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Tau S, Chamberlin MD, Yang H, Marotti JD, Roberts AM, Carmichael MM, Cressey L, Dragnev C, Demidenko E, Hampsch RA, Soucy SM, Kolling F, Samkoe KS, Alvarez JV, Kettenbach AN, Miller TW. Endocrine persistence in ER+ breast cancer is accompanied by metabolic vulnerability in oxidative phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.26.615177. [PMID: 39386444 PMCID: PMC11463551 DOI: 10.1101/2024.09.26.615177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Despite adjuvant treatment with endocrine therapies, estrogen receptor-positive (ER+) breast cancers recur in a significant proportion of patients. Recurrences are attributable to clinically undetectable endocrine-tolerant persister cancer cells that retain tumor-forming potential. Therefore, strategies targeting such persister cells may prevent recurrent disease. Using CRISPR-Cas9 genome-wide knockout screening in ER+ breast cancer cells, we identified a survival mechanism involving metabolic reprogramming with reliance upon mitochondrial respiration in endocrine-tolerant persister cells. Quantitative proteomic profiling showed reduced levels of glycolytic proteins in persisters. Metabolic tracing of glucose revealed an energy-depleted state in persisters where oxidative phosphorylation was required to generate ATP. A phase II clinical trial was conducted to evaluate changes in mitochondrial markers in primary ER+/HER2-breast tumors induced by neoadjuvant endocrine therapy ( NCT04568616 ). In an analysis of tumor specimens from 32 patients, tumors exhibiting residual cell proliferation after aromatase inhibitor-induced estrogen deprivation with letrozole showed increased mitochondrial content. Genetic profiling and barcode lineage tracing showed that endocrine-tolerant persistence occurred stochastically without genetic predisposition. Mice bearing cell line- and patient-derived xenografts were used to measure the anti-tumor effects of mitochondrial complex I inhibition in the context of endocrine therapy. Pharmacological inhibition of complex I suppressed the tumor-forming potential of persisters and synergized with the anti-estrogen fulvestrant to induce regression of patient-derived xenografts. These findings indicate that mitochondrial metabolism is essential in endocrine-tolerant persister ER+ breast cancer cells and warrant the development of treatment strategies to leverage this vulnerability in the context of endocrine-sensitive disease. Statement of Significance Endocrine-tolerant persister cancer cells that survive endocrine therapy can cause recurrent disease. Persister cells exhibit increased energetic dependence upon mitochondria for survival and tumor re-growth potential.
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Zhu J, Zhao Z, Li S, Zhou Y, Kong L, Fu X, Li H, Feng J, Tang W, Wu D, Kong X. High-Resolution Haplotyping of the PAH Gene Enables Early Gestation Noninvasive Prenatal Diagnosis of Phenylketonuria and Evolution Analysis of Recurrent Pathogenic Variations. Prenat Diagn 2024. [PMID: 39153191 DOI: 10.1002/pd.6645] [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: 03/13/2024] [Revised: 07/21/2024] [Accepted: 07/26/2024] [Indexed: 08/19/2024]
Abstract
BACKGROUND The clinical performance of RHDO-based NIPD for PKU during early gestation remains under-evaluated. Furthermore, studies focused on SNP loci obtained by next-generation sequencing to analyze the genetic evolution of pathogenic variations in PKU is limited. METHODS Maternal peripheral blood, along with proband and paternal samples, was collected between 7 and 12 weeks of gestation. The PAH gene and surrounding high heterozygosity SNPs were targeted for enrichment and sequencing. Fetal genotypes were inferred using RHDO-based NIPD. High-resolution PAH haplotypes were used for the analysis of two common pathogenic variants in the Chinese population: c.728G>A and c.1238G>C. RESULTS Sixty one PKU families participated with an average fetal fraction of 6.08%. The median gestational age was 8+6 weeks. RHDO-based NIPD successfully identified fetal genotypes in 59 cases (96.72%, 59/62). Two cases failed because of insufficient informative SNPs. In addition, a recombination event was assessed in one fetus of 59 cases. Six, and three haplotypes were identified for c.728G>A(p.Arg243Gln) and c.1238G>C(p.Arg413Pro), respectively. Hap_3 and hap_8 were identified as the ancestral haplotypes for these pathogenic variants, with other haplotypes arising from mutations or recombination based on these ancestral haplotypes. CONCLUSIONS This study validates the feasibility of an RHDO-based assay for NIPD of PKU in early pregnancy and introduces its application in the demonstration of founder effects in recurrent pathogenic variations, offering new insights into the evolutionary analysis of PAH variations.
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Affiliation(s)
- Jingqi Zhu
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Zhao
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shaojun Li
- Celula (China) Medical Technology Co., Ltd, Chengdu, China
| | - Yifan Zhou
- Celula (China) Medical Technology Co., Ltd, Chengdu, China
| | - Lingrong Kong
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xinyu Fu
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huanyun Li
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Feng
- Celula (China) Medical Technology Co., Ltd, Chengdu, China
| | - Weiqin Tang
- Celula (China) Medical Technology Co., Ltd, Chengdu, China
| | - Di Wu
- Celula (China) Medical Technology Co., Ltd, Chengdu, China
| | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Schupp PG, Shelton SJ, Brody DJ, Eliscu R, Johnson BE, Mazor T, Kelley KW, Potts MB, McDermott MW, Huang EJ, Lim DA, Pieper RO, Berger MS, Costello JF, Phillips JJ, Oldham MC. Deconstructing Intratumoral Heterogeneity through Multiomic and Multiscale Analysis of Serial Sections. Cancers (Basel) 2024; 16:2429. [PMID: 39001492 PMCID: PMC11240479 DOI: 10.3390/cancers16132429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Tumors may contain billions of cells, including distinct malignant clones and nonmalignant cell types. Clarifying the evolutionary histories, prevalence, and defining molecular features of these cells is essential for improving clinical outcomes, since intratumoral heterogeneity provides fuel for acquired resistance to targeted therapies. Here we present a statistically motivated strategy for deconstructing intratumoral heterogeneity through multiomic and multiscale analysis of serial tumor sections (MOMA). By combining deep sampling of IDH-mutant astrocytomas with integrative analysis of single-nucleotide variants, copy-number variants, and gene expression, we reconstruct and validate the phylogenies, spatial distributions, and transcriptional profiles of distinct malignant clones. By genotyping nuclei analyzed by single-nucleus RNA-seq for truncal mutations, we further show that commonly used algorithms for identifying cancer cells from single-cell transcriptomes may be inaccurate. We also demonstrate that correlating gene expression with tumor purity in bulk samples can reveal optimal markers of malignant cells and use this approach to identify a core set of genes that are consistently expressed by astrocytoma truncal clones, including AKR1C3, whose expression is associated with poor outcomes in several types of cancer. In summary, MOMA provides a robust and flexible strategy for precisely deconstructing intratumoral heterogeneity and clarifying the core molecular properties of distinct cellular populations in solid tumors.
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Affiliation(s)
- Patrick G. Schupp
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Samuel J. Shelton
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Daniel J. Brody
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Rebecca Eliscu
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Brett E. Johnson
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Tali Mazor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kevin W. Kelley
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew B. Potts
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Michael W. McDermott
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Eric J. Huang
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA;
| | - Daniel A. Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Russell O. Pieper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Mitchel S. Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Joseph F. Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Joanna J. Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA;
| | - Michael C. Oldham
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
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Fu X, Zhao Z, Kong L, Li S, Li F, Han X, Sun L, Wu D, Wang Y, Kong X. First-trimester noninvasive prenatal diagnosis of seven facioscapulohumeral muscular dystrophy type 1 families using SNP-based amplicon sequencing: An earlier, rapid and safer way. Am J Med Genet A 2024; 194:e63560. [PMID: 38329169 DOI: 10.1002/ajmg.a.63560] [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: 11/18/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 02/09/2024]
Abstract
The study is to explore the feasibility and value of SNP-based noninvasive prenatal diagnosis (NIPD) for facioscapulohumeral muscular dystrophy type 1 (FSHD1) in early pregnancy weeks. We prospectively collected seven FSHD1 families, with an average gestational age of 8+6. Among these seven couples, there were three affected FSHD1 mothers and four affected fathers. A multiplex-PCR panel comprising 402 amplicons was designed to selective enrich for highly heterozygous SNPs upstream of the DUX4 gene. Risk haplotype was constructed based on familial linkage analysis. Fetal genotypes were accurately inferred through relative haplotype dosage analysis using Bayes Factor. All tests were successfully completed in a single attempt, and no recombination events were detected. NIPD results were provided within a week, which is 4 weeks earlier than karyomapping and 7 weeks earlier than Bionano single-molecule optical mapping (BOM). Ultimately, five FSHD1 fetuses and two normal fetuses were successfully identified, with a 100% concordance rate with karyomapping and BOM. Therefore, SNP-based NIPD for FSHD1 was demonstrated to be feasible and accurate in early weeks of gestation, although the risk of recombination events cannot be completely eliminated. In the future, testing of more cases is still necessary to fully determine the clinical utility.
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Affiliation(s)
- Xinyu Fu
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Zhao
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lingrong Kong
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shaojun Li
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Feifei Li
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Xiujuan Han
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Luming Sun
- Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Di Wu
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Yanan Wang
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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5
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Zhang J, Wu L, Su T, Liu H, Jiang L, Jiang Y, Wu Z, Chen L, Li H, Zheng J, Sun Y, Peng H, Han R, Ning G, Ye L, Wang W. Pharmacogenomic analysis in adrenocortical carcinoma reveals genetic features associated with mitotane sensitivity and potential therapeutics. Front Endocrinol (Lausanne) 2024; 15:1365321. [PMID: 38779454 PMCID: PMC11109426 DOI: 10.3389/fendo.2024.1365321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
Background Adrenocortical carcinoma (ACC) is an aggressive endocrine malignancy with limited therapeutic options. Treating advanced ACC with mitotane, the cornerstone therapy, remains challenging, thus underscoring the significance to predict mitotane response prior to treatment and seek other effective therapeutic strategies. Objective We aimed to determine the efficacy of mitotane via an in vitro assay using patient-derived ACC cells (PDCs), identify molecular biomarkers associated with mitotane response and preliminarily explore potential agents for ACC. Methods In vitro mitotane sensitivity testing was performed in 17 PDCs and high-throughput screening against 40 compounds was conducted in 8 PDCs. Genetic features were evaluated in 9 samples using exomic and transcriptomic sequencing. Results PDCs exhibited variable sensitivity to mitotane treatment. The median cell viability inhibition rate was 48.4% (IQR: 39.3-59.3%) and -1.2% (IQR: -26.4-22.1%) in responders (n=8) and non-responders (n=9), respectively. Median IC50 and AUC were remarkably lower in responders (IC50: 53.4 µM vs 74.7 µM, P<0.0001; AUC: 158.0 vs 213.5, P<0.0001). Genomic analysis revealed CTNNB1 somatic alterations were only found in responders (3/5) while ZNRF3 alterations only in non-responders (3/4). Transcriptomic profiling found pathways associated with lipid metabolism were upregulated in responder tumors whilst CYP27A1 and ABCA1 expression were positively correlated to in vitro mitotane sensitivity. Furthermore, pharmacologic analysis identified that compounds including disulfiram, niclosamide and bortezomib exhibited efficacy against PDCs. Conclusion ACC PDCs could be useful for testing drug response, drug repurposing and guiding personalized therapies. Our results suggested response to mitotane might be associated with the dependency on lipid metabolism. CYP27A1 and ABCA1 expression could be predictive markers for mitotane response, and disulfiram, niclosamide and bortezomib could be potential therapeutics, both warranting further investigation.
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Affiliation(s)
- Jie Zhang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Luming Wu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tingwei Su
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haoyu Liu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Jiang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiran Jiang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyuan Wu
- Department of Interventional Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu Chen
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haorong Li
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingkai Sun
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hangya Peng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rulai Han
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang Ning
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Ye
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiqing Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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6
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Schupp PG, Shelton SJ, Brody DJ, Eliscu R, Johnson BE, Mazor T, Kelley KW, Potts MB, McDermott MW, Huang EJ, Lim DA, Pieper RO, Berger MS, Costello JF, Phillips JJ, Oldham MC. Deconstructing intratumoral heterogeneity through multiomic and multiscale analysis of serial sections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.21.545365. [PMID: 37645893 PMCID: PMC10461981 DOI: 10.1101/2023.06.21.545365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Tumors may contain billions of cells including distinct malignant clones and nonmalignant cell types. Clarifying the evolutionary histories, prevalence, and defining molecular features of these cells is essential for improving clinical outcomes, since intratumoral heterogeneity provides fuel for acquired resistance to targeted therapies. Here we present a statistically motivated strategy for deconstructing intratumoral heterogeneity through multiomic and multiscale analysis of serial tumor sections (MOMA). By combining deep sampling of IDH-mutant astrocytomas with integrative analysis of single-nucleotide variants, copy-number variants, and gene expression, we reconstruct and validate the phylogenies, spatial distributions, and transcriptional profiles of distinct malignant clones. By genotyping nuclei analyzed by single-nucleus RNA-seq for truncal mutations, we further show that commonly used algorithms for identifying cancer cells from single-cell transcriptomes may be inaccurate. We also demonstrate that correlating gene expression with tumor purity in bulk samples can reveal optimal markers of malignant cells and use this approach to identify a core set of genes that is consistently expressed by astrocytoma truncal clones, including AKR1C3, whose expression is associated with poor outcomes in several types of cancer. In summary, MOMA provides a robust and flexible strategy for precisely deconstructing intratumoral heterogeneity and clarifying the core molecular properties of distinct cellular populations in solid tumors.
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Affiliation(s)
- Patrick G. Schupp
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, California, USA
| | - Samuel J. Shelton
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Daniel J. Brody
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Rebecca Eliscu
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Brett E. Johnson
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Tali Mazor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, California, USA
- Medical Scientist Training Program and Neuroscience Graduate Program, University of California San Francisco, San Francisco, California, USA
| | - Kevin W. Kelley
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Medical Scientist Training Program and Neuroscience Graduate Program, University of California San Francisco, San Francisco, California, USA
- Neuroscience Graduate Program, University of California San Francisco, San Francisco, California, USA
| | - Matthew B. Potts
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Michael W. McDermott
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Eric J. Huang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Daniel A. Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Russell O. Pieper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Mitchel S. Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Joseph F. Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Joanna J. Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Michael C. Oldham
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
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Kong L, Li S, Zhao Z, Feng J, Fu X, Li H, Zhu J, Wang Y, Tang W, Yuan C, Li F, Han X, Wu D, Kong X, Sun L. Exploring factors impacting haplotype-based noninvasive prenatal diagnosis for single-gene recessive disorders. Clin Genet 2024; 105:52-61. [PMID: 37822034 DOI: 10.1111/cge.14434] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]
Abstract
Haplotype-based noninvasive prenatal diagnosis (NIPD) is applicable for various recessive single-gene disorders in proband families. However, a comprehensive exploration of critical factors influencing the assay performance, such as fetal fraction, informative single nucleotide polymorphism (SNP) count, and recombination events, has yet to be performed. It is critical to identify key factors affecting NIPD performance, including its accuracy and success rate, and their impact on clinical diagnostics to guide clinical practice. We conducted a prospective study, recruiting 219 proband families with singleton pregnancies at risk for eight recessive single-gene disorders (Duchenne muscular dystrophy, spinal muscular atrophy, phenylketonuria, methylmalonic acidemia, hemophilia A, hemophilia B, non-syndromic hearing loss, and congenital adrenal hyperplasia) at 7-14 weeks of gestation. Haplotype-based NIPD was performed by evaluating the relative haplotype dosage (RHDO) in maternal circulation, and the results were validated via invasive prenatal diagnosis or newborn follow-ups. Among the 219 families, the median gestational age at first blood draw was 8+5 weeks. Initial testing succeeded for 190 families and failed for 29 due to low fetal fraction (16), insufficient informative SNPs (9), and homologous recombination near pathogenic variation (4). Among low fetal fraction families, successful testing was achieved for 11 cases after a redraw, while 5 remained inconclusive. Test failures linked to insufficient informative SNPs correlated with linkage disequilibrium near the genes, with F8 and MMUT exhibiting the highest associated failure rates (14.3% and 25%, respectively). Homologous recombination was relatively frequent around the DMD and SMN1 genes (8.8% and 4.8%, respectively) but led to detection failure in only 44.4% (4/9) of such cases. All NIPD results from the 201 successful families were consistent with invasive diagnostic findings or newborn follow-up. Fetal fraction, informative SNPs count, and homologous recombination are pivotal to NIPD performance. Redrawing blood effectively improves the success rate for low fetal fraction samples. However, informative SNPs count and homologous recombination rates vary significantly across genes, necessitating careful consideration in clinical practice. We have designed an in silico method based on linkage disequilibrium data to predict the number of informative SNPs. This can identify genomic regions where there might be an insufficient number of SNPs, thereby guiding panel design. With these factors properly accounted for, NIPD is highly accurate and reliable.
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Affiliation(s)
- Lingrong Kong
- Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shaojun Li
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Zhao
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Feng
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Xinyu Fu
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huanyun Li
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jingqi Zhu
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanan Wang
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Weiqin Tang
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Chao Yuan
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Feifei Li
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Xiujuan Han
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Di Wu
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Luming Sun
- Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
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8
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Chang J, Zhao X, Wang Y, Liu T, Zhong C, Lao Y, Zhang S, Liao H, Bai F, Lin D, Wu C. Genomic alterations driving precancerous to cancerous lesions in esophageal cancer development. Cancer Cell 2023; 41:2038-2050.e5. [PMID: 38039962 DOI: 10.1016/j.ccell.2023.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/26/2023] [Accepted: 11/04/2023] [Indexed: 12/03/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) develops through a series of increasingly abnormal precancerous lesions. Previous studies have revealed the striking differences between normal esophageal epithelium and ESCC in copy number alterations (CNAs) and mutations in genes driving clonal expansion. However, due to limited data on early precancerous lesions, the timing of these transitions and which among them are prerequisites for malignant transformation remained unclear. Here, we analyze 1,275 micro-biopsies from normal esophagus, early and late precancerous lesions, and esophageal cancers to decipher the genomic alterations at each stage. We show that the frequency of TP53 biallelic inactivation increases dramatically in early precancerous lesion stage while CNAs and APOBEC mutagenesis substantially increase at late stages. TP53 biallelic loss is the prerequisite for the development of CNAs of genes in cell cycle, DNA repair, and apoptosis pathways, suggesting it might be one of the earliest steps initiating malignant transformation.
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Affiliation(s)
- Jiang Chang
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Xuan Zhao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Yichen Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Tianyuan Liu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Ce Zhong
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Yueqiong Lao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Shaosen Zhang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Han Liao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China; Center for Translational Cancer Research, Peking University First Hospital, Beijing 100034, China.
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China; Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China; Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou 510060, China.
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China; Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China; CAMS Oxford Institute, Chinese Academy of Medical Sciences, Beijing 100006, China.
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9
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Fu X, Li S, Zhao Z, Kong L, Zhu J, Li H, Feng J, Tang W, Wu D, Kong X. Haplotype-based noninvasive prenatal diagnosis of methylmalonic acidemia and the discovery of a recurrent pathogenic haplotype associated with c.609G>A. Prenat Diagn 2023; 43:1544-1555. [PMID: 37957774 DOI: 10.1002/pd.6458] [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: 07/31/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Early diagnosis and intervention are crucial for the prognosis of methylmalonic acidemia (MMA). However, research focused on early prenatal diagnosis of MMA is limited. METHODS A 161.89kb capture panel was designed for selectively enriching highly heterozygous SNPs. Fetal genotypes were inferred using relative haplotype dosage (RHDO) and Bayes factor, followed by invasive prenatal diagnosis (IPD) for validation. A core pathogenic haplotype associated with c.609G>A was identified based on the frequency differences between pathogenic and normal haplotypes. RESULTS We recruited 41 pregnancies at risk of MMA with a median gestational age of 8+2 weeks. The assay success rate of NIPD-MMA for maternal variants was 92.7% (38/41), and after incorporating the paternal result, the overall assay success rate reached 100% (41/41). All NIPD results were concordant with IPD. Notably, a core haplotype (hap_2), comprising 28 SNPs, demonstrates significant enrichment within pathogenic haplotypes bearing the c.609G>A variation. On average, c.609G>A carriers had 22.38 heterozygous loci within these 28 SNPs. CONCLUSION NIPD-MMA presents a viable choice for early, accurate, and safe prenatal diagnosis. Furthermore, the discovery of the recurrent core pathogenic haplotype provides a novel approach for haplotype phasing and has the potential for realizing proband-independent NIPD in the future.
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Affiliation(s)
- Xinyu Fu
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shaojun Li
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Zhenhua Zhao
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lingrong Kong
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jingqi Zhu
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huanyun Li
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Feng
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Weiqin Tang
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Di Wu
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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10
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Faldynová L, Walczysková S, Černá D, Kudrejová M, Hilscherová Š, Kaniová R, Širůčková S. Non-invasive prenatal testing (NIPT): Combination of copy number variant and gene analyses using an "in-house" target enrichment next generation sequencing-Solution for non-centralized NIPT laboratory? Prenat Diagn 2023; 43:1320-1332. [PMID: 37602788 DOI: 10.1002/pd.6421] [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: 05/24/2023] [Revised: 07/18/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023]
Abstract
OBJECTIVE Recent studies have integrated copy number variant (CNV) and gene analysis using target enrichment. Here, we transferred this concept to our routine genetics laboratory, which is not linked to centralized non-invasive prenatal testing (NIPT) facilities. METHOD From a cohort of 100 pregnant women, 22 were selected for the analysis of maternal genomic DNA (gDNA) along with fetal cell-free DNA. Using targeted enrichment, 135 genes were analyzed, combined with aberrations of chromosomes 21, 18, 13, X, and Y. The data were subjected to specificity and sensitivity analyses, and correlated with the results from invasive testing methods. RESULTS The sensitivity/specificity was determined for the CNV analysis of chromosomes: 21 (80%/75%), 18 (-/82%), 13 (100%/67%), and Y (100%/100%). The gene detection was valid for maternal gDNA. However, for cell-free fetal DNA, it was not possible to determine the boundary between an artifact and a real sequence variant. CONCLUSION The target enrichment method combining CNV and gene detection seems feasible in a regular laboratory. However, this method can only be responsibly optimized with a sufficient number of controls and further validation on a strong bioinformatic background. The present results showed that NIPT should be performed in specialized centers, and that its introduction to isolated laboratories may not provide valid data.
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Affiliation(s)
- Lucie Faldynová
- Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic
| | - Sylwia Walczysková
- Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic
| | - Dita Černá
- Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic
| | - Monika Kudrejová
- Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic
| | - Šárka Hilscherová
- Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic
| | - Romana Kaniová
- Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic
| | - Simona Širůčková
- Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic
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11
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Bedics G, Egyed B, Kotmayer L, Benard-Slagter A, de Groot K, Bekő A, Hegyi LL, Bátai B, Krizsán S, Kriván G, Erdélyi DJ, Müller J, Haltrich I, Kajtár B, Pajor L, Vojcek Á, Ottóffy G, Ujfalusi A, Szegedi I, Tiszlavicz LG, Bartyik K, Csanádi K, Péter G, Simon R, Hauser P, Kelemen Á, Sebestyén E, Jakab Z, Matolcsy A, Kiss C, Kovács G, Savola S, Bödör C, Alpár D. PersonALL: a genetic scoring guide for personalized risk assessment in pediatric B-cell precursor acute lymphoblastic leukemia. Br J Cancer 2023; 129:455-465. [PMID: 37340093 PMCID: PMC10403542 DOI: 10.1038/s41416-023-02309-8] [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: 09/20/2022] [Revised: 05/08/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND Recurrent genetic lesions provide basis for risk assessment in pediatric acute lymphoblastic leukemia (ALL). However, current prognostic classifiers rely on a limited number of predefined sets of alterations. METHODS Disease-relevant copy number aberrations (CNAs) were screened genome-wide in 260 children with B-cell precursor ALL. Results were integrated with cytogenetic data to improve risk assessment. RESULTS CNAs were detected in 93.8% (n = 244) of the patients. First, cytogenetic profiles were combined with IKZF1 status (IKZF1normal, IKZF1del and IKZF1plus) and three prognostic subgroups were distinguished with significantly different 5-year event-free survival (EFS) rates, IKAROS-low (n = 215): 86.3%, IKAROS-medium (n = 27): 57.4% and IKAROS-high (n = 18): 37.5%. Second, contribution of genetic aberrations to the clinical outcome was assessed and an aberration-specific score was assigned to each prognostically relevant alteration. By aggregating the scores of aberrations emerging in individual patients, personalized cumulative values were calculated and used for defining four prognostic subgroups with distinct clinical outcomes. Two favorable subgroups included 60% of patients (n = 157) with a 5-year EFS of 96.3% (excellent risk, n = 105) and 87.2% (good risk, n = 52), respectively; while 40% of patients (n = 103) showed high (n = 74) or ultra-poor (n = 29) risk profile (5-year EFS: 67.4% and 39.0%, respectively). CONCLUSIONS PersonALL, our conceptually novel prognostic classifier considers all combinations of co-segregating genetic alterations, providing a highly personalized patient stratification.
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Affiliation(s)
- Gábor Bedics
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Bálint Egyed
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Lili Kotmayer
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | | | | | - Anna Bekő
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Lajos László Hegyi
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Bence Bátai
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Szilvia Krizsán
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Gergely Kriván
- Central Hospital of Southern Pest - National Institute of Hematology and Infectious Diseases, Budapest, Hungary
| | - Dániel J Erdélyi
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Judit Müller
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Irén Haltrich
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Béla Kajtár
- Department of Pathology, University of Pécs Medical School, Pécs, Hungary
| | - László Pajor
- Department of Pathology, University of Pécs Medical School, Pécs, Hungary
| | - Ágnes Vojcek
- Department of Pediatrics, University of Pécs Medical School, Pécs, Hungary
| | - Gábor Ottóffy
- Department of Pediatrics, University of Pécs Medical School, Pécs, Hungary
| | - Anikó Ujfalusi
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - István Szegedi
- Division of Pediatric Hematology-Oncology, Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Lilla Györgyi Tiszlavicz
- Department of Paediatrics and Paediatric Health Care Center, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Katalin Bartyik
- Department of Paediatrics and Paediatric Health Care Center, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Krisztina Csanádi
- Hemato-Oncology Unit, Heim Pál Children's Hospital, Budapest, Hungary
| | - György Péter
- Hemato-Oncology Unit, Heim Pál Children's Hospital, Budapest, Hungary
| | - Réka Simon
- Hemato-Oncology and Stem Cell Transplantation Unit, Velkey László Children's Health Center, Miskolc, Hungary
| | - Péter Hauser
- Hemato-Oncology and Stem Cell Transplantation Unit, Velkey László Children's Health Center, Miskolc, Hungary
| | - Ágnes Kelemen
- Hemato-Oncology and Stem Cell Transplantation Unit, Velkey László Children's Health Center, Miskolc, Hungary
| | - Endre Sebestyén
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Zsuzsanna Jakab
- Hungarian Childhood Cancer Registry, Hungarian Pediatric Oncology Network, Budapest, Hungary
| | - András Matolcsy
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
- Department of Laboratory Medicine, Karolinska Institute, Solna, Sweden
| | - Csongor Kiss
- Division of Pediatric Hematology-Oncology, Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gábor Kovács
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | | | - Csaba Bödör
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Donát Alpár
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary.
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Ishikawa T, Ogawa T, Shiihara M, Usubuchi H, Omori Y, Hirose K, Itoh T, Yoshida T, Nakanome A, Okoshi A, Higashi K, Ishii R, Rokugo M, Wakamori S, Okamura Y, Kinoshita K, Katori Y, Furukawa T. Salivary gland cancer organoids are valid for preclinical genotype-oriented medical precision trials. iScience 2023; 26:106695. [PMID: 37207275 PMCID: PMC10189274 DOI: 10.1016/j.isci.2023.106695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/02/2023] [Accepted: 04/13/2023] [Indexed: 05/21/2023] Open
Abstract
Salivary gland cancers (SGCs) are heterogeneous tumors, and precision oncology represents a promising therapeutic approach; however, its impact on SGCs remains obscure. This study aimed to establish a translational model for testing molecular-targeted therapies by combining patient-derived organoids and genomic analyses of SGCs. We enrolled 29 patients, including 24 with SGCs and 5 with benign tumors. Resected tumors were subjected to organoid and monolayer cultures, as well as whole-exome sequencing. Organoid and monolayer cultures of SGCs were successfully established in 70.8% and 62.5% of cases, respectively. Organoids retained most histopathological and genetic profiles of their original tumors. In contrast, 40% of the monolayer-cultured cells did not harbor somatic mutations of their original tumors. The efficacy of molecular-targeted drugs tested on organoids depended on their oncogenic features. Organoids recapitulated the primary tumors and were useful for testing genotype-oriented molecular targeted therapy, which is valuable for precision medicine in patients with SGCs.
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Affiliation(s)
- Tomohiko Ishikawa
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Takenori Ogawa
- Department of Otolaryngology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Masahiro Shiihara
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Hajime Usubuchi
- Department of Pathology, Sendai Kousei Hospital, Sendai 980-0873, Japan
| | - Yuko Omori
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Katsuya Hirose
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Taito Itoh
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Takuya Yoshida
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Ayako Nakanome
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Akira Okoshi
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Kenjiro Higashi
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Ryo Ishii
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Masahiro Rokugo
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Shun Wakamori
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Yasunobu Okamura
- Tohoku University Advanced Research Center for Innovations in Next-Generation Medicine, Sendai 980-8573, Japan
- Tohoku University Tohoku Medical Megabank Organization, Sendai 980-8573, Japan
| | - Kengo Kinoshita
- Tohoku University Advanced Research Center for Innovations in Next-Generation Medicine, Sendai 980-8573, Japan
- Tohoku University Tohoku Medical Megabank Organization, Sendai 980-8573, Japan
- Tohoku University Graduate School of Information Sciences, Sendai 980-8579, Japan
| | - Yukio Katori
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Toru Furukawa
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
- Corresponding author
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13
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Tsui DCC, Drusbosky LM, Wienke S, Gao D, Bubie A, Barbacioru C, Camidge DR. Oncogene Overlap Analysis of Circulating Cell-free Tumor DNA to Explore the Appropriate Criteria for Defining MET Copy Number-Driven Lung Cancer. Clin Lung Cancer 2022; 23:630-638. [PMID: 35961935 PMCID: PMC10552597 DOI: 10.1016/j.cllc.2022.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/10/2022] [Indexed: 01/27/2023]
Abstract
INTRODUCTION Defining clinically relevant MET amplification levels in non-small cell lung cancer (NSCLC) remains challenging. We hypothesize that oncogene overlap and MET amplicon size decline with increase in MET plasma copy number (pCN), thus enriching for MET-dependent states. PATIENTS AND METHODS We interrogated cell-free DNA NGS results of 16,782 patients with newly diagnosed advanced NSCLC to identify those with MET amplification as reported using Guardant360. Co-occurring genomic mutations and copy number alterations within each sample were evaluated. An exploratory method of adjusting for tumor fraction was also performed and amplicon size for MET was analyzed when available. RESULTS MET amplification was detected in 207 (1.2%) of samples. pCN ranged from 2.1 to 52.9. Of these, 43 (20.8%) had an overlapping oncogenic driver, including 23 (11.1%) METex14 skipping or other MET mutations. The degree of (non-MET) oncogene overlap decreased with increases in pCN. Patients with MET pCN ≥ 2.7 had lower rates of overlapping drivers compared to those with MET pCN < 2.7 (6.1% vs. 16.3%, P = .033). None of the 7 patients with pCN > 6.7 had an overlapping driver. After adjusting for tumor fraction, adjusted pCN (ApCN) was also lower for those with overlapping drivers than those without (median ApCN 4.9 vs. 7.3, P =.024). There was an inverse relationship between amplicon size and pCN. CONCLUSIONS We propose that a high MET pCN and/or ApCN, together with the absence of overlapping oncogenic drivers and small MET amplicon size, will enrich for patients most likely to derive benefit from MET targeted therapy.
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Affiliation(s)
- David C C Tsui
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO
| | | | | | - Dexiang Gao
- Department of Pediatrics, Biostatistics and Bioinformatics Shared Resource, University of Colorado School of Medicine, University of Colorado Cancer Center, Aurora, CO
| | | | | | - D Ross Camidge
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO.
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14
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Pape K, Lößner AJ, William D, Czempiel T, Beyreuther E, Klimova A, Lehmann C, Schmäche T, Merker SR, Naumann M, Ada AM, Baenke F, Seidlitz T, Bütof R, Dietrich A, Krause M, Weitz J, Klink B, von Neubeck C, Stange DE. Sensitization of Patient-Derived Colorectal Cancer Organoids to Photon and Proton Radiation by Targeting DNA Damage Response Mechanisms. Cancers (Basel) 2022; 14:4984. [PMID: 36291768 PMCID: PMC9599341 DOI: 10.3390/cancers14204984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/27/2022] [Accepted: 10/05/2022] [Indexed: 12/04/2022] Open
Abstract
Pathological complete response (pCR) has been correlated with overall survival in several cancer entities including colorectal cancer. Novel total neoadjuvant treatment (TNT) in rectal cancer has achieved pathological complete response in one-third of the patients. To define better treatment options for nonresponding patients, we used patient-derived organoids (PDOs) as avatars of the patient's tumor to apply both photon- and proton-based irradiation as well as single and combined chemo(radio)therapeutic treatments. While response to photon and proton therapy was similar, PDOs revealed heterogeneous responses to irradiation and different chemotherapeutic drugs. Radiotherapeutic response of the PDOs was significantly correlated with their ability to repair irradiation-induced DNA damage. The classical combination of 5-FU and irradiation could not sensitize radioresistant tumor cells. Ataxia-telangiectasia mutated (ATM) kinase was activated upon radiation, and by inhibition of this central sensor of DNA damage, radioresistant PDOs were resensitized. The study underlined the capability of PDOs to define nonresponders to irradiation and could delineate therapeutic approaches for radioresistant patients.
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Affiliation(s)
- Kristin Pape
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine Carl Gustav Carus, University Hospital, Technische Universität Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
| | - Anna J. Lößner
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine Carl Gustav Carus, University Hospital, Technische Universität Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
| | - Doreen William
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), Partner Site Dresden, 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Hereditary Cancer Syndrome Center Dresden, ERN-GENTURIS, Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Tabea Czempiel
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), Partner Site Dresden, 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Hereditary Cancer Syndrome Center Dresden, ERN-GENTURIS, Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Elke Beyreuther
- OncoRay–National Center for Radiation Research in Oncology, Helmholtz-Zentrum Dresden-Rossendorf, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 1307 Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiation Physics, 01307 Dresden, Germany
| | - Anna Klimova
- National Center for Tumor Diseases (NCT/UCC), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
| | - Claudia Lehmann
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine Carl Gustav Carus, University Hospital, Technische Universität Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
| | - Tim Schmäche
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine Carl Gustav Carus, University Hospital, Technische Universität Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
| | - Sebastian R. Merker
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine Carl Gustav Carus, University Hospital, Technische Universität Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
| | - Max Naumann
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- OncoRay–National Center for Radiation Research in Oncology, Helmholtz-Zentrum Dresden-Rossendorf, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 1307 Dresden, Germany
| | - Anne-Marlen Ada
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine Carl Gustav Carus, University Hospital, Technische Universität Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
| | - Franziska Baenke
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine Carl Gustav Carus, University Hospital, Technische Universität Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
| | - Therese Seidlitz
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine Carl Gustav Carus, University Hospital, Technische Universität Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
| | - Rebecca Bütof
- National Center for Tumor Diseases (NCT/UCC), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
- OncoRay–National Center for Radiation Research in Oncology, Helmholtz-Zentrum Dresden-Rossendorf, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 1307 Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology–OncoRay, 01307 Dresden, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Antje Dietrich
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- OncoRay–National Center for Radiation Research in Oncology, Helmholtz-Zentrum Dresden-Rossendorf, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 1307 Dresden, Germany
| | - Mechthild Krause
- National Center for Tumor Diseases (NCT/UCC), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- OncoRay–National Center for Radiation Research in Oncology, Helmholtz-Zentrum Dresden-Rossendorf, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 1307 Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology–OncoRay, 01307 Dresden, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Jürgen Weitz
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine Carl Gustav Carus, University Hospital, Technische Universität Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
| | - Barbara Klink
- National Center for Tumor Diseases (NCT/UCC), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), Partner Site Dresden, 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Hereditary Cancer Syndrome Center Dresden, ERN-GENTURIS, Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- National Center of Genetics (NCG), Laboratoire National de Santé, 3555 Dudelange, Luxembourg
| | - Cläre von Neubeck
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- OncoRay–National Center for Radiation Research in Oncology, Helmholtz-Zentrum Dresden-Rossendorf, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 1307 Dresden, Germany
- Department of Particle Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Daniel E. Stange
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine Carl Gustav Carus, University Hospital, Technische Universität Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
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15
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Freeman CL, Pararajalingam P, Jin L, Balasubramanian S, Jiang A, Xu W, Grau M, Zapukhlyak M, Boyle M, Hodkinson B, Schaffer M, Enny C, Deshpande S, Sun S, Vermeulen J, Morin RD, Scott DW, Lenz G. Molecular determinants of outcomes in relapsed or refractory mantle cell lymphoma treated with ibrutinib or temsirolimus in the MCL3001 (RAY) trial. Leukemia 2022; 36:2479-2487. [PMID: 35963941 DOI: 10.1038/s41375-022-01658-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 11/10/2022]
Abstract
Mantle cell lymphoma (MCL) is a rare, incurable lymphoma subtype characterized by heterogeneous outcomes. To better understand the clinical behavior and response to treatment, predictive biomarkers are needed. Using residual archived material from patients enrolled in the MCL3001 (RAY) study, we performed detailed analyses of gene expression and targeted genetic sequencing. This phase III clinical trial randomized patients with relapsed or refractory MCL to treatment with either ibrutinib or temsirolimus. We confirmed the prognostic capability of the gene expression proliferation assay MCL35 in this cohort treated with novel agents; it outperformed the simplified MCL International Prognostic Index in discriminating patients with different outcomes. Regardless of treatment arm, our data demonstrated that this assay captures the risk conferred by known biological factors, including increased MYC expression, blastoid morphology, aberrations of TP53, and truncated CCND1 3' untranslated region. We showed the negative impact of BIRC3 mutations/deletions on outcomes in this cohort and identified that deletion of chromosome 8p23.3 also negatively impacts survival. Restricted to patients with deletions/alterations in TP53, ibrutinib appeared to abrogate the deleterious impact on outcome. These data illustrate the potential to perform a molecular analysis of predictive biomarkers on routine patient samples that can meaningfully inform clinical practice.
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Affiliation(s)
- Ciara L Freeman
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada. .,Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Centre and Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Prasath Pararajalingam
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Ling Jin
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | | | - Aixiang Jiang
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Wendan Xu
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Michael Grau
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Myroslav Zapukhlyak
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Merrill Boyle
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Brendan Hodkinson
- Oncology Translational Research, Janssen Research & Development, Spring House, PA, USA
| | - Michael Schaffer
- Oncology Translational Research, Janssen Research & Development, Spring House, PA, USA
| | - Christopher Enny
- Clinical Oncology, Janssen Research & Development, Raritan, NJ, USA
| | - Sanjay Deshpande
- Clinical Oncology, Janssen Research & Development, Raritan, NJ, USA
| | - Steven Sun
- Clinical Biostats, Janssen Research & Development, Raritan, NJ, USA
| | - Jessica Vermeulen
- Clinical Oncology, Janssen Research & Development, Leiden, The Netherlands
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Georg Lenz
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
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16
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Wang Y, Li S, Wu D, Yan H. Title: Noninvasive prenatal testing of hereditary colorectal cancer syndromes using cell-free DNA in maternal plasma. Prenat Diagn 2022; 42:557-566. [PMID: 35343616 DOI: 10.1002/pd.6137] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/07/2022]
Abstract
OBJECTIVE This study aimed to establish a practical protocol for early noninvasive prenatal testing (NIPT) for fetuses at risk of Peutz-Jeghers syndrome (PJS) or familial adenomatous polyposis (FAP), two classical types of hereditary colorectal cancer syndromes, for risk evaluation and whole-life monitoring. METHOD Target enrichment was performed using hybridization probes coordinating the STK11 gene region and APC gene region, with 1,458 highly heterozygous SNPs included. Semitarget amplification random sequencing was used for large fragment deletion detection. For relative haplotype dosage (RHDO) analysis, haplotype construction was performed by SHAPEIT software, the CBS algorithm was used for recombination event calculation, and Bayes factor was used for the determination of whether the fetus was affected. RESULTS Haplotypes were successfully constructed in the nine recruited families with different pedigree characteristics, and the results for the RHDO analysis were consistent with the amniocentesis sampling detection results. The cell-free fetal DNA fraction can be detected as low as 2% in maternal plasma. CONCLUSION This is the first NIPT assay on hereditary colorectal cancer syndromes based upon RHDO analysis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yao Wang
- Center for Reproductive Medicine, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Suqing Li
- Celula Medical Technology Co., Ltd. Chengdu, Chengdu, China
| | - Di Wu
- Celula Medical Technology Co., Ltd. Chengdu, Chengdu, China
| | - Hongli Yan
- Center for Reproductive Medicine, Changhai Hospital, Naval Medical University, Shanghai, China
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17
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Kong L, Li S, Zhao Z, Feng J, Liu L, Tang W, Zhang H, Wu D, Sun L, Kong X. Noninvasive prenatal testing of Duchenne muscular dystrophy in a twin gestation. Prenat Diagn 2022; 42:518-523. [PMID: 35220584 DOI: 10.1002/pd.6124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/11/2022] [Accepted: 02/24/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Lingrong Kong
- Department of Fetal Medicine & Prenatal Diagnosis Center Shanghai First Maternity and Infant Hospital School of Medicine Tongji University Shanghai China
- Genetic and Prenatal Diagnosis Center Department of Obstetrics and Gynecology The First Affiliated Hospital of Zhengzhou University Zhengzhou China
| | - Shaojun Li
- Celula (China) Medical Technology Co. Ltd. Chengdu China
| | - Zhenhua Zhao
- Genetic and Prenatal Diagnosis Center Department of Obstetrics and Gynecology The First Affiliated Hospital of Zhengzhou University Zhengzhou China
| | - Jun Feng
- Celula (China) Medical Technology Co. Ltd. Chengdu China
| | - Lina Liu
- Genetic and Prenatal Diagnosis Center Department of Obstetrics and Gynecology The First Affiliated Hospital of Zhengzhou University Zhengzhou China
| | - Weiqin Tang
- Celula (China) Medical Technology Co. Ltd. Chengdu China
| | - Haichuan Zhang
- Celula (China) Medical Technology Co. Ltd. Chengdu China
| | - Di Wu
- Celula (China) Medical Technology Co. Ltd. Chengdu China
| | - Luming Sun
- Department of Fetal Medicine & Prenatal Diagnosis Center Shanghai First Maternity and Infant Hospital School of Medicine Tongji University Shanghai China
| | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center Department of Obstetrics and Gynecology The First Affiliated Hospital of Zhengzhou University Zhengzhou China
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18
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Kong L, Li S, Zhao Z, Feng J, Chen G, Liu L, Tang W, Li S, Li F, Han X, Wu D, Zhang H, Sun L, Kong X. Haplotype-Based Noninvasive Prenatal Diagnosis of 21 Families With Duchenne Muscular Dystrophy: Real-World Clinical Data in China. Front Genet 2022; 12:791856. [PMID: 34970304 PMCID: PMC8712857 DOI: 10.3389/fgene.2021.791856] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/18/2021] [Indexed: 11/13/2022] Open
Abstract
Noninvasive prenatal diagnosis (NIPD) of single-gene disorders has recently become the focus of clinical laboratories. However, reports on the clinical application of NIPD of Duchenne muscular dystrophy (DMD) are limited. This study aimed to evaluate the detection performance of haplotype-based NIPD of DMD in a real clinical environment. Twenty-one DMD families at 7-12 weeks of gestation were prospectively recruited. DNA libraries of cell-free DNA from the pregnant and genomic DNA from family members were captured using a custom assay for the enrichment of DMD gene exons and spanning single-nucleotide polymorphisms, followed by next-generation sequencing. Parental haplotype phasing was based on family linkage analysis, and fetal genotyping was inferred using the Bayes factor through target maternal plasma sequencing. Finally, the entire experimental process was promoted in the local clinical laboratory. We recruited 13 complete families, 6 families without paternal samples, and 2 families without probands in which daughter samples were collected. Two different maternal haplotypes were constructed based on family members in all 21 pedigrees at as early as 7 gestational weeks. Among the included families, the fetal genotypes of 20 families were identified at the first blood collection, and a second blood collection was performed for another family due to low fetal concentration. The NIPD result of each family was reported within 1 week. The fetal fraction in maternal cfDNA ranged from 1.87 to 11.68%. In addition, recombination events were assessed in two fetuses. All NIPD results were concordant with the findings of invasive prenatal diagnosis (chorionic villus sampling or amniocentesis). Exon capture and haplotype-based NIPD of DMD are regularly used for DMD genetic diagnosis, carrier screening, and noninvasive prenatal diagnosis in the clinic. Our method, haplotype-based early screening for DMD fetal genotyping via cfDNA sequencing, has high feasibility and accuracy, a short turnaround time, and is inexpensive in a real clinical environment.
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Affiliation(s)
- Lingrong Kong
- Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China.,Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shaojun Li
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Zhenhua Zhao
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Feng
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Guangquan Chen
- Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lina Liu
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Weiqin Tang
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Suqing Li
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Feifei Li
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Xiujuan Han
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Di Wu
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Haichuan Zhang
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Luming Sun
- Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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19
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Yoon CJ, Kim SY, Nam CH, Lee J, Park JW, Mun J, Park S, Lee S, Yi B, Min KI, Wiley B, Bolton KL, Lee JH, Kim E, Yoo HJ, Jun JK, Choi JS, Griffith M, Griffith OL, Ju YS. Estimation of intrafamilial DNA contamination in family trio genome sequencing using deviation from Mendelian inheritance. Genome Res 2022; 32:2134-2144. [PMID: 36617634 PMCID: PMC9808622 DOI: 10.1101/gr.276794.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 10/31/2022] [Indexed: 12/12/2022]
Abstract
With the increasing number of sequencing projects involving families, quality control tools optimized for family genome sequencing are needed. However, accurately quantifying contamination in a DNA mixture is particularly difficult when genetically related family members are the sources. We developed TrioMix, a maximum likelihood estimation (MLE) framework based on Mendel's law of inheritance, to quantify DNA mixture between family members in genome sequencing data of parent-offspring trios. TrioMix can accurately deconvolute any intrafamilial DNA contamination, including parent-offspring, sibling-sibling, parent-parent, and even multiple familial sources. In addition, TrioMix can be applied to detect genomic abnormalities that deviate from Mendelian inheritance patterns, such as uniparental disomy (UPD) and chimerism. A genome-wide depth and variant allele frequency plot generated by TrioMix facilitates tracing the origin of Mendelian inheritance deviations. We showed that TrioMix could accurately deconvolute genomes in both simulated and real data sets.
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Affiliation(s)
- Christopher J. Yoon
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,Research Center for Natural Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea;,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea;,McDonnell Genome Institute, St. Louis, Missouri 63108, USA
| | - Su Yeon Kim
- Research Center for Natural Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Chang Hyun Nam
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Junehawk Lee
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon 34141, Korea
| | - Jung Woo Park
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon 34141, Korea
| | - Jihyeob Mun
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon 34141, Korea
| | | | - Soyoung Lee
- GENOME INSIGHT Incorporated, Daejeon 34051, Korea
| | - Boram Yi
- GENOME INSIGHT Incorporated, Daejeon 34051, Korea
| | - Kyoung Il Min
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Brian Wiley
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Kelly L. Bolton
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Eunjoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea;,Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon 34141, Korea
| | - Hee Jeong Yoo
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam 13620, Korea;,Department of Psychiatry, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jong Kwan Jun
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Ji Seon Choi
- Department of Laboratory Medicine, International St. Mary's Hospital, Catholic Kwandong University College of Medicine, Incheon 22711, Korea
| | - Malachi Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,McDonnell Genome Institute, St. Louis, Missouri 63108, USA
| | - Obi L. Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,McDonnell Genome Institute, St. Louis, Missouri 63108, USA
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea;,GENOME INSIGHT Incorporated, Daejeon 34051, Korea
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20
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Au L, Hatipoglu E, Robert de Massy M, Litchfield K, Beattie G, Rowan A, Schnidrig D, Thompson R, Byrne F, Horswell S, Fotiadis N, Hazell S, Nicol D, Shepherd STC, Fendler A, Mason R, Del Rosario L, Edmonds K, Lingard K, Sarker S, Mangwende M, Carlyle E, Attig J, Joshi K, Uddin I, Becker PD, Sunderland MW, Akarca A, Puccio I, Yang WW, Lund T, Dhillon K, Vasquez MD, Ghorani E, Xu H, Spencer C, López JI, Green A, Mahadeva U, Borg E, Mitchison M, Moore DA, Proctor I, Falzon M, Pickering L, Furness AJS, Reading JL, Salgado R, Marafioti T, Jamal-Hanjani M, Kassiotis G, Chain B, Larkin J, Swanton C, Quezada SA, Turajlic S. Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma. Cancer Cell 2021; 39:1497-1518.e11. [PMID: 34715028 PMCID: PMC8599450 DOI: 10.1016/j.ccell.2021.10.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/19/2021] [Accepted: 10/06/2021] [Indexed: 02/08/2023]
Abstract
ADAPTeR is a prospective, phase II study of nivolumab (anti-PD-1) in 15 treatment-naive patients (115 multiregion tumor samples) with metastatic clear cell renal cell carcinoma (ccRCC) aiming to understand the mechanism underpinning therapeutic response. Genomic analyses show no correlation between tumor molecular features and response, whereas ccRCC-specific human endogenous retrovirus expression indirectly correlates with clinical response. T cell receptor (TCR) analysis reveals a significantly higher number of expanded TCR clones pre-treatment in responders suggesting pre-existing immunity. Maintenance of highly similar clusters of TCRs post-treatment predict response, suggesting ongoing antigen engagement and survival of families of T cells likely recognizing the same antigens. In responders, nivolumab-bound CD8+ T cells are expanded and express GZMK/B. Our data suggest nivolumab drives both maintenance and replacement of previously expanded T cell clones, but only maintenance correlates with response. We hypothesize that maintenance and boosting of a pre-existing response is a key element of anti-PD-1 mode of action.
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Affiliation(s)
- Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Emine Hatipoglu
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Marc Robert de Massy
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Gordon Beattie
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Desiree Schnidrig
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachael Thompson
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Stuart Horswell
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, UK
| | - Nicos Fotiadis
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London SW3 6JJ, UK
| | - Steve Hazell
- Department of Pathology, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - David Nicol
- Department of Urology, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Annika Fendler
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Robert Mason
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Lyra Del Rosario
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Kim Edmonds
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Karla Lingard
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Sarah Sarker
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Mary Mangwende
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Eleanor Carlyle
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Jan Attig
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Kroopa Joshi
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Imran Uddin
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Pablo D Becker
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK
| | - Mariana Werner Sunderland
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK
| | - Ayse Akarca
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Ignazio Puccio
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - William W Yang
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Tom Lund
- Translational Immune Oncology Lab, Centre for Molecular Pathology, The Royal Marsden Hospital, Sutton SM2 5PT, UK
| | - Kim Dhillon
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Marcos Duran Vasquez
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Ehsan Ghorani
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Hang Xu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Charlotte Spencer
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - José I López
- Department of Pathology, Cruces University Hospital, Biocruces-Bizkaia Institute, 48903 Barakaldo, Bizkaia, Spain
| | - Anna Green
- Department of Cellular Pathology, Guy's & St Thomas' NHS Foundation Trust, St Thomas' Hospital, London SE1 7EH, UK
| | - Ula Mahadeva
- Department of Cellular Pathology, Guy's & St Thomas' NHS Foundation Trust, St Thomas' Hospital, London SE1 7EH, UK
| | - Elaine Borg
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Miriam Mitchison
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Ian Proctor
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Mary Falzon
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Lisa Pickering
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Andrew J S Furness
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Roberto Salgado
- Division of Research, Peter MacCallum Cancer Centre, Melbourne VIC 300, Australia; Department of Pathology, GZA-ZNA Hospitals, Wilrijk, Antwerp, Belgium
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London WC1E 6DD, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK; University College London Cancer Institute, London WC1E 6DD, UK
| | - James Larkin
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK; University College London Cancer Institute, London WC1E 6DD, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK.
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK.
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21
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Papathanasiou S, Markoulaki S, Blaine LJ, Leibowitz ML, Zhang CZ, Jaenisch R, Pellman D. Whole chromosome loss and genomic instability in mouse embryos after CRISPR-Cas9 genome editing. Nat Commun 2021; 12:5855. [PMID: 34615869 PMCID: PMC8494802 DOI: 10.1038/s41467-021-26097-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022] Open
Abstract
Karyotype alterations have emerged as on-target complications from CRISPR-Cas9 genome editing. However, the events that lead to these karyotypic changes in embryos after Cas9-treatment remain unknown. Here, using imaging and single-cell genome sequencing of 8-cell stage embryos, we track both spontaneous and Cas9-induced karyotype aberrations through the first three divisions of embryonic development. We observe the generation of abnormal structures of the nucleus that arise as a consequence of errors in mitosis, including micronuclei and chromosome bridges, and determine their contribution to common karyotype aberrations including whole chromosome loss that has been recently reported after editing in embryos. Together, these data demonstrate that Cas9-mediated germline genome editing can lead to unwanted on-target side effects, including major chromosome structural alterations that can be propagated over several divisions of embryonic development.
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Affiliation(s)
- Stamatis Papathanasiou
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Logan J Blaine
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mitchell L Leibowitz
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cheng-Zhong Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rudolf Jaenisch
- Whitehead Institute, Cambridge, MA, USA.
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA.
| | - David Pellman
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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22
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Wang A, Neill SG, Newman S, Tryfonidou MA, Ioachimescu A, Rossi MR, Meij BP, Oyesiku NM. The genomic profiling and MAMLD1 expression in human and canines with Cushing's disease. BMC Endocr Disord 2021; 21:185. [PMID: 34517852 PMCID: PMC8438999 DOI: 10.1186/s12902-021-00845-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Cushing's disease (CD) is defined as hypercortisolemia caused by adrenocorticotropic hormone (ACTH)-secreting pituitary adenomas (corticotroph PA) that afflicts humans and dogs. In order to map common aberrant genomic features of CD between humans and dogs, we performed genomic sequencing and immunostaining on corticotroph PA. METHODS For inclusion, humans and dog were diagnosed with CD. Whole exome sequencing (WES) was conducted on 6 human corticotroph PA. Transcriptome RNA-Seq was performed on 6 human and 7 dog corticotroph PA. Immunohistochemistry (IHC) was complete on 31 human corticotroph PA. Corticotroph PA were compared with normal tissue and between species analysis were also performed. RESULTS Eight genes (MAMLD1, MNX1, RASEF, TBX19, BIRC5, TK1, GLDC, FAM131B) were significantly (P < 0.05) overexpressed across human and canine corticotroph PA. IHC revealed MAMLD1 to be positively (3+) expressed in the nucleus of ACTH-secreting tumor cells of human corticotroph PA (22/31, 70.9%), but absent in healthy human pituitary glands. CONCLUSIONS In this small exploratory cohort, we provide the first preliminary insights into profiling the genomic characterizations of human and dog corticotroph PA with respect to MAMLD1 overexpression, a finding of potential direct impact to CD microadenoma diagnosis. Our study also offers a rationale for potential use of the canine model in development of precision therapeutics.
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Affiliation(s)
- Andrew Wang
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- College of Medicine, Charles R. Drew University of Medicine and Science, Los Angeles, CA, USA
| | - Stewart G Neill
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Scott Newman
- Department of Computational Biology, St. Jude Children's Research Hospital, Anchorage, TN, USA
| | - Marianna A Tryfonidou
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Adriana Ioachimescu
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA , USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael R Rossi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Björn P Meij
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Nelson M Oyesiku
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA , USA.
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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23
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Kumagai A, Dunphy WG. Binding of the Treslin-MTBP Complex to Specific Regions of the Human Genome Promotes the Initiation of DNA Replication. Cell Rep 2021; 32:108178. [PMID: 32966791 PMCID: PMC7523632 DOI: 10.1016/j.celrep.2020.108178] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/12/2020] [Accepted: 08/31/2020] [Indexed: 12/16/2022] Open
Abstract
The processes that control where higher eukaryotic cells initiate DNA replication throughout the genome are not understood clearly. In metazoans, the Treslin-MTBP complex mediates critical final steps in formation of the activated replicative helicase prior to initiation of replication. Here, we map the genome-wide distribution of the MTBP subunit of this complex in human cells. Our results indicate that MTBP binds to at least 30,000 sites in the genome. A majority of these sites reside in regions of open chromatin that contain transcriptional-regulatory elements (e.g., promoters, enhancers, and super-enhancers), which are known to be preferred areas for initiation of replication. Furthermore, many binding sites encompass two genomic features: a nucleosome-free DNA sequence (e.g., G-quadruplex DNA or AP-1 motif) and a nucleosome bearing histone marks characteristic of open chromatin, such as H3K4me2. Taken together, these findings indicate that Treslin-MTBP associates coordinately with multiple genomic signals to promote initiation of replication. Kumagai and Dunphy show that Treslin-MTBP, activator of the replicative helicase, binds to at least 30,000 sites in the human genome. Many sites contain a nucleosome with active chromatin marks and nucleosome-free DNA (G-quadruplex or AP-1 site). Thus, Treslin-MTBP associates with multiple genomic elements to promote initiation of DNA replication.
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Affiliation(s)
- Akiko Kumagai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - William G Dunphy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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24
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Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J, Vázquez-García I, Kleinheinz K, Livitz DG, Malikic S, Donmez N, Sengupta S, Anur P, Jolly C, Cmero M, Rosebrock D, Schumacher SE, Fan Y, Fittall M, Drews RM, Yao X, Watkins TBK, Lee J, Schlesner M, Zhu H, Adams DJ, McGranahan N, Swanton C, Getz G, Boutros PC, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Martincorena I, Markowetz F, Mustonen V, Yuan K, Gerstung M, Spellman PT, Wang W, Morris QD, Wedge DC, Van Loo P. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell 2021; 184:2239-2254.e39. [PMID: 33831375 PMCID: PMC8054914 DOI: 10.1016/j.cell.2021.03.009] [Citation(s) in RCA: 249] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 09/21/2020] [Accepted: 03/03/2021] [Indexed: 02/07/2023]
Abstract
Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin, and drivers of ITH across cancer types are poorly understood. To address this, we extensively characterize ITH across whole-genome sequences of 2,658 cancer samples spanning 38 cancer types. Nearly all informative samples (95.1%) contain evidence of distinct subclonal expansions with frequent branching relationships between subclones. We observe positive selection of subclonal driver mutations across most cancer types and identify cancer type-specific subclonal patterns of driver gene mutations, fusions, structural variants, and copy number alterations as well as dynamic changes in mutational processes between subclonal expansions. Our results underline the importance of ITH and its drivers in tumor evolution and provide a pan-cancer resource of comprehensively annotated subclonal events from whole-genome sequencing data.
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Affiliation(s)
- Stefan C Dentro
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK; Big Data Institute, University of Oxford, Oxford OX3 7LF, UK
| | | | - Kerstin Haase
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Maxime Tarabichi
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Jeff Wintersinger
- University of Toronto, Toronto, ON M5S 3E1, Canada; Vector Institute, Toronto, ON M5G 1L7, Canada
| | - Amit G Deshwar
- University of Toronto, Toronto, ON M5S 3E1, Canada; Vector Institute, Toronto, ON M5G 1L7, Canada
| | - Kaixian Yu
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yulia Rubanova
- University of Toronto, Toronto, ON M5S 3E1, Canada; Vector Institute, Toronto, ON M5G 1L7, Canada
| | - Geoff Macintyre
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Jonas Demeulemeester
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Ignacio Vázquez-García
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK; University of Cambridge, Cambridge CB2 0QQ, UK; Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA
| | - Kortine Kleinheinz
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Heidelberg University, 69120 Heidelberg, Germany
| | | | - Salem Malikic
- Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Nilgun Donmez
- Simon Fraser University, Burnaby, BC V5A 1S6, Canada; Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | | | - Pavana Anur
- Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97231, USA
| | - Clemency Jolly
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Marek Cmero
- University of Melbourne, Melbourne, VIC 3010, Australia; Walter + Eliza Hall Institute, Melbourne, VIC 3000, Australia
| | | | | | - Yu Fan
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Fittall
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ruben M Drews
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Xiaotong Yao
- Weill Cornell Medicine, New York, NY 10065, USA; New York Genome Center, New York, NY 10013, USA
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Juhee Lee
- University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Hongtu Zhu
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David J Adams
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK; Cancer Genome Evolution Research Group, University College London Cancer Institute, London WC1E 6DD, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Massachusetts General Hospital, Department of Pathology, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Paul C Boutros
- University of Toronto, Toronto, ON M5S 3E1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marcin Imielinski
- Weill Cornell Medicine, New York, NY 10065, USA; New York Genome Center, New York, NY 10013, USA
| | - Rameen Beroukhim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - S Cenk Sahinalp
- Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yuan Ji
- NorthShore University HealthSystem, Evanston, IL 60201, USA; The University of Chicago, Chicago, IL 60637, USA
| | - Martin Peifer
- Department of Translational Genomics, Center for Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | | | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Ke Yuan
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; School of Computing Science, University of Glasgow, Glasgow G12 8RZ, UK
| | - Moritz Gerstung
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK; European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Paul T Spellman
- Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97231, USA
| | - Wenyi Wang
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Quaid D Morris
- University of Toronto, Toronto, ON M5S 3E1, Canada; Vector Institute, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David C Wedge
- Big Data Institute, University of Oxford, Oxford OX3 7LF, UK; Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, UK; Manchester Cancer Research Centre, University of Manchester, Manchester M20 4GJ, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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25
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Brezina S, Feigl M, Gumpenberger T, Staudinger R, Baierl A, Gsur A. Genome-wide association study of germline copy number variations reveals an association with prostate cancer aggressiveness. Mutagenesis 2021; 35:283-290. [PMID: 32255470 DOI: 10.1093/mutage/geaa010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/16/2020] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer is a major health burden, being the second most commonly diagnosed malignancy in men worldwide. Overtreatment represents a major problem in prostate cancer therapy, leading to significant long-term quality-of-life effects for patients and a broad socio-ecological burden. Biomarkers that could facilitate risk stratification of prostate cancer aggressiveness at the time of diagnosis may help to guide clinical treatment decisions and reduce overtreatment. Previous research on genetic variations in prostate cancer has shown that germline copy number variations as well as somatic copy number alterations are commonly present in cancer patients, altering a greater portion of the cancer genome than any other type of genetic variation. To investigate the effect of germline copy number variations on cancer aggressiveness we have compared genome-wide screening data from genomic DNA isolated from the blood of 120 patients with aggressive prostate cancer, 231 patients with non-aggressive prostate cancer and 87 controls with benign prostatic hyperplasia from the Prostate Cancer Study of Austria biobank using the Affymetrix SNP 6.0 array. We could show that patients with an aggressive form of prostate cancer had a higher frequency of copy number variations [mean count of copy number segments (CNS) = 12.9, median count of CNS = 9] compared to patients with non-aggressive prostate cancer (mean count of CNS = 10.4, median count of CNS = 8) or control patients diagnosed with benign prostatic hyperplasia (mean count of CNS = 9.3, median count of CNS = 8). In general, we observed that copy number gain is a rarer event, compared to copy number loss within all three patient groups. Furthermore, we could show a significant effect of copy number losses located on chromosomes 8, 9 and 10 on prostate cancer aggressiveness (P = 0.040, P = 0.037 and P = 0.005, respectively). Applying a cross-validation analysis yielded an area under the curve of 0.63. Our study reports promising findings suggesting that copy number losses might play an important role in the establishment of novel biomarkers to predict prostate cancer aggressiveness at the time of diagnosis. Such markers could be used to facilitate risk stratification to reduce overtreatment of prostate cancer patients.
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Affiliation(s)
- Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Moritz Feigl
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria.,Institute for Hydrology and Water Management, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Tanja Gumpenberger
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Ricarda Staudinger
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Andreas Baierl
- Department of Statistics and Operations Research, University of Vienna, Vienna, Austria
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
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26
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Nachmanson D, Steward J, Yao H, Officer A, Jeong E, O'Keefe TJ, Hasteh F, Jepsen K, Hirst GL, Esserman LJ, Borowsky AD, Harismendy O. Mutational profiling of micro-dissected pre-malignant lesions from archived specimens. BMC Med Genomics 2020; 13:173. [PMID: 33208147 PMCID: PMC7672910 DOI: 10.1186/s12920-020-00820-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Systematic cancer screening has led to the increased detection of pre-malignant lesions (PMLs). The absence of reliable prognostic markers has led mostly to over treatment resulting in potentially unnecessary stress, or insufficient treatment and avoidable progression. Importantly, most mutational profiling studies have relied on PML synchronous to invasive cancer, or performed in patients without outcome information, hence limiting their utility for biomarker discovery. The limitations in comprehensive mutational profiling of PMLs are in large part due to the significant technical and methodological challenges: most PML specimens are small, fixed in formalin and paraffin embedded (FFPE) and lack matching normal DNA. METHODS Using test DNA from a highly degraded FFPE specimen, multiple targeted sequencing approaches were evaluated, varying DNA input amount (3-200 ng), library preparation strategy (BE: Blunt-End, SS: Single-Strand, AT: A-Tailing) and target size (whole exome vs. cancer gene panel). Variants in high-input DNA from FFPE and mirrored frozen specimens were used for PML-specific variant calling training and testing, respectively. The resulting approach was applied to profile and compare multiple regions micro-dissected (mean area 5 mm2) from 3 breast ductal carcinoma in situ (DCIS). RESULTS Using low-input FFPE DNA, BE and SS libraries resulted in 4.9 and 3.7 increase over AT libraries in the fraction of whole exome covered at 20x (BE:87%, SS:63%, AT:17%). Compared to high-confidence somatic mutations from frozen specimens, PML-specific variant filtering increased recall (BE:85%, SS:80%, AT:75%) and precision (BE:93%, SS:91%, AT:84%) to levels expected from sampling variation. Copy number alterations were consistent across all tested approaches and only impacted by the design of the capture probe-set. Applied to DNA extracted from 9 micro-dissected regions (8 PML, 1 normal epithelium), the approach achieved comparable performance, illustrated the data adequacy to identify candidate driver events (GATA3 mutations, ERBB2 or FGFR1 gains, TP53 loss) and measure intra-lesion genetic heterogeneity. CONCLUSION Alternate experimental and analytical strategies increased the accuracy of DNA sequencing from archived micro-dissected PML regions, supporting the deeper molecular characterization of early cancer lesions and achieving a critical milestone in the development of biology-informed prognostic markers and precision chemo-prevention strategies.
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Affiliation(s)
- Daniela Nachmanson
- Bioinformatics and Systems Biology Graduate Program - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Joseph Steward
- Moores Cancer Center - UC San Diego Health - 3855 Health Sciences Dr., La Jolla, CA, 92093, USA
| | - Huazhen Yao
- Institute for Genomic Medicine - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Adam Officer
- Bioinformatics and Systems Biology Graduate Program - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.,Division of Biomedical Informatics, Department of Medicine - UC San Diego School of Medicine, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Eliza Jeong
- Moores Cancer Center - UC San Diego Health - 3855 Health Sciences Dr., La Jolla, CA, 92093, USA
| | - Thomas J O'Keefe
- Division of Breast Surgery and The Comprehensive Breast Health Center - UC San Diego School of Medicine, 3855 Health Sciences Dr., La Jolla, CA, 92093, USA
| | - Farnaz Hasteh
- Department of Pathology - UC San Diego School of Medicine, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Gillian L Hirst
- Helen Diller Family Comprehensive Cancer Center - UC San Francisco School of Medicine, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Laura J Esserman
- Helen Diller Family Comprehensive Cancer Center - UC San Francisco School of Medicine, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Alexander D Borowsky
- Department of Pathology and Laboratory Medicine - UC Davis Comprehensive Cancer Center, UC Davis School of Medicine, 2279 45th Street, Sacramento, CA, 95817, USA
| | - Olivier Harismendy
- Moores Cancer Center - UC San Diego Health - 3855 Health Sciences Dr., La Jolla, CA, 92093, USA. .,Division of Biomedical Informatics, Department of Medicine - UC San Diego School of Medicine, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
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27
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Evolution from adherent to suspension: systems biology of HEK293 cell line development. Sci Rep 2020; 10:18996. [PMID: 33149219 PMCID: PMC7642379 DOI: 10.1038/s41598-020-76137-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 10/22/2020] [Indexed: 01/28/2023] Open
Abstract
The need for new safe and efficacious therapies has led to an increased focus on biologics produced in mammalian cells. The human cell line HEK293 has bio-synthetic potential for human-like production attributes and is currently used for manufacturing of several therapeutic proteins and viral vectors. Despite the increased popularity of this strain we still have limited knowledge on the genetic composition of its derivatives. Here we present a genomic, transcriptomic and metabolic gene analysis of six of the most widely used HEK293 cell lines. Changes in gene copy and expression between industrial progeny cell lines and the original HEK293 were associated with cellular component organization, cell motility and cell adhesion. Changes in gene expression between adherent and suspension derivatives highlighted switching in cholesterol biosynthesis and expression of five key genes (RARG, ID1, ZIC1, LOX and DHRS3), a pattern validated in 63 human adherent or suspension cell lines of other origin.
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28
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Jones LE, Hilz S, Grimmer MR, Mazor T, Najac C, Mukherjee J, McKinney A, Chow T, Pieper RO, Ronen SM, Chang SM, Phillips JJ, Costello JF. Patient-derived cells from recurrent tumors that model the evolution of IDH-mutant glioma. Neurooncol Adv 2020; 2:vdaa088. [PMID: 32904945 PMCID: PMC7462278 DOI: 10.1093/noajnl/vdaa088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background IDH-mutant lower-grade gliomas (LGGs) evolve under the selective pressure of therapy, but well-characterized patient-derived cells (PDCs) modeling evolutionary stages are lacking. IDH-mutant LGGs may develop therapeutic resistance associated with chemotherapy-driven hypermutation and malignant progression. The aim of this study was to establish and characterize PDCs, single-cell-derived PDCs (scPDCs), and xenografts (PDX) of IDH1-mutant recurrences representing distinct stages of tumor evolution. Methods We derived and validated cell cultures from IDH1-mutant recurrences of astrocytoma and oligodendroglioma. We used exome sequencing and phylogenetic reconstruction to examine the evolutionary stage represented by PDCs, scPDCs, and PDX relative to corresponding spatiotemporal tumor tissue and germline DNA. PDCs were also characterized for growth and tumor immortality phenotypes, and PDX were examined histologically. Results The integrated astrocytoma phylogeny revealed 2 independent founder clonal expansions of hypermutated (HM) cells in tumor tissue that are faithfully represented by independent PDCs. The oligodendroglioma phylogeny showed more than 4000 temozolomide-associated mutations shared among tumor samples, PDCs, scPDCs, and PDX, suggesting a shared monoclonal origin. The PDCs from both subtypes exhibited hallmarks of tumorigenesis, retention of subtype-defining genomic features, production of 2-hydroxyglutarate, and subtype-specific telomere maintenance mechanisms that confer tumor cell immortality. The oligodendroglioma PDCs formed infiltrative intracranial tumors with characteristic histology. Conclusions These PDCs, scPDCs, and PDX are unique and versatile community resources that model the heterogeneous clonal origins and functions of recurrent IDH1-mutant LGGs. The integrated phylogenies advance our knowledge of the complex evolution and immense mutational load of IDH1-mutant HM glioma.
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Affiliation(s)
- Lindsey E Jones
- Department of Neurological Surgery, University of California, San Francisco, California, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, California, USA
| | - Stephanie Hilz
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Matthew R Grimmer
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Tali Mazor
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Chloé Najac
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Joydeep Mukherjee
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Andrew McKinney
- Department of Neurological Surgery, University of California, San Francisco, California, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, California, USA
| | - Tracy Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Russell O Pieper
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Sabrina M Ronen
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, California, USA
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29
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Palmisano A, Krushkal J, Li MC, Fang J, Sonkin D, Wright G, Yee L, Zhao Y, McShane L. Bioinformatics Tools and Resources for Cancer Immunotherapy Study. Methods Mol Biol 2020; 2055:649-678. [PMID: 31502173 DOI: 10.1007/978-1-4939-9773-2_29] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In recent years, cancer immunotherapy has emerged as a highly promising approach to treat patients with cancer, as the patient's own immune system is harnessed to attack cancer cells. However, the application of these approaches is still limited to a minority of patients with cancer and it is difficult to predict which patients will derive the greatest clinical benefit.One of the challenges faced by the biomedical community in the search of more effective biomarkers is the fact that translational research efforts involve collecting and accessing data at many different levels: from the type of material examined (e.g., cell line, animal models, clinical samples) to multiple data type (e.g., pharmacodynamic markers, genetic sequencing data) to the scale of a study (e.g., small preclinical study, moderate retrospective study on stored specimen sets, clinical trials with large cohorts).This chapter reviews several publicly available bioinformatics tools and data resources for high throughput molecular analyses applied to a range of data types, including those generated from microarray, whole-exome sequencing (WES), RNA-seq, DNA copy number, and DNA methylation assays, that are extensively used for integrative multidimensional data analysis and visualization.
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Affiliation(s)
- Alida Palmisano
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ming-Chung Li
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jianwen Fang
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dmitriy Sonkin
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - George Wright
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laura Yee
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Lisa McShane
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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30
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Hassan S, Purdie KJ, Wang J, Harwood CA, Proby CM, Pourreyron C, Mladkova N, Nagano A, Dhayade S, Athineos D, Caley M, Mannella V, Blyth K, Inman GJ, Leigh IM. A Unique Panel of Patient-Derived Cutaneous Squamous Cell Carcinoma Cell Lines Provides a Preclinical Pathway for Therapeutic Testing. Int J Mol Sci 2019; 20:E3428. [PMID: 31336867 PMCID: PMC6678499 DOI: 10.3390/ijms20143428] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 06/28/2019] [Accepted: 07/04/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Cutaneous squamous cell carcinoma (cSCC) incidence continues to rise with increasing morbidity and mortality, with limited treatment options for advanced disease. Future improvements in targeted therapy will rely on advances in genomic/transcriptomic understanding and the use of model systems for basic research. We describe here the panel of 16 primary and metastatic cSCC cell lines developed and characterised over the past three decades in our laboratory in order to provide such a resource for future preclinical research and drug screening. METHODS Primary keratinocytes were isolated from cSCC tumours and metastases, and cell lines were established. These were characterised using short tandem repeat (STR) profiling and genotyped by whole exome sequencing. Multiple in vitro assays were performed to document their morphology, growth characteristics, migration and invasion characteristics, and in vivo xenograft growth. RESULTS STR profiles of the cSCC lines allow the confirmation of their unique identity. Phylogenetic trees derived from exome sequence analysis of the matched primary and metastatic lines provide insight into the genetic basis of disease progression. The results of in vivo and in vitro analyses allow researchers to select suitable cell lines for specific experimentation. CONCLUSIONS There are few well-characterised cSCC lines available for widespread preclinical experimentation and drug screening. The described cSCC cell line panel provides a critical tool for in vitro and in vivo experimentation.
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Affiliation(s)
- Sakinah Hassan
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Karin J Purdie
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Jun Wang
- Barts Cancer Institute, QMUL, London EC1M 6BQ, UK
| | - Catherine A Harwood
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Charlotte M Proby
- Division of Cancer, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Celine Pourreyron
- Division of Cancer, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Nikol Mladkova
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Ai Nagano
- Barts Cancer Institute, QMUL, London EC1M 6BQ, UK
| | - Sandeep Dhayade
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK
| | - Dimitris Athineos
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK
| | - Matthew Caley
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Viviana Mannella
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Karen Blyth
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK
| | - Gareth J Inman
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1GH, UK
| | - Irene M Leigh
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK.
- Division of Cancer, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK.
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31
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Jakubek YA, San Lucas FA, Scheet P. Directional allelic imbalance profiling and visualization from multi-sample data with RECUR. Bioinformatics 2019; 35:2300-2302. [PMID: 30462146 PMCID: PMC6596882 DOI: 10.1093/bioinformatics/bty885] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/27/2018] [Accepted: 11/20/2018] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION Genetic analysis of cancer regularly includes two or more samples from the same patient. Somatic copy number alterations leading to allelic imbalance (AI) play a critical role in cancer initiation and progression. Directional analysis and visualization of the alleles in imbalance in multi-sample settings allow for inference of recurrent mutations, providing insights into mutation rates, clonality and the genomic architecture and etiology of cancer. RESULTS The REpeat Chromosomal changes Uncovered by Reflection (RECUR) is an R application for the comparative analysis of AI profiles derived from SNP array and next-generation sequencing data. The algorithm accepts genotype calls and 'B allele' frequencies (BAFs) from at least two samples derived from the same individual. For a predefined set of genomic regions with AI, RECUR compares BAF values among samples. In the presence of AI, the expected value of a BAF can shift in two possible directions, reflecting an increased or decreased abundance of the maternal haplotype, relative to the paternal. The phenomenon of opposite haplotype shifts, or 'mirrored subclonal allelic imbalance', is a form of heterogeneity, and has been linked to clinico-pathological features of cancer. RECUR detects such genomic segments of opposite haplotypes in imbalance and plots BAF values for all samples, using a two-color scheme for intuitive visualization. AVAILABILITY AND IMPLEMENTATION RECUR is available as an R application. Source code and documentation are available at scheet.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yasminka A Jakubek
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - F Anthony San Lucas
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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32
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Yu CY, Xiang S, Huang Z, Johnson TS, Zhan X, Han Z, Abu Zaid M, Huang K. Gene Co-expression Network and Copy Number Variation Analyses Identify Transcription Factors Associated With Multiple Myeloma Progression. Front Genet 2019; 10:468. [PMID: 31156714 PMCID: PMC6533571 DOI: 10.3389/fgene.2019.00468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 05/01/2019] [Indexed: 11/29/2022] Open
Abstract
Multiple myeloma (MM) has two clinical precursor stages of disease: monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM). However, the mechanism of progression is not well understood. Because gene co-expression network analysis is a well-known method for discovering new gene functions and regulatory relationships, we utilized this framework to conduct differential co-expression analysis to identify interesting transcription factors (TFs) in two publicly available datasets. We then used copy number variation (CNV) data from a third public dataset to validate these TFs. First, we identified co-expressed gene modules in two publicly available datasets each containing three conditions: normal, MGUS, and SMM. These modules were assessed for condition-specific gene expression, and then enrichment analysis was conducted on condition-specific modules to identify their biological function and upstream TFs. TFs were assessed for differential gene expression between normal and MM precursors, then validated with CNV analysis to identify candidate genes. Functional enrichment analysis reaffirmed known functional categories in MM pathology, the main one relating to immune function. Enrichment analysis revealed a handful of differentially expressed TFs between normal and either MGUS or SMM in gene expression and/or CNV. Overall, we identified four genes of interest (MAX, TCF4, ZNF148, and ZNF281) that aid in our understanding of MM initiation and progression.
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Affiliation(s)
- Christina Y Yu
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, United States.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Shunian Xiang
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN, United States.,National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China
| | - Zhi Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, United States
| | - Travis S Johnson
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, United States.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Xiaohui Zhan
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China
| | - Zhi Han
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,Regenstrief Institute, Indianapolis, IN, United States
| | - Mohammad Abu Zaid
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Kun Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,Regenstrief Institute, Indianapolis, IN, United States
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33
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Rodrigues-Peres RM, de S Carvalho B, Anurag M, Lei JT, Conz L, Gonçalves R, Cardoso Filho C, Ramalho S, de Paiva GR, Derchain SFM, Lopes-Cendes I, Ellis MJ, Sarian LO. Copy number alterations associated with clinical features in an underrepresented population with breast cancer. Mol Genet Genomic Med 2019; 7:e00750. [PMID: 31099189 PMCID: PMC6625096 DOI: 10.1002/mgg3.750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/22/2019] [Accepted: 04/26/2019] [Indexed: 12/14/2022] Open
Abstract
Background As the most incident tumor among women worldwide, breast cancer is a heterogeneous disease. Tremendous efforts have been made to understand how tumor characteristics as histological type, molecular subtype, and tumor microenvironment collectively influence disease diagnosis to treatment, which impact outcomes. Differences between populations and environmental and cultural factors have impacts on the origin and evolution of the disease, as well as the therapeutic challenges that arise due to these factors. We, then, compared copy number variations (CNVs) in mucinous and nonmucinous luminal breast tumors from a Brazilian cohort to investigate major CNV imbalances in mucinous tumors versus non‐mucinous luminal tumors, taking into account their clinical and pathological features. Methods 48 breast tumor samples and 48 matched control blood samples from Brazilian women were assessed for CNVs by chromosome microarray. Logistic regression and random forest models were used in order to assess CNVs in chromosomal regions from tumors. Results CNVs that were identified in chromosomes 1, 5, 8, 17, 19, and 21 classify tumors according to their histological type, ethnicity, disease stage, and familial history. Conclusion Copy number alterations described in this study provide a better understanding of the landscape of genomic aberrations in mucinous breast cancers that are associated with clinical features.
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Affiliation(s)
- Raquel M Rodrigues-Peres
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Benilton de S Carvalho
- Department of Statistics, Institute of Mathematics, Statistics and Scientific Computing, State University of Campinas-UNICAMP, Campinas, Brazil.,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Meenakshi Anurag
- Department of Medicine, Baylor College of Medicine, Houston, TX.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX
| | - Jonathan T Lei
- Department of Medicine, Baylor College of Medicine, Houston, TX.,Interdepartmental Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX
| | - Livia Conz
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Rodrigo Gonçalves
- Department of Mastology, Hospital das Clínicas, Discipline of Gynecology, Department of Obstetrics and Gynecology, Faculty of Medicine, University of São Paulo, Brazil
| | - Cássio Cardoso Filho
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Susana Ramalho
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Geisilene R de Paiva
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Sophie F M Derchain
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Iscia Lopes-Cendes
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil.,Department of Medical Genetics, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Matthew J Ellis
- Department of Medicine, Baylor College of Medicine, Houston, TX.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX.,Interdepartmental Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | - Luis O Sarian
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
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Defective homologous recombination DNA repair as therapeutic target in advanced chordoma. Nat Commun 2019; 10:1635. [PMID: 30967556 PMCID: PMC6456501 DOI: 10.1038/s41467-019-09633-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 03/19/2019] [Indexed: 12/21/2022] Open
Abstract
Chordomas are rare bone tumors with few therapeutic options. Here we show, using whole-exome and genome sequencing within a precision oncology program, that advanced chordomas (n = 11) may be characterized by genomic patterns indicative of defective homologous recombination (HR) DNA repair and alterations affecting HR-related genes, including, for example, deletions and pathogenic germline variants of BRCA2, NBN, and CHEK2. A mutational signature associated with HR deficiency was significantly enriched in 72.7% of samples and co-occurred with genomic instability. The poly(ADP-ribose) polymerase (PARP) inhibitor olaparib, which is preferentially toxic to HR-incompetent cells, led to prolonged clinical benefit in a patient with refractory chordoma, and whole-genome analysis at progression revealed a PARP1 p.T910A mutation predicted to disrupt the autoinhibitory PARP1 helical domain. These findings uncover a therapeutic opportunity in chordoma that warrants further exploration, and provide insight into the mechanisms underlying PARP inhibitor resistance. Chordomas are rare bone tumors with limited therapeutic options. Here, the authors identify molecular alterations associated with defective homologous recombination DNA repair in advanced chordomas and report prolonged response in a patient treated with a PARP inhibitor, which later acquired resistance due to a newly gained PARP1 mutation.
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35
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Wojtas B, Gielniewski B, Wojnicki K, Maleszewska M, Mondal SS, Nauman P, Grajkowska W, Glass R, Schüller U, Herold-Mende C, Kaminska B. Gliosarcoma Is Driven by Alterations in PI3K/Akt, RAS/MAPK Pathways and Characterized by Collagen Gene Expression Signature. Cancers (Basel) 2019; 11:cancers11030284. [PMID: 30818875 PMCID: PMC6468745 DOI: 10.3390/cancers11030284] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 01/15/2023] Open
Abstract
Gliosarcoma is a very rare brain tumor reported to be a variant of glioblastoma (GBM), IDH-wildtype. While differences in molecular and histological features between gliosarcoma and GBM were reported, detailed information on the genetic background of this tumor is lacking. We intend to fill in this knowledge gap by the complex analysis of somatic mutations, indels, copy number variations, translocations and gene expression patterns in gliosarcomas. Using next generation sequencing, we determined somatic mutations, copy number variations (CNVs) and translocations in 10 gliosarcomas. Six tumors have been further subjected to RNA sequencing analysis and gene expression patterns have been compared to those of GBMs. We demonstrate that gliosarcoma bears somatic alterations in gene coding for PI3K/Akt (PTEN, PI3K) and RAS/MAPK (NF1, BRAF) signaling pathways that are crucial for tumor growth. Interestingly, the frequency of PTEN alterations in gliosarcomas was much higher than in GBMs. Aberrations of PTEN were the most frequent and occurred in 70% of samples. We identified genes differentially expressed in gliosarcoma compared to GBM (including collagen signature) and confirmed a difference in the protein level by immunohistochemistry. We found several novel translocations (including translocations in the RABGEF1 gene) creating potentially unfavorable combinations. Collected results on genetic alterations and transcriptomic profiles offer new insights into gliosarcoma pathobiology, highlight differences in gliosarcoma and GBM genetic backgrounds and point out to distinct molecular cues for targeted treatment.
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Affiliation(s)
- Bartosz Wojtas
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland.
| | - Bartlomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland.
| | - Kamil Wojnicki
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland.
| | - Marta Maleszewska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland.
| | - Shamba S Mondal
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, Warsaw 02-093, Poland.
| | - Pawel Nauman
- Department of Neurosurgery, Institute of Psychiatry and Neurology, Warsaw 02-957, Poland.
| | - Wieslawa Grajkowska
- Department of Pathology, The Children's Memorial Health Institute, Warsaw 04-730, Poland.
| | - Rainer Glass
- Neurosurgical Research, University Clinics, LMU Munich 80539, Germany.
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center, Hamburg-Eppendorf 20251, Germany.
- Research Institute Children's Cancer Center Hamburg, Hamburg 20251, Germany.
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany.
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University of Heidelberg, Heidelberg 69120, Germany.
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland.
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36
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Hayes J, Yu Y, Jalbert LE, Mazor T, Jones LE, Wood MD, Walsh KM, Bengtsson H, Hong C, Oberndorfer S, Roetzer T, Smirnov IV, Clarke JL, Aghi MK, Chang SM, Nelson SJ, Woehrer A, Phillips JJ, Solomon DA, Costello JF. Genomic analysis of the origins and evolution of multicentric diffuse lower-grade gliomas. Neuro Oncol 2019; 20:632-641. [PMID: 29077933 DOI: 10.1093/neuonc/nox205] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background Rare multicentric lower-grade gliomas (LGGs) represent a unique opportunity to study the heterogeneity among distinct tumor foci in a single patient and to infer their origins and parallel patterns of evolution. Methods In this study, we integrate clinical features, histology, and immunohistochemistry for 4 patients with multicentric LGG, arising both synchronously and metachronously. For 3 patients we analyze the phylogeny of the lesions using exome sequencing, including one case with a total of 8 samples from the 2 lesions. Results One patient was diagnosed with multicentric isocitrate dehydrogenase 1 (IDH1) mutated diffuse astrocytomas harboring distinct IDH1 mutations, R132H and R132C; the latter mutation has been associated with Li-Fraumeni syndrome, which was subsequently confirmed in the patient's germline DNA and shown in additional cases with The Cancer Genome Atlas data. In another patient, phylogenetic analysis of synchronously arising grade II and grade III diffuse astrocytomas demonstrated a single shared mutation, IDH1 R132H, and revealed convergent evolution via non-overlapping mutations in ATRX and TP53. In 2 cases, there was divergent evolution of IDH1-mutated and 1p/19q-codeleted oligodendroglioma and IDH1-mutated and 1p/19q-intact diffuse astrocytoma, occurring synchronously in one case and metachronously in a second. Conclusions Each tumor in multicentric LGG cases may arise independently or may diverge very early in their development, presenting as genetically and histologically distinct tumors. Comprehensive sampling of these lesions can therefore significantly alter diagnosis and management. Additionally, somatic IDH1 R132C mutation in either multicentric or solitary LGG identifies unsuspected germline TP53 mutation, validating the limited number of published cases.
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Affiliation(s)
- Josie Hayes
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Yao Yu
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
| | - Llewellyn E Jalbert
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Tali Mazor
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Lindsey E Jones
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Matthew D Wood
- Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Kyle M Walsh
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Henrik Bengtsson
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Stefan Oberndorfer
- Department of Neurology, University Hospital of St Poelten, St Poelten, Austria
| | - Thomas Roetzer
- Institute of Neurology and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Ivan V Smirnov
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Jennifer L Clarke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA.,UCSF Brain Tumor Center, Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA.,Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Manish K Aghi
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA.,UCSF Brain Tumor Center, Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Sarah J Nelson
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Adelheid Woehrer
- Institute of Neurology and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA.,Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - David A Solomon
- Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
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37
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Torabi K, Erola P, Alvarez-Mora MI, Díaz-Gay M, Ferrer Q, Castells A, Castellví-Bel S, Milà M, Lozano JJ, Miró R, Ried T, Ponsa I, Camps J. Quantitative analysis of somatically acquired and constitutive uniparental disomy in gastrointestinal cancers. Int J Cancer 2018; 144:513-524. [PMID: 30350313 PMCID: PMC6635747 DOI: 10.1002/ijc.31936] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/31/2018] [Accepted: 10/02/2018] [Indexed: 12/20/2022]
Abstract
Somatically acquired uniparental disomies (aUPDs) are frequent events in solid tumors and have been associated with cancer‐related genes. Studies assessing their functional consequences across several cancer types are therefore necessary. Here, we aimed at integrating aUPD profiles with the mutational status of cancer‐related genes in a tumor‐type specific manner. Using TCGA datasets for 1,032 gastrointestinal cancers, including colon (COAD), rectum (READ), stomach (STAD), esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC), we show a non‐random distribution of aUPD, suggesting the existence of a cancer‐specific landscape of aUPD events. Our analysis indicates that aUPD acts as a “second hit” in Knudson's model in order to achieve biallelic inactivation of tumor suppressor genes. In particular, APC, ARID1A and NOTCH1 were recurrently inactivated by the presence of homozygous mutation as a consequence of aUPD in COAD and READ, STAD and ESCC, respectively. Furthermore, while TP53 showed inactivation caused by aUPD at chromosome arm 17p across all tumor types, copy number losses at this genomic position were also frequent. By experimental and computationally inferring genome ploidy, we demonstrate that an increased number of aUPD events, both affecting the whole chromosome or segments of it, were present in highly aneuploid genomes compared to near‐diploid tumors. Finally, the presence of mosaic UPD was detected at a higher frequency in DNA extracted from peripheral blood lymphocytes of patients with colorectal cancer compared to healthy individuals. In summary, our study defines specific profiles of aUPD in gastrointestinal cancers and provides unequivocal evidence of their relevance in cancer. What's new? Somatically acquired uniparental disomies (aUPDs), in which two copies of a chromosome originate from the same parent, have been documented in various human cancers. Here, the authors examined the frequency of aUPDs in different gastrointestinal cancer types. Events involving aUPDs were found to occur at high incidence in gastrointestinal cancers and at increased frequency particularly in highly aneuploid genomes. The data also reveal a nonrandom distribution of aUPDs, with evidence of biallelic inactivation of tumor suppressor genes and activation of oncogenes in a tumor type‐specific manner. The findings suggest that aUPDs are functionally relevant in gastrointestinal malignancies.
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Affiliation(s)
- Keyvan Torabi
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain.,Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Pau Erola
- Bioinformatics Unit, CIBEREHD, Barcelona, Catalonia, Spain.,Roslin Institute, University of Edinburgh, Midlothian, Scotland, United Kingdom
| | - Maria Isabel Alvarez-Mora
- Biochemistry and Molecular Genetics Department, Hospital Clínic, IDIBAPS, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Catalonia, Spain
| | - Marcos Díaz-Gay
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain
| | - Queralt Ferrer
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain
| | - Antoni Castells
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain
| | - Sergi Castellví-Bel
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain
| | - Montserrat Milà
- Biochemistry and Molecular Genetics Department, Hospital Clínic, IDIBAPS, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Catalonia, Spain
| | | | - Rosa Miró
- Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain.,Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Immaculada Ponsa
- Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain.,Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain.,Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
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Cheng Y, Dai JY, Wang X, Kooperberg C. Identifying disease-associated copy number variations by a doubly penalized regression model. Biometrics 2018; 74:1341-1350. [PMID: 29894562 PMCID: PMC6663092 DOI: 10.1111/biom.12920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 05/01/2018] [Accepted: 05/01/2018] [Indexed: 11/27/2022]
Abstract
Copy number variation (CNV) of DNA plays an important role in the development of many diseases. However, due to the irregularity and sparsity of the CNVs, studying the association between CNVs and a disease outcome or a trait can be challenging. Up to now, not many methods have been proposed in the literature for this problem. Most of the current researchers reply on an ad hoc two-stage procedure by first identifying CNVs in each individual genome and then performing an association test using these identified CNVs. This potentially leads to information loss and as a result a lower power to identify disease associated CNVs. In this article, we describe a new method that combines the two steps into a single coherent model to identify the common CNV across patients that are associated with certain diseases. We use a double penalty model to capture CNVs' association with both the intensities and the disease trait. We validate its performance in simulated datasets and a data example on platinum resistance and CNV in ovarian cancer genome.
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Affiliation(s)
- Yichen Cheng
- Institute for Insight, Georgia State University, Atlanta, Georgia, USA
| | - James Y. Dai
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
| | - Xiaoyu Wang
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
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39
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Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer. Nat Commun 2018; 9:4782. [PMID: 30429477 PMCID: PMC6235880 DOI: 10.1038/s41467-018-07041-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 10/15/2018] [Indexed: 12/23/2022] Open
Abstract
Incomplete understanding of the metastatic process hinders personalized therapy. Here we report the most comprehensive whole-genome study of colorectal metastases vs. matched primary tumors. 65% of somatic mutations originate from a common progenitor, with 15% being tumor- and 19% metastasis-specific, implicating a higher mutation rate in metastases. Tumor- and metastasis-specific mutations harbor elevated levels of BRCAness. We confirm multistage progression with new components ARHGEF7/ARHGEF33. Recurrently mutated non-coding elements include ncRNAs RP11-594N15.3, AC010091, SNHG14, 3’ UTRs of FOXP2, DACH2, TRPM3, XKR4, ANO5, CBL, CBLB, the latter four potentially dual protagonists in metastasis and efferocytosis-/PD-L1 mediated immunosuppression. Actionable metastasis-specific lesions include FAT1, FGF1, BRCA2, KDR, and AKT2-, AKT3-, and PDGFRA-3’ UTRs. Metastasis specific mutations are enriched in PI3K-Akt signaling, cell adhesion, ECM and hepatic stellate activation genes, suggesting genetic programs for site-specific colonization. Our results put forward hypotheses on tumor and metastasis evolution, and evidence for metastasis-specific events relevant for personalized therapy. The evolution and genetic nature of metastatic lesions is not completely characterized. Here the authors perform a comprehensive whole-genome study of colorectal metastases in comparison to matched primary tumors and define a multistage progression model and metastasis-specific changes that, in part, are therapeutically actionable.
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40
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Gara SK, Lack J, Zhang L, Harris E, Cam M, Kebebew E. Metastatic adrenocortical carcinoma displays higher mutation rate and tumor heterogeneity than primary tumors. Nat Commun 2018; 9:4172. [PMID: 30301885 PMCID: PMC6178360 DOI: 10.1038/s41467-018-06366-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 08/15/2018] [Indexed: 12/21/2022] Open
Abstract
Adrenocortical cancer (ACC) is a rare cancer with poor prognosis and high mortality due to metastatic disease. All reported genetic alterations have been in primary ACC, and it is unknown if there is molecular heterogeneity in ACC. Here, we report the genetic changes associated with metastatic ACC compared to primary ACCs and tumor heterogeneity. We performed whole-exome sequencing of 33 metastatic tumors. The overall mutation rate (per megabase) in metastatic tumors was 2.8-fold higher than primary ACC tumor samples. We found tumor heterogeneity among different metastatic sites in ACC and discovered recurrent mutations in several novel genes. We observed 37–57% overlap in genes that are mutated among different metastatic sites within the same patient. We also identified new therapeutic targets in recurrent and metastatic ACC not previously described in primary ACCs. Adrenocortical cancer (ACC) is a rarely diagnosed and aggressive cancer whose metastatic form has been scarcely studied. Here, the authors study primary and metastatic ACC to investigate genomic heterogeneity, discovering higher mutation rates in metastatic lesions and novel recurrent mutations.
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Affiliation(s)
- Sudheer Kumar Gara
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Justin Lack
- Center for Cancer Research, Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lisa Zhang
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Emerson Harris
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Margaret Cam
- Center for Cancer Research, Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Electron Kebebew
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA. .,Department of Surgery and Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA.
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41
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Sayles LC, Breese MR, Koehne AL, Leung SG, Lee AG, Liu HY, Spillinger A, Shah AT, Tanasa B, Straessler K, Hazard FK, Spunt SL, Marina N, Kim GE, Cho SJ, Avedian RS, Mohler DG, Kim MO, DuBois SG, Hawkins DS, Sweet-Cordero EA. Genome-Informed Targeted Therapy for Osteosarcoma. Cancer Discov 2018; 9:46-63. [PMID: 30266815 DOI: 10.1158/2159-8290.cd-17-1152] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 08/01/2018] [Accepted: 09/25/2018] [Indexed: 11/16/2022]
Abstract
Osteosarcoma is a highly aggressive cancer for which treatment has remained essentially unchanged for more than 30 years. Osteosarcoma is characterized by widespread and recurrent somatic copy-number alterations (SCNA) and structural rearrangements. In contrast, few recurrent point mutations in protein-coding genes have been identified, suggesting that genes within SCNAs are key oncogenic drivers in this disease. SCNAs and structural rearrangements are highly heterogeneous across osteosarcoma cases, suggesting the need for a genome-informed approach to targeted therapy. To identify patient-specific candidate drivers, we used a simple heuristic based on degree and rank order of copy-number amplification (identified by whole-genome sequencing) and changes in gene expression as identified by RNA sequencing. Using patient-derived tumor xenografts, we demonstrate that targeting of patient-specific SCNAs leads to significant decrease in tumor burden, providing a road map for genome-informed treatment of osteosarcoma. SIGNIFICANCE: Osteosarcoma is treated with a chemotherapy regimen established 30 years ago. Although osteosarcoma is genomically complex, we hypothesized that tumor-specific dependencies could be identified within SCNAs. Using patient-derived tumor xenografts, we found a high degree of response for "genome-matched" therapies, demonstrating the utility of a targeted genome-informed approach.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Leanne C Sayles
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, California
| | - Marcus R Breese
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, California
| | - Amanda L Koehne
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, California
| | - Stanley G Leung
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, California
| | - Alex G Lee
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, California
| | - Heng-Yi Liu
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, California
| | - Aviv Spillinger
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, California
| | - Avanthi T Shah
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, California
| | - Bogdan Tanasa
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, California
| | - Krystal Straessler
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, California
| | - Florette K Hazard
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Sheri L Spunt
- Division of Hematology and Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Neyssa Marina
- Division of Hematology and Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Grace E Kim
- Department of Pathology, University of California, San Francisco, California
| | - Soo-Jin Cho
- Department of Pathology, University of California, San Francisco, California
| | - Raffi S Avedian
- Department of Orthopedic Surgery, Stanford University School of Medicine, Stanford University, Stanford, California
| | - David G Mohler
- Department of Orthopedic Surgery, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Mi-Ok Kim
- Biostatistics Core, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Division of Biostatistics, Department of Epidemiology and Biostatistics, University of California, San Francisco, California
| | - Steven G DuBois
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Boston, Massachusetts
| | - Douglas S Hawkins
- Seattle Children's Hospital, University of Washington, Fred Hutchison Cancer Research Center, Seattle, Washington
| | - E Alejandro Sweet-Cordero
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, California.
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The clinical implications of G1-G6 transcriptomic signature and 5-gene score in Korean patients with hepatocellular carcinoma. BMC Cancer 2018; 18:571. [PMID: 29776391 PMCID: PMC5960090 DOI: 10.1186/s12885-018-4192-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 03/06/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Efforts have been made to classify Hepatocellular Carcinoma (HCC) at surgically curable stages because molecular classification, which is prognostically informative, can accurately identify patients in need of additional early therapeutic interventions. Recently, HCC classification based French studies on the expression of 16 genes and 5 genes were proposed. In 16-gene classification, transcriptomic signatures (G1-G6) were used to classify HCC patients into clinical, genomic and pathway-specific subgroups. In 5-gene score classification, the good or poor prognosis of HCC patients was predicted. The patient's cohort in these studies was mainly from Caucasian and African populations. Here, we aimed to validate G1-G6 and 5-gene score signatures in 205 Korean HCC patients since genomic profiles of Korean patients are distinct from other regions. METHODS Integrated analyses using whole-exome sequencing, copy number variation and clinical data was performed against these two signatures to find statistical correlations. Kaplan-Meier, univariate and multivariate COX regression analysis were performed for Disease-Specific Survival (DSS) and Recurrence-Free Survival (RFS). RESULTS The G2 and G3 subgroups of transcriptomic signature were significantly associated with TP53 mutations while G5 and G6 subgroups were significantly associated with CTNNB1 mutations which is in concordance with original French studies. Similarly, the poor prognosis group of 5-gene score showed shorter DSS (p = 0.045) and early RFS (p = 0.023) as well as a significant association with microvascular invasion, tumor size (> 5 cm), elevated AFP levels, and RB1 mutations. However, the 5-gene score was not an independent prognostic factor for survival. CONCLUSION The G1-G6 and 5-gene signatures showed significant concordance between genetic profiles of Korean HCC patients and patients in original French studies. Thus, G1-G6 and 5-gene score signatures can be targeted as potential therapeutic biomarkers against HCC patients worldwide.
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Spatial mutation patterns as markers of early colorectal tumor cell mobility. Proc Natl Acad Sci U S A 2018; 115:5774-5779. [PMID: 29760052 DOI: 10.1073/pnas.1716552115] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A growing body of evidence suggests that a subset of human cancers grows as single clonal expansions. In such a nearly neutral evolution scenario, it is possible to infer the early ancestral tree of a full-grown tumor. We hypothesized that early tree reconstruction can provide insights into the mobility phenotypes of tumor cells during their first few cell divisions. We explored this hypothesis by means of a computational multiscale model of tumor expansion incorporating the glandular structure of colorectal tumors. After calibrating the model to multiregional and single gland data from 19 human colorectal tumors using approximate Bayesian computation, we examined the role of early tumor cell mobility in shaping the private mutation patterns of the final tumor. The simulations showed that early cell mixing in the first tumor gland can result in side-variegated patterns where the same private mutations could be detected on opposite tumor sides. In contrast, absence of early mixing led to nonvariegated, sectional mutation patterns. These results suggest that the patterns of detectable private mutations in colorectal tumors may be a marker of early cell movement and hence the invasive and metastatic potential of the tumor at the start of the growth. In alignment with our hypothesis, we found evidence of early abnormal cell movement in 9 of 15 invasive colorectal carcinomas ("born to be bad"), but in none of 4 benign adenomas. If validated with a larger dataset, the private mutation patterns may be used for outcome prediction among screen-detected lesions with unknown invasive potential.
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Genomic features of renal cell carcinoma with venous tumor thrombus. Sci Rep 2018; 8:7477. [PMID: 29748622 PMCID: PMC5945671 DOI: 10.1038/s41598-018-25544-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 04/25/2018] [Indexed: 12/17/2022] Open
Abstract
A venous tumor thrombus (VTT) is a potentially lethal complication of renal cell carcinoma (RCC) but virtually nothing is known about the underlying natural history. Based on our observation that venous thrombi contain significant numbers of viable tumor cells, we applied multiregion whole exome sequencing to a total of 37 primary tumor and VTT samples including normal tissue specimens from five consecutive patients. Our findings demonstrate mutational heterogeneity between primary tumor and VTT with 106 of 483 genes (22%) harboring functional SNVs and/or indels altered in either primary tumor or thrombus. Reconstruction of the clonal phylogeny showed clustering of tumor samples and VTT samples, respectively, in the majority of tumors. However, no new subclones were detected suggesting that pre-existing subclones of the primary tumor drive VTT formation. Importantly, we found several lines of evidence for “BRCAness” in a subset of tumors. These included mutations in genes that confer “BRCAness”, a mutational signature and an increase of small indels. Re-analysis of SNV calls from the TCGA KIRC-US cohort confirmed a high frequency of the “BRCAness” mutational signature AC3 in clear cell RCC. Our findings warrant further pre-clinical experiments and may lead to novel personalized therapies for RCC patients.
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45
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Wawrocka A, Skorczyk-Werner A, Wicher K, Niedziela Z, Ploski R, Rydzanicz M, Sykulski M, Kociecki J, Weisschuh N, Kohl S, Biskup S, Wissinger B, Krawczynski MR. Novel variants identified with next-generation sequencing in Polish patients with cone-rod dystrophy. Mol Vis 2018; 24:326-339. [PMID: 29769798 PMCID: PMC5937672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 04/24/2018] [Indexed: 11/30/2022] Open
Abstract
Purpose The aim of this study was to identify the molecular genetic basis of cone-rod dystrophy in 18 unrelated families of Polish origin. Cone-rod dystrophy is one of the inherited retinal dystrophies, which constitute a highly heterogeneous group of disorders characterized by progressive dysfunction of photoreceptors and retinal pigment epithelium (RPE) cells. Methods The study group was composed of four groups of patients representing different Mendelian inheritance of the disease: autosomal dominant (AD), autosomal recessive (AR), X-linked recessive (XL), and autosomal recessive or X-linked recessive (AR/XL). The combined molecular strategy included Sanger sequencing of the RPGR-ORF15 gene (three families with XL and three families with the AR/XL mode of inheritance), mutation-specific microarray analysis of the ABCA4 gene (five families with the AR mode of inheritance and two families with the AR/XL mode of inheritance), targeted next-generation sequencing (NGS) of inherited retinal disease-associated (IRD) genes (seven families with the AD mode of inheritance and five families with the AR mode of inheritance), and whole exome sequencing, performed in select families who had been mutation-negative in the analysis with the targeted NGS panel (one family with the AD mode of inheritance, one family with the AR mode of inheritance, and two families with the AR/XL mode of inheritance). Results Based on this combined strategy, we managed to identify potentially causative variants in seven out of 18 families with CRD. Five of these variants are novel: c.3142_3143dupAA, p.(Glu1049Argfs*41) in the RPGR-ORF15 gene, two variants: c.1612delT, p.(Trp538Glyfs*15) and c.2389dupG, p.(Ile798Hisfs*20) in the PROM1 gene in one family, c.592A>C, p.(Ser198Arg) in the PRPH2 gene and the variant c.1691A>G, p.(Asp564Gly) in the ATF6 gene that we have already reported to be pathogenic. NGS on the IRD panel allowed the molecular basis of CRD to be identified in four out of 14 families with a total detection rate of 38%. WES allowed identification of the molecular genetic basis of CRD in one family. Conclusions This is the first report on the spectrum of disease genes and pathogenic variants causing CRD in the Polish population. The study presents five novel variants identified in four genes and therefore, broadens the spectrum of probable pathogenic variants associated with CRD.
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Affiliation(s)
- Anna Wawrocka
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Skorczyk-Werner
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Katarzyna Wicher
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Zuzanna Niedziela
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Clinical Eye Unit and Pediatric Ophthalmology Service, Heliodor Swiecicki University Hospital, Poznan University of Medical Sciences, Poznan, Poland
| | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Maciej Sykulski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Jaroslaw Kociecki
- Department of Ophthalmology, Poznan University of Medical Sciences, Poznan, Poland
| | - Nicole Weisschuh
- Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Susanne Kohl
- Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | | | - Bernd Wissinger
- Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Maciej R. Krawczynski
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Centers for Medical Genetics GENESIS, Poznan, Poland
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Gray PN, Tsai P, Chen D, Wu S, Hoo J, Mu W, Li B, Vuong H, Lu HM, Batth N, Willett S, Uyeda L, Shah S, Gau CL, Umali M, Espenschied C, Janicek M, Brown S, Margileth D, Dobrea L, Wagman L, Rana H, Hall MJ, Ross T, Terdiman J, Cullinane C, Ries S, Totten E, Elliott AM. TumorNext-Lynch-MMR: a comprehensive next generation sequencing assay for the detection of germline and somatic mutations in genes associated with mismatch repair deficiency and Lynch syndrome. Oncotarget 2018; 9:20304-20322. [PMID: 29755653 PMCID: PMC5945525 DOI: 10.18632/oncotarget.24854] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/06/2018] [Indexed: 12/12/2022] Open
Abstract
The current algorithm for Lynch syndrome diagnosis is highly complex with multiple steps which can result in an extended time to diagnosis while depleting precious tumor specimens. Here we describe the analytical validation of a custom probe-based NGS tumor panel, TumorNext-Lynch-MMR, which generates a comprehensive genetic profile of both germline and somatic mutations that can accelerate and streamline the time to diagnosis and preserve specimen. TumorNext-Lynch-MMR can detect single nucleotide variants, small insertions and deletions in 39 genes that are frequently mutated in Lynch syndrome and colorectal cancer. Moreover, the panel provides microsatellite instability status and detects loss of heterozygosity in the five Lynch genes; MSH2, MSH6, MLH1, PMS2 and EPCAM. Clinical cases are described that highlight the assays ability to differentiate between somatic and germline mutations, precisely classify variants and resolve discordant cases.
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Affiliation(s)
- Phillip N Gray
- Advanced Genomic Services, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Pei Tsai
- Advanced Genomic Services, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Daniel Chen
- Clinical Diagnostics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Sitao Wu
- Bioinformatics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Jayne Hoo
- Bioinformatics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Wenbo Mu
- Bioinformatics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Bing Li
- Bioinformatics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Huy Vuong
- Bioinformatics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Hsiao-Mei Lu
- Bioinformatics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Navanjot Batth
- Clinical Diagnostics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Sara Willett
- Advanced Genomic Services, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Lisa Uyeda
- Clinical Diagnostics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Swati Shah
- Clinical Diagnostics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Chia-Ling Gau
- Clinical Diagnostics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Monalyn Umali
- Clinical Diagnostics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Carin Espenschied
- Clinical Diagnostics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Mike Janicek
- Cancer Genetic Risk Assessment Program, Arizona Oncology, Scottsdale, AZ 85258, USA
| | - Sandra Brown
- Cancer Genetics Program, Saint Joseph of Orange, Orange, CA 92868, USA
| | - David Margileth
- Cancer Genetics Program, Saint Joseph of Orange, Orange, CA 92868, USA
| | - Lavinia Dobrea
- Oncology Research and Biospecimen Program, Saint Joseph of Orange, Orange, CA 92868, USA
| | - Lawrence Wagman
- The Center for Cancer Prevention and Treatment, Saint Joseph of Orange, Orange, CA 92868, USA
| | - Huma Rana
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02461, USA
| | - Michael J Hall
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia PA 19111, USA
| | - Theodora Ross
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jonathan Terdiman
- Department of Medicine - Gastroenterology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Carey Cullinane
- Department of Pathology, Long Beach Memorial Medical Center, Long Beach, CA 90801, USA
| | - Savita Ries
- Department of Pathology, Long Beach Memorial Medical Center, Long Beach, CA 90801, USA
| | - Ellen Totten
- Advocate Medical Group, Park Ridge, Illinois 60068, USA
| | - Aaron M Elliott
- Advanced Genomic Services, Ambry Genetics, Aliso Viejo, CA 92656, USA
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47
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The landscape of genomic alterations across childhood cancers. Nature 2018; 555:321-327. [PMID: 29489754 DOI: 10.1038/nature25480] [Citation(s) in RCA: 947] [Impact Index Per Article: 157.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 12/24/2017] [Indexed: 02/07/2023]
Abstract
Pan-cancer analyses that examine commonalities and differences among various cancer types have emerged as a powerful way to obtain novel insights into cancer biology. Here we present a comprehensive analysis of genetic alterations in a pan-cancer cohort including 961 tumours from children, adolescents, and young adults, comprising 24 distinct molecular types of cancer. Using a standardized workflow, we identified marked differences in terms of mutation frequency and significantly mutated genes in comparison to previously analysed adult cancers. Genetic alterations in 149 putative cancer driver genes separate the tumours into two classes: small mutation and structural/copy-number variant (correlating with germline variants). Structural variants, hyperdiploidy, and chromothripsis are linked to TP53 mutation status and mutational signatures. Our data suggest that 7-8% of the children in this cohort carry an unambiguous predisposing germline variant and that nearly 50% of paediatric neoplasms harbour a potentially druggable event, which is highly relevant for the design of future clinical trials.
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Dou H, Fang Y, Zheng X. Universal informative CpG sites for inferring tumor purity from DNA methylation microarray data. J Bioinform Comput Biol 2018; 16:1750030. [PMID: 29347875 DOI: 10.1142/s0219720017500305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Tumor purity is an intrinsic property of tumor samples and potentially has severe impact on many types of data analysis. We have previously developed a statistical method, InfiniumPurify, which could infer purity of a tumor sample given its tumor type (available in TCGA) or a set of informative CpG (iDMC) sites. However, in many clinical practices, researchers may focus on a specific type of tumor samples that is not included in TCGA, and samples which are too few to identify reliable iDMCs. This greatly restricts the application of InfiniumPurify in cancer research. In this paper, we proposed an updated version of InfiniumPurify (termed as uiInfiniumPurify) through identifying a universal set of iDMCs (uiDMCs) and redesigning the algorithm to determine hyper- and hypo-methylation status of each uiDMC. Through the application, we estimated tumor purities of 8830 tumor samples from TCGA. Result shows that our estimates are highly consistent with those by other available methods. Consequently, the updated uiInfiniumPurify, can be applied to a single sample (or a few samples) of interest whose tumor type is not included in TCGA. This characteristic will greatly broaden the application of uiInfiniumPurify in cancer research.
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Affiliation(s)
- Haixia Dou
- 1 Department of Mathematics, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Yun Fang
- 1 Department of Mathematics, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Xiaoqi Zheng
- 1 Department of Mathematics, Shanghai Normal University, Shanghai 200234, P. R. China
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49
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Integrative genomic and transcriptomic analysis of leiomyosarcoma. Nat Commun 2018; 9:144. [PMID: 29321523 PMCID: PMC5762758 DOI: 10.1038/s41467-017-02602-0] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 12/13/2017] [Indexed: 02/07/2023] Open
Abstract
Leiomyosarcoma (LMS) is an aggressive mesenchymal malignancy with few therapeutic options. The mechanisms underlying LMS development, including clinically actionable genetic vulnerabilities, are largely unknown. Here we show, using whole-exome and transcriptome sequencing, that LMS tumors are characterized by substantial mutational heterogeneity, near-universal inactivation of TP53 and RB1, widespread DNA copy number alterations including chromothripsis, and frequent whole-genome duplication. Furthermore, we detect alternative telomere lengthening in 78% of cases and identify recurrent alterations in telomere maintenance genes such as ATRX, RBL2, and SP100, providing insight into the genetic basis of this mechanism. Finally, most tumors display hallmarks of "BRCAness", including alterations in homologous recombination DNA repair genes, multiple structural rearrangements, and enrichment of specific mutational signatures, and cultured LMS cells are sensitive towards olaparib and cisplatin. This comprehensive study of LMS genomics has uncovered key biological features that may inform future experimental research and enable the design of novel therapies.
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50
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Northcott PA, Buchhalter I, Morrissy AS, Hovestadt V, Weischenfeldt J, Ehrenberger T, Gröbner S, Segura-Wang M, Zichner T, Rudneva VA, Warnatz HJ, Sidiropoulos N, Phillips AH, Schumacher S, Kleinheinz K, Waszak SM, Erkek S, Jones DTW, Worst BC, Kool M, Zapatka M, Jäger N, Chavez L, Hutter B, Bieg M, Paramasivam N, Heinold M, Gu Z, Ishaque N, Jäger-Schmidt C, Imbusch CD, Jugold A, Hübschmann D, Risch T, Amstislavskiy V, Gonzalez FGR, Weber UD, Wolf S, Robinson GW, Zhou X, Wu G, Finkelstein D, Liu Y, Cavalli FMG, Luu B, Ramaswamy V, Wu X, Koster J, Ryzhova M, Cho YJ, Pomeroy SL, Herold-Mende C, Schuhmann M, Ebinger M, Liau LM, Mora J, McLendon RE, Jabado N, Kumabe T, Chuah E, Ma Y, Moore RA, Mungall AJ, Mungall KL, Thiessen N, Tse K, Wong T, Jones SJM, Witt O, Milde T, Von Deimling A, Capper D, Korshunov A, Yaspo ML, Kriwacki R, Gajjar A, Zhang J, Beroukhim R, Fraenkel E, Korbel JO, Brors B, Schlesner M, Eils R, Marra MA, Pfister SM, Taylor MD, Lichter P. The whole-genome landscape of medulloblastoma subtypes. Nature 2017; 547:311-317. [PMID: 28726821 PMCID: PMC5905700 DOI: 10.1038/nature22973] [Citation(s) in RCA: 725] [Impact Index Per Article: 103.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 05/10/2017] [Indexed: 12/14/2022]
Abstract
Current therapies for medulloblastoma, a highly malignant childhood brain tumour, impose debilitating effects on the developing child, and highlight the need for molecularly targeted treatments with reduced toxicity. Previous studies have been unable to identify the full spectrum of driver genes and molecular processes that operate in medulloblastoma subgroups. Here we analyse the somatic landscape across 491 sequenced medulloblastoma samples and the molecular heterogeneity among 1,256 epigenetically analysed cases, and identify subgroup-specific driver alterations that include previously undiscovered actionable targets. Driver mutations were confidently assigned to most patients belonging to Group 3 and Group 4 medulloblastoma subgroups, greatly enhancing previous knowledge. New molecular subtypes were differentially enriched for specific driver events, including hotspot in-frame insertions that target KBTBD4 and ‘enhancer hijacking’ events that activate PRDM6. Thus, the application of integrative genomics to an extensive cohort of clinical samples derived from a single childhood cancer entity revealed a series of cancer genes and biologically relevant subtype diversity that represent attractive therapeutic targets for the treatment of patients with medulloblastoma. Genomic analysis of 491 medulloblastoma samples, including methylation profiling of 1,256 cases, effectively assigns candidate drivers to most tumours across all molecular subgroups. Medulloblastomas are highly malignant brain tumours that develop during childhood. Paul Northcott and colleagues analysed the whole-genome sequences of 491 medulloblastomas in order to characterize the genomic landscape across tumours and identify new drivers and mutational signatures. Their integrative genomic analyses, including methylation profiling of 1,256 medulloblastomas, identifies subgroup-specific driver mutations and suggests additional tumour subtypes. The authors assign driver mutations to a high proportion of the less well characterized Group 3 and Group 4, which together contribute to more than 60% of all medulloblastomas.
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Affiliation(s)
- Paul A Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ivo Buchhalter
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - A Sorana Morrissy
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joachim Weischenfeldt
- Biotech Research &Innovation Centre (BRIC), Copenhagen University and Finsen Laboratory, Rigshospitalet, Denmark
| | - Tobias Ehrenberger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Susanne Gröbner
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Maia Segura-Wang
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Thomas Zichner
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Vasilisa A Rudneva
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Hans-Jörg Warnatz
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Nikos Sidiropoulos
- Biotech Research &Innovation Centre (BRIC), Copenhagen University and Finsen Laboratory, Rigshospitalet, Denmark
| | - Aaron H Phillips
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Kortine Kleinheinz
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian M Waszak
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Serap Erkek
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Barbara C Worst
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Natalie Jäger
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lukas Chavez
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Barbara Hutter
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Bieg
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nagarajan Paramasivam
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Michael Heinold
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Zuguang Gu
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Naveed Ishaque
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christina Jäger-Schmidt
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Charles D Imbusch
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alke Jugold
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Hübschmann
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Risch
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | | | | | - Ursula D Weber
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephan Wolf
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Giles W Robinson
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Xin Zhou
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gang Wu
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David Finkelstein
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yanling Liu
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Florence M G Cavalli
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario
| | - Betty Luu
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario
| | - Vijay Ramaswamy
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario
| | - Xiaochong Wu
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario
| | - Jan Koster
- Department of Oncogenomics, Amsterdam Medical Center, Amsterdam, Netherlands
| | - Marina Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - Yoon-Jae Cho
- Department of Pediatrics, Papé Family Pediatric Research Institute, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Scott L Pomeroy
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Christel Herold-Mende
- Department of Neurosurgery, University Clinic, Heidelberg University, Heidelberg Hospital, Germany
| | - Martin Schuhmann
- Department of Neurosurgery, University Hospital Tübingen, Tübingen, Germany
| | - Martin Ebinger
- Department of Hematology and Oncology, Children's University Hospital Tübingen, Tübingen, Germany
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Roger E McLendon
- Department of Pathology, Duke University, Durham, North County, USA
| | - Nada Jabado
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada
| | - Toshihiro Kumabe
- Department of Neurosurgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Eric Chuah
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Richard A Moore
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Karen L Mungall
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Nina Thiessen
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Kane Tse
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Tina Wong
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Olaf Witt
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Till Milde
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas Von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marie-Laure Yaspo
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Richard Kriwacki
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Amar Gajjar
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rameen Beroukhim
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Benedikt Brors
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marco A Marra
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael D Taylor
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario.,Division of Neurosurgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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