Novel Tumor-Specific Antigens for Immunotherapy Identified From Multi-omics Profiling in Thymic Carcinomas

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.

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.

The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I-Associated Peptides

Tumor antigens can emerge through multiple mechanisms, including translation of noncoding genomic regions. This noncanonical category of tumor antigens has recently gained attention; however, our understanding of how they recur within and between cancer types is still in its infancy. Therefore, we developed a proteogenomic pipeline based on deep learning de novo mass spectrometry (MS) to enable the discovery of noncanonical MHC class I-associated peptides (ncMAP) from noncoding regions. Considering that the emergence of tumor antigens can also involve posttranslational modifications (PTM), we included an open search component in our pipeline. Leveraging the wealth of MS-based immunopeptidomics, we analyzed data from 26 MHC class I immunopeptidomic studies across 11 different cancer types. We validated the de novo identified ncMAPs, along with the most abundant PTMs, using spectral matching and controlled their FDR to 1%. The noncanonical presentation appeared to be 5 times enriched for the A03 HLA supertype, with a projected population coverage of 55%. The data reveal an atlas of 8,601 ncMAPs with varying levels of cancer selectivity and suggest 17 cancer-selective ncMAPs as attractive therapeutic targets according to a stringent cutoff. In summary, the combination of the open-source pipeline and the atlas of ncMAPs reported herein could facilitate the identification and screening of ncMAPs as targets for T-cell therapies or vaccine development.

Harnessing gene fusion-derived neoantigens for 'cold' breast and prostate tumor immunotherapy

Breast and prostate cancers are generally considered immunologically 'cold' tumors due to multiple mechanisms rendering them unresponsive to immune checkpoint blockade therapies. With little success in garnering positive outcomes in modern immunotherapeutic clinical trials, it is prudent to re-examine the role of immunogenic neoantigens in these cold tumors. Gene fusions are driver mutations in hormone-driven cancers that can result in alternative mutation-specific neoantigens to promote immunotherapy sensitivity. This review focuses on 1) gene fusion formation mechanisms in neoantigen generation; 2) gene fusion neoantigens in cancer immunotherapeutic strategies and associated clinical trials; and 3) challenges and opportunities in computational and liquid biopsy technologies. This review is anticipated to initiate further research into gene fusion neoantigens of cold tumors for further experimental validation.