1
|
Lee MK, Azizgolshani N, Zhang Z, Perreard L, Kolling FW, Nguyen LN, Zanazzi GJ, Salas LA, Christensen BC. Associations in cell type-specific hydroxymethylation and transcriptional alterations of pediatric central nervous system tumors. Nat Commun 2024; 15:3635. [PMID: 38688903 PMCID: PMC11061294 DOI: 10.1038/s41467-024-47943-9] [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: 02/18/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
Although intratumoral heterogeneity has been established in pediatric central nervous system tumors, epigenomic alterations at the cell type level have largely remained unresolved. To identify cell type-specific alterations to cytosine modifications in pediatric central nervous system tumors, we utilize a multi-omic approach that integrated bulk DNA cytosine modification data (methylation and hydroxymethylation) with both bulk and single-cell RNA-sequencing data. We demonstrate a large reduction in the scope of significantly differentially modified cytosines in tumors when accounting for tumor cell type composition. In the progenitor-like cell types of tumors, we identify a preponderance differential Cytosine-phosphate-Guanine site hydroxymethylation rather than methylation. Genes with differential hydroxymethylation, like histone deacetylase 4 and insulin-like growth factor 1 receptor, are associated with cell type-specific changes in gene expression in tumors. Our results highlight the importance of epigenomic alterations in the progenitor-like cell types and its role in cell type-specific transcriptional regulation in pediatric central nervous system tumors.
Collapse
Affiliation(s)
- Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
| | - Nasim Azizgolshani
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Surgery, Columbia University Medical Center, New York, NY, USA
| | - Ze Zhang
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Laurent Perreard
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Fred W Kolling
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Lananh N Nguyen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - George J Zanazzi
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Pathology and Laboratory Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
| |
Collapse
|
2
|
Alonso‐Luna O, Mercado‐Celis GE, Melendez‐Zajgla J, Barquera R, Zapata‐Tarres M, Juárez‐Villegas LE, Mendoza‐Caamal EC, Rey‐Helo E, Borges‐Yañez SA. Germline mutations in pediatric cancer cohort with mixed-ancestry Mexicans. Mol Genet Genomic Med 2024; 12:e2332. [PMID: 38093606 PMCID: PMC10767611 DOI: 10.1002/mgg3.2332] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/11/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Childhood cancer is one of the primary causes of disease-related death in 5- to 14-year-old children and currently no prevention strategies exist to reduce the incidence of this disease. Childhood cancer has a larger hereditary component compared with cancer in adults. Few genetic studies have been conducted on children with cancer. Additionally, Latin American populations are underrepresented in genomic studies compared with other populations. Therefore, the aim of this study is to analyze germline mutations in a group of mixed-ancestry Mexican pediatric patients with solid and hematological cancers. METHODS We analyzed genetic variants from 40 Mexican childhood cancer patients and their relatives. DNA from saliva or blood samples was used for whole-exome sequencing. All variants were identified following GATK best practices. RESULTS We found that six patients (15%) were carriers of germline mutations in CDKN2A, CHEK2, DICER1, FANCA, MSH6, MUTYH, NF1, and SBDS cancer predisposition genes, and additional new variants predicted to be deleterious by in silico algorithms. A population genetics analysis detected five components consistent with the demographic models assumed for modern mixed-ancestry Mexicans. CONCLUSIONS This report identifies potential genetic risk factors and provides a better understanding of the underlying mechanisms of childhood cancer in this population.
Collapse
Grants
- 365882 Consejo Nacional de Ciencia y Tecnología, CONACyT, Mexico
- 253316 Consejo Nacional de Ciencia y Tecnología, CONACyT, Mexico
- Fundacion Carlos Slim as part of the inaugural phase of Slim Initiative in Genomic Medicine for the Americas, SIGMA
- Broad Institute of MIT and Harvard
- Instituto Nacional de Medicina Genomica (INMEGEN)
- Division de Estudios de Posgrado e Investigacion de la Facultad de Odontologia
- Programa de Maestria y Doctorado en Ciencias Medicas, Odontologicas y de la Salud, UNAM
- "Aqui nadie se rinde, ANSER (I.A.P)
- Max Planck Institute for Evolutionary Anthropology (MPI-EVA)
- Consejo Nacional de Ciencia y Tecnología, CONACyT, Mexico
- Max Planck Institute for Evolutionary Anthropology (MPI‐EVA)
Collapse
Affiliation(s)
- Oscar Alonso‐Luna
- Programa de Maestria y Doctorado en Ciencias Medicas, Odontologicas y de la SaludCiudad Universitaria, Universidad Nacional Autonoma de MexicoMexico CityMexico
| | | | - Jorge Melendez‐Zajgla
- Laboratorio de Genomica Funcional del CancerInstituto Nacional de Medicina GenomicaMexico CityMexico
| | - Rodrigo Barquera
- Department of ArchaeogeneticsMax Plank Institute for Evolutionary Anthropology (MPI‐EVA)LeipzigGermany
| | | | | | | | | | | |
Collapse
|
3
|
Papadimitriou DT, Stratakis CA, Kattamis A, Glentis S, Dimitrakakis C, Spyridis GP, Christopoulos P, Mastorakos G, Vlahos NF, Iacovidou N. A Novel Variant in the TP53 Gene Causing Li-Fraumeni Syndrome. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1150. [PMID: 37508646 PMCID: PMC10378136 DOI: 10.3390/children10071150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023]
Abstract
Li-Fraumeni syndrome (LFS) is an autosomal dominant hereditary cancer syndrome associated with germline pathogenic variants in the tumor protein p53 (TP53) gene and elevated risk of a broad range of early-onset malignancies. Patients with LFS are at risk of a second and third primary tumor. A 15-month-old girl consulted for clitoromegaly and pubic hair. Adrenal ultrasound detected a large left adrenal tumor. Left total adrenalectomy confirmed adrenocortical carcinoma. Family history revealed multiple highly malignant neoplasms at an early age across five generations, and a genetic dominant trait seemed probable. Whole-genome sequencing was performed. Multiple members of the family were found positive for a novel likely pathogenic variant (c. 892delGinsTTT, p. Glu298PhefsX48, NM_000546.6) in the TP53 gene, causing the loss of normal protein function through non-sense-mediated mRNA decay. According to the PSV1 supporting criteria and the Auto PVS1 online tool this frameshift variant: hg19/17-7577045-TC-TAAA:NM_000546.6 has a very strong, definitive clinical validity for LFS with autosomal dominant inheritance. Proper guidance resulted in timely diagnosis of a second tumor (primary osteosarcoma) in the index case and in the early detection of breast and cervical cancer in her young mother. Patients with cancer predisposition syndromes like LFS require close multidisciplinary cancer surveillance and appropriate referral to expert centers.
Collapse
Affiliation(s)
- Dimitrios T Papadimitriou
- Endocrine Unit, Second Department of Obstetrics and Gynecology, Aretaieion Hospital, 11528 Athens, Greece
- Pediatric-Adolescent Endocrinology and Diabetes, Athens Medical Center, 15125 Marousi, Greece
| | - Constantine A Stratakis
- Section on Endocrinology & Genetics, The Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20814, USA
| | - Antonis Kattamis
- Division of Pediatric Hematology and Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, 11527 Athens, Greece
- 'Aghia Sophia' Children's Hospital ERN-Genturis Center, 11527 Athina, Greece
| | - Stavros Glentis
- Division of Pediatric Hematology and Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, 11527 Athens, Greece
- 'Aghia Sophia' Children's Hospital ERN-Genturis Center, 11527 Athina, Greece
| | - Constantine Dimitrakakis
- First Department of Obstetrics and Gynecology, Alexandra University Hospital, National and Kapodistrian University of Athens, 11528 Athens, Greece
| | - George P Spyridis
- Surgical Pediatric Oncology, Mitera Children's Hospital, 15123 Marousi, Greece
| | | | - George Mastorakos
- Endocrine Unit, Second Department of Obstetrics and Gynecology, Aretaieion Hospital, 11528 Athens, Greece
| | - Nikolaos F Vlahos
- Second Department of Obstetrics and Gynecology, Aretaieion Hospital, 11528 Athens, Greece
| | - Nicoletta Iacovidou
- Neonatal Department, Aretaieion Hospital, National and Kapodistrian University of Athens, 11528 Athens, Greece
| |
Collapse
|
4
|
Zage PE, Huo Y, Subramonian D, Le Clorennec C, Ghosh P, Sahoo D. Identification of a novel gene signature for neuroblastoma differentiation using a Boolean implication network. Genes Chromosomes Cancer 2023; 62:313-331. [PMID: 36680522 PMCID: PMC10257350 DOI: 10.1002/gcc.23124] [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: 04/01/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023] Open
Abstract
Although induction of differentiation represents an effective strategy for neuroblastoma treatment, the mechanisms underlying neuroblastoma differentiation are poorly understood. We generated a computational model of neuroblastoma differentiation consisting of interconnected gene clusters identified based on symmetric and asymmetric gene expression relationships. We identified a differentiation signature consisting of series of gene clusters comprised of 1251 independent genes that predicted neuroblastoma differentiation in independent datasets and in neuroblastoma cell lines treated with agents known to induce differentiation. This differentiation signature was associated with patient outcomes in multiple independent patient cohorts and validated the role of MYCN expression as a marker of neuroblastoma differentiation. Our results further identified novel genes associated with MYCN via asymmetric Boolean implication relationships that would not have been identified using symmetric computational approaches and that were associated with both neuroblastoma differentiation and patient outcomes. Our differentiation signature included a cluster of genes involved in intracellular signaling and growth factor receptor trafficking pathways that is strongly associated with neuroblastoma differentiation, and we validated the associations of UBE4B, a gene within this cluster, with neuroblastoma cell and tumor differentiation. Our findings demonstrate that Boolean network analyses of symmetric and asymmetric gene expression relationships can identify novel genes and pathways relevant for neuroblastoma tumor differentiation that could represent potential therapeutic targets.
Collapse
Affiliation(s)
- Peter E. Zage
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego (UCSD), La Jolla, CA
| | - Yuchen Huo
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego (UCSD), La Jolla, CA
| | - Divya Subramonian
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego (UCSD), La Jolla, CA
| | - Christophe Le Clorennec
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego (UCSD), La Jolla, CA
| | - Pradipta Ghosh
- Department of Medicine, UCSD, La Jolla, CA
- Department of Cellular and Molecular Medicine, UCSD, La Jolla, CA
- Veterans Affairs Medical Center, La Jolla, CA
| | - Debashis Sahoo
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego (UCSD), La Jolla, CA
- Department of Computer Science and Engineering, Jacobs School of Engineering, UCSD, La Jolla, CA
| |
Collapse
|
5
|
Sharma I, Son MJ, Motamedi S, Hoeft A, Teller C, Hamby T, Ray A. Utilization of Genomic Tumor Profiling in Pediatric Liquid Tumors: A Clinical Series. Hematol Rep 2023; 15:256-265. [PMID: 37092520 PMCID: PMC10123750 DOI: 10.3390/hematolrep15020026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/09/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023] Open
Abstract
Hematologic tumors are mostly treated with chemotherapies that have poor toxicity profiles. While molecular tumor profiling can expand therapeutic options, our understanding of potential targetable drivers comes from studies of adult liquid tumors, which does not necessarily translate to efficacious treatment in pediatric liquid tumors. There is also no consensus on when profiling should be performed and its use in guiding therapies. We describe a single institution's experience in integrating profiling for liquid tumors. Pediatric patients diagnosed with leukemia or lymphoma and who underwent tumor profiling were retrospectively reviewed. Ten (83.3%) patients had relapsed disease prior to tumor profiling. Eleven (91.7%) patients had targetable alterations identified on profiling, and three (25%) received targeted therapy based on these variants. Of the three patients that received targeted therapy, two (66.7%) were living, and one (33.3%) decreased. For a portion of our relapsing and/or treatment-refractory patients, genetic profiling was feasible and useful in tailoring therapy to obtain stable or remission states. Practitioners may hesitate to deviate from the 'standard of therapy', resulting in the underutilization of profiling results. Prospective studies should identify actionable genetic variants found more frequently in pediatric liquid tumors and explore the benefits of proactive tumor profiling prior to the first relapse.
Collapse
Affiliation(s)
- Ishna Sharma
- Texas College of Osteopathic Medicine, The University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Min Ji Son
- Texas College of Osteopathic Medicine, The University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Shoaleh Motamedi
- Texas College of Osteopathic Medicine, The University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Alice Hoeft
- Department of Hematology/Oncology, Cook Children's Medical Center, Fort Worth, TX 76104, USA
- Department of Research Operations, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Christa Teller
- Department of Hematology/Oncology, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Tyler Hamby
- Department of Research Operations, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Anish Ray
- Texas College of Osteopathic Medicine, The University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Department of Hematology/Oncology, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| |
Collapse
|
6
|
Desai S, Guddati AK. Bimodal Age Distribution in Cancer Incidence. World J Oncol 2022; 13:329-336. [PMID: 36660209 PMCID: PMC9822681 DOI: 10.14740/wjon1424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/05/2022] [Indexed: 12/26/2022] Open
Abstract
Cancer is caused by accumulation of genetic changes which include activation of protooncogenes and loss of tumor suppressor genes. The age-specific incidence of cancer in general increases with advancing age. However, some cancers exhibit a bimodal distribution. Commonly recognized cancers with bimodal age distribution include acute lymphoblastic leukemia, osteosarcoma, Hodgkin's lymphoma, germ cell tumors and breast cancer. Delayed infection hypothesis has been used to provide explanation for the early childhood peak in leukemias and lymphomas, whereas the peak at an older age is associated with accumulation of protooncogenes and weakened immune system. Further genetic analysis and histopathological variations point to distinctly different cancers, varying genetically and histologically, which are often combined under a single category of cancers. Tumor characteristics and age distribution of these cancers varies also by population groups and has further implications on cancer screening methods. Although significant advances have been made to explain the bimodal nature of such cancers, the specific genetic mechanisms for each age distribution remain to be elucidated. Further distinction among the different cancer subtypes may lead to improvements in individual risk assessments, prevention and enhancement of treatment strategies.
Collapse
Affiliation(s)
- Shreya Desai
- Division of Hematology/Oncology, Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
| | - Achuta K. Guddati
- Division of Hematology/Oncology, Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA,Corresponding Author: Achuta Kumar Guddati, Division of Hematology/Oncology, Georgia Cancer Center, Augusta University, Augusta, GA 30909, USA.
| |
Collapse
|
7
|
Gonzalez Malagon SG, Liu KJ. Linking neural crest development to neuroblastoma pathology. Development 2022; 149:276149. [DOI: 10.1242/dev.200331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Although rare, childhood (paediatric) cancers are a major cause of death in young children. Unlike many adult cancers, paediatric cancers, such as neuroblastoma (NB), are developmental diseases that rarely show genetic predispositions. NB is the most common extracranial solid tumour in children, accounting for ∼15% of paediatric cancer deaths. This heterogeneous cancer arises from undifferentiated neural crest-derived progenitor cells. As neural crest cells are multipotent and migratory, they are often considered the embryonic paradigm of cancer stem cells. However, very little is known about the events that trigger tumour initiation and progression. Here, we discuss recent insights into sympathoadrenal lineage specification, as well as genetic factors associated with NB. With this in mind, we consider the molecular underpinnings of NB in the context of developmental trajectories of the neural crest lineage. This allows us to compare distinct subtypes of the disease and gene-function interactions during sensitive phases of neural crest development.
Collapse
Affiliation(s)
- Sandra Guadalupe Gonzalez Malagon
- Biomedical Research Institute, Foundation for Research and Technology, University of Ioannina Campus 1 , 45115 Ioannina , Greece
- School of Health Sciences and Institute of Biosciences, University Research Centre, University of Ioannina 2 Department of Biological Applications and Technology , , 45110 Ioannina , Greece
| | - Karen J. Liu
- Centre for Craniofacial and Regenerative Biology, King's College London 3 , London SE1 9RT , UK
| |
Collapse
|
8
|
Tozzi AE, Fabozzi F, Eckley M, Croci I, Dell’Anna VA, Colantonio E, Mastronuzzi A. Gaps and Opportunities of Artificial Intelligence Applications for Pediatric Oncology in European Research: A Systematic Review of Reviews and a Bibliometric Analysis. Front Oncol 2022; 12:905770. [PMID: 35712463 PMCID: PMC9194810 DOI: 10.3389/fonc.2022.905770] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 05/04/2022] [Indexed: 12/23/2022] Open
Abstract
The application of artificial intelligence (AI) systems is emerging in many fields in recent years, due to the increased computing power available at lower cost. Although its applications in various branches of medicine, such as pediatric oncology, are many and promising, its use is still in an embryonic stage. The aim of this paper is to provide an overview of the state of the art regarding the AI application in pediatric oncology, through a systematic review of systematic reviews, and to analyze current trends in Europe, through a bibliometric analysis of publications written by European authors. Among 330 records found, 25 were included in the systematic review. All papers have been published since 2017, demonstrating only recent attention to this field. The total number of studies included in the selected reviews was 674, with a third including an author with a European affiliation. In bibliometric analysis, 304 out of the 978 records found were included. Similarly, the number of publications began to dramatically increase from 2017. Most explored AI applications regard the use of diagnostic images, particularly radiomics, as well as the group of neoplasms most involved are the central nervous system tumors. No evidence was found regarding the use of AI for process mining, clinical pathway modeling, or computer interpreted guidelines to improve the healthcare process. No robust evidence is yet available in any of the domains investigated by systematic reviews. However, the scientific production in Europe is significant and consistent with the topics covered in systematic reviews at the global level. The use of AI in pediatric oncology is developing rapidly with promising results, but numerous gaps and challenges persist to validate its utilization in clinical practice. An important limitation is the need for large datasets for training algorithms, calling for international collaborative studies.
Collapse
Affiliation(s)
- Alberto Eugenio Tozzi
- Multifactorial and Complex Diseases Research Area, Bambino Gesù Children’s Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Francesco Fabozzi
- Department of Onco Hematology and Cell and Gene Therapy, Bambino Gesù Pediatric Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Pediatrics, University of Rome Tor Vergata, Rome, Italy
| | - Megan Eckley
- Department of Onco Hematology and Cell and Gene Therapy, Bambino Gesù Pediatric Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Ileana Croci
- Multifactorial and Complex Diseases Research Area, Bambino Gesù Children’s Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Vito Andrea Dell’Anna
- Department of Onco Hematology and Cell and Gene Therapy, Bambino Gesù Pediatric Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Erica Colantonio
- Department of Onco Hematology and Cell and Gene Therapy, Bambino Gesù Pediatric Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Angela Mastronuzzi
- Department of Onco Hematology and Cell and Gene Therapy, Bambino Gesù Pediatric Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- *Correspondence: Angela Mastronuzzi,
| |
Collapse
|
9
|
Aguiar T, Teixeira A, Scliar MO, Sobral de Barros J, Lemes RB, Souza S, Tolezano G, Santos F, Tojal I, Cypriano M, Caminada de Toledo SR, Valadares E, Borges Pinto R, Pinto Artigalas OA, Caetano de Aguirre Neto J, Novak E, Cristofani LM, Miura Sugayama SM, Odone V, Cunha IW, Lima da Costa CM, Rosenberg C, Krepischi A. Unraveling the Genetic Architecture of Hepatoblastoma Risk: Birth Defects and Increased Burden of Germline Damaging Variants in Gastrointestinal/Renal Cancer Predisposition and DNA Repair Genes. Front Genet 2022; 13:858396. [PMID: 35495172 PMCID: PMC9039399 DOI: 10.3389/fgene.2022.858396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/08/2022] [Indexed: 12/21/2022] Open
Abstract
The ultrarare hepatoblastoma (HB) is the most common pediatric liver cancer. HB risk is related to a few rare syndromes, and the molecular bases remain elusive for most cases. We investigated the burden of rare damaging germline variants in 30 Brazilian patients with HB and the presence of additional clinical signs. A high frequency of prematurity (20%) and birth defects (37%), especially craniofacial (17%, including craniosynostosis) and kidney (7%) anomalies, was observed. Putative pathogenic or likely pathogenic monoallelic germline variants mapped to 10 cancer predisposition genes (CPGs: APC, CHEK2, DROSHA, ERCC5, FAH, MSH2, MUTYH, RPS19, TGFBR2 and VHL) were detected in 33% of the patients, only 40% of them with a family history of cancer. These findings showed a predominance of CPGs with a known link to gastrointestinal/colorectal and renal cancer risk. A remarkable feature was an enrichment of rare damaging variants affecting different classes of DNA repair genes, particularly those known as Fanconi anemia genes. Moreover, several potentially deleterious variants mapped to genes impacting liver functions were disclosed. To our knowledge, this is the largest assessment of rare germline variants in HB patients to date, contributing to elucidate the genetic architecture of HB risk.
Collapse
Affiliation(s)
- Talita Aguiar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Columbia University Irving Medical Center, New York, NY, United States
| | - Anne Teixeira
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Marília O. Scliar
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Juliana Sobral de Barros
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Renan B. Lemes
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Silvia Souza
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Giovanna Tolezano
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Fernanda Santos
- Department of Pediatric Oncology, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Israel Tojal
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Monica Cypriano
- GRAACC—Grupo de Apoio Ao Adolescente e Criança Com Câncer, Federal University of São Paulo, São Paulo, Brazil
| | | | - Eugênia Valadares
- Benjamim Guimarães Foundation - Department of Pediatrics Hospital da Baleia, Belo Horizonte, Brazil
| | - Raquel Borges Pinto
- Department of Genetics, Hospital da Criança Conceição, Hospitalar Conceição Group, Porto Alegre, Brazil
| | | | | | - Estela Novak
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
- Molecular Genetics—Foundation Pro Sangue Blood Center of São Paulo, São Paulo, Brazil
| | - Lilian Maria Cristofani
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Sofia M. Miura Sugayama
- Department of Pediatric, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Vicente Odone
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | | | | | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- *Correspondence: Ana Krepischi,
| |
Collapse
|
10
|
The Use of Inhibitors of Tyrosine Kinase in Paediatric Haemato-Oncology-When and Why? Int J Mol Sci 2021; 22:ijms222112089. [PMID: 34769519 PMCID: PMC8584725 DOI: 10.3390/ijms222112089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 12/25/2022] Open
Abstract
The fundamental pathophysiology of malignancies is dysregulation of the signalling pathways. Protein tyrosine kinases (PTKs) are among the enzymes which, if mutated, play a critical role in carcinogenesis. The best-studied rearrangement, which enhances PTK activity and causes atypical proliferation, is BCR-ABL1. Abnormal expression of PTKs has proven to play a significant role in the development of various malignancies, such as chronic myelogenous leukaemia, brain tumours, neuroblastoma, and gastrointestinal stromal tumours. The use of tyrosine kinase inhibitors (TKIs) is an outstanding example of successful target therapy. TKIs have been effectively applied in the adult oncology setting, but there is a need to establish TKIs’ importance in paediatric patients. Many years of research have allowed a significant improvement in the outcome of childhood cancers. However, there are still groups of patients who have a poor prognosis, where the intensification of chemotherapy could even cause death. TKIs are designed to target specific PTKs, which lead to the limitation of severe adverse effects and increase overall survival. These advances will hopefully allow new therapeutic approaches in paediatric haemato-oncology to emerge. In this review, we present an analysis of the current data on tyrosine kinase inhibitors in childhood cancers.
Collapse
|
11
|
Manzano-Muñoz A, Alcon C, Menéndez P, Ramírez M, Seyfried F, Debatin KM, Meyer LH, Samitier J, Montero J. MCL-1 Inhibition Overcomes Anti-apoptotic Adaptation to Targeted Therapies in B-Cell Precursor Acute Lymphoblastic Leukemia. Front Cell Dev Biol 2021; 9:695225. [PMID: 34568318 PMCID: PMC8458912 DOI: 10.3389/fcell.2021.695225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/20/2021] [Indexed: 12/30/2022] Open
Abstract
Multiple targeted therapies are currently explored for pediatric and young adult B-cell precursor acute lymphoblastic leukemia (BCP-ALL) treatment. However, this new armamentarium of therapies faces an old problem: choosing the right treatment for each patient. The lack of predictive biomarkers is particularly worrying for pediatric patients since it impairs the implementation of new treatments in the clinic. In this study, we used the functional assay dynamic BH3 profiling (DBP) to evaluate two new treatments for BCP-ALL that could improve clinical outcome, especially for relapsed patients. We found that the MEK inhibitor trametinib and the multi-target tyrosine kinase inhibitor sunitinib exquisitely increased apoptotic priming in an NRAS-mutant and in a KMT2A-rearranged cell line presenting a high expression of FLT3, respectively. Following these observations, we sought to study potential adaptations to these treatments. Indeed, we identified with DBP anti-apoptotic changes in the BCL-2 family after treatment, particularly involving MCL-1 - a pro-survival strategy previously observed in adult cancers. To overcome this adaptation, we employed the BH3 mimetic S63845, a specific MCL-1 inhibitor, and evaluated its sequential addition to both kinase inhibitors to overcome resistance. We observed that the metronomic combination of both drugs with S63845 was synergistic and showed an increased efficacy compared to single agents. Similar observations were made in BCP-ALL KMT2A-rearranged PDX cells in response to sunitinib, showing an analogous DBP profile to the SEM cell line. These findings demonstrate that rational sequences of targeted agents with BH3 mimetics, now extensively explored in clinical trials, may improve treatment effectiveness by overcoming anti-apoptotic adaptations in BCP-ALL.
Collapse
Affiliation(s)
- Albert Manzano-Muñoz
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Clara Alcon
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Pablo Menéndez
- Stem Cell Biology, Developmental Leukemia and Immunotherapy, Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Manuel Ramírez
- Department of Pediatric Hematology and Oncology, Niño Jesús University Children’s Hospital, Madrid, Spain
| | - Felix Seyfried
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Klaus-Michael Debatin
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Lüder H. Meyer
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Josep Samitier
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, University of Barcelona, Barcelona, Spain
- Networking Biomedical Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Joan Montero
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| |
Collapse
|
12
|
Bruckner TA, Catalano R, Das A, Lu Y. Cohort Selection In Utero against Male Twins and Childhood Cancers: A Population-Based Register Study. Cancer Epidemiol Biomarkers Prev 2021; 30:1834-1840. [PMID: 34272267 PMCID: PMC8974355 DOI: 10.1158/1055-9965.epi-21-0053] [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: 01/12/2021] [Revised: 03/28/2021] [Accepted: 06/15/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Cancer ranks as the second leading cause of death among children ages 1 to 14 years in the United States. Previous research finds that strong cohort selection in utero against males precedes a reduction in live-born males considered frail. We examine whether such cohort selection in utero may similarly affect the frequency of childhood cancers among male live births. METHODS We examined 1,368 childhood cancers among males born in Sweden over 144 months, from January 1990 to December 2001, and followed to age 15 in the Swedish Cancer Registry. We retrieved the count of male twins by birth month from the Swedish Birth Registry. We applied autoregressive, integrated, moving average time-series methods to identify and control for temporal patterns in monthly childhood cancers and to evaluate robustness of results. RESULTS Fewer childhood cancers occur among monthly male birth cohorts with elevated selection in utero (i.e., a low count of live-born male twins). This association appears in the concurrent month (coef = 0.04; 95% CI, 0.001-0.079) as well as in the following month in which most births from the twin's conception cohort are "scheduled" to be born (coef = 0.055; 95% CI, 0.017-0.094). CONCLUSIONS Elevated cohort selection in utero may reduce the number of frail male gestations that would otherwise have survived to birth and received a cancer diagnosis during childhood. IMPACT This novel result warrants further investigation of prenatal exposures, including those at the population level, that may induce cohort selection in utero for some cancer types but not others.
Collapse
Affiliation(s)
- Tim A. Bruckner
- Program in Public Health, University of California, Irvine, Irvine, California.,Center for Population, Inequality, and Policy, University of California, Irvine, Irvine, California.,Corresponding Author: Tim A. Bruckner, Program in Public Health, University of California, Irvine, Irvine, CA 92617. E-mail:
| | - Ralph Catalano
- School of Public Health, University of California, Berkeley, Berkeley, California
| | - Abhery Das
- Program in Public Health, University of California, Irvine, Irvine, California
| | - Yunxia Lu
- Program in Public Health, University of California, Irvine, Irvine, California
| |
Collapse
|
13
|
Barbet V, Broutier L. Future Match Making: When Pediatric Oncology Meets Organoid Technology. Front Cell Dev Biol 2021; 9:674219. [PMID: 34327198 PMCID: PMC8315550 DOI: 10.3389/fcell.2021.674219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
Unlike adult cancers that frequently result from the accumulation in time of mutational “hits” often linked to lifestyle, childhood cancers are emerging as diseases of dysregulated development through massive epigenetic alterations. The ability to reconstruct these differences in cancer models is therefore crucial for better understanding the uniqueness of pediatric cancer biology. Cancer organoids (i.e., tumoroids) represent a promising approach for creating patient-derived in vitro cancer models that closely recapitulate the overall pathophysiological features of natural tumorigenesis, including intra-tumoral heterogeneity and plasticity. Though largely applied to adult cancers, this technology is scarcely used for childhood cancers, with a notable delay in technological transfer. However, tumoroids could provide an unprecedented tool to unravel the biology of pediatric cancers and improve their therapeutic management. We herein present the current state-of-the-art of a long awaited and much needed matchmaking.
Collapse
Affiliation(s)
- Virginie Barbet
- Childhood Cancer & Cell Death (C3), Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon (CRCL), Lyon, France
| | - Laura Broutier
- Childhood Cancer & Cell Death (C3), Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon (CRCL), Lyon, France
| |
Collapse
|
14
|
Keskin T, Rucci B, Cornaz-Buros S, Martin P, Fusco C, Broye L, Cisarova K, Perez EM, Letovanec I, La Rosa S, Cherix S, Diezi M, Renella R, Provero P, Suvà ML, Stamenkovic I, Riggi N. A live single-cell reporter assay links intratumor heterogeneity to metastatic proclivity in Ewing sarcoma. SCIENCE ADVANCES 2021; 7:eabf9394. [PMID: 34215585 PMCID: PMC11060044 DOI: 10.1126/sciadv.abf9394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
Targeting of the most aggressive tumor cell subpopulations is key for effective management of most solid malignancies. However, the metastable nature of tumor heterogeneity, which allows cells to transition between strong and weak tumorigenic phenotypes, and the lack of reliable markers of tumor-promoting properties hamper identification of the most relevant cells. To overcome these obstacles, we designed a functional microRNA (miR)-based live-cell reporter assay to identify highly tumorigenic cells in xenotransplants of primary Ewing sarcoma (EwS) 3D cultures. Leveraging the inverse relationship between cell pluripotency and miR-145 expression, we successfully separated highly tumorigenic, metastasis-prone (miR-145low) cells from poorly tumorigenic, nonmetastatic (miR-145high) counterparts. Gene expression and functional studies of the two cell populations identified the EPHB2 receptor as a prognostic biomarker in patients with EwS and a major promoter of metastasis. Our study provides a simple and powerful means to identify and isolate tumor cells that display aggressive behavior.
Collapse
Affiliation(s)
- Tugba Keskin
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Beatrice Rucci
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Sandrine Cornaz-Buros
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Patricia Martin
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Carlo Fusco
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Liliane Broye
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Katarina Cisarova
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Elizabeth M Perez
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Igor Letovanec
- Department of Histopathology, Central Institute, Valais Hospital, Sion, Switzerland
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Stefano La Rosa
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Stephane Cherix
- Department of Orthopedics, Faculty of Biology and Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Manuel Diezi
- Department Woman-Mother-Child, Division of Pediatrics, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Raffaele Renella
- Department Woman-Mother-Child, Division of Pediatrics, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Paolo Provero
- Department of Neurosciences Rita Levi Montalcini, University of Turin, Center of Omics Sciences, Ospedale San Raffaele IRCSS, Milan, Italy
| | - Mario L Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Ivan Stamenkovic
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland.
| | - Nicolò Riggi
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
15
|
Jehl F, Degalez F, Bernard M, Lecerf F, Lagoutte L, Désert C, Coulée M, Bouchez O, Leroux S, Abasht B, Tixier-Boichard M, Bed'hom B, Burlot T, Gourichon D, Bardou P, Acloque H, Foissac S, Djebali S, Giuffra E, Zerjal T, Pitel F, Klopp C, Lagarrigue S. RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species. Front Genet 2021; 12:655707. [PMID: 34262593 PMCID: PMC8273700 DOI: 10.3389/fgene.2021.655707] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 06/01/2021] [Indexed: 12/19/2022] Open
Abstract
In addition to their common usages to study gene expression, RNA-seq data accumulated over the last 10 years are a yet-unexploited resource of SNPs in numerous individuals from different populations. SNP detection by RNA-seq is particularly interesting for livestock species since whole genome sequencing is expensive and exome sequencing tools are unavailable. These SNPs detected in expressed regions can be used to characterize variants affecting protein functions, and to study cis-regulated genes by analyzing allele-specific expression (ASE) in the tissue of interest. However, gene expression can be highly variable, and filters for SNP detection using the popular GATK toolkit are not yet standardized, making SNP detection and genotype calling by RNA-seq a challenging endeavor. We compared SNP calling results using GATK suggested filters, on two chicken populations for which both RNA-seq and DNA-seq data were available for the same samples of the same tissue. We showed, in expressed regions, a RNA-seq precision of 91% (SNPs detected by RNA-seq and shared by DNA-seq) and we characterized the remaining 9% of SNPs. We then studied the genotype (GT) obtained by RNA-seq and the impact of two factors (GT call-rate and read number per GT) on the concordance of GT with DNA-seq; we proposed thresholds for them leading to a 95% concordance. Applying these thresholds to 767 multi-tissue RNA-seq of 382 birds of 11 chicken populations, we found 9.5 M SNPs in total, of which ∼550,000 SNPs per tissue and population with a reliable GT (call rate ≥ 50%) and among them, ∼340,000 with a MAF ≥ 10%. We showed that such RNA-seq data from one tissue can be used to (i) detect SNPs with a strong predicted impact on proteins, despite their scarcity in each population (16,307 SIFT deleterious missenses and 590 stop-gained), (ii) study, on a large scale, cis-regulations of gene expression, with ∼81% of protein-coding and 68% of long non-coding genes (TPM ≥ 1) that can be analyzed for ASE, and with ∼29% of them that were cis-regulated, and (iii) analyze population genetic using such SNPs located in expressed regions. This work shows that RNA-seq data can be used with good confidence to detect SNPs and associated GT within various populations and used them for different analyses as GTEx studies.
Collapse
Affiliation(s)
- Frédéric Jehl
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, Saint-Gilles, France
| | - Fabien Degalez
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, Saint-Gilles, France
| | - Maria Bernard
- INRAE, SIGENAE, Genotoul Bioinfo MIAT, Castanet-Tolosan, France.,INRAE, AgroParisTech, Université Paris-Saclay, GABI UMR 1313, Jouy-en-Josas, France
| | | | | | - Colette Désert
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, Saint-Gilles, France
| | - Manon Coulée
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, Saint-Gilles, France
| | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Sophie Leroux
- INRAE, INPT, ENVT, Université de Toulouse, GenPhySE UMR 1388, Castanet-Tolosan, France
| | - Behnam Abasht
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, United States
| | | | - Bertrand Bed'hom
- INRAE, AgroParisTech, Université Paris-Saclay, GABI UMR 1313, Jouy-en-Josas, France
| | | | | | - Philippe Bardou
- INRAE, SIGENAE, Genotoul Bioinfo MIAT, Castanet-Tolosan, France
| | - Hervé Acloque
- INRAE, AgroParisTech, Université Paris-Saclay, GABI UMR 1313, Jouy-en-Josas, France
| | - Sylvain Foissac
- INRAE, INPT, ENVT, Université de Toulouse, GenPhySE UMR 1388, Castanet-Tolosan, France
| | - Sarah Djebali
- INRAE, INPT, ENVT, Université de Toulouse, GenPhySE UMR 1388, Castanet-Tolosan, France
| | - Elisabetta Giuffra
- INRAE, AgroParisTech, Université Paris-Saclay, GABI UMR 1313, Jouy-en-Josas, France
| | - Tatiana Zerjal
- INRAE, AgroParisTech, Université Paris-Saclay, GABI UMR 1313, Jouy-en-Josas, France
| | - Frédérique Pitel
- INRAE, INPT, ENVT, Université de Toulouse, GenPhySE UMR 1388, Castanet-Tolosan, France
| | | | | |
Collapse
|
16
|
Homicsko K. Deep Tumor Profiling for Molecular Tumor Boards. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11680-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
17
|
Abstract
This review aims to reflect upon the major developments in PARP14 research from late 2017 to early 2020. In doing so, this report will focus on the continual elucidation of PARP14's function including an emerging role in viral replication. This is in addition to other functional developments in cancer and inflammation, along with reflecting upon the leads in inhibitor design, including the increased attention toward the macrodomain. This report will also include a brief recap on contemporary poly(ADP-ribose) polymerase inhibitors and reflect upon the development surrounding the other poly(ADP-ribose) polymerases to overall give a succinct update to assist the development of selective PARP14 inhibitors.
Collapse
Affiliation(s)
- Amanda L Tauber
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast 4229, Queensland, Australia
| | - Stephan M Levonis
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast 4229, Queensland, Australia
| | - Stephanie S Schweiker
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast 4229, Queensland, Australia
| |
Collapse
|