Genomic characterization of thymic epithelial tumors in a real-world dataset

Immunotherapy in thymic epithelial tumors: an attractive dilemma

Thymomas and thymic carcinomas are the most prevalent tumors that develop in the thymus's epithelial tissue. Thymomas are malignant tumors that develop from the epithelial cells of the thymus and frequently include mixed populations of lymphocytes. In contrast, thymic carcinomas are also tumors of the thymic epithelium, but they are characterized by a lack of lymphocytes, exhibit more aggressive behavior, and are associated with a poorer prognosis. Surgical intervention is the primary approach for managing resectable cases, while advanced, unresectable tumors are treated with platinum-based chemotherapy. The recurrence of the disease can happen months to years after initial treatment. Some patients do benefit from biologic therapies, but there is still a significant need for new treatment options. Immune checkpoint inhibitors have proven safe and clinically effective, improving survival in various cancers. However, their use in thymic cancers is currently limited to treating recurrent thymic carcinoma due to potential immune toxicity risks. This manuscript reviews the current applications of immunotherapy for thymic epithelial tumors and discusses strategies to enhance safety and expand treatment options for patients with these cancers.

Association between homologous recombination deficiency and time to treatment failure to platinum-based chemotherapy for pancreatic cancer by using the C-CAT database

BACKGROUND

Since homologous recombination deficiency (HRD) is relatively uncommon in pancreatic cancer (PC), its impact on time-to-treatment failure (TTF) among patients undergoing systemic chemotherapy for unresectable and recurrent PC remains uncertain.

METHODS

Among patients with unresectable and recurrent PC enrolled in the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) database by July 2023, a total of 1394 patients who underwent first-line chemotherapy with either gemcitabine plus nab-paclitaxel (GnP) or FOLFIRINOX (FFX) and received tissue-based CGP tests after disease progression were included in this study. HRD was defined as the presence of germline or somatic genetic mutations in homologous recombination repair (HRR)-related genes such as ATM, BARD1, BRIP1, BRCA1/2, CHEK2, CDK12, PALB, and RAD51C/D. We investigated the correlation between HRD and TTF among patients treated with GnP and FFX.

RESULTS

First-line chemotherapy consisted of GnP in 69% of the cases and FFX in 31%. The CGP tests used were NCC OncoPanel and FoundationOne CDx in 26% and 74%, respectively. HRR-related genetic abnormalities were identified in 107 patients (7.6%): BRCA2 (n = 51), ATM (n = 34), BRCA1 (n = 9), PALB2 (n = 9), among others. In the GnP cohort, the median TTF was comparable between the HRD and non-HRD groups (5.3 vs 4.6 months, P = 0.44). Conversely, in the FFX cohort, it was significantly longer in the HRD group compared to the non-HRD group (7.3 vs. 4.7 months, p < 0.01).

CONCLUSIONS

Our findings suggest that HRR-related genetic abnormalities might be predictive of TTF in platinum-based chemotherapy for PC.

DNA methylation analysis of multiple genes in thymic epithelial tumors

Aim: To investigate DNA methylation levels of a panel of genes in thymic epithelial tumors (TETs).Materials & methods: We selected 15 genes among the most promising epigenetic biomarkers of TETs and evaluated their methylation levels in 71 TET samples.Results: thymic carcinomas (TCs) showed hypermethylation of GHSR and ELF3 genes and reduced IL1RN methylation levels compared with thymomas (TMs) and healthy thymic tissues. RAG1 was hypomethylated in TMs compared with healthy thymic tissues. No difference in the methylation levels of the investigated genes was seen among TM stages and subtypes. No changes in blood methylation levels of the investigated genes were seen among TET subtypes.Conclusion: The present study confirms GHSR, ELF3, IL1RN and RAG1 as TET epigenetic biomarkers.

Comparative Analysis of Comprehensive Genomic Profile in Thymomas and Recurrent Thymomas Reveals Potentially Actionable Mutations for Target Therapies

Molecular profiles of thymomas and recurrent thymomas are far from being defined. Herein, we report an analysis of a comprehensive genetic profile (CGP) in a highly selected cohort of recurrent thymomas. Among a cohort of 426 thymomas, the tissue was available in 23 recurrent tumors for matching the biomolecular results obtained from primary and relapse samples. A control group composed of non-recurrent thymoma patients was selected through a propensity score match analysis. CGP was performed using the NGS Tru-SightOncology assay to evaluate TMB, MSI, and molecular alterations in 523 genes. CGP does not differ when comparing initial tumor with tumor relapse. A significantly higher frequency of cell cycle control genes alterations (100.0% vs. 57.1%, p = 0.022) is detected in patients with early recurrence (<32 months) compared to late recurrent cases. The CGPs were similar in recurrent thymomas and non-recurrent thymomas. Finally, based on NGS results, an off-label treatment or clinical trial could be potentially proposed in >50% of cases (oncogenic Tier-IIC variants). In conclusion, CGPs do not substantially differ between initial tumor vs. tumor recurrence and recurrent thymomas vs. non-recurrent thymomas. Cell cycle control gene alterations are associated with an early recurrence after thymectomy. Multiple target therapies are potentially available by performing a comprehensive CGP, suggesting that a precision medicine approach on these patients could be further explored.

Evolving treatment landscape in thymic epithelial tumors: From mechanism to therapy

Thymic epithelial tumors (TETs) are rare neoplasms of the anterior mediastinum that arise from thymic epithelial cells. Although surgery is the preferred treatment for resectable TETs, the options for unresectable or recurrent advanced-stage TETs are limited beyond platinum-based chemotherapy. The evolving landscape of TET treatments is marked by significant advancements in targeted therapies and immunotherapies, particularly with anti-angiogenic agents and immune checkpoint inhibitors (ICIs). While monotherapies demonstrated certain efficacy, the development of combination strategies is vital for improving patient outcomes. This review consolidates progress in anti-angiogenic therapies and ICIs, emphasizing the evolution of combination therapies of TETs. Furtherly, we particularly discuss new first-line strategies based on these advancements and emphasizes exploring novel treatments like antibody-drug conjugates, immunomodulatory drugs and cytokine-based agents for TETs. Mechanistically, the molecular features of TETs integrated with clinical diagnosis and targeted therapy, and immunophenotyping of TETs along with its impact on the efficacy and safety of immunotherapy are discussed. Thus, this review systemizes the development in the treatment landscape of TETs, integrating the corresponding molecular and immune mechanisms, aiming to provide new references for the treatment of TETs.

Genomic insights into molecular profiling of thymic carcinoma: a narrative review

Background and Objective

Thymic carcinoma is an exceptionally rare cancer, with an annual incidence of just 0.15-0.29 per 100,000 people. Owing to its rarity, only few proven treatments have been developed. Understanding its genetic profile is crucial for the development of targeted therapies. However, limited studies have exclusively examined thymic carcinoma mutations, with most investigation combining thymomas and thymic carcinomas. This paper reviews findings from genetic studies focusing on thymic carcinoma alone and compares them to those of thymoma.

Methods

We conducted a PubMed search for relevant English studies on thymic carcinoma genomics. Then, key papers utilizing target sequencing or whole-exome sequencing were analyzed.

Key Content and Findings

The most frequently mutated genes were TP53, CDKN2A, CDKN2B, CYLD, KIT, TET2, SETD2, BAP1, and ASXL1. TP53 and CDKN2A are correlated with poor prognosis. CYLD, which regulates signaling related with proliferation and interacts with AIRE expression and T cell development, might predict the immunotherapy response. KIT mutations might enable targeted therapy. TET2, SETD2, BAP1, and ASXL1 regulate epigenetics, suggesting disruption of these mechanisms. Higher tumor mutational burden (TMB) and 16q loss distinguish thymic carcinoma from thymoma. Although some copy number aberrations are shared, thymic carcinoma exhibits a mutational profile distinct from that of thymoma.

Conclusions

Thymic carcinoma demonstrates a unique genomic landscape, suggesting a molecular pathogenesis distinct from that of thymoma. Our findings revealed prognostic biomarkers such as TP53/CDKN2A and potential therapeutic targets such as KIT. Because thymic carcinoma is extremely rare, sharing molecular profiling data could provide valuable insights into the molecular mechanisms driving the development of these tumors.

Immunotherapy for Thymomas and Thymic Carcinomas: Current Status and Future Directions

Thymic epithelial tumors are a histologically diverse group of cancers arising from the epithelial compartment of the thymus. These tumors are characterized by a low tumor mutation burden, a lack of actionable genomic changes, and, especially with thymomas, defects in immune tolerance. Surgery is the mainstay of the management of resectable disease, whereas advanced, unresectable tumors are treated with platinum-based chemotherapy. Disease recurrence can occur months to years after frontline treatment. Although several options are available for conventional treatment of recurrent thymic tumors, response rates are generally low, and treatment-related toxicity can affect quality of life. A subset of patients benefit from biologic therapies, but there remains an unmet need for the development of new treatments. Immune checkpoint inhibitors are safe, clinically active, and have contributed to an improvement in survival for patients with a wide variety of cancers. However, the application of these revolutionary treatments for thymic cancers is limited to their use for the management of recurrent thymic carcinoma because of the risk of immune toxicity. In this paper, we review the current uses of immunotherapy for the management of thymic epithelial tumors and highlight potential strategies to improve safety and broaden the application of these treatments for patients with thymic cancers.

Insights into molecular aspects and targeted therapy of thymic carcinoma: a narrative review

Background and Objective

Thymic carcinomas are rare tumors derived from thymic epithelial cells. Owing to their rarity, the search for molecular biology has been conducted in combination with thymoma as one histological subtype, and only a few studies have exclusively focused on thymic carcinoma. Currently, no therapy is more effective than complete surgical resection, and the development of novel therapies, including targeted therapies, is hampered. In this review, we summarize the knowledge regarding altered genes and pathways in thymic carcinoma with recent preclinical and clinical targeted therapies.

Methods

We conducted a narrative review of the relevant English literature available in PubMed and Google Scholar on genomic characteristics and targeted therapies for thymic carcinoma.

Key Content and Findings

Although the literature consists of a relatively small series, it suggests that the frequently involved genes or pathways associated with thymic carcinoma are tumor suppressor genes, including TP53 and CDKN2A/B, and the receptor tyrosine kinase pathway. Targeted therapy demonstrated antitumor activity with encouraging results. However, potential predictive biomarkers have not been identified and the response to these therapies appears to be irrelevant to gene alterations.

Conclusions

Some studies have revealed the molecular characteristics of thymic carcinoma, although the results of these studies have shown a different pattern of gene alterations. The further accumulation of data would be helpful in revealing the genomic landscape and establishing molecular-targeted therapies.

Perspectives on surgical treatment for thymic epithelial tumors: a narrative review

Background and Objective

Thymic epithelial tumors are relatively rare; thus, mostly retrospective studies and a few prospective randomized controlled trials have been conducted on the treatment and the biomarkers, with no standard therapy established. Indications for extended thymectomy, robot-assisted thoracic surgery, and multidisciplinary treatment are controversial. Here, we considered the prospects of surgical treatment and the possibility of immune checkpoint inhibitor (ICI) treatment for thymic epithelial tumors.

Methods

This is a narrative review; PubMed was searched using a set of keywords related to thymoma and its proposed treatments over the last 5 years.

Key Content and Findings

Thymic epithelial tumors are associated with autoimmune diseases. They are relatively rare, and their pathology remains unclear. Therefore, accumulating more case reports is important. Surgical resection is generally considered for both diagnosis and treatment. If the tumor has a strong tendency to invade surrounding areas, such as thymic carcinoma/thymoma, the diagnosis may be confirmed preoperatively by needle biopsy, and induction chemotherapy may be selected. Surgical resection is the most effective treatment, and complete resection is important. In cases where complete resection is difficult, multidisciplinary treatment is performed. Although there are various obstacles, using ICIs may prove effective for treatment both as preoperative and postoperative chemotherapy in the future, as shown for other cancers. Programmed cell death-ligand 1 (PD-L1) is an immunoinhibitory molecule that suppresses T cells activation, leading to tumor progression. Overexpression of PD-L1 in some cancers is associated with poor clinical outcomes. However, the role of PD-L1 expression as a prognostic factor remains controversial. Therefore, various biomarkers other than PD-L1 have been identified.

Conclusions

We reviewed the latest treatments for thymic epithelial tumors. If new therapeutic agents such as ICIs and molecular-targeted drugs are developed, this review suggests that surgery will become more important not only as therapy but also as part of multidisciplinary treatment that includes tissue collection.

Non-Mutational Key Features in the Biology of Thymomas

Thymomas (THs) are a unique group of heterogeneous tumors of the thymic epithelium. In particular, the subtypes B2 and B3 tend to be aggressive and metastatic. Radical tumor resection remains the only curative option for localized tumors, while more advanced THs require multimodal treatment. Deep sequencing analyses have failed to identify known oncogenic driver mutations in TH, with the notable exception of the GTF2I mutation, which occurs predominantly in type A and AB THs. However, there are multiple alternative non-mutational mechanisms (e.g., perturbed thymic developmental programs, metabolism, non-coding RNA networks) that control cellular behavior and tumorigenesis through the deregulation of critical molecular pathways. Here, we attempted to show how the results of studies investigating such alternative mechanisms could be integrated into a current model of TH biology. This model could be used to focus ongoing research and therapeutic strategies.

Aberrant DNA Methylation of NPTX2 as an Indicator of Malignant Behavior in Thymic Epithelial Tumors

Thymic epithelial tumors (TET) consist of thymomas, thymic carcinoma (TC), and neuroendocrine tumors of the thymus (NECTT). Genetic and epigenetic alterations in TET have been the focus of recent research. In the present study, genome-wide screening was performed on aberrantly methylated CpG islands in TET, and this identified neuronal pentraxin 2 (NTPX2) as a significantly hypermethylated CpG island in TC relative to thymomas. NPTX2 is released from pre-synaptic cells in response to neuronal activity/seizure, and plays a role in host immunity and acute inflammation. TET samples were obtained from 38 thymomas, 25 TC, and 6 NECTT. The DNA methylation, mRNA, and protein expression levels of NPTX2 were examined. The DNA methylation rate of the NPTX2 gene was significantly higher in TC than in the normal thymus and thymomas, except B3. The mRNA expression level of NPTX2 was lower in TC than in the normal thymus. An inverse relationship was observed between mRNA expression levels and methylation levels. Relapse-free survival was shorter in patients with high NPTX2 DNA methylation levels than in those with low DNA methylation levels. NECTT showed very high mRNA and protein expression levels and low DNA methylation levels of NPTX2. NPTX2 may function as a tumor suppressor in TC, and have an oncogenic function in NECTT.

Molecular and Functional Key Features and Oncogenic Drivers in Thymic Carcinomas

Thymic epithelial tumors, comprising thymic carcinomas and thymomas, are rare neoplasms. They differ in histology, prognosis, and association with autoimmune diseases such as myasthenia gravis. Thymomas, but not thymic carcinomas, often harbor GTF2I mutations. Mutations of CDKN2A, TP53, and CDKN2B are the most common thymic carcinomas. The acquisition of mutations in genes that control chromatin modifications and epigenetic regulation occurs in the advanced stages of thymic carcinomas. Anti-angiogenic drugs and immune checkpoint inhibitors targeting the PD-1/PD-L1 axis have shown promising results for the treatment of unresectable tumors. Since thymic carcinomas are frankly aggressive tumors, this report presents insights into their oncogenic drivers, categorized under the established hallmarks of cancer.