BCL10 down-regulation in peripheral T-cell lymphomas

Integration of ubiquitination-related genes in predictive signatures for prognosis and immunotherapy response in sarcoma

Background

Ubiquitination is one of the most prevalent and complex post-translational modifications of proteins in eukaryotes, playing a critical role in regulating various physiological and pathological processes. Targeting ubiquitination pathways, either through inhibition or activation, holds promise as a novel therapeutic approach for cancer treatment. However, the expression patterns, prognostic significance, and underlying mechanisms of ubiquitination-related genes (URGs) in sarcoma (SARC) remain unclear.

Methods

We analyzed URG expression patterns and prognostic implications in TCGA-SARC using public databases, identifying DEGs related to ubiquitination among SARC molecular subtypes. Functional enrichment analysis elucidated their biological significance. Prognostic signatures were developed using LASSO-Cox regression, and a predictive nomogram was constructed. External validation was performed using GEO datasets and clinical tissue samples. The association between URG risk scores and various clinical parameters, immune response, drug sensitivity, and RNA modification regulators was investigated. Integration of data from multiple sources and RT-qPCR confirmed upregulated expression of prognostic URGs in SARC. Single-cell RNA sequencing data analyzed URG distribution across immune cell types. Prediction analysis identified potential target genes of microRNAs and long non-coding RNAs.

Results

We identified five valuable genes (CALR, CASP3, BCL10, PSMD7, PSMD10) and constructed a prognostic model, simultaneously identifying two URG-related subtypes in SARC. The UEGs between subtypes in SARC are mainly enriched in pathways such as Cell cycle, focal adhesion, and ECM-receptor interaction. Analysis of URG risk scores reveals that patients with a low-risk score have better prognoses compared to those with high-risk scores. There is a significant correlation between DRG riskscore and clinical features, immune therapy response, drug sensitivity, and genes related to pan-RNA epigenetic modifications. High-risk SARC patients were identified as potential beneficiaries of immune checkpoint inhibitor therapy. We established regulatory axes in SARC, including CALR/hsa-miR-29c-3p/LINC00943, CASP3/hsa-miR-143-3p/LINC00944, and MIR503HG. RT-qPCR data further confirmed the upregulation of prognostic URGs in SARC. Finally, we validated the prognostic model's excellent predictive performance in predicting outcomes for SARC patients.

Conclusion

We discovered a significant correlation between aberrant expression of URGs and prognosis in SARC patients, identifying a prognostic model related to ubiquitination. This model provides a basis for individualized treatment and immunotherapy decisions for SARC patients.

Genomic analysis reveals molecular characterization of CD30+ and CD30- extranodal natural killer/T-cell lymphomas (ENKTLs)

Extranodal natural killer (NK)/T-cell lymphoma (ENKTL) is prevalent in the Asian population; however, little is known about its molecular characteristics. In this study, we examined the CD30 expression in ENKTLs and then performed whole exome sequencing on ten CD30+ ENKTL and CD30- ENKTL paired samples. CD30 was positive in 55.74% of the ENKTLs. Single nucleotide and insertion/deletion polymorphism analyses revealed that 53.41% of the somatic mutations in CD30+ ENKTLs were shared with CD30- ENKTLs, including mutations in SERPINA9, MEGF6, MUC6, and KDM5A. Frequently mutated genes were primarily associated with cell proliferation and migration, the tumor microenvironment, energy and metabolism, epigenetic modulators, vascular remodeling, and neurological function. PI3K-AKT, cAMP, cGMP-PKG, and AMPK pathways were enriched in both CD30+ and CD30- ENKTLs. Copy number variation analysis identified a unique set of genes in CD30+ ENKTLs, including T-cell receptor genes (TRBV6-1 and TRBV8), cell cycle-related genes (MYC and CCND3), immune-related genes (GPS2, IFNA14, TTC38, and CTSV), and a large number of ubiquitination-related genes (USP32, TRIM23, TRIM2, DUSP7, and UBE2QL1). BCL10 mutation was identified in 6/10 CD30+ ENKTLs and 7/10 CD30- ENKTLs. Immunohistochemical analysis revealed that the expression pattern of BCL10 in normal lymphoid tissues was similar to that of BCL2; however, its expression in ENKTL cells was significantly higher (67.92% vs. 16.98%), implying the potential application of BCL10 inhibitors for treating ENKTLs. These results provide new insights into the genetic characteristics of CD30+ and CD30- ENKTLs, and could facilitate the clinical development of novel therapies for ENKTL.

Conserved Molecular Underpinnings and Characterization of a Role for Caveolin-1 in the Tumor Microenvironment of Mature T-Cell Lymphomas

Neoplasms of extra-thymic T-cell origin represent a rare and difficult population characterized by poor clinical outcome, aggressive presentation, and poorly defined molecular characteristics. Much work has been done to gain greater insights into distinguishing features among malignant subtypes, but there also exists a need to identify unifying characteristics to assist in rapid diagnosis and subsequent potential treatment. Herein, we investigated gene expression data of five different mature T-cell lymphoma subtypes (n = 187) and found 21 genes to be up- and down-regulated across all malignancies in comparison to healthy CD4⁺ and CD8⁺ T-cell controls (n = 52). From these results, we sought to characterize a role for caveolin-1 (CAV1), a gene with previous description in the progression of both solid and hematological tumors. Caveolin-1 was upregulated, albeit with a heterogeneous nature, across all mature T-cell lymphoma subtypes, a finding confirmed using immunohistochemical staining on an independent sampling of mature T-cell lymphoma biopsies (n = 65 cases). Further, stratifying malignant samples in accordance with high and low CAV1 expression revealed that higher expression of CAV1 in mature T-cell lymphomas is analogous with an enhanced inflammatory and invasive gene expression profile. Taken together, these results demonstrate a role for CAV1 in the tumor microenvironment of mature T-cell malignancies and point toward potential prognostic implications.

The TCR γδ repertoire and relative gene expression characteristics of T-ALL cases with biclonal malignant Vδ1 and Vδ2 T cells

Despite significant improvement in our understanding of T-cell acute lymphoblastic leukemia (T-ALL) biology and pathogenesis, many questions remain unanswered. In previous studies, we found a T-ALL case with two malignant T-cell clones with Vδ1Dδ2Dδ3Jδ1 and Vδ2Dδ3Jδ2 rearrangements. In this study, we further characterized T-ALL cases with two malignant clones containing Vδ1Dδ3Jδ1 and Vδ2Dδ1Jδ1 rearrangements using fine-tiling array comparative genomic hybridization, ligation-mediated polymerase chain reaction (LM-PCR), sequencing, and reverse transcription polymerase chain reaction (RT-PCR) analysis. We further analyzed the distribution and clonality of the T-cell receptor (TCR) Vγ and Vδ subfamily T cells in the two T-ALL cases by RT-PCR and GeneScan. Monoclonal Vδ1 and Vδ2 subfamilies were confirmed in both samples, the Vδ3 through Vδ7 subfamilies could not be detected in the T-ALL samples, whereas the oligoclonal Vδ8 subfamily could be identified. Based on the clinical finding that both of the T-ALL cases with two malignant T-cell clones had a poor outcome, we attempted to compare the expression pattern of genes related to T-cell activation and proliferation between cases with the malignant Vδ1 and Vδ2 T-cell clones and T-ALL cases with a mono-malignant Vα T-cell clone. We selected two T-ALL cases with VαJα rearrangements and analyzed the expression level of Notch1, TAL1, and the CARMA-BCL10-MALT-A20-NF-κB pathway genes by real-time PCR. A20 had significantly higher expression in the biclonal compared with the monoclonal T-ALL group (p=0.0354), and there was a trend toward higher expression for the other genes in the biclonal group with the exception of TAL1, although the differences were not statistically significant. In conclusion, we identified two T-ALL cases with biclonal malignant T-cell clones and described the characteristics of the biclonal T-ALL subtype and its gene expression pattern. Thus, our findings may improve the understanding of biclonal T-ALL.

New molecular insights into peripheral T cell lymphomas

Peripheral T cell lymphomas (PTCLs) are heterogeneous neoplasms and represent about 12% of all lymphoid malignancies. They are often regarded as "orphan diseases," a designation that does not reflect their real incidence but rather signifies the difficulties encountered in their classification, diagnosis, and treatment. Here we revise the current understanding of the pathobiological characteristics of the most common nodal PTCLs by focusing on the contribution given by high-throughput technologies and the identification of potential therapeutic targets proposed by translational studies.