1
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Bindu S, Bibi R, Pradeep R, Sarkar K. The evolving role of B cells in malignancies. Hum Immunol 2025; 86:111301. [PMID: 40132250 DOI: 10.1016/j.humimm.2025.111301] [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: 08/06/2024] [Revised: 03/07/2025] [Accepted: 03/19/2025] [Indexed: 03/27/2025]
Abstract
B cells play diverse roles in different pathological circumstances, such as neoplastic diseases, autoimmune disorders, and neurological maladies. B cells, which are essential elements of the adaptive immune system, demonstrate exceptional functional variety, including the generation of antibodies, the presentation of antigens, and the secretion of cytokines. Within the field of oncology, B cells display a multifaceted nature in the tumor microenvironment, simultaneously manifesting both tumor-promoting and tumor-suppressing characteristics. Studies have found that the existence of tertiary lymphoid structures, which consist of B cells, is linked to better survival rates in different types of cancers. This article examines the involvement of B cells in different types of malignancies, emphasizing their importance in the development of the diseases and their potential as biomarkers. Additionally, the review also examines the crucial role of B cells in autoimmune illnesses and their potential as targets for therapy. The article also analyses the role of B cells in immunization and exploring their potential uses in cancer immunotherapy. This analysis highlights the intricate and occasionally contradictory roles of B cells, underlining the necessity for additional research to clarify their varied actions in various illness scenarios.
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Affiliation(s)
- Soham Bindu
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603203, India
| | - Roshni Bibi
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603203, India
| | - R Pradeep
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603203, India
| | - Koustav Sarkar
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603203, India.
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2
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Kratz CP. Re-envisioning genetic predisposition to childhood and adolescent cancers. Nat Rev Cancer 2025; 25:109-128. [PMID: 39627375 DOI: 10.1038/s41568-024-00775-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/28/2024] [Indexed: 01/31/2025]
Abstract
Although cancer is rare in children and adolescents, it remains a leading cause of death within this age range, and genetic predisposition is the main known risk factor. Since the discovery of retinoblastoma-predisposing RB1 pathogenic germline variants in 1985, several additional high-penetrance cancer predisposition genes (CPGs) have been identified. Although few clinically recognizable genetic conditions display moderate cancer phenotypes, burden testing has revealed low-to-moderate penetrance CPGs. In addition to germline pathogenic variants in CPGs, postzygotic somatic mosaic CPG pathogenic variants acquired during embryonic development are increasingly recognized as factors that predispose children and adolescents to malignancies. Genome-wide association studies of various childhood and adolescent cancer types have identified some common low-risk cancer susceptibility alleles. Although the clinical utility of polygenic risk scores is currently limited in children and adolescents, polygenic risk scores developed for adults can predict subsequent cancer risks in childhood and adolescent cancer survivors. In this Review, I describe our current knowledge of genetic predisposition to childhood and adolescent cancers. Survival rates in children and adolescents with cancer and CPGs are often poor, necessitating better integration of genomic testing into clinical care to improve cancer prevention, surveillance and therapies.
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Affiliation(s)
- Christian P Kratz
- Department of Paediatric Haematology and Oncology, Hannover Medical School, Hannover, Germany.
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3
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Hoang TT, Scheurer ME, Lupo PJ. Overview of the etiology of childhood cancer and future directions. Curr Opin Pediatr 2025; 37:59-66. [PMID: 39699102 DOI: 10.1097/mop.0000000000001419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2024]
Abstract
PURPOSE OF REVIEW We provide an overview of the etiology of childhood cancer, the state of the literature, and highlight some opportunities for future research, including technological advancements that could be applied to etiologic studies of childhood cancer to accelerate our understanding. RECENT FINDINGS Risk factors of childhood cancer were summarized based on demographics and perinatal factors, environmental risk factors, and genetic risk factors. Overall, demographics and perinatal factors are the most well studied in relation to childhood cancer. While environmental risk factors have been implicated, more work is needed to pinpoint specific exposures, identify window(s) of susceptibility, and understand mechanisms. With genome-wide association studies (GWAS), genetic risk factors of eight childhood cancers have emerged, and opportunities remain to conduct GWAS for other cancer types and determine whether risk variants are inherited or de novo. Technological advancements that can shed light into the susceptibility of childhood cancer include metabolomics, using primary teeth as an exposure matrix, and long-read sequencing. SUMMARY The development of childhood cancer remains largely not well understood. Collaboration to increase sample size to conduct analyses by histology and/or molecular subtype and application of novel technologies will accelerate our understanding of childhood cancer.
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Affiliation(s)
- Thanh T Hoang
- Department of Pediatrics, Division of Hematology-Oncology
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine
- Texas Children's Cancer and Hematology Center, Texas Children's Hospital, Houston, Texas, USA
| | - Michael E Scheurer
- Department of Pediatrics, Division of Hematology-Oncology
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine
- Texas Children's Cancer and Hematology Center, Texas Children's Hospital, Houston, Texas, USA
| | - Philip J Lupo
- Department of Pediatrics, Division of Hematology-Oncology
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine
- Texas Children's Cancer and Hematology Center, Texas Children's Hospital, Houston, Texas, USA
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4
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Langie J, Chan TF, Yang W, Kang AY, Morimoto L, Stram DO, Mancuso N, Ma X, Metayer C, Lupo PJ, Rabin KR, Scheurer ME, Wiemels JL, Yang JJ, de Smith AJ, Chiang CWK. The impact of Indigenous American-like ancestry on risk of acute lymphoblastic leukemia in Hispanic/Latino children. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.01.14.25320563. [PMID: 39867407 PMCID: PMC11759616 DOI: 10.1101/2025.01.14.25320563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer, with Hispanic/Latino children having a higher incidence of ALL than other racial/ethnic groups. Genetic variants, particularly ones found enriched in Indigenous American (IA)-like ancestry and inherited by Hispanics/Latinos, may contribute to this disparity. In this study, we characterized the impact of IA-like ancestry on overall ALL risk and the frequency and effect size of known risk alleles in a large cohort of self-reported Hispanic/Latino individuals. We also performed genome-wide admixture mapping analysis to identify potentially novel ALL risk loci. We found that global IA ancestry was positively associated with ALL risk, but the association was not significant after adjusting for socio-economic indicators. In a series of local ancestry analyses, we uncovered that at known ALL risk loci, increasing copies of the IA-like haplotype were positively and significantly associated with ALL case-control status. Further, the IA-like haplotype had ~1.33 times the odds of harboring the risk allele compared to non-IA-like haplotypes. We found no evidence of interaction between genotype and ancestry (local or global) in relation to ALL risk. Admixture mapping identified association signals on chromosomes 2 (2q21.2), 7 (7p12.2), 10 (10q21.2), and 15 (15q22.31); however, only the variants at 7p12.2 and 10q21.2 replicated in additional cohorts. Taken together, our results suggest that increased risk of ALL in Hispanic/Latino children may be conferred by higher frequency of risk alleles within IA-like ancestry, which can be leveraged as targets of new precision health strategies and therapeutics.
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Affiliation(s)
- Jalen Langie
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Tsz Fung Chan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Alice Y Kang
- School of Public Health, University of California Berkeley, Berkeley, CA, USA
| | - Libby Morimoto
- School of Public Health, University of California Berkeley, Berkeley, CA, USA
| | - Daniel O Stram
- Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Catherine Metayer
- School of Public Health, University of California Berkeley, Berkeley, CA, USA
| | - Philip J Lupo
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Houston, TX, USA
| | - Karen R Rabin
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Houston, TX, USA
| | - Michael E Scheurer
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Houston, TX, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
- Co-senior authors
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Co-senior authors
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Jung EM, Raduski AR, Mills LJ, Spector LG. A phenome-wide association study of polygenic scores for selected childhood cancer: Results from the UK Biobank. HGG ADVANCES 2025; 6:100356. [PMID: 39340156 PMCID: PMC11538869 DOI: 10.1016/j.xhgg.2024.100356] [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: 05/31/2024] [Revised: 09/24/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024] Open
Abstract
The aim of this study was to scan phenotypes in adulthood associated with polygenic risk scores (PRS) for childhood cancers with well-articulated genetic architectures-acute lymphoblastic leukemia (ALL), Ewing sarcoma, and neuroblastoma-to examine genetic pleiotropy. Furthermore, we aimed to determine which SNPs could drive associations. Per-SNP summary statistics were extracted for PRS calculation. Participants with white British ancestry were exclusively included for analyses. SNPs were queried from the UK Biobank genotype imputation data. Records from the cancer registry, death registry, and inpatient diagnoses were abstracted for phenome-wide scans. Firth logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) alongside corresponding p values, adjusting for age at recruitment and sex. A total of 244,332 unrelated white British participants were included. We observed a significant association between ALL-PRS and ALL (OR: 1.20e+24, 95% CI: 9.08e+14-1.60e+33). In addition, we observed a significant association between high-risk neuroblastoma PRS and nonrheumatic aortic valve disorders (OR: 43.9, 95% CI: 7.42-260). There were no significant phenotype associations with Ewing sarcoma and neuroblastoma PRS. Regarding individual SNPs, rs17607816 increased the risk of ALL (OR: 6.40, 95% CI: 3.26-12.57). For high-risk neuroblastoma, rs80059929 elevated the risk of atrioventricular block (OR: 3.04, 95% CI: 1.85-4.99). Our findings suggest that individuals with genetic susceptibility to ALL may face a lifelong risk for developing ALL, along with a genetic pleiotropic association between high-risk neuroblastoma and circulatory diseases.
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Affiliation(s)
- Eun Mi Jung
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.
| | - Andrew R Raduski
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Lauren J Mills
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Logan G Spector
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
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6
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Liu X, Guo H, Kang M, Fu W, Li H, Ji H, Zhao J, Fang Y, Du M, Xue Y. Multi-step gene set analysis identified HTR3 family genes involving childhood acute lymphoblastic leukemia susceptibility. Arch Toxicol 2025; 99:299-307. [PMID: 39322821 DOI: 10.1007/s00204-024-03881-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Accepted: 09/19/2024] [Indexed: 09/27/2024]
Abstract
In our previous conventional genome-wide association study (GWAS), WWOX was a susceptibility gene associated with acute lymphoblastic leukemia (ALL) development. Nowadays, advancements in genetic association analyses promote an in-depth exploration of ALL genomics. We conducted a two-step enrichment analysis at both gene and pathway levels based on ALL GWAS data including 269 cases and 1039 controls of Chinese descent. The following functional prediction and experiments were used to evaluate the genetic biology of candidate variants and genes. The serotonin-activated cation-selective channel complex gene-set was a potential biological pathway involved in ALL occurrence. Of which, individuals carrying the T allele of rs33940208 exhibited a prominent reduced risk of ALL [odds ratio (OR) = 0.71, 95% confidence interval (CI) = 0.53 to 0.96, P = 2.81 × 10-2], whereas those with the A allele of rs6779545 demonstrated an increased risk (OR = 1.23, 95% CI = 1.01 to 1.51, P = 4.11 × 10-2). Notably, the two variants displayed a better prediction capability when combined, that the risk of developing childhood ALL increased by 131% in subjects with 2-4 risk alleles compared to those with 0-1 risk alleles (Ptrend = 2.05 × 10-3). In addition, the T allele of rs33940208 could reduce HTR3A mRNA level, while the A allele of rs6779545 increased HTR3D mRNA expression. In this study, we identified HTR3A rs33940208 and HTR3D rs6779545 as potential susceptibility loci for ALL in Chinese children. Future validation and functional research will elucidate the underlying molecular processes, refining preventive strategies for this disease.
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Affiliation(s)
- Xiao Liu
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, No. 101 Longmian Avenue, Nanjing, 211166, China
| | - Honghao Guo
- Department of Hematology, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, China
| | - Meiyun Kang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Wenfeng Fu
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Huiqin Li
- Department of Genetic Toxicology and Environmental Genomics, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongsheng Ji
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, No. 101 Longmian Avenue, Nanjing, 211166, China
| | - Jiou Zhao
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Yongjun Fang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China.
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China.
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Key Laboratory of Hematology, Nanjing Medical University, No. 72 Guangzhou Road, Nanjing, 210008, China.
| | - Mulong Du
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, No. 101 Longmian Avenue, Nanjing, 211166, China.
- Department of Genetic Toxicology and Environmental Genomics, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China.
| | - Yao Xue
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China.
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China.
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Key Laboratory of Hematology, Nanjing Medical University, No. 72 Guangzhou Road, Nanjing, 210008, China.
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7
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Bigge J, Koebbe LL, Giel AS, Bornholdt D, Buerfent B, Dasmeh P, Zink AM, Maj C, Schumacher J. Expression quantitative trait loci influence DNA damage-induced apoptosis in cancer. BMC Genomics 2024; 25:1168. [PMID: 39623312 PMCID: PMC11613471 DOI: 10.1186/s12864-024-11068-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 11/19/2024] [Indexed: 12/06/2024] Open
Abstract
BACKGROUND Genomic instability and evading apoptosis are two fundamental hallmarks of cancer and closely linked to DNA damage response (DDR). By analyzing expression quantitative trait loci (eQTL) upon cell stimulation (called exposure eQTL (e2QTL)) it is possible to identify context specific gene regulatory variants and connect them to oncological diseases based on genome-wide association studies (GWAS). RESULTS We isolate CD8+ T cells from 461 healthy donors and stimulate them with high doses of 5 different carcinogens to identify regulatory mechanisms of DNA damage-induced apoptosis. Across all stimuli, we find 5,373 genes to be differentially expressed, with 85% to 99% of these genes being suppressed. While upregulated genes are specific to distinct stimuli, downregulated genes are shared across conditions but exhibit enrichment in biological processes depending on the DNA damage type. Analysis of eQTL reveals 654 regulated genes across conditions. Among them, 47 genes are significant e2QTL, representing a fraction of 4% to 5% per stimulus. To unveil disease relevant genetic variants, we compare eQTL and e2QTL with GWAS risk variants. We identify gene regulatory variants for KLF2, PIP4K2A, GPR160, RPS18, ARL17B and XBP1 that represent risk variants for oncological diseases. CONCLUSION Our study highlights the relevance of gene regulatory variants influencing DNA damage-induced apoptosis in cancer. The results provide new insights in cellular mechanisms and corresponding genes contributing to inter-individual effects in cancer development.
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Affiliation(s)
- Jessica Bigge
- Philipps University of Marburg, Center for Human Genetics, Marburg, Germany
| | - Laura L Koebbe
- Philipps University of Marburg, Center for Human Genetics, Marburg, Germany
| | - Ann-Sophie Giel
- Philipps University of Marburg, Center for Human Genetics, Marburg, Germany
| | - Dorothea Bornholdt
- Philipps University of Marburg, Center for Human Genetics, Marburg, Germany
| | - Benedikt Buerfent
- Philipps University of Marburg, Center for Human Genetics, Marburg, Germany
| | - Pouria Dasmeh
- Philipps University of Marburg, Center for Human Genetics, Marburg, Germany
| | | | - Carlo Maj
- Philipps University of Marburg, Center for Human Genetics, Marburg, Germany
| | - Johannes Schumacher
- Philipps University of Marburg, Center for Human Genetics, Marburg, Germany.
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8
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Garcia C, Miller-Awe MD, Witkowski MT. Concepts in B cell acute lymphoblastic leukemia pathogenesis. J Leukoc Biol 2024; 116:18-32. [PMID: 38243586 PMCID: PMC11869204 DOI: 10.1093/jleuko/qiae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024] Open
Abstract
B cell acute lymphoblastic leukemia (B-ALL) arises from genetic alterations impacting B cell progenitors, ultimately leading to clinically overt disease. Extensive collaborative efforts in basic and clinical research have significantly improved patient prognoses. Nevertheless, a subset of patients demonstrate resistance to conventional chemotherapeutic approaches and emerging immunotherapeutic interventions. This review highlights the mechanistic underpinnings governing B-ALL transformation. Beginning with exploring normative B cell lymphopoiesis, we delineate the influence of recurrent germline and somatic genetic aberrations on the perturbation of B cell progenitor differentiation and protumorigenic signaling, thereby facilitating the neoplastic transformation underlying B-ALL progression. Additionally, we highlight recent advances in the multifaceted landscape of B-ALL, encompassing metabolic reprogramming, microbiome influences, inflammation, and the discernible impact of socioeconomic and racial disparities on B-ALL transformation and patient survival.
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Affiliation(s)
- Clarissa Garcia
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, United States
| | - Megan D. Miller-Awe
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, United States
| | - Matthew T. Witkowski
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, United States
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Pagliaro L, Chen SJ, Herranz D, Mecucci C, Harrison CJ, Mullighan CG, Zhang M, Chen Z, Boissel N, Winter SS, Roti G. Acute lymphoblastic leukaemia. Nat Rev Dis Primers 2024; 10:41. [PMID: 38871740 DOI: 10.1038/s41572-024-00525-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 06/15/2024]
Abstract
Acute lymphoblastic leukaemia (ALL) is a haematological malignancy characterized by the uncontrolled proliferation of immature lymphoid cells. Over past decades, significant progress has been made in understanding the biology of ALL, resulting in remarkable improvements in its diagnosis, treatment and monitoring. Since the advent of chemotherapy, ALL has been the platform to test for innovative approaches applicable to cancer in general. For example, the advent of omics medicine has led to a deeper understanding of the molecular and genetic features that underpin ALL. Innovations in genomic profiling techniques have identified specific genetic alterations and mutations that drive ALL, inspiring new therapies. Targeted agents, such as tyrosine kinase inhibitors and immunotherapies, have shown promising results in subgroups of patients while minimizing adverse effects. Furthermore, the development of chimeric antigen receptor T cell therapy represents a breakthrough in ALL treatment, resulting in remarkable responses and potential long-term remissions. Advances are not limited to treatment modalities alone. Measurable residual disease monitoring and ex vivo drug response profiling screening have provided earlier detection of disease relapse and identification of exceptional responders, enabling clinicians to adjust treatment strategies for individual patients. Decades of supportive and prophylactic care have improved the management of treatment-related complications, enhancing the quality of life for patients with ALL.
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Affiliation(s)
- Luca Pagliaro
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics (THEC), University of Parma, Parma, Italy
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Daniel Herranz
- Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Cristina Mecucci
- Department of Medicine, Hematology and Clinical Immunology, University of Perugia, Perugia, Italy
| | - Christine J Harrison
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ming Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Nicolas Boissel
- Hôpital Saint-Louis, APHP, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
| | - Stuart S Winter
- Children's Minnesota Cancer and Blood Disorders Program, Minneapolis, MN, USA
| | - Giovanni Roti
- Department of Medicine and Surgery, University of Parma, Parma, Italy.
- Translational Hematology and Chemogenomics (THEC), University of Parma, Parma, Italy.
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy.
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10
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Bhattarai KR, Mobley RJ, Barnett KR, Ferguson DC, Hansen BS, Diedrich JD, Bergeron BP, Yoshimura S, Yang W, Crews KR, Manring CS, Jabbour E, Paietta E, Litzow MR, Kornblau SM, Stock W, Inaba H, Jeha S, Pui CH, Cheng C, Pruett-Miller SM, Relling MV, Yang JJ, Evans WE, Savic D. Investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment. Nat Commun 2024; 15:3681. [PMID: 38693155 PMCID: PMC11063049 DOI: 10.1038/s41467-024-48124-4] [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: 02/10/2023] [Accepted: 04/18/2024] [Indexed: 05/03/2024] Open
Abstract
Defining genetic factors impacting chemotherapy failure can help to better predict response and identify drug resistance mechanisms. However, there is limited understanding of the contribution of inherited noncoding genetic variation on inter-individual differences in chemotherapy response in childhood acute lymphoblastic leukemia (ALL). Here we map inherited noncoding variants associated with treatment outcome and/or chemotherapeutic drug resistance to ALL cis-regulatory elements and investigate their gene regulatory potential and target gene connectivity using massively parallel reporter assays and three-dimensional chromatin looping assays, respectively. We identify 54 variants with transcriptional effects and high-confidence gene connectivity. Additionally, functional interrogation of the top variant, rs1247117, reveals changes in chromatin accessibility, PU.1 binding affinity and gene expression, and deletion of the genomic interval containing rs1247117 sensitizes cells to vincristine. Together, these data demonstrate that noncoding regulatory variants associated with diverse pharmacological traits harbor significant effects on allele-specific transcriptional activity and impact sensitivity to antileukemic agents.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - Daniel C Ferguson
- 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
| | - Baranda S Hansen
- 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
| | - 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
| | - Satoshi Yoshimura
- 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
- Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, Japan
| | - 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 MD Anderson Cancer Center, Houston, TX, 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 MD Anderson Cancer Center, Houston, TX, USA
| | - Wendy Stock
- Comprehensive Cancer Center, University of Chicago Medicine, Chicago, IL, 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
| | - Cheng Cheng
- Department of Biostatistics, 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
| | - 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, 38163, 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, 38163, USA.
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11
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Yu X, Chen Y, Chen J, Fan Y, Lu H, Wu D, Xu Y. Shared genetic architecture between autoimmune disorders and B-cell acute lymphoblastic leukemia: insights from large-scale genome-wide cross-trait analysis. BMC Med 2024; 22:161. [PMID: 38616254 PMCID: PMC11017616 DOI: 10.1186/s12916-024-03385-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024] Open
Abstract
BACKGROUND To study the shared genetic structure between autoimmune diseases and B-cell acute lymphoblastic leukemia (B-ALL) and identify the shared risk loci and genes and genetic mechanisms involved. METHODS Based on large-scale genome-wide association study (GWAS) summary-level data sets, we observed genetic overlaps between autoimmune diseases and B-ALL, and cross-trait pleiotropic analysis was performed to detect shared pleiotropic loci and genes. A series of functional annotation and tissue-specific analysis were performed to determine the influence of pleiotropic genes. The heritability enrichment analysis was used to detect crucial immune cells and tissues. Finally, bidirectional Mendelian randomization (MR) methods were utilized to investigate the casual associations. RESULTS Our research highlighted shared genetic mechanisms between seven autoimmune disorders and B-ALL. A total of 73 pleiotropic loci were identified at the genome-wide significance level (P < 5 × 10-8), 16 of which had strong evidence of colocalization. We demonstrated that several loci have been previously reported (e.g., 17q21) and discovered some novel loci (e.g., 10p12, 5p13). Further gene-level identified 194 unique pleiotropic genes, for example IKZF1, GATA3, IKZF3, GSDMB, and ORMDL3. Pathway analysis determined the key role of cellular response to cytokine stimulus, B cell activation, and JAK-STAT signaling pathways. SNP-level and gene-level tissue enrichment suggested that crucial role pleiotropic mechanisms involved in the spleen, whole blood, and EBV-transformed lymphocytes. Also, hyprcoloc and stratified LD score regression analyses revealed that B cells at different developmental stages may be involved in mechanisms shared between two different diseases. Finally, two-sample MR analysis determined causal effects of asthma and rheumatoid arthritis on B-ALL. CONCLUSIONS Our research proved shared genetic architecture between autoimmune disorders and B-ALL and shed light on the potential mechanism that might involve in.
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Affiliation(s)
- Xinghao Yu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China
| | - Yiyin Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China
| | - Jia Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yi Fan
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Huimin Lu
- Department of Outpatient and Emergency, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China.
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China.
| | - Yang Xu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China.
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China.
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12
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de Smith AJ, Wahlster L, Jeon S, Kachuri L, Black S, Langie J, Cato LD, Nakatsuka N, Chan TF, Xia G, Mazumder S, Yang W, Gazal S, Eng C, Hu D, Burchard EG, Ziv E, Metayer C, Mancuso N, Yang JJ, Ma X, Wiemels JL, Yu F, Chiang CWK, Sankaran VG. A noncoding regulatory variant in IKZF1 increases acute lymphoblastic leukemia risk in Hispanic/Latino children. CELL GENOMICS 2024; 4:100526. [PMID: 38537633 PMCID: PMC11019360 DOI: 10.1016/j.xgen.2024.100526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/11/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Hispanic/Latino children have the highest risk of acute lymphoblastic leukemia (ALL) in the US compared to other racial/ethnic groups, yet the basis of this remains incompletely understood. Through genetic fine-mapping analyses, we identified a new independent childhood ALL risk signal near IKZF1 in self-reported Hispanic/Latino individuals, but not in non-Hispanic White individuals, with an effect size of ∼1.44 (95% confidence interval = 1.33-1.55) and a risk allele frequency of ∼18% in Hispanic/Latino populations and <0.5% in European populations. This risk allele was positively associated with Indigenous American ancestry, showed evidence of selection in human history, and was associated with reduced IKZF1 expression. We identified a putative causal variant in a downstream enhancer that is most active in pro-B cells and interacts with the IKZF1 promoter. This variant disrupts IKZF1 autoregulation at this enhancer and results in reduced enhancer activity in B cell progenitors. Our study reveals a genetic basis for the increased ALL risk in Hispanic/Latino children.
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Affiliation(s)
- Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.
| | - Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Soyoung Jeon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Susan Black
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jalen Langie
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Liam D Cato
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Tsz-Fung Chan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Guangze Xia
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Soumyaa Mazumder
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Celeste Eng
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Biotherapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Donglei Hu
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Esteban González Burchard
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Biotherapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaomei Ma
- Yale School of Public Health, New Haven, CT 06520, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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13
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Abstract
Lymphoid neoplasms represent a heterogeneous group of disease entities and subtypes with markedly different molecular and clinical features. Beyond genetic alterations, lymphoid tumors also show widespread epigenomic changes. These severely affect the levels and distribution of DNA methylation, histone modifications, chromatin accessibility, and three-dimensional genome interactions. DNA methylation stands out as a tracer of cell identity and memory, as B cell neoplasms show epigenetic imprints of their cellular origin and proliferative history, which can be quantified by an epigenetic mitotic clock. Chromatin-associated marks are informative to uncover altered regulatory regions and transcription factor networks contributing to the development of distinct lymphoid tumors. Tumor-intrinsic epigenetic and genetic aberrations cooperate and interact with microenvironmental cells to shape the transcriptome at different phases of lymphoma evolution, and intraclonal heterogeneity can now be characterized by single-cell profiling. Finally, epigenetics offers multiple clinical applications, including powerful diagnostic and prognostic biomarkers as well as therapeutic targets.
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Affiliation(s)
- Martí Duran-Ferrer
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain;
| | - José Ignacio Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain;
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain
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14
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Jeon S, Lo YC, Morimoto LM, Metayer C, Ma X, Wiemels JL, de Smith AJ, Chiang CWK. Evaluating genomic polygenic risk scores for childhood acute lymphoblastic leukemia in Latinos. HGG ADVANCES 2023; 4:100239. [PMID: 37710962 PMCID: PMC10550840 DOI: 10.1016/j.xhgg.2023.100239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/16/2023] Open
Abstract
The utility of polygenic risk score (PRS) models has not been comprehensively evaluated for childhood acute lymphoblastic leukemia (ALL), the most common type of cancer in children. Previous PRS models for ALL were based on significant loci observed in genome-wide association studies (GWASs), even though genomic PRS models have been shown to improve prediction performance for a number of complex diseases. In the United States, Latino (LAT) children have the highest risk of ALL, but the transferability of PRS models to LAT children has not been studied. In this study, we constructed and evaluated genomic PRS models based on either non-Latino White (NLW) GWAS or a multi-ancestry GWAS. We found that the best PRS models performed similarly between held-out NLW and LAT samples (PseudoR2 = 0.086 ± 0.023 in NLW vs. 0.060 ± 0.020 in LAT), and can be improved for LAT if we performed GWAS in LAT-only (PseudoR2 = 0.116 ± 0.026) or multi-ancestry samples (PseudoR2 = 0.131 ± 0.025). However, the best genomic models currently do not have better prediction accuracy than a conventional model using all known ALL-associated loci in the literature (PseudoR2 = 0.166 ± 0.025), which includes loci from GWAS populations that we could not access to train genomic PRS models. Our results suggest that larger and more inclusive GWASs may be needed for genomic PRS to be useful for ALL. Moreover, the comparable performance between populations may suggest a more oligogenic architecture for ALL, where some large effect loci may be shared between populations. Future PRS models that move away from the infinite causal loci assumption may further improve PRS for ALL.
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Affiliation(s)
- Soyoung Jeon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ying Chu Lo
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Libby M Morimoto
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Catherine Metayer
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA, USA.
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15
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Sharma G, Tran TM, Bansal I, Beg MS, Bhardwaj R, Bassi J, Tan Y, Jaiswal AK, Tso C, Jain A, Singh J, Chattopadhyay P, Singh A, Chopra A, Bakhshi S, Casero D, Rao DS, Palanichamy JK. RNA binding protein IGF2BP1 synergizes with ETV6-RUNX1 to drive oncogenic signaling in B-cell Acute Lymphoblastic Leukemia. J Exp Clin Cancer Res 2023; 42:231. [PMID: 37670323 PMCID: PMC10478443 DOI: 10.1186/s13046-023-02810-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 08/27/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Acute lymphoblastic leukemia (ALL) is the most common pediatric hematological malignancy, with ETV6::RUNX1 being the most prevalent translocation whose exact pathogenesis remains unclear. IGF2BP1 (Insulin-like Growth Factor 2 Binding Protein 1) is an oncofetal RNA binding protein seen to be specifically overexpressed in ETV6::RUNX1 positive B-ALL. In this study, we have studied the mechanistic role of IGF2BP1 in leukemogenesis and its synergism with the ETV6::RUNX1 fusion protein. METHODS Gene expression was analyzed from patient bone marrow RNA using Real Time RT-qPCR. Knockout cell lines were created using CRISPR-Cas9 based lentiviral vectors. RNA-Seq and RNA Immunoprecipitation sequencing (RIP-Seq) after IGF2BP1 pulldown were performed using the Illumina platform. Mouse experiments were done by retroviral overexpression of donor HSCs followed by lethal irradiation of recipients using a bone marrow transplant model. RESULTS We observed specific overexpression of IGF2BP1 in ETV6::RUNX1 positive patients in an Indian cohort of pediatric ALL (n=167) with a positive correlation with prednisolone resistance. IGF2BP1 expression was essential for tumor cell survival in multiple ETV6::RUNX1 positive B-ALL cell lines. Integrated analysis of transcriptome sequencing after IGF2BP1 knockout and RIP-Seq after IGF2BP1 pulldown in Reh cell line revealed that IGF2BP1 targets encompass multiple pro-oncogenic signalling pathways including TNFα/NFκB and PI3K-Akt pathways. These pathways were also dysregulated in primary ETV6::RUNX1 positive B-ALL patient samples from our center as well as in public B-ALL patient datasets. IGF2BP1 showed binding and stabilization of the ETV6::RUNX1 fusion transcript itself. This positive feedback loop led to constitutive dysregulation of several oncogenic pathways. Enforced co-expression of ETV6::RUNX1 and IGF2BP1 in mouse bone marrow resulted in marrow hypercellularity which was characterized by multi-lineage progenitor expansion and strong Ki67 positivity. This pre-leukemic phenotype confirmed their synergism in-vivo. Clonal expansion of cells overexpressing both ETV6::RUNX1 and IGF2BP1 was clearly observed. These mice also developed splenomegaly indicating extramedullary hematopoiesis. CONCLUSION Our data suggest a combined impact of the ETV6::RUNX1 fusion protein and RNA binding protein, IGF2BP1 in activating multiple oncogenic pathways in B-ALL which makes IGF2BP1 and these pathways as attractive therapeutic targets and biomarkers.
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Affiliation(s)
- Gunjan Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Tiffany M Tran
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Ishu Bansal
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Mohammad Sabique Beg
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Ruchi Bhardwaj
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Jaspal Bassi
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Yuande Tan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Amit Kumar Jaiswal
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Christine Tso
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Ayushi Jain
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Jay Singh
- Department of Laboratory Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Parthaprasad Chattopadhyay
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Archna Singh
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Anita Chopra
- Department of Laboratory Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Sameer Bakhshi
- Department of Medical Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - David Casero
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dinesh S Rao
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Jayanth Kumar Palanichamy
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India.
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16
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Svyatova G, Boranbayeva R, Berezina G, Manzhuova L, Murtazaliyeva A. Genes of Predisposition to Childhood Beta-Cell Acute Lymphoblastic Leukemia in the Kazakh Population. Asian Pac J Cancer Prev 2023; 24:2653-2666. [PMID: 37642051 PMCID: PMC10685230 DOI: 10.31557/apjcp.2023.24.8.2653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Today, acute lymphoblastic leukemia is one of the most common malignant diseases of the hematopoietic system. The genetic predisposition to ALL is not fully explored in various ethnic populations. OBJECTIVE The study aimed to conduct a comparative analysis of the population frequencies of alleles and genotypes of polymorphic gene variants: immune regulation GATA3 (rs3824662); transcription and differentiation of B cells: ARID5B (rs7089424, rs10740055), IKZF1 (rs4132601); differentiation of hematopoietic cells: PIP4K2A (rs7088318); apoptosis: CEBPE (rs2239633), tumor suppressors: CDKN2A (rs3731249), TP53 (rs1042522); carcinogen metabolism: CBR3 (rs1056892), CYP1A1 (rs104894, rs4646903), according to genome-wide association studies analyses associated with the risk of developing pediatric beta-cell acute lymphoblastic leukemia (B-cell ALL), in an ethnically homogeneous population of Kazakhs with studied populations. METHODS The genomic database consists of 1800 conditionally healthy persons of Kazakh nationality, genotyped using OmniChip 2.5-8 Illumina chips at the deCODE genetics as part of the InterPregGen 7 project of the European Union (EU) framework program under Grant Agreement No. 282540. RESULTS High population frequencies of single nucleotide polymorphism (SNP) minor alleles identified for immune regulation genes - GATA3 rs3824662 - 42.5%; transcription and differentiation of B-cells genes - ARID5B rs7089424 - 33.1% and rs10740055 - 48.5%, which suggests their significant genetic contribution to the risk of development and prognosis of the effectiveness of B-cell ALL therapy in the Kazakh population. The significantly lower population frequency of the minor allele G rs1056892 CBR3 gene - 38.6% in the Kazakhs suggests its significant protective effect in reducing the risk of childhood B-cell ALL and the smaller number of cardiac complications after anthracycline therapy. CONCLUSION The obtained results will serve as a basis for developing effective methods for predicting the risk of development, early diagnosis, and effectiveness of treatment of B-cell ALL in children.
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Affiliation(s)
- Gulnara Svyatova
- Republican Medical Genetic Consultation, Scientific Center of Obstetrics, Gynecology and Perinatology, 050020, 125 Dostyk Ave., Almaty, Kazakhstan.
| | - Riza Boranbayeva
- Scientific Center of Pediatrics and Pediatric Surgery, 050060, 146 Al-Farabi Ave., Almaty, Kazakhstan.
| | - Galina Berezina
- Republican Medical Genetic Consultation, Scientific Center of Obstetrics, Gynecology and Perinatology, 050020, 125 Dostyk Ave., Almaty, Kazakhstan.
| | - Lyazat Manzhuova
- Scientific Center of Pediatrics and Pediatric Surgery, 050060, 146 Al-Farabi Ave., Almaty, Kazakhstan.
| | - Alexandra Murtazaliyeva
- Republican Medical Genetic Consultation, Scientific Center of Obstetrics, Gynecology and Perinatology, 050020, 125 Dostyk Ave., Almaty, Kazakhstan.
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17
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Li Z, Chang TC, Junco JJ, Devidas M, Li Y, Yang W, Huang X, Hedges DJ, Cheng Z, Shago M, Carroll AJ, Heerema NA, Gastier-Foster J, Wood BL, Borowitz MJ, Sanclemente L, Raetz EA, Hunger SP, Feingold E, Rosser TC, Sherman SL, Loh ML, Mullighan CG, Yu J, Wu G, Lupo PJ, Rabin KR, Yang JJ. Genomic landscape of Down syndrome-associated acute lymphoblastic leukemia. Blood 2023; 142:172-184. [PMID: 37001051 PMCID: PMC10352600 DOI: 10.1182/blood.2023019765] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 04/03/2023] Open
Abstract
Trisomy 21, the genetic cause of Down syndrome (DS), is the most common congenital chromosomal anomaly. It is associated with a 20-fold increased risk of acute lymphoblastic leukemia (ALL) during childhood and results in distinctive leukemia biology. To comprehensively define the genomic landscape of DS-ALL, we performed whole-genome sequencing and whole-transcriptome sequencing (RNA-Seq) on 295 cases. Our integrated genomic analyses identified 15 molecular subtypes of DS-ALL, with marked enrichment of CRLF2-r, IGH::IGF2BP1, and C/EBP altered (C/EBPalt) subtypes compared with 2257 non-DS-ALL cases. We observed abnormal activation of the CEBPD, CEBPA, and CEBPE genes in 10.5% of DS-ALL cases via a variety of genomic mechanisms, including chromosomal rearrangements and noncoding mutations leading to enhancer hijacking. A total of 42.3% of C/EBP-activated DS-ALL also have concomitant FLT3 point mutations or insertions/deletions, compared with 4.1% in other subtypes. CEBPD overexpression enhanced the differentiation of mouse hematopoietic progenitor cells into pro-B cells in vitro, particularly in a DS genetic background. Notably, recombination-activating gene-mediated somatic genomic abnormalities were common in DS-ALL, accounting for a median of 27.5% of structural alterations, compared with 7.7% in non-DS-ALL. Unsupervised hierarchical clustering analyses of CRLF2-rearranged DS-ALL identified substantial heterogeneity within this group, with the BCR::ABL1-like subset linked to an inferior event-free survival, even after adjusting for known clinical risk factors. These results provide important insights into the biology of DS-ALL and point to opportunities for targeted therapy and treatment individualization.
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Affiliation(s)
- Zhenhua Li
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jacob J. Junco
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Meenakshi Devidas
- Global Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yizhen Li
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
| | - Xin Huang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Dale J. Hedges
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Zhongshan Cheng
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Mary Shago
- Department of Pathobiology and Laboratory Medicine, University of Toronto, Toronto, ON, Canada
| | - Andrew J. Carroll
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL
| | - Nyla A. Heerema
- Department of Pathology, The Ohio State University, Columbus, OH
| | - Julie Gastier-Foster
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Brent L. Wood
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA
| | | | | | - Elizabeth A. Raetz
- Department of Pediatrics and Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY
| | - Stephen P. Hunger
- Department of Pediatrics and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA
- The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA
| | | | | | - Mignon L. Loh
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Department of Pediatrics, Seattle Children’s Hospital, University of Washington, Seattle, WA
| | | | - Jiyang Yu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Philip J. Lupo
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Karen R. Rabin
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Jun J. Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
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18
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Jeon S, Lo YC, Morimoto LM, Metayer C, Ma X, Wiemels JL, de Smith AJ, Chiang CW. Evaluating Genomic Polygenic Risk Scores for Childhood Acute Lymphoblastic Leukemia in Latinos. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.08.23291167. [PMID: 37398036 PMCID: PMC10312899 DOI: 10.1101/2023.06.08.23291167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The utility of polygenic risk score (PRS) models has not been comprehensively evaluated for childhood acute lymphoblastic leukemia (ALL), the most common type of cancer in children. Previous PRS models for ALL were based on significant loci observed in genome-wide association studies (GWAS), even though genomic PRS models have been shown to improve prediction performance for a number of complex diseases. In the United States, Latino (LAT) children have the highest risk of ALL, but the transferability of PRS models to LAT children has not been studied. In this study we constructed and evaluated genomic PRS models based on either non-Latino white (NLW) GWAS or a multi-ancestry GWAS. We found that the best PRS models performed similarly between held-out NLW and LAT samples (PseudoR 2 = 0.086 ± 0.023 in NLW vs. 0.060 ± 0.020 in LAT), and can be improved for LAT if we performed GWAS in LAT-only (PseudoR 2 = 0.116 ± 0.026) or multi-ancestry samples (PseudoR 2 = 0.131 ± 0.025). However, the best genomic models currently do not have better prediction accuracy than a conventional model using all known ALL-associated loci in the literature (PseudoR 2 = 0.166 ± 0.025), which includes loci from GWAS populations that we could not access to train genomic PRS models. Our results suggest that larger and more inclusive GWAS may be needed for genomic PRS to be useful for ALL. Moreover, the comparable performance between populations may suggest a more oligo-genic architecture for ALL, where some large effect loci may be shared between populations. Future PRS models that move away from the infinite causal loci assumption may further improve PRS for ALL.
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Affiliation(s)
- Soyoung Jeon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ying Chu Lo
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Libby M. Morimoto
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Catherine Metayer
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Joseph L. Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Adam J. de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Charleston W.K. Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
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19
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Aref S, El-Ghonemy M, Shimaa H, Darwish A, Abdelmabood S, Khaled N. Significance of CEBPE Gene Promoter Polymorphism (Rs2239630 G > A ) Assessment in Childhood B-cell Acute Lymphoblastic Leukemia. J Pediatr Hematol Oncol 2023; 45:e334-e338. [PMID: 36897378 DOI: 10.1097/mph.0000000000002648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 01/16/2023] [Indexed: 03/11/2023]
Abstract
BACKGROUND A significant association has been reported between CEBPE gene promoter polymorphisms (rs2239630 G > A ) and the incidence of B-cell acute lymphoblastic leukemia (B-ALL). However, no previous study on this issue has been included among the Egyptian cohort of pediatric patients with B-ALL. Therefore, this study was designed to address the associations between CEBPE polymorphisms and susceptibility to B-ALL, as well as its impact on the outcome of B-ALL Egyptian patients with B-ALL. PATIENTS AND METHODS In the current study, we evaluated the rs2239630 polymorphism in 225 pediatric patients and 228 controls to assess the association of different rs2239630 genotypes with childhood susceptibility to B-ALL and the impact on the outcome of the patients. RESULTS The frequency of the A allele was significantly higher in the cases of B-ALL compared with the control group ( P = 0.004). By analyzing different genotypes for the predictive value of disease development, the GA and AA genotypes have been identified to be the highest among multivariate factors with an odds ratio of 3.330 (95% CI: 1.105-10.035). Likewise, the A allele was significantly associated with the shortest overall survival. CONCLUSIONS CEBPE gene promoter polymorphism (rs2239630 G > A ) AA is frequently associated with B-ALL; and has the worst overall survival among the 3 genotypes, followed by the GA and GG genotypes ( P < 0.001).
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Affiliation(s)
| | | | | | - Ahmad Darwish
- Pediatrics Department; Hematology and Oncology unit; Faculty of Medicine; Mansoura University, Egypt
| | - Suzy Abdelmabood
- Pediatrics Department; Hematology and Oncology unit; Faculty of Medicine; Mansoura University, Egypt
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20
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Gundry M, Sankaran VG. Hacking hematopoiesis - emerging tools for examining variant effects. Dis Model Mech 2023; 16:dmm049857. [PMID: 36826849 PMCID: PMC9983777 DOI: 10.1242/dmm.049857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Hematopoiesis is a continuous process of blood and immune cell production. It is orchestrated by thousands of gene products that respond to extracellular signals by guiding cell fate decisions to meet the needs of the organism. Although much of our knowledge of this process comes from work in model systems, we have learned a great deal from studies on human genetic variation. Considerable insight has emerged from studies on presumed monogenic blood disorders, which continue to provide key insights into the mechanisms critical for hematopoiesis. Furthermore, the emergence of large-scale biobanks and cohorts has uncovered thousands of genomic loci associated with blood cell traits and diseases. Some of these blood cell trait-associated loci act as modifiers of what were once thought to be monogenic blood diseases. However, most of these loci await functional validation. Here, we discuss the validation bottleneck and emerging methods to more effectively connect variant to function. In particular, we highlight recent innovations in genome editing, which have paved the path forward for high-throughput functional assessment of loci. Finally, we discuss existing barriers to progress, including challenges in manipulating the genomes of primary hematopoietic cells.
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Affiliation(s)
- Michael Gundry
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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21
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Bhattarai KR, Mobley RJ, Barnett KR, Ferguson DC, Hansen BS, Diedrich JD, Bergeron BP, Yang W, Crews KR, Manring CS, Jabbour E, Paietta E, Litzow MR, Kornblau SM, Stock W, Inaba H, Jeha S, Pui CH, Cheng C, Pruett-Miller SM, Relling MV, Yang JJ, Evans WE, Savic D. Functional investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.10.23285762. [PMID: 36798219 PMCID: PMC9934807 DOI: 10.1101/2023.02.10.23285762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Although acute lymphoblastic leukemia (ALL) is the most common childhood cancer, there is limited understanding of the contribution of inherited genetic variation on inter-individual differences in chemotherapy response. Defining genetic factors impacting therapy failure can help better predict response and identify drug resistance mechanisms. We therefore mapped inherited noncoding variants associated with chemotherapeutic drug resistance and/or treatment outcome to ALL cis-regulatory elements and investigated their gene regulatory potential and genomic connectivity using massively parallel reporter assays and promoter capture Hi-C, respectively. We identified 53 variants with reproducible allele-specific effects on transcription and high-confidence gene targets. Subsequent functional interrogation of the top variant (rs1247117) determined that it disrupted a PU.1 consensus motif and PU.1 binding affinity. Importantly, deletion of the genomic interval containing rs1247117 sensitized ALL cells to vincristine. Together, these data demonstrate that noncoding regulatory variation associated with diverse pharmacological traits harbor significant effects on allele-specific transcriptional activity and impact sensitivity to chemotherapeutic agents in ALL.
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Affiliation(s)
- Kashi Raj Bhattarai
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Robert J. Mobley
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Kelly R. Barnett
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Daniel C. Ferguson
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Baranda S. Hansen
- 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
| | - Jonathan D. Diedrich
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Brennan P. Bergeron
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Wenjian Yang
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Kristine R. Crews
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - 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 MD Anderson Cancer Center, Houston, TX
| | | | - 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 MD Anderson Cancer Center, Houston, TX
| | - Wendy Stock
- Comprehensive Cancer Center, University of Chicago Medicine, Chicago, IL
| | - Hiroto Inaba
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Sima Jeha
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Ching-Hon Pui
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - 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
| | - Mary V. Relling
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Jun J. Yang
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN
| | - William E. Evans
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Daniel Savic
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN
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22
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Junk SV, Schaeffeler E, Zimmermann M, Möricke A, Beier R, Schütte P, Fedders B, Alten J, Hinze L, Klein N, Kulozik A, Muckenthaler MU, Koehler R, Borkhardt A, Vijayakrishnan J, Ellinghaus D, Forster M, Franke A, Wintering A, Kratz CP, Schrappe M, Schwab M, Houlston RS, Cario G, Stanulla M. Chemotherapy-related hyperbilirubinemia in pediatric acute lymphoblastic leukemia: a genome-wide association study from the AIEOP-BFM ALL study group. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2023; 42:21. [PMID: 36639636 PMCID: PMC9838013 DOI: 10.1186/s13046-022-02585-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/26/2022] [Indexed: 01/15/2023]
Abstract
BACKGROUND Characterization of clinical phenotypes in context with tumor and host genomic information can aid in the development of more effective and less toxic risk-adapted and targeted treatment strategies. To analyze the impact of therapy-related hyperbilirubinemia on treatment outcome and to identify contributing genetic risk factors of this well-recognized adverse effect we evaluated serum bilirubin levels in 1547 pediatric patients with acute lymphoblastic leukemia (ALL) and conducted a genome-wide association study (GWAS). PATIENTS AND METHODS Patients were treated in multicenter trial AIEOP-BFM ALL 2000 for pediatric ALL. Bilirubin toxicity was graded 0 to 4 according to the Common Toxicity Criteria (CTC) of the National Cancer Institute. In the GWAS discovery cohort, including 650 of the 1547 individuals, genotype frequencies of 745,895 single nucleotide variants were compared between 435 patients with hyperbilirubinemia (CTC grades 1-4) during induction/consolidation treatment and 215 patients without it (grade 0). Replication analyses included 224 patients from the same trial. RESULTS Compared to patients with no (grade 0) or moderate hyperbilirubinemia (grades 1-2) during induction/consolidation, patients with grades 3-4 had a poorer 5-year event free survival (76.6 ± 3% versus 87.7 ± 1% for grades 1-2, P = 0.003; 85.2 ± 2% for grade 0, P < 0.001) and a higher cumulative incidence of relapse (15.6 ± 3% versus 9.0 ± 1% for grades 1-2, P = 0.08; 11.1 ± 1% for grade 0, P = 0.007). GWAS identified a strong association of the rs6744284 variant T allele in the UGT1A gene cluster with risk of hyperbilirubinemia (allelic odds ratio (OR) = 2.1, P = 7 × 10- 8). TT-homozygotes had a 6.5-fold increased risk of hyperbilirubinemia (grades 1-4; 95% confidence interval (CI) = 2.9-14.6, P = 7 × 10- 6) and a 16.4-fold higher risk of grade 3-4 hyperbilirubinemia (95% CI 6.1-43.8, P = 2 × 10- 8). Replication analyses confirmed these associations with joint analysis yielding genome-wide significance (allelic OR = 2.1, P = 6 × 10- 11; 95% CI 1.7-2.7). Moreover, rs6744284 genotypes were strongly linked to the Gilbert's syndrome-associated UGT1A1*28/*37 allele (r2 = 0.70), providing functional support for study findings. Of clinical importance, the rs6744284 TT genotype counterbalanced the adverse prognostic impact of high hyperbilirubinemia on therapy outcome. CONCLUSIONS Chemotherapy-related hyperbilirubinemia is a prognostic factor for treatment outcome in pediatric ALL and genetic variation in UGT1A aids in predicting the clinical impact of hyperbilirubinemia. TRIAL REGISTRATION http://www. CLINICALTRIALS gov ; #NCT00430118.
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Affiliation(s)
- Stefanie V. Junk
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Elke Schaeffeler
- Margarete-Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Martin Zimmermann
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Anja Möricke
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Rita Beier
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Peter Schütte
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Birthe Fedders
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Julia Alten
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Laura Hinze
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Norman Klein
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Andreas Kulozik
- grid.7700.00000 0001 2190 4373Department of Pediatric Hematology, Oncology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Martina U. Muckenthaler
- grid.7700.00000 0001 2190 4373Department of Pediatric Hematology, Oncology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Rolf Koehler
- grid.7700.00000 0001 2190 4373Department of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Arndt Borkhardt
- grid.411327.20000 0001 2176 9917Clinic for Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Jayaram Vijayakrishnan
- grid.18886.3fDivision of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, UK
| | - David Ellinghaus
- grid.9764.c0000 0001 2153 9986Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Michael Forster
- grid.9764.c0000 0001 2153 9986Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Andre Franke
- grid.9764.c0000 0001 2153 9986Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Astrid Wintering
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Christian P. Kratz
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Martin Schrappe
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Matthias Schwab
- Margarete-Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany ,grid.10392.390000 0001 2190 1447Departments of Clinical Pharmacology, and of Biochemistry and Pharmacy, University of Tuebingen, Tuebingen, Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, Tuebingen, Germany ,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
| | - Richard S. Houlston
- grid.18886.3fDivision of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, UK
| | - Gunnar Cario
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Martin Stanulla
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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23
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Brum da Silva Nunes V, Kehl Dias C, Nathali Scholl J, Nedel Sant'Ana A, de Fraga Dias A, Granero Farias M, Alegretti AP, Sosnoski M, Esteves Daudt L, Bohns Michalowski M, Oliveira Battastini AM, Paz AA, Figueiró F. Lymphocytes from B-acute lymphoblastic leukemia patients present differential regulation of the adenosinergic axis depending on risk stratification. Discov Oncol 2022; 13:143. [PMID: 36581667 PMCID: PMC9800668 DOI: 10.1007/s12672-022-00602-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Although risk-stratified chemotherapy regimens improve B-cell acute lymphoblastic leukemia (B-ALL) clinical outcome, relapse occurs in a significant number of cases. The identification of new therapeutic targets as well as prognostic and diagnostic biomarkers can improve B-ALL patients' clinical outcomes. Purinergic signaling is an important pathway in cancer progression, however the expression of ectonucleotidases and their impact on immune cells in B-ALL lacks exploration. We aimed to analyze the expression of ectonucleotidases in B-ALL patients' lymphocyte subpopulations. METHODS Peripheral blood samples from 15 patients diagnosed with B-ALL were analyzed. Flow cytometry was used to analyze cellularity, expression level of CD38, CD39, and CD73, and frequency of [Formula: see text], and [Formula: see text] in lymphocyte subpopulations. Plasma was used for cytokines (by CBA kit) and adenine nucleosides/nucleotides detection (by HPLC). RESULTS Comparing B-ALL patients to health donors, we observed an increase of CD4 + and CD8 + T-cells. In addition, a decrease in CD38 expression in B and Treg subpopulations and an increase in CD39+ CD73+ frequency in Breg and CD8+ T-cells. Analyzing cytokines and adenine nucleosides/nucleotides, we found a decrease in TNF, IL-1β, and ADO concentrations, together with an increase in AMP in B-ALL patients' plasma. CONCLUSION As immunomodulators, the expression of ectonucleotidases might be associated with activation states, as well as the abundance of different cellular subsets. We observed a pro-tumor immunity expression profile in B-ALL patients at diagnosis, being associated with cell exhaustion and immune evasion in B-ALL.
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Affiliation(s)
- Vitória Brum da Silva Nunes
- Laboratório de Imunobioquímica do Câncer, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, UFRGS, Porto Alegre, RS, CEP 90035-003, Brazil
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, UFRGS, Porto Alegre, RS, CEP 90035-003, Brazil
| | - Camila Kehl Dias
- Laboratório de Imunobioquímica do Câncer, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, UFRGS, Porto Alegre, RS, CEP 90035-003, Brazil
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, UFRGS, Porto Alegre, RS, CEP 90035-003, Brazil
| | - Juliete Nathali Scholl
- Laboratório de Imunobioquímica do Câncer, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, UFRGS, Porto Alegre, RS, CEP 90035-003, Brazil
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, UFRGS, Porto Alegre, RS, CEP 90035-003, Brazil
| | - Alexia Nedel Sant'Ana
- Laboratório de Imunobioquímica do Câncer, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, UFRGS, Porto Alegre, RS, CEP 90035-003, Brazil
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, UFRGS, Porto Alegre, RS, CEP 90035-003, Brazil
| | - Amanda de Fraga Dias
- Laboratório de Imunobioquímica do Câncer, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, UFRGS, Porto Alegre, RS, CEP 90035-003, Brazil
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, UFRGS, Porto Alegre, RS, CEP 90035-003, Brazil
| | | | - Ana Paula Alegretti
- Hospital de Clínicas de Porto Alegre/HCPA, Porto Alegre, RS, CEP 90035-903, Brazil
| | - Monalisa Sosnoski
- Hospital de Clínicas de Porto Alegre/HCPA, Porto Alegre, RS, CEP 90035-903, Brazil
| | - Liane Esteves Daudt
- Hospital de Clínicas de Porto Alegre/HCPA, Porto Alegre, RS, CEP 90035-903, Brazil
| | - Mariana Bohns Michalowski
- Hospital de Clínicas de Porto Alegre/HCPA, Porto Alegre, RS, CEP 90035-903, Brazil
- Programa de Pós-Graduação em Saúde da Criança e do Adolescente, Faculdade de Medicina, UFRGS, Porto Alegre, RS, 90035-003, Brazil
| | - Ana Maria Oliveira Battastini
- Laboratório de Imunobioquímica do Câncer, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, UFRGS, Porto Alegre, RS, CEP 90035-003, Brazil
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, UFRGS, Porto Alegre, RS, CEP 90035-003, Brazil
| | | | - Fabrício Figueiró
- Laboratório de Imunobioquímica do Câncer, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, UFRGS, Porto Alegre, RS, CEP 90035-003, Brazil.
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, UFRGS, Porto Alegre, RS, CEP 90035-003, Brazil.
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24
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Haas OA, Borkhardt A. Hyperdiploidy: the longest known, most prevalent, and most enigmatic form of acute lymphoblastic leukemia in children. Leukemia 2022; 36:2769-2783. [PMID: 36266323 PMCID: PMC9712104 DOI: 10.1038/s41375-022-01720-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
Abstract
Hyperdiploidy is the largest genetic entity B-cell precursor acute lymphoblastic leukemia in children. The diagnostic hallmark of its two variants that will be discussed in detail herein is a chromosome count between 52 and 67, respectively. The classical HD form consists of heterozygous di-, tri-, and tetrasomies, whereas the nonclassical one (usually viewed as "duplicated hyperhaploid") contains only disomies and tetrasomies. Despite their apparently different clinical behavior, we show that these two sub-forms can in principle be produced by the same chromosomal maldistribution mechanism. Moreover, their respective array, gene expression, and mutation patterns also indicate that they are biologically more similar than hitherto appreciated. Even though in-depth analyses of the genomic intricacies of classical HD leukemias are indispensable for the elucidation of the disease process, the ensuing results play at present surprisingly little role in treatment stratification, a fact that can be attributed to the overall good prognoses and low relapse rates of the concerned patients and, consequently, their excellent treatment outcome. Irrespective of this underutilization, however, the detailed genetic characterization of HD leukemias may, especially in planned treatment reduction trials, eventually become important for further treatment stratification, patient management, and the clinical elucidation of outcome data. It should therefore become an integral part of all upcoming treatment studies.
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Affiliation(s)
- Oskar A Haas
- St. Anna Children's Hospital, Pediatric Clinic, Medical University, Vienna, Austria.
- Labdia Labordiagnostik, Vienna, Austria.
| | - Arndt Borkhardt
- Department for Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany.
- German Cancer Consortium (DKTK), partnering site Essen/Düsseldorf, Düsseldorf, Germany.
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25
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Kratz CP, Smirnov D, Autry R, Jäger N, Waszak SM, Großhennig A, Berutti R, Wendorff M, Hainaut P, Pfister SM, Prokisch H, Ripperger T, Malkin D. Heterozygous BRCA1 and BRCA2 and Mismatch Repair Gene Pathogenic Variants in Children and Adolescents With Cancer. J Natl Cancer Inst 2022; 114:1523-1532. [PMID: 35980168 DOI: 10.1093/jnci/djac151] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 03/21/2022] [Accepted: 07/20/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Genetic predisposition is has been identified as a cause of cancer, yet little is known about the role of adult cancer predisposition syndromes in childhood cancer. We examined the extent to which heterozygous pathogenic germline variants in BRCA1, BRCA2, PALB2, ATM, CHEK2, MSH2, MSH6, MLH1, and PMS2 contribute to cancer risk in children and adolescents. METHODS We conducted a meta-analysis of 11 studies that incorporated comprehensive germline testing for children and adolescents with cancer. ClinVar pathogenic or likely pathogenic variants (PVs) in genes of interest were compared with 2 control groups. Results were validated in a cohort of mainly European patients and controls. We employed the Proxy External Controls Association Test to account for different pipelines. RESULTS Among 3975 children and adolescents with cancer, statistically significant associations with cancer risk were observed for PVs in BRCA1 and 2 (26 PVs vs 63 PVs among 27 501 controls, odds ratio = 2.78, 95% confidence interval = 1.69 to 4.45; P < .001) and mismatch repair genes (19 PVs vs 14 PVs among 27 501 controls, odds ratio = 7.33, 95% confidence interval = 3.64 to 14.82; P <.001). Associations were seen in brain and other solid tumors but not in hematologic neoplasms. We confirmed similar findings in 1664 pediatric cancer patients primarily of European descent. CONCLUSION These data suggest that heterozygous PVs in BRCA1 and 2 and mismatch repair genes contribute with reduced penetrance to cancer risk in children and adolescents. No changes to predictive genetic testing and surveillance recommendations are required.
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Affiliation(s)
- Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Dmitrii Smirnov
- Institute of Human Genetics, School of Medicine, Technische Universität München, München, Germany.,Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Robert Autry
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic European Molecular Biology Laboratory (EMBL) Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Anika Großhennig
- Institute of Biostatistics, Hannover Medical School, Hannover, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, School of Medicine, Technische Universität München, München, Germany.,Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Pierre Hainaut
- Univ. Grenoble Alpes, Inserm 1209, CNRS 5309, Institute for Advanced Biosciences, F38000, Grenoble, France
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technische Universität München, München, Germany.,Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - David Malkin
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Paediatrics, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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26
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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: 2] [Impact Index Per Article: 0.7] [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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27
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Zhao X, Qian M, Goodings C, Zhang Y, Yang W, Wang P, Xu B, Tian C, Pui CH, Hunger SP, Raetz EA, Devidas M, Relling MV, Loh ML, Savic D, Li C, Yang JJ. Molecular Mechanisms of ARID5B-Mediated Genetic Susceptibility to Acute Lymphoblastic Leukemia. J Natl Cancer Inst 2022; 114:1287-1295. [PMID: 35575404 PMCID: PMC9468286 DOI: 10.1093/jnci/djac101] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/05/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND There is growing evidence for the inherited basis of susceptibility to childhood acute lymphoblastic leukemia (ALL). Genome-wide association studies have identified non-coding ALL risk variants at the ARID5B gene locus, but their exact functional effects and the molecular mechanism linking ARID5B to B-cell ALL leukemogenesis remain largely unknown. METHODS We performed targeted sequencing of ARID5B in germline DNA of 5008 children with ALL. Variants were evaluated for association with ALL susceptibility using 3644 patients from the UK10K cohort as non-ALL controls, under an additive model. Cis-regulatory elements in ARID5B were systematically identified using dCas9-KRAB-mediated enhancer interference system enhancer screen in ALL cells. Disruption of transcription factor binding by ARID5B variant was predicted informatically and then confirmed using chromatin immunoprecipitation and coimmunoprecipitation. ARID5B variant association with hematological traits was examined using UK Biobank dataset. All statistical tests were 2-sided. RESULTS We identified 54 common variants in ARID5B statistically significantly associated with leukemia risk, all of which were noncoding. Six cis-regulatory elements at the ARID5B locus were discovered using CRISPR-based high-throughput enhancer screening. Strikingly, the top ALL risk variant (rs7090445, P = 5.57 × 10-45) is located precisely within the strongest enhancer element, which is also distally tethered to the ARID5B promoter. The variant allele disrupts the MEF2C binding motif sequence, resulting in reduced MEF2C affinity and decreased local chromosome accessibility. MEF2C influences ARID5B expression in ALL, likely via a transcription factor complex with RUNX1. Using the UK Biobank dataset (n = 349 861), we showed that rs7090445 was also associated with lymphocyte percentage and count in the general population (P = 8.6 × 10-22 and 2.1 × 10-18, respectively). CONCLUSIONS Our results indicate that ALL risk variants in ARID5B function by modulating cis-regulatory elements at this locus.
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Affiliation(s)
- Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Maoxiang Qian
- Institute of Pediatrics and Department of Hematology and Oncology, Children's Hospital of Fudan University, National Children's Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Charnise Goodings
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yang Zhang
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ping Wang
- Department of Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheng Tian
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen P Hunger
- Department of Pediatrics 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, PA, USA
| | - Elizabeth A Raetz
- Department of Pediatrics and Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Meenakshi Devidas
- Department of Global Pediatric Medicine, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Daniel Savic
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
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28
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Lin X, Liu Y, Liu S, Zhu X, Wu L, Zhu Y, Zhao D, Xu X, Chemparathy A, Wang H, Cao Y, Nakamura M, Noordermeer JN, La Russa M, Wong WH, Zhao K, Qi LS. Nested epistasis enhancer networks for robust genome regulation. Science 2022; 377:1077-1085. [PMID: 35951677 DOI: 10.1126/science.abk3512] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mammalian genomes possess multiple enhancers spanning an ultralong distance (>megabases) to modulate important genes, yet it is unclear how these enhancers coordinate to achieve this task. Here, we combine multiplexed CRISPRi screening with machine learning to define quantitative enhancer-enhancer interactions. We find that the ultralong distance enhancer network possesses a nested multi-layer architecture that confers functional robustness of gene expression. Experimental characterization reveals that enhancer epistasis is maintained by three-dimensional chromosomal interactions and BRD4 condensation. Machine learning prediction of synergistic enhancers provides an effective strategy to identify non-coding variant pairs associated with pathogenic genes in diseases beyond Genome-Wide Association Studies (GWAS) analysis. Our work unveils nested epistasis enhancer networks, which can better explain enhancer functions within cells and in diseases.
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Affiliation(s)
- Xueqiu Lin
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yanxia Liu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Shuai Liu
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute NIH, Bethesda, MD 20892, USA
| | - Xiang Zhu
- Department of Statistics, Stanford University, Stanford, CA 94305, USA.,Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lingling Wu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yanyu Zhu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Dehua Zhao
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Xiaoshu Xu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Haifeng Wang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yaqiang Cao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute NIH, Bethesda, MD 20892, USA
| | - Muneaki Nakamura
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Marie La Russa
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, CA 94305, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute NIH, Bethesda, MD 20892, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,ChEM-H, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg BioHub, San Francisco, CA 94158, USA
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29
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Goodings C, Zhao X, McKinney-Freeman S, Zhang H, Yang JJ. ARID5B influences B-cell development and function in mouse. Haematologica 2022; 108:502-512. [PMID: 35924577 PMCID: PMC9890020 DOI: 10.3324/haematol.2022.281157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Indexed: 02/03/2023] Open
Abstract
There is growing evidence for an inherited basis of susceptibility to childhood acute lymphoblastic leukemia. Genomewide association studies by us and others have identified non-coding acute lymphoblastic leukemia risk variants at the ARID5B gene locus, but the molecular mechanisms linking ARID5B to normal and malignant hematopoiesis remain largely unknown. Using a Vav1-driven transgenic mouse model, we characterized the role of Arid5b in hematopoiesis in vivo. Arid5b overexpression resulted in a dramatic reduction in the proportion of circulating B cells, immature, and mature Bcell fractions in the peripheral blood and the bone marrow, and also a decrease of follicular B cells in the spleen. There were significant defects in B-cell activation upon Arid5b overexpression in vitro with hyperactivation of B-cell receptor signaling at baseline. In addition, increased mitochondrial oxygen consumption rate of naïve or stimulated B cells of Arid5b-overexpressing mice was observed, compared to the rate of wild-type counterparts. Taken together, our results indicate that ARID5B may play an important role in B-cell development and function.
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Affiliation(s)
- Charnise Goodings
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA,*CG and XZ contributed equally as co-first authors
| | - Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA,*CG and XZ contributed equally as co-first authors
| | | | - Hui Zhang
- Department of Hematology/Oncology, Shanghai Children’s Medical Center, Shanghai, China
| | - Jun J. Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA,Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA,J. J. Yang
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30
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Leitão LPC, de Carvalho DC, Rodrigues JCG, Fernandes MR, Wanderley AV, Vinagre LWMS, da Silva NM, Pastana LF, Gellen LPA, Assunção MCE, Fernandes SSM, Pereira EEB, Ribeiro-Dos-Santos AM, Guerreiro JF, Ribeiro-dos-Santos Â, de Assumpção PP, dos Santos SEB, dos Santos NPC. Identification of Genomic Variants Associated with the Risk of Acute Lymphoblastic Leukemia in Native Americans from Brazilian Amazonia. J Pers Med 2022; 12:jpm12060856. [PMID: 35743641 PMCID: PMC9224820 DOI: 10.3390/jpm12060856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/17/2022] [Accepted: 04/18/2022] [Indexed: 12/04/2022] Open
Abstract
A number of genomic variants related to native American ancestry may be associated with an increased risk of developing Acute Lymphoblastic Leukemia (ALL), which means that Latin American and hispanic populations from the New World may be relatively susceptible to this disease. However, there has not yet been any comprehensive investigation of the variants associated with susceptibility to ALL in traditional Amerindian populations from Brazilian Amazonia. We investigated the exomes of the 18 principal genes associated with susceptibility to ALL in samples of 64 Amerindians from this region, including cancer-free individuals and patients with ALL. We compared the findings with the data on populations representing five continents available in the 1000 Genomes database. The variation in the allele frequencies found between the different groups was evaluated using Fisher’s exact test. The analyses of the exomes of the Brazilian Amerindians identified 125 variants, seven of which were new. The comparison of the allele frequencies between the two Amerindian groups analyzed in the present study (ALL patients vs. cancer-free individuals) identified six variants (rs11515, rs2765997, rs1053454, rs8068981, rs3764342, and rs2304465) that may be associated with susceptibility to ALL. These findings contribute to the identification of genetic variants that represent a potential risk for ALL in Amazonian Amerindian populations and might favor precision oncology measures.
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Affiliation(s)
- Luciana P. C. Leitão
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
- Faculdade de Ciências Médicas do Pará (FACIMPA), Marabá 68508-030, PA, Brazil
| | - Darlen C. de Carvalho
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Juliana C. G. Rodrigues
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Marianne R. Fernandes
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Alayde V. Wanderley
- Pediatrics Department, Ophir Loyola Hospital, Belém 66063-240, PA, Brazil; (A.V.W.); (S.S.M.F.)
| | - Lui W. M. S. Vinagre
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Natasha M. da Silva
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Lucas F. Pastana
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Laura P. A. Gellen
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Matheus C. E. Assunção
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Sweny S. M. Fernandes
- Pediatrics Department, Ophir Loyola Hospital, Belém 66063-240, PA, Brazil; (A.V.W.); (S.S.M.F.)
| | - Esdras E. B. Pereira
- Human and Medical Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (E.E.B.P.); (A.M.R.-D.-S.); (J.F.G.); (Â.R.-d.-S.); (S.E.B.d.S.)
- Instituto Tocantinense Presidente Antônio Carlos (ITPAC), Abaetetuba 68440-000, PA, Brazil
| | - André M. Ribeiro-Dos-Santos
- Human and Medical Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (E.E.B.P.); (A.M.R.-D.-S.); (J.F.G.); (Â.R.-d.-S.); (S.E.B.d.S.)
| | - João F. Guerreiro
- Human and Medical Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (E.E.B.P.); (A.M.R.-D.-S.); (J.F.G.); (Â.R.-d.-S.); (S.E.B.d.S.)
| | - Ândrea Ribeiro-dos-Santos
- Human and Medical Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (E.E.B.P.); (A.M.R.-D.-S.); (J.F.G.); (Â.R.-d.-S.); (S.E.B.d.S.)
| | - Paulo P. de Assumpção
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
| | - Sidney E. B. dos Santos
- Human and Medical Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (E.E.B.P.); (A.M.R.-D.-S.); (J.F.G.); (Â.R.-d.-S.); (S.E.B.d.S.)
| | - Ney P. C. dos Santos
- Oncology Research Nucleus, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (L.P.C.L.); (D.C.d.C.); (J.C.G.R.); (M.R.F.); (L.W.M.S.V.); (N.M.d.S.); (L.F.P.); (L.P.A.G.); (M.C.E.A.); (P.P.d.A.)
- Correspondence: ; Tel.: +55-(91)-3201-6778
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31
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Zhu H, Zhang R, Li R, Wang Z, Li H, Zhong H, Yin L, Ruan X, Ye C, Yuan H, Cheng Z, Peng H. Identification of diagnosis and prognosis gene markers in B-ALL with ETV6-RUNX1 fusion by integrated bioinformatics analysis. Gene 2022; 815:146132. [PMID: 34999180 DOI: 10.1016/j.gene.2021.146132] [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: 09/23/2021] [Revised: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022]
Abstract
B-acute lymphoblastic leukemia (B-ALL) is characterized by clonal expansion of immature B-lymphocytes in the bone marrow, blood, or other tissues. Chromosomal translocations have often been reported in B-ALL, which are important for its prognosis. B-ALL patients with ETV6-RUNX1 fusion have favorable outcomes, but the mechanisms remain to be clarified. In the present study, we crossed the selected WGCNA module genes and differential expression genes to obtain core genes, and random forest algorithm, a type of supervised learning analysis, was conducted to evaluate the importance of those core genes in distinguishing B-ALL samples with ETV6-RUNX2 fusion with extracting 5 genes as gene markers for ETV6-RUNX2 fusion. Moreover, we calculated the immune infiltration profiles and screened out the ETV6-RUNX2 association immune cells using the CIBERSORT algorithm. In conclusion, combined with various solid informatics methods, we depicted the underlying molecular and immune mechanism of ETV6-RUNX2 fusion and providing potential biological targets for diagnosing and treating B-ALL in the future.
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Affiliation(s)
- Hongkai Zhu
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Rong Zhang
- National Cancer Center Exploratory Oncology Research & Clinical Trial Center, Japan
| | - Ruijuan Li
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Zhihua Wang
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Heng Li
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Haiying Zhong
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Le Yin
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Xueqin Ruan
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Can Ye
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Huan Yuan
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China
| | - Zhao Cheng
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Hongling Peng
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, Changsha, Hunan 410011, PR China.
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32
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Jeon S, de Smith AJ, Li S, Chen M, Chan TF, Muskens IS, Morimoto LM, DeWan AT, Mancuso N, Metayer C, Ma X, Wiemels JL, Chiang CWK. Genome-wide trans-ethnic meta-analysis identifies novel susceptibility loci for childhood acute lymphoblastic leukemia. Leukemia 2022; 36:865-868. [PMID: 34750507 PMCID: PMC9075725 DOI: 10.1038/s41375-021-01465-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/12/2021] [Accepted: 10/21/2021] [Indexed: 02/08/2023]
Affiliation(s)
- Soyoung Jeon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Cancer Biology and Genomics Graduate Program, Program in Biological and Biomedical Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Cancer Biology and Genomics Graduate Program, Program in Biological and Biomedical Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Minhui Chen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tsz Fung Chan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ivo S Muskens
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Libby M Morimoto
- Division of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
| | - Andrew T DeWan
- Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, CT, USA
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Catherine Metayer
- Division of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
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33
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Ajrouche R, Chandab G, Petit A, Strullu M, Nelken B, Plat G, Michel G, Domenech C, Clavel J, Bonaventure A. Allergies, genetic polymorphisms of Th2 interleukins, and childhood acute lymphoblastic leukemia: The ESTELLE study. Pediatr Blood Cancer 2022; 69:e29402. [PMID: 34662484 DOI: 10.1002/pbc.29402] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 08/12/2021] [Accepted: 09/16/2021] [Indexed: 11/07/2022]
Abstract
CONTEXT A negative association between a history of allergy and childhood acute lymphoblastic leukemia (ALL) has been reported in previous studies, but remains debated. This work aimed to investigate this association accounting for genetic polymorphisms of the Th2 pathway cytokines (IL4, IL10, IL13, and IL4R). METHODS Analyses were based on the French case-control study ESTELLE (2010-2011). The complete sample included 629 ALL cases and 1421 population-based controls frequency-matched on age and gender. The child's medical history was collected through standardized maternal interview. Biological samples were collected, and genotyping data were available for 411 cases and 704 controls of European origin. Odds ratios (OR) were estimated using unconditional regression models adjusted for potential confounders. RESULTS In the complete sample, a significant inverse association was observed between ALL and reported history of allergic rhinitis or sinusitis (OR = 0.65 [0.42-0.98]; P = 0.04), but there was no obvious association with allergies overall. There was an interaction between genetic polymorphisms in IL4 and IL4R (Pinteraction = 0.003), as well as a gene-environment interaction between IL4R-rs1801275 and a reported history of asthma (IOR = 0.23; Pint = 0.008) and eczema (IOR = 0.47; Pint = 0.06). We observed no interaction with the candidate polymorphisms in IL4 and IL13. CONCLUSION These results suggest that the association between allergic symptoms and childhood ALL could be modified by IL4R-rs1801275, and that this variant could also interact with a functional variant in IL4 gene. Although they warrant confirmation, these results could help understand the pathological mechanisms under the reported inverse association between allergy and childhood ALL.
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Affiliation(s)
- Roula Ajrouche
- CRESS, Université de Paris INSERM, UMR 1153, Epidemiology of Childhood and Adolescent Cancers Team, Villejuif, France.,Faculty of Pharmacy, Lebanese University, Hadath, Lebanon
| | - Ghinaj Chandab
- CRESS, Université de Paris INSERM, UMR 1153, Epidemiology of Childhood and Adolescent Cancers Team, Villejuif, France.,Faculty of Pharmacy, Lebanese University, Hadath, Lebanon
| | - Arnaud Petit
- Sorbonne Université, UMRS_938, AP-HP, Hôpital Armand Trousseau, Paris, France
| | | | | | | | | | - Carine Domenech
- Institut d'Hématologie et d'Oncologie Pédiatrique, Hospices Civils de Lyon, Université Lyon 1, Lyon, France
| | - Jacqueline Clavel
- CRESS, Université de Paris INSERM, UMR 1153, Epidemiology of Childhood and Adolescent Cancers Team, Villejuif, France.,National Registry of Childhood Cancers, Groupe Hospitalier Universitaire Paris-Sud, Assistance Publique Hôpitaux de Paris (AP-HP) Hôpital Paul Brousse, Villejuif, France and CHU de Nancy, Vandoeuvre-lès-Nancy, Nancy, France
| | - Audrey Bonaventure
- CRESS, Université de Paris INSERM, UMR 1153, Epidemiology of Childhood and Adolescent Cancers Team, Villejuif, France
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34
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Impact of Variants in the ATIC and ARID5B Genes on Therapeutic Failure with Imatinib in Patients with Chronic Myeloid Leukemia. Genes (Basel) 2022; 13:genes13020330. [PMID: 35205374 PMCID: PMC8872593 DOI: 10.3390/genes13020330] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/24/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm derived from the balanced reciprocal translocation of chromosomes 9 and 22 t (9q34 and 22q11), which leads to the formation of the Philadelphia chromosome and fusion of the BCR-ABL genes. The first-line treatment for CML is imatinib, a tyrosine kinase inhibitor that acts on the BCR-ABL protein. However, even though it is a target-specific drug, about 25% of patients do not respond to this treatment. The resistance mechanisms involved in this process have been investigated and studies have shown that germinal alterations can influence this mechanism. The aim of this work was to investigate 32 polymorphisms in 24 genes of carcinogenic pathway to verify the influence of these genetic variants on the response to treatment with imatinib. Our results demonstrated that individuals with the recessive GG genotype for the rs2372536 variant in the ATIC gene are approximately three times more likely to experience treatment failure with imatinib (p = 0.045, HR = 2.726, 95% CI = 0.9986–7.441), as well as individuals with the TT genotype for the rs10821936 variant in the ARID5B gene, who also have a higher risk for treatment failure with imatinib over time (p = 0.02, HR = 0.4053, IC 95% = 0.1802–0.911). In conclusion, we show that variants in the ATIC and ARIDB5 gene, never screened in previous studies, could potentially influence the therapeutic response to imatinib in patients treated for CML.
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35
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Cardesa-Salzmann TM, Simon A, Graf N. Antibiotics in early life and childhood pre-B-ALL. Reasons to analyze a possible new piece in the puzzle. Discov Oncol 2022; 13:5. [PMID: 35201533 PMCID: PMC8777491 DOI: 10.1007/s12672-022-00465-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/23/2021] [Indexed: 11/29/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer with precursor B-cell ALL (pB-ALL) accounting for ~ 85% of the cases. Childhood pB-ALL development is influenced by genetic susceptibility and host immune responses. The role of the intestinal microbiome in leukemogenesis is gaining increasing attention since Vicente-Dueñas' seminal work demonstrated that the gut microbiome is distinct in mice genetically predisposed to ALL and that the alteration of this microbiome by antibiotics is able to trigger pB-ALL in Pax5 heterozygous mice in the absence of infectious stimuli. In this review we provide an overview on novel insights on the role of the microbiome in normal and preleukemic hematopoiesis, inflammation, the effect of dysbiosis on hematopoietic stem cells and the emerging importance of the innate immune responses in the conversion from preleukemic to leukemic state in childhood ALL. Since antibiotics, which represent one of the most widely used medical interventions, alter the gut microbial composition and can cause a state of dysbiosis, this raises exciting epidemiological questions regarding the implications for antibiotic use in early life, especially in infants with a a preleukemic "first hit". Sheading light through a rigorous study on this piece of the puzzle may have broad implications for clinical practice.
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Affiliation(s)
- T. M. Cardesa-Salzmann
- Department of Pediatric Hematology and Oncology, Universitätsklinikum des Saarlandes, Homburg, Saarland Germany
| | - A. Simon
- Department of Pediatric Hematology and Oncology, Universitätsklinikum des Saarlandes, Homburg, Saarland Germany
| | - N. Graf
- Department of Pediatric Hematology and Oncology, Universitätsklinikum des Saarlandes, Homburg, Saarland Germany
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36
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McEachron TA, Helman LJ. Recent Advances in Pediatric Cancer Research. Cancer Res 2021; 81:5783-5799. [PMID: 34561271 DOI: 10.1158/0008-5472.can-21-1191] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/05/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022]
Abstract
Over the past few years, the field of pediatric cancer has experienced a shift in momentum, and this has led to new and exciting findings that have relevance beyond pediatric malignancies. Here we present the current status of key aspects of pediatric cancer research. We have focused on genetic and epigenetic drivers of disease, cellular origins of different pediatric cancers, disease models, the tumor microenvironment, and cellular immunotherapies.
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Affiliation(s)
| | - Lee J Helman
- Osteosarcoma Institute, Dallas, Texas
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, California
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37
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Yang T, Mills LJ, Xue H, Raduski A, Williams LA, Spector LG. Impact of fetal expression quantitative trait loci on transcriptome-wide association study of childhood leukemia. Hum Mol Genet 2021; 31:3207-3215. [PMID: 34791233 DOI: 10.1093/hmg/ddab336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/08/2021] [Accepted: 11/07/2021] [Indexed: 11/12/2022] Open
Abstract
Transcriptome-wide association studies increase the yield of loci associated with disease phenotypes by focusing on expression quantitative trait loci (eQTL). The major source of eQTL data for is the Gene and Tissue Expression (GTEx) project, which is comprised entirely of adults, mainly those > 50 years of age at death. Since gene expression levels differ by developmental stage, it is not clear whether eQTLs derived from adult data sources are best suited for use in young-onset diseases such as pediatric cancers. To fill in this knowledge gap, we performed a large-scale eQTL mapping analysis in the GenCord study with newborn samples and compared it with GTEx. Under matched conditions, we found around 80% of the eQTLs in one study can be replicated in the other. However, among all eQTLs identified in GenCord (GTEx), 584 (1045) showed statistically significant differences in effect sizes in GTEx (GenCord). We further investigated how using fetal eQTL data can facilitate the genetic association study of acute lymphoblastic leukemia. GenCord and GTEx identified the same genetic loci with statistical significance; however, the overall association pattern was only weakly correlated. Our paper demonstrates age-differential eQTLs and shows their potential influence on childhood leukemia research.
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Affiliation(s)
- Tianzhong Yang
- Department of Biostatistics, School of Public Health, University of Minnesota, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Lauren J Mills
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Haoran Xue
- Department of Statistics, University of Minnesota, MN, USA
| | - Andrew Raduski
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Lindsay A Williams
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota School of Medicine, Minneapolis, MN, USA.,Brain Tumor Program, University of Minnesota, Minneapolis, MN, USA
| | - Logan G Spector
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota School of Medicine, Minneapolis, MN, USA
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Hauer J, Fischer U, Borkhardt A. Toward prevention of childhood ALL by early-life immune training. Blood 2021; 138:1412-1428. [PMID: 34010407 PMCID: PMC8532195 DOI: 10.1182/blood.2020009895] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/21/2021] [Indexed: 11/21/2022] Open
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most common form of childhood cancer. Chemotherapy is associated with life-long health sequelae and fails in ∼20% of cases. Thus, prevention of leukemia would be preferable to treatment. Childhood leukemia frequently starts before birth, during fetal hematopoiesis. A first genetic hit (eg, the ETV6-RUNX1 gene fusion) leads to the expansion of preleukemic B-cell clones, which are detectable in healthy newborn cord blood (up to 5%). These preleukemic clones give rise to clinically overt leukemia in only ∼0.2% of carriers. Experimental evidence suggests that a major driver of conversion from the preleukemic to the leukemic state is exposure to immune challenges. Novel insights have shed light on immune host responses and how they shape the complex interplay between (1) inherited or acquired genetic predispositions, (2) exposure to infection, and (3) abnormal cytokine release from immunologically untrained cells. Here, we integrate the recently emerging concept of "trained immunity" into existing models of childhood BCP-ALL and suggest future avenues toward leukemia prevention.
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Affiliation(s)
- Julia Hauer
- National Center for Tumor Diseases (NCT), Dresden, Germany
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Ute Fischer
- Department for Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany; and
- German Cancer Consortium (DKTK), partnering site Essen/Düsseldorf, Germany
| | - Arndt Borkhardt
- Department for Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany; and
- German Cancer Consortium (DKTK), partnering site Essen/Düsseldorf, Germany
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39
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Kachuri L, Jeon S, DeWan AT, Metayer C, Ma X, Witte JS, Chiang CWK, Wiemels JL, de Smith AJ. Genetic determinants of blood-cell traits influence susceptibility to childhood acute lymphoblastic leukemia. Am J Hum Genet 2021; 108:1823-1835. [PMID: 34469753 PMCID: PMC8546033 DOI: 10.1016/j.ajhg.2021.08.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/06/2021] [Indexed: 01/07/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Despite overlap between genetic risk loci for ALL and hematologic traits, the etiological relevance of dysregulated blood-cell homeostasis remains unclear. We investigated this question in a genome-wide association study (GWAS) of childhood ALL (2,666 affected individuals, 60,272 control individuals) and a multi-trait GWAS of nine blood-cell indices in the UK Biobank. We identified 3,000 blood-cell-trait-associated (p < 5.0 × 10-8) variants, explaining 4.0% to 23.9% of trait variation and including 115 loci associated with blood-cell ratios (LMR, lymphocyte-to-monocyte ratio; NLR, neutrophil-to-lymphocyte ratio; PLR, platelet-to-lymphocyte ratio). ALL susceptibility was genetically correlated with lymphocyte counts (rg = 0.088, p = 4.0 × 10-4) and PLR (rg = -0.072, p = 0.0017). In Mendelian randomization analyses, genetically predicted increase in lymphocyte counts was associated with increased ALL risk (odds ratio [OR] = 1.16, p = 0.031) and strengthened after accounting for other cell types (OR = 1.43, p = 8.8 × 10-4). We observed positive associations with increasing LMR (OR = 1.22, p = 0.0017) and inverse effects for NLR (OR = 0.67, p = 3.1 × 10-4) and PLR (OR = 0.80, p = 0.002). Our study shows that a genetically induced shift toward higher lymphocyte counts, overall and in relation to monocytes, neutrophils, and platelets, confers an increased susceptibility to childhood ALL.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Soyoung Jeon
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Andrew T DeWan
- Center for Perinatal, Pediatric, and Environmental Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA; Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA
| | - Catherine Metayer
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.
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40
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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: 25] [Impact Index Per Article: 6.3] [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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41
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Li X, Sundquist K, Sundquist J, Försti A, Hemminki K. Family history of any cancer for childhood leukemia patients in Sweden. EJHAEM 2021; 2:421-427. [PMID: 35844716 PMCID: PMC9175698 DOI: 10.1002/jha2.166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 11/10/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood leukemia, while the other types, acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL), and chronic myeloid leukemia (CML) are much rarer. While data on familial risks for childhood ALL have been emerging, such data for the other childhood leukemias are hardly available. We aim to fill in the gap of knowledge by assessing familial clustering of each childhood leukemia with childhood and adult leukemia and with any cancer. We identified 4461 childhood leukemias from the Swedish Cancer Registry and obtained their family members from the Multigeneration Register. Standardized incidence ratios (SIRs) were 3.34 for singleton siblings both diagnosed with ALL before age 20 years and 1.64 for those who had a family member diagnosed with ALL in adult age. Other childhood leukemias showed no familial risk, but childhood ALL risk was increased to 1.40 when adult family members were diagnosed with CLL. Childhood ALL was associated with endometrial cancer, and female ALL patients showed increased risk when family members were diagnosed with testicular cancer, melanoma, and skin squamous cell carcinoma. Childhood CLL was associated with rectal cancer, and childhood AML was associated with pancreatic and bladder cancers. As most of these associations are reported for the first time, there is a need to replicate the findings from independent sources.
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Affiliation(s)
- Xinjun Li
- Center for Primary Health Care ResearchLund UniversityMalmöSweden
| | - Kristina Sundquist
- Center for Primary Health Care ResearchLund UniversityMalmöSweden
- Department of Family Medicine and Community HealthDepartment of Population Health Science and PolicyIcahn School of Medicine at Mount SinaiNew YorkNew York
- Center for Community‐based Healthcare Research and Education (CoHRE)Department of Functional PathologySchool of MedicineShimane UniversityShimaneJapan
| | - Jan Sundquist
- Center for Primary Health Care ResearchLund UniversityMalmöSweden
- Department of Family Medicine and Community HealthDepartment of Population Health Science and PolicyIcahn School of Medicine at Mount SinaiNew YorkNew York
- Center for Community‐based Healthcare Research and Education (CoHRE)Department of Functional PathologySchool of MedicineShimane UniversityShimaneJapan
| | - Asta Försti
- Center for Primary Health Care ResearchLund UniversityMalmöSweden
- Hopp Children's Cancer Center (KiTZ)HeidelbergGermany
- Division of Pediatric NeurooncologyGerman Cancer Research Center (DKFZ)German Cancer Consortium (DKTK)HeidelbergGermany
| | - Kari Hemminki
- Center for Primary Health Care ResearchLund UniversityMalmöSweden
- Faculty of Medicine and Biomedical Center in PilsenCharles University in PraguePilsenCzech Republic
- Division of Cancer EpidemiologyGerman Cancer Research Centre (DKFZ)HeidelbergGermany
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42
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Yamamoto-Fukuda T, Akiyama N, Kojima H. Super-enhancer Acquisition Drives FOXC2 Expression in Middle Ear Cholesteatoma. J Assoc Res Otolaryngol 2021; 22:405-424. [PMID: 33861394 PMCID: PMC8329101 DOI: 10.1007/s10162-021-00801-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/29/2021] [Indexed: 12/21/2022] Open
Abstract
Distinct histone modifications regulate gene expression in certain diseases, but little is known about histone epigenetics in middle ear cholesteatoma. It is known that histone acetylation destabilizes the nucleosome and chromatin structure and induces gene activation. The association of histone acetylation with chronic inflammatory diseases has been indicated in recent studies. In this study, we examined the localization of variously modified histone H3 acetylation at lysine 9, 14, 18, 23, and 27 in paraffin-embedded sections of human middle ear cholesteatoma (cholesteatoma) tissues and the temporal bones of an animal model of cholesteatoma immunohistochemically. As a result, we found that there was a significant increase of the expression levels of H3K27ac both in human cholesteatoma tissues and the animal model. In genetics, super-enhancers are clusters of enhancers that drive the transcription of genes involved in cell identity. Super-enhancers were originally defined using the H3K27ac signal, and then we used H3K27ac chromatin immunoprecipitation followed by sequencing to map the active cis-regulatory landscape in human cholesteatoma. Based on the results, we identified increased H3K27ac signals as super-enhancers of the FOXC2 loci, as well as increased protein of FOXC2 in cholesteatoma. Recent studies have indicated that menin-MLL inhibitor could suppress tumor growth through the control of histone H3 modification. In this study, we demonstrated that the expression of FOXC2 was inhibited by menin-MLL inhibitor in vivo. These findings indicate that FOXC2 expression under histone modifications promoted the pathogenesis of cholesteatoma and suggest that it may be a therapeutic target of cholesteatoma.
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Affiliation(s)
- Tomomi Yamamoto-Fukuda
- Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan.
- Department of Histology and Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.
| | - Naotaro Akiyama
- Department of Histology and Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Department of Otorhinolaryngology, Toho University School of Medicine, Tokyo, Japan
| | - Hiromi Kojima
- Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
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43
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Marcotte EL, Domingues AM, Sample JM, Richardson MR, Spector LG. Racial and ethnic disparities in pediatric cancer incidence among children and young adults in the United States by single year of age. Cancer 2021; 127:3651-3663. [PMID: 34151418 DOI: 10.1002/cncr.33678] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/05/2021] [Accepted: 04/26/2021] [Indexed: 01/28/2023]
Abstract
BACKGROUND Incidence rates of pediatric cancers in the United States are typically reported in 5-year age groups, obscuring variation by single year of age. Additionally, racial and ethnic variation in incidence is typically presented in broad categories rather than by narrow age ranges. METHODS The Surveillance, Epidemiology, and End Results (SEER) 18 data (2000-2017) were examined to calculate frequencies and age-adjusted incidence rates among individuals aged birth to 39 years. Incidence rate ratios (IRRs) and 95% confidence intervals (95% CIs) were estimated as the measure of association for rate comparisons by race and Hispanic origin overall and by single year of age. RESULTS Several histologic types showed substantial variation in race/ethnicity-specific and overall rates by single year of age. Overall, Black children and young adults experienced substantially decreased incidence of acute lymphoid leukemia (IRR, 0.52; 95% CI, 0.49-0.55) compared to Whites, and this decreased incidence was strongest at ages 1 through 7 years and 16 through 20 years. Hispanic individuals experienced decreased overall incidence of Hodgkin lymphoma (IRR, 0.50; 95% CI, 0.48-0.52) and astrocytoma (IRR, 0.54; 95% CI, 0.52-0.56) and increased risk of acute lymphoblastic leukemia (IRR, 1.46; 95% CI, 1.42-1.51) compared to non-Hispanic Whites, and the increased risk was strongest at ages 10 through 23 years. Substantial decreased risk across many tumor types was also observed for Asian/Pacific Islanders and American Indian/Alaska Natives. CONCLUSIONS Examination of incidence rates for pediatric cancers by narrow age groups may provide insights regarding etiological differences in subgroups. Additionally, variation in age-specific incidence rates by race and ethnicity may enable hypothesis generation on drivers of disparities observed.
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Affiliation(s)
- Erin L Marcotte
- Division of Pediatric Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota.,University of Minnesota Masonic Cancer Center, Minneapolis, Minnesota
| | - Allison M Domingues
- Division of Pediatric Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Jeannette M Sample
- Division of Pediatric Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Michaela R Richardson
- Division of Pediatric Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Logan G Spector
- Division of Pediatric Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota.,University of Minnesota Masonic Cancer Center, Minneapolis, Minnesota
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44
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Wang J, Clay-Gilmour AI, Karaesmen E, Rizvi A, Zhu Q, Yan L, Preus L, Liu S, Wang Y, Griffiths E, Stram DO, Pooler L, Sheng X, Haiman C, Van Den Berg D, Webb A, Brock G, Spellman S, Pasquini M, McCarthy P, Allan J, Stölzel F, Onel K, Hahn T, Sucheston-Campbell LE. Genome-Wide Association Analyses Identify Variants in IRF4 Associated With Acute Myeloid Leukemia and Myelodysplastic Syndrome Susceptibility. Front Genet 2021; 12:554948. [PMID: 34220922 PMCID: PMC8248805 DOI: 10.3389/fgene.2021.554948] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 04/19/2021] [Indexed: 12/22/2022] Open
Abstract
The role of common genetic variation in susceptibility to acute myeloid leukemia (AML), and myelodysplastic syndrome (MDS), a group of rare clonal hematologic disorders characterized by dysplastic hematopoiesis and high mortality, remains unclear. We performed AML and MDS genome-wide association studies (GWAS) in the DISCOVeRY-BMT cohorts (2,309 cases and 2,814 controls). Association analysis based on subsets (ASSET) was used to conduct a summary statistics SNP-based analysis of MDS and AML subtypes. For each AML and MDS case and control we used PrediXcan to estimate the component of gene expression determined by their genetic profile and correlate this imputed gene expression level with risk of developing disease in a transcriptome-wide association study (TWAS). ASSET identified an increased risk for de novo AML and MDS (OR = 1.38, 95% CI, 1.26-1.51, Pmeta = 2.8 × 10-12) in patients carrying the T allele at s12203592 in Interferon Regulatory Factor 4 (IRF4), a transcription factor which regulates myeloid and lymphoid hematopoietic differentiation. Our TWAS analyses showed increased IRF4 gene expression is associated with increased risk of de novo AML and MDS (OR = 3.90, 95% CI, 2.36-6.44, Pmeta = 1.0 × 10-7). The identification of IRF4 by both GWAS and TWAS contributes valuable insight on the role of genetic variation in AML and MDS susceptibility.
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Affiliation(s)
- Junke Wang
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Alyssa I. Clay-Gilmour
- Department of Epidemiology, Mayo Clinic, Rochester, MN, United States
- Department of Epidemiology & Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, United States
| | - Ezgi Karaesmen
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Abbas Rizvi
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Leah Preus
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Yiwen Wang
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Elizabeth Griffiths
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Daniel O. Stram
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - Loreall Pooler
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - Xin Sheng
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - Christopher Haiman
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - David Van Den Berg
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - Amy Webb
- Department on Biomedical Informatics, The Ohio State University, Columbus, OH, United States
| | - Guy Brock
- Department on Biomedical Informatics, The Ohio State University, Columbus, OH, United States
| | - Stephen Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, United States
| | - Marcelo Pasquini
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Philip McCarthy
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - James Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Friedrich Stölzel
- Department of Internal Medicine I, University Hospital Carl Gustav Carus Dresden, Technical University Dresden, Dresden, Germany
| | - Kenan Onel
- Department of Pediatrics, Mount Sinai Medical Center, Miami Beach, NY, United States
| | - Theresa Hahn
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Lara E. Sucheston-Campbell
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
- College of Veterinary Medicine, The Ohio State University, Columbus, OH, United States
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45
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Family history of early onset acute lymphoblastic leukemia is suggesting genetic associations. Sci Rep 2021; 11:12370. [PMID: 34117277 PMCID: PMC8195979 DOI: 10.1038/s41598-021-90542-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/21/2021] [Indexed: 11/08/2022] Open
Abstract
Childhood acute lymphoblastic leukemia (ALL) has an origin in the fetal period which may distinguish it from ALL diagnosed later in life. We wanted to test whether familial risks differ in ALL diagnosed in the very early childhood from ALL diagnosed later. The Swedish nation-wide family-cancer data were used until year 2016 to calculate standardized incidence ratios (SIRs) for familial risks in ALL in three diagnostic age-groups: 0–4, 5–34 and 35 + years. Among 1335 ALL patients diagnosed before age 5, familial risks were increased for esophageal (4.78), breast (1.42), prostate (1.40) and connective tissue (2.97) cancers and leukemia (2.51, ALL 7.81). In age-group 5–34 years, rectal (1.73) and endometrial (2.40) cancer, myeloma (2.25) and leukemia (2.00, ALL 4.60) reached statistical significance. In the oldest age-group, the only association was with Hodgkin lymphoma (3.42). Diagnostic ages of family members of ALL patients were significantly lower compared to these cancers in the population for breast, prostate and rectal cancers. The patterns of increased familial cancers suggest that BRCA2 mutations could contribute to associations of ALL with breast and prostate cancers, and mismatch gene PMS2 mutations with rectal and endometrial cancers. Future DNA sequencing data will be a test for these familial predictions.
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46
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Hao Q, Cao M, Zhang C, Yin D, Wang Y, Ye Y, Zhao S, Yang Y, Chen KL, Ying B, Wang L, Zhang Y, Xu C, Zhu Y, Wu Y, Gao J, Zhao JN, Zhang Y, Lu X. Age-related differences of genetic susceptibility to patients with acute lymphoblastic leukemia. Aging (Albany NY) 2021; 13:12456-12465. [PMID: 33891562 PMCID: PMC8148462 DOI: 10.18632/aging.202903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/05/2021] [Indexed: 02/05/2023]
Abstract
Inherited predispositions to acute lymphoblastic leukemia have been well investigated in pediatric patients, but studies on adults, particularly Chinese patients, are limited. In this study, we conducted a genome-wide association study in 466 all-age Chinese patients with Acute lymphoblastic leukemia (ALL) and 1,466 non-ALL controls to estimate the impact of age on ALL susceptibility in the Chinese population. Among the 17 reported loci, 8 have been validated in pediatric and 1 in adult patients. The strongest association signal was identified at ARID5B locus and gradually decreased with age, while the signal at GATA3 exhibited the opposite trend and significantly impact on adult patients. With genome-wide approaches, germline variants at 2q14.3 rank as the top inherited predisposition to adult patients (e.g., rs73956024, P = 4.3 × 10-5) and separate the genetic risk of pediatric vs. adult patients (P = 3.6 × 10-6), whereas variants at 15q25.3 (e.g., rs11638062) have a similar impact on patients in different age groups (overall P = 2.9 × 10-7). Our analysis highlights the impact of age on genetic susceptibility to ALL in Chinese patients.
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Affiliation(s)
- Qing Hao
- Department of Thoracic Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China.,College of Pharmaceutical Sciences, Southwest Medical University, Luzhou, China.,Sichuan Center for Translational Medicine of Traditional Chinese Medicine, Institute of Translational Pharmacology, Sichuan Academy of Chinese Medicine Sciences, Chengdu, China
| | - Minyuan Cao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Chunlan Zhang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Dandan Yin
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yuelan Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yuanxin Ye
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Shan Zhao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yunfan Yang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Ke-Ling Chen
- Digestive Surgery Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Lanlan Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yiguan Zhang
- Sichuan Center for Translational Medicine of Traditional Chinese Medicine, Institute of Translational Pharmacology, Sichuan Academy of Chinese Medicine Sciences, Chengdu, China
| | - Caigang Xu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Yiping Zhu
- Department of Hematology/Oncology, West China Second Hospital, Sichuan University, Chengdu, China
| | - Yu Wu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Ju Gao
- Department of Hematology/Oncology, West China Second Hospital, Sichuan University, Chengdu, China
| | - Jun-Ning Zhao
- Sichuan Center for Translational Medicine of Traditional Chinese Medicine, Institute of Translational Pharmacology, Sichuan Academy of Chinese Medicine Sciences, Chengdu, China
| | - Yan Zhang
- Department of Thoracic Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoxi Lu
- Department of Hematology/Oncology, West China Second Hospital, Sichuan University, Chengdu, China
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47
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Spector LG, Turcotte LM. Germline Genetic Risk Stratification in ALL? GATA Get More Information. J Natl Cancer Inst 2021; 113:353-354. [PMID: 32894770 DOI: 10.1093/jnci/djaa139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Logan G Spector
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Lucie M Turcotte
- Division of Hematology/Oncology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
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48
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Yao L, Yin H, Hong M, Wang Y, Yu T, Teng Y, Li T, Wu Q. RNA methylation in hematological malignancies and its interactions with other epigenetic modifications. Leukemia 2021; 35:1243-1257. [PMID: 33767371 DOI: 10.1038/s41375-021-01225-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 02/12/2021] [Accepted: 03/11/2021] [Indexed: 01/18/2023]
Abstract
Hematological malignancies are a class of malignant neoplasms attributed to abnormal differentiation of hematopoietic stem cells (HSCs). The systemic involvement, poor prognosis, chemotherapy resistance, and recurrence common in hematological malignancies urge researchers to look for novel treatment targets and mechanisms. In recent years, epigenetic abnormalities have been shown to play a vital role in tumorigenesis and progression in hematological malignancies. In addition to DNA methylation and histone modifications, which are most studied, RNA methylation has become increasingly significant. In this review, we elaborate recent advances in the understanding of RNA modification in the pathogenesis, diagnosis and molecular targeted therapies of hematological malignancies and discuss its intricate interactions with other epigenetic modifications, including DNA methylation, histone modifications and noncoding RNAs.
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Affiliation(s)
- Lan Yao
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hua Yin
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mei Hong
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Yajun Wang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tingting Yu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yao Teng
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tingting Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiuling Wu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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49
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Cobaleda C, Vicente-Dueñas C, Sánchez-García I. An immune window of opportunity to prevent childhood B cell leukemia. Trends Immunol 2021; 42:371-374. [PMID: 33773925 DOI: 10.1016/j.it.2021.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/11/2022]
Abstract
The prevalence of childhood B cell acute lymphoblastic leukemia (B-ALL) is increasing, particularly in developed countries. There is no clear explanation for this increment, but recent data suggest that, besides genetic predisposition, stress in the immune system (e.g., an infection) might have an important role in B-ALL leukemogenesis. Here, we speculate on how this knowledge might impact B-ALL prevention strategies.
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Affiliation(s)
- César Cobaleda
- Immune System Development and Function Unit, Centro de Biología Molecular Severo Ochoa (CSIC -Universidad Autónoma de Madrid), Madrid, Spain. *
| | | | - Isidro Sánchez-García
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain; Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Salamanca, Spain.
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An intact gut microbiome protects genetically predisposed mice against leukemia. Blood 2021; 136:2003-2017. [PMID: 32911536 DOI: 10.1182/blood.2019004381] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 08/21/2020] [Indexed: 12/22/2022] Open
Abstract
The majority of childhood leukemias are precursor B-cell acute lymphoblastic leukemias (pB-ALLs) caused by a combination of prenatal genetic predispositions and oncogenic events occurring after birth. Although genetic predispositions are frequent in children (>1% to 5%), fewer than 1% of genetically predisposed carriers will develop pB-ALL. Although infectious stimuli are believed to play a major role in leukemogenesis, the critical determinants are not well defined. Here, by using murine models of pB-ALL, we show that microbiome disturbances incurred by antibiotic treatment early in life were sufficient to induce leukemia in genetically predisposed mice, even in the absence of infectious stimuli and independent of T cells. By using V4 and full-length 16S ribosomal RNA sequencing of a series of fecal samples, we found that genetic predisposition to pB-ALL (Pax5 heterozygosity or ETV6-RUNX1 fusion) shaped a distinct gut microbiome. Machine learning accurately (96.8%) predicted genetic predisposition using 40 of 3983 amplicon sequence variants as proxies for bacterial species. Transplantation of either wild-type (WT) or Pax5+/- hematopoietic bone marrow cells into WT recipient mice revealed that the microbiome is shaped and determined in a donor genotype-specific manner. Gas chromatography-mass spectrometry (GC-MS) analyses of sera from WT and Pax5+/- mice demonstrated the presence of a genotype-specific distinct metabolomic profile. Taken together, our data indicate that it is a lack of commensal microbiota rather than the presence of specific bacteria that promotes leukemia in genetically predisposed mice. Future large-scale longitudinal studies are required to determine whether targeted microbiome modification in children predisposed to pB-ALL could become a successful prevention strategy.
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