Macroautophagy (autophagy) is an essential cellular catabolic process required for survival under conditions of starvation. The role of autophagy in cancer is complex, context-dependent and at times ...contradictory, as it has been shown to inhibit, promote or be dispensable for tumor progression. In this study, we evaluated the contribution of the immune system to the reliance of tumors on autophagy by depleting autophagy-related 7 (ATG7) in murine tumor cells and grafting into immunocompetent versus immunodeficient hosts. Although loss of ATG7 did not affect tumor growth in vitro or in immunodeficient mice, our studies revealed that cancer cell reliance on autophagy was influenced by anti-tumor immune responses, including those mediated by CD8
T cells. Furthermore, we provide insights into possible mechanisms by which autophagy disruption can enhance anti-tumor immune responses and suggest that autophagy disruption may further benefit patients with immunoreactive tumors.
Cyclin-dependent kinase 4/6 inhibitor (CDK4/6) therapy plus endocrine therapy (ET) is an effective treatment for patients with hormone receptor-positive/human epidermal receptor 2-negative metastatic ...breast cancer (HR+/HER2- MBC); however, resistance is common and poorly understood. A comprehensive genomic and transcriptomic analysis of pretreatment and post-treatment tumors from patients receiving palbociclib plus ET was performed to delineate molecular mechanisms of drug resistance.
Tissue was collected from 89 patients with HR+/HER2- MBC, including those with recurrent and/or metastatic disease, receiving palbociclib plus an aromatase inhibitor or fulvestrant at Samsung Medical Center and Seoul National University Hospital from 2017 to 2020. Tumor biopsy and blood samples obtained at pretreatment, on-treatment (6 weeks and/or 12 weeks), and post-progression underwent RNA sequencing and whole-exome sequencing. Cox regression analysis was performed to identify the clinical and genomic variables associated with progression-free survival.
Novel markers associated with poor prognosis, including genomic scar features caused by homologous repair deficiency (HRD), estrogen response signatures, and four prognostic clusters with distinct molecular features were identified. Tumors with TP53 mutations co-occurring with a unique HRD-high cluster responded poorly to palbociclib plus ET. Comparisons of paired pre- and post-treatment samples revealed that tumors became enriched in APOBEC mutation signatures, and many switched to aggressive molecular subtypes with estrogen-independent characteristics. We identified frequent genomic alterations upon disease progression in RB1, ESR1, PTEN, and KMT2C.
We identified novel molecular features associated with poor prognosis and molecular mechanisms that could be targeted to overcome resistance to CKD4/6 plus ET.
ClinicalTrials.gov, NCT03401359. The trial was posted on 18 January 2018 and registered prospectively.
The fetal oncogene 5T4 is a cell surface protein, with overexpression observed in a variety of cancers as compared to normal adult tissue. The ability to select patients with tumors that express high ...levels of 5T4 may enrich a clinical trial cohort with patients most likely to respond to 5T4 targeted therapy. To that end, we developed assays to measure 5T4 in both tumors and in circulating tumor cells (CTCs). We identified the presence of 5T4 in both adenocarcinoma and squamous cell carcinoma of lung, in all clinical stages and grades of disease. CTCs were identified in peripheral blood from the majority of patients with NSCLC, and 5T4 was detectable in most samples. Although 5T4 was present in both CTCs and tumors in most patients, there was no concordance between relative amount in either sample type. Clinical response rates of patients treated with the therapies directed against 5T4 in early stage clinical trials, as determined by these assays, may provide important insights into the biology of 5T4 in tumors and the mechanisms of action of 5T4-targeting therapy.
The recently approved ALK kinase inhibitor crizotinib has demonstrated successful treatment of metastatic and late stage ALK fusion positive non-small cell lung cancer (NSCLC). However, the median ...duration of clinical benefit is ~10–11months due to the emergence of multiple and simultaneous resistance mechanisms in these tumors. Mutations in the ALK kinase domain confer resistance to crizotinib in about one-third of these patients. We developed a multiplex deep sequencing method using semiconductor sequencing technology to quickly detect resistance mutations within the ALK kinase domain from tumor biopsies. By applying a base-pair specific error-weighted mutation calling algorithm (BASCA) that we developed for this assay, genomic DNA analysis from thirteen relapsed patients revealed three known crizotinib resistance mutations, C1156Y, L1196M and G1269A. Our assay demonstrates robust and sensitive detection of ALK kinase mutations in NSCLC tumor samples and aids in the elucidation of resistance mechanisms pertinent to the clinical setting.
► A sensitive and accurate assay to identify crizotinib resistance mutations in ALK. ► A simple method to multiplex deep sequencing patient samples. ► Identified 3 resistance mutations in 13 crizotinib-refactory patients.
Anaplastic lymphoma kinase gene ( ALK ) fusions have been identified in approximately 5% of non-small-cell lung carcinomas (NSCLCs) and define a distinct subpopulation of patients with lung cancer ...who are highly responsive to ALK kinase inhibitors, such as crizotinib. Because of this profound therapeutic implication, the latest National Comprehensive Cancer Network Clinical Practice Guidelines in Oncology recommend upfront ALK screening for all patients with NSCLC. The Food and Drug Administration–approved companion diagnostic test (ie, fluorescence in situ hybridization) for identification of ALK-positive patients, however, is complex and has considerable limitations in terms of cost and throughput, making it difficult to screen many patients. To explore alternative screening modalities for detecting ALK fusions, we designed a combination of two transcript-based assays to detect for presence or absence of ALK fusions using NanoString’s nCounter technology. By using this combined gene expression and ALK fusion detection strategy, we developed a multiplexed assay with a quantitative scoring modality that is highly sensitive, reproducible, and capable of detecting low-abundant ALK fusion transcripts, even in samples with a low tumor cell content. In 66 archival NSCLC samples, our results were highly concordant to prior results obtained by fluorescence in situ hybridization and IHC. Our assay offers a cost-effective, easy-to-perform, high-throughput, and FFPE-compatible screening alternative for detection of ALK fusions.
BackgroundPreclinical studies of avelumab (anti–PD-L1) + binimetinib (MEK inhibitor MEKi) showed encouraging antitumor activity. We report results from the phase 1b JAVELIN PARP MEKi trial ...(NCT03637491) evaluating avelumab + binimetinib in patients with mPDAC.MethodsEligible patients had mPDAC and disease progression during or following 1–2 prior lines for advanced or metastatic disease. Patients received avelumab 800 mg intravenously every 2 weeks and binimetinib 30 or 45 mg orally twice daily. The primary endpoint for phase 1b was dose-limiting toxicity (DLT). Secondary endpoints included safety, confirmed objective response per investigator (RECIST 1.1), pharmacokinetics, immunogenicity, and biomarker analyses. PD-L1 expression (SP263 assay) and CD8+ tumor-infiltrating lymphocytes (TILs) in baseline tumor samples were assessed using immunohistochemistry. Molecular alterations were assessed via plasma ctDNA analyses. Blood samples were collected to assess trough concentrations for avelumab, binimetinib, and AR00426032 (binimetinib metabolite) and end-of-infusion concentration for avelumab.Results22 patients received avelumab + binimetinib 30 mg (n=10) or 45 mg (n=12); all discontinued treatment. Among 21 DLT-evaluable patients, DLTs occurred in 3/10 (30.0%) in the 30-mg group (mucosal inflammation, dermatitis acneiform, blood creatine phosphokinase increased n=1 each) and 5/11 (45.5%) in the 45-mg group (detachment of retinal pigment epithelium, abdominal pain, diarrhea, nausea, vomiting, rash pustular, hypertension, blood creatine phosphokinase increased n=1 each). Any-grade treatment-related adverse events (TRAEs) occurred in all 22 patients; grade =3 TRAEs occurred in 8 (80.0%) and 4 (33.3%) in the 30- and 45-mg groups, respectively, most commonly blood creatine phosphokinase increased (n=3 30.0%, n=2 16.7%, respectively). No treatment-related deaths occurred. Objective response rates (95% CI) in the 30- and 45-mg groups were 0% (0.0–30.8) and 8.3% (0.2–38.5; 1 partial response), respectively; 1 (10.0%) and 6 (50.0%) had a best overall response of stable disease. Tumor shrinkage was associated with higher baseline PD-L1 expression, higher number of CD8+ TILs, and MEK1/2, PIK3CA, and RNF43 alterations, whereas ERBB4 alterations correlated inversely with tumor size change. Available data indicate that avelumab, binimetinib, and AR00426032 exposures were within range of previous monotherapy studies.ConclusionsThis study was terminated before a recommended phase 2 dose was established. In patients with mPDAC who received avelumab + binimetinib, DLTs occurred in both dose groups, although TRAEs were generally consistent with single agent safety profiles. The 45-mg binimetinib dose had a higher number of patients with stable disease and one confirmed partial response. Biomarker findings provide insights into potential mechanisms of treatment resistance and response.Trial RegistrationNCT03637491Ethics ApprovalThe trial was approved by each site’s independent ethics committee.
Prolongation of the electrocardiogram QT interval by some, but not all drugs, has been associated with increased incidence of sudden cardiac death. Current preclinical regulatory assays cannot ...discriminate the arrhythmia liability of these drugs. Consequently, many new medications that prolong the QT interval are not developed despite their potential therapeutic benefit. Alternans (action potential duration alternations) is a measure of cardiac instability in humans and animals associated with the onset of ventricular fibrillation. Due to potential arrhythmia risk from observed QT prolongation, alternans was assessed in the anesthetized guinea pig after azithromycin or chloroquine alone and after combination treatment at clinically relevant concentrations proposed for the management of malaria. Chloroquine alone, but not azithromycin, caused a profound increase in action potential duration but with only minimal effects on alternans (approximately 10 ms). Azithromycin alone and in combination with chloroquine showed no increase in alternans beyond vehicle baseline responses indicating no additional arrhythmia liability.
The genotoxicity testing battery is highly sensitive for detection of chemical carcinogens. However, it features a low specificity and provides only limited mechanistic information required for risk ...assessment of positive findings. This is especially important in case of positive findings in the in vitro chromosome damage assays, because chromosome damage may be also induced secondarily to cell death. An increasing body of evidence indicates that toxicogenomic analysis of cellular stress responses provides an insight into mechanisms of action of genotoxicants. To evaluate the utility of such a toxicogenomic analysis we evaluated gene expression profiles of TK6 cells treated with four model genotoxic agents using a targeted high density real-time PCR approach in a multilaboratory project coordinated by the Health and Environmental Sciences Institute Committee on the Application of Genomics in Mechanism-based Risk Assessment. We show that this gene profiling technology produced reproducible data across laboratories allowing us to conclude that expression analysis of a relevant gene set is capable of distinguishing compounds that cause DNA adducts or double strand breaks from those that interfere with mitotic spindle function or that cause chromosome damage as a consequence of cytotoxicity. Furthermore, our data suggest that the gene expression profiles at early time points are most likely to provide information relevant to mechanisms of genotoxic damage and that larger gene expression arrays will likely provide richer information for differentiating molecular mechanisms of action of genotoxicants. Although more compounds need to be tested to identify a robust molecular signature, this study confirms the potential of toxicogenomic analysis for investigation of genotoxic mechanisms.
In early oncology clinical trials there is often limited data for biomarkers and their association with response to treatment. Thus, it is challenging to decide whether a biomarker should be used for ...patient selection and enrollment. Most evidence about any potential predictive biomarker comes from preclinical research and, sometimes, clinical observations. How to translate the preclinical predictive biomarker data to clinical study remains an active field of research. Here, we propose a method to incorporate existing knowledge about a predictive biomarker - its prevalence, association with response and the performance of the assay used to measure the biomarker - to estimate the response rate in a clinical study designed with or without using the predictive biomarker. Importantly, we quantify the uncertainty associated with the biomarker and its predictability in a probabilistic model. This model estimates the distribution of the clinical response when a predictive biomarker is used to select patients and compares it to unselected cohort. We applied this method to two real world cases of approved biomarker-guided therapies to demonstrate its utility and potential value. This approach helps to make a data-driven decision whether to select patients with a predictive biomarker in early oncology clinical development.
Purpose: To determine the effect of increasing the aerobic component of the school’s physical activity program and improving the knowledge about weight control and blood pressure on the blood ...pressure and body fat of early adolescents.
Methods: The subjects were 1140 youth aged 11 to 14 years (630 females, 510 males; 64% white, 24.4% African-American, and 11.6% “other”), who were randomly assigned by school into four treatment groups: exercise only, education only, exercise and education combined, and control group. Heights, weights, and skinfold thicknesses were measured, and body mass index (BMI) was computed (kg/m
2). Blood pressure was obtained in duplicate using a random-zero mercury sphygmomanometer. Maximal oxygen uptake was predicted from a submaximal cycle ergometer test. Data were analyzed using analysis of covariance statistics, adjusting for gender, ethnicity, age, socioeconomic status, and initial baseline characteristics.
Results: Systolic and diastolic blood pressures increased more in the control group than in the intervention groups (
p = .001). The BMI did not change significantly (
p = .709), but the sum of skinfolds increased less in subjects in the exercise intervention groups than the education only or control groups (
p = .0001). The small increase in
pVO
2max of the combined exercise and education group was significantly greater than the education only group (
p = .0001).
Conclusion: An exercise program for youth can have a positive effect on blood pressure independent of body weight loss.
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