Melanoma Cohort Research Articles

Omission of Completion Lymph Node Dissection in Sentinel Node Biopsy Positive Head and Neck Cutaneous Melanoma Patients.

Recent studies evaluating patients with a positive sentinel lymph node biopsy (SLNB+) show no melanoma-specific survival difference between patients undergoing lymph node basin surveillance and completion lymph node dissection (CLND). This has been broadly applied, despite underrepresentation of head and neck (HN) cutaneous melanoma patients. We evaluated whether this was upheld in the HN melanoma cohort. Patients with HN melanoma with a SLNB+ were selected from the National Cancer Database (NCDB) from 2012 to 2019. Overall survival (OS) of patients who underwent SLNB only versus SLNB + CLND were compared. Subgroup analyses were performed based on pathologic N (pN) and receipt of immunotherapy. Adjusted hazard ratio (aHR) and 95% confidence interval (CI) were calculated. Analysis of 634 patients with multivariable Cox regression showed no difference in OS in SLNB only versus SLNB + CLND cohorts (hazard ratio [HR] 1.13; 95% confidence interval [CI] 0.71-1.81; p = 0.610). Charlson-Deyo score (CDS) 1 versus 0 (HR 1.70; 95% CI 1.10-2.63; p = 0.016), pN2+ versus pN1 (HR 1.74; 95% CI 1.23-2.45; p = 0.002), and lymphovascular invasion (LVI) versus no (HR 2.07; 95% CI 1.34-3.19; p = 0.001) were associated with worse prognosis. Subgroup analysis by pN showed no OS benefit for CLND in either pN1 (HR 1.04; 95% CI 0.51-2.10; p = 0.922) or pN2+ (HR 1.31; 95% CI 0.67-2.57; p = 0.427) patients or in patients who received immunotherapy (HR 1.32; 95% CI 0.54-3.22; p = 0.549). This study of SLNB + HN melanoma patients showed no OS difference in SLNB only versus SLNB + CLND. Further studies need to be performed to better define the role of CLND.

Dynamic thresholding and tissue dissociation optimization for CITE-seq identifies differential surface protein abundance in metastatic melanoma

Multi-omics profiling by CITE-seq bridges the RNA-protein gap in single-cell analysis but has been largely applied to liquid biopsies. Applying CITE-seq to clinically relevant solid biopsies to characterize healthy tissue and the tumor microenvironment is an essential next step in single-cell translational studies. In this study, gating of cell populations based on their transcriptome signatures for use in cell type-specific ridge plots allowed identification of positive antibody signals and setting of manual thresholds. Next, we compare five skin dissociation protocols by taking into account dissociation efficiency, captured cell type heterogeneity and recovered surface proteome. To assess the effect of enzymatic digestion on transcriptome and epitope expression in immune cell populations, we analyze peripheral blood mononuclear cells (PBMCs) with and without dissociation. To further assess the RNA-protein gap, RNA-protein we perform codetection and correlation analyses on thresholded protein values. Finally, in a proof-of-concept study, using protein abundance analysis on selected surface markers in a cohort of healthy skin, primary, and metastatic melanoma we identify CD56 surface marker expression on metastatic melanoma cells, which was further confirmed by multiplex immunohistochemistry. This work provides practical guidelines for processing and analysis of clinically relevant solid tissue biopsies for biomarker discovery.

Immune Inhibitory Molecule PD-1 Homolog (VISTA) Colocalizes with CD11b Myeloid Cells in Melanoma and Is Associated with Poor Outcomes

Tumors evade immunity through the overexpression of immune inhibitory molecules in the tumor microenvironment such as PD-L1/B7-H1. An immune inhibitory molecule named PD-1 homolog (also known as V-domain Ig-containing suppressor of T cell activation [VISTA]) functions to control both T cells and myeloid cells. Current clinical trials using anti-VISTA-blocking agents for treatment of cancer are ongoing. We sought to determine the extent of VISTA expression in primary cutaneous melanomas (n= 190), identify the critical cell types expressing VISTA, and correlate its expression with PD-L1 expression using multiplexed quantitative immunofluorescence. Within the tumor subcompartments, VISTA is most highly expressed on CD11b myeloid cells, and PD-L1 is most highly expressed on CD68 myeloid cells in our melanoma cohort. There is little correlation between VISTA and PD-L1 expression intensity, suggesting that individual tumors have distinct immunosuppressive tumor microenvironments. High levels of VISTA expression on CD11b myeloid cells but not PD-L1 expression were associated with greater melanoma recurrence and greater all-cause mortality. Our findings suggest that cell-specific VISTA expression may be a negative prognostic biomarker for melanoma and a future potential therapeutic target.

EGFR expression is associated with relapse in a melanoma cohort receiving adjuvant PD-1-based immunotherapy

EGFR expression is associated with relapse in a melanoma cohort receiving adjuvant PD-1-based immunotherapy

Causes of death among patients with cutaneous melanoma: a US population-based study

Research on mortality outcomes and non-cancer-related causes of death in patients with cutaneous melanoma (CM) remains limited. This study aimed to identify the prevalence of non-cancer-related deaths following CM diagnosis. The data of 224,624 patients diagnosed with malignant CM in the United States between 2000 and 2019 were extracted from the Surveillance, Epidemiology, and End Results (SEER) database. We stratified our cohort based on their melanoma stage at diagnosis and further calculated standardized mortality ratios (SMRs) for each cause of death, comparing their relative risk to that of the general US population. The total number of fatalities among melanoma patients was 60,110, representing 26.8% of the total cases. The percentage of deaths is directly proportional to the disease stage, reaching 80% in distant melanoma. The highest fatalities among the localized melanoma group (25,332; 60.5%) occurred from non-cancer causes, followed by melanoma-attributable deaths (10,817; 25.8%). Conversely, melanoma is the leading cause of death in regional and distant melanoma cohorts. Cardiovascular and cerebrovascular diseases were the most prevalent non-cancer causes of death among the three disease-stage cohorts. Compared to the general population, we did not observe an increased risk of death due to non-cancer causes in the localized CM cohort, while patients diagnosed with regional and distant CMs had a statistically significant higher risk of death from all the reported major causes of death.

Artificial Intelligence Applied to a First Screening of Naevoid Melanoma: A New Use of Fast Random Forest Algorithm in Dermatopathology.

Malignant melanoma (MM) is the "great mime" of dermatopathology, and it can present such rare variants that even the most experienced pathologist might miss or misdiagnose them. Naevoid melanoma (NM), which accounts for about 1% of all MM cases, is a constant challenge, and when it is not diagnosed in a timely manner, it can even lead to death. In recent years, artificial intelligence has revolutionised much of what has been achieved in the biomedical field, and what once seemed distant is now almost incorporated into the diagnostic therapeutic flow chart. In this paper, we present the results of a machine learning approach that applies a fast random forest (FRF) algorithm to a cohort of naevoid melanomas in an attempt to understand if and how this approach could be incorporated into the business process modelling and notation (BPMN) approach. The FRF algorithm provides an innovative approach to formulating a clinical protocol oriented toward reducing the risk of NM misdiagnosis. The work provides the methodology to integrate FRF into a mapped clinical process.

Expression of lymphoid structure-associated cytokine/chemokine gene transcripts in tumor and protein in serum are prognostic of melanoma patient outcomes.

Proinflammatory chemokines/cytokines support development and maturation of tertiary lymphoid structures (TLS) within the tumor microenvironment (TME). In the current study, we sought to investigate the prognostic value of TLS-associated chemokines/cytokines (TLS-kines) expression levels in melanoma patients by performing serum protein and tissue transcriptomic analyses, and to then correlate these data with patients clinicopathological and TME characteristics. Levels of TLS-kines in patients' sera were quantitated using a custom Luminex Multiplex Assay. The Cancer Genomic Atlas melanoma cohort (TCGA-SKCM) and a Moffitt Melanoma cohort were used for tissue transcriptomic analyses. Associations between target analytes and survival outcomes, clinicopathological variables, and correlations between TLS-kines were statistically analyzed. Serum of 95 patients with melanoma were evaluated; 48 (50%) female, median age of 63, IQR 51-70 years. Serum levels of APRIL/TNFSF13 were positively correlated with levels of both CXCL10 and CXCL13. In multivariate analyses, high levels of serum APRIL/TNFSF13 were associated with improved event-free survival after adjusting for age and stage (HR = 0.64, 95% CI 0.43-0.95; p = 0.03). High expression of APRIL/TNFSF13 tumor transcripts was significantly associated with improved OS in TCGA-SKCM (HR = 0.69, 95% CI 0.52-0.93; p = 0.01) and in Moffitt Melanoma patients (HR = 0.51, 95% CI: 0.32-0.82; p = 0.006). Further incorporation of CXCL13 and CXCL10 tumor transcript levels in a 3-gene index revealed that high APRIL/CXCL10/CXCL13 expression was associated with improved OS in the TCGA SKCM cohort (HR = 0.42, 95% CI 0.19-0.94; p = 0.035). Melanoma differentially expressed genes positively associated with high APRIL/CXCL10/CXCL13 tumor expression were linked to tumor infiltration by a diverse array of proinflammatory immune cell types. Serum protein and tumor transcript levels of APRIL/TNFSF13 are associated with improved survival outcomes. Patients exhibiting high coordinate expression of APRIL/CXCL10/CXCL13 transcripts in their tumors displayed superior OS. Further investigation of TLS-kine expression profiles related to clinical outcomes in larger cohort studies is warranted.

Correlation of low B7-H6 expression with efficacy of immunotherapy inpatients with melanoma.

e21556 Background: B7-H6 (NCR3LG1) can bind to NKp30 to trigger antitumor NK cell activation and cytokine secretion. Our previous studies have shown that in gastric cancer, B7-H6 high expression was associated with better prognosis and the low expression of B7-H6 group was correlated with better immune microenvironment. However, the effect of B7-H6 expression on immunotherapy is unknown. Herein, we used the data from a clinically annotated cohort of melanoma patients treated with ICI to analyze the influence of B7-H6 expression on immunotherapy. Methods: The gene expression profile, gene mutation information and clinical data were extracted from the supplementary data in melanoma cohort (PMID: 31792460). Maximally selected rank statistics was used to select the optimum threshold for B7-H6 expression, and the patients was divided into two groups according to the expression of B7-H6, high group and low group. Kaplan-Meier survival analysis was used to evaluate the influence of B7-H6 expression on OS prognosis. Associations between variables and OS survival were tested using univariate and multivariate Cox and displayed by forest (R package). Results: We selected 3.14 as the optimum threshold of B7-H6 expression, and the patients was divided into high group (B7-H6 expression＞3.14) and low group (B7-H6 expression≤3.14). The results showed that low group was significantly associated with longer overall survival (p value = 0.048) in cohort of melanoma patients treated with anti-PD1 ICI, which was consistent with our previous results that low expression of B7-H6 group was correlated with better immune microenvironment. We selected primary lesion type, TMB and the expression of B7-H6 factors for univariate and multivariate analysis. TMB-H (top 25%) (p value = 0.051) and B7-H6 (p value = 0.051) low expression were associated with a better OS. Then the patients were divided into four groups according to the TMB and B7-H6 expression and analyzed the difference in the four groups. The results showed that in patients with TMB-L, B7-H6 low group had significant better OS than the B7-H6 high group (p value = 0.032). Conclusions: The low B7-H6 expression was correlated with better efficacy immunotherapy. The effect of B7-H6 expression on immunotherapy needs to be further prospective trial validation.

The DIET study: A randomized controlled trial of a high fiber diet in cancer patients (pts) receiving immune checkpoint blockade (ICB).

TPS9609 Background: Gut microbiome modulation is a promising strategy to enhance response to ICB Fecal microbiota transplant studies have shown positive signals of improved outcomes in both ICB naïve and refractory melanoma; however, this strategy is challenging to scale. Diet is a key determinant of the gut microbiota and we have previously shown that a) habitual high dietary fiber intake is associated with improved response to ICB and b) fiber manipulation in mice impacts ant-tumor immunity. We recently demonstrated feasibility of a controlled high-fiber dietary intervention (HFDI) conducted in melanoma survivors with excellent compliance and tolerance. Building on this, we are now conducting a single center Phase II randomized trial of HFDI versus healthy control diet in cancer pts receiving ICB (NCT04645680). Methods: 57 pts starting standard of care (SOC) ICB will be enrolled in 4 cohorts: 3 melanoma cohorts in the adjuvant (n = 21), neoadjuvant (n = 12), and unresectable (n = 12) settings and 1 metastatic renal cell carcinoma (RCC) cohort (n = 12). Key inclusion criteria include BMI 18.5-40 kg/m2, and willingness to exclusively eat the diet. Key exclusion criteria include diabetes mellitus, inflammatory bowel disease, total colectomy or bariatric surgery, recent use of prebiotic/probiotic supplements, steroids (within 14 days), antibiotics (within 21 days), current smoker or heavy drinker, and dietary fiber > 20g/day. Pts are randomized 2:1 to the HFDI (target fiber 50g/day) or control diet (fiber 15-20g/day) stratified by BMI and cohort. Both diets have same macronutrient composition but differ in fiber content. The primary objective is to establish the effects of a dietary intervention on the structure and function of the gut microbiome. Secondary endpoints include change in circulating and stool metabolites, systemic and tumor immunity, and safety and tolerability of dietary intervention. As a controlled feeding study, all meals are isocaloric and prepared by MD Anderson Bionutrition Research Core for up to 11 weeks. Meals follow American Cancer Society and American Institute for Cancer Research recommendations which include whole foods plant-forward diet, little to no processed meats or added sugars, and no alcohol consumption. Meals are shipped weekly within the contiguous United States and include breakfast, lunch, dinner, and snacks. The HFDI group start at 30g fiber/day, up titrated every 2 weeks up to 50g/day based on tolerance. Blood and stool samples are collected longitudinally. Tumor biopsies are required in the neoadjuvant cohort and optional in unresectable. A Fitbit is provided to monitor physical activity and a scale to measure daily weight. 24 of the planned 57 pts have been enrolled: n = 13 adjuvant, n = 5 neoadjuvant, n = 5 unresectable, n = 1 RCC. 14 treated with PD1 monotherapy, 9 with ipilimumab + nivolumab, and 1 with nivolumab + relatlimab. Clinical trial information: NCT04645680 .

Weight loss (WL) as a predictive factor for immune oncology (IO).

e14528 Background: WL is an adverse prognostic factor/symptom reported in ~40% cancer (ca) patients (pts) at diagnosis agnostic to site or histologic grade. The mechanism of WL in ca, however, remains elusive. The role of energetic waste in ca WL is doubtful (it neglects likely dietary compensation). On the other hand, lymphocytic activation, a clonal, energetically demanding process is accompanied with anorexia limiting caloric intake which leads frequently to WL if protracted over months as seen in lymphoma (B-symptom) or indecisive immune engagement (Eng) with tuberculosis. WL of > 5% of body weight, was an adverse prognosticator and exclusion criterion in non-small cell lung cancer (NSCLC) chemotherapy (CT) trials, likely due to CT or steroids' abrogation of the putative, limited immune ca containment. We hypothesized that WL in ca reflects months of immune Eng, ineffective as it may be at containing the tumor, but nevertheless representing immune Eng with the ca. Such cases stand the best chance for IO benefit. Notably, IO impact in ca mirrors the 40% of WL in ca pts. Methods: Tumor registry retrieved data from all stage 4 cancers treated with monotherapy IO in our institution. We dichotomized pts to beneficiaries (B) or non-beneficiaries (NB). Bs survive longer than median survival for the respective stage/line of therapy in each ca derived from published trials. To account for missing WL data prior to IO, we reasoned that weight gain of ≥10 lbs (reliably charted over 1 year from IO infusions) is acceptable surrogate for WL and met our criteria. Results: WL in our cohort (n = 53) of Melanoma, NSCLC, renal cell carcinoma, and bladder ca was 43% of B; 10% in NB (ratio > 4:1) rejecting the null hypothesis (p < 0.05). PDL-1, Tumor Mutation Burden, both inconclusive in identifying durable benefit, were limited in our set precluding further analysis. Conclusions: Our results support, though do not prove, that WL identifies the appropriate IO pts. Improved outcome despite a historically-adverse prognosticator (WL); the fact that IO was the only ca therapy used, both support our interpretation. We hope to stimulate others to examine independent larger datasets to confirm this notion and to allow comprehensive subset analyses. For WL to be utilized properly the relevant clinical context is crucial, accounting for GI obstructing ca (esophageal ca), enzymatic anomalies (pancreatic ca), volume fluctuations (cirrhosis), catabolism (prolonged hospitalization), or dental issues, to name a few. Additionally, factors such as tumor bulk, perhaps discerned from the T of TNM staging, deserve examination since more vigorous immune activation against larger targets could produce more impact on appetite and caloric intake. Finally, available clinical trial datasets, not tumor registries, might provide a more crisp, reliable source as we continue this investigation. WL can, with confirmatory work, be clinically incorporated as a predictive factor for IO benefit.

Phase 1/2 study of mRNA-4359 administered alone and in combination with immune checkpoint blockade in adult participants with advanced solid tumors.

TPS2676 Background: mRNA-4359 is a lipid nanoparticle encapsulated mRNA-based cancer vaccine encoding for concatemerized program death-ligand 1 (PD-L1) and indoleamine 2,3-dioxygenase 1 (IDO1) antigens given as an intramuscular injection. These proteins are found across a wide range of cancer types. PD-L1 is a cell surface receptor expressed on both tumor and regulatory immune cells and functions as a checkpoint to inhibit T cell function, while IDO1 is an L-tryptophan metabolizing enzyme involved in T cell suppression and immune tolerance. Both are thought to impart an inhibitory tumor microenvironment which allows tumor cells to escape immune monitoring and clearance. T cells that can target PD-L1 and IDO1 are known to pre-exist in cancer patients and a recent study leveraging a peptide-based vaccine approach demonstrated they can be induced to elicit clinically meaningful and durable tumor responses in patients with metastatic melanoma when combined with PD-1 inhibition. mRNA-4359 encodes immunogenic peptides proposed to generate anti-PD-L1/IDO1-specific T-cells to kill immunosuppressive regulatory cells as well as cancer cells which express those antigens and thus tip the balance towards an inflammatory and/or immune permissive tumor microenvironment. Additionally, combination with checkpoint inhibition may further amplify this anti-tumor immunostimulatory effect, resulting in superior clinical outcomes. Methods: The primary objective of this first in human, open label Phase 1/2 study is to assess safety and tolerability, with secondary objectives to measure T cell profile changes and initial anti-tumor activity. Arm 1a entails dose escalation of mRNA-4359 monotherapy with dose levels guided by a modified continual reassessment method in participants with locally advanced/metastatic cancers, including cutaneous melanoma, non-small cell lung cancer (NSCLC), non-muscle invasive bladder cancer, head/ neck squamous cell carcinoma, microsatellite stable colorectal cancer, basal cell carcinoma or triple negative breast cancer. Arm 1b will be dose confirmatory and will run concurrently with a pharmacodynamic arm; both will assess mRNA-4359 in combination with pembrolizumab in patients with primary/secondary checkpoint inhibitor refractory locally advanced/metastatic melanoma or NSCLC. The totality of available data from these arms will be used to support determination of a recommended phase 2 dose. Arm 2 includes two single arm expansion cohorts evaluating mRNA-4359 in combination with pembrolizumab therapy in patients who have not received any prior therapy for their cancer in this setting of locally advanced/metastatic melanoma (Cohort 1) or locally advanced/metastatic NSCLC with PD-L1 TPS of ≥ 1% (Cohort 2). Study enrollment into Arm 1a has commenced in the United States and Australia with plans to open sites in Europe later in 2023. Clinical trial information: NCT05533697 .

Risk of inpatient and emergency department visits among lung cancer patients receiving immunotherapies as first line treatment: Findings from a linked population dataset.

e18817 Background: Immunotherapy harnesses cancer patients’ immune systems to eradicate cancer cells, and has become the standard of care as first line or combination therapy in advanced lung cancer. While immunotherapy is more tolerable than other treatments such as chemotherapy, a minority of patients experience toxicities requiring clinical intervention. The aim of this study is to examine the risk of all-cause inpatient and emergency department visits among lung cancer patients diagnosed with cancer receiving immunotherapies as first line treatments using a linked population dataset. Methods: We analyzed administrative data from N = 3,268 lung cancer patients diagnosed between 2013 and 2018 from the Immunotherapy, Palliative and End-of-life Treatment Utilization and Spousal Outcomes (ImmPETUS) cohort, a linked population-based cohort of melanoma, lung, breast, colorectal and bladder cancer patients and their spouses in Utah. Analyses were conducted with multivariable logistic regression models in R and adjusted for sex, age, age at diagnosis, cancer stage, race, ethnicity, marital status, neighborhood education and household income, insurance type, rurality and comorbidity. Results: Among patients diagnosed with lung and bronchus cancers (53.1% male, 46.9% female), 9.5% received immunotherapy as a first line treatment and 57.3% had distant stages at diagnosis. Adjusting for race, ethnicity, neighborhood education and income, and rurality, lung cancer patients who received immunotherapies as a first course of treatment had greater odds of all-cause emergency department encounters (aOR = 1.94, 95% CI = 1.49-2.53, p < 0.001) compared to patients receiving other first line treatments. Non-Medicaid patients and patients with greater comorbidities were less likely to have all-cause emergency department encounters (aOR = 0.66, 95% CI = 0.53-0.82, p < 0.001; 0.92, 95% CI = 0.89-0.96, p < 0.001) and all-cause inpatient visits (aOR = 0.60, 95% CI = 0.46-0.77, p < 0.001; aOR = 0.89, 95% CI = 0.85-0.93, p < 0.001) compared with Medicaid patients and patients with no comorbidities. Nonmarried patients (aOR = 0.71, 95% CI 0.59-0.86, p < 0.001) were less likely to have all-cause inpatient visits compared with those who were married/partnered. Conclusions: Our findings support that patients receiving immunotherapies as first line treatment have increased risk of all-cause emergency department encounters. This analysis of real-world data enabled the examination of downstream healthcare utilization outcomes of immunotherapy cancer patients within Utah, and provides insight into groups at risk for adverse events. Future directions include examining the clinical and social pathways of these disparities, such as immune-related adverse events, access to supportive care, and supports for patient and family decision making.

Initial efficacy and safety of RP1 + nivolumab in patients with anti–PD-1–failed melanoma from the ongoing phase 1/2 IGNYTE study.

9509 Background: Patients (pts) with melanoma who progress on anti–PD-1 therapy (anti–PD-1–failed) have limited treatment options. RP1 is an HSV-1–based oncolytic immunotherapy expressing human GM-CSF and a fusogenic protein (GALV-GP-R−). Here, we present data from the first 75 pts enrolled into the registration-directed (R-D) cohort in anti–PD-1–failed melanoma (target enrollment N = 125) from the phase 1/2 IGNYTE study (NCT03767348). Methods: Pts must have locally advanced or metastatic cutaneous melanoma with ≥1 measurable and injectable tumor (≥1 cm) and confirmed progressive disease (PD) on 2 assessments ≥28 days apart while on ≥8 consecutive weeks of anti–PD-1 ± anti–CTLA-4 therapy, with anti–PD-1 being the last treatment received. Pts on prior adjuvant anti–PD-1 therapy must have had PD confirmed by biopsy while on adjuvant therapy. RP1 is initially given intratumorally at 106 PFU/mL and then every 2 weeks (Q2W) at 107 PFU/mL for ≤8 total cycles (≤10 mL/dose) combined with nivolumab (nivo; cycles 2–8, 240 mg IV); pts then receive nivo alone (240 mg Q2W or 480 mg Q4W IV) for ≤2 years, with the option to reinitiate RP1 if specified criteria are met. Results: A total of 91 pts are included in this analysis (initial melanoma cohort, 16 pts; R-D cohort, 75 pts; data cut: Dec 30, 2022). The overall objective response rate (ORR) was 37.4% (initial cohort, 37.5%; R-D cohort, 37.3%) and 18.7% of pts achieved complete response (CR; Table). The response rates seen were also encouraging when evaluated by prior anti–PD-1 therapy setting and disease stage (Table). Responses were seen in uninjected lesions in most responding patients, including in pts with bulky and visceral disease. The majority of responses were observed in pts with PD-L1–negative tumors at baseline (17 of 52 pts with PD-L1–negative tumors responded, compared to 15 of 26 pts with PD-L1–positive tumors, and 2 of 13 pts for whom PD-L1 status was unknown). 85.3% of responses were ongoing 3.7–36.6 months from initiating therapy. Most treatment-related adverse events (TRAEs) were Grade 1–2 with the most common (>20%) being fatigue, chills, pyrexia, and nausea. Conclusions: The initial data from this expanded cohort show that RP1 + nivo provides durable and clinically meaningful antitumor activity in pts with anti–PD-1–failed melanoma. Responses were observed in both injected and uninjected lesions, including visceral lesions. The combination continues to be well tolerated, with mostly on-target TRAEs. Additional and updated data will be presented. Clinical trial information: NCT03767348 . [Table: see text]

Identification of RPTOR mutation as a novel predictor of efficacious immunotherapy in melanoma.

9524 Background: mTOR pathway is known to influence cancer immunity by metabolism reprogramming. RPTOR (Regulatory Associated Protein of MTOR Complex 1), one of mTOR pathway genes, which is involving in control of mammalian target of mTORC1 activity for regulating cell growth and survival. Whether mutations of RPTOR are associated with clinical efficacy of immune checkpoint inhibitors (ICIs) in melanoma is still ambiguous. Methods: In discovery cohort, we retrospective analyzed the genomic data of 418 melanoma samples which derived from seven immunotherapy studies ( http://www.cbioportal.org/ ) to evaluate the relationship between RPTOR mutation status and efficacy of immunotherapy. Then in validation cohort, the predictive value of RPTOR mutation was confirmed in 320 melanomas from MSKCC cohort (http://www.cbioportal.org/). TMB was calculated as the total count of nonsynonymous mutations in coding sequence. We used the CIBERSORT to evaluate the 22 types immune cell infiltration status in TCGA melanoma cohort. Results: The TMB level of RPTOR-mutant patients was higher than RPTOR-wildtype patients in both discovery (Median [IQR]: 43.11[23.76-140.15] vs. 6.13[2.07-13.66], P < 0.001) and validation (Median [IQR]: 37.38[20.17-84.95] vs. 8.85[3.35-21.07], P < 0.001) cohort. In discovery cohort, compared to RPTOR-wildtype patients, the RPTOR-mutant patients achieved prolonged OS (median OS: not reach, NR vs 22.7 months, HR (95%CI): 0.47(0.22-0.99), P = 0.043). This result was confirmed in validation cohort (median OS: NR vs. 42; HR (95%CI): 0.34 (0.11-1.0); P = 0.049). According to analysis of immune cell infiltration status, the mechanism of the predictive values of RPTOR mutations to ICI efficacy may be activated CD4 memory T cell more abundant in RPTOR-mutant tumors. Conclusions: RPTOR mutation is associated with higher TMB in ICI-treated melanoma patients. Survival analysis shows RPTOR mutation have a good link with longer OS after immunotherapy. These findings indicate that RPTOR mutation may serve as a potential predictive biomarker for ICIs in melanoma.

Predicting the immunotherapy response based on molecular subtypes of pan-immune signatures in gastrointestinal stromal tumor.

e23512 Background: Gastrointestinal stromal tumor (GIST) is the most common sarcoma, often originate in the stomach or the small intestine. Although the application of imatinib has brought a breakthrough in the clinical treatment of GIST, not all GIST patients are effective, and most GIST patients who receive imatinib sensitivity will develop drug resistance and eventually malignant progression. The tumor microenvironment (TME) is a key mediator of cancer progression and treatment outcome, and plays an important role in predicting cancer prognosis and treatment response. This study aims to investigate the role of TME in the treatment of GIST and the response to immunotherapy. Methods: Raw microarray data of 199 GIST patients were downloaded from GEO, including 159 KIT-mutant, 21 PDGFRA-mutant and 19 WT. All affymetrix datasets were re-normalized using the gcRMA package with default parameters. We integrated 275 TME and malignant signaling pathways related signatures from different database and previous researches, including CIBERSORT, MCP-counter, TIMER, and others. Fisher exact test's was used to identify signatures that differential between KIT-mutant, PDGFRA-mutant, and WT (p < 0.05), and 85 signatures were finally obtained. To classify the molecular profiles, the expression patterns were assessed in all 199 GIST patients using unsupervised clustering based on their ssGSEA scores, and can be clustered into three distinct microenvironments. Results: Using GSEA with all TME signatures genes ranked by the log2(fold change) between the threee clustes, we found that gene sets were considered immune favorable in cluster A, including gene sets related to activated CD8+ T cells (p = 0.0003)and activated CD4 T cell signaling pathway (p = 0.009). Cluster B enriched to the epithelial mesenchymal transformation pathway (p = 0.04) and TGFb signaling pathway (p = 0.003), cluster C enriched into DNA-repair pathway (p = 0.02). In an independent skin cutaneous melanoma cohorts (n = 86) treated with anti-PD-1 therapy, patients were classified into three molecular clusters, which significantly corrleated with response to ipilimumab (p = 0.007). The percentage of responders to anti-PD-1 therapy in cluster A was 75% in contrast to only 10% in cluster B. The three molecular clusters discern a potential responder versus non-responder (AUC = 0.87; p = 0.0015), with essentially a 80% chance of correctly predicting the response, which supporting the utilization of the classification method. Conclusions: In this study, the immuno-infiltrating landscape was characterized based on pan-immune signatures using transcriptomic profile in GIST. The molecular subtypes derived from pan-immune signatures have the potential to predict the efficacy of immunotherapy.

31-Gene Expression Profile Testing in Cutaneous Melanoma and Survival Outcomes in a Population-Based Analysis: A SEER Collaboration.

The DecisionDx-Melanoma 31-gene expression profile (31-GEP) test is validated to classify cutaneous malignant melanoma (CM) patient risk of recurrence, metastasis, or death as low (class 1A), intermediate (class 1B/2A), or high (class 2B). This study aimed to examine the effect of 31-GEP testing on survival outcomes and confirm the prognostic ability of the 31-GEP at the population level. Patients with stage I-III CM with a clinical 31-GEP result between 2016 and 2018 were linked to data from 17 SEER registries (n = 4,687) following registries' operation procedures for linkages. Melanoma-specific survival (MSS) and overall survival (OS) differences by 31-GEP risk category were examined using Kaplan-Meier analysis and the log-rank test. Crude and adjusted hazard ratios (HRs) were calculated using Cox regression model to evaluate variables associated with survival. 31-GEP tested patients were propensity score-matched to a cohort of non-31-GEP tested patients from the SEER database. Robustness of the effect of 31-GEP testing was assessed using resampling. Patients with a 31-GEP class 1A result had higher 3-year MSS and OS than patients with a class 1B/2A or class 2B result (MSS: 99.7% v 97.1% v 89.6%, P < .001; OS: 96.6% v 90.2% v 79.4%, P < .001). A class 2B result was an independent predictor of MSS (HR, 7.00; 95% CI, 2.70 to 18.00) and OS (HR, 2.39; 95% CI, 1.54 to 3.70). 31-GEP testing was associated with a 29% lower MSS mortality (HR, 0.71; 95% CI, 0.53 to 0.94) and 17% lower overall mortality (HR, 0.83; 95% CI, 0.70 to 0.99) relative to untested patients. In a population-based, clinically tested melanoma cohort, the 31-GEP stratified patients by their risk of dying from melanoma.

Long-term follow-up of anti-PD-1 naïve patients with metastatic melanoma treated with IDO/PD-L1 targeting peptide vaccine and nivolumab

BackgroundWe have previously published initial efficacy of the indoleamine 2,3-dioxygenase (IDO)/anti-programmed death ligand 1 (PD-L1) vaccine in combination with nivolumab in 30 anti-PD-1 therapy naïve patients with metastatic melanoma (cohort...

Multi-organ landscape of therapy-resistant melanoma

Metastasis and failure of present-day therapies represent the most common causes of mortality in patients with cutaneous melanoma. To identify the underlying genetic and transcriptomic landscapes, in this study we analyzed multi-organ metastases and tumor-adjacent tissues from 11 rapid autopsies after treatment with MAPK inhibitor (MAPKi) and/or immune checkpoint blockade (ICB) and death due to acquired resistance. Either treatment elicits shared genetic alterations that suggest immune-evasive, cross-therapy resistance mechanisms. Large, non-clustered deletions, inversions and inter-chromosomal translocations dominate rearrangements. Analyzing data from separate melanoma cohorts including 345 therapy-naive patients and 35 patients with patient-matched pre-treatment and post-acquired resistance tumor samples, we performed cross-cohort analyses to identify MAPKi and ICB as respective contributors to gene amplifications and deletions enriched in autopsy versus therapy-naive tumors. In the autopsy cohort, private/late mutations and structural variants display shifted mutational and rearrangement signatures, with MAPKi specifically selecting for signatures of defective homologous-recombination, mismatch and base-excision repair. Transcriptomic signatures and crosstalks with tumor-adjacent macroenvironments nominated organ-specific adaptive pathways. An immune-desert, CD8+-macrophage-biased archetype, T-cell exhaustion and type-2 immunity characterized the immune contexture. This multi-organ analysis of therapy-resistant melanoma presents preliminary insights with potential to improve therapeutic strategies.

Chromosome instability-associated prognostic signature and cluster investigation for cutaneous melanoma cases.

Chromosomal instability (CIN) is closely associated to the early detection of several clinical tumours. In this study, the authors first established a novel prognostic model of melanoma using the hub genes of CIN, based on the datasets of The cancer genome atlas-skin cutaneous melanoma (TCGA-SKCM) and GSE65904 cohorts. Based on the risk scores of our model, the disease-specific survival (DSS) prognosis was worse in the high-risk group. Combining risk score, stage, age, ulceration, and clark factors, a Nomogram was generated to predict 1, 3, 5-year survival rates, which indicated a good clinical validity. Our finding also showed a correlation between high/low risk and tumour infiltration levels of 'activated CD8 T cells' and 'effector memory CD8 T cells'. Moreover, the authors first performed a CIN-based tumour clustering analysis using TCGA-SKCM cases, and identified two melanoma clusters, which exhibit the distinct DSS prognosis and the tumour-infiltrating levels of CD8 T cells. Taken together, a promising CIN-related prognostic signature and clustering for melanoma cases were first established in our study.

Abstract 5472: Utilizing response in immune checkpoint inhibitor treated cohorts improves clinical applicability of neoantigen immunogenicity predictions

Abstract Introduction: Neoantigen-based biomarkers have improved predictions of response to immune checkpoint blockade (ICB) therapy, highlighting the importance of accurate prediction of immunogenic neoantigen candidates. A challenge in developing robust immunogenicity prediction models is limited availability of sequencing-associated immunogenicity data for evaluating methods due to the complexity of generating such datasets. We propose a novel approach to optimize prediction models of immunogenic neoantigens using a meta-analysis framework based on multiple ICB cohorts. Methods: To build on the 110 mono-allelic immunopeptidomics-derived SHERPA® MHC binding prediction framework, we engineered T-cell recognition features on two datasets: peptide-centric data aggregated by Schmidt et al. and patient-specific exome and transcriptome sequencing data from the TESLA consortium. We developed two-tiered models based on the feature landscapes of both datasets to predict peptide-MHC (pMHC) immunogenicity, incorporating features with significant performance gains. We systematically re-processed publicly available DNA and RNA sequencing data from over 500 ICB treated patients spanning 12 different cohorts across five different cancer types with a harmonized bioinformatics pipeline. We then evaluated the performance of each model consisting of a unique combination of immunogenic features across the ICB training (N=7) and validation (N=5) cohorts using a meta-analysis framework. Results: We evaluated iterations of SHERPA-Immunogenicity (SI) models using the Schmidt et al. and TESLA datasets, resulting in a range of performance metrics (area under the precision recall curves of 0.74-0.84 and positive predictive values of 0.32-0.54). After aggregating pMHC predictions into patient-specific scores based on the most immunogenic peptide present (SHERPA-Immunogenicity Maximum - SIM) or the quantity of immunogenic peptides identified (SHERPA-Immunogenicity Burden - SIB), we observed that responders had higher SIM and SIB scores compared to non-responders across the melanoma training cohorts. We found SIM scores outperformed SIB scores, suggesting the degree of epitope immunogenicity may be a critical factor in predicting response. The model with the most significant meta p-value for ICB response in melanoma cohorts (OR=2.43, p=0.006) also predicted overall survival in 3/5 melanoma cohorts (p&amp;lt0.05). Conclusions: We developed a novel framework to predict neoantigen immunogenicity utilizing meta-analysis of ICB cohorts to overcome dataset limitations and gain prediction performance confidence. We look forward to supporting personalized cancer vaccine development with our pMHC immunogenicity predictions and applying our predictive biomarker on additional ICB cohorts. Citation Format: Hima Anbunathan, Neeraja Ravi, Rachel Marty Pyke, Steven Dea, Richard O. Chen, Sean Michael Boyle. Utilizing response in immune checkpoint inhibitor treated cohorts improves clinical applicability of neoantigen immunogenicity predictions. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5472.