1
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Forrest SJ, Gupta H, Ward A, Li YY, Doan D, Al-Ibraheemi A, Alexandrescu S, Bandopadhayay P, Shusterman S, Mullen EA, Collins NB, Chi SN, Wright KD, Kumari P, Mazor T, Ligon KL, Shivdasani P, Manam M, MacConaill LE, Ceca E, Benich SN, London WB, Schilsky RL, Bruinooge SS, Guidry Auvil JM, Cerami E, Rollins BJ, Meyerson ML, Lindeman NI, Johnson BE, Cherniak AD, Church AJ, Janeway KA. Molecular profiling of 888 pediatric tumors informs future precision trials and data-sharing initiatives in pediatric cancer. Nat Commun 2024; 15:5837. [PMID: 38992034 PMCID: PMC11239876 DOI: 10.1038/s41467-024-49944-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 06/18/2024] [Indexed: 07/13/2024] Open
Abstract
To inform clinical trial design and real-world precision pediatric oncology practice, we classified diagnoses, assessed the landscape of mutations, and identified genomic variants matching trials in a large unselected institutional cohort of solid tumors patients sequenced at Dana-Farber / Boston Children's Cancer and Blood Disorders Center. Tumors were sequenced with OncoPanel, a targeted next-generation DNA sequencing panel. Diagnoses were classified according to the International Classification of Diseases for Oncology (ICD-O-3.2). Over 6.5 years, 888 pediatric cancer patients with 95 distinct diagnoses had successful tumor sequencing. Overall, 33% (n = 289/888) of patients had at least 1 variant matching a precision oncology trial protocol, and 14% (41/289) were treated with molecularly targeted therapy. This study highlights opportunities to use genomic data from hospital-based sequencing performed either for research or clinical care to inform ongoing and future precision oncology clinical trials. Furthermore, the study results emphasize the importance of data sharing to define the genomic landscape and targeted treatment opportunities for the large group of rare pediatric cancers we encounter in clinical practice.
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Affiliation(s)
- Suzanne J Forrest
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Hersh Gupta
- Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Abigail Ward
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Yvonne Y Li
- Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Duong Doan
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Alyaa Al-Ibraheemi
- Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Sanda Alexandrescu
- Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Pratiti Bandopadhayay
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Suzanne Shusterman
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Elizabeth A Mullen
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Natalie B Collins
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Susan N Chi
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Karen D Wright
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Tali Mazor
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keith L Ligon
- Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | | | | | | | - Evelina Ceca
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Sidney N Benich
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Wendy B London
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | | | | | | | | | - Barrett J Rollins
- Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew L Meyerson
- Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Bruce E Johnson
- Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Andrew D Cherniak
- Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alanna J Church
- Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Katherine A Janeway
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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2
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Hodder A, Leiter SM, Kennedy J, Addy D, Ahmed M, Ajithkumar T, Allinson K, Ancliff P, Bailey S, Barnard G, Burke GAA, Burns C, Cano-Flanagan J, Chalker J, Coleman N, Cheng D, Clinch Y, Dryden C, Ghorashian S, Griffin B, Horan G, Hubank M, May P, McDerra J, Nagrecha R, Nicholson J, O'Connor D, Pavasovic V, Quaegebeur A, Rao A, Roberts T, Samarasinghe S, Stasevich I, Tadross JA, Trayers C, Trotman J, Vora A, Watkins J, Chitty LS, Bowdin S, Armstrong R, Murray MJ, Hook CE, Tarpey P, Vedi A, Bartram J, Behjati S. Benefits for children with suspected cancer from routine whole-genome sequencing. Nat Med 2024:10.1038/s41591-024-03056-w. [PMID: 38956197 DOI: 10.1038/s41591-024-03056-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/08/2024] [Indexed: 07/04/2024]
Abstract
Clinical whole-genome sequencing (WGS) has been shown to deliver potential benefits to children with cancer and to alter treatment in high-risk patient groups. It remains unknown whether offering WGS to every child with suspected cancer can change patient management. We collected WGS variant calls and clinical and diagnostic information from 281 children (282 tumors) across two English units (n = 152 from a hematology center, n = 130 from a solid tumor center) where WGS had become a routine test. Our key finding was that variants uniquely attributable to WGS changed the management in ~7% (20 out of 282) of cases while providing additional disease-relevant findings, beyond standard-of-care molecular tests, in 108 instances for 83 (29%) cases. Furthermore, WGS faithfully reproduced every standard-of-care molecular test (n = 738) and revealed several previously unknown genomic features of childhood tumors. We show that WGS can be delivered as part of routine clinical care to children with suspected cancer and can change clinical management by delivering unexpected genomic insights. Our experience portrays WGS as a clinically impactful assay for routine practice, providing opportunities for assay consolidation and for delivery of molecularly informed patient care.
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Affiliation(s)
- Angus Hodder
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Sarah M Leiter
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Jonathan Kennedy
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Dilys Addy
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Munaza Ahmed
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | | | - Kieren Allinson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Phil Ancliff
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Shivani Bailey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Gemma Barnard
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - G A Amos Burke
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Charlotte Burns
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Danny Cheng
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | | | - Caryl Dryden
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Sara Ghorashian
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Blanche Griffin
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- North Thames Genomic Laboratory Hub, London, UK
| | - Gail Horan
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Michael Hubank
- North Thames Genomic Laboratory Hub, London, UK
- The Institute of Cancer Research, London, UK
| | - Phillippa May
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Joanna McDerra
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Rajvi Nagrecha
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - James Nicholson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - David O'Connor
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Vesna Pavasovic
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Annelies Quaegebeur
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Anupama Rao
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Thomas Roberts
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | | | - Iryna Stasevich
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - John A Tadross
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Claire Trayers
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jamie Trotman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | - Ajay Vora
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - James Watkins
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | - Lyn S Chitty
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- North Thames Genomic Laboratory Hub, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sarah Bowdin
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | - Ruth Armstrong
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Matthew J Murray
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Catherine E Hook
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Patrick Tarpey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- East Genomics Laboratory Hub, Cambridge, UK.
| | - Aditi Vedi
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
| | - Jack Bartram
- Great Ormond Street Hospital NHS Foundation Trust, London, UK.
- North Thames Genomic Laboratory Hub, London, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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3
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Mangum R, Lin FY, Parsons DW. Recent Advancements and Innovations in Pediatric Precision Oncology. J Pediatr Hematol Oncol 2024; 46:262-271. [PMID: 38857189 DOI: 10.1097/mph.0000000000002871] [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: 08/26/2023] [Accepted: 03/29/2024] [Indexed: 06/12/2024]
Abstract
Precision oncology incorporates comprehensive genomic profiling into the individualized clinical care of pediatric cancer patients. In recent years, comprehensive pan-cancer analyses have led to the successful implementation of genomics-based pediatric trials and accelerated approval of novel targeted agents. In addition, disease-specific studies have resulted in molecular subclassification of myriad cancer types with subsequent tailoring of treatment intensity based on the patient's prognostic factors. This review discusses the progress of the field and highlights developments that are leading to more personalized cancer care and improved patient outcomes. Increased understanding of the evolution of precision oncology over recent decades emphasizes the tremendous impact of improved genomic applications. New technologies and improved diagnostic modalities offer further promise for future advancements within the field.
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Affiliation(s)
- Ross Mangum
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, AZ
| | - Frank Y Lin
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
| | - D Williams Parsons
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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4
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Zhao C, Su KJ, Wu C, Cao X, Sha Q, Li W, Luo Z, Qing T, Qiu C, Zhao LJ, Liu A, Jiang L, Zhang X, Shen H, Zhou W, Deng HW. Multi-scale variational autoencoder for imputation of missing values in untargeted metabolomics using whole-genome sequencing data. Comput Biol Med 2024; 179:108813. [PMID: 38955127 DOI: 10.1016/j.compbiomed.2024.108813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
BACKGROUND Missing data is a common challenge in mass spectrometry-based metabolomics, which can lead to biased and incomplete analyses. The integration of whole-genome sequencing (WGS) data with metabolomics data has emerged as a promising approach to enhance the accuracy of data imputation in metabolomics studies. METHOD In this study, we propose a novel method that leverages the information from WGS data and reference metabolites to impute unknown metabolites. Our approach utilizes a multi-scale variational autoencoder to jointly model the burden score, polygenetic risk score (PGS), and linkage disequilibrium (LD) pruned single nucleotide polymorphisms (SNPs) for feature extraction and missing metabolomics data imputation. By learning the latent representations of both omics data, our method can effectively impute missing metabolomics values based on genomic information. RESULTS We evaluate the performance of our method on empirical metabolomics datasets with missing values and demonstrate its superiority compared to conventional imputation techniques. Using 35 template metabolites derived burden scores, PGS and LD-pruned SNPs, the proposed methods achieved R2-scores > 0.01 for 71.55 % of metabolites. CONCLUSION The integration of WGS data in metabolomics imputation not only improves data completeness but also enhances downstream analyses, paving the way for more comprehensive and accurate investigations of metabolic pathways and disease associations. Our findings offer valuable insights into the potential benefits of utilizing WGS data for metabolomics data imputation and underscore the importance of leveraging multi-modal data integration in precision medicine research.
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Affiliation(s)
- Chen Zhao
- Department of Computer Science, Kennesaw State University, 680 Arntson Dr, Marietta, GA, 30060, USA
| | - Kuan-Jui Su
- Division of Biomedical Informatics and Genomics, Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Chong Wu
- Department of Biostatistics, University of Texas MD Anderson, Pickens Academic Tower, 1400 Pressler St., Houston, TX, 77030, USA
| | - Xuewei Cao
- Department of Mathematical Sciences, Michigan Technological University, 1400 Townsend Dr, Houghton, MI, 49931, USA
| | - Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, 1400 Townsend Dr, Houghton, MI, 49931, USA
| | - Wu Li
- Division of Biomedical Informatics and Genomics, Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Zhe Luo
- Division of Biomedical Informatics and Genomics, Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Tian Qing
- Division of Biomedical Informatics and Genomics, Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Chuan Qiu
- Division of Biomedical Informatics and Genomics, Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Lan Juan Zhao
- Division of Biomedical Informatics and Genomics, Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Anqi Liu
- Division of Biomedical Informatics and Genomics, Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Lindong Jiang
- Division of Biomedical Informatics and Genomics, Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Xiao Zhang
- Division of Biomedical Informatics and Genomics, Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Hui Shen
- Division of Biomedical Informatics and Genomics, Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Weihua Zhou
- Department of Applied Computing, Michigan Technological University, 1400 Townsend Dr, Houghton, MI, 49931, USA; Center for Biocomputing and Digital Health, Institute of Computing and Cybersystems, and Health Research Institute, Michigan Technological University, Houghton, MI, 49931, USA.
| | - Hong-Wen Deng
- Division of Biomedical Informatics and Genomics, Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University, New Orleans, LA, 70112, USA
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5
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Chapple RH, Liu X, Natarajan S, Alexander MIM, Kim Y, Patel AG, LaFlamme CW, Pan M, Wright WC, Lee HM, Zhang Y, Lu M, Koo SC, Long C, Harper J, Savage C, Johnson MD, Confer T, Akers WJ, Dyer MA, Sheppard H, Easton J, Geeleher P. An integrated single-cell RNA-seq map of human neuroblastoma tumors and preclinical models uncovers divergent mesenchymal-like gene expression programs. Genome Biol 2024; 25:161. [PMID: 38898465 PMCID: PMC11186099 DOI: 10.1186/s13059-024-03309-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 06/14/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Neuroblastoma is a common pediatric cancer, where preclinical studies suggest that a mesenchymal-like gene expression program contributes to chemotherapy resistance. However, clinical outcomes remain poor, implying we need a better understanding of the relationship between patient tumor heterogeneity and preclinical models. RESULTS Here, we generate single-cell RNA-seq maps of neuroblastoma cell lines, patient-derived xenograft models (PDX), and a genetically engineered mouse model (GEMM). We develop an unsupervised machine learning approach ("automatic consensus nonnegative matrix factorization" (acNMF)) to compare the gene expression programs found in preclinical models to a large cohort of patient tumors. We confirm a weakly expressed, mesenchymal-like program in otherwise adrenergic cancer cells in some pre-treated high-risk patient tumors, but this appears distinct from the presumptive drug-resistance mesenchymal programs evident in cell lines. Surprisingly, however, this weak-mesenchymal-like program is maintained in PDX and could be chemotherapy-induced in our GEMM after only 24 h, suggesting an uncharacterized therapy-escape mechanism. CONCLUSIONS Collectively, our findings improve the understanding of how neuroblastoma patient tumor heterogeneity is reflected in preclinical models, provides a comprehensive integrated resource, and a generalizable set of computational methodologies for the joint analysis of clinical and pre-clinical single-cell RNA-seq datasets.
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Affiliation(s)
- Richard H Chapple
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Xueying Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Sivaraman Natarajan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Margaret I M Alexander
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yuna Kim
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Anand G Patel
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Christy W LaFlamme
- Department of Cell and Molecular Biology, 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
| | - Min Pan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - William C Wright
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Hyeong-Min Lee
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yinwen Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Meifen Lu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Selene C Koo
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Courtney Long
- Animal Resources Center, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - John Harper
- Animal Resources Center, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Chandra Savage
- Animal Resources Center, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Melissa D Johnson
- Center for In Vivo Imaging and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Thomas Confer
- Center for In Vivo Imaging and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Walter J Akers
- Department of Biomedical Engineering, University of Texas Southwestern Medical School, Dallas, TX, 75390, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Heather Sheppard
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Paul Geeleher
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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6
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Zheng Y, Zhang C, Sun X, Kang K, Luo R, Zhao A, Wu Y. Survival trend and outcome prediction for pediatric Hodgkin and non-Hodgkin lymphomas based on machine learning. Clin Exp Med 2024; 24:132. [PMID: 38890203 PMCID: PMC11189314 DOI: 10.1007/s10238-024-01402-3] [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: 04/24/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024]
Abstract
Pediatric Hodgkin and non-Hodgkin lymphomas differ from adult cases in biology and management, yet there is a lack of survival analysis tailored to pediatric lymphoma. We analyzed lymphoma data from 1975 to 2018, comparing survival trends between 7,871 pediatric and 226,211 adult patients, identified key risk factors for pediatric lymphoma survival, developed a predictive nomogram, and utilized machine learning to predict long-term lymphoma-specific mortality risk. Between 1975 and 2018, we observed substantial increases in 1-year (19.3%), 5-year (41.9%), and 10-year (48.8%) overall survival rates in pediatric patients with lymphoma. Prognostic factors such as age, sex, race, Ann Arbor stage, lymphoma subtypes, and radiotherapy were incorporated into the nomogram. The nomogram exhibited excellent predictive performance with area under the curve (AUC) values of 0.766, 0.724, and 0.703 for one-year, five-year, and ten-year survival, respectively, in the training cohort, and AUC values of 0.776, 0.712, and 0.696 in the validation cohort. Importantly, the nomogram outperformed the Ann Arbor staging system in survival prediction. Machine learning models achieved AUC values of approximately 0.75, surpassing the conventional method (AUC = ~ 0.70) in predicting the risk of lymphoma-specific death. We also observed that pediatric lymphoma survivors had a substantially reduced risk of lymphoma after ten years b,ut faced an increasing risk of non-lymphoma diseases. The study highlights substantial improvements in pediatric lymphoma survival, offers reliable predictive tools, and underscores the importance of long-term monitoring for non-lymphoma health issues in pediatric patients.
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Grants
- No. 82303773, No. 82303772, No. 82204490, No. 82303694 National Natural Science Foundation of China
- No. 82303773, No. 82303772, No. 82204490, No. 82303694 National Natural Science Foundation of China
- No. 82303773, No. 82303772, No. 82204490, No. 82303694 National Natural Science Foundation of China
- No. 82303773, No. 82303772, No. 82204490, No. 82303694 National Natural Science Foundation of China
- No. 2023NSFSC1885 Natural Science Foundation of Sichuan Province
- No. 2023NSFSC1885 Natural Science Foundation of Sichuan Province
- No. 2023YFS0306 Key Research, Development Program of Sichuan Province
- No. 2023YFS0306 Key Research, Development Program of Sichuan Province
- No. GZB20230481 Postdoctoral Fellowship Program of CPSF
- No. 2024HXBH149, No. 2024HXBH006 Post-Doctor Research Project, West China Hospital, Sichuan University
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Affiliation(s)
- Yue Zheng
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Clinical Cell Therapy, West China Hospital, Sichuan University, Chengdu, China
| | - Chunlan Zhang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Xu Sun
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Kai Kang
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Clinical Cell Therapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ren Luo
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Clinical Cell Therapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ailin Zhao
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China.
| | - Yijun Wu
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
- Laboratory of Clinical Cell Therapy, West China Hospital, Sichuan University, Chengdu, China.
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7
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Pathania AS. Immune Microenvironment in Childhood Cancers: Characteristics and Therapeutic Challenges. Cancers (Basel) 2024; 16:2201. [PMID: 38927907 PMCID: PMC11201451 DOI: 10.3390/cancers16122201] [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: 02/09/2024] [Revised: 05/23/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
The tumor immune microenvironment is pivotal in cancer initiation, advancement, and regulation. Its molecular and cellular composition is critical throughout the disease, as it can influence the balance between suppressive and cytotoxic immune responses within the tumor's vicinity. Studies on the tumor immune microenvironment have enriched our understanding of the intricate interplay between tumors and their immunological surroundings in various human cancers. These studies illuminate the role of significant components of the immune microenvironment, which have not been extensively explored in pediatric tumors before and may influence the responsiveness or resistance to therapeutic agents. Our deepening understanding of the pediatric tumor immune microenvironment is helping to overcome challenges related to the effectiveness of existing therapeutic strategies, including immunotherapies. Although in the early stages, targeted therapies that modulate the tumor immune microenvironment of pediatric solid tumors hold promise for improved outcomes. Focusing on various aspects of tumor immune biology in pediatric patients presents a therapeutic opportunity that could improve treatment outcomes. This review offers a comprehensive examination of recent literature concerning profiling the immune microenvironment in various pediatric tumors. It seeks to condense research findings on characterizing the immune microenvironment in pediatric tumors and its impact on tumor development, metastasis, and response to therapeutic modalities. It covers the immune microenvironment's role in tumor development, interactions with tumor cells, and its impact on the tumor's response to immunotherapy. The review also discusses challenges targeting the immune microenvironment for pediatric cancer therapies.
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Affiliation(s)
- Anup Singh Pathania
- Department of Biochemistry and Molecular Biology, The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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8
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Ferrena A, Zhang R, Wang J, Zheng XY, Göker B, Borjihan H, Chae SS, Lo Y, Zhao H, Schwartz E, Loeb D, Yang R, Geller D, Zheng D, Hoang B. Comprehensive single cell transcriptomics analysis of murine osteosarcoma uncovers Skp2 function in metastasis, genomic instability and immune activation and reveals additional target pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597347. [PMID: 38895216 PMCID: PMC11185585 DOI: 10.1101/2024.06.04.597347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Osteosarcoma (OS) is the most common primary pediatric bone malignancy. One promising new therapeutic target is SKP2, encoding a substrate recognition factor of the SCF E3 ubiquitin ligase responsible for ubiquitination and proteasome degradation of substrate p27, thus driving cellular proliferation. We have shown previously that knockout of Skp2 in an immunocompetent transgenic mouse model of OS improved survival, drove apoptosis, and induced tumor inflammation. Here, we applied single-cell RNA-sequencing (scRNA-seq) to study primary OS tumors derived from Osx-Cre driven conditional knockout of Rb1 and Trp53. We showed that murine OS models recapitulate the tumor heterogeneity and microenvironment complexity observed in patient tumors. We further compared this model with OS models with functional disruption of Skp2: one with Skp2 knockout and the other with the Skp2-p27 interaction disrupted (resulting in p27 overexpression). We found reduction of T cell exhaustion and upregulation of interferon activation, along with evidence of replicative and endoplasmic reticulum-related stress in the Skp2 disruption models, and showed that interferon induction was correlated with improved survival in OS patients. Additionally, our scRNA-seq analysis uncovered decreased activities of metastasis-related gene signatures in the Skp2-disrupted OS, which we validated by observation of a strong reduction in lung metastasis in the Skp2 knockout mice. Finally, we report several potential mechanisms of escape from targeting Skp2 in OS, including upregulation of Myc targets, DNA copy number amplification and overexpression of alternative E3 ligase genes, and potential alternative lineage activation. These mechanistic insights into OS tumor biology and Skp2 function suggest novel targets for new, synergistic therapies, while the data and our comprehensive analysis may serve as a public resource for further big data-driven OS research.
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Affiliation(s)
- Alexander Ferrena
- Institute for Clinical and Translational Research, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ranxin Zhang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
- Musculoskeletal Tumor Center, Beijing Key Laboratory for Musculoskeletal Tumors, Peking University People’s Hospital, Beijing, China
| | - Jichuan Wang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
- Musculoskeletal Tumor Center, Beijing Key Laboratory for Musculoskeletal Tumors, Peking University People’s Hospital, Beijing, China
| | - Xiang Yu Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Barlas Göker
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hasibagan Borjihan
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sung-Suk Chae
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yungtai Lo
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hongling Zhao
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Edward Schwartz
- Department of Oncology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - David Loeb
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rui Yang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - David Geller
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bang Hoang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
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9
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Kartal-Kaess M, Karow A, Bacher U, Pabst T, Joncourt R, Zweier C, Kuehni CE, Porret NA, Roessler J. Clonal hematopoiesis of indeterminate potential is rare in pediatric patients undergoing autologous stem cell transplantation. Pediatr Hematol Oncol 2024:1-10. [PMID: 38840569 DOI: 10.1080/08880018.2024.2362885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/28/2024] [Indexed: 06/07/2024]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) describes recurrent somatic gene mutations in the blood of healthy individuals, associated with higher risk for hematological malignancies and higher all-cause mortality by cardiovascular disease. CHIP increases with age and is more common in adult patients after chemotherapy or radiation for cancer. Furthermore, in some adult patients undergoing autologous stem cell transplantation (ASCT) or thereafter, CHIP has been identified. In children and adolescents, it remains unclear how cellular stressors such as cytotoxic therapy influence the incidence and expansion of CHIP. We conducted a retrospective study on 33 pediatric patients mostly with solid tumors undergoing ASCT for presence of CHIP. We analyzed CD34+ selected peripheral blood stem cell grafts after several cycles of chemotherapy, prior to cell infusion, by next-generation sequencing including 18 "CHIP-genes". Apart from a somatic variant in TP53 in one patient no other variants indicative of CHIP were identified. As a CHIP-unrelated finding, germline variants in CHEK2 and in ATM were identified in two and four patients, respectively. In conclusion, we could not detect "typical" CHIP variants in our cohort of pediatric cancer patients undergoing ASCT. However, more studies with larger patient numbers are necessary to assess if chemotherapy in the pediatric setting contributes to an increased CHIP incidence and at what time point.
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Affiliation(s)
- Mutlu Kartal-Kaess
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Inselspital, University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Axel Karow
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Inselspital, University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Ulrike Bacher
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Thomas Pabst
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Medical Oncology, Inselspital, Bern University Hospital, Bern, University of Bern, Bern, Switzerland
| | - Raphael Joncourt
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Claudia E Kuehni
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Inselspital, University Hospital, University of Bern, Bern, Switzerland
- Childhood Cancer Research Group, Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Naomi Azur Porret
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jochen Roessler
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Inselspital, University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
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10
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Church AJ, Wakefield CE, Hetherington K, Shern JF. Promise and Perils of Precision Oncology for Patients With Pediatric and Young Adult Sarcomas. Am Soc Clin Oncol Educ Book 2024; 44:e432794. [PMID: 38924707 DOI: 10.1200/edbk_432794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
The completion of multiple national pediatric precision oncology platform trials and the incorporation of standardized molecular profiling into the diagnostic care of pediatric and young adult patients with sarcomas have proven the feasibility and potential of the approach. In this work, we explore the current state of the art of precision oncology for pediatric and young adults with sarcoma. We highlight important lessons learned and the challenges that should be addressed in the next generation of trials. The chapter outlines current efforts to improve standardization of molecular assays, harmonization of data collection, and novel molecular tools such as cell-free DNA analyses. Finally, we discuss the impacts and psychosocial outcomes experienced by patients and communication strategies for providers.
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Affiliation(s)
- Alanna J Church
- Department of Pathology, Boston Children's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Claire E Wakefield
- School of Clinical Medicine, Faculty of Medicine, UNSW Sydney, Randwick, NSW, Australia
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Kate Hetherington
- School of Clinical Medicine, Faculty of Medicine, UNSW Sydney, Randwick, NSW, Australia
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Jack F Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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11
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Chen X, Yang W, Roberts CWM, Zhang J. Developmental origins shape the paediatric cancer genome. Nat Rev Cancer 2024; 24:382-398. [PMID: 38698126 DOI: 10.1038/s41568-024-00684-9] [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: 03/18/2024] [Indexed: 05/05/2024]
Abstract
In the past two decades, technological advances have brought unprecedented insights into the paediatric cancer genome revealing characteristics distinct from those of adult cancer. Originating from developing tissues, paediatric cancers generally have low mutation burden and are driven by variants that disrupt the transcriptional activity, chromatin state, non-coding cis-regulatory regions and other biological functions. Within each tumour, there are multiple populations of cells with varying states, and the lineages of some can be tracked to their fetal origins. Genome-wide genetic screening has identified vulnerabilities associated with both the cell of origin and transcription deregulation in paediatric cancer, which have become a valuable resource for designing new therapeutic approaches including those for small molecules, immunotherapy and targeted protein degradation. In this Review, we present recent findings on these facets of paediatric cancer from a pan-cancer perspective and provide an outlook on future investigations.
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Affiliation(s)
- Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wentao Yang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Comprehensive Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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12
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Padhye BD, Nawaz U, Hains PG, Reddel RR, Robinson PJ, Zhong Q, Poulos RC. Proteomic insights into paediatric cancer: Unravelling molecular signatures and therapeutic opportunities. Pediatr Blood Cancer 2024; 71:e30980. [PMID: 38556739 DOI: 10.1002/pbc.30980] [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: 11/28/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/02/2024]
Abstract
Survival rates in some paediatric cancers have improved greatly over recent decades, in part due to the identification of diagnostic, prognostic and predictive molecular signatures, and the development of risk-directed therapies. However, other paediatric cancers have proved difficult to treat, and there is an urgent need to identify novel biomarkers that reveal therapeutic opportunities. The proteome is the total set of expressed proteins present in a cell or tissue at a point in time, and is vastly more dynamic than the genome. Proteomics holds significant promise for cancer research, as proteins are ultimately responsible for cellular phenotype and are the target of most anticancer drugs. Here, we review the discoveries, opportunities and challenges of proteomic analyses in paediatric cancer, with a focus on mass spectrometry (MS)-based approaches. Accelerating incorporation of proteomics into paediatric precision medicine has the potential to improve survival and quality of life for children with cancer.
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Affiliation(s)
- Bhavna D Padhye
- Cancer Centre for Children, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Kids Research, Children's Cancer Research Unit, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Urwah Nawaz
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Peter G Hains
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Roger R Reddel
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Phillip J Robinson
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Qing Zhong
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Rebecca C Poulos
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
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13
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Bousquets-Muñoz P, Molina O, Varela I, Álvarez-Eguiluz Á, Fernández-Mateos J, Gómez A, Sánchez EG, Balbín M, Ruano D, Ramírez-Orellana M, Puente XS, Menéndez P, Velasco-Hernandez T. Backtracking NOM1::ETV6 fusion to neonatal pathogenesis of t(7;12) (q36;p13) infant AML. Leukemia 2024:10.1038/s41375-024-02293-9. [PMID: 38806630 DOI: 10.1038/s41375-024-02293-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Affiliation(s)
- Pablo Bousquets-Muñoz
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Oscar Molina
- Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Red Española de Terapias Avanzadas (TERAV), Instituto de Salud Carlos III, Madrid, Spain
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Ángel Álvarez-Eguiluz
- Laboratorio de Oncología Molecular, Laboratorio de Medicina, Instituto Universitario de Oncología (IUOPA), Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Javier Fernández-Mateos
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Ana Gómez
- Department of Pediatric Hematology and Oncology, Hospital Infantil Universitario Niño Jesús, Autonomous University of Madrid, Madrid, Spain
| | - Elena G Sánchez
- Unidad de Terapias Avanzadas, Laboratorio de Oncohematología, Fundación para la Investigación Biomédica del Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Milagros Balbín
- Laboratorio de Oncología Molecular, Laboratorio de Medicina, Instituto Universitario de Oncología (IUOPA), Hospital Universitario Central de Asturias, Oviedo, Spain
| | - David Ruano
- Department of Pediatric Hematology and Oncology, Hospital Infantil Universitario Niño Jesús, Autonomous University of Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria La Princesa, Madrid, Spain
| | - Manuel Ramírez-Orellana
- Department of Pediatric Hematology and Oncology, Hospital Infantil Universitario Niño Jesús, Autonomous University of Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria La Princesa, Madrid, Spain
| | - Xose S Puente
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Pablo Menéndez
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
- Josep Carreras Leukemia Research Institute, Barcelona, Spain.
- Red Española de Terapias Avanzadas (TERAV), Instituto de Salud Carlos III, Madrid, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.
| | - Talia Velasco-Hernandez
- Josep Carreras Leukemia Research Institute, Barcelona, Spain.
- Red Española de Terapias Avanzadas (TERAV), Instituto de Salud Carlos III, Madrid, Spain.
- Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.
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14
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Linga BG, Mohammed SGAA, Farrell T, Rifai HA, Al-Dewik N, Qoronfleh MW. Genomic Newborn Screening for Pediatric Cancer Predisposition Syndromes: A Holistic Approach. Cancers (Basel) 2024; 16:2017. [PMID: 38893137 PMCID: PMC11171256 DOI: 10.3390/cancers16112017] [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: 04/19/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
As next-generation sequencing (NGS) has become more widely used, germline and rare genetic variations responsible for inherited illnesses, including cancer predisposition syndromes (CPSs) that account for up to 10% of childhood malignancies, have been found. The CPSs are a group of germline genetic disorders that have been identified as risk factors for pediatric cancer development. Excluding a few "classic" CPSs, there is no agreement regarding when and how to conduct germline genetic diagnostic studies in children with cancer due to the constant evolution of knowledge in NGS technologies. Various clinical screening tools have been suggested to aid in the identification of individuals who are at greater risk, using diverse strategies and with varied outcomes. We present here an overview of the primary clinical and molecular characteristics of various CPSs and summarize the existing clinical genomics data on the prevalence of CPSs in pediatric cancer patients. Additionally, we discuss several ethical issues, challenges, limitations, cost-effectiveness, and integration of genomic newborn screening for CPSs into a healthcare system. Furthermore, we assess the effectiveness of commonly utilized decision-support tools in identifying patients who may benefit from genetic counseling and/or direct genetic testing. This investigation highlights a tailored and systematic approach utilizing medical newborn screening tools such as the genome sequencing of high-risk newborns for CPSs, which could be a practical and cost-effective strategy in pediatric cancer care.
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Affiliation(s)
- BalaSubramani Gattu Linga
- Department of Research, Women’s Wellness and Research Center, Hamad Medical Corporation (HMC), P.O. Box 3050, Doha 0974, Qatar
- Translational and Precision Medicine Research, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
| | | | - Thomas Farrell
- Department of Research, Women’s Wellness and Research Center, Hamad Medical Corporation (HMC), P.O. Box 3050, Doha 0974, Qatar
| | - Hilal Al Rifai
- Neonatal Intensive Care Unit (NICU), Newborn Screening Unit, Department of Pediatrics and Neonatology, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
| | - Nader Al-Dewik
- Department of Research, Women’s Wellness and Research Center, Hamad Medical Corporation (HMC), P.O. Box 3050, Doha 0974, Qatar
- Translational and Precision Medicine Research, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
- Neonatal Intensive Care Unit (NICU), Newborn Screening Unit, Department of Pediatrics and Neonatology, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
- Genomics and Precision Medicine (GPM), College of Health & Life Science (CHLS), Hamad Bin Khalifa University (HBKU), Doha 0974, Qatar
- Faculty of Health and Social Care Sciences, Kingston University and St George’s University of London, Kingston upon Thames, Surrey, London KT1 2EE, UK
| | - M. Walid Qoronfleh
- Healthcare Research & Policy Division, Q3 Research Institute (QRI), Ann Arbor, MI 48197, USA
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15
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Novoloaca A, Broc C, Beloeil L, Yu WH, Becker J. Comparative analysis of integrative classification methods for multi-omics data. Brief Bioinform 2024; 25:bbae331. [PMID: 38985929 PMCID: PMC11234228 DOI: 10.1093/bib/bbae331] [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: 12/19/2023] [Revised: 05/31/2024] [Indexed: 07/12/2024] Open
Abstract
Recent advances in sequencing, mass spectrometry, and cytometry technologies have enabled researchers to collect multiple 'omics data types from a single sample. These large datasets have led to a growing consensus that a holistic approach is needed to identify new candidate biomarkers and unveil mechanisms underlying disease etiology, a key to precision medicine. While many reviews and benchmarks have been conducted on unsupervised approaches, their supervised counterparts have received less attention in the literature and no gold standard has emerged yet. In this work, we present a thorough comparison of a selection of six methods, representative of the main families of intermediate integrative approaches (matrix factorization, multiple kernel methods, ensemble learning, and graph-based methods). As non-integrative control, random forest was performed on concatenated and separated data types. Methods were evaluated for classification performance on both simulated and real-world datasets, the latter being carefully selected to cover different medical applications (infectious diseases, oncology, and vaccines) and data modalities. A total of 15 simulation scenarios were designed from the real-world datasets to explore a large and realistic parameter space (e.g. sample size, dimensionality, class imbalance, effect size). On real data, the method comparison showed that integrative approaches performed better or equally well than their non-integrative counterpart. By contrast, DIABLO and the four random forest alternatives outperform the others across the majority of simulation scenarios. The strengths and limitations of these methods are discussed in detail as well as guidelines for future applications.
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Affiliation(s)
- Alexei Novoloaca
- BIOASTER Research Institute, 40 avenue Tony Garnier, F-69007 Lyon, France
| | - Camilo Broc
- BIOASTER Research Institute, 40 avenue Tony Garnier, F-69007 Lyon, France
| | - Laurent Beloeil
- BIOASTER Research Institute, 40 avenue Tony Garnier, F-69007 Lyon, France
| | - Wen-Han Yu
- Bill & Melinda Gates Medical Research Institute, Cambridge, Massachusetts, MA 02139, United States
| | - Jérémie Becker
- BIOASTER Research Institute, 40 avenue Tony Garnier, F-69007 Lyon, France
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16
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Polychronopoulos PA, Bedoya-Reina OC, Johnsen JI. The Neuroblastoma Microenvironment, Heterogeneity and Immunotherapeutic Approaches. Cancers (Basel) 2024; 16:1863. [PMID: 38791942 PMCID: PMC11119056 DOI: 10.3390/cancers16101863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Neuroblastoma is a peripheral nervous system tumor that almost exclusively occurs in young children. Although intensified treatment modalities have led to increased patient survival, the prognosis for patients with high-risk disease is still around 50%, signifying neuroblastoma as a leading cause of cancer-related deaths in children. Neuroblastoma is an embryonal tumor and is shaped by its origin from cells within the neural crest. Hence, neuroblastoma usually presents with a low mutational burden and is, in the majority of cases, driven by epigenetically deregulated transcription networks. The recent development of Omic techniques has given us detailed knowledge of neuroblastoma evolution, heterogeneity, and plasticity, as well as intra- and intercellular molecular communication networks within the neuroblastoma microenvironment. Here, we discuss the potential of these recent discoveries with emphasis on new treatment modalities, including immunotherapies which hold promise for better future treatment regimens.
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Affiliation(s)
- Panagiotis Alkinoos Polychronopoulos
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 11883 Stockholm, Sweden; (P.A.P.); (O.C.B.-R.)
| | - Oscar C. Bedoya-Reina
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 11883 Stockholm, Sweden; (P.A.P.); (O.C.B.-R.)
- School of Medical Sciences, Örebro University, 70182 Örebro, Sweden
| | - John Inge Johnsen
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 11883 Stockholm, Sweden; (P.A.P.); (O.C.B.-R.)
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17
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Schmitt AD, Sikkink K, Ahmed AA, Melnyk S, Reid D, Van Meter L, Guest EM, Lansdon LA, Pastinen T, Pushel I, Yoo B, Farooqi MS. Evaluation of Hi-C sequencing for the detection of gene fusions in hematologic and solid pediatric cancer samples. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.10.24306838. [PMID: 38765974 PMCID: PMC11100933 DOI: 10.1101/2024.05.10.24306838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome and has shown promise in detecting genomic rearrangements in translational research studies. To evaluate HiC as a potential clinical diagnostic platform, analytical concordance with routine laboratory testing was assessed using primary pediatric leukemia and sarcoma specimens previously positive for clinically significant genomic rearrangements. Archived specimen types tested included viable and nonviable frozen leukemic cells, as well as formalin-fixed paraffin-embedded (FFPE) tumor tissues. Initially, pediatric acute myeloid leukemia (AML) and alveolar rhabdomyosarcoma (A-RMS) specimens with known genomic rearrangements were subjected to HiC analysis to assess analytical concordance. Subsequently, a discovery cohort consisting of AML and acute lymphoblastic leukemia (ALL) cases with no known genomic rearrangements based on prior clinical diagnostic testing were evaluated to determine whether HiC could detect rearrangements. Using a standard sequencing depth of 50 million raw read-pairs per sample, or approximately 5X raw genomic coverage, 100% concordance was observed between HiC and previous clinical cytogenetic and molecular testing. In the discovery cohort, a clinically relevant gene fusion was detected in 45% of leukemia cases (5/11). This study demonstrates the value of HiC sequencing to medical diagnostic testing as it identified several clinically significant rearrangements, including those that might have been missed by current clinical testing workflows. Key points HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome, facilitating detection of genomic rearrangements.HiC was 100% concordant with clinical diagnostic testing workflows for detecting clinically significant genomic rearrangements in pediatric leukemia and rhabdomyosarcoma specimens.HiC detected clinically significant genomic rearrangements not previously detected by prior clinical cytogenetic and molecular testing.HiC performed well with archived non-viable and viable frozen leukemic cell samples, as well as archived formalin-fixed paraffin-embedded tumor tissue specimens.
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18
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Song L, Li Q, Xia L, Sahay A, Qiu Q, Li Y, Li H, Sasaki K, Susztak K, Wu H, Wan L. Single-Cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.591709. [PMID: 38766219 PMCID: PMC11100752 DOI: 10.1101/2024.05.09.591709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Cell differentiation during organogenesis relies on precise epigenetic and transcriptional control. Disruptions to this regulation can result in developmental abnormalities and malignancies, yet the underlying mechanisms are not well understood. Wilms tumors, a type of embryonal tumor closely linked to disrupted organogenesis, harbor mutations in epigenetic regulators in 30-50% of cases. However, the role of these regulators in kidney development and pathogenesis remains unexplored. By integrating mouse modeling, histological characterizations, and single-cell transcriptomics and chromatin accessibility profiling, we show that a Wilms tumor-associated mutation in the chromatin reader protein ENL disrupts kidney development trajectory by rewiring the gene regulatory landscape. Specifically, the mutant ENL promotes the commitment of nephron progenitors while simultaneously restricting their differentiation by dysregulating key transcription factor regulons, particularly the HOX clusters. It also induces the emergence of abnormal progenitor cells that lose their chromatin identity associated with kidney specification. Furthermore, the mutant ENL might modulate stroma-nephron interactions via paracrine Wnt signaling. These multifaceted effects caused by the mutation result in severe developmental defects in the kidney and early postnatal mortality in mice. Notably, transient inhibition of the histone acetylation binding activity of mutant ENL with a small molecule displaces transcriptional condensates formed by mutant ENL from target genes, abolishes its gene activation function, and restores developmental defects in mice. This work provides new insights into how mutations in epigenetic regulators can alter the gene regulatory landscape to disrupt kidney developmental programs at single-cell resolution in vivo . It also offers a proof-of-concept for the use of epigenetics-targeted agents to rectify developmental defects.
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19
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Jin C, Zhao L, Zhao G, Liu Y, Ma W, Ma S, Yao L, Liu Y, Wu Q, Yuan H, Yang K, Ohgi K, Rich JN, Rosenfeld MG. Gene Amplification of Mediator Subunit 30 Redirects the MYC Transcriptional Program and Oncogenesis. RESEARCH SQUARE 2024:rs.3.rs-4326418. [PMID: 38766212 PMCID: PMC11100879 DOI: 10.21203/rs.3.rs-4326418/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Understanding the molecular mechanisms underlying tumorigenesis is crucial for developing effective cancer therapies. Here, we investigate the co-amplification of MED30 and MYC across diverse cancer types and its impact on oncogenic transcriptional programs. Transcriptional profiling of MYC and MED30 single or both overexpression/amplification revealed the over amount of MED30 lead MYC to a new transcriptional program that associate with poor prognosis. Mechanistically, MED30 overexpression/amplification recruits other Mediator components and binding of MYC to a small subset of novel genomic regulatory sites, changing the epigenetic marks and inducing the formation of new enhancers, which drive the expression of target genes crucial for cancer progression. In vivo studies in pancreatic ductal adenocarcinoma (PDAC) further validate the oncogenic potential of MED30, as its overexpression promotes tumor growth and can be attenuated by knockdown of MYC. Using another cancer type as an example, MED30 knockdown reduces tumor growth particularly in MYC high-expressed glioblastoma (GBM) cell lines. Overall, our study elucidates the critical role of MED30 overexpression in orchestrating oncogenic transcriptional programs and highlights its potential as a therapeutic target for MYC-amplified cancer.
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Affiliation(s)
| | | | | | | | - Wubin Ma
- University of California, San Diego
| | | | | | - Yuan Liu
- University of California, San Diego
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20
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Zhang Q, Luo Y, Qian B, Cao X, Xu C, Guo K, Wan R, Jiang Y, Wang T, Mei Z, Liu J, Lv C. A systematic pan-cancer analysis identifies LDHA as a novel predictor for immunological, prognostic, and immunotherapy resistance. Aging (Albany NY) 2024; 16:8000-8018. [PMID: 38709280 PMCID: PMC11132014 DOI: 10.18632/aging.205800] [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: 08/31/2023] [Accepted: 03/18/2024] [Indexed: 05/07/2024]
Abstract
Lactate dehydrogenase A (LDHA), a critical enzyme involved in glycolysis, is broadly involved multiple biological functions in human cancers. It is reported that LDHA can impact tumor immune surveillance and induce the transformation of tumor-associated macrophages, highlighting its unnoticed function of LDHA in immune system. However, in human cancers, the role of LDHA in prognosis and immunotherapy hasn't been investigated. In this study, we analyzed the expression pattern and prognostic value of LDHA in pan-cancer and explored its association between tumor microenvironment (TME), immune infiltration subtype, stemness scores, tumor mutation burden (TMB), and immunotherapy resistance. We found that LDHA expression is tumor heterogeneous and that its high expression is associated with poor prognosis in multiple human cancers. In addition, LDHA expression was positively correlated with the presence of mononuclear/macrophage cells, and also promoted the infiltration of a range of immune cells. Genomic alteration of LDHA was common in different types of cancer, while with prognostic value in pan-cancers. Pan-cancer analysis revealed that the significant correlations existed between LDHA expression and tumor microenvironment (including stromal cells and immune cells) as well as stemness scores (DNAss and RNAss) across cancer types. Drug sensitivity analysis also revealed that LDHA was able to predict response to chemotherapy and immunotherapy. Furthermore, it was confirmed that knockdown of LDHA reduced proliferation and migration ability of lung cancer cells. Taken together, LDHA could serve as a prognostic biomarker and a potential immunotherapy marker.
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Affiliation(s)
- Qiqi Zhang
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, P.R. China
- Southwest Medical University, Luzhou, P.R. China
| | - Yuanning Luo
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, P.R. China
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, P.R. China
| | - Bingshuo Qian
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, P.R. China
- School of Pharmacy, Henan University, Kaifeng, P.R. China
| | - Xiuhua Cao
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, P.R. China
| | - Caijun Xu
- Southwest Medical University, Luzhou, P.R. China
| | - Kan Guo
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, P.R. China
- Southwest Medical University, Luzhou, P.R. China
| | - Runlan Wan
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, P.R. China
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, P.R. China
| | - Yaling Jiang
- Southwest Medical University, Luzhou, P.R. China
| | - Tiecheng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, P.R. China
| | - Zhiqiang Mei
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, P.R. China
- Southwest Medical University, Luzhou, P.R. China
| | - Jinbiao Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, P.R. China
| | - Chaoxiang Lv
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, P.R. China
- Southwest Medical University, Luzhou, P.R. China
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, P.R. China
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21
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Saldana-Guerrero IM, Montano-Gutierrez LF, Boswell K, Hafemeister C, Poon E, Shaw LE, Stavish D, Lea RA, Wernig-Zorc S, Bozsaky E, Fetahu IS, Zoescher P, Pötschger U, Bernkopf M, Wenninger-Weinzierl A, Sturtzel C, Souilhol C, Tarelli S, Shoeb MR, Bozatzi P, Rados M, Guarini M, Buri MC, Weninger W, Putz EM, Huang M, Ladenstein R, Andrews PW, Barbaric I, Cresswell GD, Bryant HE, Distel M, Chesler L, Taschner-Mandl S, Farlik M, Tsakiridis A, Halbritter F. A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations. Nat Commun 2024; 15:3745. [PMID: 38702304 PMCID: PMC11068915 DOI: 10.1038/s41467-024-47945-7] [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: 01/06/2023] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
Early childhood tumours arise from transformed embryonic cells, which often carry large copy number alterations (CNA). However, it remains unclear how CNAs contribute to embryonic tumourigenesis due to a lack of suitable models. Here we employ female human embryonic stem cell (hESC) differentiation and single-cell transcriptome and epigenome analysis to assess the effects of chromosome 17q/1q gains, which are prevalent in the embryonal tumour neuroblastoma (NB). We show that CNAs impair the specification of trunk neural crest (NC) cells and their sympathoadrenal derivatives, the putative cells-of-origin of NB. This effect is exacerbated upon overexpression of MYCN, whose amplification co-occurs with CNAs in NB. Moreover, CNAs potentiate the pro-tumourigenic effects of MYCN and mutant NC cells resemble NB cells in tumours. These changes correlate with a stepwise aberration of developmental transcription factor networks. Together, our results sketch a mechanistic framework for the CNA-driven initiation of embryonal tumours.
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Affiliation(s)
- Ingrid M Saldana-Guerrero
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
- Sheffield Institute for Nucleic Acids (SInFoNiA), School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | | | - Katy Boswell
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | | | - Evon Poon
- Division of Clinical Studies, The Institute of Cancer Research (ICR) & Royal Marsden NHS Trust, London, UK
| | - Lisa E Shaw
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Dylan Stavish
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Rebecca A Lea
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Sara Wernig-Zorc
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Eva Bozsaky
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Irfete S Fetahu
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Medical University of Vienna, Department of Neurology, Division of Neuropathology and Neurochemistry, Vienna, Austria
| | - Peter Zoescher
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ulrike Pötschger
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Marie Bernkopf
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik GmbH, Vienna, Austria
| | | | - Caterina Sturtzel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Celine Souilhol
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
- Biomolecular Sciences Research Centre, Department of Biosciences and Chemistry, Sheffield Hallam University, Sheffield, UK
| | - Sophia Tarelli
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Mohamed R Shoeb
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Polyxeni Bozatzi
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Magdalena Rados
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Maria Guarini
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Michelle C Buri
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Eva M Putz
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Miller Huang
- Children's Hospital Los Angeles, Cancer and Blood Disease Institutes, and The Saban Research Institute, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ruth Ladenstein
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Peter W Andrews
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | | | - Helen E Bryant
- Sheffield Institute for Nucleic Acids (SInFoNiA), School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Martin Distel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research (ICR) & Royal Marsden NHS Trust, London, UK
| | | | - Matthias Farlik
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Anestis Tsakiridis
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK.
- Neuroscience Institute, The University of Sheffield, Sheffield, UK.
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22
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Walia Y, de Bock CE, Huang Y. The landscape of alterations affecting epigenetic regulators in T-cell acute lymphoblastic leukemia: Roles in leukemogenesis and therapeutic opportunities. Int J Cancer 2024; 154:1522-1536. [PMID: 38155420 DOI: 10.1002/ijc.34819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/25/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy accounting for 10%-15% of pediatric and 20%-25% of adult ALL cases. Epigenetic irregularities in T-ALL include alterations in both DNA methylation and the post-translational modifications on histones which together play a critical role in the initiation and development of T-ALL. Characterizing the oncogenic mutations that result in these epigenetic changes combined with the reversibility of epigenetic modifications represents an opportunity for the development of epigenetic therapies. Oncogenic mutations and deregulated expression of DNA methyltransferases (DNMTs), Ten-Eleven Translocation dioxygenases (TETs), Histone acetyltransferases (HATs) and members of Polycomb Repressor Complex 2 (PRC2) have all been identified in T-ALL. This review focuses on the current understanding of how these mutations lead to epigenetic changes in T-ALL, their association with disease pathogenesis and the current efforts to exploit these clinically through the development of epigenetic therapies in T-ALL treatment.
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Affiliation(s)
- Yashna Walia
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, New South Wales, Australia
| | - Charles E de Bock
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, New South Wales, Australia
| | - Yizhou Huang
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, New South Wales, Australia
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23
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Fraire CR, Desai K, Obalapuram UA, Mendyka LK, Rajaram V, Sebastian T, Wang Y, Onel K, Lee J, Chen KS. An imbalance between proliferation and differentiation underlies the development of microRNA-defective pineoblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590638. [PMID: 38712047 PMCID: PMC11071395 DOI: 10.1101/2024.04.23.590638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Mutations in the microRNA processing genes DICER1 and DROSHA drive several cancers that resemble embryonic progenitors. To understand how microRNAs regulate tumorigenesis, we ablated Drosha or Dicer1 in the developing pineal gland to emulate the pathogenesis of pineoblastoma, a brain tumor that resembles undifferentiated precursors of the pineal gland. Accordingly, these mice develop pineal tumors marked by loss of microRNAs, including the let-7/miR-98-5p family, and de-repression of microRNA target genes. Pineal tumors driven by loss of Drosha or Dicer1 mimic tumors driven by Rb1 loss, as they exhibit upregulation of S-phase genes and homeobox transcription factors that regulate pineal development. Blocking proliferation of these tumors facilitates expression of pinealocyte maturation markers, with a concomitant reduction in embryonic markers. Select embryonic markers remain elevated, however, as the microRNAs that normally repress these target genes remain absent. One such microRNA target gene is the oncofetal transcription factor Plagl2, which regulates expression of pro-growth genes, and inhibiting their signaling impairs tumor growth. Thus, we demonstrate that tumors driven by loss of microRNA processing may be therapeutically targeted by inhibiting downstream drivers of proliferation.
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Affiliation(s)
- Claudette R. Fraire
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Kavita Desai
- Division of Oncology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | | | | | - Veena Rajaram
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Teja Sebastian
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Kenan Onel
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Jeon Lee
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX USA
| | - Kenneth S. Chen
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX USA
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX USA
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24
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Chapple RH, Liu X, Natarajan S, Alexander MIM, Kim Y, Patel AG, LaFlamme CW, Pan M, Wright WC, Lee HM, Zhang Y, Lu M, Koo SC, Long C, Harper J, Savage C, Johnson MD, Confer T, Akers WJ, Dyer MA, Sheppard H, Easton J, Geeleher P. An integrated single-cell RNA-seq map of human neuroblastoma tumors and preclinical models uncovers divergent mesenchymal-like gene expression programs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.13.536639. [PMID: 38712039 PMCID: PMC11071300 DOI: 10.1101/2023.04.13.536639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Neuroblastoma is a common pediatric cancer, where preclinical studies suggest that a mesenchymal-like gene expression program contributes to chemotherapy resistance. However, clinical outcomes remain poor, implying we need a better understanding of the relationship between patient tumor heterogeneity and preclinical models. Here, we generated single-cell RNA-seq maps of neuroblastoma cell lines, patient-derived xenograft models (PDX), and a genetically engineered mouse model (GEMM). We developed an unsupervised machine learning approach ('automatic consensus nonnegative matrix factorization' (acNMF)) to compare the gene expression programs found in preclinical models to a large cohort of patient tumors. We confirmed a weakly expressed, mesenchymal-like program in otherwise adrenergic cancer cells in some pre-treated high-risk patient tumors, but this appears distinct from the presumptive drug-resistance mesenchymal programs evident in cell lines. Surprisingly however, this weak-mesenchymal-like program was maintained in PDX and could be chemotherapy-induced in our GEMM after only 24 hours, suggesting an uncharacterized therapy-escape mechanism. Collectively, our findings improve the understanding of how neuroblastoma patient tumor heterogeneity is reflected in preclinical models, provides a comprehensive integrated resource, and a generalizable set of computational methodologies for the joint analysis of clinical and pre-clinical single-cell RNA-seq datasets.
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25
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Choochuen P, Nokchan N, Khongcharoen N, Laochareonsuk W, Surachat K, Chotsampancharoen T, Sila T, Consortium SS. Discovery of Novel Potential Prognostic Markers and Targeted Therapy to Overcome Chemotherapy Resistance in an Advanced-Stage Wilms Tumor. Cancers (Basel) 2024; 16:1567. [PMID: 38672648 PMCID: PMC11049388 DOI: 10.3390/cancers16081567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Wilms tumor (WT), the most prevalent type of renal cancer in children, exhibits overall survival rates exceeding 90%. However, chemotherapy resistance, which occurs in approximately 10% of WT cases, is a major challenge for the treatment of WT, particularly for advanced-stage patients. In this study, we aimed to discover potential mutation markers and drug targets associated with chemotherapy resistance in advanced-stage WT. We performed exome sequencing to detect somatic mutations and molecular targets in 43 WT samples, comprising 26 advanced-stage WTs, of which 7 cases were chemotherapy-resistant. Our analysis revealed four genes (ALPK2, C16orf96, PRKDC, and SVIL) that correlated with chemotherapy resistance and reduced disease-free survival in advanced-stage WT. Additionally, we identified driver mutations in 55 genes within the chemotherapy-resistant group, including 14 druggable cancer driver genes. Based on the mutation profiles of the resistant WT samples, we propose potential therapeutic strategies involving platinum-based agents, PARP inhibitors, and antibiotic/antineoplastic agents. Our findings provide insights into the genetic landscape of WT and offer potential avenues for targeted treatment, particularly for patients with chemotherapy resistance.
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Affiliation(s)
- Pongsakorn Choochuen
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (P.C.); (N.N.); (N.K.); (W.L.); (K.S.)
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Natakorn Nokchan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (P.C.); (N.N.); (N.K.); (W.L.); (K.S.)
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Natthapon Khongcharoen
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (P.C.); (N.N.); (N.K.); (W.L.); (K.S.)
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Wison Laochareonsuk
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (P.C.); (N.N.); (N.K.); (W.L.); (K.S.)
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (P.C.); (N.N.); (N.K.); (W.L.); (K.S.)
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | | | - Thanit Sila
- Department of Pathology, Facualty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand;
| | - Surasak Sangkhathat Consortium
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (P.C.); (N.N.); (N.K.); (W.L.); (K.S.)
- Department of Surgery, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
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26
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Silver KI, Mannheimer JD, Saba C, Hendricks WPD, Wang G, Day K, Warrier M, Beck JA, Mazcko C, LeBlanc AK. Clinical, pathologic and molecular findings in 2 Rottweiler littermates with appendicular osteosarcoma. RESEARCH SQUARE 2024:rs.3.rs-4223759. [PMID: 38659878 PMCID: PMC11042397 DOI: 10.21203/rs.3.rs-4223759/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Appendicular osteosarcoma was diagnosed and treated in a pair of littermate Rottweiler dogs, resulting in distinctly different clinical outcomes despite similar therapy within the context of a prospective, randomized clinical trial (NCI-COTC021/022). Histopathology, immunohistochemistry, mRNA sequencing, and targeted DNA hotspot sequencing techniques were applied to both dogs' tumors to define factors that could underpin their differential response to treatment. We describe the comparison of their clinical, histologic and molecular features, as well as those from a companion cohort of Rottweiler dogs, providing new insight into potential prognostic biomarkers for canine osteosarcoma.
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Affiliation(s)
| | | | | | - William P D Hendricks
- Vidium Animal Health, A Subsidiary of The Translational Genomics Research Institute (TGen)
| | - Guannan Wang
- Vidium Animal Health, A Subsidiary of The Translational Genomics Research Institute (TGen)
| | - Kenneth Day
- Vidium Animal Health, A Subsidiary of The Translational Genomics Research Institute (TGen)
| | - Manisha Warrier
- Vidium Animal Health, A Subsidiary of The Translational Genomics Research Institute (TGen)
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27
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Pusch FF, Dorado García H, Xu R, Gürgen D, Bei Y, Brückner L, Röefzaad C, von Stebut J, Bardinet V, Chamorro Gonzalez R, Eggert A, Schulte JH, Hundsdörfer P, Seifert G, Haase K, Schäfer BW, Wachtel M, Kühl AA, Ortiz MV, Wengner AM, Scheer M, Henssen AG. Elimusertib has Antitumor Activity in Preclinical Patient-Derived Pediatric Solid Tumor Models. Mol Cancer Ther 2024; 23:507-519. [PMID: 38159110 PMCID: PMC10985474 DOI: 10.1158/1535-7163.mct-23-0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 09/12/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The small-molecule inhibitor of ataxia telangiectasia and Rad3-related protein (ATR), elimusertib, is currently being tested clinically in various cancer entities in adults and children. Its preclinical antitumor activity in pediatric malignancies, however, is largely unknown. We here assessed the preclinical activity of elimusertib in 38 cell lines and 32 patient-derived xenograft (PDX) models derived from common pediatric solid tumor entities. Detailed in vitro and in vivo molecular characterization of the treated models enabled the evaluation of response biomarkers. Pronounced objective response rates were observed for elimusertib monotherapy in PDX, when treated with a regimen currently used in clinical trials. Strikingly, elimusertib showed stronger antitumor effects than some standard-of-care chemotherapies, particularly in alveolar rhabdomysarcoma PDX. Thus, elimusertib has strong preclinical antitumor activity in pediatric solid tumor models, which may translate to clinically meaningful responses in patients.
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Affiliation(s)
- Fabian F. Pusch
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Heathcliff Dorado García
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Robin Xu
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dennis Gürgen
- Experimental Pharmacology and Oncology (EPO), Berlin, Germany
| | - Yi Bei
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lotte Brückner
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany
| | - Claudia Röefzaad
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jennifer von Stebut
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Victor Bardinet
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
| | - Rocío Chamorro Gonzalez
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johannes H. Schulte
- Department of Pediatric Oncology and Hematology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, University Hospital Tübingen, Tübingen, Germany
| | - Patrick Hundsdörfer
- Department of Pediatric Oncology and Hematology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Helios Klinikum Berlin-Buch, Berlin, Germany
| | - Georg Seifert
- Department of Pediatric Oncology and Hematology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kerstin Haase
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
| | | | | | - Anja A. Kühl
- iPATH.Berlin—Core Unit Immunopathology for Experimental Models, Charité Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael V. Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York City, New York
| | | | - Monika Scheer
- Department of Pediatric Oncology and Hematology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anton G. Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
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Lee WG, Kim ES. Precision Oncology in Pediatric Cancer Surgery. Surg Oncol Clin N Am 2024; 33:409-446. [PMID: 38401917 DOI: 10.1016/j.soc.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2024]
Abstract
Pediatric precision oncology has provided a greater understanding of the wide range of molecular alterations in difficult-to-treat or rare tumors with the aims of increasing survival as well as decreasing toxicity and morbidity from current cytotoxic therapies. In this article, the authors discuss the current state of pediatric precision oncology which has increased access to novel targeted therapies while also providing a framework for clinical implementation in this unique population. The authors evaluate the targetable mutations currently under investigation-with a focus on pediatric solid tumors-and discuss the key surgical implications associated with novel targeted therapies.
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Affiliation(s)
- William G Lee
- Department of Surgery, Cedars-Sinai Medical Center, 116 North Robertson Boulevard, Suite PACT 700, Los Angeles, CA 90048, USA. https://twitter.com/william_ghh_lee
| | - Eugene S Kim
- Division of Pediatric Surgery, Department of Surgery, Cedars-Sinai Medical Center, 116 North Robertson Boulevard, Suite PACT 700, Los Angeles, CA 90048, USA.
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29
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Charlab R, Leong R, Shord SS, Reaman GH. Pediatric Cancer Drug Development: Leveraging Insights in Cancer Biology and the Evolving Regulatory Landscape to Address Challenges and Guide Further Progress. Cold Spring Harb Perspect Med 2024; 14:a041656. [PMID: 38467448 PMCID: PMC10982696 DOI: 10.1101/cshperspect.a041656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The discovery and development of anticancer drugs for pediatric patients have historically languished when compared to both past and recent activity in drug development for adult patients, notably the dramatic spike of targeted and immune-oncology therapies. The reasons for this difference are multifactorial. Recent changes in the regulatory landscape surrounding pediatric cancer drug development and the understanding that some pediatric cancers are driven by genetic perturbations that also drive disparate adult cancers afford new opportunities. The unique cancer-initiating events and dependencies of many pediatric cancers, however, require additional pediatric-specific strategies. Research efforts to unravel the underlying biology of pediatric cancers, innovative clinical trial designs, model-informed drug development, extrapolation from adult data, addressing the unique considerations in pediatric patients, and use of pediatric appropriate formulations, should all be considered for efficient development and dosage optimization of anticancer drugs for pediatric patients.
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Affiliation(s)
- Rosane Charlab
- Office of Clinical Pharmacology, Office of Translational Sciences, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, USA
| | - Ruby Leong
- Office of Clinical Pharmacology, Office of Translational Sciences, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, USA
| | - Stacy S Shord
- Office of Clinical Pharmacology, Office of Translational Sciences, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, USA
| | - Gregory H Reaman
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland 20892, USA
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30
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Zhang X, Zhang X, Yang Q, Han R, Fadhul W, Sachdeva A, Zhang X. Comprehensive analysis of ADGRE5 gene in human tumors: Clinical relevance, prognostic implications, and potential for personalized immunotherapy. Heliyon 2024; 10:e27459. [PMID: 38501000 PMCID: PMC10945187 DOI: 10.1016/j.heliyon.2024.e27459] [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: 10/15/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Purpose The Adhesion G protein receptor E5 (ADGRE5) gene is involved in a wide range of biological functions in human tumors; however, its specific molecular mechanism and significance in the analysis of human tumors have not yet been determined. Here, we provide a comprehensive genomic architecture of ADGRE5 in the tumor immune microenvironment and its clinical relevance across a broad range of solid tumors. Methods In this study, we used publicly available bioinformatics databases, with a primary focus on The Cancer Genome Atlas (TCGA) database and GTEx data, to conduct a comprehensive analysis of the impact on patient prognosis associated with ADGRE5. Results Statistics of more than 30 solid tumors from TCGA and Cancer Cell Line Encyclopedia (CCLE) were examined. ADGRE5 was differentially expressed in several cancers and was significantly associated with survival outcomes. Higher ADGRE5 levels were associated with worse prognosis in adrenocortical carcinoma, low grade glioma of the brain (LGG), lung squamous cell carcinoma, liver hepatocellular carcinoma, and uveal melanoma (UVM). Additionally, ADGRE5 was found to be an independent risk factor for LGG and UVM. The clinical relevance of ADGRE5 in tumor immunogenicity was further investigated. The expression level of ADGRE5 was not only strongly associated with tumor infiltration, such as tumor-infiltrating immune cells and immune subtypes, but also with tumor mutation burden, pyroptosis, and epithelial-mesenchymal transition in various types of cancer (P < 0.05). Furthermore, we noted that ADGRE5 exhibited a positive association with targeted drug sensitivity and conversely, a negative association with traditional chemotherapeutic drug sensitivity. Thus, ADGRE5 is expected to be a guiding marker gene for clinical prognosis and personalized tumor immunotherapy.
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Affiliation(s)
- Xiangjian Zhang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xinxin Zhang
- Department of Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Qiuhui Yang
- Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Ruokuo Han
- Department of Surgical Oncology, Wenzhou Central Hospital, Wenzhou, Zhejiang, 325000, China
| | - Walaa Fadhul
- Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Alisha Sachdeva
- Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xianbo Zhang
- Department of Surgical Oncology, Wenzhou Central Hospital, Wenzhou, Zhejiang, 325000, China
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31
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Li J, Wang Z, Fan X, Yao R, Zhang G, Fan R, Wang Z. Rapid multiple protein sequence search by parallel and heterogeneous computation. Bioinformatics 2024; 40:btae151. [PMID: 38547405 PMCID: PMC11021808 DOI: 10.1093/bioinformatics/btae151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 02/21/2024] [Accepted: 03/26/2024] [Indexed: 04/18/2024] Open
Abstract
MOTIVATION Protein sequence database search and multiple sequence alignment generation is a fundamental task in many bioinformatics analyses. As the data volume of sequences continues to grow rapidly, there is an increasing need for efficient and scalable multiple sequence query algorithms for super-large databases without expensive time and computational costs. RESULTS We introduce Chorus, a novel protein sequence query system that leverages parallel model and heterogeneous computation architecture to enable users to query thousands of protein sequences concurrently against large protein databases on a desktop workstation. Chorus achieves over 100× speedup over BLASTP without sacrificing sensitivity. We demonstrate the utility of Chorus through a case study of analyzing a ∼1.5-TB large-scale metagenomic datasets for novel CRISPR-Cas protein discovery within 30 min. AVAILABILITY AND IMPLEMENTATION Chorus is open-source and its code repository is available at https://github.com/Bio-Acc/Chorus.
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Affiliation(s)
- Jiefu Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Ziyuan Wang
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xuwei Fan
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ruijie Yao
- Institute of Intelligent Computing Technology, Chinese Academy of Sciences, 88 Jinjihu Avenue, Suzhou, Jiangsu 215000, China
| | - Guoqing Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Rui Fan
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- School of Life Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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32
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Zhang Q, Zhang J, Lan T, He J, Lei B, Wang H, Mei Z, Lv C. Integrative analysis revealed a correlation of PIAS family genes expression with prognosis, immunomodulation and chemotherapy. Eur J Med Res 2024; 29:195. [PMID: 38528630 DOI: 10.1186/s40001-024-01795-7] [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] [Accepted: 03/13/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Protein inhibitor of activated STATs (PIAS) has pleiotropic biological effects, such as protein post-translational modification, transcriptional coregulation and gene editing. It is reported that PIAS family genes are also correlated with immune cells infiltration in cancers that highlights their unnoticed biological role in tumor progression. However, the relationship of their expression with prognosis, immune cell infiltration, tumor microenvironment, and immunotherapy in pan-cancer has been rarely reported. METHODS The multi-omics data were used to investigate the expression level of PIAS family members in pan-cancer, and the prognostic value of their expression in different tumors was analyzed by univariate Cox regression and Kaplan-Meier. Correlation analysis was used to investigate the relationship of PIAS gene expression with tumor microenvironment, immune infiltrating subtypes, stemness score and drug sensitivity. In addition, we also used wound healing and transwell assays to verify the biological effects of PIAS family gene expression on invasion and metastasis of HCC cells. RESULTS We found that PIAS family genes expression is significantly heterogeneous in tumors by multi-genomic analysis, and associated with poor prognosis in patients with multiple types of cancer. Furthermore, we also found that genetic alterations of PIAS family genes were not only common in different types of human tumors, but were also significantly associated with disease-free survival (DFS) across pan-cancer. Single-cell analysis revealed that PIAS family genes were mainly distributed in monocytes/macrophages. Additionally, we also found that their expression was associated with tumor microenvironment (including stromal cells and immune cells) and stemness score (DNAss and RNAss). Drug sensitivity analysis showed that PIAS family genes were able to predict the response to chemotherapy and immunotherapy. PIAS family genes expression is closely related to tumor metastasis, especially PIAS3. High PIAS3 expression significantly promotes the migration and invasion of liver cancer cell lines (HCC-LM3 and MHCC97-H). CONCLUSIONS Taking together, these findings contribute to determine whether the PIAS family genes are a potential oncogenic target gene, which have important contribution for the development of cancer immunotherapy.
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Affiliation(s)
- Qiqi Zhang
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Junkui Zhang
- Pharmaceutical Institute, Henan University, Kaifeng, 475004, China
| | - Tianyi Lan
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jiayue He
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Bin Lei
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Hongnan Wang
- College of Integrative Chinese and Western Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Zhiqiang Mei
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
| | - Chaoxiang Lv
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
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33
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Cornel AM, van der Sman L, van Dinter JT, Arrabito M, Dunnebach E, van Hoesel M, Kluiver TA, Lopes AP, Dautzenberg NMM, Dekker L, van Rijn JM, van den Beemt DAMH, Buhl JL, du Chatinier A, Barneh F, Lu Y, Lo Nigro L, Krippner-Heidenreich A, Sebestyén Z, Kuball J, Hulleman E, Drost J, van Heesch S, Heidenreich OT, Peng WC, Nierkens S. Targeting pediatric cancers via T-cell recognition of the monomorphic MHC class I-related protein MR1. J Immunother Cancer 2024; 12:e007538. [PMID: 38519054 PMCID: PMC10961533 DOI: 10.1136/jitc-2023-007538] [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] [Accepted: 12/18/2023] [Indexed: 03/24/2024] Open
Abstract
Human leukocyte antigen (HLA) restriction of conventional T-cell targeting introduces complexity in generating T-cell therapy strategies for patients with cancer with diverse HLA-backgrounds. A subpopulation of atypical, major histocompatibility complex-I related protein 1 (MR1)-restricted T-cells, distinctive from mucosal-associated invariant T-cells (MAITs), was recently identified recognizing currently unidentified MR1-presented cancer-specific metabolites. It is hypothesized that the MC.7.G5 MR1T-clone has potential as a pan-cancer, pan-population T-cell immunotherapy approach. These cells are irresponsive to healthy tissue while conferring T-cell receptor(TCR) dependent, HLA-independent cytotoxicity to a wide range of adult cancers. Studies so far are limited to adult malignancies. Here, we investigated the potential of MR1-targeting cellular therapy strategies in pediatric cancer. Bulk RNA sequencing data of primary pediatric tumors were analyzed to assess MR1 expression. In vitro pediatric tumor models were subsequently screened to evaluate their susceptibility to engineered MC.7.G5 TCR-expressing T-cells. Targeting capacity was correlated with qPCR-based MR1 mRNA and protein overexpression. RNA expression of MR1 in primary pediatric tumors varied widely within and between tumor entities. Notably, embryonal tumors exhibited significantly lower MR1 expression than other pediatric tumors. In line with this, most screened embryonal tumors displayed resistance to MR1T-targeting in vitro MR1T susceptibility was observed particularly in pediatric leukemia and diffuse midline glioma models. This study demonstrates potential of MC.7.G5 MR1T-cell immunotherapy in pediatric leukemias and diffuse midline glioma, while activity against embryonal tumors was limited. The dismal prognosis associated with relapsed/refractory leukemias and high-grade brain tumors highlights the promise to improve survival rates of children with these cancers.
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Affiliation(s)
- Annelisa M Cornel
- Prinses Maxima Centrum voor Kinderoncologie, Utrecht, The Netherlands
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Loutje van der Sman
- Prinses Maxima Centrum voor Kinderoncologie, Utrecht, The Netherlands
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Jip T van Dinter
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Marta Arrabito
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
- Center of Pediatric Hematology & Oncology, University of Catania, Catania, Italy
| | - Ester Dunnebach
- Prinses Maxima Centrum voor Kinderoncologie, Utrecht, The Netherlands
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | | | - Thomas A Kluiver
- Prinses Maxima Centrum voor Kinderoncologie, Utrecht, The Netherlands
| | - Ana P Lopes
- Prinses Maxima Centrum voor Kinderoncologie, Utrecht, The Netherlands
| | | | - Linde Dekker
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Jorik M van Rijn
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | | | - Juliane L Buhl
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Aimee du Chatinier
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Farnaz Barneh
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Yuyan Lu
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Luca Lo Nigro
- Center of Pediatric Hematology & Oncology, University of Catania, Catania, Italy
| | | | - Zsolt Sebestyén
- Prinses Maxima Centrum voor Kinderoncologie, Utrecht, The Netherlands
| | - Jurgen Kuball
- Prinses Maxima Centrum voor Kinderoncologie, Utrecht, The Netherlands
- Department of Hematology, UMC Utrecht, Utrecht, The Netherlands
| | - Esther Hulleman
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Jarno Drost
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | | | - Olaf T Heidenreich
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Weng Chuan Peng
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Stefan Nierkens
- Prinses Maxima Centrum voor Kinderoncologie, Utrecht, The Netherlands
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
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Wang T, Liu L, Fang J, Jin H, Natarajan S, Sheppard H, Lu M, Turner G, Confer T, Johnson M, Steinberg J, Ha L, Yadak N, Jain R, Picketts DJ, Ma X, Murphy A, Davidoff AM, Glazer ES, Easton J, Chen X, Wang R, Yang J. Conditional c-MYC activation in catecholaminergic cells drives distinct neuroendocrine tumors: neuroblastoma vs somatostatinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584622. [PMID: 38559042 PMCID: PMC10980015 DOI: 10.1101/2024.03.12.584622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The MYC proto-oncogenes (c-MYC, MYCN , MYCL ) are among the most deregulated oncogenic drivers in human malignancies including high-risk neuroblastoma, 50% of which are MYCN -amplified. Genetically engineered mouse models (GEMMs) based on the MYCN transgene have greatly expanded the understanding of neuroblastoma biology and are powerful tools for testing new therapies. However, a lack of c-MYC-driven GEMMs has hampered the ability to better understand mechanisms of neuroblastoma oncogenesis and therapy development given that c-MYC is also an important driver of many high-risk neuroblastomas. In this study, we report two transgenic murine neuroendocrine models driven by conditional c-MYC induction in tyrosine hydroxylase (Th) and dopamine β-hydroxylase (Dbh)-expressing cells. c-MYC induction in Th-expressing cells leads to a preponderance of Pdx1 + somatostatinomas, a type of pancreatic neuroendocrine tumor (PNET), resembling human somatostatinoma with highly expressed gene signatures of δ cells and potassium channels. In contrast, c-MYC induction in Dbh-expressing cells leads to onset of neuroblastomas, showing a better transforming capacity than MYCN in a comparable C57BL/6 genetic background. The c-MYC murine neuroblastoma tumors recapitulate the pathologic and genetic features of human neuroblastoma, express GD2, and respond to anti-GD2 immunotherapy. This model also responds to DFMO, an FDA-approved inhibitor targeting ODC1, which is a known MYC transcriptional target. Thus, establishing c-MYC-overexpressing GEMMs resulted in different but related tumor types depending on the targeted cell and provide useful tools for testing immunotherapies and targeted therapies for these diseases.
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35
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Wang J, Ferrena A, Zhang R, Singh S, Viscarret V, Al-Harden W, Aldahamsheh O, Borjihan H, Singla A, Yaguare S, Tingling J, Zi X, Lo Y, Gorlick R, Schwartz EL, Zhao H, Yang R, Geller DS, Zheng D, Hoang BH. Targeted inhibition of SCF SKP2 confers anti-tumor activities resulting in a survival benefit in osteosarcoma. Oncogene 2024; 43:962-975. [PMID: 38355807 PMCID: PMC10959747 DOI: 10.1038/s41388-024-02942-4] [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: 10/27/2022] [Revised: 12/21/2023] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
Osteosarcoma(OS) is a highly aggressive bone cancer for which treatment has remained essentially unchanged for decades. Although OS is characterized by extensive genomic heterogeneity and instability, RB1 and TP53 have been shown to be the most commonly inactivated tumor suppressors in OS. We previously generated a mouse model with a double knockout (DKO) of Rb1 and Trp53 within cells of the osteoblastic lineage, which largely recapitulates human OS with nearly complete penetrance. SKP2 is a repression target of pRb and serves as a substrate recruiting subunit of the SCFSKP2 complex. In addition, SKP2 plays a central role in regulating the cell cycle by ubiquitinating and promoting the degradation of p27. We previously reported the DKOAA transgenic model, which harbored a knock-in mutation in p27 that impaired its binding to SKP2. Here, we generated a novel p53-Rb1-SKP2 triple-knockout model (TKO) to examine SKP2 function and its potential as a therapeutic target in OS. First, we observed that OS tumorigenesis was significantly delayed in TKO mice and their overall survival was markedly improved. In addition, the loss of SKP2 also promoted an apoptotic microenvironment and reduced the stemness of DKO tumors. Furthermore, we found that small-molecule inhibitors of SKP2 exhibited anti-tumor activities in vivo and in OS organoids as well as synergistic effects when combined with a standard chemotherapeutic agent. Taken together, our results suggest that SKP2 inhibitors may reduce the stemness plasticity of OS and should be leveraged as next-generation adjuvants in this cancer.
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Affiliation(s)
- Jichuan Wang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
- Musculoskleletal Tumor Center, Beijing Key Laboratory for Musculoskeletal Tumors, Peking University People's Hospital, Beijing, China
| | - Alexander Ferrena
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
- Institute for Clinical and Translational Research, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ranxin Zhang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Swapnil Singh
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Valentina Viscarret
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Waleed Al-Harden
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Osama Aldahamsheh
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
- Orthopedic Department, Al-Balqa Applied University, As-Salt, Jordan
| | - Hasibagan Borjihan
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Amit Singla
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Simon Yaguare
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Janet Tingling
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Xiaolin Zi
- Department of Urology, University of California, Irvine Medical Center, Orange, CA, USA
| | - Yungtai Lo
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Richard Gorlick
- Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edward L Schwartz
- Departments of Oncology, Molecular Pharmacology, and Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hongling Zhao
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rui Yang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - David S Geller
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deyou Zheng
- Departments of Genetics, Neurology and Neuroscience. Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Bang H Hoang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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Hoffman JA, Muse GW, Langer LF, Patterson AI, Gandara I, Ward JM, Archer TK. BRG1 establishes the neuroectodermal chromatin landscape to restrict dorsal cell fates. SCIENCE ADVANCES 2024; 10:eadj5107. [PMID: 38427725 PMCID: PMC10906928 DOI: 10.1126/sciadv.adj5107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
Cell fate decisions are achieved with gene expression changes driven by lineage-specific transcription factors (TFs). These TFs depend on chromatin remodelers including the Brahma-related gene 1 (BRG1)-associated factor (BAF) complex to activate target genes. BAF complex subunits are essential for development and frequently mutated in cancer. Thus, interrogating how BAF complexes contribute to cell fate decisions is critical for human health. We examined the requirement for the catalytic BAF subunit BRG1 in neural progenitor cell (NPC) specification from human embryonic stem cells. During the earliest stages of differentiation, BRG1 was required to establish chromatin accessibility at neuroectoderm-specific enhancers. Depletion of BRG1 dorsalized NPCs and promoted precocious neural crest specification and enhanced neuronal differentiation. These findings demonstrate that BRG1 mediates NPC specification by ensuring proper expression of lineage-specific TFs and appropriate activation of their transcriptional programs.
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Affiliation(s)
- Jackson A. Hoffman
- Epigenetics and Stem Cell Biology Laboratory, National Institutes of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Ginger W. Muse
- Epigenetics and Stem Cell Biology Laboratory, National Institutes of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Lee F. Langer
- Epigenetics and Stem Cell Biology Laboratory, National Institutes of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - A. Isabella Patterson
- Epigenetics and Stem Cell Biology Laboratory, National Institutes of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Isabella Gandara
- Epigenetics and Stem Cell Biology Laboratory, National Institutes of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - James M. Ward
- Integrative Bioinformatics, National Institutes of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Trevor K. Archer
- Epigenetics and Stem Cell Biology Laboratory, National Institutes of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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Stoltze UK, Foss-Skiftesvik J, Hansen TVO, Rasmussen S, Karczewski KJ, Wadt KAW, Schmiegelow K. The evolutionary impact of childhood cancer on the human gene pool. Nat Commun 2024; 15:1881. [PMID: 38424437 PMCID: PMC10904397 DOI: 10.1038/s41467-024-45975-9] [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: 03/16/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Germline pathogenic variants associated with increased childhood mortality must be subject to natural selection. Here, we analyze publicly available germline genetic metadata from 4,574 children with cancer [11 studies; 1,083 whole exome sequences (WES), 1,950 whole genome sequences (WGS), and 1,541 gene panel] and 141,456 adults [125,748 WES and 15,708 WGS]. We find that pediatric cancer predisposition syndrome (pCPS) genes [n = 85] are highly constrained, harboring only a quarter of the loss-of-function variants that would be expected. This strong indication of selective pressure on pCPS genes is found across multiple lines of germline genomics data from both pediatric and adult cohorts. For six genes [ELP1, GPR161, VHL and SDHA/B/C], a clear lack of mutational constraint calls the pediatric penetrance and/or severity of associated cancers into question. Conversely, out of 23 known pCPS genes associated with biallelic risk, two [9%, DIS3L2 and MSH2] show significant constraint, indicating that they may monoallelically increase childhood cancer risk. In summary, we show that population genetic data provide empirical evidence that heritable childhood cancer leads to natural selection powerful enough to have significantly impacted the present-day gene pool.
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Affiliation(s)
- Ulrik Kristoffer Stoltze
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark.
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark.
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Merkin Building, 415 Main St, Cambridge, MA, 02142, USA.
| | - Jon Foss-Skiftesvik
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark
- Department of Neurosurgery, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Merkin Building, 415 Main St, Cambridge, MA, 02142, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, 55 Fruit St, Boston, MA, 02114, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit St, Boston, MA, 02114, USA
| | - Karin A W Wadt
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark.
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Filipek-Gorzała J, Kwiecińska P, Szade A, Szade K. The dark side of stemness - the role of hematopoietic stem cells in development of blood malignancies. Front Oncol 2024; 14:1308709. [PMID: 38440231 PMCID: PMC10910019 DOI: 10.3389/fonc.2024.1308709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/02/2024] [Indexed: 03/06/2024] Open
Abstract
Hematopoietic stem cells (HSCs) produce all blood cells throughout the life of the organism. However, the high self-renewal and longevity of HSCs predispose them to accumulate mutations. The acquired mutations drive preleukemic clonal hematopoiesis, which is frequent among elderly people. The preleukemic state, although often asymptomatic, increases the risk of blood cancers. Nevertheless, the direct role of preleukemic HSCs is well-evidenced in adult myeloid leukemia (AML), while their contribution to other hematopoietic malignancies remains less understood. Here, we review the evidence supporting the role of preleukemic HSCs in different types of blood cancers, as well as present the alternative models of malignant evolution. Finally, we discuss the clinical importance of preleukemic HSCs in choosing the therapeutic strategies and provide the perspective on further studies on biology of preleukemic HSCs.
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Affiliation(s)
- Jadwiga Filipek-Gorzała
- Laboratory of Stem Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Patrycja Kwiecińska
- Laboratory of Stem Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Agata Szade
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Krzysztof Szade
- Laboratory of Stem Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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Wachter F, Pikman Y. Pathophysiology of Acute Myeloid Leukemia. Acta Haematol 2024; 147:229-246. [PMID: 38228114 DOI: 10.1159/000536152] [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: 07/25/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is a biologically heterogenous disease arising in clonally proliferating hematopoietic stem cells. Sequential acquisition of mutations leads to expanded proliferation of clonal myeloid progenitors and failure of differentiation, leading to fulminant AML. SUMMARY Here, we review the pathophysiology of AML with a focus on factors predisposing to AML development, including prior chemo- and radiation therapy, environmental factors, and germline predisposition. KEY MESSAGE Increasing genomic characterization of AML and insight into mechanisms of its development will be critical to improvement in AML prognostication and therapy.
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Affiliation(s)
- Franziska Wachter
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA
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Kolekar P, Balagopal V, Dong L, Liu Y, Foy S, Tran Q, Mulder H, Huskey AL, Plyler E, Liang Z, Ma J, Nakitandwe J, Gu J, Namwanje M, Maciaszek J, Payne-Turner D, Mallampati S, Wang L, Easton J, Klco JM, Ma X. SJPedPanel: A pan-cancer gene panel for childhood malignancies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.27.23299068. [PMID: 38076942 PMCID: PMC10705664 DOI: 10.1101/2023.11.27.23299068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Background Large scale genomics projects have identified driver alterations for most childhood cancers that provide reliable biomarkers for clinical diagnosis and disease monitoring using targeted sequencing. However, there is lack of a comprehensive panel that matches the list of known driver genes. Here we fill this gap by developing SJPedPanel for childhood cancers. Results SJPedPanel covers 5,275 coding exons of 357 driver genes, 297 introns frequently involved in rearrangements that generate fusion oncoproteins, commonly amplified/deleted regions (e.g., MYCN for neuroblastoma, CDKN2A and PAX5 for B-/T-ALL, and SMARCB1 for AT/RT), and 7,590 polymorphism sites for interrogating tumors with aneuploidy, such as hyperdiploid and hypodiploid B-ALL or 17q gain neuroblastoma. We used driver alterations reported from an established real-time clinical genomics cohort (n=253) to validate this gene panel. Among the 485 pathogenic variants reported, our panel covered 417 variants (86%). For 90 rearrangements responsible for oncogenic fusions, our panel covered 74 events (82%). We re-sequenced 113 previously characterized clinical specimens at an average depth of 2,500X using SJPedPanel and recovered 354 (91%) of the 389 reported pathogenic variants. We then investigated the power of this panel in detecting mutations from specimens with low tumor purity (as low as 0.1%) using cell line-based dilution experiments and discovered that this gene panel enabled us to detect ∼80% variants with allele fraction of 0.2%, while the detection rate decreases to ∼50% when the allele fraction is 0.1%. We finally demonstrate its utility in disease monitoring on clinical specimens collected from AML patients in morphologic remission. Conclusions SJPedPanel enables the detection of clinically relevant genetic alterations including rearrangements responsible for subtype-defining fusions for childhood cancers by targeted sequencing of ∼0.15% of human genome. It will enhance the analysis of specimens with low tumor burdens for cancer monitoring and early detection.
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Zhang M, Wei T, Guo D. The role of abnormal ubiquitination in hepatocellular carcinoma pathology. Cell Signal 2024; 114:110994. [PMID: 38036196 DOI: 10.1016/j.cellsig.2023.110994] [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: 09/13/2023] [Revised: 11/17/2023] [Accepted: 11/23/2023] [Indexed: 12/02/2023]
Abstract
Primary liver cancer is known for its high incidence and fatality rate. Over the years, therapeutic strategies for primary liver cancer have advanced significantly. Nonetheless, a substantial number of patients have not benefited from these methods, underscoring the pressing need for new and effective treatments for primary liver cancer. Ubiquitination is a critical post-translational modification that enables proteins to fulfill their normal biological functions and maintain their expression stability within cells. Importantly, increasing evidence suggests that the progression of liver cancer cells is often accompanied by disruptions in protein ubiquitination and deubiquitination processes. In this comprehensive review, we have compiled pertinent research about dysregulated ubiquitination in hepatocellular carcinoma (HCC) to broaden our understanding in this field. We elucidate the connections between the ubiquitination proteasome system, deubiquitination, and HCC. Furthermore, we shed light on the role of ubiquitination in cells situated within the tumor microenvironment of HCC including its involvement in mediating the activation of oncogenic pathways, reprogramming metabolic processes, and perturbing normal cellular functions. In conclusion, targeting the dysregulation of ubiquitination in HCC holds promise as a prospective and complementary therapeutic approach to existing treatments.
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Affiliation(s)
- Ming Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China; Henan Key Laboratory for Digestive Organ Transplantation, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Tingju Wei
- Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Danfeng Guo
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China; Henan Key Laboratory for Digestive Organ Transplantation, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China.
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Ferrena A, Wang J, Zhang R, Karadal-Ferrena B, Al-Hardan W, Singh S, Borjihan H, Schwartz EL, Zhao H, Oktay MH, Yang R, Geller DS, Hoang BH, Zheng D. SKP2 Knockout in Rb1/p53-Deficient Mouse Models of Osteosarcoma Induces Immune Infiltration and Drives a Transcriptional Program with a Favorable Prognosis. Mol Cancer Ther 2024; 23:223-234. [PMID: 37871911 PMCID: PMC10842346 DOI: 10.1158/1535-7163.mct-23-0173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/27/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023]
Abstract
Osteosarcoma is an aggressive bone malignancy with a poor prognosis. One putative proto-oncogene in osteosarcoma is SKP2, encoding a substrate recognition factor of the SCF E3 ubiquitin ligase. We previously demonstrated that Skp2 knockout in murine osteosarcoma improved survival and delayed tumorigenesis. Here, we performed RNA sequencing (RNA-seq) on tumors from a transgenic osteosarcoma mouse model with conditional Trp53 and Rb1 knockouts in the osteoblast lineage ("DKO": Osx1-Cre;Rb1lox/lox;p53lox/lox) and a triple-knockout model with additional Skp2 germline knockout ("TKO": Osx1-Cre;Rb1lox/lox;p53lox/lox;Skp2-/-), followed by qPCR and immunohistochemistry validation. To investigate the clinical implications of our results, we analyzed a human osteosarcoma patient cohort ("NCI-TARGET OS") with RNA-seq and clinical data. We found large differences in gene expression after SKP2 knockout. Surprisingly, we observed increased expression of genes related to immune microenvironment infiltration in TKO tumors, especially the signature genes for macrophages and to a lesser extent, T cells, B cells, and vascular cells. We also uncovered a set of relevant transcription factors that may mediate these changes. In osteosarcoma patient cohorts, high expression of genes upregulated in TKO was correlated with favorable overall survival, which was largely explained by the macrophage gene signatures. This relationship was further supported by our finding that SKP2 expression was negatively correlated with macrophage infiltration in the NCI-TARGET osteosarcoma and the TCGA Sarcoma cohorts. Overall, our findings indicate that SKP2 may mediate immune exclusion from the osteosarcoma tumor microenvironment, suggesting that SKP2 modulation in osteosarcoma may induce antitumor immune activation.
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Affiliation(s)
- Alexander Ferrena
- Institute for Clinical and Translational Research, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jichuan Wang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ranxin Zhang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Waleed Al-Hardan
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Swapnil Singh
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hasibagan Borjihan
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Edward L. Schwartz
- Department of Oncology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hongling Zhao
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Maja H. Oktay
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
- Gruss-Lipper Biophotonics Center, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
- Integrated Imaging Program, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rui Yang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - David S Geller
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bang H Hoang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
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Buckley J, Schmidt RJ, Ostrow D, Maglinte D, Bootwalla M, Ruble D, Govindarajan A, Ji J, Kovach AE, Orgel E, Raca G, Navid F, Mascarenhas L, Pawel B, Robison N, Gai X, Biegel JA. An Exome Capture-Based RNA-Sequencing Assay for Genome-Wide Identification and Prioritization of Clinically Important Fusions in Pediatric Tumors. J Mol Diagn 2024; 26:127-139. [PMID: 38008288 DOI: 10.1016/j.jmoldx.2023.11.003] [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: 10/10/2022] [Revised: 08/14/2023] [Accepted: 11/07/2023] [Indexed: 11/28/2023] Open
Abstract
This study reports the development of an exome capture-based RNA-sequencing assay to detect recurring and novel fusions in hematologic, solid, and central nervous system tumors. The assay used Twist Comprehensive Exome capture with either fresh or formalin-fixed samples and a bioinformatic platform that provides fusion detection, prioritization, and downstream curation. A minimum of 50 million uniquely mapped reads, a consensus read alignment/fusion calling approach using four callers (Arriba, FusionCatcher, STAR-Fusion, and Dragen), and custom software were used to integrate, annotate, and rank the candidate fusion calls. In an evaluation of 50 samples, the number of calls varied substantially by caller, from a mean of 24.8 with STAR-Fusion to 259.6 with FusionCatcher; only 1.1% of calls were made by all four callers. Therefore a filtering and ranking algorithm was developed based on multiple criteria, including number of supporting reads, calling consensus, genes involved, and cross-reference against databases of known cancer-associated or likely false-positive fusions. This approach was highly effective in pinpointing known clinically relevant fusions, ranking them first in 47 of 50 samples (94%). Detection of pathogenic gene fusions in three diagnostically challenging cases highlights the importance of a genome-wide and nontargeted method for fusion detection in pediatric cancer.
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Affiliation(s)
- Jonathan Buckley
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Ryan J Schmidt
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Dejerianne Ostrow
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Dennis Maglinte
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Moiz Bootwalla
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - David Ruble
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Ananthanarayanan Govindarajan
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Jianling Ji
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Alexandra E Kovach
- Keck School of Medicine of University of Southern California, Los Angeles, California; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Etan Orgel
- Keck School of Medicine of University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Gordana Raca
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Fariba Navid
- Keck School of Medicine of University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Leo Mascarenhas
- Keck School of Medicine of University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Bruce Pawel
- Keck School of Medicine of University of Southern California, Los Angeles, California; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Nathan Robison
- Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Jaclyn A Biegel
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California.
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Lim WC, Marques Da Costa ME, Godefroy K, Jacquet E, Gragert L, Rondof W, Marchais A, Nhiri N, Dalfovo D, Viard M, Labaied N, Khan AM, Dessen P, Romanel A, Pasqualini C, Schleiermacher G, Carrington M, Zitvogel L, Scoazec JY, Geoerger B, Salmon J. Divergent HLA variations and heterogeneous expression but recurrent HLA loss-of- heterozygosity and common HLA-B and TAP transcriptional silencing across advanced pediatric solid cancers. Front Immunol 2024; 14:1265469. [PMID: 38318504 PMCID: PMC10839790 DOI: 10.3389/fimmu.2023.1265469] [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: 07/22/2023] [Accepted: 11/06/2023] [Indexed: 02/07/2024] Open
Abstract
The human leukocyte antigen (HLA) system is a major factor controlling cancer immunosurveillance and response to immunotherapy, yet its status in pediatric cancers remains fragmentary. We determined high-confidence HLA genotypes in 576 children, adolescents and young adults with recurrent/refractory solid tumors from the MOSCATO-01 and MAPPYACTS trials, using normal and tumor whole exome and RNA sequencing data and benchmarked algorithms. There was no evidence for narrowed HLA allelic diversity but discordant homozygosity and allele frequencies across tumor types and subtypes, such as in embryonal and alveolar rhabdomyosarcoma, neuroblastoma MYCN and 11q subtypes, and high-grade glioma, and several alleles may represent protective or susceptibility factors to specific pediatric solid cancers. There was a paucity of somatic mutations in HLA and antigen processing and presentation (APP) genes in most tumors, except in cases with mismatch repair deficiency or genetic instability. The prevalence of loss-of-heterozygosity (LOH) ranged from 5.9 to 7.7% in HLA class I and 8.0 to 16.7% in HLA class II genes, but was widely increased in osteosarcoma and glioblastoma (~15-25%), and for DRB1-DQA1-DQB1 in Ewing sarcoma (~23-28%) and low-grade glioma (~33-50%). HLA class I and HLA-DR antigen expression was assessed in 194 tumors and 44 patient-derived xenografts (PDXs) by immunochemistry, and class I and APP transcript levels quantified in PDXs by RT-qPCR. We confirmed that HLA class I antigen expression is heterogeneous in advanced pediatric solid tumors, with class I loss commonly associated with the transcriptional downregulation of HLA-B and transporter associated with antigen processing (TAP) genes, whereas class II antigen expression is scarce on tumor cells and occurs on immune infiltrating cells. Patients with tumors expressing sufficient HLA class I and TAP levels such as some glioma, osteosarcoma, Ewing sarcoma and non-rhabdomyosarcoma soft-tissue sarcoma cases may more likely benefit from T cell-based approaches, whereas strategies to upregulate HLA expression, to expand the immunopeptidome, and to target TAP-independent epitopes or possibly LOH might provide novel therapeutic opportunities in others. The consequences of HLA class II expression by immune cells remain to be established. Immunogenetic profiling should be implemented in routine to inform immunotherapy trials for precision medicine of pediatric cancers.
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Affiliation(s)
- Wan Ching Lim
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
| | | | - Karine Godefroy
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Loren Gragert
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Windy Rondof
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Naima Nhiri
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Davide Dalfovo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Mathias Viard
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Nizar Labaied
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Asif M. Khan
- School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
| | - Philippe Dessen
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Alessandro Romanel
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Claudia Pasqualini
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Gudrun Schleiermacher
- INSERM U830, Recherche Translationnelle en Oncologie Pédiatrique (RTOP), and SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), PSL Research University, Institut Curie, Paris, France
| | - Mary Carrington
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, United States
| | - Laurence Zitvogel
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Jean-Yves Scoazec
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Birgit Geoerger
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Jerome Salmon
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
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Wang S, Jiang Y, Zheng R, Yu Y, Wei W, Li N. Mobilizing China and the Global Community to Confront the Treatment Desert for Pediatric Solid Tumors. Cancer Discov 2024; 14:26-29. [PMID: 38213295 PMCID: PMC10784741 DOI: 10.1158/2159-8290.cd-23-0451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
SUMMARY Pediatric solid tumors are distinct clinical entities that impose heavy socioeconomic burden and while their incidence has increased in recent years, treatment options are often limited, with only 27 drugs approved for pediatric solid tumors in the United States, and fewer still, 13, in China. The scale of the unmet medical need is immense and new efforts are urgently needed to develop efficient therapeutics and improve these children's lives.
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Affiliation(s)
- Shuhang Wang
- Clinical Trial Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yale Jiang
- Clinical Trial Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rongshou Zheng
- National Central Cancer Registry, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Yu
- Clinical Trial Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenqiang Wei
- National Central Cancer Registry, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ning Li
- Clinical Trial Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Randall MP, Egolf LE, Vaksman Z, Samanta M, Tsang M, Groff D, Evans JP, Rokita JL, Layeghifard M, Shlien A, Maris JM, Diskin SJ, Bosse KR. BARD1 germline variants induce haploinsufficiency and DNA repair defects in neuroblastoma. J Natl Cancer Inst 2024; 116:138-148. [PMID: 37688570 PMCID: PMC10777668 DOI: 10.1093/jnci/djad182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND High-risk neuroblastoma is a complex genetic disease that is lethal in more than 50% of patients despite intense multimodal therapy. Through genome-wide association studies (GWAS) and next-generation sequencing, we have identified common single nucleotide polymorphisms and rare, pathogenic or likely pathogenic germline loss-of-function variants in BARD1 enriched in neuroblastoma patients. The functional implications of these findings remain poorly understood. METHODS We correlated BARD1 genotype with expression in normal tissues and neuroblastomas, along with the burden of DNA damage in tumors. To validate the functional consequences of germline pathogenic or likely pathogenic BARD1 variants, we used CRISPR-Cas9 to generate isogenic neuroblastoma (IMR-5) and control (RPE1) cellular models harboring heterozygous BARD1 loss-of-function variants (R112*, R150*, E287fs, and Q564*) and quantified genomic instability in these cells via next-generation sequencing and with functional assays measuring the efficiency of DNA repair. RESULTS Both common and rare neuroblastoma-associated BARD1 germline variants were associated with lower levels of BARD1 mRNA and an increased burden of DNA damage. Using isogenic heterozygous BARD1 loss-of-function variant cellular models, we functionally validated this association with inefficient DNA repair. BARD1 loss-of-function variant isogenic cells exhibited reduced efficiency in repairing Cas9-induced DNA damage, ineffective RAD51 focus formation at DNA double-strand break sites, and enhanced sensitivity to cisplatin and poly (ADP-ribose) polymerase (PARP) inhibition both in vitro and in vivo. CONCLUSIONS Taken together, we demonstrate that germline BARD1 variants disrupt DNA repair fidelity. This is a fundamental molecular mechanism contributing to neuroblastoma initiation that may have important therapeutic implications.
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Affiliation(s)
- Michael P Randall
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura E Egolf
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Zalman Vaksman
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Current affiliation: New York Genome Center, New York, NY
| | - Minu Samanta
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Matthew Tsang
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - David Groff
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - J Perry Evans
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Current affiliation: Genomics and Data Sciences, Spark Therapeutics, Philadelphia, PA
| | - Jo Lynne Rokita
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mehdi Layeghifard
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Adam Shlien
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Sharon J Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Kristopher R Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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Liu CH, Lai YL, Shen PC, Liu HC, Tsai MH, Wang YD, Lin WJ, Chen FH, Li CY, Wang SC, Hung MC, Cheng WC. DriverDBv4: a multi-omics integration database for cancer driver gene research. Nucleic Acids Res 2024; 52:D1246-D1252. [PMID: 37956338 PMCID: PMC10767848 DOI: 10.1093/nar/gkad1060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/12/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Advancements in high-throughput technology offer researchers an extensive range of multi-omics data that provide deep insights into the complex landscape of cancer biology. However, traditional statistical models and databases are inadequate to interpret these high-dimensional data within a multi-omics framework. To address this limitation, we introduce DriverDBv4, an updated iteration of the DriverDB cancer driver gene database (http://driverdb.bioinfomics.org/). This updated version offers several significant enhancements: (i) an increase in the number of cohorts from 33 to 70, encompassing approximately 24 000 samples; (ii) inclusion of proteomics data, augmenting the existing types of omics data and thus expanding the analytical scope; (iii) implementation of multiple multi-omics algorithms for identification of cancer drivers; (iv) new visualization features designed to succinctly summarize high-context data and redesigned existing sections to accommodate the increased volume of datasets and (v) two new functions in Customized Analysis, specifically designed for multi-omics driver identification and subgroup expression analysis. DriverDBv4 facilitates comprehensive interpretation of multi-omics data across diverse cancer types, thereby enriching the understanding of cancer heterogeneity and aiding in the development of personalized clinical approaches. The database is designed to foster a more nuanced understanding of the multi-faceted nature of cancer.
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Affiliation(s)
- Chia-Hsin Liu
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
| | - Yo-Liang Lai
- Department of Radiation Oncology, China Medical University, Taichung 404328, Taiwan
| | - Pei-Chun Shen
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
| | - Hsiu-Cheng Liu
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
| | - Meng-Hsin Tsai
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
| | - Yu-De Wang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404328, Taiwan
- Department of Urology, China Medical University, Taichung 404328, Taiwan
| | - Wen-Jen Lin
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
- School of Medicine, China Medical University, Taichung 404328, Taiwan
| | - Fang-Hsin Chen
- Institute of Nuclear Engineering and Science, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Chia-Yang Li
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Shu-Chi Wang
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Mien-Chie Hung
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404328, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung 404328, Taiwan
- Molecular Medicine Center, China Medical University Hospital, China Medical University, Taichung 404328, Taiwan
- Department of Biotechnology, Asia University, Taichung 413305, Taiwan
| | - Wei-Chung Cheng
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404328, Taiwan
- The Ph.D. program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung 404328, Taiwan
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Quesnel-Vallières M, Jewell S, Lynch KW, Thomas-Tikhonenko A, Barash Y. MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer. Nucleic Acids Res 2024; 52:D213-D221. [PMID: 37953365 PMCID: PMC10767883 DOI: 10.1093/nar/gkad1043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023] Open
Abstract
Quantification of RNA splicing variations based on RNA-Sequencing can reveal tissue- and disease-specific splicing patterns. To study such splicing variations, we introduce MAJIQlopedia, an encyclopedia of splicing variations that encompasses 86 human tissues and 41 cancer datasets. MAJIQlopedia reports annotated and unannotated splicing events for a total of 486 175 alternative splice junctions in normal tissues and 338 317 alternative splice junctions in cancer. This database, available at https://majiq.biociphers.org/majiqlopedia/, includes a user-friendly interface that provides graphical representations of junction usage quantification for each junction across all tissue or cancer types. To demonstrate case usage of MAJIQlopedia, we review splicing variations in genes WT1, MAPT and BIN1, which all have known tissue or cancer-specific splicing variations. We also use MAJIQlopedia to highlight novel splicing variations in FDX1 and MEGF9 in normal tissues, and we uncover a novel exon inclusion event in RPS6KA6 that only occurs in two cancer types. Users can download the database, request the addition of data to the webtool, or install a MAJIQlopedia server to integrate proprietary data. MAJIQlopedia can serve as a reference database for researchers seeking to understand what splicing variations exist in genes of interest, and those looking to understand tissue- or cancer-specific splice isoform usage.
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Affiliation(s)
- Mathieu Quesnel-Vallières
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - San Jewell
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yoseph Barash
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA
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Wang Y, Jiang H, Fu L, Guan L, Yang J, Ren J, Liu F, Li X, Ma X, Li Y, Cai H. Prognostic value and immunological role of PD-L1 gene in pan-cancer. BMC Cancer 2024; 24:20. [PMID: 38166842 PMCID: PMC10763229 DOI: 10.1186/s12885-023-11267-6] [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: 02/09/2023] [Accepted: 08/07/2023] [Indexed: 01/05/2024] Open
Abstract
OBJECTIVE PD-L1, a target of immune checkpoint blockade, has been proven to take the role of an oncogene in most human tumors. However, the role of PD-L1 in human pan-cancers has not yet been fully investigated. MATERIALS AND METHODS Pan-cancer analysis was conducted to analyze expression, genetic alterations, prognosis analysis, and immunological characteristics of PD-L1. Estimating the correlation between PD-L1 expression and survival involved using pooled odds ratios and hazard ratios with 95% CI. The Kaplan-Meier (K-M) technique, COX analysis, and receiver operating characteristic (ROC) curves were applied to the survival analysis. Additionally, we investigated the relationships between PD-L1 and microsatellite instability (MSI), tumor mutational burden (TMB), DNA methyltransferases (DNMTs), the associated genes of mismatch repair (MMR), and immune checkpoint biomarkers using Spearman's correlation analysis. Also, immunohistochemical analysis and qRT-PCR were employed in evaluating PD-L1's protein and mRNA expression in pan-caner. RESULTS PD-L1 showed abnormal mRNA and protein expression in a variety of cancers and predicted prognosis in cancer patients. Furthermore, across a variety of cancer types, the aberrant PD-L1 expression was connected to the MSI, MMR, TMB, drug sensitivity, and tumor immune microenvironment (TIME). Moreover, PD-L1 was significantly correlated with infiltrating levels of immune cells (T cell CD8 + , neutrophil, and so on). CONCLUSION Our study provides a better theoretical basis and guidance for the clinical treatment of PD-L1.
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Affiliation(s)
- Yongfeng Wang
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, 730000, China
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, Gansu, 730000, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Gansu, 730000, China
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, 204 Donggang West Road, Lanzhou, Gansu, 730000, China
| | - Hong Jiang
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Liangyin Fu
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, Gansu, 730000, China
| | - Ling Guan
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Jiaxin Yang
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Jingyao Ren
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, Gansu, 730000, China
| | - Fangyu Liu
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Xiangyang Li
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Xuhui Ma
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, Gansu, 730000, China
| | - Yonghong Li
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, 204 Donggang West Road, Lanzhou, Gansu, 730000, China.
| | - Hui Cai
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, 730000, China.
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, Gansu, 730000, China.
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Gansu, 730000, China.
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, 204 Donggang West Road, Lanzhou, Gansu, 730000, China.
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Calderon A, Han C, Karma S, Wang E. Non-genetic mechanisms of drug resistance in acute leukemias. Trends Cancer 2024; 10:38-51. [PMID: 37839973 DOI: 10.1016/j.trecan.2023.09.003] [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: 06/20/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023]
Abstract
Acute leukemia is characterized by clonal heterogeneity that contributes to poor drug responses in patients. Despite treatment advances, the occurrence of relapse remains a major barrier to achieving cures as current therapeutic approaches are inadequate to effectively prevent or overcome resistance. Given that only a few genetic mutations are associated with relapse in acute leukemia patients, there is a growing focus on 'non-genetic' mechanisms that affect the hallmarks of cancer to allow leukemic cells to survive post therapy. In this review, we provide an overview of the therapeutic landscape in acute leukemias. Importantly, we discuss non-genetic mechanisms exploited by leukemic cells to promote their survival after treatment. Last, we present current strategies to prevent or overcome drug resistance in this disease.
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Affiliation(s)
| | - Cuijuan Han
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Sadik Karma
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Graduate Program in Genetics and Development, UConn Health, Farmington, CT, USA
| | - Eric Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA; Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
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