Clinical Application of Next-Generation Sequencing-Based Panel to BRAF Wild-Type Advanced Melanoma Identifies Key Oncogenic Alterations and Therapeutic Strategies

Molecular profiling with next-generation sequencing (NGS) has been applied in multiple solid cancers to discover potential therapeutic targets. Here, we describe the results of a clinical NGS panel in patients with advanced melanoma. Thirty-six tumor tissues from patients with BRAF wild-type melanoma at Seoul National University Hospital (SNUH; Seoul, Republic of Korea) were collected and deep-sequenced using the SNUH FIRST-Cancer NGS panel to assess single-nucleotide variants, small insertions/deletions, copy number variations, and structural variations to estimate tumor mutation burden (TMB). We discovered 106 oncogenic alterations and most of the patients (n = 33, 92%) harbored at least one oncogenic alteration, including 2 patients who were initially diagnosed as BRAF V600E-negative but were later confirmed to be positive. Altogether, 36 samples were classified into RAS/BRAF/NF1-mutant (n = 14, 39%) or triple wild-type (n = 22, 61%) melanoma subtypes. The estimated median TMB was 8.2 mutations per Mb, ranging from 0 to 146.67 mutations per Mb. Of the 36 patients, 25 (70%) had actionable alterations with currently developed drugs, and 7 (19.4%) were enrolled in dinical trials with an RAF inhibitor, multiple receptor tyrosine kinase inhibitor, and anti-programmed cell death-1 (PD-1) antibody. TMB tended to associate with progression-free survival (PFS) of treatment with anti-PD-1/PDL-1 antibody (HR, 0.96; 95% confidence interval, 0.92-1.00; P = 0.07). High-TMB (>= 13) group was associated with longer PFS than the low-TMB group (median 34.0 vs. 11.0 weeks, P = 0.04). Overall, the dinical use of a NGS panel in patients with advanced melanoma shows association with clinical outcomes and several therapeutic strategies.

Clinical factors affecting progression-free survival with crizotinib in ALK-positive non-small cell lung cancer

Background/Aims: Although crizotinib is standard chemotherapy for advanced anaplastic lymphoma kinase (ALK)-positive non-small cell lung cancer (NSCLC), clinical factors affecting progression-free survival (PFS) have not been reported. The purpose of this study was to identify clinical factors affecting PFS of crizotinib and develop a prognostic model for advanced ALK-positive NSCLC. Methods: Clinicopathologic features of patients enrolled in PROFILE 1001, 1005, 1007, and 1014 (training cohort) were reviewed. We conducted multivariate Cox analysis for PFS and overall survival (OS) in the training cohort (n = 159) and generated a proportional hazards model based on significant clinicopathologic factors, and then validated the model in an independent validation cohort (n = 40). Results: In the training cohort, the objective response rate was 81.5%. Median PFS and OS from the start of crizotinib were 12.4 and 31.3 months, respectively. Multivariate Cox analysis showed poor performance status, number of metastatic organs (>= 3), and no response to crizotinib independently associated shorter PFS. Based on a score derived from these three factors, median PFS and OS of patients with one or two factors were significantly shorter compared to those without these factors (median PFS, 22.4 months vs. 10.5 months vs. 6.5 months; median OS, not reached vs. 29.1 months vs. 11.8 months, respectively; p < 0.001 for each group). This model also had validated in an independent validation cohort. Conclusions: Performance status, number of metastatic organs, and response to crizotinib affected PFS of crizotinib in ALK-positive NSCLC. Based on these factors, we developed a simple and useful prediction model for PFS.

The efficacy of immune checkpoint inhibitors in anaplastic lymphoma kinase-positive non-small cell lung cancer

Background Despite recent advances in treating non-small cell lung cancer (NSCLC) with immune checkpoint inhibitors (ICIs), their role in ALK-positive NSCLC patients is unclear. We investigated the efficacy of ICIs in patients with ALK-positive NSCLC. Methods Between 2011 and 2018, a total of 14 ALK-positive NSCLC patients treated with ICIs were evaluated retrospectively. Clinicopathologic features including age, PD-L1 expression, and treatment outcomes were analyzed. RNA expression level and cytolytic activity by ALK positivity were analyzed using The Cancer Genome Atlas (TCGA) and National Cancer Center Research Institute (NCCRI) data sets. Results A total of 13 patients (92.9%) received ALK inhibitors. Patients received a median of three (range 2-8) courses of therapy. The study included nine patients (64.3%) who were PD-L1-high (>50%) and four (28.6%) who were PD-L1-low (<50%). The objective response rate was 14.3% (2/14). The median progression-free survival time was 2.18 months (95% confidence interval [CI] 1.13 months-not reached [NR]). The median overall survival time was 5.67 months (95% CI 3.00 months-NR). RNA expression levels of CD274 were similar between the ALK-positive and negative groups in both TCGA and NCCRI datasets. RNA levels of CD8A in both TCGA and NCCRI data sets were nonsignificantly lower in the ALK-positive group. Cytolytic activity scores including interferon-gamma-related response were lower in the ALK-positive group in the NCCRI but not TCGA dataset. Conclusions Despite high PD-L1-positive rates, ICIs show limited efficacy in ALK-positive NSCLC. Decreased interferon-gamma-related response may underlie these findings.

Induction chemotherapy in head and neck squamous cell carcinoma of the paranasal sinus and nasal cavity: A role in organ preservation

Background/Aims: The role of induction chemotherapy (IC) for eyeball preservation has not been established in head and neck squamous cell carcinoma (HNSCC) of the paranasal sinus and nasal cavity (PNSNC). Periorbital involvement frequently leads to eyeball exenteration with a margin of safety. We evaluated the treatment outcomes, including survival and eyeball preservation, of patients who received IC for HNSCC of the PNSNC. Methods: We reviewed 21 patients diagnosed with HNSCC of the PNSNC who were treated with IC. We analyzed response, eyeball preservation rate, and overall survival. Results: Tumors were located in the paranasal sinus (n = 14) or nasal cavity (n = 7). Most patients had stage T4a (n = 10) or T4b (n = 7) disease. More than half of the patients received a chemotherapy regimen of docetaxel, fluorouracil, and cisplatin (n = 11). Thirteen patients (61.9%) achieved a partial response after IC and 15 patients (71.4%) achieved T down-staging. Among 17 patients with stage T4 disease, which confers a high risk of orbital exenteration, 14 (82.4%) achieved preservation of the involved eye. The 3-year overall survival (OS) rate of patients who achieved a partial response to IC was 84.6%. The 3-year OS rate of patients with stable disease or disease progression after IC was 25.0% (p = 0.038). Conclusions: IC could be considered for down-staging patients with advanced T-stage disease. It could also be a reasonable option for eyeball preservation in locally advanced HNSCC of the PNSNC.

Tumor immune profiles noninvasively estimated by FDG PET with deep learning correlate with immunotherapy response in lung adenocarcinoma

Rationale: The clinical application of biomarkers reflecting tumor immune microenvironment is hurdled by the invasiveness of obtaining tissues despite its importance in immunotherapy. We developed a deep learning-based biomarker which noninvasively estimates a tumor immune profile with fluorodeoxyglucose positron emission tomography (FDG-PET) in lung adenocarcinoma (LUAD). Methods: A deep learning model to predict cytolytic activity score (CytAct) using semi-automatically segmented tumors on FDG-PET trained by a publicly available dataset paired with tissue RNA sequencing (n = 93). This model was validated in two independent cohorts of LUAD: SNUH (n = 43) and The Cancer Genome Atlas (TCGA) cohort (n = 16). The model was applied to the immune checkpoint blockade (ICB) cohort, which consists of patients with metastatic LUAD who underwent ICB treatment (n = 29). Results: The predicted CytAct showed a positive correlation with CytAct of RNA sequencing in validation cohorts (Spearman rho = 0.32, p = 0.04 in SNUH cohort; spearman rho = 0.47, p = 0.07 in TCGA cohort). In ICB cohort, the higher predicted CytAct of individual lesion was associated with more decrement in tumor size after ICB treatment (Spearman rho = -0.54, p < 0.001). Higher minimum predicted CytAct in each patient associated with significantly prolonged progression free survival and overall survival (Hazard ratio 0.25, p = 0.001 and 0.18, p = 0.004, respectively). In patients with multiple lesions, ICB responders had significantly lower variance of predicted CytActs (p = 0.005). Conclusion: The deep learning model that predicts CytAct using FDG-PET of LUAD was validated in independent cohorts. Our approach may be used to noninvasively assess an immune profile and predict outcomes of LUAD patients treated with ICB.

Effects of dietary energy and crude protein levels on growth performance, blood profiles, and nutrient digestibility in weaning pigs

Objective This experiment was conducted to investigate the effect of reducing dietary metabolic energy (ME) and crude protein (CP) levels on growth performance, blood profiles, and nutrient digestibility in weaning pigs. Methods A total of 240 crossbred pigs (Duroc×[Landrace×Yorkshire]) with an average body weight of 8.67±1.13 kg were used for a 6-week feeding trial. Experimental pigs were allotted to a 2×3 factorial arrangement using a randomized complete block design. The first factor was two levels of dietary ME density (low ME level, 13.40 MJ/kg or high ME level, 13.82 MJ/kg) and the second factor was three dietary CP levels based on subdivision of early and late weaning phases (low CP level, 19.7%/16.9%; middle CP level, 21.7%/18.9%; or high CP level, 23.7%/20.9%). Results Over the entire experimental period, there were no significant difference in body weight among groups, but a decrease in diet energy level was associated with an increase in average daily feed intake (p = 0.02) and decrease in gain-feed ratio (G:F) ratio (p<0.01). Decreased CP levels in the diet were associated with a linear increase in average daily gain (p< 0.05) and quadratic increase in G:F ratio (p<0.05). In the early weaning period, blood urea nitrogen concentration tended to increase when ME in the diet decreased and decrease when CP level in the diet decreased (p = 0.09, p<0.01, respectively). Total protein concentration tended to increase when CP level was reduced (p = 0.08). In the late weaning period, blood urea nitrogen concentration decreased linearly as CP level decreased (p<0.01). The CP and crude fat digestibility decreased when ME was decreased by 0.42 MJ/kg (p = 0.05, p = 0.01, respectively). The CP digestibility increased linearly as CP level decreased (p = 0.01). Conclusion A weaning pig diet containing high ME level (13.82 MJ/kg) and low CP level (19.7%/16.9%) can improve pig growth performance and nutrient digestibility

Effects of dietary energy and crude protein levels on growth performance, blood profiles, and carcass traits in growing-finishing pigs

This experiment was conducted to evaluate the effect of dietary energy and crude protein (CP) levels on growth performance, blood profiles, and carcass traits in growing-finishing pigs. A total of 180 crossbred pigs ([Yorkshire x Landrace] x Duroc) with an average body weight of 30.96 +/- 3.068 kg were used for a 12-week feeding trial. Experimental pigs were allotted to a 2 x 3 factorial arrangement using a randomized complete block (RCB) design. The first factor was two levels of dietary metabolizable energy (ME) density (13.40 MJ/kg or 13.82 MJ/kg), and the second factor was three dietary CP levels based on subdivision of growing-finishing phases (high: 18%/16.3%/16.3%/13.2% middle: 17%/15.3%/15.3%/12.2% and low: 16%/14.3%/14.3%/11.2%). Average daily gain (ADG) and gain-feed ratio (G: F ratio) decreased as dietary CP level was decreased linearly (linear, p &lt; 0.05; p &lt; 0.05, respectively) in the early growing period, and G: F ration also decreased as dietary CP level was decreased linearly (linearly, p &lt; 0.05) over the whole growing phase. Over the entire experimental period, G: F ratio decreased as dietary ME level decreased (p = 0.01). Blood urea nitrogen (BUN) concentration was increased as dietary energy level decreased in growing period (p &lt; 0.01). During finishing period, total protein concentration was decreased by lower dietary energy level (p &lt; 0.05). In this study, there were no significant differences in proximate factors, physiochemical properties, muscle TBARS assay results, pH changes, or color of pork by dietary treatments. However, saturated fatty acid (SFA) increased (p &lt; 0.01) and polyunsaturated fatty acid (PUFA) decreased (p &lt; 0.05) when ME was decreased by 0.42 MJ/kg in growing-finishing pig diets. In addition, monounsaturated fatty acid (MUFA) tended to increase when CP level was decreased in growing-finishing pig diets (p = 0.06). A growing-finishing diet of 13.82 MJ/kg diet of ME with the high CP level can improve growth performance and show better fatty acids composition of pork.N

Okanin, a chalcone found in the genus Bidens, and 3-penten-2-one inhibit inducible nitric oxide synthase expression via heme oxygenase-1 induction in RAW264.7 macrophages activated with lipopolysaccharide

Excess production of nitric oxide by activated macrophages via inducible nitric oxide synthase leads to the development of various inflammatory diseases. Heme oxygenase-1 expression via activation of nuclear factor-erythroid 2-related factor 2 inhibits nitric oxide production and inducible nitric oxide synthase expression in activated macrophages. Okanin is one of the most abundant chalcones found in the genus Bidens (Asteraceae) that is used as various folk medications in Korea and China for treating inflammation. Here, we found that okanin (possessing the α-β unsaturated carbonyl group) induced heme oxygenase-1 expression via nuclear factor-erythroid 2-related factor 2 activation in RAW264.7 macrophages. 3-Penten-2-one, of which structure, as in okanin, possesses the α-β unsaturated carbonyl group, also induced nuclear factor-erythroid 2-related factor 2-dependent heme oxygenase-1 expression, while both 2-pentanone (lacking a double bond) and 2-pentene (lacking a carbonyl group) were virtually inactive. In lipopolysaccharide-activated RAW264.7 macrophages, both okanin and 3-penten-2-one inhibited nitric oxide production and inducible nitric oxide synthase expression via heme oxygenase-1 expression. Collectively, our findings suggest that by virtue of its α-β unsaturated carbonyl functional group, okanin can inhibit nitric oxide production and inducible nitric oxide synthase expression via nuclear factor-erythroid 2-related factor 2-dependent heme oxygenase-1 expression in lipopolysaccharide-activated macrophages

Immunogenicity of influenza vaccination in patients with cancer receiving immune checkpoint inhibitors

Among prospectively enrolled adult patients with cancer receiving immune checkpoint inhibitors (ICIs; n = 46) or cytotoxic agents (n = 90), seroprotection and seroconversion rates after seasonal quadrivalent influenza vaccinations were higher with ICI than with cytotoxic chemotherapy. These results support annual influenza vaccinations for cancer patients receiving ICIs.