Abstract Extrachromosomal DNA (ecDNA) drives oncogene amplification, transcriptional deregulation, and therapeutic resistance in cancer, but its prevalence and impact in melanoma remain unclear. We analyzed 470 TCGA-SKCM samples with whole-genome (n = 223), whole-exome (n = 247), and RNA sequencing (n = 469). Tumors were classified as BRAF/NRAS/NF1-mutant (BNN, n = 396) or triple wild-type (TWT, n = 74). ecDNA detection was performed using AmpliconArchitect (AA) and Gene-level Circular Amplicon Prediction (GCAP). Multi-omic analyses assessed transcriptional, immunologic, and clinical correlates. ecDNA was detected in 133 tumors (28%; 47 by AA, 133 by GCAP, 39 overlapping), with higher prevalence in TWT tumors (51%) than BNN tumors (26%; χ2 = 17.88, p = 2.4 × 10−5). Frequently amplified ecDNA genes included MDM2, CDK4, CCND1, BIRC2/3, PAK1, GAB2, and RSF1, implicating proliferation, apoptosis evasion, and chromatin regulation. In an effort to assess putative functional impact, we performed various transcriptomic analyses which identified upregulation of amplified oncogenes (GAB2, MDM2, RSF1, CCND1, PAK1). In addition, gene set enrichment analyses with MutSigDB (against Hallmark genes) shows strong enrichment of pathways associated with enhanced cell proliferation, such as MYC and E2F targets in ecDNA+ tumors. In addition, cell deconvolution methods reveal immune cell composition varies across subtypes, highlighting potential unique immunomodulatory effects. Survival analysis indicated worse overall survival in ecDNA+ tumors (p = 0.016), driven by TWT cases (p = 0.0048). ecDNA is prevalent in melanoma, particularly in TWT tumors, where it promotes oncogene amplification, immunomodulatory reprogramming, and poor prognosis. These results highlight ecDNA as a potential biomarker for stratification and targetable vulnerability in TWT melanoma. Citation Format: Sharadha Sakthikumar, Bryce Turner, Jeffrey Trent, ALEKSANDAR SEKULIC. Integrative multi-omic analysis reveals subtype-specific impact of extrachromosomal DNA in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1994.

Cutaneous squamous cell carcinoma is one of the most common cancers in humans and kills as many people annually as melanoma. The understanding of the transcriptional changes with respect to high-risk clinical/histopathologic features and outcome is poor. In this study, we examine stage-matched, outcome-differentiated cutaneous squamous cell carcinoma using whole-exome and transcriptome sequencing. Exome analysis identified key driver mutations, including TP53, CDKN2A, NOTCH1, SHC4, MIIP, CNOT1, C17orf66, LPHN2, and TTC16, and pathway enrichment of driver mutations in replicative senescence, cellular response to UV, cell-cell adhesion, and cell cycle. Transcriptomic analysis identified pathway enrichment of immune signaling/inflammation, cell-cycle pathways, extracellular matrix function, and chromatin function. Integrative analysis identified 183 critical genes in carcinogenesis and were used to develop a gene expression panel for outcome. Three outcome-related gene clusters included those involved in keratinization, cell division, and metabolism. We found 16 genes whose expressions may be associated with metastasis (risk score ≥ 9 Met and risk score < 9 NoMet) with an area under the curve of 97.1%, sensitivity of 95.5%, specificity of 85.7%, and overall accuracy of 90%. Eleven genes were chosen to generate the risk score for overall survival, with an overall survival prediction of 80.8% and each risk gene increasing the risk of death by 2.47 (hazard ratio = 2.47, P < .001).

BACKGROUND:The Fitzpatrick skin type (FST) is commonly used in clinical settings to stratify melanoma risk across different skin types. However, it is subjective and does not capture intra-type variability in risk. These limitations are particularly evident among lighter-skinned individuals, who constitute the majority of those with European ancestry and generally have a higher melanoma risk. METHODS:We assessed whether supplementing FST with validated polygenic scores for skin color (PGSSC) and melanoma (PGSM) improves risk stratification in 479,607 UK Biobank participants. Melanoma prevalence in individuals by FST, PGSSC, and PGSM was estimated, and their differences were tested, adjusting for age, gender, and genetic background (top 10 principal components). RESULTS:FST distribution was as follows: Very fair (7.77%), fair (68.06%), light olive (18.56%), olive (1.87%), brown (2.96%), and black (0.78%), with corresponding melanoma prevalence of 1.94%, 1.31%, 0.70%, 0.45%, 0.15%, and 0% (P-trend < 0.001). Notably, PGSSC significantly differentiated melanoma prevalence within each lighter-skinned type (very fair, fair, and light olive), P-trend < 0.001. Among lighter-skinned individuals, the melanoma prevalence ranged widely across the lowest to highest deciles of PGSSC (0.62%-2.12%). In addition, PGSM also differentiated risk, with prevalence ranging from 0.39%-2.08% between low- and high-risk groups. Among darker skin types (olive and brown), only PGSM significantly differentiated melanoma risk, with prevalence ranging from 0.13% to 0.80% between low- and high-risk groups. CONCLUSIONS:Integrating PGS of skin color and melanoma with the conventional FST classification significantly improves melanoma risk stratification and addresses key limitations of the FST, which, while widely used, lacks sensitivity to intra-type risk variation.

AbstractBackgroundA phase 2 cemiplimab study (NCT03132636) demonstrated a 24.1% objective response rate in patients diagnosed with metastatic basal cell carcinoma (mBCC) who were not candidates for continued hedgehog inhibitor (HHI) therapy due to intolerance to previous HHI therapy, disease progression while receiving HHI therapy, or having not better than stable disease on HHI therapy after 9 months. Here, health‐related quality of life (QoL) for this patient population is reported.MethodsAdult patients with mBCC were treated with intravenous cemiplimab at a dose of 350 mg every 3 weeks for 5 treatment cycles of 9 weeks/cycle then 4 treatment cycles of 12 weeks/cycle. Patients completed the European Organisation for Research and Treatment of Cancer Quality of Life‐Core 30 (QLQ‐C30) and Skindex‐16 questionnaires at baseline and Day 1 of each cycle. Across Cycles 2 to 9, the overall change from baseline was analyzed using a mixed model with repeated measures. Responder analyses determined clinically meaningful improvement or deterioration (changes ≥10 points) or maintenance across all scales.ResultsPatients reported low symptom burden and moderate‐to‐high functioning at baseline. Maintenance for QLQ‐C30 global health status (GHS)/QoL and across all functioning and symptom scales was indicated by overall mean changes from baseline. Clinically meaningful improvement or maintenance was reported at Cycle 2 for GHS/QoL (77%), functioning scales (77% to 86%), and symptom scales (70% to 93%), with similar proportions of improvement or maintenance at Cycles 6 and 9, excluding fatigue. On the Skindex‐16, clinically meaningful improvement or maintenance was reported across the emotional, symptom, and functional subscales, in 76%–88% of patients at Cycle 2, which were generally maintained at Cycles 6 and 9. Overall mean changes from baseline showed maintenance across these subscales.ConclusionsThe majority of patients treated with cemiplimab reported improvement or maintenance in GHS/QoL and functioning while maintaining a low symptom burden.

The NCCN Guidelines for Merkel Cell Carcinoma (MCC) provide recommendations for diagnostic workup, clinical stage, and treatment options for patients. The panel meets annually to discuss updates to the guidelines based on comments from expert review from panel members, institutional review, as well as submissions from within NCCN and external organizations. These NCCN Guidelines Insights focus on the introduction of a new page for locally advanced disease in the setting of clinical node negative status, entitled "Clinical N0 Disease, Locally Advanced MCC." This new algorithm page addresses locally advanced disease, and the panel clarifies the meaning behind the term "nonsurgical" by further defining locally advanced disease. In addition, the guideline includes the management of in-transit disease and updates to the systemic therapy options.

Drug repurposing is an attractive strategy for therapy development, particularly in rare diseases where traditional drug development approaches may be challenging owing to high cost and small numbers of patients. In this study, we used a drug identification and repurposing pipeline to identify candidate targetable drivers of disease and corresponding therapies through application of causal reasoning using a combination of openaccess resources and transcriptomics data. We optimized our approach on psoriasis as a disease model, demonstrating the ability to identify known and, to date, unrecognized molecular drivers of psoriasis and link them to current and emerging therapies. Application of our approach to a cohort of tissue samples of necrobiosis lipoidica (an unrelated; rare; and, to date, molecularly poorly characterized cutaneous inflammatory disorder) identified a unique set of upstream regulators, particularly highlighting the role of IFNG and the Jak-signal transducer and activator of transcription pathway as a likely driver of disease pathogenesis and linked it to Jak inhibitors as potential therapy. Analysis of an independent cohort of necrobiosis lipoidica samples validated these findings, with the overall agreement of drug-matched upstream regulators above 96%. These data highlight the utility of our approach in rare diseases and offer an opportunity for drug discovery in other rare diseases in dermatology and beyond.

Background• Patients with metastatic basal cell carcinoma (mBCC) who are not candidates for surgery or radiation therapy are generally treated with hedgehog signaling pathway inhibitors (HHIs). 1 -However, intolerance and resistance to HHIs are common. 1• Cemiplimab-rwlc is approved in the United States for patients with mBCC and locally advanced BCC (laBCC) following HHI treatment or for whom HHIs are not appropriate. 2• In a Phase 2 clinical trial (NCT03132636), cemiplimab demonstrated an objective response rate of 24.1% (95% CI: 13.5-37.6%) in patients with mBCC who progressed on or were intolerant to HHIs. 3• Efficacy and health-related quality of life (HRQoL) data for patients with laBCC were previously reported. 4 Objective• To evaluate HRQoL in patients with mBCC who were treated with cemiplimab in the phase 2 clinical trial (NCT03132636). Methods• In this phase 2, non-randomized, multicenter, pivotal trial of cemiplimab, adults (≥18 years old) with mBCC and Eastern Cooperative Oncology Group performance status ≤1 (N=54) received cemiplimab 350 mg intravenous every 3 weeks for up to 9 treatment cycles.-mBCC was based on histologic confirmation of distant BCC metastases to lung, liver, bone, or lymph node, and included patients with both nodal and distant metastatic disease.• At baseline and Day 1 of each treatment cycle, patients were administered the European Organisation forResearch and Treatment of Cancer Quality of Life-Core 30 (EORTC QLQ-C30) 6 and Skindex-16 7 questionnaires (Table 1).-Follow-up assessment was conducted 28-42 days after the last study treatment administration if a patient discontinued early.• Analyses were conducted on the full analysis set, which consisted of all enrolled patients who were deemed eligible for the study.• Mixed-model repeated-measures (MMRM) analyses were used to estimate overall least-squares (LS) mean change from baseline and 95% CI across Cycles 2-9 on all scales for patients with baseline and ≥1 post-baseline value. Conclusions• Results of this pivotal clinical trial of cemiplimab showed that, in addition to providing clinically meaningful antitumour activity and durable responses in patients with mBCC, 3 patient-reported HRQoL was maintained during the study.-From baseline to Cycle 9, most patients treated with cemiplimab reported:• Maintenance or improvement in QLQ-C30 GHS/QoL and functioning while maintaining a low symptom burden.• Maintenance across all 3 subscales on the Skindex-16.

9566 Background: Cemiplimab-rwlc is the first immunotherapy to receive approval in the US, fully for pts with laBCC and accelerated for metastatic BCC, post hedgehog inhibitors or for whom hedgehog inhibitors are not appropriate. Cemiplimab resulted in clinically meaningful anti-tumor activity in pts with laBCC who progressed on or were intolerant to hedgehog inhibitor therapy (NCT03132636). This analysis evaluated HRQoL in these pts. Methods: Adults with laBCC and ECOG performance status ≤1 (n=84) received IV cemiplimab 350 mg Q3W for up to 9 treatment cycles. At baseline (BL) and day 1 of each cycle (C), pts completed EORTC QLQ-C30 and SKINDEX-16 questionnaires that assess Global Health Status (GHS)/QoL, functioning, and BCC-related symptoms. Mixed-effects repeated measures (MMRM) models were used to estimate least squares (LS) mean (standard error [SE]) change from BL during treatment (i.e., across C2 to C9); changes ≥|10| points were considered clinically meaningful. Responder analyses were conducted in pts with non-missing data from BL to determine the proportions with clinically meaningful improvement or deterioration, or stability on QLQ-C30 and SKINDEX-16 at C2 and C9; a 10-point threshold was considered meaningful for both instruments. Results: BL scores showed moderate to high levels of functioning and low symptom burden. In MMRM models, overall changes from BL on QLQ-C30 indicated stability for GHS/QoL and all scales except for clinically meaningful worsening of fatigue (LS mean [SE] change 12.5 [3.9]; P<.05). In responder analysis, the majority of pts reported clinically meaningful improvement or stability at C2 and C9 on all QLQ-C30 functioning scales and the key symptom of pain but not fatigue (Table). On SKINDEX-16, MMRM models showed clinically meaningful improvement on the emotional subscale (LS mean [SE] change –13.2 [3.9]; P<.05) and stability on the symptom and functional subscales. Responder analysis showed clinically meaningful improvements or stability across the SKINDEX-16 subscales in approximately 80% of pts at C2, and 70–80% of pts at C9. Conclusions: In laBCC pts treated with cemiplimab, the majority reported clinically meaningful improvement or stability in GHS/QoL and functional status while maintaining a low symptom burden except for fatigue. Clinical trial information: NCT03132636. [Table: see text]

Cutaneous squamous cell carcinoma (cSCC) is one of the most common cancers in humans and kills as many people annually as melanoma. The mutational and transcriptional landscape of cSCC has identified driver mutations associated with disease progression as well as key pathway activation in the progression of pre-cancerous lesions. The understanding of the transcriptional changes with respect to high-risk clinical/histopathological features and outcome is poor. Here, we examine stage-matched, outcome-differentiated cSCC and associated clinicopathologic risk factors using whole exome and transcriptome sequencing on matched samples. Exome analysis identified key driver mutations including TP53, CDKN2A, NOTCH1, SHC4, MIIP, CNOT1, C17orf66, LPHN22, and TTC16 and pathway enrichment of driver mutations in replicative senescence, cellular response to UV, cell-cell adhesion, and cell cycle. Transcriptomic analysis identified pathway enrichment of immune signaling/inflammation, cell-cycle pathways, extracellular matrix function, and chromatin function. Our integrative analysis identified 183 critical genes in carcinogenesis and were used to develop a gene expression panel (GEP) model for cSCC. Three outcome-related gene clusters included those involved in keratinization, cell division, and metabolism. We found 16 genes were predictive of metastasis (Risk score ≥ 9 Met & Risk score < 9 NoMet). The Risk score has an AUC of 97.1% (95% CI: 93.5% - 100%), sensitivity 95.5%, specificity 85.7%, and overall accuracy of 90%. Eleven genes were chosen to generate the risk score for Overall Survival (OS). The Harrell's C-statistic to predict OS is 80.8%. With each risk score increase, the risk of death increases by 2.47 (HR: 2.47, 95% CI: 1.64-3.74; p<0.001) after adjusting for age, immunosuppressant use, and metastasis status.### Competing Interest StatementThe authors have declared no competing interest.### Funding StatementThis study was funded by: Dermatology Foundation Medical Dermatology Career Development Award, Mayo Clinic Investment for Extramural Grants Awards Program, Mayo Clinic Comprehensive Cancer Center Arnold and Kit Palmer Career Development Award in Cancer Research, and Mayo Clinic Cancer Center Desert Mountain Cares Program. ### Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:The Mayo Clinic Institutional Review Board IRB 21-012833 gave ethical approval of this work.I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.YesAll data produced in the present study are available upon reasonable request to the authors.

Background: Anastomotic leak rates after colorectal surgery remain high. In most left-sided colon and rectal resection surgeries, a circular stapler is utilized to create the primary bowel anastomosis. However, it remains unclear whether a relationship between circular stapler technology and anastomotic leak in left-sided colorectal surgery exists. Methods: A post-hoc analysis was conducted using a prospectively collected data set of patients from the 2017 European Society of Coloproctology snapshot audit who underwent elective left-sided resection (left hemicolectomy, sigmoid colectomy, or rectal resection) with a manual circular stapled anastomosis. Rates of anastomotic leak and unplanned intensive care unit stay in association with manual circular stapling were assessed. Patient-, disease-, geographical-, and surgeon-related factors as well as stapler brand were explored using multivariable regression models to identify predictors of adverse outcomes. Results: Across 3305 procedures, 8.0% of patients had an anastomotic leak and 2.1% had an unplanned intensive care unit stay. Independent predictors of anastomotic leak were male sex, minimal-access surgery converted to open surgery, and anastomosis height C11 (lower third rectum) (all P < 0.050). Independent predictors of unplanned intensive care unit stay were minimal-access surgery converted to open surgery and American Society of Anesthesiologists grade IV (all P < 0.050). Stapler device brand was not a predictor of anastomotic leak or unplanned intensive care unit stay in multivariable regression analysis. There were no differences in rates of anastomotic leak and unplanned intensive care unit stay according to stapler head diameter, geographical region, or surgeon experience. Conclusion: In patients undergoing left-sided bowel anastomosis, choice of manual circular stapler, in terms of manufacturer or head diameter, is not associated with rates of anastomotic leak and unplanned intensive care unit stay.

California is one of the major uncertainty hotspots for climate change, as climate models have historically been split between projecting wetter and drier future conditions over the region. We analysed the future (mid-century and end-century) projections of California's winter precipitation changes from the latest Coupled Model Intercomparison Project Phase 6 (CMIP6), and studied its respective model agreement in comparison to the previous CMIP5 projections. Over northern California more than two thirds of the models in each ensemble agree on wetter future conditions. However, over southern California both ensembles show highly uncertain precipitation changes, with model projections almost equally divided between wetter or drier conditions. Projected end-century precipitation changes range from -30% to +70% in CMIP5 and -20% to +80% in CMIP6. The CMIP6 ensemble mean changes are generally wetter and show larger model disagreement compared to CMIP5. Distribution of year-to-year precipitation indicates more extremely wet or dry years over southern California in CMIP6 compared to CMIP5, with some models suggesting that the five wettest years account for as much as similar to 55% of the 20-year rainfall, and the five driest for as little as similar to 5%. Dynamically, both ensembles project weakened subsidence over Baja California that is stronger in CMIP6 than in CMIP5, in line with the wetter mean conditions in CMIP6. In the western tropical Pacific we find strengthening of the Hadley circulation in CMIP6 that is not seen in CMIP5, and more El Nino than La Nina conditions in the equatorial Pacific. More CMIP6 models also project an increase in ENSO events compared to CMIP5, and a stronger impact of ENSO on California's precipitation is found in CMIP6 than in CMIP5. These factors also contribute to larger model disagreement and more extremely wet or dry years over southern California in CMIP6.

Necrobiosis lipoidica (NL) is a rare granulomatous disease. There are few effective treatments for NL. We sought to investigate the efficacy and safety of the Jak1/2 inhibitor, ruxolitnib, in the treatment of NL and identify the biomarkers associated with the disease and treatment response. We conducted an open-label, phase 2 study of ruxolitinib in 12 patients with NL. We performed transcriptomic analysis of tissue samples before and after treatment. At week 12, the mean NL lesion score decreased by 58.2% (SD = 28.7%, P = .003). Transcriptomic analysis demonstrated enrichment of type I and type II IFN pathways in baseline disease. Weighted gene coexpression network analysis demonstrated post-treatment changes in IFN pathways with key hub genes IFNG and signal transducer and activator of transcription 1 gene STAT1. Limitations include small sample size and a study group limited to patients with <10% body surface area. In conclusion, ruxolitinib is an effective treatment for NL and targets the key pathogenic mediators of the disease.

Basal cell carcinoma (BCC) is the most common form of skin cancer in the United States. Due to the high frequency, BCC occurrences are not typically recorded, and annual rates of incidence can only be estimated. Current estimated rates are 2 million Americans affected annually, and this continues to rise. Exposure to radiation, from either sunlight or previous medical therapy, is a key player in BCC development. BCC is not as aggressive as other skin cancers because it is less likely to metastasize. However, surgery and radiation are prevalent treatment options, therefore disfigurement and limitation of function are significant considerations. The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) outline an updated risk stratification and treatment options available for BCC.

List of validated siRNA screen hits.

List of high-throughput drug screen hits.

Supplemental Table 5. SCCOHT-1 ABPP data; Supplemental Table 6. BIN67 ABPP data.

Summary of hits from ponatinib analyses and target expression.

Supplemental Materials and Methods

Background: Necrobiosis lipoidica (NL) is a rare, chronic granulomatous disease of unclear etiology that is often associated with diabetes mellitus. No consistently effective treatments for NL exist in the current landscape. Ruxolitinib is a Janus kinase (JAK)-1/2 inhibitor that targets the JAK-signal transducer and activator of transcription proteins (STAT) pathway. Given that constitutive activation of the JAK-STAT pathway is a feature of granulomatous diseases, JAK inhibitors show promise as a novel treatment option for NL. Twelve patients with clinical and histopathologic diagnosis of NL were enrolled in our open-label, single-arm clinical trial. Topical ruxolitinib was applied twice daily for twelve weeks. Pre- and post-treatment biopsies were taken at week 0 and week 4, respectively. We characterized the effects of ruxolitinib in NL using transcriptomic analysis. Comparison of lesional NL and control tissue identified 3,211 upregulated genes in NL. Interferon (IFN) gamma, STAT1, STAT4, STAT5A, IL2, IL6, and tumor necrosis factor (TNF) were elevated at baseline in disease samples, which is in concordance with genes upregulated in other granulomatous diseases including sarcoidosis and granuloma annulare. Type I and II interferon pathways were enriched in NL, and responsive disease demonstrated downregulation of the IFN gamma pathway. In our pilot study, topical ruxolitinib was highly effective with therapeutic response achieved in nine (81.8%) patients as measured by the Physician Global Assessment at week 12. Our findings support the use of topical ruxolitinib as an effective treatment option for NL. Future studies with larger sample size and longer treatment duration are warranted.