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Lu H, Wang Y, Chaudhary S, Balaga V, Ke H, Shi F, Liu J, Huo Y, Romanienko PJ, Xia B, De S, Chan CS, Shen Z. Medulloblastomas Initiated by Homologous Recombination Defects in Mice. THE AMERICAN JOURNAL OF PATHOLOGY 2024:S0002-9440(24)00294-3. [PMID: 39168365 DOI: 10.1016/j.ajpath.2024.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/08/2024] [Accepted: 07/31/2024] [Indexed: 08/23/2024]
Abstract
Germline mutations of homologous-recombination (HR) genes are among the top contributors to medulloblastomas. A significant portion of human medulloblastomas exhibit genomic signatures of HR defects. We queried whether ablation of Brca2 and Palb2, and their related Brca1 and Bccip genes, in the mouse brain can differentially initiate medulloblastomas. Conditional knockout mouse models of these HR genes and a conditional knockdown of Bccip (shBccip-KD) were established. Deletion of any of these genes led to microcephaly and neurologic defects, with Brca1- and Bccip- producing the worst. Trp53 co-deletion significantly rescued the microcephaly with Brca1, Palb2, and Brca2 deficiency but exhibited limited impact on Bccip- mice. For the first time, inactivation of either Brca1 or Palb2 with Trp53 was found to induce medulloblastomas. Despite shBccip-CKD being highly penetrative, Bccip/Trp53 deletions failed to induce medulloblastomas. The tumors displayed diverse immunohistochemical features and chromosome copy number variation. Although there were widespread up-regulations of cell proliferative pathways, most of the tumors expressed biomarkers of the sonic hedgehog subgroup. The medulloblastomas developed from Brca1-, Palb2-, and Brca2- mice were highly sensitive to a poly (ADP-ribose) polymerase inhibitor but not the ones from shBccip-CKD mice. These models recapitulate the spontaneous medulloblastoma development with high penetrance and a narrow time window, providing ideal platforms to test therapeutic agents with the ability to differentiate HR-defective and HR-proficient tumors.
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Affiliation(s)
- Huimei Lu
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Yuan Wang
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Shipra Chaudhary
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Varshita Balaga
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Hua Ke
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Fuqian Shi
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Jingmei Liu
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Yangyin Huo
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | | | - Bing Xia
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Subhajyoti De
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Chang S Chan
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Zhiyuan Shen
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey.
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Yoon JY, Sharma A, Ligon AH, Ramesh RG, Soong TR, Xian W, Chapel DB, Crum CP. Genomic Catastrophe (Chromothripsis and Polyploidy) Correlates With Tumor Distribution in Extrauterine High-grade Serous Carcinoma. Am J Surg Pathol 2024; 48:1017-1023. [PMID: 38639044 PMCID: PMC11254554 DOI: 10.1097/pas.0000000000002229] [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] [Indexed: 04/20/2024]
Abstract
Most extrauterine high-grade serous carcinomas (HGSCs) are thought to develop first in the distal fallopian tube. Most models of HGSC assume origin from relatively stable, noninvasive serous tubal intraepithelial carcinomas. However, widespread tumor involvement in the absence of a serous tubal intraepithelial carcinoma could occur after catastrophic genomic events (CGEs; such as chromothripsis or polyploidy). Twenty-six HGSCs assigned to fallopian tube (n = 9, group 1) and/or ovary (n = 9, group 2), and primary peritoneal (n = 8, group 3) were assessed by microarray (Oncoscan). CGEs were identified in 15/26 (57.7%); chromothripsis-like pattern in 13/26 (50.0%) and polyploidy in 6/26 (23.1%). CGE was seen in 4/9 (44.4%), 9/9 (100%), and 2/8 (25%) cases in groups 1. 2, and 3, respectively. Overall, CGEs were seen in 9/9 (100%) cases with grossly evident ovarian parenchymal involvement versus 6/17 (35.3%) without ( P = 0.0024). Ovarian size (measured on the long axis) correlated with CGE positivity ( P = 0.016). CGEs are significantly more common in HGSCs with ovarian parenchymal involvement compared with those limited to the fallopian tube and/or extraovarian tissues. These associations suggest geographically different tumor growth patterns and support the subdivision of HGSCs according to not only the stage but also tumor distribution. They have implications for clinical and pathologic presentation, trajectory of tumor evolution, and in the case of primary peritoneal HGSCs, potentially unique precursors to tumor transitions that could inform or influence cancer prevention efforts.
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Affiliation(s)
- Ju Yoon Yoon
- Unity Health Toronto, Department of Pathology, Toronto, Canada
| | - Aarti Sharma
- Brigham and Women’s Hospital, Division of Women’s and Perinatal pathology, Department of Pathology, Boston, USA
| | - Azra H. Ligon
- Brigham and Women’s Hospital, Department of Pathology, Division of Clinical Cytogenetics, Boston, USA
| | - Rebecca G. Ramesh
- Hospital of the University of Pennsylvania, Department of Pathology and Laboratory Medicine, Philadelphia, USA
| | - T. Rinda Soong
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Wa Xian
- University of Houston, Department of Biology and Biochemistry, Stem Cell Center, Houston TX
| | - David B. Chapel
- University of Michigan Health, Department of Pathology, Ann Arbor Michigan
| | - Christopher P. Crum
- Brigham and Women’s Hospital, Division of Women’s and Perinatal pathology, Department of Pathology, Boston, USA
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Zhang M, He D, Zhang Y, Cheng K, Li H, Zhou Y, Long Q, Liu R, Liu J. Chromothripsis is a novel biomarker for prognosis and differentiation diagnosis of pancreatic neuroendocrine neoplasms. MedComm (Beijing) 2024; 5:e623. [PMID: 38988495 PMCID: PMC11234462 DOI: 10.1002/mco2.623] [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: 10/25/2023] [Revised: 04/22/2024] [Accepted: 05/20/2024] [Indexed: 07/12/2024] Open
Abstract
This study aimed to identify the role of chromothripsis as a novel biomarker in the prognosis and differentiation diagnosis of pancreatic neuroendocrine neoplasms (pNENs). We conducted next-generation gene sequencing in a cohort of 30 patients with high-grade (G3) pNENs. As a reference, a similar analysis was also performed on 25 patients with low-grade (G1/G2) pancreatic neuroendocrine tumors (pNETs). Chromothripsis and its relationship with clinicopathological features and prognosis were investigated. The results showed that DNA damage response and repair gene alteration and TP53 mutation were found in 29 and 11 patients, respectively. A total of 14 out of 55 patients had chromothripsis involving different chromosomes. Chromothripsis had a close relationship with TP53 alteration and higher grade. In the entire cohort, chromothripsis was associated with a higher risk of distant metastasis; both chromothripsis and metastasis (ENETS Stage IV) suggested a significantly shorter overall survival (OS). Importantly, in the high-grade pNENs group, chromothripsis was the only independent prognostic indicator significantly associated with a shorter OS, other than TP53 alteration or pathological pancreatic neuroendocrine carcinomas (pNECs) diagnosis. Chromothripsis can guide worse prognosis in pNENs, and help differentiate pNECs from high-grade (G3) pNETs.
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Affiliation(s)
- Ming‐Yi Zhang
- Department of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Du He
- Department of Pathology, West China HospitalSichuan UniversityChengduSichuanChina
| | - Yi Zhang
- Center of Life SciencesPeking UniversityBeijingChina
| | - Ke Cheng
- Department of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Hong‐Shuai Li
- Department of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Yu‐Wen Zhou
- Department of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Qiong‐Xian Long
- Department of Pathology, Nan Chong Central Hospitalthe Second Affiliated Hospital of North Sichuan Medical CollegeNanchongSichuanChina
| | - Rui‐Zhi Liu
- School of Medical and Life SciencesChengdu University of Traditional Chinese MedicineChengduSichuanChina
| | - Ji‐Yan Liu
- Department of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
- Sichuan Clinical Research Center of BiotherapyChengduSichuanChina
- Department of OncologyThe First People's Hospital of ZiyangZiyangSichuanChina
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Agarwal H, Tal P, Goldfinger N, Chattopadhyay E, Malkin D, Rotter V, Attery A. Mutant p53 reactivation restricts the protumorigenic consequences of wild type p53 loss of heterozygosity in Li-Fraumeni syndrome patient-derived fibroblasts. Cell Death Differ 2024; 31:855-867. [PMID: 38745079 PMCID: PMC11239894 DOI: 10.1038/s41418-024-01307-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 04/13/2024] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
The p53 tumor suppressor, encoded by the TP53 gene, serves as a major barrier against malignant transformation. Patients with Li-Fraumeni syndrome (LFS) inherit a mutated TP53 allele from one parent and a wild-type TP53 allele from the other. Subsequently, the wild-type allele is lost and only the mutant TP53 allele remains. This process, which is termed loss of heterozygosity (LOH), results in only mutant p53 protein expression. We used primary dermal fibroblasts from LFS patients carrying the hotspot p53 gain-of-function pathogenic variant, R248Q to study the LOH process and characterize alterations in various pathways before and after LOH. We previously described the derivation of mutant p53 reactivating peptides, designated pCAPs (p53 Conformation Activating Peptides). In this study, we tested the effect of lead peptide pCAP-250 on LOH and on its associated cellular changes. We report that treatment of LFS fibroblasts with pCAP-250 prevents the accumulation of mutant p53 protein, inhibits LOH, and alleviates its cellular consequences. Furthermore, prolonged treatment with pCAP-250 significantly reduces DNA damage and restores long-term genomic stability. pCAPs may thus be contemplated as a potential preventive treatment to prevent or delay early onset cancer in carriers of mutant p53.
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Affiliation(s)
- Himanshi Agarwal
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Perry Tal
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Naomi Goldfinger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Esita Chattopadhyay
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - David Malkin
- Department of Genetics and Genome Biology and the Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
- Departments of Medical Biophysics and Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Varda Rotter
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Ayush Attery
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
- Department of Tumor Cell Biology, St Jude Children's Research Hospital, Memphis, TN, USA.
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Carey-Smith SL, Kotecha RS, Cheung LC, Malinge S. Insights into the Clinical, Biological and Therapeutic Impact of Copy Number Alteration in Cancer. Int J Mol Sci 2024; 25:6815. [PMID: 38999925 PMCID: PMC11241182 DOI: 10.3390/ijms25136815] [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: 05/21/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/14/2024] Open
Abstract
Copy number alterations (CNAs), resulting from the gain or loss of genetic material from as little as 50 base pairs or as big as entire chromosome(s), have been associated with many congenital diseases, de novo syndromes and cancer. It is established that CNAs disturb the dosage of genomic regions including enhancers/promoters, long non-coding RNA and gene(s) among others, ultimately leading to an altered balance of key cellular functions. In cancer, CNAs have been associated with almost all steps of the disease: predisposition, initiation, development, maintenance, response to treatment, resistance, and relapse. Therefore, understanding how specific CNAs contribute to tumourigenesis may provide prognostic insight and ultimately lead to the development of new therapeutic approaches to improve patient outcomes. In this review, we provide a snapshot of what is currently known about CNAs and cancer, incorporating topics regarding their detection, clinical impact, origin, and nature, and discuss the integration of innovative genetic engineering strategies, to highlight the potential for targeting CNAs using novel, dosage-sensitive and less toxic therapies for CNA-driven cancer.
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Affiliation(s)
- Shannon L. Carey-Smith
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
| | - Rishi S. Kotecha
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children’s Hospital, Perth, WA 6009, Australia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
| | - Laurence C. Cheung
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Sébastien Malinge
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
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Zhang S, Xiao X, Yi Y, Wang X, Zhu L, Shen Y, Lin D, Wu C. Tumor initiation and early tumorigenesis: molecular mechanisms and interventional targets. Signal Transduct Target Ther 2024; 9:149. [PMID: 38890350 PMCID: PMC11189549 DOI: 10.1038/s41392-024-01848-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 06/20/2024] Open
Abstract
Tumorigenesis is a multistep process, with oncogenic mutations in a normal cell conferring clonal advantage as the initial event. However, despite pervasive somatic mutations and clonal expansion in normal tissues, their transformation into cancer remains a rare event, indicating the presence of additional driver events for progression to an irreversible, highly heterogeneous, and invasive lesion. Recently, researchers are emphasizing the mechanisms of environmental tumor risk factors and epigenetic alterations that are profoundly influencing early clonal expansion and malignant evolution, independently of inducing mutations. Additionally, clonal evolution in tumorigenesis reflects a multifaceted interplay between cell-intrinsic identities and various cell-extrinsic factors that exert selective pressures to either restrain uncontrolled proliferation or allow specific clones to progress into tumors. However, the mechanisms by which driver events induce both intrinsic cellular competency and remodel environmental stress to facilitate malignant transformation are not fully understood. In this review, we summarize the genetic, epigenetic, and external driver events, and their effects on the co-evolution of the transformed cells and their ecosystem during tumor initiation and early malignant evolution. A deeper understanding of the earliest molecular events holds promise for translational applications, predicting individuals at high-risk of tumor and developing strategies to intercept malignant transformation.
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Affiliation(s)
- Shaosen Zhang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyi Xiao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yonglin Yi
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyu Wang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Lingxuan Zhu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Changping Laboratory, 100021, Beijing, China
| | - Yanrong Shen
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, 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 and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- CAMS Oxford Institute, Chinese Academy of Medical Sciences, 100006, Beijing, China.
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Chen CY. Chromothripsis in myeloid malignancies. Ann Hematol 2024:10.1007/s00277-024-05814-9. [PMID: 38814446 DOI: 10.1007/s00277-024-05814-9] [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: 03/06/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]
Abstract
Chromothripsis refers to massive genomic rearrangements developed during a catastrophic event. In total acute myeloid leukemia (AML), the incidence of chromothripsis ranges from 0 to 6.6%, in cases of complex karyotype AML, the incidence of chromothripsis ranges from 27.3 to 100%, whereas in cases of AML with TP53 mutations, the incidence ranges from 11.1 to 90%. For other types of malignancies, the incidence of chromothripsis also varies, from 0 to 10.5% in myelodysplastic syndrome to up to 61.5% in cases of myelodysplastic syndrome with TP53 mutations.Chromothripsis is typically associated with complex karyotypes and TP53 mutations, and monosomal karyotypes are associated with the condition. ERG amplifications are frequently noted in cases of chromothripsis, whereas MYC amplifications are not. Moreover, FLT3 and NPM1 mutations are negatively associated with chromothripsis. Chromothripsis typically occurs in older patients with AML with low leukocyte counts and bone marrow blast counts. Rare cases of patients with chromothripsis who received intensive induction chemotherapy revealed low response rates and poor overall prognosis. Signal pathways in chromothripsis typically involve copy number gain and upregulation of oncogene gene sets that promote cancer growth and a concomitant copy number loss and downregulation of gene sets associated with tumor suppression functions.Patients with chromothripsis showed a trend of lower complete remission rate and worse overall survival in myeloid malignancy. Large-scale studies are required to further elucidate the causes and treatments of the condition.
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Affiliation(s)
- Chien-Yuan Chen
- Department of Internal Medicine, Division of Hematology, National Taiwan University Hospital, No. 7, Chung-Shan South Road, Taipei, 100, Taiwan.
- Department of Pathology, Cytogenetic laboratory, National Taiwan University Hospital, Taipei, Taiwan.
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Dermawan JK, Slotkin E, Tap WD, Meyers P, Wexler L, Healey J, Vanoli F, Vanderbilt CM, Antonescu CR. Chromoplexy Is a Frequent Early Clonal Event in EWSR1-Rearranged Round Cell Sarcomas That Can Be Detected Using Clinically Validated Targeted Sequencing Panels. Cancer Res 2024; 84:1504-1516. [PMID: 38335254 DOI: 10.1158/0008-5472.can-23-2573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/09/2023] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Chromoplexy is a phenomenon defined by large-scale chromosomal chained rearrangements. A previous study observed chromoplectic events in a subset of Ewing sarcomas (ES), which was linked to an increased relapse rate. Chromoplexy analysis could potentially facilitate patient risk stratification, particularly if it could be detected with clinically applied targeted next-generation sequencing (NGS) panels. Using DELLY, a structural variant (SV) calling algorithm that is part of the MSK-IMPACT pipeline, we characterized the spectrum of SVs in EWSR1-fused round cell sarcomas, including 173 ES and 104 desmoplastic small round cell tumors (DSRCT), to detect chromoplexy and evaluate its association with clinical and genomic features. Chromoplectic events were detected in 31% of the ES cases and 19% of the DSRCT cases. EWSR1 involvement accounted for 76% to 93% of these events, being rearranged with diverse noncanonical gene partners across the genome, involving mainly translocations but also intrachromosomal deletions and inversions. A major breakpoint cluster was located on EWSR1 exons 8-13. In a subset of cases, the SVs disrupted adjacent loci, forming deletion bridges. Longitudinal sequencing and breakpoint allele fraction analysis showed that chromoplexy is an early event that remains detectable throughout disease progression and likely develops simultaneously with the driver fusion. The presence of chromoplexy was validated in an external ES patient cohort with whole exome sequencing. Chromoplexy was significantly more likely to be present in cases that were metastatic at presentation. Together, this study identifies chromoplexy as a frequent genomic alteration in diverse EWSR1-rearranged tumors that can be captured by targeted NGS panels. SIGNIFICANCE Chromoplexy is detectable using targeted NGS in a substantial portion of EWSR1-rearranged round cell sarcomas as an early and persistent clonal event, expanding the genomic complexity of fusion-associated sarcomas.
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Affiliation(s)
- Josephine K Dermawan
- Department of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Emily Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Paul Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Leonard Wexler
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John Healey
- Department of Surgery, Orthopedic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fabio Vanoli
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chad M Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cristina R Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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Wu H, Liu S, Wu D, Zhou H, Wu G. Tumor extrachromosomal DNA: Biogenesis and recent advances in the field. Biomed Pharmacother 2024; 174:116588. [PMID: 38613997 DOI: 10.1016/j.biopha.2024.116588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/02/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024] Open
Abstract
Extrachromosomal DNA (ecDNA) is a self-replicating circular DNA originating from the chromosomal genome and exists outside the chromosome. It contains specific gene sequences and non-coding regions that regulate transcription. Recent studies have demonstrated that ecDNA is present in various malignant tumors. Malignant tumor development and poor prognosis may depend on ecDNA's distinctive ring structure, which assists in amplifying oncogenes. During cell division, an uneven distribution of ecDNA significantly enhances tumor cells' heterogeneity, allowing tumor cells to adapt to changes in the tumor microenvironment and making them more resistant to treatments. The application of ecDNA as a cancer biomarker and therapeutic target holds great potential. This article examines the latest advancements in this area and discusses the potential clinical applications of ecDNA.
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Affiliation(s)
- Haomin Wu
- Department of General Surgery, the First Hospital of China Medical University, 155# Nanjing Street, Shenyang 110001, China
| | - Shiqi Liu
- Department of General Surgery, the First Hospital of China Medical University, 155# Nanjing Street, Shenyang 110001, China
| | - Di Wu
- Department of General Surgery, the First Hospital of China Medical University, 155# Nanjing Street, Shenyang 110001, China
| | - Haonan Zhou
- Department of General Surgery, the First Hospital of China Medical University, 155# Nanjing Street, Shenyang 110001, China
| | - Gang Wu
- Department of General Surgery, the First Hospital of China Medical University, 155# Nanjing Street, Shenyang 110001, China.
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Holmberg KO, Borgenvik A, Zhao M, Giraud G, Swartling FJ. Drivers Underlying Metastasis and Relapse in Medulloblastoma and Targeting Strategies. Cancers (Basel) 2024; 16:1752. [PMID: 38730706 PMCID: PMC11083189 DOI: 10.3390/cancers16091752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/12/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Medulloblastomas comprise a molecularly diverse set of malignant pediatric brain tumors in which patients are stratified according to different prognostic risk groups that span from very good to very poor. Metastasis at diagnosis is most often a marker of poor prognosis and the relapse incidence is higher in these children. Medulloblastoma relapse is almost always fatal and recurring cells have, apart from resistance to standard of care, acquired genetic and epigenetic changes that correlate with an increased dormancy state, cell state reprogramming and immune escape. Here, we review means to carefully study metastasis and relapse in preclinical models, in light of recently described molecular subgroups. We will exemplify how therapy resistance develops at the cellular level, in a specific niche or from therapy-induced secondary mutations. We further describe underlying molecular mechanisms on how tumors acquire the ability to promote leptomeningeal dissemination and discuss how they can establish therapy-resistant cell clones. Finally, we describe some of the ongoing clinical trials of high-risk medulloblastoma and suggest or discuss more individualized treatments that could be of benefit to specific subgroups.
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Affiliation(s)
- Karl O. Holmberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (K.O.H.); (M.Z.); (G.G.)
| | - Anna Borgenvik
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA;
- Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Miao Zhao
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (K.O.H.); (M.Z.); (G.G.)
| | - Géraldine Giraud
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (K.O.H.); (M.Z.); (G.G.)
- Department of Women and Child Health, Uppsala University, 75124 Uppsala, Sweden
- Department of Pediatric Hematology and Oncology, Uppsala University Children’s Hospital, 75185 Uppsala, Sweden
| | - Fredrik J. Swartling
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (K.O.H.); (M.Z.); (G.G.)
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11
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Zhou L, Tang W, Ye B, Zou L. Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA. Front Genet 2024; 15:1385150. [PMID: 38746056 PMCID: PMC11092383 DOI: 10.3389/fgene.2024.1385150] [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: 02/12/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024] Open
Abstract
Human extrachromosomal circular DNA, or eccDNA, has been the topic of extensive investigation in the last decade due to its prominent regulatory role in the development of disorders including cancer. With the rapid advancement of experimental, sequencing and computational technology, millions of eccDNA records are now accessible. Unfortunately, the literature and databases only provide snippets of this information, preventing us from fully understanding eccDNAs. Researchers frequently struggle with the process of selecting algorithms and tools to examine eccDNAs of interest. To explain the underlying formation mechanisms of the five basic classes of eccDNAs, we categorized their characteristics and functions and summarized eight biogenesis theories. Most significantly, we created a clear procedure to help in the selection of suitable techniques and tools and thoroughly examined the most recent experimental and bioinformatics methodologies and data resources for identifying, measuring and analyzing eccDNA sequences. In conclusion, we highlighted the current obstacles and prospective paths for eccDNA research, specifically discussing their probable uses in molecular diagnostics and clinical prediction, with an emphasis on the potential contribution of novel computational strategies.
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Affiliation(s)
- Lina Zhou
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Wenyi Tang
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Bo Ye
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Lingyun Zou
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
- School of Medicine, Jinan University, Guangzhou, Guangdong, China
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12
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Li Z, Qian D. Extrachromosomal circular DNA (eccDNA): from carcinogenesis to drug resistance. Clin Exp Med 2024; 24:83. [PMID: 38662139 PMCID: PMC11045593 DOI: 10.1007/s10238-024-01348-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/03/2024] [Indexed: 04/26/2024]
Abstract
Extrachromosomal circular DNA (eccDNA) is a circular form of DNA that exists outside of the chromosome. Although it has only been a few decades since its discovery, in recent years, it has been found to have a close relationship with cancer, which has attracted widespread attention from researchers. Thus far, under the persistent research of researchers from all over the world, eccDNA has been found to play an important role in a variety of tumors, including breast cancer, lung cancer, ovarian cancer, etc. Herein, we review the sources of eccDNA, classifications, and the mechanisms responsible for their biogenesis. In addition, we introduce the relationship between eccDNA and various cancers and the role of eccDNA in the generation and evolution of cancer. Finally, we summarize the research significance and importance of eccDNA in cancer, and highlight new prospects for the application of eccDNA in the future detection and treatment of cancer.
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Affiliation(s)
- Zhaoxing Li
- Department of Hepatobiliary Surgery, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Daohai Qian
- Department of Hepatobiliary Surgery, Yijishan Hospital of Wannan Medical College, Wuhu, China.
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13
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Chen Z, Huang H, Hong H, Huang H, Weng H, Yu L, Xiao J, Wang Z, Fang X, Yao Y, Yue JX, Lin T. Full-spectral genome analysis of natural killer/T cell lymphoma highlights impacts of genome instability in driving its progression. Genome Med 2024; 16:48. [PMID: 38566223 PMCID: PMC10986005 DOI: 10.1186/s13073-024-01324-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Natural killer/T cell lymphoma (NKTCL) is a clinically and genetically heterogeneous disease with poor prognosis. Genome sequencing and mutation characterization provides a powerful approach for patient stratification, treatment target discovery, and etiology identification. However, previous studies mostly concentrated on base-level mutations in primary NKTCL, whereas the large-scale genomic alterations in NKTCL and the mutational landscapes in relapsed/refractory NKTCL remain largely unexplored. METHODS Here, we assembled whole-genome sequencing and whole-exome sequencing data from 163 patients with primary or relapsed/refractory NKTCL and compared their somatic mutational landscapes at both nucleotide and structure levels. RESULTS Our study not only confirmed previously reported common NKTCL mutational targets like STAT3, TP53, and DDX3X but also unveiled several novel high-frequency mutational targets such as PRDM9, DST, and RBMX. In terms of the overall mutational landscape, we observed striking differences between primary and relapsed/refractory NKTCL patient groups, with the latter exhibits higher levels of tumor mutation burden, copy number variants (CNVs), and structural variants (SVs), indicating a strong signal of genomic instability. Complex structural rearrangements such as chromothripsis and focal amplification are also significantly enriched in relapsed/refractory NKTCL patients, exerting a substantial impact on prognosis. Accordingly, we devised a novel molecular subtyping system (i.e., C0-C4) with distinct prognosis by integrating potential driver mutations at both nucleotide and structural levels, which further provides an informative guidance for novel treatments that target these specific driver mutations and genome instability as a whole. CONCLUSIONS The striking differences underlying the mutational landscapes between the primary and relapsed/refractory NKTCL patients highlight the importance of genomic instability in driving the progression of NKTCL. Our newly proposed molecular subtyping system is valuable in assisting patient stratification and novel treatment design towards a better prognosis in the age of precision medicine.
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Affiliation(s)
- Zegeng Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - He Huang
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Huangming Hong
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Huageng Huang
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Huawei Weng
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Le Yu
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Jian Xiao
- Department of Medical Oncology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China
| | - Zhao Wang
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Xiaojie Fang
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Yuyi Yao
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
| | - Tongyu Lin
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China.
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14
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Yan X, Mischel P, Chang H. Extrachromosomal DNA in cancer. Nat Rev Cancer 2024; 24:261-273. [PMID: 38409389 DOI: 10.1038/s41568-024-00669-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
Extrachromosomal DNA (ecDNA) has recently been recognized as a major contributor to cancer pathogenesis that is identified in most cancer types and is associated with poor outcomes. When it was discovered over 60 years ago, ecDNA was considered to be rare, and its impact on tumour biology was not well understood. The application of modern imaging and computational techniques has yielded powerful new insights into the importance of ecDNA in cancer. The non-chromosomal inheritance of ecDNA during cell division results in high oncogene copy number, intra-tumoural genetic heterogeneity and rapid tumour evolution that contributes to treatment resistance and shorter patient survival. In addition, the circular architecture of ecDNA results in altered patterns of gene regulation that drive elevated oncogene expression, potentially enabling the remodelling of tumour genomes. The generation of clusters of ecDNAs, termed ecDNA hubs, results in interactions between enhancers and promoters in trans, yielding a new paradigm in oncogenic transcription. In this Review, we highlight the rapid advancements in ecDNA research, providing new insights into ecDNA biogenesis, maintenance and transcription and its role in promoting tumour heterogeneity. To conclude, we delve into a set of unanswered questions whose answers will pave the way for the development of ecDNA targeted therapeutic approaches.
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Affiliation(s)
- Xiaowei Yan
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Paul Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| | - Howard Chang
- Department of Dermatology, Stanford University, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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15
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Bibbò F, Asadzadeh F, Boccia A, Sorice C, Bianco O, Saccà CD, Majello B, Donofrio V, Bifano D, De Martino L, Quaglietta L, Cristofano A, Covelli EM, Cinalli G, Ferrucci V, De Antonellis P, Zollo M. Targeting Group 3 Medulloblastoma by the Anti-PRUNE-1 and Anti-LSD1/KDM1A Epigenetic Molecules. Int J Mol Sci 2024; 25:3917. [PMID: 38612726 PMCID: PMC11011515 DOI: 10.3390/ijms25073917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Medulloblastoma (MB) is a highly malignant childhood brain tumor. Group 3 MB (Gr3 MB) is considered to have the most metastatic potential, and tailored therapies for Gr3 MB are currently lacking. Gr3 MB is driven by PRUNE-1 amplification or overexpression. In this paper, we found that PRUNE-1 was transcriptionally regulated by lysine demethylase LSD1/KDM1A. This study aimed to investigate the therapeutic potential of inhibiting both PRUNE-1 and LSD1/KDM1A with the selective inhibitors AA7.1 and SP-2577, respectively. We found that the pharmacological inhibition had a substantial efficacy on targeting the metastatic axis driven by PRUNE-1 (PRUNE-1-OTX2-TGFβ-PTEN) in Gr3 MB. Using RNA seq transcriptomic feature data in Gr3 MB primary cells, we provide evidence that the combination of AA7.1 and SP-2577 positively affects neuronal commitment, confirmed by glial fibrillary acidic protein (GFAP)-positive differentiation and the inhibition of the cytotoxic components of the tumor microenvironment and the epithelial-mesenchymal transition (EMT) by the down-regulation of N-Cadherin protein expression. We also identified an impairing action on the mitochondrial metabolism and, consequently, oxidative phosphorylation, thus depriving tumors cells of an important source of energy. Furthermore, by overlapping the genomic mutational signatures through WES sequence analyses with RNA seq transcriptomic feature data, we propose in this paper that the combination of these two small molecules can be used in a second-line treatment in advanced therapeutics against Gr3 MB. Our study demonstrates that the usage of PRUNE-1 and LSD1/KDM1A inhibitors in combination represents a novel therapeutic approach for these highly aggressive metastatic MB tumors.
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Affiliation(s)
- Francesca Bibbò
- Department of Molecular Medicine and Medical Biotechnological DMMBM, University Federico II of Naples, 80131 Naples, Italy; (F.B.); (V.F.); (P.D.A.)
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
| | - Fatemeh Asadzadeh
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
- SEMM European School of Molecular Medicine, 20139 Milan, Italy
| | - Angelo Boccia
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
| | - Carmen Sorice
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
| | - Orazio Bianco
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
| | - Carmen Daniela Saccà
- Department of Biology, University Federico II of Naples, 80138 Naples, Italy; (C.D.S.); (B.M.)
| | - Barbara Majello
- Department of Biology, University Federico II of Naples, 80138 Naples, Italy; (C.D.S.); (B.M.)
| | - Vittoria Donofrio
- Department of Pathology, Santobono-Pausilipon Children’s Hospital, AORN, 80129 Naples, Italy; (V.D.); (D.B.)
| | - Delfina Bifano
- Department of Pathology, Santobono-Pausilipon Children’s Hospital, AORN, 80129 Naples, Italy; (V.D.); (D.B.)
| | - Lucia De Martino
- Pediatric Neuro-Oncology, Santobono-Pausilipon Children’s Hospital, AORN, 80129 Naples, Italy; (L.D.M.); (L.Q.)
| | - Lucia Quaglietta
- Pediatric Neuro-Oncology, Santobono-Pausilipon Children’s Hospital, AORN, 80129 Naples, Italy; (L.D.M.); (L.Q.)
| | - Adriana Cristofano
- Pediatric Neuroradiology, Santobono-Pausilipon Children’s Hospital, AORN, 80129 Naples, Italy; (A.C.); (E.M.C.)
| | - Eugenio Maria Covelli
- Pediatric Neuroradiology, Santobono-Pausilipon Children’s Hospital, AORN, 80129 Naples, Italy; (A.C.); (E.M.C.)
| | - Giuseppe Cinalli
- Pediatric Neurosurgery, Santobono-Pausilipon Children’s Hospital, AORN, 80129 Naples, Italy;
| | - Veronica Ferrucci
- Department of Molecular Medicine and Medical Biotechnological DMMBM, University Federico II of Naples, 80131 Naples, Italy; (F.B.); (V.F.); (P.D.A.)
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
| | - Pasqualino De Antonellis
- Department of Molecular Medicine and Medical Biotechnological DMMBM, University Federico II of Naples, 80131 Naples, Italy; (F.B.); (V.F.); (P.D.A.)
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
| | - Massimo Zollo
- Department of Molecular Medicine and Medical Biotechnological DMMBM, University Federico II of Naples, 80131 Naples, Italy; (F.B.); (V.F.); (P.D.A.)
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, 80131 Naples, Italy; (F.A.); (A.B.); (C.S.); (O.B.)
- DAI Medicina di Laboratorio e Trasfusionale, ‘AOU Federico II Policlinico’, 80131 Naples, Italy
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16
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Krupina K, Goginashvili A, Cleveland DW. Scrambling the genome in cancer: causes and consequences of complex chromosome rearrangements. Nat Rev Genet 2024; 25:196-210. [PMID: 37938738 PMCID: PMC10922386 DOI: 10.1038/s41576-023-00663-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2023] [Indexed: 11/09/2023]
Abstract
Complex chromosome rearrangements, known as chromoanagenesis, are widespread in cancer. Based on large-scale DNA sequencing of human tumours, the most frequent type of complex chromosome rearrangement is chromothripsis, a massive, localized and clustered rearrangement of one (or a few) chromosomes seemingly acquired in a single event. Chromothripsis can be initiated by mitotic errors that produce a micronucleus encapsulating a single chromosome or chromosomal fragment. Rupture of the unstable micronuclear envelope exposes its chromatin to cytosolic nucleases and induces chromothriptic shattering. Found in up to half of tumours included in pan-cancer genomic analyses, chromothriptic rearrangements can contribute to tumorigenesis through inactivation of tumour suppressor genes, activation of proto-oncogenes, or gene amplification through the production of self-propagating extrachromosomal circular DNAs encoding oncogenes or genes conferring anticancer drug resistance. Here, we discuss what has been learned about the mechanisms that enable these complex genomic rearrangements and their consequences in cancer.
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Affiliation(s)
- Ksenia Krupina
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Alexander Goginashvili
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.
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17
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Ravi Kiran AVVV, Kumari GK, Krishnamurthy PT, Johnson AP, Kenchegowda M, Osmani RAM, Abu Lila AS, Moin A, Gangadharappa HV, Rizvi SMD. An Update on Emergent Nano-Therapeutic Strategies against Pediatric Brain Tumors. Brain Sci 2024; 14:185. [PMID: 38391759 PMCID: PMC10886772 DOI: 10.3390/brainsci14020185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
Pediatric brain tumors are the major cause of pediatric cancer mortality. They comprise a diverse group of tumors with different developmental origins, genetic profiles, therapeutic options, and outcomes. Despite many technological advancements, the treatment of pediatric brain cancers has remained a challenge. Treatment options for pediatric brain cancers have been ineffective due to non-specificity, inability to cross the blood-brain barrier, and causing off-target side effects. In recent years, nanotechnological advancements in the medical field have proven to be effective in curing challenging cancers like brain tumors. Moreover, nanoparticles have emerged successfully, particularly in carrying larger payloads, as well as their stability, safety, and efficacy monitoring. In the present review, we will emphasize pediatric brain cancers, barriers to treating these cancers, and novel treatment options.
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Affiliation(s)
- Ammu V V V Ravi Kiran
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Rocklands, Ooty 643001, The Nilgiris, Tamil Nadu, India
| | - G Kusuma Kumari
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Rocklands, Ooty 643001, The Nilgiris, Tamil Nadu, India
| | - Praveen T Krishnamurthy
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Rocklands, Ooty 643001, The Nilgiris, Tamil Nadu, India
| | - Asha P Johnson
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India
| | - Madhuchandra Kenchegowda
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India
| | - Riyaz Ali M Osmani
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India
| | - Amr Selim Abu Lila
- Department of Pharmaceutics, College of Pharmacy, University of Ha'il, Ha'il 81442, Saudi Arabia
| | - Afrasim Moin
- Department of Pharmaceutics, College of Pharmacy, University of Ha'il, Ha'il 81442, Saudi Arabia
| | - H V Gangadharappa
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India
| | - Syed Mohd Danish Rizvi
- Department of Pharmaceutics, College of Pharmacy, University of Ha'il, Ha'il 81442, Saudi Arabia
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18
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Ijaz J, Harry E, Raine K, Menzies A, Beal K, Quail MA, Zumalave S, Jung H, Coorens THH, Lawson ARJ, Leongamornlert D, Francies HE, Garnett MJ, Ning Z, Campbell PJ. Haplotype-specific assembly of shattered chromosomes in esophageal adenocarcinomas. CELL GENOMICS 2024; 4:100484. [PMID: 38232733 PMCID: PMC10879010 DOI: 10.1016/j.xgen.2023.100484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/13/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
The epigenetic landscape of cancer is regulated by many factors, but primarily it derives from the underlying genome sequence. Chromothripsis is a catastrophic localized genome shattering event that drives, and often initiates, cancer evolution. We characterized five esophageal adenocarcinoma organoids with chromothripsis using long-read sequencing and transcriptome and epigenome profiling. Complex structural variation and subclonal variants meant that haplotype-aware de novo methods were required to generate contiguous cancer genome assemblies. Chromosomes were assembled separately and scaffolded using haplotype-resolved Hi-C reads, producing accurate assemblies even with up to 900 structural rearrangements. There were widespread differences between the chromothriptic and wild-type copies of chromosomes in topologically associated domains, chromatin accessibility, histone modifications, and gene expression. Differential epigenome peaks were most enriched within 10 kb of chromothriptic structural variants. Alterations in transcriptome and higher-order chromosome organization frequently occurred near differential epigenetic marks. Overall, chromothripsis reshapes gene regulation, causing coordinated changes in epigenetic landscape, transcription, and chromosome conformation.
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Affiliation(s)
- Jannat Ijaz
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
| | | | - Keiran Raine
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Health Innovation East, Unit C, Magog Court, Shelford Bottom, Cambridge CB22 3AD, UK
| | | | | | | | - Sonia Zumalave
- Mobile Genomes and Disease, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | | | - Tim H H Coorens
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Hayley E Francies
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; GSK, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | | | - Zemin Ning
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
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19
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Baker TM, Waise S, Tarabichi M, Van Loo P. Aneuploidy and complex genomic rearrangements in cancer evolution. NATURE CANCER 2024; 5:228-239. [PMID: 38286829 PMCID: PMC7616040 DOI: 10.1038/s43018-023-00711-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/14/2023] [Indexed: 01/31/2024]
Abstract
Mutational processes that alter large genomic regions occur frequently in developing tumors. They range from simple copy number gains and losses to the shattering and reassembly of entire chromosomes. These catastrophic events, such as chromothripsis, chromoplexy and the formation of extrachromosomal DNA, affect the expression of many genes and therefore have a substantial effect on the fitness of the cells in which they arise. In this review, we cover large genomic alterations, the mechanisms that cause them and their effect on tumor development and evolution.
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Affiliation(s)
- Toby M Baker
- The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sara Waise
- The Francis Crick Institute, London, UK
- Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Maxime Tarabichi
- The Francis Crick Institute, London, UK
- Institute for Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Peter Van Loo
- The Francis Crick Institute, London, UK.
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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20
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Mazzagatti A, Engel JL, Ly P. Boveri and beyond: Chromothripsis and genomic instability from mitotic errors. Mol Cell 2024; 84:55-69. [PMID: 38029753 PMCID: PMC10842135 DOI: 10.1016/j.molcel.2023.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023]
Abstract
Mitotic cell division is tightly monitored by checkpoints that safeguard the genome from instability. Failures in accurate chromosome segregation during mitosis can cause numerical aneuploidy, which was hypothesized by Theodor Boveri over a century ago to promote tumorigenesis. Recent interrogation of pan-cancer genomes has identified unexpected classes of chromosomal abnormalities, including complex rearrangements arising through chromothripsis. This process is driven by mitotic errors that generate abnormal nuclear structures that provoke extensive yet localized shattering of mis-segregated chromosomes. Here, we discuss emerging mechanisms underlying chromothripsis from micronuclei and chromatin bridges, as well as highlight how this mutational cascade converges on the DNA damage response. A fundamental understanding of these catastrophic processes will provide insight into how initial errors in mitosis can precipitate rapid cancer genome evolution.
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Affiliation(s)
- Alice Mazzagatti
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Justin L Engel
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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21
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Sourty B, Basset L, Fontaine A, Garcion E, Rousseau A. Chromothripsis is rare in IDH-mutant gliomas compared to IDH-wild-type glioblastomas whereas whole-genome duplication is equally frequent in both tumor types. Neurooncol Adv 2024; 6:vdae059. [PMID: 38800696 PMCID: PMC11125406 DOI: 10.1093/noajnl/vdae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024] Open
Abstract
Background Adult-type diffuse gliomas comprise IDH (isocitrate dehydrogenase)-mutant astrocytomas, IDH-mutant 1p/19q-codeleted oligodendrogliomas (ODG), and IDH-wild-type glioblastomas (GBM). GBM displays genome instability, which may result from 2 genetic events leading to massive chromosome alterations: Chromothripsis (CT) and whole-genome duplication (WGD). These events are scarcely described in IDH-mutant gliomas. The better prognosis of the latter may be related to their genome stability compared to GBM. Methods Pangenomic profiles of 297 adult diffuse gliomas were analyzed at initial diagnosis using SNP arrays, including 192 GBM and 105 IDH-mutant gliomas (61 astrocytomas and 44 ODG). Tumor ploidy was assessed with Genome Alteration Print and CT events with CTLPScanner and through manual screening. Survival data were compared using the Kaplan-Meier method. Results At initial diagnosis, 37 GBM (18.7%) displayed CT versus 5 IDH-mutant gliomas (4.7%; P = .0008), the latter were all high-grade (grade 3 or 4) astrocytomas. WGD was detected at initial diagnosis in 18 GBM (9.3%) and 9 IDH-mutant gliomas (5 astrocytomas and 4 oligodendrogliomas, either low- or high-grade; 8.5%). Neither CT nor WGD was associated with overall survival in GBM or in IDH-mutant gliomas. Conclusions CT is less frequent in IDH-mutant gliomas compared to GBM. The absence of CT in ODG and grade 2 astrocytomas might, in part, explain their genome stability and better prognosis, while CT might underlie aggressive biological behavior in some high-grade astrocytomas. WGD is a rare and early event occurring equally in IDH-mutant gliomas and GBM.
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Affiliation(s)
- Baptiste Sourty
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000Angers, France
- Department of Pathology, University Hospital of Angers, Angers, France
| | - Laëtitia Basset
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000Angers, France
- Department of Pathology, University Hospital of Angers, Angers, France
| | - Alix Fontaine
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000Angers, France
- Department of Pathology, University Hospital of Angers, Angers, France
| | - Emmanuel Garcion
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000Angers, France
| | - Audrey Rousseau
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000Angers, France
- Department of Pathology, University Hospital of Angers, Angers, France
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22
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Buccilli B, Rodriguez Molina MA, Redrovan Palomeque DP, Herrera Sabán CA, C Caliwag FM, Contreras Flores CJS, Abeysiriwardana CWJ, Diarte E, Arruarana VS, Calderon Martinez E. Liquid Biopsies for Monitoring Medulloblastoma: Circulating Tumor DNA as a Biomarker for Disease Progression and Treatment Response. Cureus 2024; 16:e51712. [PMID: 38313884 PMCID: PMC10838584 DOI: 10.7759/cureus.51712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2024] [Indexed: 02/06/2024] Open
Abstract
Pediatric brain tumors, including medulloblastoma (MB), represent a significant challenge in clinical oncology. Early diagnosis, accurate monitoring of therapeutic response, and the detection of minimal residual disease (MRD) are crucial for improving outcomes in these patients. This review aims to explore recent advancements in liquid biopsy techniques for monitoring pediatric brain tumors, with a specific focus on medulloblastoma. The primary research question is how liquid biopsy techniques can be effectively utilized for these purposes. Liquid biopsies, particularly the analysis of circulating tumor DNA (ctDNA) in cerebrospinal fluid (CSF), are investigated as promising noninvasive tools. This comprehensive review examines the components of liquid biopsies, including ctDNA, cell-free DNA (cfDNA), and microRNA (miRNA). Their applications in diagnosis, prognosis, and MRD assessment are critically assessed. The review also discusses the role of liquid biopsies in categorizing medulloblastoma subgroups, risk stratification, and the identification of therapeutic targets. Liquid biopsies have shown promising applications in the pediatric brain tumor field, particularly in medulloblastoma. They offer noninvasive means of diagnosis, monitoring treatment response, and detecting MRD. These biopsies have played a pivotal role in subgroup classification and risk stratification of medulloblastoma patients, aiding in the identification of therapeutic targets. However, challenges related to sensitivity and specificity are noted. In conclusion, this review highlights the growing importance of liquid biopsies, specifically ctDNA analysis in CSF, in pediatric brain tumor management, with a primary focus on medulloblastoma. Liquid biopsies have the potential to revolutionize patient care by enabling early diagnosis, accurate monitoring, and MRD detection. Nevertheless, further research is essential to validate their clinical utility fully. The evolving landscape of liquid biopsy applications underscores their promise in improving outcomes for pediatric brain tumor patients.
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Affiliation(s)
- Barbara Buccilli
- Department of Human Neuroscience, Sapienza University of Rome, Rome, ITA
- Department of Neurosurgery, Mount Sinai Hospital, New York, USA
| | | | | | - Cindy A Herrera Sabán
- Department of General Practice, Facultad de Ciencias Médicas, Universidad de San Carlos de Guatemala, San Carlos, GTM
| | - Fides M C Caliwag
- Department of General Practice, Ateneo School of Medicine and Public Health, Pasig City, PHL
| | | | | | - Edna Diarte
- Department of Medicine, Universidad Autónoma de Sinaloa, Culiacán, MEX
| | - Victor S Arruarana
- Department of Internal Medicine, Brookdale University Hospital Medical Center, New York, USA
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23
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Jiang H, Chan YW. Chromatin bridges: stochastic breakage or regulated resolution? Trends Genet 2024; 40:69-82. [PMID: 37891096 DOI: 10.1016/j.tig.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023]
Abstract
Genetic material is organized in the form of chromosomes, which need to be segregated accurately into two daughter cells in each cell cycle. However, chromosome fusion or the presence of unresolved interchromosomal linkages lead to the formation of chromatin bridges, which can induce DNA lesions and genome instability. Persistent chromatin bridges are trapped in the cleavage furrow and are broken at or after abscission, the final step of cytokinesis. In this review, we focus on recent progress in understanding the mechanism of bridge breakage and resolution. We discuss the molecular machinery and enzymes that have been implicated in the breakage and processing of bridge DNA. In addition, we outline both the immediate outcomes and genomic consequences induced by bridge breakage.
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Affiliation(s)
- Huadong Jiang
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Ying Wai Chan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China.
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24
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Clairmont CD, Gell JJ, Lau CC. Pediatric Tumors as Disorders of Development: The Case for In Vitro Modeling Based on Human Stem Cells. Cancer Control 2024; 31:10732748241270564. [PMID: 39118322 PMCID: PMC11311176 DOI: 10.1177/10732748241270564] [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: 11/30/2023] [Revised: 05/31/2024] [Accepted: 06/13/2024] [Indexed: 08/10/2024] Open
Abstract
Despite improvements in patient outcomes, pediatric cancer remains a leading cause of non-accidental death in children. Recent genetic analysis of patients with pediatric cancers indicates an important role for both germline genetic predisposition and cancer-specific somatic driver mutations. Increasingly, evidence demonstrates that the developmental timepoint at which the cancer cell-of-origin transforms is critical to tumor identity and therapeutic response. Therefore, future therapeutic development would be bolstered by the use of disease models that faithfully recapitulate the genetic context, cell-of-origin, and developmental window of vulnerability in pediatric cancers. Human stem cells have the potential to incorporate all of these characteristics into a pediatric cancer model, while serving as a platform for rapid genetic and pharmacological testing. In this review, we describe how human stem cells have been used to model pediatric cancers and how these models compare to other pediatric cancer model modalities.
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Affiliation(s)
- Cullen D. Clairmont
- University of Connecticut School of Medicine, Farmington, CT, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Joanna J. Gell
- University of Connecticut School of Medicine, Farmington, CT, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Connecticut Children’s Medical Center, Center for Cancer and Blood Disorders, Hartford, CT, USA
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, UConn Health, Farmington, CT, USA
| | - Ching C. Lau
- University of Connecticut School of Medicine, Farmington, CT, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Connecticut Children’s Medical Center, Center for Cancer and Blood Disorders, Hartford, CT, USA
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, UConn Health, Farmington, CT, USA
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25
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Kolodziejczak AS, Guerrini-Rousseau L, Planchon JM, Ecker J, Selt F, Mynarek M, Obrecht D, Sill M, Autry RJ, Stutheit-Zhao E, Hirsch S, Amouyal E, Dufour C, Ayrault O, Torrejon J, Waszak SM, Ramaswamy V, Pentikainen V, Demir HA, Clifford SC, Schwalbe EC, Massimi L, Snuderl M, Galbraith K, Karajannis MA, Hill K, Li BK, Walsh M, White CL, Redmond S, Loizos L, Jakob M, Kordes UR, Schmid I, Hauer J, Blattmann C, Filippidou M, Piccolo G, Scheurlen W, Farrag A, Grund K, Sutter C, Pietsch T, Frank S, Schewe DM, Malkin D, Ben-Arush M, Sehested A, Wong TT, Wu KS, Liu YL, Carceller F, Mueller S, Stoller S, Taylor MD, Tabori U, Bouffet E, Kool M, Sahm F, von Deimling A, Korshunov A, von Hoff K, Kratz CP, Sturm D, Jones DTW, Rutkowski S, van Tilburg CM, Witt O, Bougeard G, Pajtler KW, Pfister SM, Bourdeaut F, Milde T. Clinical outcome of pediatric medulloblastoma patients with Li-Fraumeni syndrome. Neuro Oncol 2023; 25:2273-2286. [PMID: 37379234 PMCID: PMC10708940 DOI: 10.1093/neuonc/noad114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND The prognosis for Li-Fraumeni syndrome (LFS) patients with medulloblastoma (MB) is poor. Comprehensive clinical data for this patient group is lacking, challenging the development of novel therapeutic strategies. Here, we present clinical and molecular data on a retrospective cohort of pediatric LFS MB patients. METHODS In this multinational, multicenter retrospective cohort study, LFS patients under 21 years with MB and class 5 or class 4 constitutional TP53 variants were included. TP53 mutation status, methylation subgroup, treatment, progression free- (PFS) and overall survival (OS), recurrence patterns, and incidence of subsequent neoplasms were evaluated. RESULTS The study evaluated 47 LFS individuals diagnosed with MB, mainly classified as DNA methylation subgroup "SHH_3" (86%). The majority (74%) of constitutional TP53 variants represented missense variants. The 2- and 5-year (y-) PFS were 36% and 20%, and 2- and 5y-OS were 53% and 23%, respectively. Patients who received postoperative radiotherapy (RT) (2y-PFS: 44%, 2y-OS: 60%) or chemotherapy before RT (2y-PFS: 32%, 2y-OS: 48%) had significantly better clinical outcome then patients who were not treated with RT (2y-PFS: 0%, 2y-OS: 25%). Patients treated according to protocols including high-intensity chemotherapy and patients who received only maintenance-type chemotherapy showed similar outcomes (2y-PFS: 42% and 35%, 2y-OS: 68% and 53%, respectively). CONCLUSIONS LFS MB patients have a dismal prognosis. In the presented cohort use of RT significantly increased survival rates, whereas chemotherapy intensity did not influence their clinical outcome. Prospective collection of clinical data and development of novel treatments are required to improve the outcome of LFS MB patients.
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Affiliation(s)
- Anna S Kolodziejczak
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Lea Guerrini-Rousseau
- Department of Children and Adolescents Oncology, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France
- Molecular Predictors and New Targets in Oncology, Inserm U981 Team “Genomics and Oncogenesis of pediatric Brain Tumors,” Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Julien Masliah Planchon
- Department of Diagnostic and Theranostic Medicine, Somatic Genetics Unit, Institut Curie, Paris-Science Lettres University, Paris, France
| | - Jonas Ecker
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Selt
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Mynarek
- Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Denise Obrecht
- Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Sill
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Robert J Autry
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Eric Stutheit-Zhao
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Steffen Hirsch
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Elsa Amouyal
- SIREDO Pediatric Oncology Center, Institut Curie, Paris-Science Lettres University, Paris, France
| | - Christelle Dufour
- Department of Children and Adolescents Oncology, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France
- Molecular Predictors and New Targets in Oncology, Inserm U981 Team “Genomics and Oncogenesis of pediatric Brain Tumors,” Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Olivier Ayrault
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Jacob Torrejon
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Vijay Ramaswamy
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Hematology and Oncology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Virve Pentikainen
- Division of Hematology-Oncology and Stem Cell Transplantation, Children’s Hospital, Helsinki University Hospital, Helsinki, Finland
| | - Haci Ahmet Demir
- Department of Pediatric Hematology-Oncology, Private Memorial Ankara Hospital, Ankara, Turkey
| | - Steven C Clifford
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, United Kingdom
| | - Ed C Schwalbe
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, United Kingdom
- Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Luca Massimi
- Pediatric Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, Catholic University Medical School, Rome, Italy
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York City, NY, USA
| | - Kristyn Galbraith
- Department of Pathology, New York University Langone Health, New York City, NY, USA
| | - Matthias A Karajannis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Katherine Hill
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Bryan K Li
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Mike Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Christine L White
- Victorian Clinical Genetics Services, Parkville, Australia
- Hudson Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Shelagh Redmond
- Childhood Cancer Registry, Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Loizou Loizos
- Pediatric Oncology/Hematology/Immunology at the Medical School of the University of Nicosia, Nicosia, Cyprus
| | - Marcus Jakob
- Department of Paediatric Haematology, Oncology and Stem-Cell Transplantation, University Hospital Regensburg, Regensburg, Germany
| | - Uwe R Kordes
- Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Irene Schmid
- Paediatric Haematology and Oncology, Dr. von Hauner Children’s Hospital, Ludwig Maximilians University Munich, Munich, Germany
| | - Julia Hauer
- Pediatric Haematology and Oncology, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Claudia Blattmann
- Paediatric Haematology, Oncology and Immunology, Olgahospital, Klinikum Stuttgart, Stuttgart, Germany
| | - Maria Filippidou
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, “Aghia Sophia” Children’s Hospital, Athens, Greece
| | - Gianluca Piccolo
- Neuro-Oncology Unit, IRCCS Istituto Giannina Gaslini, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Wolfram Scheurlen
- Paediatric Haematology and Oncology, Cnopfsche Paediatric Clinic, Nurnberg, Germany
| | - Ahmed Farrag
- Department of Paediatric Haematology, Oncology and Stem-Cell Transplantation, Paediatric Clinic, University Hospital Aachen, Aachen, Germany
- Department of Pediatric Oncology, South Egypt Cancer Institute, Assiut University, Egypt
| | - Kerstin Grund
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Christian Sutter
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn Medical Center, Bonn, Germany
| | - Stephan Frank
- Division of Neuropathology, Institute of Pathology, Basel University Hospital, Basel, Switzerland
| | - Denis M Schewe
- Department of Pediatrics, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - David Malkin
- Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Myriam Ben-Arush
- Pediatric Hematology Oncology, Rambam Medical Center, Haifa, Israel
| | - Astrid Sehested
- Department of Paediatrics and Adolescent Medicine, Juliane Marie Centre, Copenhagen University Hospital, Copenhagen, Denmark
| | - Tai-Tong Wong
- Division of Pediatric Neurosurgery, Department of Neurosurgery, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan
| | - Kuo-Sheng Wu
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yen-Lin Liu
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Fernando Carceller
- Paediatric and Adolescent Oncology Drug Development Team, Children and Young People’s Unit, The Royal Marsden NHS Foundation Trust and The Institute of Cancer Research, Sutton, United Kingdom
| | - Sabine Mueller
- Department of Neurology, Neurosurgery and Pediatrics, University of California, San Francisco, USA
| | - Schuyler Stoller
- Department of Neurology, University of California, San Francisco, USA
| | - Michael D Taylor
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Uri Tabori
- Division of Hematology and Oncology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Eric Bouffet
- Division of Hematology and Oncology, Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Division of Haematology/ Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Marcel Kool
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Felix Sahm
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, and CCU Neuropathology, German Cancer Institute (DKF), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, and CCU Neuropathology, German Cancer Institute (DKF), Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, and CCU Neuropathology, German Cancer Institute (DKF), Heidelberg, Germany
| | - Katja von Hoff
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Christian P Kratz
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Dominik Sturm
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - David T W Jones
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan Rutkowski
- Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cornelis M van Tilburg
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Olaf Witt
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Gaëlle Bougeard
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics, F-76000 Rouen, France
| | - Kristian W Pajtler
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Franck Bourdeaut
- SIREDO Pediatric Oncology Center, Institut Curie, Paris-Science Lettres University, Paris, France
| | - Till Milde
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
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26
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Gharbaran R. Insights into the molecular roles of FOXR2 in the pathology of primary pediatric brain tumors. Crit Rev Oncol Hematol 2023; 192:104188. [PMID: 37879492 DOI: 10.1016/j.critrevonc.2023.104188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 08/23/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023] Open
Abstract
Forkhead box gene R2 (FOXR2) belongs to the family of FOX genes which codes for highly conserved transcription factors (TFs) with critical roles in biological processes ranging from development to organogenesis to metabolic and immune regulation to cellular homeostasis. A number of FOX genes are associated with cancer development and progression and poor prognosis. A growing body of evidence suggests that FOXR2 is an oncogene. Studies suggested important roles for FOXR2 in cancer cell growth, metastasis, and drug resistance. Recent studies showed that FOXR2 is overexpressed by a subset of newly identified entities of embryonal tumors. This review discusses the role(s) FOXR2 plays in the pathology of pediatric brain cancers and its potential as a therapeutic target.
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Affiliation(s)
- Rajendra Gharbaran
- Biological Sciences Department, Bronx Community College/City University of New York, 2155 University Avenue, Bronx, NY 10453, USA.
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Chapman OS, Luebeck J, Sridhar S, Wong ITL, Dixit D, Wang S, Prasad G, Rajkumar U, Pagadala MS, Larson JD, He BJ, Hung KL, Lange JT, Dehkordi SR, Chandran S, Adam M, Morgan L, Wani S, Tiwari A, Guccione C, Lin Y, Dutta A, Lo YY, Juarez E, Robinson JT, Korshunov A, Michaels JEA, Cho YJ, Malicki DM, Coufal NG, Levy ML, Hobbs C, Scheuermann RH, Crawford JR, Pomeroy SL, Rich JN, Zhang X, Chang HY, Dixon JR, Bagchi A, Deshpande AJ, Carter H, Fraenkel E, Mischel PS, Wechsler-Reya RJ, Bafna V, Mesirov JP, Chavez L. Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma. Nat Genet 2023; 55:2189-2199. [PMID: 37945900 PMCID: PMC10703696 DOI: 10.1038/s41588-023-01551-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/22/2023] [Indexed: 11/12/2023]
Abstract
Circular extrachromosomal DNA (ecDNA) in patient tumors is an important driver of oncogenic gene expression, evolution of drug resistance and poor patient outcomes. Applying computational methods for the detection and reconstruction of ecDNA across a retrospective cohort of 481 medulloblastoma tumors from 465 patients, we identify circular ecDNA in 82 patients (18%). Patients with ecDNA-positive medulloblastoma were more than twice as likely to relapse and three times as likely to die within 5 years of diagnosis. A subset of tumors harbored multiple ecDNA lineages, each containing distinct amplified oncogenes. Multimodal sequencing, imaging and CRISPR inhibition experiments in medulloblastoma models reveal intratumoral heterogeneity of ecDNA copy number per cell and frequent putative 'enhancer rewiring' events on ecDNA. This study reveals the frequency and diversity of ecDNA in medulloblastoma, stratified into molecular subgroups, and suggests copy number heterogeneity and enhancer rewiring as oncogenic features of ecDNA.
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Affiliation(s)
- Owen S Chapman
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Sunita Sridhar
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Department of Pediatrics, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Ivy Tsz-Lo Wong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Deobrat Dixit
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
- Department of Neurology and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Shanqing Wang
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Gino Prasad
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Meghana S Pagadala
- Medical Scientist Training Program, University of California San Diego, San Diego, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, San Diego, CA, USA
| | - Jon D Larson
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Britney Jiayu He
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Joshua T Lange
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Siavash R Dehkordi
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | | | - Miriam Adam
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ling Morgan
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Sameena Wani
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Ashutosh Tiwari
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Caitlin Guccione
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Yingxi Lin
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Aditi Dutta
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Yan Yuen Lo
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital and Healthcare Center, San Diego, CA, USA
| | - Edwin Juarez
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - James T Robinson
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - John-Edward A Michaels
- Papé Pediatric Research Institute, Department of Pediatrics and Knight Cancer Insitute, Oregon Health and Sciences University, Portland, OR, USA
| | - Yoon-Jae Cho
- Papé Pediatric Research Institute, Department of Pediatrics and Knight Cancer Insitute, Oregon Health and Sciences University, Portland, OR, USA
| | - Denise M Malicki
- Division of Pathology, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Nicole G Coufal
- Department of Pediatrics, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Michael L Levy
- Division of Pathology, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Charlotte Hobbs
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital and Healthcare Center, San Diego, CA, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, San Diego, CA, USA
| | - John R Crawford
- Department of Pediatrics, University of California Irvine and Children's Hospital Orange County, Irvine, CA, USA
| | - Scott L Pomeroy
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jeremy N Rich
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xinlian Zhang
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, San Diego, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jesse R Dixon
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anindya Bagchi
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | | | - Hannah Carter
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Robert J Wechsler-Reya
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
- Department of Neurology and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Jill P Mesirov
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Lukas Chavez
- Department of Medicine, University of California San Diego, San Diego, CA, USA.
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA.
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital and Healthcare Center, San Diego, CA, USA.
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA.
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Espejo Valle-Inclán J, Cortés-Ciriano I. ReConPlot: an R package for the visualization and interpretation of genomic rearrangements. Bioinformatics 2023; 39:btad719. [PMID: 38058190 PMCID: PMC10710371 DOI: 10.1093/bioinformatics/btad719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 09/13/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023] Open
Abstract
MOTIVATION Whole-genome sequencing studies of human tumours have revealed that complex forms of structural variation, collectively known as complex genome rearrangements (CGRs), are pervasive across diverse cancer types. Detection, classification, and mechanistic interpretation of CGRs requires the visualization of complex patterns of somatic copy number aberrations (SCNAs) and structural variants (SVs). However, there is a lack of tools specifically designed to facilitate the visualization and study of CGRs. RESULTS We present ReConPlot (REarrangement and COpy Number PLOT), an R package that provides functionalities for the joint visualization of SCNAs and SVs across one or multiple chromosomes. ReConPlot is based on the popular ggplot2 package, thus allowing customization of plots and the generation of publication-quality figures with minimal effort. Overall, ReConPlot facilitates the exploration, interpretation, and reporting of CGR patterns. AVAILABILITY AND IMPLEMENTATION The R package ReConPlot is available at https://github.com/cortes-ciriano-lab/ReConPlot. Detailed documentation and a tutorial with examples are provided with the package.
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Affiliation(s)
- Jose Espejo Valle-Inclán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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Lanceta J, Tripodi J, Karp L, Shaham M, Mahmood N, Najfeld V, Edelman M, Cohen N. Chromothripsis in lipoblastoma: second reported case with complex PLAG1 rearrangement. Mol Cytogenet 2023; 16:32. [PMID: 38012697 PMCID: PMC10683218 DOI: 10.1186/s13039-023-00665-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023] Open
Abstract
Lipoblastomas (LPBs) are rare benign neoplasms derived from embryonal adipose that occur predominantly in childhood. LPBs typically present with numeric or structural rearrangements of chromosome 8, the majority of which involve the pleomorphic adenoma gene 1 (PLAG1) proto-oncogene on chromosome 8q12. Here, we report on a LPB case on which showed evidence of chromothripsis. This is the second reported case of chromothripsis in LPB.
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Affiliation(s)
- Joel Lanceta
- Department of Pathology and Laboratory Medicine, Northwell Health/Donald and Barbara Zucker School of Medicine at Hofstra, Manhasset, New York, USA.
| | - Joseph Tripodi
- Tumor CytoGenomics, Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lynne Karp
- Department of Pathology and Laboratory Medicine, Northwell Health/Donald and Barbara Zucker School of Medicine at Hofstra, Manhasset, New York, USA
- Division of Cytogenetics and Molecular Pathology, North Shore University Hospital, Manhasset, NY, USA
| | - Meira Shaham
- Department of Pathology and Laboratory Medicine, Northwell Health/Donald and Barbara Zucker School of Medicine at Hofstra, Manhasset, New York, USA
- Division of Cytogenetics and Molecular Pathology, North Shore University Hospital, Manhasset, NY, USA
| | - Nayyara Mahmood
- Department of Pathology and Laboratory Medicine, Northwell Health/Donald and Barbara Zucker School of Medicine at Hofstra, Manhasset, New York, USA
- Division of Cytogenetics and Molecular Pathology, North Shore University Hospital, Manhasset, NY, USA
| | - Vesna Najfeld
- Tumor CytoGenomics, Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Morris Edelman
- Department of Pathology and Laboratory Medicine, Northwell Health/Donald and Barbara Zucker School of Medicine at Hofstra, Manhasset, New York, USA
- Division of Pediatric Pathology, Cohen Children's Medical Center, New Hyde Park, NY, USA
| | - Ninette Cohen
- Department of Pathology and Laboratory Medicine, Northwell Health/Donald and Barbara Zucker School of Medicine at Hofstra, Manhasset, New York, USA
- Division of Cytogenetics and Molecular Pathology, North Shore University Hospital, Manhasset, NY, USA
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30
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Hatano Y. The Pathology according to p53 Pathway. Pathobiology 2023; 91:230-243. [PMID: 37963443 PMCID: PMC11313058 DOI: 10.1159/000535203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/12/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND Observations play a pivotal role in the progress of science, including in pathology. The cause of a disease such as cancer is analyzed by breaking it down into smaller organs, tissues, cells, and molecules. The current standard cancer diagnostic procedure, microscopic observation, relies on preserved morphological characteristics. In contrast, molecular analyses explore oncogenic pathway activation that leads to genetic mutations and aberrant protein expression. Such molecular analyses could potentially identify therapeutic targets and has gained considerable attention in clinical oncology. SUMMARY This review summarizes the cardinal biomarkers of the p53 pathway, p53, p16, and mouse double minute 2 (MDM2), in the context of traditional surgical pathology and emerging genomic oncology. The p53 pathway, which is dysregulated in more than a half of all cancers, can be applied in several diagnostic settings. A four-classification model of immunophenotype for p53 pathway gene status, tumor types with a high frequency of abnormalities for each p53 pathway gene, and a minimal p53 pathway immunohistochemical panel is also described. KEY MESSAGES Immunohistochemistry of oncogenic signals should be interpreted according to molecular findings based on genomic oncology, in addition to the microscopic findings of diagnostic pathology.
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Affiliation(s)
- Yuichiro Hatano
- Department of Pathology, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka, Japan
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31
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Wu S, Tao T, Zhang L, Zhu X, Zhou X. Extrachromosomal DNA (ecDNA): Unveiling its role in cancer progression and implications for early detection. Heliyon 2023; 9:e21327. [PMID: 38027570 PMCID: PMC10643110 DOI: 10.1016/j.heliyon.2023.e21327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Extrachromosomal DNA (ecDNA) is a special class of circular DNA in eukaryotes, which is independent of conventional chromosomes. These circular molecules play important roles in biology, especially in cancer biology. The emergence of sequencing technologies such as CCDA-seq and Amplicon Architect has led to a progressive unraveling of the mystery of ecDNA. Consequently, insights into its function and potential applications have begun to surface. Among these studies, the most noteworthy research pertains to cancer-related investigations into ecDNA. Numerous studies have underscored the significance of ecDNA in the pathogenesis of cancer and its role in accelerating cancer evolution. This review provides an overview of the source, structure, and function of ecDNA, while compiling recent advancements in ecDNA in the field of cancer. Nonetheless, further research is imperative to determine its effectiveness and specificity as a biomarker for early cancer detection.
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Affiliation(s)
- Shuhong Wu
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Tao Tao
- Department of Gastroenterology, Zibo Central Hospital, Zibo, China
| | - Lin Zhang
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhu
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
- Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou Medical College, Hangzhou, China
| | - Xiaorong Zhou
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
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Yang Y, Yang L. Somatic structural variation signatures in pediatric brain tumors. Cell Rep 2023; 42:113276. [PMID: 37851574 PMCID: PMC10748741 DOI: 10.1016/j.celrep.2023.113276] [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: 05/17/2023] [Revised: 08/26/2023] [Accepted: 09/28/2023] [Indexed: 10/20/2023] Open
Abstract
Brain cancer is the leading cause of cancer-related death in children. Somatic structural variations (SVs), large-scale alterations in DNA, remain poorly understood in pediatric brain tumors. Here, we detect a total of 13,199 high-confidence somatic SVs in 744 whole-genome sequences of pediatric brain tumors from the Pediatric Brain Tumor Atlas. The somatic SV occurrences have tremendous diversity among the cohort and across different tumor types. We decompose mutational signatures of clustered complex SVs, non-clustered complex SVs, and simple SVs separately to infer their mutational mechanisms. Our finding of many tumor types carrying unique sets of SV signatures suggests that distinct molecular mechanisms shape genome instability in different tumor types. The patterns of somatic SV signatures in pediatric brain tumors are substantially different from those in adult cancers. The convergence of multiple SV signatures on several major cancer driver genes implies vital roles of somatic SVs in disease progression.
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Affiliation(s)
- Yang Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Lixing Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; University of Chicago Comprehensive Cancer Center, Chicago, IL 60637, USA.
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Li O, Li L, Sheng Y, Ke K, Wu J, Mou Y, Liu M, Jin W. Biological characteristics of pancreatic ductal adenocarcinoma: Initiation to malignancy, intracellular to extracellular. Cancer Lett 2023; 574:216391. [PMID: 37714257 DOI: 10.1016/j.canlet.2023.216391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 09/04/2023] [Accepted: 09/10/2023] [Indexed: 09/17/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly life-threatening tumour with a low early-detection rate, rapid progression and a tendency to develop resistance to chemotherapy. Therefore, understanding the regulatory mechanisms underlying the initiation, development and metastasis of pancreatic cancer is necessary for enhancing therapeutic effectiveness. In this review, we summarised single-gene mutations (including KRAS, CDKN2A, TP53, SMAD4 and some other less prevalent mutations), epigenetic changes (including DNA methylation, histone modifications and RNA interference) and large chromosome alterations (such as copy number variations, chromosome rearrangements and chromothripsis) associated with PDAC. In addition, we discussed variations in signalling pathways that act as intermediate oncogenic factors in PDAC, including PI3K/AKT, MAPK/ERK, Hippo and TGF-β signalling pathways. The focus of this review was to investigate alterations in the microenvironment of PDAC, particularly the role of immunosuppressive cells, cancer-associated fibroblasts, lymphocytes, other para-cancerous cells and tumour extracellular matrix in tumour progression. Peripheral axons innervating the pancreas have been reported to play a crucial role in the development of cancer. In addition, tumour cells can influence the behaviour of neighbouring non-tumour cells by secreting certain factors, both locally and at a distance. In this review, we elucidated the alterations in intracellular molecules and the extracellular environment that occur during the progression of PDAC. Altogether, this review may enhance the understanding of the biological characteristics of PDAC and guide the development of more precise treatment strategies.
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Affiliation(s)
- Ou Li
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China; Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Li Li
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China; Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yunru Sheng
- Center for Rehabilitation Medicine, Department of Anesthesiology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Kun Ke
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China; Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Jianzhang Wu
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China; Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yiping Mou
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China; Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Mingyang Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center, China; National Clinical Research Center for Cancer, China; Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Weiwei Jin
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China; Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China.
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Moore JA, Chen KT, Madison R, Newberg JY, Fleischmann Z, Wang S, Sharaf R, Murugesan K, Fendler BJ, Hughes J, Schrock AB, Hegde PS, Oxnard GR, Fabrizio D, Frampton GM, Antonarakis ES, Sokol ES, Jin DX. Pan-Cancer Analysis of Copy-Number Features Identifies Recurrent Signatures and a Homologous Recombination Deficiency Biomarker to Predict Poly (ADP-Ribose) Polymerase Inhibitor Response. JCO Precis Oncol 2023; 7:e2300093. [PMID: 37769224 DOI: 10.1200/po.23.00093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/21/2023] [Accepted: 07/21/2023] [Indexed: 09/30/2023] Open
Abstract
PURPOSE Copy-number (CN) features reveal the molecular state of cancers and may have predictive and prognostic value in the treatment of cancer. We sought to apply published CN analysis methods to a large pan-cancer data set and characterize ubiquitous CN signatures across tumor types, including potential utility for treatment selection. METHODS We analyzed the landscape of CN features in 260,333 pan-cancer samples. We examined the association of 10 signatures with genomic alterations and clinical characteristics and trained a machine learning classifier using CN and insertion and deletion features to detect homologous recombination deficiency signature (HRDsig) positivity. Clinical outcomes were assessed using a real-world clinicogenomic database (CGDB) of comprehensive genomic profiling linked to deidentified, electronic health record-derived clinical data. RESULTS CN signatures were prevalent across cancer types and associated with diverse processes including focal tandem duplications, seismic amplifications, genome-wide loss of heterozygosity (gLOH), and HRD. Our novel HRDsig outperformed gLOH in predicting BRCAness and effectively distinguished biallelic BRCA and homologous recombination-repair wild-type (HRRwt) samples pan-tumor, demonstrating high sensitivity to detect biallelic BRCA in ovarian (93%) and other HRD-associated cancers (80%-87%). Pan-tumor prevalence of HRDsig was 6.4%. HRRwt cases represented a significant fraction of the HRDsig-positive cohort, likely reflecting a population with nongenomic mechanisms of HRD. In ovarian and prostate CGDBs, HRDsig identified more patients than gLOH and had predictive value for poly (ADP-ribose) polymerase inhibitor (PARPi) benefit. CONCLUSION Tumor CN profiles are informative, revealing diverse processes active in cancer. We describe the landscape of 10 CN signatures in a large pan-cancer cohort, including two associated with HRD. We trained a machine learning-based HRDsig that robustly identified BRCAness and associated with biallelic BRCA pan-tumor, and was predictive of PARPi benefit in real-world ovarian and prostate data sets.
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35
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Zwaig M, Johnston MJ, Lee JJ, Farooq H, Gallo M, Jabado N, Taylor MD, Ragoussis J. Linked-read based analysis of the medulloblastoma genome. Front Oncol 2023; 13:1221611. [PMID: 37576901 PMCID: PMC10419201 DOI: 10.3389/fonc.2023.1221611] [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: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Medulloblastoma is the most common type of malignant pediatric brain tumor with group 4 medulloblastomas (G4 MBs) accounting for 40% of cases. However, the molecular mechanisms that underlie this subgroup are still poorly understood. Point mutations are detected in a large number of genes at low incidence per gene while the detection of complex structural variants in recurrently affected genes typically requires the application of long-read technologies. Methods Here, we applied linked-read sequencing, which combines the long-range genome information of long-read sequencing with the high base pair accuracy of short read sequencing and very low sample input requirements. Results We demonstrate the detection of complex structural variants and point mutations in these tumors, and, for the first time, the detection of extrachromosomal DNA (ecDNA) with linked-reads. We provide further evidence for the high heterogeneity of somatic mutations in G4 MBs and add new complex events associated with it. Discussion We detected several enhancer-hijacking events, an ecDNA containing the MYCN gene, and rare structural rearrangements, such a chromothripsis in a G4 medulloblastoma, chromoplexy involving 8 different chromosomes, a TERT gene rearrangement, and a PRDM6 duplication.
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Affiliation(s)
- Melissa Zwaig
- Victor Phillip Dahdaleh Institute of Genomic Medicine and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Michael J. Johnston
- Alberta Children’s Hospital Research Institute, Arnie Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - John J.Y. Lee
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, United States
| | | | - Marco Gallo
- Alberta Children’s Hospital Research Institute, Arnie Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
| | - Michael D. Taylor
- Division of Neurosurgery, The Arthur and Sonia Labatt Brain Tumour Research Centre and the Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Texas Children’s Cancer Center , Hematology-Oncology Section and Department of Pediatrics – Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, TX, United States
| | - Jiannis Ragoussis
- Victor Phillip Dahdaleh Institute of Genomic Medicine and Department of Human Genetics, McGill University, Montreal, QC, Canada
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36
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Zhou RW, Parsons RE. Etiology of super-enhancer reprogramming and activation in cancer. Epigenetics Chromatin 2023; 16:29. [PMID: 37415185 DOI: 10.1186/s13072-023-00502-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/10/2023] [Indexed: 07/08/2023] Open
Abstract
Super-enhancers are large, densely concentrated swaths of enhancers that regulate genes critical for cell identity. Tumorigenesis is accompanied by changes in the super-enhancer landscape. These aberrant super-enhancers commonly form to activate proto-oncogenes, or other genes upon which cancer cells depend, that initiate tumorigenesis, promote tumor proliferation, and increase the fitness of cancer cells to survive in the tumor microenvironment. These include well-recognized master regulators of proliferation in the setting of cancer, such as the transcription factor MYC which is under the control of numerous super-enhancers gained in cancer compared to normal tissues. This Review will cover the expanding cell-intrinsic and cell-extrinsic etiology of these super-enhancer changes in cancer, including somatic mutations, copy number variation, fusion events, extrachromosomal DNA, and 3D chromatin architecture, as well as those activated by inflammation, extra-cellular signaling, and the tumor microenvironment.
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Affiliation(s)
- Royce W Zhou
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Molecular Medicine Program, University of California San Francisco Internal Medicine Residency, San Francisco, CA, USA
| | - Ramon E Parsons
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Casimir L, Zimmer S, Racine-Brassard F, Goudreau F, Jacques PÉ, Maréchal A. Chronic treatment with ATR and CHK1 inhibitors does not substantially increase the mutational burden of human cells. Mutat Res 2023; 827:111834. [PMID: 37531716 DOI: 10.1016/j.mrfmmm.2023.111834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023]
Abstract
DNA replication stress (RS) entails the frequent slow down and arrest of replication forks by a variety of conditions that hinder accurate and processive genome duplication. Elevated RS leads to genome instability, replication catastrophe and eventually cell death. RS is particularly prevalent in cancer cells and its exacerbation to unsustainable levels by chemotherapeutic agents remains a cornerstone of cancer treatments. The adverse consequences of RS are normally prevented by the ATR and CHK1 checkpoint kinases that stabilize stressed forks, suppress origin firing and promote cell cycle arrest when replication is perturbed. Specific inhibitors of these kinases have been developed and shown to potentiate RS and cell death in multiple in vitro cancer settings. Ongoing clinical trials are now probing their efficacy against various cancer types, either as single agents or in combination with mainstay chemotherapeutics. Despite their promise as valuable additions to the anti-cancer pharmacopoeia, we still lack a genome-wide view of the potential mutagenicity of these new drugs. To investigate this question, we performed chronic long-term treatments of TP53-depleted human cancer cells with ATR and CHK1 inhibitors (ATRi, AZD6738/ceralasertib and CHK1i, MK8776/SCH-900776). ATR or CHK1 inhibition did not significantly increase the mutational burden of cells, nor generate specific mutational signatures. Indeed, no notable changes in the numbers of base substitutions, short insertions/deletions and larger scale rearrangements were observed despite induction of replication-associated DNA breaks during treatments. Interestingly, ATR inhibition did induce a slight increase in closely-spaced mutations, a feature previously attributed to translesion synthesis DNA polymerases. The results suggest that ATRi and CHK1i do not have substantial mutagenic effects in vitro when used as standalone agents.
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Affiliation(s)
- Lisa Casimir
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Samuel Zimmer
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Félix Racine-Brassard
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Félix Goudreau
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Pierre-Étienne Jacques
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke J1H 5N3, QC, Canada.
| | - Alexandre Maréchal
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke J1H 5N3, QC, Canada.
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38
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Dong Y, He Q, Chen X, Yang F, He L, Zheng Y. Extrachromosomal DNA (ecDNA) in cancer: mechanisms, functions, and clinical implications. Front Oncol 2023; 13:1194405. [PMID: 37448518 PMCID: PMC10338009 DOI: 10.3389/fonc.2023.1194405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/05/2023] [Indexed: 07/15/2023] Open
Abstract
Extrachromosomal DNA (ecDNA) is circular DNA that plays an important role in the development and heterogeneity of cancer. The rapid evolution of methods to detect ecDNA, including microscopic and sequencing approaches, has greatly enhanced our knowledge of the role of ecDNA in cancer development and evolution. Here, we review the molecular characteristics, functions, mechanisms of formation, and detection methods of ecDNA, with a focus on the potential clinical implications of ecDNA in cancer. Specifically, we consider the role of ecDNA in acquired drug resistance, as a diagnostic and prognostic biomarker, and as a therapeutic target in the context of cancer. As the pathological and clinical significance of ecDNA continues to be explored, it is anticipated that ecDNA will have broad applications in the diagnosis, prognosis, and treatment of patients with cancer.
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Affiliation(s)
- Yucheng Dong
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qi He
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xinyu Chen
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fan Yang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li He
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Yongchang Zheng
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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39
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Arshadi A, Tolomeo D, Venuto S, Storlazzi CT. Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications. Genes (Basel) 2023; 14:1304. [PMID: 37372484 PMCID: PMC10298061 DOI: 10.3390/genes14061304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Focal amplifications (FAs) are crucial in cancer research due to their significant diagnostic, prognostic, and therapeutic implications. FAs manifest in various forms, such as episomes, double minute chromosomes, and homogeneously staining regions, arising through different mechanisms and mainly contributing to cancer cell heterogeneity, the leading cause of drug resistance in therapy. Numerous wet-lab, mainly FISH, PCR-based assays, next-generation sequencing, and bioinformatics approaches have been set up to detect FAs, unravel the internal structure of amplicons, assess their chromatin compaction status, and investigate the transcriptional landscape associated with their occurrence in cancer cells. Most of them are tailored for tumor samples, even at the single-cell level. Conversely, very limited approaches have been set up to detect FAs in liquid biopsies. This evidence suggests the need to improve these non-invasive investigations for early tumor detection, monitoring disease progression, and evaluating treatment response. Despite the potential therapeutic implications of FAs, such as, for example, the use of HER2-specific compounds for patients with ERBB2 amplification, challenges remain, including developing selective and effective FA-targeting agents and understanding the molecular mechanisms underlying FA maintenance and replication. This review details a state-of-the-art of FA investigation, with a particular focus on liquid biopsies and single-cell approaches in tumor samples, emphasizing their potential to revolutionize the future diagnosis, prognosis, and treatment of cancer patients.
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Affiliation(s)
| | | | | | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (A.A.); (D.T.); (S.V.)
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40
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Lin YF, Hu Q, Mazzagatti A, Valle-Inclán JE, Maurais EG, Dahiya R, Guyer A, Sanders JT, Engel JL, Nguyen G, Bronder D, Bakhoum SF, Cortés-Ciriano I, Ly P. Mitotic clustering of pulverized chromosomes from micronuclei. Nature 2023; 618:1041-1048. [PMID: 37165191 PMCID: PMC10307639 DOI: 10.1038/s41586-023-05974-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 03/17/2023] [Indexed: 05/12/2023]
Abstract
Complex genome rearrangements can be generated by the catastrophic pulverization of missegregated chromosomes trapped within micronuclei through a process known as chromothripsis1-5. As each chromosome contains a single centromere, it remains unclear how acentric fragments derived from shattered chromosomes are inherited between daughter cells during mitosis6. Here we tracked micronucleated chromosomes with live-cell imaging and show that acentric fragments cluster in close spatial proximity throughout mitosis for asymmetric inheritance by a single daughter cell. Mechanistically, the CIP2A-TOPBP1 complex prematurely associates with DNA lesions within ruptured micronuclei during interphase, which poises pulverized chromosomes for clustering upon mitotic entry. Inactivation of CIP2A-TOPBP1 caused acentric fragments to disperse throughout the mitotic cytoplasm, stochastically partition into the nucleus of both daughter cells and aberrantly misaccumulate as cytoplasmic DNA. Mitotic clustering facilitates the reassembly of acentric fragments into rearranged chromosomes lacking the extensive DNA copy-number losses that are characteristic of canonical chromothripsis. Comprehensive analysis of pan-cancer genomes revealed clusters of DNA copy-number-neutral rearrangements-termed balanced chromothripsis-across diverse tumour types resulting in the acquisition of known cancer driver events. Thus, distinct patterns of chromothripsis can be explained by the spatial clustering of pulverized chromosomes from micronuclei.
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Affiliation(s)
- Yu-Fen Lin
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qing Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alice Mazzagatti
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jose Espejo Valle-Inclán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elizabeth G Maurais
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rashmi Dahiya
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alison Guyer
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Interdisciplinary Biomedical Graduate Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jacob T Sanders
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Justin L Engel
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Giaochau Nguyen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Daniel Bronder
- Human Oncology and Pathogenesis Program, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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41
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Ntenti C, Lallas K, Papazisis G. Clinical, Histological, and Molecular Prognostic Factors in Childhood Medulloblastoma: Where Do We Stand? Diagnostics (Basel) 2023; 13:diagnostics13111915. [PMID: 37296767 DOI: 10.3390/diagnostics13111915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023] Open
Abstract
Medulloblastomas, highly aggressive neoplasms of the central nervous system (CNS) that present significant heterogeneity in clinical presentation, disease course, and treatment outcomes, are common in childhood. Moreover, patients who survive may be diagnosed with subsequent malignancies during their life or could develop treatment-related medical conditions. Genetic and transcriptomic studies have classified MBs into four subgroups: wingless type (WNT), Sonic Hedgehog (SHH), Group 3, and Group 4, with distinct histological and molecular profiles. However, recent molecular findings resulted in the WHO updating their guidelines and stratifying medulloblastomas into further molecular subgroups, changing the clinical stratification and treatment management. In this review, we discuss most of the histological, clinical, and molecular prognostic factors, as well the feasibility of their application, for better characterization, prognostication, and treatment of medulloblastomas.
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Affiliation(s)
- Charikleia Ntenti
- First Department of Pharmacology, School of Medicine, Aristotle University of Thessaloniki, 54621 Thessaloniki, Greece
| | - Konstantinos Lallas
- Department of Medical Oncology, School of Medicine, Aristotle University of Thessaloniki, 54621 Thessaloniki, Greece
| | - Georgios Papazisis
- Clinical Research Unit, Special Unit for Biomedical Research and Education (BRESU), School of Medicine, Aristotle University of Thessaloniki, 54621 Thessaloniki, Greece
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42
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Maslenkina K, Mikhaleva L, Naumenko M, Vandysheva R, Gushchin M, Atiakshin D, Buchwalow I, Tiemann M. Signaling Pathways in the Pathogenesis of Barrett's Esophagus and Esophageal Adenocarcinoma. Int J Mol Sci 2023; 24:ijms24119304. [PMID: 37298253 DOI: 10.3390/ijms24119304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Barrett's esophagus (BE) is a premalignant lesion that can develop into esophageal adenocarcinoma (EAC). The development of Barrett's esophagus is caused by biliary reflux, which causes extensive mutagenesis in the stem cells of the epithelium in the distal esophagus and gastro-esophageal junction. Other possible cellular origins of BE include the stem cells of the mucosal esophageal glands and their ducts, the stem cells of the stomach, residual embryonic cells and circulating bone marrow stem cells. The classical concept of healing a caustic lesion has been replaced by the concept of a cytokine storm, which forms an inflammatory microenvironment eliciting a phenotypic shift toward intestinal metaplasia of the distal esophagus. This review describes the roles of the NOTCH, hedgehog, NF-κB and IL6/STAT3 molecular pathways in the pathogenesis of BE and EAC.
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Affiliation(s)
- Ksenia Maslenkina
- A.P. Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119991 Moscow, Russia
| | - Liudmila Mikhaleva
- A.P. Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119991 Moscow, Russia
| | - Maxim Naumenko
- A.P. Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119991 Moscow, Russia
| | - Rositsa Vandysheva
- A.P. Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119991 Moscow, Russia
| | - Michail Gushchin
- A.P. Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119991 Moscow, Russia
| | - Dmitri Atiakshin
- Research and Educational Resource Centre for Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis Innovative Technologies, Peoples' Friendship University of Russia Named after Patrice Lumumba, 117198 Moscow, Russia
| | - Igor Buchwalow
- Research and Educational Resource Centre for Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis Innovative Technologies, Peoples' Friendship University of Russia Named after Patrice Lumumba, 117198 Moscow, Russia
- Institute for Hematopathology, Fangdieckstr. 75a, 22547 Hamburg, Germany
| | - Markus Tiemann
- Institute for Hematopathology, Fangdieckstr. 75a, 22547 Hamburg, Germany
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43
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Yang Y, Yang L. Somatic structural variation signatures in pediatric brain tumors. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.18.23290139. [PMID: 37292789 PMCID: PMC10246126 DOI: 10.1101/2023.05.18.23290139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Brain cancer is the leading cause of cancer-related death in children. Somatic structural variations (SVs), large scale alterations in DNA, remain poorly understood in pediatric brain tumors. Here, we detect a total of 13,199 high confidence somatic SVs in 744 whole-genome-sequenced pediatric brain tumors from Pediatric Brain Tumor Atlas. The somatic SV occurrences have tremendous diversity among the cohort and across different tumor types. We decompose mutational signatures of clustered complex SVs, non-clustered complex SVs, and simple SVs separately to infer the mutational mechanisms of SV formation. Our finding of many tumor types carrying unique sets of SV signatures suggests that distinct molecular mechanisms are active in different tumor types to shape genome instability. The patterns of somatic SV signatures in pediatric brain tumors are substantially different from those in adult cancers. The convergence of multiple signatures to alter several major cancer driver genes suggesting the functional importance of somatic SVs in disease progression.
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Affiliation(s)
- Yang Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Lixing Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
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44
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Comaills V, Castellano-Pozo M. Chromosomal Instability in Genome Evolution: From Cancer to Macroevolution. BIOLOGY 2023; 12:biology12050671. [PMID: 37237485 DOI: 10.3390/biology12050671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023]
Abstract
The integrity of the genome is crucial for the survival of all living organisms. However, genomes need to adapt to survive certain pressures, and for this purpose use several mechanisms to diversify. Chromosomal instability (CIN) is one of the main mechanisms leading to the creation of genomic heterogeneity by altering the number of chromosomes and changing their structures. In this review, we will discuss the different chromosomal patterns and changes observed in speciation, in evolutional biology as well as during tumor progression. By nature, the human genome shows an induction of diversity during gametogenesis but as well during tumorigenesis that can conclude in drastic changes such as the whole genome doubling to more discrete changes as the complex chromosomal rearrangement chromothripsis. More importantly, changes observed during speciation are strikingly similar to the genomic evolution observed during tumor progression and resistance to therapy. The different origins of CIN will be treated as the importance of double-strand breaks (DSBs) or the consequences of micronuclei. We will also explain the mechanisms behind the controlled DSBs, and recombination of homologous chromosomes observed during meiosis, to explain how errors lead to similar patterns observed during tumorigenesis. Then, we will also list several diseases associated with CIN, resulting in fertility issues, miscarriage, rare genetic diseases, and cancer. Understanding better chromosomal instability as a whole is primordial for the understanding of mechanisms leading to tumor progression.
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Affiliation(s)
- Valentine Comaills
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, University of Pablo de Olavide-University of Seville-CSIC, Junta de Andalucía, 41092 Seville, Spain
| | - Maikel Castellano-Pozo
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, University of Pablo de Olavide-University of Seville-CSIC, Junta de Andalucía, 41092 Seville, Spain
- Genetic Department, Faculty of Biology, University of Seville, 41080 Seville, Spain
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45
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Rausch T, Snajder R, Leger A, Simovic M, Giurgiu M, Villacorta L, Henssen AG, Fröhling S, Stegle O, Birney E, Bonder MJ, Ernst A, Korbel JO. Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures. CELL GENOMICS 2023; 3:100281. [PMID: 37082141 PMCID: PMC10112291 DOI: 10.1016/j.xgen.2023.100281] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 06/14/2022] [Accepted: 02/22/2023] [Indexed: 04/22/2023]
Abstract
Cancer genomes harbor a broad spectrum of structural variants (SVs) driving tumorigenesis, a relevant subset of which escape discovery using short-read sequencing. We employed Oxford Nanopore Technologies (ONT) long-read sequencing in a paired diagnostic and post-therapy medulloblastoma to unravel the haplotype-resolved somatic genetic and epigenetic landscape. We assembled complex rearrangements, including a 1.55-Mbp chromothripsis event, and we uncover a complex SV pattern termed templated insertion (TI) thread, characterized by short (mostly <1 kb) insertions showing prevalent self-concatenation into highly amplified structures of up to 50 kbp in size. TI threads occur in 3% of cancers, with a prevalence up to 74% in liposarcoma, and frequent colocalization with chromothripsis. We also perform long-read-based methylome profiling and discover allele-specific methylation (ASM) effects, complex rearrangements exhibiting differential methylation, and differential promoter methylation in cancer-driver genes. Our study shows the advantage of long-read sequencing in the discovery and characterization of complex somatic rearrangements.
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Affiliation(s)
- Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), GeneCore, Heidelberg, Germany
| | - Rene Snajder
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty for Biosciences, Heidelberg University, Heidelberg, Germany
- HIDSS4Health, Helmholtz Information and Data Science School for Health, Heidelberg, Germany
| | - Adrien Leger
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Milena Simovic
- Group “Genome Instability in Tumors,” German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mădălina Giurgiu
- Experimental and Clinical Research Center (ECRC) of the Max Delbrück Center (MDC) and Charité-Universitätsmedizin, Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | - Laura Villacorta
- European Molecular Biology Laboratory (EMBL), GeneCore, Heidelberg, Germany
| | - Anton G. Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the Max Delbrück Center (MDC) and Charité-Universitätsmedizin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Fröhling
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Oliver Stegle
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Ewan Birney
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Marc Jan Bonder
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aurelie Ernst
- Group “Genome Instability in Tumors,” German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan O. Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Bridging Research Division on Mechanisms of Genomic Variation and Data Science, DKFZ, Heidelberg, Germany
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46
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Rahmé R, Braun T, Manfredi JJ, Fenaux P. TP53 Alterations in Myelodysplastic Syndromes and Acute Myeloid Leukemia. Biomedicines 2023; 11:biomedicines11041152. [PMID: 37189770 DOI: 10.3390/biomedicines11041152] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
TP53 mutations are less frequent in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) than in solid tumors, except in secondary and therapy-related MDS/AMLs, and in cases with complex monosomal karyotype. As in solid tumors, missense mutations predominate, with the same hotspot mutated codons (particularly codons 175, 248, 273). As TP53-mutated MDS/AMLs are generally associated with complex chromosomal abnormalities, it is not always clear when TP53 mutations occur in the pathophysiological process. It is also uncertain in these MDS/AML cases, which often have inactivation of both TP53 alleles, if the missense mutation is only deleterious through the absence of a functional p53 protein, or through a potential dominant-negative effect, or finally a gain-of-function effect of mutant p53, as demonstrated in some solid tumors. Understanding when TP53 mutations occur in the disease course and how they are deleterious would help to design new treatments for those patients who generally show poor response to all therapeutic approaches.
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Affiliation(s)
- Ramy Rahmé
- Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Institut de Recherche Saint Louis (IRSL), INSERM U1131, Université Paris Cité, 75010 Paris, France
- Ecole Doctorale Hématologie-Oncogenèse-Biothérapies, Université Paris Cité, 75010 Paris, France
- Clinical Hematology Department, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Sorbonne Paris Nord, 93000 Bobigny, France
| | - Thorsten Braun
- Clinical Hematology Department, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Sorbonne Paris Nord, 93000 Bobigny, France
| | - James J Manfredi
- Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pierre Fenaux
- Senior Hematology Department, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, 75010 Paris, France
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Dharanipragada P, Zhang X, Liu S, Lomeli SH, Hong A, Wang Y, Yang Z, Lo KZ, Vega-Crespo A, Ribas A, Moschos SJ, Moriceau G, Lo RS. Blocking Genomic Instability Prevents Acquired Resistance to MAPK Inhibitor Therapy in Melanoma. Cancer Discov 2023; 13:880-909. [PMID: 36700848 PMCID: PMC10068459 DOI: 10.1158/2159-8290.cd-22-0787] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/27/2022] [Accepted: 01/23/2023] [Indexed: 01/27/2023]
Abstract
Blocking cancer genomic instability may prevent tumor diversification and escape from therapies. We show that, after MAPK inhibitor (MAPKi) therapy in patients and mice bearing patient-derived xenografts (PDX), acquired resistant genomes of metastatic cutaneous melanoma specifically amplify resistance-driver, nonhomologous end-joining (NHEJ), and homologous recombination repair (HRR) genes via complex genomic rearrangements (CGR) and extrachromosomal DNAs (ecDNA). Almost all sensitive and acquired-resistant genomes harbor pervasive chromothriptic regions with disproportionately high mutational burdens and significant overlaps with ecDNA and CGR spans. Recurrently, somatic mutations within ecDNA and CGR amplicons enrich for HRR signatures, particularly within acquired resistant tumors. Regardless of sensitivity or resistance, breakpoint-junctional sequence analysis suggests NHEJ as critical to double-stranded DNA break repair underlying CGR and ecDNA formation. In human melanoma cell lines and PDXs, NHEJ targeting by a DNA-PKCS inhibitor prevents/delays acquired MAPKi resistance by reducing the size of ecDNAs and CGRs early on combination treatment. Thus, targeting the causes of genomic instability prevents acquired resistance. SIGNIFICANCE Acquired resistance often results in heterogeneous, redundant survival mechanisms, which challenge strategies aimed at reversing resistance. Acquired-resistant melanomas recurrently evolve resistance-driving and resistance-specific amplicons via ecDNAs and CGRs, thereby nominating chromothripsis-ecDNA-CGR biogenesis as a resistance-preventive target. Specifically, targeting DNA-PKCS/NHEJ prevents resistance by suppressing ecDNA/CGR rearrangements in MAPKi-treated melanomas. This article is highlighted in the In This Issue feature, p. 799.
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Affiliation(s)
- Prashanthi Dharanipragada
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Xiao Zhang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Sixue Liu
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Shirley H. Lomeli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Aayoung Hong
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Yan Wang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Zhentao Yang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Kara Z. Lo
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Agustin Vega-Crespo
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Antoni Ribas
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Stergios J. Moschos
- Division of Medical Oncology, Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Gatien Moriceau
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Roger S. Lo
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
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Schandl CA, Mazzoni S, Znoyko I, Nahhas GJ, Chung D, Ding Y, Hess B, Wolff DJ. Novel high-risk acute myeloid leukemia subgroup with ERG amplification and Biallelic loss of TP53. Cancer Genet 2023; 272-273:23-28. [PMID: 36657266 DOI: 10.1016/j.cancergen.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/21/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
ETS-related gene (ERG) amplification, observed in 4-6% of acute myeloid leukemia (AML), is associated with unfavorable prognosis. To determine coincident effects of additional genomic abnormalities in AML with ERG amplification (ERGamp), we examined 11 ERGamp cases of 205 newly diagnosed AML using chromosomal microarray analysis and next generation sequencing. ERGamp cases demonstrated a distinct pattern of high genetic complexity: loss of 5q, chromothripsis and TP53 loss of function variants. Remarkably, allelic TP53 loss or loss of heterozygosity (LOH) co-occurring with TP53 inactivating mutation dramatically effected ERGamp tumor patient outcome. In the presence of homozygous TP53 loss of function, ERGamp patients demonstrated no response to induction chemotherapy with median overall survival (OS) of 3.8 months (N = 9). Two patients with heterozygous loss of TP53 function underwent alloSCT without evidence of relapse at one year. Similarly, a validation TCGA cohort, 6 of the 8 ERGamp cases with TP53 loss of function demonstrated median OS of 2.5 months. This suggests that with TP53 mutant ERGamp AML, successive loss of the second TP53 allele, typically by 17p deletion or LOH identifies a specific high-risk subtype of AML patients who are resistant to standard induction chemotherapy and need novel approaches to avert the very poor prognosis.
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Affiliation(s)
- Cynthia A Schandl
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Sandra Mazzoni
- Departmant of Hematology and Oncology, Cleveland Clinic Taussig Cancer Center, Cleveland, OH, USA.
| | - Iya Znoyko
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Georges J Nahhas
- Department of Public Health-Division of Biostatistics and Bioinformatics, Medical University of South Carolina, Charleston, SC, USA
| | - Dongjun Chung
- Department of Public Health-Division of Biostatistics and Bioinformatics, Medical University of South Carolina, Charleston, SC, USA
| | - Yanna Ding
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Brian Hess
- Department of Hematology and Oncology, Medical University of South Carolina Hollings Cancer Center, Charleston, SC, USA
| | - Daynna J Wolff
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
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Gorini F, Miceli M, de Antonellis P, Amente S, Zollo M, Ferrucci V. Epigenetics and immune cells in medulloblastoma. Front Genet 2023; 14:1135404. [PMID: 36968588 PMCID: PMC10036437 DOI: 10.3389/fgene.2023.1135404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
Medulloblastoma (MB) is a highly malignant childhood tumor of the cerebellum. Transcriptional and epigenetic signatures have classified MB into four molecular subgroups, further stratified into biologically different subtypes with distinct somatic copy-number aberrations, driver genes, epigenetic alterations, activated pathways, and clinical outcomes. The brain tumor microenvironment (BTME) is of importance to regulate a complex network of cells, including immune cells, involved in cancer progression in brain malignancies. MB was considered with a “cold” immunophenotype due to the low influx of immune cells across the blood brain barrier (BBB). Recently, this assumption has been reconsidered because of the identification of infiltrating immune cells showing immunosuppressive phenotypes in the BTME of MB tumors. Here, we are providing a comprehensive overview of the current status of epigenetics alterations occurring during cancer progression with a description of the genomic landscape of MB by focusing on immune cells within the BTME. We further describe how new immunotherapeutic approaches could influence concurring epigenetic mechanisms of the immunosuppressive cells in BTME. In conclusion, the modulation of these molecular genetic complexes in BTME during cancer progression might enhance the therapeutic benefit, thus firing new weapons to fight MB.
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Affiliation(s)
- Francesca Gorini
- Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples, Naples, Italy
| | - Marco Miceli
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, Naples, Italy
| | - Pasqualino de Antonellis
- Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples, Naples, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples, Naples, Italy
| | - Massimo Zollo
- Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples, Naples, Italy
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, Naples, Italy
- DAI Medicina di Laboratorio e Trasfusionale, ‘AOU Federico II Policlinico, Naples, Italy
| | - Veronica Ferrucci
- Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples, Naples, Italy
- CEINGE Biotecnologie Avanzate “Franco Salvatore”, Naples, Italy
- *Correspondence: Veronica Ferrucci,
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Ni Y, Liu X, Simeneh ZM, Yang M, Li R. Benchmarking of Nanopore R10.4 and R9.4.1 flow cells in single-cell whole-genome amplification and whole-genome shotgun sequencing. Comput Struct Biotechnol J 2023; 21:2352-2364. [PMID: 37025654 PMCID: PMC10070092 DOI: 10.1016/j.csbj.2023.03.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
Third-generation sequencing can be used in human cancer genomics and epigenomic research. Oxford Nanopore Technologies (ONT) recently released R10.4 flow cell, which claimed an improved read accuracy compared to R9.4.1 flow cell. To evaluate the benefits and defects of R10.4 flow cell for cancer cell profiling on MinION devices, we used the human non-small-cell lung-carcinoma cell line HCC78 to construct libraries for both single-cell whole-genome amplification (scWGA) and whole-genome shotgun sequencing. The R10.4 and R9.4.1 reads were benchmarked in terms of read accuracy, variant detection, modification calling, genome recovery rate and compared with the next generation sequencing (NGS) reads. The results highlighted that the R10.4 outperforms R9.4.1 reads, achieving a higher modal read accuracy of over 99.1%, superior variation detection, lower false-discovery rate (FDR) in methylation calling, and comparable genome recovery rate. To achieve high yields scWGA sequencing in the ONT platform as NGS, we recommended multiple displacement amplification with a modified T7 endonuclease Ⅰ cutting procedure as a promising method. In addition, we provided a possible solution to filter the likely false positive sites among the whole genome region with R10.4 by using scWGA sequencing result as a negative control. Our study is the first benchmark of whole genome single-cell sequencing using ONT R10.4 and R9.4.1 MinION flow cells by clarifying the capacity of genomic and epigenomic profiling within a single flow cell. A promising method for scWGA sequencing together with the methylation calling results can benefit researchers who work on cancer cell genomic and epigenomic profiling using third-generation sequencing.
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Affiliation(s)
- Ying Ni
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, China
- Department of Biomedical Sciences and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
| | - Xudong Liu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Zemenu Mengistie Simeneh
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, China
- Department of Biomedical Sciences and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
| | - Mengsu Yang
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, China
- Department of Biomedical Sciences and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
- Corresponding author at: Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, China.
| | - Runsheng Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Corresponding author at: Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.
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