Thymic epithelial tumors (TETs) are localized in the anterior mediastinum and comprise several forms of thymomas with different malignant potentials, aggressive forms of thymic carcinoma (TC), and thymic neuroendocrine thymoma.1 Thymomas originate from thymic epithelial tissue. Thymoma and TC are similar and overlapping in many characteristics, but despite these histopathological and cytological features, thymomas could be considered a more benign form of TETs in comparison with TC with aggressive forms. That is the reason why thymomas and TC, exhibit main differences in therapy approach.2,3 Here we analyze thymoma including the following subtypes A, AB, B1, B2, and B3.4 A and AB subtypes belong to
To that end, advances in high-throughput technology (next-generation sequencing-NGS) have enabled assess of the mutational profiling of various types of diseases including cancer. NGS in genomics includes whole-genome sequencing (WGS), whole-exome sequencing (WES), and targeted sequencing (TS).10 WGS covers all genomes but provides lower sequencing coverage in comparison to TS. Advances in NGS have contributed to a better understanding of molecular events that lead to disease origin as well as the development of various genetic tests and potential targeted therapy. TS approach targets specific regions of interest and is more cost-effective and often suitable for diagnostic panels which include a specific set of genes characteristic of the disease. Thus, TS provides a patient-specific mutational landscape for effective targeted therapy and better patient management.11,12 Different approaches are used depending on the need required by the type of study. WGS represents the most comprehensive method for genome analysis and covers the entire DNA of interest. The main limitation of WGS is low sequencing coverage (25 - 30x), high cost per sample (which is lower with the increasing role of methodology), and complex and demanding computation analyzed genome, in comparison to WGS or TS.13
This study aimed to identify all relevant articles that evaluate the frequency of SNVs and InDels in thymomas using NGS technology through PubMed, Web of Science, and SCOPUS databases, and to perform a meta-analysis of the prevalence to get better insight into their possible involvement in thymomas. The introduction should summarize the rationale for the study or observation, citing only the essential references and stating the aim of the study.
This systematic review was performed by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses.14
Publications were screened for inclusion and exclusion in the meta-analysis of prevalence in two phases, and all disagreements were solved by a discussion with the third reviewer. We included studies that analyze the molecular landscape of thymoma using next-generation sequencing (NGS) genomics. Studies were excluded if they: 1) investigated related diseases but not thymoma; 2) evaluated other outcomes (NGS genomics for gene expression); 2) explored populations other than human (animal models, cell lines); 3) were abstracts; 4) were not original articles (reviews, systematic reviews, case reports, etc.).
Two researchers have conducted a meta-analysis of the prevalence of the genes and variants involved in thymoma disease. The meta-analysis of all published peer-reviewed articles related to the study was performed by searching the PubMed, Web of Science (WoS), and SCOPUS electronic databases, until the 12th of December 2022. Keywords used for article search in all databases were next-generation sequencing (NGS) and thymoma. Only publications written in English were considered. Additionally, reference lists of articles identified through electronic retrieval were manually searched, as well as relevant reviews and editorials. Experts in the field were contacted to identify other potentially relevant articles.
Two reviewers (JKP, AC) independently evaluated the eligibility of all titles and abstracts. Studies were included in the full-text screening if either reviewer identified the study as being potentially eligible, or if the abstract and title did not include sufficient information. Studies were eligible for full-text screening if they included NGS genomics analysis of thymoma. TETs include thymoma and TC forms, which have been distinguished. The same reviewers independently performed full-text screening to select articles for inclusion according to the criteria listed under the Inclusion and Exclusion Criteria. Disagreements were resolved by consensus (JKP, AC) or arbitration (SP).
Two reviewers independently abstracted the following data: author(s), country of research, year of publication, study design, sample size, study population, type of thymoma, inclusion and exclusion criteria used in the original articles, method of NGS variant detection, genes harboring variants, number of patients having genes with SNVs/InDel variants. Each reviewer independently evaluated the quality of selected manuscripts.
The primary outcome was the number of patients harboring SNVs/InDels variants per gene. The odds ratio was evaluated as the ratio between patients with variants in a specific gene per total number of observed patients with thymoma.
Heterogeneity was assessed using the Chisquare Q and I2 statistics. I2 presents the inconsistency between the study results and quantifies the proportion of observed dispersion that is real, i.e., due to between-study differences and not due to random error. The categorization of heterogeneity was based on the Cochrane Handbook and states that I2 < 30%, 30% to 60%, or > 60%, corresponds to low, moderate, and high heterogeneity, respectively.15 Funnel plots were used to evaluate publication bias. Forest plots were constructed for each analysis showing the Odds Ratio (box), 95% confidence interval (lines), and weight (size of box) for each trial. The overall effect size was represented by a diamond. A p-value < 0.05 was considered to be statistically significant. For graph plots (Forest and Funnel) we used Cohrain’s RevMan 5.4 version.16
The literature search for original articles was conducted according to the Preferred Reporting Items for Systematic reviews and Meta-Analysis (PRISMA) statement. A total of 166 potentially eligible publications were found in search of PubMed, WoS, and SCOPUS electronic databases PubMed 49 articles, WoS 44 articles, and SCOPUS 71. Moreover, we included 3 additional studies from an additional PubMed search (Additional records). After duplication removal, and exclusion of review articles, case reports, abstracts, investigations on animals, cell lines, and articles with unsuitable outcomes, 65 articles were excluded. After exclusion, according to previously defined criteria, 44 articles were assessed in full text. Totally, 12 full-text articles were considered for final analyses. The flow diagram represents the selection workflow of publications (Figure 1).
Selected studies have been presented with the names of studies’ authors, year of published works, NGS approach, type of tumor, and genes that harbored any single nucleotide variants (SNVs) or small insertions/deletions (InDels) in Table 1.
Characteristics of 12 selected studies
Author | Year | Study design | Thymoma | Gene (SNV) | Number of cases | number Total of cases | NGS genomics |
---|---|---|---|---|---|---|---|
23 | |||||||
12 | |||||||
22 | |||||||
Chen K, China | 2020 | Cross-sectional | Type A, AB, B1, B2, B3 | 5 | 50 | TS | |
12 | |||||||
19 | |||||||
2 | |||||||
2 | |||||||
3 | |||||||
Enkner F, Austria | 2017 | Cross-sectional | Type A, B | 1 | 19 | TS | |
1 | |||||||
Higuchi R, Japan | 2020 | Cross-sectional | Type A, AB, B | 14 | 22 | TS | |
Petrini I, Italia | 2014 | Cross-sectional | Type A, AB | 119 | 270 | ES | |
44 | |||||||
Radovich M, USA | 2017 | Case-control | Type A, AB | 10 | 105 | MOPA | |
2 | |||||||
1 | |||||||
2 | SNaPshot | ||||||
Sakane T, Japan | 2020 | Cross-sectional | Type A, B2, B3, B4, B5 | 1 | 33 | ||
1 | Multiplex | ||||||
3 | |||||||
Song ZB, China | 2016 | Type B2, B3 | 1 | 37 | TS | ||
1 | IonAmpliSeq | ||||||
27 | |||||||
27 | |||||||
Peric J, Serbia | 2020 | Case-control | Type A, B1, B2, B3 | 26 | 35 | TSACP | |
24 | |||||||
26 | |||||||
Xu S, China | 2021 | Cross-sectional | Type A, AB B1, B2, B3 | 9 | 17 | ES | |
2 | |||||||
Liang N, China | 2021 | Cross-sectional | Type A, AB, B1, B2, B3 | 15 | 24 | SureSelectXT TS | |
Szpechcinski A, Poland | 2022 | Cross-sectional | Type B2B3 | ERBBKIT 2 | 11 | 19 | TS |
KIT | 1 | ||||||
Girard N, France | 2022 | Cross-sectional | Type A, B1, B2, B3 | TPHRAS 53 | 81 | 90 | WES |
Other genes | 80 |
MOPA = multi-omics platform analysis; SNaPshot Multiplex = Snapshot multiplex assay for point mutation; TS = targeted enrichment-based sequencing: TSACP = TruSeq amplicon cancer panel; (WES) = whole exome sequencing
The number of patients harboring or not genes with variants, as well as a total number of patients is shown in the same table. Finally, selected studies were published from 2014 to 12th December 2022. The total number of patients analyzed for
The analyses of the original articles related to the next-generation sequencing genomics of thymoma have suggested the prevalence of three genes, namely,
The prevalence of the
The aim of this study was to explore genomic background of indolent forms of thymoma using genomic high-throughput approach. Thymoma epithelial tumors (TETs) comprise thymoma, thymic carcinoma (TC), and thymic neuroendocrine thymoma, as we said previously. In this meta-analysis, we take into consideration several forms of thymomas, including A, AB, B1, B2, and B3 subtypes, which have diverse invasive (malignant) potential. Thymoma is a tumor type that belongs to rare types of thoracic tumors, which is the reason for a lower number of studies that we have finally selected as eligible for analysis, along with the relatively recently developed method of analysis that we have applied.
As well, keywords used in this research are limited to the NGS genomics approach to analyzing genes included in thymoma. The potential of high-throughput sequencing or NGS enables the detection of the molecular profile, typical for specific tumors or a variety of diseases. All genomic sequencing methods, including WGS, WES, and TS have been applied in the research or in diagnostics. The selection of methodology depends on all advantages or disadvantages suitable for appropriate use. Applying previously explained inclusion/exclusion criteria we were able to select and analyze articles related to this topic, and we were able to find genes associated with thymoma.
Meta-analysis of the prevalence of the gene variants that we performed using selected studies, has indicated that the majority of patients exhibited variants in
The molecular background of this pathology is still poorly understood, including all types of A, AB, B1, B2, and B3 thymoma. We have analyzed only NGS genomics-based articles. Further in the discussion will also be considered other methodological approaches to better explain obtained results. The newest data that appeared 2022, have indicated that
The most pathogenic variants in this gene are Chr 7 c.1211T > A and c.1271 (COSM5095139) which could be used in targeted therapy that could lead to successful clinical application.21,22 Despite
Our meta-analysis of articles that analyze a mutational portrait using NGS of thymoma has pointed out