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Patients with unresectable dedifferentiated liposarcoma (DDLPS) have poor overall outcomes. Few genomic alterations have been identified with limited therapeutic options.Patients treated at Levine Cancer Institute with DDLPS were identified. Next generation sequencing (NGS), immunohistochemistry (IHC), and fluorescence in situ hybridization (FISH) testing were performed on tumor tissue collected at diagnosis or recurrence/progression. Confirmation of genomic alterations was performed by orthologous methods and correlated with clinical outcomes. Univariate Cox regression was used to identify genomic alterations associated with clinical outcomes.Thirty-eight DDLPS patients with adequate tissue for genomic profiling and clinical data were identified. Patient characteristics included: median age at diagnosis (66 years), race (84.2% Caucasian), and median follow-up time for the entire cohort was 12.1 years with a range from approximately 3.5 months to 14.1 years. Genes involved in cell cycle regulation, including MDM2 (74%) CDK4 (65%), and CDKN2A (23%), were amplified along with WNT/Notch pathway markers: HMGA2, LGR5, MCL1, and CALR (19%-29%). While common gene mutations were identified, PDE4DIP and FOXO3 were also mutated in 47% and 34% of patients, respectively, neither of which have been previously reported. FOXO3 was associated with improved overall survival (OS) (HR 0.37; p = 0.043) along with MAML2 (HR 0.30; p = 0.040). Mutations that portended worse prognosis included RECQL4 (disease-specific survival HR 4.67; p = 0.007), MN1 (OS HR = 3.38; p = 0.013), NOTCH1 (OS HR 2.28, p = 0.086), and CNTRL (OS HR 2.42; p = 0.090).This is one of the largest retrospective reports analyzing genomic aberrations in relation to clinical outcomes for patients with DDLPS. Our results suggest therapies targeting abnormalities should be explored and confirmation of prognostic markers is needed. Dedifferentiated liposarcoma is one of the most common subtypes of soft tissue sarcoma yet little is known of its molecular aberrations and possible impact on outcomes. The work presented here is an evaluation of genetic abnormalities among a population of patients with dedifferentiated liposarcoma and how they corresponded with survival and risk of metastases. There were notable gene mutations and amplifications commonly found, some of which had interesting prognostic implications.

Circulating tumor DNA; Non–small cell lung cancer; Tumor biomarker ADN tumoral circulante; Cáncer de pulmón de células no pequeñas; Biomarcador tumoral ADN tumoral circulant; Càncer de pulmó de cèl·lules no petites; Biomarcador tumoral Introduction Brigatinib is a potent next-generation ALK tyrosine kinase inhibitor approved for treatment-naive and crizotinib-refractory advanced ALK-positive (ALK+) NSCLC. We evaluated brigatinib after other next-generation ALK tyrosine kinase inhibitors. Methods In this single-arm, phase 2, ALK in Lung Cancer Trial of brigAtinib-2 (NCT03535740), patients with advanced ALK+ NSCLC whose disease progressed on alectinib or ceritinib received brigatinib 180 mg once daily (after 7-d 90-mg lead-in). Primary end point was independent review committee (IRC)-assessed overall response rate (ORR). Circulating tumor DNA (ctDNA) was analyzed. Results Among 103 patients (data cutoff: September 30, 2020; median follow-up [range]: 10.8 [0.5–17.7] mo), confirmed IRC-ORR was 26.2% (95% confidence interval [CI]: 18.0–35.8), median duration of response, 6.3 months (95% CI: 5.6–not reached), and median progression-free survival (mPFS), 3.8 months (95% CI: 3.5–5.8). mPFS was 1.9 months (95% CI: 1.8–3.7) in patients with ctDNA-detectable baseline ALK fusion (n = 64). Among 86 patients who progressed on alectinib, IRC-ORR was 29.1% (95% CI: 19.8–39.9); mPFS was 3.8 months (95% CI: 1.9–5.4). Resistance mutations were present in 33.3% (26 of 78) of baseline ctDNA; 54% (14 of 26) of mutations were G1202R; 52% (33 of 64) of patients with detectable ALK fusion had EML4-ALK variant 3. Most common all-grade treatment-related adverse events were increased creatine phosphokinase (32%) and diarrhea (27%). The mean dose intensity of brigatinib (180 mg once daily) was 85.9%. Conclusions In ALK in Lung Cancer Trial of brigAtinib-2, brigatinib was found to have a limited activity in patients with ALK+ NSCLC post-ceritinib or post-alectinib therapy. mPFS was longer with brigatinib in patients without baseline detectable plasma ALK fusion.

Inflammation in the tumor microenvironment is a complicit and known carcinogenesis driver. Inhibition of IL-1β, one of the most abundant and influential cytokines in the tumor microenvironment, may enhance the efficacy of PD-1. In aIL-1β is a small molecule involved in the spreading of cancer cells and scouting for cells that work against the body’s protective inflammatory response. In a follow-up analysis of the CANTOS study, people with atherosclerosis who received canakinumab, a drug which limits the activity of IL-1β in the body, were diagnosed with lung cancer less often than people who received an inactive substance. Immunotherapy is a treatment that can boost the natural defenses of the immune system, but how well it works varies from patient to patient. Recent efforts aim to understand whether blocking unhealthy inflammation with canakinumab and stimulating the body’s protective system with immunotherapy at the same time could be an efficacious treatment for patients with lung cancer. Currently there are limited data from experiments in cell and animal models; however, data from the ongoing CANOPY-N clinical trial, which is investigating this treatment combination prior to surgery for patients with lung cancer, are expected by the first half of this year.

Rapid advancements in cancer discovery, diagnosis, and treatment options available to patients with cancer have highlighted the need for enhancements in clinical trial design. The drug development process is costly, with more than 80% of trials failing to reach recruitment targets. Historical approaches to trial design are increasingly burdensome and lack real-world application in the intent-to-treat patient population. Equitable access to clinical trials combined with increased availability of real-world data are creating new opportunities for inclusiveness, improved outcomes, and evidence-based advances in therapies that will generate more generalizable data to better inform clinical decision-making. Clinical trials need to be inclusive if lifesaving data are not to be missed and investigational therapies are to be more accessible to a broader patient base. Real-world data can facilitate the conduct of studies that are identifying and understanding where disparities exist and developing new interventions to improve patient care. The clinical trial design process should be a multistakeholder and consensus- and evidence-driven process in which stakeholders are working together across the health care industry to close the care gap and ensure elimination of barriers that prevent equal access to specialized cancer care and advanced therapies available in clinical trials. The patient voice is essential throughout the trial process; however, it is often excluded from the design process. Integrating real-world data as well as ensuring patient involvement in early trial design during drug development can enhance enrollment and retention, leading to greater diversity.

Supplementary Material 3 from Gene Expression Profiling Predicts the Development of Oral Cancer

Supplementary Material 7 from Gene Expression Profiling Predicts the Development of Oral Cancer

XLSX file - 102K, Supplementary table depicting 263 genes comprising a cluster of genes with highest average expression in adjacent airways

PDF file - 6272K, Sweave report depicting complete codes used for microarray analysis and identification of genes differentially expressed by site and time

Perspective on this Article from Biological Activity of Celecoxib in the Bronchial Epithelium of Current and Former Smokers

Related Article from Cotargeting Cyclin D1 Starts a New Chapter in Lung Cancer Prevention and Therapy

PDF file - 125K, Histograms of the p-values for site- and time-dependent differential expression; Site-dependent differential gene expression patterns identified by expression profiling of airways excluding main carinas; Smoothened scatter plot of transformed p-values for site and time effects

DNA promoter methylation of tumor suppressor genes and global DNA hypomethylation are common features of head and neck cancers. Our goal was to identify early DNA methylation changes in oral premalignant lesions (OPL) that may serve as predictive markers of developing oral squamous cell carcinoma (OSCC). Using high-throughput DNA methylation profiles of 24 OPLs, we found that the top 86 genes differentially methylated between patients who did or did not develop OSCC were simultaneously hypermethylated, suggesting that a CpG island methylation phenotype may occur early during OSCC development. The vast majority of the 86 genes were nonmethylated in normal tissues and hypermethylated in OSCC versus normal mucosa. We used pyrosequencing in a validation cohort of 44 patients to evaluate the degree of methylation of AGTR1, FOXI2, and PENK promoters CpG sites that were included in the top 86 genes and of LINE1 repetitive element methylation, a surrogate of global DNA methylation. A methylation index was developed by averaging the percent methylation of AGTR1, FOXI2, and PENK promoters; patients with a high methylation index had a worse oral cancer–free survival (P = 0.0030). On the other hand, patients with low levels of LINE1 methylation had a significantly worse oral cancer–free survival (P = 0.0153). In conclusion, AGTR1, FOXI2, and PENK promoter methylation and LINE1 hypomethylation may be associated with an increased risk of OSCC development in patients with OPLs. Cancer Prev Res; 8(11); 1027–35. ©2015 AACR.

Leukoplakia is the most common premalignant lesion of the oral cavity. Epidermal growth factor receptor (EGFR) abnormalities are associated with oral tumorigenesis and progression. We hypothesized that EGFR expression and gene copy number changes are predictors of the risk of an oral premalignant lesion (OPL) progressing to oral squamous cell carcinoma (OSCC). A formalin-fixed, paraffin-embedded OPL biopsy specimen was collected from each of 162 patients in a randomized controlled clinical trial. We assessed EGFR expression by immunohistochemistry with two methods: a semiquantitative analysis (145 evaluable specimens) and an automated quantitative analysis (127 evaluable specimens). EGFR gene copy number was assessed by fluorescence in situ hybridization (FISH) in a subset of 49 OPLs with high EGFR expression defined by the semiquantitative analysis. We analyzed EGFR abnormalities for associations with OSCC development. High EGFR expression occurred in 103 (71%) of the 145 OPLs and was associated with a nonsignificantly higher risk of OSCC (P = 0.10). Twenty (41%) of 49 OPLs assessed by FISH had an increased EGFR gene copy number (FISH-positive). Patients with FISH-positive lesions had a significantly higher incidence of OSCC than did patients with FISH-negative (a normal copy number) lesions (P = 0.0007). Of note, 10 of 11 OSCCs that developed at the site of the examined OPL were in the FISH-positive group, leaving only one FISH-negative OPL that did so (P < 0.0001). Our data indicate that an increased EGFR gene copy number is common in and associated with OSCC development in patients with OPLs expressing high EGFR, particularly OSCC developing at the site of a high-expression OPL; they also suggest that EGFR inhibitors may prevent oral cancer in patients with OPLs having an increased EGFR gene copy number. Cancer Prev Res; 3(7); 800–9. ©2010 AACR.

Supplementary Tables 1-3 and Table A-1, Figure 1, Appendix and Information from The BATTLE Trial: Personalizing Therapy for Lung Cancer

Supplementary Material 2 from Gene Expression Profiling Predicts the Development of Oral Cancer

PDF file - 4670K, Sweave report depicting complete codes use for microarray analysis and identification of genes differentially expressed in the molecular field of injury after excluding main carinas from the analysis

PDF file - 129K, Sweave report depicting complete codes use for microarray analysis of paired adjacent and contralateral airways

Lung cancer has limited effective therapy and no effective prevention. Cytotoxic chemotherapy has not improved when combined with the epidermal growth factor receptor (EGFR) inhibitor erlotinib (standard lung cancer therapy) or with the rexinoid bexarotene. Combining erlotinib and bexarotene, however, to cotarget cyclin D1 via the retinoid X receptor and EGFR was active preclinically in KRAS-driven lung cancer cells derived from transgenic mice and in two clinical studies in lung cancer (including wild-type EGFR tumors, with or without KRAS mutations), as reported in this issue of the journal by Dragnev and colleagues (beginning on page 818). These results, along with closely related clinical results of the BATTLE program, support the promise of this cotargeting approach for lung cancer prevention and therapy and of cyclin D1 as a predictive, personalizing marker for it. Cancer Prev Res; 4(6); 779–82. ©2011 AACR.

Supplementary Material 4 from Gene Expression Profiling Predicts the Development of Oral Cancer

We previously showed that low-dose fenretinide (200 mg/d) had limited activity in retinoid-resistant oral leukoplakia (34% response rate) possibly because serum drug levels were insufficient to induce retinoid receptor–independent apoptosis. Therefore, we designed the single-arm phase II trial reported here to investigate whether higher-dose fenretinide would improve leukoplakia response over that of our previous study. Leukoplakia patients received fenretinide (900 mg/m2 twice daily) in four 3-week cycles (1 week on drug followed by 2 weeks off). At week 12, clinical responses were determined and blood samples were collected for serum drug level assessments. A planned interim futility analysis led to early trial closure after the initial 15 (of 25 planned) patients because only 3 (20%) had a partial response (stopping rule: ≤4 responses in first 16 patients). Fenretinide was well tolerated—only one grade 3 adverse event (diarrhea) occurred. Serum fenretinide levels changed from 0 (baseline) to 0.122 ± 0.093 μmol/L (week 12). In correlative in vitro studies, high-dose fenretinide inhibited the growth of head and neck cancer cells more and oral leukoplakia cells less than did lower doses of fenretinide. This result is consistent with our clinical finding that high-dose fenretinide did not improve on the historical response rate of lower-dose fenretinide in our previous oral leukoplakia trial.

Perspective from Oral Epithelium as a Surrogate Tissue for Assessing Smoking-Induced Molecular Alterations in the Lungs

Supplementary Figure 1: Flow-chart describing the selection of 86 candidate genes. Supplementary Figure 2: Promoter methylation of 62/86 candidate genes in head and neck cancer, normal mucosa and blood. Supplementary Figure 3: Promoter methylation of 13/86 candidate genes in normal tissues. Supplementary Fig. 4: Hierarchical clustering of paired normal, dysplastic lesions and carcinomas (in situ or invasive) collected from 10 patients (3), using methylation profiles of 60/86 of our candidate genes. Supplementary Figure 5: (A) Hierarchical cluster analysis of oral squamous cell carcinoma and oral normal mucosa using candidate genes expression profiles. Supplementary Figure 6: Correlation of the percentage methylation of AGTR1.

Supplementary Material 9 from Gene Expression Profiling Predicts the Development of Oral Cancer

XLSX file - 627K, Supplementary table depicting 1395 genes significantly differentially expressed with time in the molecular field of injury

Supplementary Material 5 from Gene Expression Profiling Predicts the Development of Oral Cancer

Perspective on this Article from High-Dose Fenretinide in Oral Leukoplakia

Supplementary Table 1: Description of the studies used for the in silico validation of the candidate genes in terms of number of samples analyzed, platform used and number of overlapping genes between our candidate gene list and the genes analyzed on the platform (HN: head and neck; SCC: squamous cell carcinoma). Supplementary Table 2: List of cell lines in which the level of promoter methylation of AGTR1, FOXI2, HOXA9, PENK and ZIC1 were evaluated (HNSCC: head and neck squamous cell carcinoma). Supplementary Table 3: Univariate Cox proportional hazards model for all other available variables. Supplementary table 4: Multi-covariable Cox Model analysis including histology (hyperplasia or dysplasia).

Perspective on this Article from Epidermal Growth Factor Receptor Expression and Gene Copy Number in the Risk of Oral Cancer

XLSX file - 68K, Supplementary table depicting 1165 genes significantly differentially expressed by site in the molecular field of injury

Supplementary Tables 1-4 from Epidermal Growth Factor Receptor Expression and Gene Copy Number in the Risk of Oral Cancer

Non–small cell lung cancer is the primary cause of cancer-related death in Western countries. One important approach taken to address this problem is the development of effective chemoprevention strategies. In this study, we examined whether the cyclooxygenase-2 inhibitor celecoxib, as evidenced by decreased cell proliferation, is biologically active in the bronchial epithelium of current and former smokers. Current or former smokers with at least a 20 pack-year (pack-year = number of packs of cigarettes per day times number of years smoked) smoking history were randomized into one of four treatment arms (3-month intervals of celecoxib then placebo, celecoxib then celecoxib, placebo then celecoxib, or placebo then placebo) and underwent bronchoscopies with biopsies at baseline, 3 months, and 6 months. The 204 patients were primarily (79.4%) current smokers: 81 received either low-dose celecoxib or placebo and 123 received either high-dose celecoxib or placebo. Celecoxib was originally administered orally at 200 mg twice daily and the protocol subsequently increased the dose to 400 mg twice daily. The primary end point was change in Ki-67 labeling (from baseline to 3 months) in bronchial epithelium. No cardiac toxicities were observed in the participants. Although the effect of low-dose treatment was not significant, high-dose celecoxib decreased Ki-67 labeling by 3.85% in former smokers and by 1.10% in current smokers—a significantly greater reduction (P = 0.02) than that seen with placebo after adjusting for metaplasia and smoking status. A 3- to 6-month celecoxib regimen proved safe to administer. Celecoxib (400 mg twice daily) was biologically active in the bronchial epithelium of current and former smokers; additional studies on the efficacy of celecoxib in non–small cell lung cancer chemoprevention may be warranted. Cancer Prev Res; 3(2); 148–59

Supplementary Material 6 from Gene Expression Profiling Predicts the Development of Oral Cancer

The lungs and oral cavity of smokers are exposed to tobacco carcinogens. We hypothesized that tobacco-induced molecular alterations in the oral epithelium are similar to those in the lungs, and thus the oral epithelium may be used as a surrogate tissue for assessing alterations in the lungs. We used methylation-specific PCR to analyze promoter methylation of the p16 and FHIT genes at baseline and 3 months after intervention in 1,774 oral and bronchial brush specimens from 127 smokers enrolled in a randomized placebo-controlled chemoprevention trial. The association between methylation patterns in oral tissues and bronchial methylation indices (methylated sites / total sites per subject) was analyzed in a blinded fashion. At baseline, promoter methylation in bronchial tissue was present in 23% of samples for p16, 17% for FHIT, and 35% for p16 and FHIT; these percentages were comparable to methylation in oral tissue: 19% (p16), 15% (FHIT), and 31% (p16 and FHIT). Data from both oral and bronchial tissues were available for 125 individuals, in whom the two sites correlated strongly with respect to alterations (P < 0.0001 for both p16 and FHIT). At baseline, the mean bronchial methylation index was far higher in patients with oral tissue methylation (in either of the two genes; 39 patients) than in patients without oral tissue methylation (86 patients): 0.53 ± 0.29 versus 0.27 + 0.26 methylation index (P < 0.0001). Similar correlations occurred at 3 months after intervention. Our results support the potential of oral epithelium as a surrogate tissue for assessing tobacco-induced molecular damage in the lungs and thus have important implications for designing future lung cancer prevention trials and for research into the risk and early detection of lung cancer.

XLSX file - 65K, Supplementary table exhibiting genes significantly differentially expressed by site in the molecular field of injury when excluding main carinas from the analysis

Supplementary Material 1 from Gene Expression Profiling Predicts the Development of Oral Cancer

PDF file - 78K, Mutation status of AZ samples acquired through Liverpool Heart and Chest Hospital.

PDF file - 167K, Different probes for the same gene vary within and across microarray platforms

Purpose: Epithelial–mesenchymal transition (EMT) has been associated with metastatic spread and EGF receptor (EGFR) inhibitor resistance. We developed and validated a robust 76-gene EMT signature using gene expression profiles from four platforms using non–small cell lung carcinoma (NSCLC) cell lines and patients treated in the Biomarker-Integrated Approaches of Targeted Therapy for Lung Cancer Elimination (BATTLE) study.Experimental Design: We conducted an integrated gene expression, proteomic, and drug response analysis using cell lines and tumors from patients with NSCLC. A 76-gene EMT signature was developed and validated using gene expression profiles from four microarray platforms of NSCLC cell lines and patients treated in the BATTLE study, and potential therapeutic targets associated with EMT were identified.Results: Compared with epithelial cells, mesenchymal cells showed significantly greater resistance to EGFR and PI3K/Akt pathway inhibitors, independent of EGFR mutation status, but more sensitivity to certain chemotherapies. Mesenchymal cells also expressed increased levels of the receptor tyrosine kinase Axl and showed a trend toward greater sensitivity to the Axl inhibitor SGI-7079, whereas the combination of SGI-7079 with erlotinib reversed erlotinib resistance in mesenchymal lines expressing Axl and in a xenograft model of mesenchymal NSCLC. In patients with NSCLC, the EMT signature predicted 8-week disease control in patients receiving erlotinib but not other therapies.Conclusion: We have developed a robust EMT signature that predicts resistance to EGFR and PI3K/Akt inhibitors, highlights different patterns of drug responsiveness for epithelial and mesenchymal cells, and identifies Axl as a potential therapeutic target for overcoming EGFR inhibitor resistance associated with the mesenchymal phenotype. Clin Cancer Res; 19(1); 279–90. ©2012 AACR.

PDF file - 129K, Reduced nuclear PTEN in SCC compared with AC (TMA Set 2).