Genomic characterization of intracranial teratomas using whole genome sequencing
BackgroundIntracranial teratoma is a rare neoplasm of the central nervous system, often classified into mature and immature types and occurs mainly in children and adolescents. To date, there has been no comprehensive genomic characterization analysis of teratoma due to its rarity of the cases.Metho...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-11-01
|
| Series: | Frontiers in Oncology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fonc.2022.1013722/full |
| _version_ | 1811312976780591104 |
|---|---|
| author | Chao Zhang Chao Zhang Chao Zhang Chao Zhang Chao Zhang Xiaoyu Zhou Xiang Huang Xiang Huang Xiang Huang Xiang Huang Xinghua Ding Xinghua Ding Xinghua Ding Xinghua Ding Yang Wang Rong Zhang Rong Zhang Rong Zhang Rong Zhang |
| author_facet | Chao Zhang Chao Zhang Chao Zhang Chao Zhang Chao Zhang Xiaoyu Zhou Xiang Huang Xiang Huang Xiang Huang Xiang Huang Xinghua Ding Xinghua Ding Xinghua Ding Xinghua Ding Yang Wang Rong Zhang Rong Zhang Rong Zhang Rong Zhang |
| author_sort | Chao Zhang |
| collection | DOAJ |
| description | BackgroundIntracranial teratoma is a rare neoplasm of the central nervous system, often classified into mature and immature types and occurs mainly in children and adolescents. To date, there has been no comprehensive genomic characterization analysis of teratoma due to its rarity of the cases.MethodsForty-six patients with intracranial teratomas were collected and 22 of them underwent whole-exome sequencing, including 8 mature teratomas and 14 immature teratomas. A comprehensive analysis was performed to analyze somatic mutations, copy number variants (CNVs), mutational signatures, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway in our cohort.ResultsThe most common somatic mutated gene in intracranial teratomas was CARD11 (18%) and IRS1 (18%), followed by PSMD11, RELN, RRAS2, SMC1A, SYNE1 and ZFHX3, with mutation rates of 14% for the latter six genes. Copy number variation was dominated by amplification, among which ARAF (50%), ATP2B3 (41%), GATA1 (41%), ATP6AP1 (36%), CCND2 (36%) and ZMYM3 (36%) were the most frequently amplified genes. Copy number deletion of SETDB2 and IL2 only appeared in immature teratoma (43% and 36%, respectively), but not in mature teratoma (p = 0.051 and 0.115, respectively). Prognostic analysis showed that TP53 mutations might be associated with poor prognosis of intracranial teratomas patients.ConclusionsOur study revealed the genetic characteristics of intracranial teratoma which might be valuable for guiding future targeted therapies. |
| first_indexed | 2024-04-13T10:46:06Z |
| format | Article |
| id | doaj.art-c718cbf195ea4ba8acd7bbd52273cbb8 |
| institution | Directory Open Access Journal |
| issn | 2234-943X |
| language | English |
| last_indexed | 2024-04-13T10:46:06Z |
| publishDate | 2022-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Oncology |
| spelling | doaj.art-c718cbf195ea4ba8acd7bbd52273cbb82022-12-22T02:49:47ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2022-11-011210.3389/fonc.2022.10137221013722Genomic characterization of intracranial teratomas using whole genome sequencingChao Zhang0Chao Zhang1Chao Zhang2Chao Zhang3Chao Zhang4Xiaoyu Zhou5Xiang Huang6Xiang Huang7Xiang Huang8Xiang Huang9Xinghua Ding10Xinghua Ding11Xinghua Ding12Xinghua Ding13Yang Wang14Rong Zhang15Rong Zhang16Rong Zhang17Rong Zhang18Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, ChinaDepartment of Pediatric Neurosurgery, Neurosurgical Institute of Fudan University, Shanghai, ChinaDepartment of Pediatric Neurosurgery, Shanghai Clinical Medical Center of Neurosurgery, Shanghai, ChinaDepartment of Pediatric Neurosurgery, National Center for Neurological Disorders, Shanghai, ChinaDepartment of Neurosurgery, Putuo District People’s Hospital of Shanghai, Shanghai, ChinaDepartment of Medicine, GenomiCare Biotechnology (Shanghai) Co. Ltd., Shanghai, ChinaDepartment of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, ChinaDepartment of Pediatric Neurosurgery, Neurosurgical Institute of Fudan University, Shanghai, ChinaDepartment of Pediatric Neurosurgery, Shanghai Clinical Medical Center of Neurosurgery, Shanghai, ChinaDepartment of Pediatric Neurosurgery, National Center for Neurological Disorders, Shanghai, ChinaDepartment of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, ChinaDepartment of Pediatric Neurosurgery, Neurosurgical Institute of Fudan University, Shanghai, ChinaDepartment of Pediatric Neurosurgery, Shanghai Clinical Medical Center of Neurosurgery, Shanghai, ChinaDepartment of Pediatric Neurosurgery, National Center for Neurological Disorders, Shanghai, ChinaDepartment of Radiotherapy, Huashan Hospital, Fudan University, Shanghai, ChinaDepartment of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, ChinaDepartment of Pediatric Neurosurgery, Neurosurgical Institute of Fudan University, Shanghai, ChinaDepartment of Pediatric Neurosurgery, Shanghai Clinical Medical Center of Neurosurgery, Shanghai, ChinaDepartment of Pediatric Neurosurgery, National Center for Neurological Disorders, Shanghai, ChinaBackgroundIntracranial teratoma is a rare neoplasm of the central nervous system, often classified into mature and immature types and occurs mainly in children and adolescents. To date, there has been no comprehensive genomic characterization analysis of teratoma due to its rarity of the cases.MethodsForty-six patients with intracranial teratomas were collected and 22 of them underwent whole-exome sequencing, including 8 mature teratomas and 14 immature teratomas. A comprehensive analysis was performed to analyze somatic mutations, copy number variants (CNVs), mutational signatures, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway in our cohort.ResultsThe most common somatic mutated gene in intracranial teratomas was CARD11 (18%) and IRS1 (18%), followed by PSMD11, RELN, RRAS2, SMC1A, SYNE1 and ZFHX3, with mutation rates of 14% for the latter six genes. Copy number variation was dominated by amplification, among which ARAF (50%), ATP2B3 (41%), GATA1 (41%), ATP6AP1 (36%), CCND2 (36%) and ZMYM3 (36%) were the most frequently amplified genes. Copy number deletion of SETDB2 and IL2 only appeared in immature teratoma (43% and 36%, respectively), but not in mature teratoma (p = 0.051 and 0.115, respectively). Prognostic analysis showed that TP53 mutations might be associated with poor prognosis of intracranial teratomas patients.ConclusionsOur study revealed the genetic characteristics of intracranial teratoma which might be valuable for guiding future targeted therapies.https://www.frontiersin.org/articles/10.3389/fonc.2022.1013722/fullteratomaintracranialgenomic characterizationwhole genome sequencingpediatric |
| spellingShingle | Chao Zhang Chao Zhang Chao Zhang Chao Zhang Chao Zhang Xiaoyu Zhou Xiang Huang Xiang Huang Xiang Huang Xiang Huang Xinghua Ding Xinghua Ding Xinghua Ding Xinghua Ding Yang Wang Rong Zhang Rong Zhang Rong Zhang Rong Zhang Genomic characterization of intracranial teratomas using whole genome sequencing Frontiers in Oncology teratoma intracranial genomic characterization whole genome sequencing pediatric |
| title | Genomic characterization of intracranial teratomas using whole genome sequencing |
| title_full | Genomic characterization of intracranial teratomas using whole genome sequencing |
| title_fullStr | Genomic characterization of intracranial teratomas using whole genome sequencing |
| title_full_unstemmed | Genomic characterization of intracranial teratomas using whole genome sequencing |
| title_short | Genomic characterization of intracranial teratomas using whole genome sequencing |
| title_sort | genomic characterization of intracranial teratomas using whole genome sequencing |
| topic | teratoma intracranial genomic characterization whole genome sequencing pediatric |
| url | https://www.frontiersin.org/articles/10.3389/fonc.2022.1013722/full |
| work_keys_str_mv | AT chaozhang genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT chaozhang genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT chaozhang genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT chaozhang genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT chaozhang genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT xiaoyuzhou genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT xianghuang genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT xianghuang genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT xianghuang genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT xianghuang genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT xinghuading genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT xinghuading genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT xinghuading genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT xinghuading genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT yangwang genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT rongzhang genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT rongzhang genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT rongzhang genomiccharacterizationofintracranialteratomasusingwholegenomesequencing AT rongzhang genomiccharacterizationofintracranialteratomasusingwholegenomesequencing |