-Hon Pui
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Richard Aplenc
- Division of Oncology and the Center for Childhood Cancer Research, The Children's Hospital of Philadelphia and The Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Stephen P Hunger
- Division of Oncology and the Center for Childhood Cancer Research, The Children's Hospital of Philadelphia and The Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Mignon Loh
- Division of Pediatric Hematology and Oncology, University of California, San Francisco
| | - Mel Greaves
- Institute of Cancer Research, London, England
| | | | - Elizabeth Raetz
- Department of Pediatrics, NYU Langone Health, New York, New York
| | - J Kimble Frazer
- Jimmy Everest Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City
| | - Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael E Engel
- Division of Pediatric Hematology Oncology, Department of Pediatrics, University of Virginia, Charlottesville
| | - Rodney R Miles
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City
| | - Karen R Rabin
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Joshua D Schiffman
- Division of Pediatric Hematology & Oncology, Department of Pediatrics, University of Utah, Salt Lake City.,Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City.,PEEL Therapeutics, Inc, Salt Lake City, Utah
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33
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Cobaleda C, Vicente-Dueñas C, Sanchez-Garcia I. Infectious triggers and novel therapeutic opportunities in childhood B cell leukaemia. Nat Rev Immunol 2021; 21:570-581. [PMID: 33558682 DOI: 10.1038/s41577-021-00505-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2021] [Indexed: 01/30/2023]
Abstract
B cell acute lymphoblastic leukaemia (B-ALL) is the most common form of childhood cancer. Although treatment has advanced remarkably in the past 50 years, it still fails in ~20% of patients. Recent studies revealed that more than 5% of healthy newborns carry preleukaemic clones that originate in utero, but only a small percentage of these carriers will progress to overt B-ALL. The drivers of progression are unclear, but B-ALL incidence seems to be increasing in parallel with the adoption of modern lifestyles. Emerging evidence shows that a major driver for the conversion from the preleukaemic state to the B-ALL state is exposure to immune stressors, such as infection. Here, we discuss our current understanding of the environmental triggers and genetic predispositions that may lead to B-ALL, highlighting lessons from epidemiology, the clinic and animal models, and identifying priority areas for future research.
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Affiliation(s)
- Cesar Cobaleda
- Immune System Development and Function Unit, Centro de Biología Molecular Severo Ochoa, CSIC and Universidad Autónoma de Madrid, Madrid, Spain.
| | | | - Isidro Sanchez-Garcia
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. .,Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC and Universidad de Salamanca, Salamanca, Spain.
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34
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Iacobucci I, Kimura S, Mullighan CG. Biologic and Therapeutic Implications of Genomic Alterations in Acute Lymphoblastic Leukemia. J Clin Med 2021; 10:3792. [PMID: 34501239 PMCID: PMC8432032 DOI: 10.3390/jcm10173792] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most successful paradigm of how risk-adapted therapy and detailed understanding of the genetic alterations driving leukemogenesis and therapeutic response may dramatically improve treatment outcomes, with cure rates now exceeding 90% in children. However, ALL still represents a leading cause of cancer-related death in the young, and the outcome for older adolescents and young adults with ALL remains poor. In the past decade, next generation sequencing has enabled critical advances in our understanding of leukemogenesis. These include the identification of risk-associated ALL subtypes (e.g., those with rearrangements of MEF2D, DUX4, NUTM1, ZNF384 and BCL11B; the PAX5 P80R and IKZF1 N159Y mutations; and genomic phenocopies such as Ph-like ALL) and the genomic basis of disease evolution. These advances have been complemented by the development of novel therapeutic approaches, including those that are of mutation-specific, such as tyrosine kinase inhibitors, and those that are mutation-agnostic, including antibody and cellular immunotherapies, and protein degradation strategies such as proteolysis-targeting chimeras. Herein, we review the genetic taxonomy of ALL with a focus on clinical implications and the implementation of genomic diagnostic approaches.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
| | - Shunsuke Kimura
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
- Comprehensive Cancer Center, Hematological Malignancies Program, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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35
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Lee SHR, Li Z, Tai ST, Oh BLZ, Yeoh AEJ. Genetic Alterations in Childhood Acute Lymphoblastic Leukemia: Interactions with Clinical Features and Treatment Response. Cancers (Basel) 2021; 13:4068. [PMID: 34439222 PMCID: PMC8393341 DOI: 10.3390/cancers13164068] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/03/2021] [Accepted: 08/08/2021] [Indexed: 12/28/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer among children. This aggressive cancer comprises multiple molecular subtypes, each harboring a distinct constellation of somatic, and to a lesser extent, inherited genetic alterations. With recent advances in genomic analyses such as next-generation sequencing techniques, we can now clearly identify >20 different genetic subtypes in ALL. Clinically, identifying these genetic subtypes will better refine risk stratification and determine the optimal intensity of therapy for each patient. Underpinning each genetic subtype are unique clinical and therapeutic characteristics, such as age and presenting white blood cell (WBC) count. More importantly, within each genetic subtype, there is much less variability in treatment response and survival outcomes compared with current risk factors such as National Cancer Institute (NCI) criteria. We review how this new taxonomy of genetic subtypes in childhood ALL interacts with clinical risk factors used widely, i.e., age, presenting WBC, IKZF1del, treatment response, and outcomes.
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Affiliation(s)
- Shawn H. R. Lee
- VIVA-University Children’s Cancer Centre, Khoo-Teck Puat-National University Children’s Medical Institute, National University Hospital, Singapore 119074, Singapore; (S.H.R.L.); (B.L.Z.O.)
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore; (Z.L.); (S.T.T.)
| | - Zhenhua Li
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore; (Z.L.); (S.T.T.)
| | - Si Ting Tai
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore; (Z.L.); (S.T.T.)
| | - Bernice L. Z. Oh
- VIVA-University Children’s Cancer Centre, Khoo-Teck Puat-National University Children’s Medical Institute, National University Hospital, Singapore 119074, Singapore; (S.H.R.L.); (B.L.Z.O.)
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore; (Z.L.); (S.T.T.)
| | - Allen E. J. Yeoh
- VIVA-University Children’s Cancer Centre, Khoo-Teck Puat-National University Children’s Medical Institute, National University Hospital, Singapore 119074, Singapore; (S.H.R.L.); (B.L.Z.O.)
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore; (Z.L.); (S.T.T.)
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36
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Genomic Analyses of Pediatric Acute Lymphoblastic Leukemia Ph+ and Ph-Like-Recent Progress in Treatment. Int J Mol Sci 2021; 22:ijms22126411. [PMID: 34203891 PMCID: PMC8232636 DOI: 10.3390/ijms22126411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/04/2021] [Accepted: 06/14/2021] [Indexed: 12/24/2022] Open
Abstract
Pediatric acute lymphoblastic leukemia (ALL) with t(9;22)(q34;q11.2) is a very rare malignancy in children. Approximately 3-5% of pediatric ALL patients present with the Philadelphia chromosome. Previously, children with Ph+ had a poor prognosis, and were considered for allogeneic stem cell transplantation (allo-HSCT) in their first remission (CR1). Over the last few years, the treatment of childhood ALL has significantly improved due to standardized research protocols. Hematopoietic stem cell transplantation (HSCT) has been the gold standard therapy in ALL Ph+ patients, but recently first-generation tyrosine kinase inhibitor (TKI)-imatinib became a major milestone in increasing overall survival. Genomic analyses give the opportunity for the investigation of new fusions or mutations, which can be used to establish effective targeted therapies. Alterations of the IKZF1 gene are present in a large proportion of pediatric and adult ALL Ph+ cases. IKZF1 deletions are present in ~15% of patients without BCR-ABL1 rearrangements. In BCR-ABL1-negative cases, IKZF1 deletions have been shown to have an independent prognostic impact, carrying a three-fold increased risk of treatment failure. The prognostic significance of IKZF1 gene aberrations in pediatric ALL Ph+ is still under investigation. More research should focus on targeted therapies and immunotherapy, which is not associated with serious toxicity in the same way as classic chemotherapy, and on the improvement of patient outcomes. In this review, we provide a molecular analysis of childhood ALL with t(9;22)(q34;q11.2), including the Ph-like subtype, and of treatment strategies.
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37
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Retinoids in hematology: a timely revival? Blood 2021; 137:2429-2437. [PMID: 33651885 DOI: 10.1182/blood.2020010100] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/17/2021] [Indexed: 12/27/2022] Open
Abstract
The retinoic acid receptors (RARA, RARB, and RARG) are ligand-regulated nuclear receptors that act as transcriptional switches. These master genes drew significant interest in the 1990s because of their key roles in embryogenesis and involvement in a rare malignancy, acute promyelocytic leukemia (APL), in which the RARA (and very rarely, RARG or RARB) genes are rearranged, underscoring the central role of deregulated retinoid signaling in leukemogenesis. Several recent provocative observations have revived interest in the roles of retinoids in non-APL acute myeloid leukemia (AML), as well as in normal hematopoietic differentiation. We review the role of retinoids in hematopoiesis, as well as in the treatment of non-APL AMLs. From this perspective, broader uses of retinoids in the management of hematopoietic tumors are discussed.
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38
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Adnan-Awad S, Kankainen M, Mustjoki S. Mutational landscape of chronic myeloid leukemia: more than a single oncogene leukemia. Leuk Lymphoma 2021; 62:2064-2078. [PMID: 33944660 DOI: 10.1080/10428194.2021.1894652] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The BCR-ABL1 fusion gene, which causes aberrant kinase activity and uncontrolled cell proliferation, is the hallmark of chronic myeloid leukemia (CML). The development of tyrosine kinase inhibitors (TKI) that target the BCR-ABL oncoprotein has led to dramatic improvement in CML management. However, some challenges remain to be addressed in the TKI era, including patient stratification and the selection of frontline TKIs and CML progression. Additionally, with the emerging goal of treatment-free remission (TFR) in CML management, biomarkers that predict the outcomes of stopping TKI remain to be identified. Notably, recent reports have revealed the power of genome screening in understanding the role of genome aberrations other than BCR-ABL1 in CML pathogenesis. These studies have discovered the presence of disease-phase specific mutations and linked certain mutations to inferior responses to TKI treatment and CML progression. A personalized approach that incorporates genetic data in tailoring treatment strategies has been successfully implemented in acute leukemia, and it represents a promising approach for the management of high-risk CML patients. In this article, we will review current knowledge about the mutational profile in different phases of CML as well as patterns of mutational dynamics in patients having different outcomes. We highlight the effects of somatic mutations involving certain genes (e.g. epigenetic modifiers) on the outcomes of TKI treatment. We also discuss the potential value of incorporating genetic data in treatment decisions and the routine care of CML patients as a future direction for optimizing CML management.
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Affiliation(s)
- Shady Adnan-Awad
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Matti Kankainen
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
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39
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Gupta SK, Bakhshi S, Gupta R, Sharma P, Pushpam D, Sahoo RK, Kamal VK. IKZF1 Deletion Subtyping and Outcome Analysis in BCR-ABL1-Negative Pediatric B-Cell Acute Lymphoblastic Leukemia: A Single-Institution Experience from North India. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2021; 21:e666-e673. [PMID: 33906825 DOI: 10.1016/j.clml.2021.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND IKZF1 deletions are associated with adverse outcomes in B-cell acute lymphoblastic leukemia (B-ALL). We assessed the prevalence and clinical impact of functional subtypes of IKZF1 deletions in pediatric BCR-ABL1-negative B-ALL. PATIENTS AND METHODS This retrospective study of IKZF1 deletions was done in cases of pediatric BCR-ABL1-negative B-ALL. The genomic DNA of cases, over a 53-month period, was analyzed using multiplex ligation-dependent probe amplification and multiplex fluorescent polymerase chain reaction. The deletions were divided into functional subgroups: (1) loss-of-function/haploinsufficiency, (2) dominant-negative, and (3) a combination of both types of deletion. The post-induction remission status, event-free survival (EFS), and overall survival (OS) were noted. RESULTS Out of 320 cases, 47 (14.7%) had IKZF1 deletions. Thirty-six of the 47 (77%) had loss-of-function deletions, 10 (21%) had dominant-negative deletions, and one (2%) had a combination of both types. The post-induction remission rates in cases with loss-of-function deletions (22/30, 73%; P = .060) and dominant-negative deletions (4/5, 80%; P = .517) were lower compared with those without deletions (215/248, 86.7%). These cases also had worse median EFS: 21.1 months (P = .006) for loss-of-function and 15.4 months (P = .156) for dominant-negative deletions, compared with 46.4 months in cases without IKZF1 deletions. They also had worse median OS: 23.4 months (P = .012) for loss-of-function deletions and 15.7 months (P = .233) for dominant-negative deletions, compared with median not reached in cases without IKZF1 deletions. CONCLUSION The IKZF1 deletions were seen in 14.7% of BCR-ABL1-negative pediatric B-ALL. Most of these deletions (77%) were loss-of-function type. The cases with loss-of-function deletions had lower remission rates and poor EFS and OS compared with cases without IKZF1 deletions. A similar trend of poor outcome was seen in the few cases with dominant-negative IKZF1 deletions.
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Affiliation(s)
- Sanjeev Kumar Gupta
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, All India Institute of Medical Sciences, New Delhi, India.
| | - Sameer Bakhshi
- Department of Medical Oncology, Dr. B.R.A. IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Preity Sharma
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Deepam Pushpam
- Department of Medical Oncology, Dr. B.R.A. IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Ranjit Kumar Sahoo
- Department of Medical Oncology, Dr. B.R.A. IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Vineet Kumar Kamal
- Division of Epidemiology and Biostatistics, National Institute of Epidemiology, Chennai, India
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Pastorczak A, Domka K, Fidyt K, Poprzeczko M, Firczuk M. Mechanisms of Immune Evasion in Acute Lymphoblastic Leukemia. Cancers (Basel) 2021; 13:1536. [PMID: 33810515 PMCID: PMC8037152 DOI: 10.3390/cancers13071536] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) results from a clonal expansion of abnormal lymphoid progenitors of B cell (BCP-ALL) or T cell (T-ALL) origin that invade bone marrow, peripheral blood, and extramedullary sites. Leukemic cells, apart from their oncogene-driven ability to proliferate and avoid differentiation, also change the phenotype and function of innate and adaptive immune cells, leading to escape from the immune surveillance. In this review, we provide an overview of the genetic heterogeneity and treatment of BCP- and T-ALL. We outline the interactions of leukemic cells in the bone marrow microenvironment, mainly with mesenchymal stem cells and immune cells. We describe the mechanisms by which ALL cells escape from immune recognition and elimination by the immune system. We focus on the alterations in ALL cells, such as overexpression of ligands for various inhibitory receptors, including anti-phagocytic receptors on macrophages, NK cell inhibitory receptors, as well as T cell immune checkpoints. In addition, we describe how developing leukemia shapes the bone marrow microenvironment and alters the function of immune cells. Finally, we emphasize that an immunosuppressive microenvironment can reduce the efficacy of chemo- and immunotherapy and provide examples of preclinical studies showing strategies for improving ALL treatment by targeting these immunosuppressive interactions.
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Affiliation(s)
- Agata Pastorczak
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 91-738 Lodz, Poland;
| | - Krzysztof Domka
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (K.D.); (K.F.); (M.P.)
- Doctoral School, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Klaudyna Fidyt
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (K.D.); (K.F.); (M.P.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Martyna Poprzeczko
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (K.D.); (K.F.); (M.P.)
| | - Malgorzata Firczuk
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (K.D.); (K.F.); (M.P.)
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41
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Wu L, Jiang M, Yu P, Li J, Ouyang W, Feng C, Zhao WL, Dai Y, Huang J. Single-Cell Transcriptome Analysis Identifies Ligand-Receptor Pairs Associated With BCP-ALL Prognosis. Front Oncol 2021; 11:639013. [PMID: 33777800 PMCID: PMC7987943 DOI: 10.3389/fonc.2021.639013] [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: 12/08/2020] [Accepted: 01/25/2021] [Indexed: 12/21/2022] Open
Abstract
B cell precursor acute lymphoblastic leukemia (BCP-ALL) is a blood cancer that originates from the abnormal proliferation of B-lymphoid progenitors. Cell population components and cell–cell interaction in the bone marrow microenvironment are significant factors for progression, relapse, and therapy resistance of BCP-ALL. In this study, we identified specifically expressed genes in B cells and myeloid cells by analyzing single-cell RNA sequencing data for seven BCP-ALL samples and four healthy samples obtained from a public database. Integrating 1356 bulk RNA sequencing samples from a public database and our previous study, we found a total of 57 significant ligand–receptor pairs (24 upregulated and 33 downregulated) in the autocrine crosstalk network of B cells. Via assessment of the communication between B cells and myeloid cells, another 29 ligand–receptor pairs were discovered, some of which notably affected survival outcomes. A score-based model was constructed with least absolute shrinkage and selection operator (LASSO) using these ligand–receptor pairs. Patients with higher scores had poorer prognoses. This model can be applied to create predictions for both pediatric and adult BCP-ALL patients.
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Affiliation(s)
- Liang Wu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minghao Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Yu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianfeng Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wen Ouyang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chong Feng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Li Zhao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuting Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jinyan Huang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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42
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Multi-species transcriptome meta-analysis of the response to retinoic acid in vertebrates and comparative analysis of the effects of retinol and retinoic acid on gene expression in LMH cells. BMC Genomics 2021; 22:146. [PMID: 33653267 PMCID: PMC7923837 DOI: 10.1186/s12864-021-07451-2] [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: 11/23/2020] [Accepted: 02/18/2021] [Indexed: 12/21/2022] Open
Abstract
Background Retinol (RO) and its active metabolite retinoic acid (RA) are major regulators of gene expression in vertebrates and influence various processes like organ development, cell differentiation, and immune response. To characterize a general transcriptomic response to RA-exposure in vertebrates, independent of species- and tissue-specific effects, four publicly available RNA-Seq datasets from Homo sapiens, Mus musculus, and Xenopus laevis were analyzed. To increase species and cell-type diversity we generated RNA-seq data with chicken hepatocellular carcinoma (LMH) cells. Additionally, we compared the response of LMH cells to RA and RO at different time points. Results By conducting a transcriptome meta-analysis, we identified three retinoic acid response core clusters (RARCCs) consisting of 27 interacting proteins, seven of which have not been associated with retinoids yet. Comparison of the transcriptional response of LMH cells to RO and RA exposure at different time points led to the identification of non-coding RNAs (ncRNAs) that are only differentially expressed (DE) during the early response. Conclusions We propose that these RARCCs stand on top of a common regulatory RA hierarchy among vertebrates. Based on the protein sets included in these clusters we were able to identify an RA-response cluster, a control center type cluster, and a cluster that directs cell proliferation. Concerning the comparison of the cellular response to RA and RO we conclude that ncRNAs play an underestimated role in retinoid-mediated gene regulation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07451-2.
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Klco JM, Mullighan CG. Advances in germline predisposition to acute leukaemias and myeloid neoplasms. Nat Rev Cancer 2021; 21:122-137. [PMID: 33328584 PMCID: PMC8404376 DOI: 10.1038/s41568-020-00315-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/28/2020] [Indexed: 12/17/2022]
Abstract
Although much work has focused on the elucidation of somatic alterations that drive the development of acute leukaemias and other haematopoietic diseases, it has become increasingly recognized that germline mutations are common in many of these neoplasms. In this Review, we highlight the different genetic pathways impacted by germline mutations that can ultimately lead to the development of familial and sporadic haematological malignancies, including acute lymphoblastic leukaemia, acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS). Many of the genes disrupted by somatic mutations in these diseases (for example, TP53, RUNX1, IKZF1 and ETV6) are the same as those that harbour germline mutations in children and adolescents who develop these malignancies. Moreover, the presumption that familial leukaemias only present in childhood is no longer true, in large part due to the numerous studies demonstrating germline DDX41 mutations in adults with MDS and AML. Lastly, we highlight how different cooperating events can influence the ultimate phenotype in these different familial leukaemia syndromes.
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Affiliation(s)
- Jeffery M Klco
- Department of Pathology and the Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Charles G Mullighan
- Department of Pathology and the Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.
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44
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Yadav V, Ganesan P, Veeramani R, Kumar V D. Philadelphia-Like Acute Lymphoblastic Leukemia: A Systematic Review. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2021; 21:e57-e65. [PMID: 33485429 DOI: 10.1016/j.clml.2020.08.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 01/10/2023]
Abstract
Philadelphia-like (Ph-like) acute lymphoblastic leukemia (ALL) is a subgroup of B-cell precursor ALL (BCP-ALL) with a gene expression profile analogous to Philadelphia-positive ALL and recurrent IKAROS Family Zinc Finger 1 (IKZF1) gene deletion despite lacking BCR-ABL1 (Breakpoint cluster region-ABL protooncogene) translocation. Although recognized to occur at all ages, the proportion of cases among BCP-ALL varies (< 10% in children and up to 30% in adolescents). In all age groups, males are more commonly affected. Generally, Ph-like ALL is associated with adverse clinical features and an increased risk of treatment failure with conventional approaches. Genetic alterations such as aberrant expression, point mutations, or fusion translocations lead to activation of cytokine receptors and signaling kinases, which affect the ABL1 (ABL class fusion) or Janus Kinase (JAK) signaling pathways. Several clinical trials are being conducted to understand whether specific tyrosine kinase inhibitor therapy can improve cure rates. This review summarizes the current literature available about this entity.
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Affiliation(s)
- Vineeta Yadav
- Department of Anatomy, Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, India
| | - Prasanth Ganesan
- Department of Medical Oncology, Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, India
| | - Raveendranath Veeramani
- Department of Anatomy, Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, India.
| | - Dinesh Kumar V
- Department of Anatomy, Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, India
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45
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Emerging molecular subtypes and therapeutic targets in B-cell precursor acute lymphoblastic leukemia. Front Med 2021; 15:347-371. [PMID: 33400146 DOI: 10.1007/s11684-020-0821-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/04/2020] [Indexed: 12/13/2022]
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is characterized by genetic alterations with high heterogeneity. Precise subtypes with distinct genomic and/or gene expression patterns have been recently revealed using high-throughput sequencing technology. Most of these profiles are associated with recurrent non-overlapping rearrangements or hotspot point mutations that are analogous to the established subtypes, such as DUX4 rearrangements, MEF2D rearrangements, ZNF384/ZNF362 rearrangements, NUTM1 rearrangements, BCL2/MYC and/or BCL6 rearrangements, ETV6-RUNX1-like gene expression, PAX5alt (diverse PAX5 alterations, including rearrangements, intragenic amplifications, or mutations), and hotspot mutations PAX5 (p.Pro80Arg) with biallelic PAX5 alterations, IKZF1 (p.Asn159Tyr), and ZEB2 (p.His1038Arg). These molecular subtypes could be classified by gene expression patterns with RNA-seq technology. Refined molecular classification greatly improved the treatment strategy. Multiagent therapy regimens, including target inhibitors (e.g., imatinib), immunomodulators, monoclonal antibodies, and chimeric antigen receptor T-cell (CAR-T) therapy, are transforming the clinical practice from chemotherapy drugs to personalized medicine in the field of risk-directed disease management. We provide an update on our knowledge of emerging molecular subtypes and therapeutic targets in BCP-ALL.
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46
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Smith KH, Budhraja A, Lynch J, Roberts K, Panetta JC, Connelly JP, Turnis ME, Pruett-Miller SM, Schuetz JD, Mullighan CG, Opferman JT. The Heme-Regulated Inhibitor Pathway Modulates Susceptibility of Poor Prognosis B-Lineage Acute Leukemia to BH3-Mimetics. Mol Cancer Res 2020; 19:636-650. [PMID: 33288732 DOI: 10.1158/1541-7786.mcr-20-0586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/28/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022]
Abstract
Antiapoptotic MCL1 is one of the most frequently amplified genes in human cancers and elevated expression confers resistance to many therapeutics including the BH3-mimetic agents ABT-199 and ABT-263. The antimalarial, dihydroartemisinin (DHA) translationally represses MCL-1 and synergizes with BH3-mimetics. To explore how DHA represses MCL-1, a genome-wide CRISPR screen identified that loss of genes in the heme synthesis pathway renders mouse BCR-ABL+ B-ALL cells resistant to DHA-induced death. Mechanistically, DHA disrupts the interaction between heme and the eIF2α kinase heme-regulated inhibitor (HRI) triggering the integrated stress response. Genetic ablation of Eif2ak1, which encodes HRI, blocks MCL-1 repression in response to DHA treatment and represses the synergistic killing of DHA and BH3-mimetics compared with wild-type leukemia. Furthermore, BTdCPU, a small-molecule activator of HRI, similarly triggers MCL-1 repression and synergizes with BH3-mimetics in mouse and human leukemia including both Ph+ and Ph-like B-ALL. Finally, combinatorial treatment of leukemia bearing mice with both BTdCPU and a BH3-mimetic extended survival and repressed MCL-1 in vivo. These findings reveal for the first time that the HRI-dependent cellular heme-sensing pathway can modulate apoptosis in leukemic cells by repressing MCL-1 and increasing their responsiveness to BH3-mimetics. This signaling pathway could represent a generalizable mechanism for repressing MCL-1 expression in malignant cells and sensitizing them to available therapeutics. IMPLICATIONS: The HRI-dependent cellular heme-sensing pathway can modulate apoptotic sensitivity in leukemic cells by repressing antiapoptotic MCL-1 and increasing their responsiveness to BH3-mimetics.
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Affiliation(s)
- Kaitlyn H Smith
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.,Integrated Program in Biomedical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Amit Budhraja
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John Lynch
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kathryn Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John C Panetta
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jon P Connelly
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.,Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Meghan E Turnis
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.,Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John D Schuetz
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Joseph T Opferman
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
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Plotnikov A, Kozer N, Cohen G, Carvalho S, Duberstein S, Almog O, Solmesky LJ, Shurrush KA, Babaev I, Benjamin S, Gilad S, Kupervaser M, Levin Y, Gershovits M, Ben-Avraham D, Barr HM. PRMT1 inhibition induces differentiation of colon cancer cells. Sci Rep 2020; 10:20030. [PMID: 33208761 PMCID: PMC7676271 DOI: 10.1038/s41598-020-77028-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/04/2020] [Indexed: 12/24/2022] Open
Abstract
Differentiation therapy has been recently revisited as a prospective approach in cancer therapy by targeting the aberrant growth, and repairing the differentiation and cell death programs of cancer cells. However, differentiation therapy of solid tumors is a challenging issue and progress in this field is limited. We performed High Throughput Screening (HTS) using a novel dual multiplex assay to discover compounds, which induce differentiation of human colon cancer cells. Here we show that the protein arginine methyl transferase (PRMT) type 1 inhibitor, MS023, is a potent inducer of colon cancer cell differentiation with a large therapeutic window. Differentiation changes in the highly aggressive human colon cancer cell line (HT-29) were proved by proteomic and genomic approaches. Growth of HT-29 xenograft in nude mice was significantly delayed upon MS023 treatment and immunohistochemistry of tumor indicated differentiation changes. These findings may lead to development of clinically effective anti-cancer drugs based on the mechanism of cancer cell differentiation.
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Affiliation(s)
- Alexander Plotnikov
- Wohl Institute for Drug Discovery, High Throughput Screening Unit, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel.
| | - Noga Kozer
- Wohl Institute for Drug Discovery, High Throughput Screening Unit, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Galit Cohen
- Wohl Institute for Drug Discovery, High Throughput Screening Unit, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Silvia Carvalho
- Wohl Institute for Drug Discovery, High Throughput Screening Unit, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Shirly Duberstein
- Wohl Institute for Drug Discovery, High Throughput Screening Unit, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Ofir Almog
- Wohl Institute for Drug Discovery, High Throughput Screening Unit, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Leonardo Javier Solmesky
- Wohl Institute for Drug Discovery, High Throughput Screening Unit, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Khriesto A Shurrush
- Wohl Institute for Drug Discovery, Medicinal Chemistry Unit, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Babaev
- Wohl Institute for Drug Discovery, Medicinal Chemistry Unit, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Sima Benjamin
- Crown Institute for Genomics, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Shlomit Gilad
- Crown Institute for Genomics, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Meital Kupervaser
- de Botton Institute for Proteomics, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- de Botton Institute for Proteomics, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Gershovits
- Mantoux Institute for Bioinformatics, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Danny Ben-Avraham
- Mantoux Institute for Bioinformatics, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Haim Michael Barr
- Wohl Institute for Drug Discovery, High Throughput Screening Unit, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
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48
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Tran TH, Hunger SP. The genomic landscape of pediatric acute lymphoblastic leukemia and precision medicine opportunities. Semin Cancer Biol 2020; 84:144-152. [PMID: 33197607 DOI: 10.1016/j.semcancer.2020.10.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and constitutes approximately 25 % of cancer diagnoses among children under the age of 15 (Howlader et al., 2013) [1]. Overall, about half of ALL cases occur in children and adolescents and it is the most common acute leukemia until the early 20s, after which acute myeloid leukemia predominates. ALL is the most successful treatment paradigm in pediatric cancer medicine as illustrated by the significant survival rate improvement from ∼10 % in the 1960s to >90 % today (Hunger et al., 2015) [2]. This remarkable success stems from the progressive improvement in the efficacy of risk-adapted multiagent chemotherapy regimens with effective central nervous system (CNS) prophylaxis via well-designed randomized clinical trials conducted by international collaborative consortia, enhanced supportive care measures to decrease treatment-related mortality, in-depth understanding of the genetic basis of ALL, and refinement in treatment response assessment through serial minimal residual disease (MRD) monitoring (Pui et al., 2015) [3]. These advances collectively contribute to a decline in mortality rate of 23.5% for children diagnosed with ALL in the US from 2000 to 2010 (Smith et al., 2014) [4]. Nevertheless, outcomes of older adolescents and young adults with ALL still lag behind those of their younger counterparts despite pediatric-inspired chemotherapy regimens (Stock et al., 2019) [5], relapsed/refractory childhood ALL is associated with poor outcomes (Rheingold et al., 2019) [6], and ALL still represents the leading causes of cancer-related deaths (Smith et al., 2010) [7]. The last two decades have witnessed important genomic discoveries in ALL, enabled by advances in next-generation sequencing (NGS) technologies to characterize the landscape of germline and somatic alterations in ALL, some of which have important diagnostic, prognostic and therapeutic implications. Comprehensive genomic analysis of large cohorts of children and adults with ALL has revised the taxonomy of ALL in the molecular era by identifying novel clonal, subtype-defined chromosomal alterations associated with distinct gene expression signatures, thus reducing the proportion of patients previously labelled as "Others" from 25 % to approximately 5 % (Mullighan et al., 2019) [8]. Insights into the genomics of ALL further provide compelling biologic rationale to expand the scope of precision medicine therapies for childhood ALL. Herein, we summarize a decade of genomic discoveries to highlight three different facets of precision medicine in pediatric ALL: 1) inherited predispositions of ALL; 2) relevant molecularly targeted therapies in genomically-defined ALL subtypes; and 3) treatment response monitoring via pharmacogenomics and novel MRD biomarkers.
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Affiliation(s)
- Thai Hoa Tran
- Division of Pediatric Hematology-Oncology, Charles-Bruneau Cancer Center, CHU Sainte-Justine, University of Montreal, Montreal, Quebec, Canada
| | - Stephen P Hunger
- Department of Pediatrics, The Center for Childhood Cancer Research, Children's Hospital of Philadelphia, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Abstract
The last decade has witnessed great advances in our understanding of the genetic and biological basis of childhood acute lymphoblastic leukemia (ALL), the development of experimental models to probe mechanisms and evaluate new therapies, and the development of more efficacious treatment stratification. Genomic analyses have revolutionized our understanding of the molecular taxonomy of ALL, and these advances have led the push to implement genome and transcriptome characterization in the clinical management of ALL to facilitate more accurate risk-stratification and, in some cases, targeted therapy. Although mutation- or pathway-directed targeted therapy (e.g., using tyrosine kinase inhibitors to treat Philadelphia chromosome [Ph]-positive and Phlike B-cell-ALL) is currently available for only a minority of children with ALL, many of the newly identified molecular alterations have led to the exploration of approaches targeting deregulated cell pathways. The efficacy of cellular or humoral immunotherapy has been demonstrated with the success of chimeric antigen receptor T-cell therapy and the bispecific engager blinatumomab in treating advanced disease. This review describes key advances in our understanding of the biology of ALL and optimal approaches to risk-stratification and therapy, and it suggests key areas for basic and clinical research.
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Affiliation(s)
- Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN; Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN.
| | - Charles G Mullighan
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN; Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN.
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Zhang X, Zhang X, Li X, Lv Y, Zhu Y, Wang J, Jin J, Yu W. The specific distribution pattern of IKZF1 mutation in acute myeloid leukemia. J Hematol Oncol 2020; 13:140. [PMID: 33081843 PMCID: PMC7574539 DOI: 10.1186/s13045-020-00972-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/29/2020] [Indexed: 11/10/2022] Open
Abstract
IKZF1 belongs to the IKAROS family of transcription factors, and its deletion/mutation frequently affects acute lymphoblastic leukemia. In acute myeloid leukemia, IKZF1 deletion has been demonstrated recurrent, but whether IKZF1 mutation also exists in AML remained largely unknown. Herein, we analyzed the IKZF1 mutation in AML. In our cohort, the frequency of IKZF1 mutation was 2.6% (5/193), and 5 frameshift/nonsense mutations as well as 2 missense mutations were identified in total. Molecularly, IKZF1 mutation was absent in fusion gene-positive AML, but it was demonstrated as the significant concomitant genetic alteration with SF3B1 or bi-alleleCEBPA mutation in AML. Clinically, two IKZF1, PTPN11 and SF3B1-mutated AML patients exhibited one aggressive clinical course and showed primary resistant to chemotherapy. Furthermore, we confirmed the recurrent IKZF1 mutation in AML with cBioPortal tool from OHSU, TCGA and TARGET studies. Interestingly, OHSU study also showed that SF3B1 mutation was the significant concomitant genetic alteration with IKZF1 mutation, indicating their strong synergy in leukemogenesis. In conclusion, IKZF1 mutation recurrently affected AML.
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Affiliation(s)
- Xiang Zhang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, #79 Qingchun Rd Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, Zhejiang, China
| | - Xuewu Zhang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, #79 Qingchun Rd Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, Zhejiang, China
| | - Xia Li
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, #79 Qingchun Rd Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, Zhejiang, China
| | - Yunfei Lv
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, #79 Qingchun Rd Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, Zhejiang, China
| | - Yanan Zhu
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, #79 Qingchun Rd Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, Zhejiang, China
| | - Jinghan Wang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, #79 Qingchun Rd Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, Zhejiang, China
| | - Jie Jin
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, #79 Qingchun Rd Zhejiang Province, Hangzhou, 310003, China. .,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, Zhejiang, China.
| | - Wenjuan Yu
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, #79 Qingchun Rd Zhejiang Province, Hangzhou, 310003, China. .,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, Zhejiang, China.
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