Dissection of Immune Gene Networks in Primary Melanoma Tumors Critical for Antitumor Surveillance of Patients with Stage II–III Resectable Disease

Abstract

Patients with resected stage II–III cutaneous melanomas remain at high risk for metastasis and death. Biomarker development has been limited by the challenge of isolating high-quality RNA for transcriptome-wide profiling from formalin-fixed and paraffin-embedded (FFPE) primary tumor specimens. Using NanoString technology, RNA from 40 stage II–III FFPE primary melanomas was analyzed and a 53-immune-gene panel predictive of non-progression (area under the curve (AUC)=0.920) was defined. The signature predicted disease-specific survival (DSS P<0.001) and recurrence-free survival (RFS P<0.001). CD2, the most differentially expressed gene in the training set, also predicted non-progression (P<0.001). Using publicly available microarray data from 46 primary human melanomas (GSE15605), a coexpression module enriched for the 53-gene panel was then identified using unbiased methods. A Bayesian network of signaling pathways based on this data identified driver genes. Finally, the proposed 53-gene panel was confirmed in an independent test population of 48 patients (AUC=0.787). The gene signature was an independent predictor of non-progression (P<0.001), RFS (P<0.001), and DSS (P=0.024) in the test population. The identified driver genes are potential therapeutic targets, and the 53-gene panel should be tested for clinical application using a larger data set annotated on the basis of prospectively gathered data.

Divergent Phenotypes of Human Regulatory T Cells Expressing the Receptors TIGIT and CD226

“…We sorted Tconv (FOXP3 − Helios − ), FOXP3 + Helios − ,, and tTreg subsets (FOXP3 + Helios + ) (Figure 1A), which then underwent direct mRNA hybridization that facilitates the direct quantitation of mRNA transcripts without reverse-transcription and amplification. This approach is compatible with partially degraded RNA samples, such as those obtained from fixed samples (35). …”

Aloe-emodin exerts a potent anticancer and immunomodulatory activity on BRAF-mutated human melanoma cells

“…The immune system plays an important role in the surveillance and initial control of tumor growth and diffusion. The outcome of the tumor immuno-surveillance is dependent from many factors (Sivendran et al, 2014) including the dynamic of cytokine secretion (Wilmott et al, 2014). Cytokines released by melanoma cells may contribute to modulate and regulate the ongoing immune response against tumor cells.…”

Evaluating Robustness and Sensitivity of the NanoString Technologies nCounter Platform to Enable Multiplexed Gene Expression Analysis of Clinical Samples

“…The Nanostring Technologies nCounter platform is a relatively new technology and has been used within various clinical and research applications (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13). The automated nCounter platform hybridizes fluorescent barcodes directly to specific nucleic acid sequences, allowing for the nonamplified measurement of up to 800 targets within one sample (1,14).…”