Upregulated Expression of ERBB2/HER2 in Multiple Myeloma as a Predictor of Poor Survival Outcomes

Identification of Hub Genes and Analysis of their Regulatory miRNAs in Patients with Thymoma Associated Myasthenia Gravis Based on TCGA Database

BACKGROUND

Myasthenia gravis is an autoimmune disease, and 30% of patients with thymoma often have myasthenia gravis. Patients with thymoma-associated MG (TAMG) have many different clinical presentations compared to non-MG thymoma (NMG), yet their gene expression differences remain unclear.

OBJECTIVE

In this study, we analyzed the Differentially Expressed Genes (DEGs) and analyzed their regulatory microRNAs (miRNAs) in TAMG, which will further clarify the possible pathogenesis of TAMG.

METHODS

DEGs were calculated using the RNA-sequencing data of TAMG and NMG downloaded from The Cancer Genome Atlas (TCGA) database. R software was then used to analyze the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of DEGs, while STRING was applied to build the protein-protein interaction (PPI) network and Cytoscape to identify and visualize the hub genes. Immune infiltration significances of hub genes were also explored by using the TIMER database and TCGA database. Upstream microRNAs (miRNAs) of the hub genes were predicted by online software.

RESULTS

We comparatively analyzed the gene expression differences between TAMG and NMG groups. A total of 977 DEGs were identified between the two groups (|log fold change (FC)| >2, adjusted P value <0.050), with 555 down-regulated genes and 422 up-regulated genes. Five top hub genes (CTNNB1, EGFR, SOX2, ERBB2, and EGF) were recognized in the PPI network. Analysis based on the TIMER and TCGA databases suggested that 5 hub genes were correlated with multiple immune cell infiltrations and immune checkpoint-related markers, such as PDCD1, CTLA-4, and CD274, in TAMG patients. Lastly, 5 miRNAs were identified to have the potential function of regulating the hub gene expression.

CONCLUSION

Our study identified 5 hub genes (CTNNB1, EGFR, SOX2, ERBB2, and EGF) and their 5 regulatory miRNAs in TAMG, and the hub genes were correlated with multiple immune cell infiltrations and immune checkpoint-related markers. Our findings could help partially clarify the pathophysiology of TAMG, which could be new potential targets for subsequent clinical immunotherapy.

Small RNA-seq and clinical evaluation of tRNA-derived fragments in multiple myeloma: Loss of mitochondrial i-tRFHisGTG results in patients' poor treatment outcome

Despite the substantial progress in multiple myeloma (MM) therapy nowadays, treatment resistance and disease relapse remain major clinical hindrances. Herein, we have investigated tRNA-derived fragment (tRF) profiles in MM and precursor stages (smoldering MM/sMM; monoclonal gammopathy of undetermined significance/MGUS), aiming to unveil potential MM-related tRFs in ameliorating MM prognosis and risk stratification. Small RNA-seq was performed to profile tRFs in bone marrow CD138+ plasma cells, revealing the significant deregulation of the mitochondrial internal tRFHisGTG (mt-i-tRFHisGTG) in MM versus sMM/MGUS. The screening cohort of the study consisted of 147 MM patients, and mt-i-tRFHisGTG levels were quantified by RT-qPCR. Disease progression was assessed as clinical end-point for survival analysis, while internal validation was performed by bootstrap and decision curve analyses. Screening cohort analysis highlighted the potent association of reduced mt-i-tRFHisGTG levels with patients' bone disease (p = 0.010), osteolysis (p = 0.023) and with significantly higher risk for short-term disease progression following first-line chemotherapy, independently of patients' clinical data (HR = 1.954; p = 0.036). Additionally, mt-i-tRFHisGTG-fitted multivariate models led to superior risk stratification of MM patients' treatment outcome and prognosis compared to disease-established markers. Notably, our study highlighted mt-i-tRFHisGTG loss as a powerful independent indicator of post-treatment progression of MM patients, leading to superior risk stratification of patients' treatment outcome.

Phase II study of nivolumab in patients with genetic alterations in DNA damage repair and response who progressed after standard treatment for metastatic solid cancers (KM-06)

BACKGROUND

Immune-modulating antibodies targeting programmed cell death protein 1/programmed death-ligand 1 (PD-1/PD-L1) have demonstrated promising antitumor efficacy in various types of cancers, especially highly mutated ones. Genetic alterations in DNA damage response and repair (DDR) genes can lead to genetic instability, often accompanied by a high tumor mutation burden (TMB). However, few studies have validated the aberration of DDR genes as a predictive biomarker for response to immune-modulating antibodies.

METHODS

The KM-06 open-label, multicenter, single-arm, phase II trial evaluated the safety and efficacy of nivolumab in refractory solid cancers with DDR gene mutations assessed by clinically targeted sequencing. Nivolumab (3 mg/kg) was administered every 2 weeks until disease progression, unacceptable toxicity, or for 24 months. The primary endpoint was the objective response rate (ORR) as per RECIST V.1.1 criteria.

RESULTS

A total of 48 patients were enrolled in the study (median age 61, 58.3% male). The most common cancer type was colorectal cancer (41.7%), followed by prostate and biliary tract cancer (8.3% each). Eight patients achieved a partial response as their best overall response, resulting in an ORR of 17.8%. The disease control rate was 60.0%. The median progression-free survival was 2.9 months. Treatment-related adverse events of any grade and grade ≥3 occurred in 44 (91.7%) and 4 (8.3%) patients, respectively. Clinically targeted sequencing data inferred both TMB and microsatellite instability (MSI). Using a TMB cut-off of 12 mut/Mb, there were significant differences in overall survival (p=0.00035), progression-free survival (p=0.0061), and the best overall response (p=0.05). In the RNA sequencing analysis, nivolumab responders showed activation of the interleukin signaling pathway. Patients who experienced early progression presented high epithelial-mesenchymal transition signaling pathway activation. The responders exhibited a marked increase in PD-1-/Ki67+CD8 T cells at the early stage of treatment (C3D1) compared with non-responders (p=0.03).

CONCLUSIONS

In this phase II trial, nivolumab demonstrated moderate efficacy and manageable toxicity in patients with solid cancer harboring DDR gene mutations. A high TMB (>12 mut/Mb) and MSI score (>2.5) determined through clinically target sequencing presented significant discriminatory power for the nivolumab response.

TRIAL REGISTRATION NUMBER

NCT04761744.