The Cancer Genome Atlas dataset-based analysis of aberrantly expressed genes by GeneAnalytics in thymoma associated myasthenia gravis: focusing on T cells

Soluble form of immune checkpoints in autoimmune diseases

Immune checkpoints are essential regulators of immune responses, either by activating or suppressing them. Consequently, they are regarded as pivotal elements in the management of infections, cancer, and autoimmune disorders. In recent years, researchers have identified numerous soluble immune checkpoints that are produced through various mechanisms and demonstrated biological activity. These soluble immune checkpoints can be produced and distributed in the bloodstream and various tissues, with their roles in immune response dysregulation and autoimmunity extensively documented. This review aims to provide a thorough overview of the generation of various soluble immune checkpoints, such as sPD-1, sCTLA-4, sTim-3, s4-1BB, sBTLA, sLAG-3, sCD200, and the B7 family, and their importance as indicators for the diagnosis and prediction of autoimmune conditions. Furthermore, the review will investigate the potential pathological mechanisms of soluble immune checkpoints in autoimmune diseases, emphasizing their association with autoimmune diseases development, prognosis, and treatment.

The Molecular Landscape of Thymic Epithelial Tumors: A Comprehensive Review

Thymic epithelial tumors (TETs) are characterized by their extreme rarity and variable clinical presentation, with the inadequacy of the use of histological classification alone to distinguish biologically indolent from aggressive cases. The utilization of Next Generation Sequencing (NGS) to unravel the intricate genetic landscape of TETs could offer us a comprehensive understanding that is crucial for precise diagnoses, prognoses, and potential therapeutic strategies. Despite the low tumor mutational burden of TETS, NGS allows for exploration of specific genetic signatures contributing to TET onset and progression. Thymomas exhibit a limited mutational load, with prevalent GTF2I and HRAS mutations. On the other hand, thymic carcinomas (TCs) exhibit an elevated mutational burden, marked by frequent mutations in TP53 and genes associated with epigenetic regulation. Moreover, signaling pathway analyses highlight dysregulation in crucial cellular functions and pathways. Targeted therapies, and ongoing clinical trials show promising results, addressing challenges rooted in the scarcity of actionable mutations and limited genomic understanding. International collaborations and data-sharing initiatives are crucial for breakthroughs in TETs research.

DCAF12 and HSPA1A May Serve as Potential Diagnostic Biomarkers for Myasthenia Gravis

Background

Myasthenia gravis (MG) is an autoimmune disease that severely affects the life quality of patients. This study explores the differences in immune cell types between MG and healthy control and the role of immune-related genes in the diagnosis of MG.

Methods

The GSE85452 dataset was downloaded from the Gene Expression Omnibus (GEO) database and analyzed using the limma package to determine differentially expressed genes (DEGs) between patients with MG and the control group. Differentially expressed immune cells were analyzed using single-sample gene set enrichment analysis (GSEA), while immune cell-associated modules were identified by weighted gene coexpression network analysis (WGCNA). Then, the expression of the identified hub genes was confirmed by RT-PCR in peripheral blood mononuclear cells (PBMCs) of MG patients. The R package pROC was used to plot the receiver operating characteristics (ROC) curves.

Results

The modules related to CD56bright natural killer cells were identified by GSEA and WGCNA. The proportion of CD56bright natural killer cells in the peripheral blood of MG patients is low. The results of RT-PCR showed that the levels of DDB1- and CUL4-associated factor 12 (DCAF12) and heat shock protein family A member 1A (HSPA1A) were significantly decreased in peripheral blood mononuclear cells of MG patients compared with healthy controls. The ROC curve results of DCAF12 and HSPA1A mRNA in MG diagnosis were 0.780 and 0.830, respectively.

Conclusions

CD56bright NK cell is lower in MG patients and may affect MG occurrence. DCAF12 and HSPA1A are lowly expressed in PBMCs of MG patients and may serve as the diagnostic biomarkers of MG.

Identification of Molecular Characteristics and New Prognostic Targets for Thymoma by Multiomics Analysis

BACKGROUND

Thymoma is a heterogeneous tumor originated from thymic epithelial cells. The molecular mechanism of thymoma remains unclear.

METHODS

The expression profile, methylation, and mutation data of thymoma were obtained from TCGA database. The coexpression network was constructed using the variance of gene expression through WGCNA. Enrichment analysis using clusterProfiler R package and overall survival (OS) analysis by Kaplan-Meier method were carried out for the intersection of differential expression genes (DEGs) screened by limma R package and important module genes. PPI network was constructed based on STRING database for genes with significant impact on survival. The impact of key genes on the prognosis of thymoma was evaluated by ROC curve and Cox regression model. Finally, the immune cell infiltration, methylation modification, and gene mutation were calculated.

RESULTS

We obtained eleven coexpression modules, and three of them were higher positively correlated with thymoma. DEGs in these three modules mainly involved in MAPK cascade and PPAR pathway. LIPE, MYH6, ACTG2, KLF4, SULT4A1, and TF were identified as key genes through the PPI network. AUC values of LIPE were the highest. Cox regression analysis showed that low expression of LIPE was a prognostic risk factor for thymoma. In addition, there was a high correlation between LIPE and T cells. Importantly, the expression of LIPE was modified by methylation. Among all the mutated genes, GTF2I had the highest mutation frequency.

CONCLUSION

These results suggested that the molecular mechanism of thymoma may be related to immune inflammation. LIPE may be the key genes affecting prognosis of thymoma. Our findings will help to elucidate the pathogenesis and therapeutic targets of thymoma.

Autoimmune disorders and paraneoplastic syndromes in thymoma

Thymomas are counted among the rare tumour entities which are associated with autoimmune disorders (AIDs) and paraneoplastic syndromes (PNS) far more often than other malignancies. Through its complex immunological function in the context of the selection and maturation of T cells, the thymus is at the same time highly susceptible to disruptive factors caused by the development and growth of thymic tumours. These T cells, which are thought to develop to competent immune cells in the thymus, can instead adopt autoreactive behaviour due to the uncontrolled interplay of thymomas and become the trigger for AID or PNS affecting numerous organs and tissues within the human body. While myasthenia gravis is the most prevalent PNS in thymoma, numerous others have been described, be they related to neurological, cardiovascular, gastrointestinal, haematological, dermatological, endocrine or systemic disorders. This review article sheds light on the pathophysiology, epidemiology, specific clinical features and therapeutic options of the various forms as well as courses and outcomes of AID/PNS in association with thymomas. Whenever suitable and backed by the limited available evidence, the perspectives from both the thymoma and the affected organ/tissue will be highlighted. Specific issues addressed are the prognostic significance of thymectomy on myasthenia gravis and other thymoma-associated AID/PND and further the impact and safety of immunotherapies on AID and PND relating to thymomas.

Correlation of genomic alterations and PD-L1 expression in thymoma

Thymic epithelial tumors (TETs) include several anterior mediastinal malignant tumours: thymomas, thymic carcinomas and thymic neuroendocrine cancers. There is significant variety in the biologic features and clinical course of TETs and many attempts have been made to identify target genes for successful therapy of TETs. Next generation sequencing (NGS) represents a huge advancement in diagnostics and these new molecular technologies revealed that thymic neoplasms have the lowest tumor mutation burden among all adult malignant tumours with a different pattern of molecular aberrations in thymomas and thymic carcinomas. As for the PD-L1 expression in tumor cells in thymoma and thymic carcinoma, it varies a lot in published studies, with findings of PD-L1 expression from 23% to 92% in thymoma and 36% to 100% in thymic carcinoma. When correlated PD-L1 expression with disease stage some controversial results were obtained, with no association with tumor stage in most studies. This is, at least in part, explained by the fact that several diverse PD-L1 immunohistochemical tests were used in each trial, with four different antibodies (SP142, SP263, 22C3, and 28-8), different definition of PD-L1 positivity and cutoff values throughout the studies as well. There is a huge interest in using genomic features to produce predictive genomic-based immunotherapy biomarkers, particularly since recent data suggest that certain tumor-specific genomic alterations, either individually or in combination, appear to influence immune checkpoint activity and better responses as the outcome, so as such in some cancer types they may complement existing biomarkers to improve the selection criteria for immunotherapy.

Pathology of thymoma-where are we today?

Thymoma is the commonest epithelial neoplasm arising from thymus gland. Tumour is slow growing and in the absence of metastasis, surgery is the treatment of choice. Complete resection and bland morphology are important prognostic features. However, a significant proportion of these tumours tend to recur. These recurrent tumours, advanced thymomas and thymic carcinomas require platinum-based combination chemotherapy and radiotherapy. Efforts are being made to explore additional treatment modalities to control disease with the aim of improving survival. Number of thymoma cases worldwide is small in comparison to lung cancers. As a result, fewer studies have been carried out to enhance our understanding of molecular events responsible for the initiation, maintenance, and progression of thymomas. Inspite of this there are advances in understanding the pathology of thymic epithelial neoplasms including genetics, PD-L1 and molecular testing which has bearing on the prognosis, post-surgical management, and testing algorithm. Similar to pulmonary pathology, thymic epithelial tumours will require adequate tumour sampling to carry out ancillary testing. Mutational analytical tests include EGFR, RAS, BRAF, RET, AKT1, PIK3CA and T53 genes. If adequate sample is available (upto100 cells), PD-L1 testing should be considered for immunotherapy in recurrent/ advanced thymomas and thymic carcinomas. This list is likely to expand in future with increasing emphasis on molecular testing to support treatment with newer therapies.

Investigation of BTLA tagging variants with risk of esophagogastric junction adenocarcinoma

Background: Variants in B- and T-lymphocyte attenuator (BTLA) gene are likely to affect the function of BTLA protein.

Methods: In the present case–control study, we selected BTLA tagging single-nucleotide polymorphisms (SNPs) (rs16859629 T>C, rs1982809 G>A, rs2171513 G>A and rs3112270 A>G) and conducted a case–control study to identify the association of BTLA SNPs with risk of esophagogastric junction adenocarcinoma (EGJA). The present study involved 1236 new incident EGJA cases and 1540 cancer-free controls.

Results: The genotypes of BTLA SNPs were analyzed using a SNPscan Kit. No association was also found between the BTLA SNPs and the susceptibility of EGJA in overall comparsion. In subgroup analyses, the BTLA rs1982809 was found to be associated with an increased susceptibility of EGJA (AA versus GG: OR^adjusted = 2.09, 95% CI 1.08–4.07, P = 0.030; and AA versus GA/GG: OR^adjusted = 1.99, 95% CI 1.04–3.82, P = 0.039). In haplotype comparison, we identified that TAAG haplotype with the order of BTLA rs16859629, rs1982809, rs2171513 and rs3112270 SNPs might increase the susceptibility of EGJA (OR = 3.07, 95% CI = 1.41–6.71; P = 0.003).

Conclusion: To conclude, the present study suggests that BTLA T_rs16859629A_rs1982809A_rs2171513G_rs3112270 haplotype may increase the susceptibility of EGJA. More studies should be conducted to evaluate whether BTLA polymorphisms may influence the susceptibility of cancer in the future.