Methylation, Gene Expression, and Risk Genotypes at the TERT-CLPTM1L Locus in Cervical Cancer.

The reverse transcriptase subunit of telomerase, TERT, is frequently activated in high-grade dysplasia and invasive cancers of the uterine cervix. Telomerase activation through hypomethylation of the TERT promoter holds promise as a biomarker for cervical cancer progression, however, specific CpG sites involved in cervical cancer risk remain to be fully defined. A recent genome-wide association study on cervical cancer identified genetic polymorphisms at 5p13.33 (close to TERT-CLPTM1L) but the underlying mechanisms are undetermined. We investigated 529 CpG sites within the TERT promoter region and 3 CpG islands nearby, and 21 CpG sites within CLPTM1L in 190 bisulfite-converted cervical tumor DNA samples from BioRAIDs (NCT02428842). We identified eight CpG sites within TERT intron 2 where methylation was significantly associated with the genotypes of cervical cancer risk variants rs27070 and rs459961 in cervical tumors after multiple testing correction (p < 9.4 × 10E-5). Hypermethylation at chr5:1289663 correlated with decreased TERT mRNA levels. In an independent series of 188 normal or dysplastic cervical tissues, rare alleles of rs27070 and rs459961 were associated with low basal CLPTM1L levels and with the absence of TERT mRNA in HPV-negative samples, consistent with their proposed role as protective variants for cervical cancer. HPV infection was associated with increased CLPTM1L and TERT levels. Collectively, our results provide a link between cervical cancer risk variants, methylation, and gene expression and implicate both TERT and CLPTM1L as genes modulated by genomic background and HPV infection during cervical cancer development.

Reconsidering conceptual knowledge: Heterogeneity of its components.

Cognitive arithmetic classically distinguishes procedural and conceptual knowledge as two determinants of the acquisition of flexible expertise. Whereas procedural knowledge relates to algorithmic routines, conceptual knowledge is defined as the knowledge of core principles, referred to as fundamental structures of arithmetic. To date, there is no consensus regarding their number, list, or even their definition, partly because they are difficult to measure. Recent findings suggest that among the most complex of these principles, some might not be "fundamental structures" but rather may articulate several components of conceptual knowledge, each specific to the arithmetic operation involved. Here, we argue that most of the arithmetic principles similarly may rather articulate several core concepts specific to the operation involved. Data were collected during a national mathematics contest based on an arithmetic game involving a large sample of 9- to 11-year-old students (N = 11,243; 53.1% boys) over several weeks. The purpose of the game was to solve complex arithmetic problems using five numbers and the four operations. A principal component analysis (PCA) was performed. The results show that both conceptual and procedural knowledge were used by children. Moreover, the PCA sorted conceptual and procedural knowledge together, with dimensions being defined by the operation rather than by the concept. This implies that "fundamental structures" rather regroup different concepts that are learned separately. This opens the way to reconsider the very nature of conceptual knowledge and has direct pedagogical implications.

Total metabolic tumor volume and spleen metabolism on baseline [18F]-FDG PET/CT as independent prognostic biomarkers of recurrence in resected breast cancer.

PURPOSE: We evaluated whether biomarkers on baseline [18F]-FDG PET/CT are associated with recurrence after surgery in patients with invasive breast cancer of no special type (NST). METHODS: In this retrospective single-center study, we included consecutive patients with non-metastatic breast cancer of NST who underwent [18F]-FDG PET/CT before treatment, including surgery, between 2011 and 2016. Clinicopathological data were collected. Tumor SUVmax, total metabolic tumor volume (TMTV), and spleen- and bone marrow-to-liver SUVmax ratios (SLR, BLR) were measured from the PET images. Cut-off values were determined using predictiveness curves to predict 5-year recurrence-free survival (5y-RFS). A multivariable prediction model was developed using Cox regression. The association with stromal tumor-infiltrating lymphocytes (TILs) levels (low if <50%) was studied by logistic regression. RESULTS: Three hundred and three women were eligible, including 93 (31%) with triple-negative breast carcinoma. After a median follow-up of 6.2 years, 56 and 35 patients experienced recurrence and death, respectively. The 5y-RFS rate was 86%. In multivariable analyses, high TMTV (>20 cm3) and high SLR (>0.76) were associated with shorter 5y-RFS (HR 2.4, 95%CI 1.3-4.5, and HR 1.9, 95%CI 1.0-3.6). In logistic regression, high SLR was the only independent factor associated with low stromal TILs (OR 2.8, 95%CI 1.4-5.7). CONCLUSION: High total metabolic tumor volume and high spleen glucose metabolism on baseline [18F]-FDG PET/CT were associated with poor 5y-RFS after surgical resection in patients with breast cancer of NST. Spleen metabolism was inversely correlated with stromal TILs and might be a surrogate for an immunosuppressive tumor microenvironment.

A review of the use of time-varying covariates in the Fine-Gray subdistribution hazard competing risk regression model.

In survival analysis, time-varying covariates are covariates whose value can change during follow-up. Outcomes in medical research are frequently subject to competing risks (events precluding the occurrence of the primary outcome). We review the types of time-varying covariates and highlight the effect of their inclusion in the subdistribution hazard model. External time-dependent covariates are external to the subject, can effect the failure process, but are not otherwise involved in the failure mechanism. Internal time-varying covariates are measured on the subject, can effect the failure process directly, and may also be impacted by the failure mechanism. In the absence of competing risks, a consequence of including internal time-dependent covariates in the Cox model is that one cannot estimate the survival function or the effect of covariates on the survival function. In the presence of competing risks, the inclusion of internal time-varying covariates in a subdistribution hazard model results in the loss of the ability to estimate the cumulative incidence function (CIF) or the effect of covariates on the CIF. Furthermore, the definition of the risk set for the subdistribution hazard function can make defining internal time-varying covariates difficult or impossible. We conducted a review of the use of time-varying covariates in subdistribution hazard models in articles published in the medical literature in 2015 and in the first 5 months of 2019. Seven percent of articles published included a time-varying covariate. Several inappropriately described a time-varying covariate as having an association with the risk of the outcome.

A covariate-specific time-dependent receiver operating characteristic curve for correlated survival data.

Several studies for the clinical validity of circulating tumor cells (CTCs) in metastatic breast cancer were conducted showing that it is a prognostic biomarker of overall survival. In this work, we consider an individual patient data meta-analysis for nonmetastatic breast cancer to assess the discrimination of CTCs regarding the risk of death. Data are collected in several centers and present correlated failure times for subjects of the same center. However, although the covariate-specific time-dependent receiver operating characteristic (ROC) curve has been widely used for assessing the performance of a biomarker, there is no methodology yet that can handle this specific setting with clustered censored failure times. We propose an estimator for the covariate-specific time-dependent ROC curves and area under the ROC curve when clustered failure times are detected. We discuss the assumptions under which the estimators are consistent and their interpretations. We assume a shared frailty model for modeling the effect of the covariates and the biomarker on the outcome in order to account for the cluster effect. A simulation study was conducted and it shows negligible bias for the proposed estimator and a nonparametric one based on inverse probability censoring weighting, while a semiparametric estimator, ignoring the clustering, is markedly biased. Finally, in our application to breast cancer data, the estimation of the covariate-specific area under the curves illustrates that the CTCs discriminate better patients with inflammatory tumor than patients with noninflammatory tumor, with respect to their risk of death.

On evaluating how well a biomarker can predict treatment response with survival data.

One of the objectives of personalized medicine is to take treatment decisions based on a biomarker measurement. Therefore, it is often interesting to evaluate how well a biomarker can predict the response to a treatment. To do so, a popular methodology consists of using a regression model and testing for an interaction between treatment assignment and biomarker. However, the existence of an interaction is not sufficient for a biomarker to be predictive. It is only necessary. Hence, the use of the marker-by-treatment predictiveness curve has been recommended. In addition to evaluate how well a single continuous biomarker predicts treatment response, it can further help to define an optimal threshold. This curve displays the risk of a binary outcome as a function of the quantiles of the biomarker, for each treatment group. Methods that assume a binary outcome or rely on a proportional hazard model for a time-to-event outcome have been proposed to estimate this curve. In this work, we propose some extensions for censored data. They rely on a time-dependent logistic model, and we propose to estimate this model via inverse probability of censoring weighting. We present simulations results and three applications to prostate cancer, liver cirrhosis, and lung cancer data. They suggest that a large number of events need to be observed to define a threshold with sufficient accuracy for clinical usefulness. They also illustrate that when the treatment effect varies with the time horizon which defines the outcome, then the optimal threshold also depends on this time horizon.

Meta-analysis of clinical trials with competing time-to-event endpoints.

Recommendations for the analysis of competing risks in the context of randomized clinical trials are well established. Meta-analysis of individual patient data (IPD) is the gold standard for synthesizing evidence for clinical interpretation based on multiple studies. Surprisingly, no formal guidelines have been yet proposed to conduct an IPD meta-analysis with competing risk endpoints. To fill this gap, this work details (i) how to handle the heterogeneity between trials via a stratified regression model for competing risks and (ii) that the usual metrics of inconsistency to assess heterogeneity can readily be employed. Our proposal is illustrated by the re-analysis of a recently published meta-analysis in nasopharyngeal carcinoma, aiming at quantifying the benefit of the addition of chemotherapy to radiotherapy on each competing endpoint.

A Note on the Measurement of Socioeconomic Inequalities in Life Years Lost by Cause of Death.

Quantifying socioeconomic inequalities in health in absolute terms is of prime interest for decision-making and for international comparisons. The Slope Index of Inequality (SII), an index that quantifies absolute socioeconomic inequalities, was recently formalized, particularly in the context of mortality differences measured in the rate or hazard scale. However, absolute inequalities using either rates or hazards do not translate into a time dimension, which makes their interpretation difficult for policymakers. We propose an extension of the (Equation is included in full-text article.)in terms of the expected number of life years lost before an upper age, as well as its decomposition by cause of death. The (Equation is included in full-text article.)in the life years lost metric quantifies the extent to which life expectancy is shortened when comparing the higher and lower ends of the socioeconomic scale. The methodology proposed builds on recent developments in survival analysis for decomposing the number of life years lost according to cause of death using a pseudo-value approach. We illustrate our proposal using a representative 1% sample of the French population. On average, the least educated men lost 7 years of life from age 30 up to age 90 compared to the most educated. The loss for women is twice as much with 3.5 years. The (Equation is included in full-text article.)in the life years lost metric is easily understood, and the decomposition of the all-cause mortality (Equation is included in full-text article.)into parts attributable to given causes provides a sound estimation of the burden of different causes of death on absolute socioeconomic inequalities in mortality.

The heart of the matter: years-saved from cardiovascular and cancer deaths in an elite athlete cohort with over a century of follow-up.

To quantify the years of life saved from cardiovascular (CVD), cancer and overall deaths among elite athletes according to their main type of physiological effort performed in the Olympic Games. All French athletes participating in the Games from 1912 to 2012, with vital status validated and cause of death (if concerned) identified by the national registries were included (n = 2814, 455 died) and classified according to 6 groups of effort: POWER (continuous effort < 45 s); INTERMEDIATE (45 s ≤ continuous effort < 600 s); ENDURANCE (continuous effort ≥ 600 s); POLYVALENT (participating in different events entering different classifications), INTERMITTENT (intermittent effort, i.e. team sports); PRECISION (targeting events). The theoretical years-lost method was adapted to calculate gains in longevity (years-saved) according to specific-risks under the competing risks model and was implemented in R software. Considering overall-deaths, all groups significantly saved, on average, 6.5 years of life (95% CI 5.8-7.2) compared to the general population. This longevity advantage is mainly driven by a lower risk of cancer which, isolated, contributed to significantly save 2.3 years of life (95% CI 1.2-1.9) on average in each group. The risk of CVD-related mortality in the ENDURANCE and PRECISION groups is not significantly different from the general population. The other groups significantly saved, on average, 1.6 years of life (95% CI 1.2-1.9) from CVD death. The longevity benefits in elite athletes are associated with the type of effort performed during their career, mainly due to differences on the CVD-risk of death.

Modeling time-varying exposure using inverse probability of treatment weights.

For estimating the causal effect of treatment exposure on the occurrence of adverse events, inverse probability weights (IPW) can be used in marginal structural models to correct for time-dependent confounding. The R package ipw allows IPW estimation by modeling the relationship between the exposure and confounders via several regression models, among which is the Cox model. For right-censored data and time-dependent exposures such as treatment switches, the ipw package allows a single switch, assuming that patients are treated once and for all. However, to accommodate multiple switches, we extend this package by implementing a function that allows for multiple and intermittent exposure status in the estimation of IPW using a survival model. This extension allows for the whole exposure treatment trajectory in the estimation of IPW. The impact of the estimated weights on the estimated causal effect, with both methods, is assessed in a simulation study. Then, the function is illustrated on a real dataset from a nationwide prospective observational cohort including patients with inflammatory bowel disease. In this study, patients received one or multiple medications (thiopurines, methotrexate, and anti-TNF) over time. We used a Cox marginal structural model to assess the effect of thiopurines exposure on the cause-specific hazard for cancer incidence considering other treatments as confounding factors. To this end, we used our extended function which is available online in the Supporting Information.

Using Automated Learning Devices for Monkeys (ALDM) to study social networks.

Social network analysis has become a prominent tool to study animal social life, and there is an increasing need to develop new systems to collect social information automatically, systematically, and reliably. Here we explore the use of a freely accessible Automated Learning Device for Monkeys (ALDM) to collect such social information on a group of 22 captive baboons (Papio papio). We compared the social network obtained from the co-presence of the baboons in ten ALDM testing booths to the social network obtained through standard behavioral observation techniques. The results show that the co-presence network accurately reflects the social organization of the group, and also indicate under which conditions the co-presence network is most informative. In particular, the best correlation between the two networks was obtained with a minimum of 40 days of computer records and for individuals with at least 500 records per day. We also show through random permutation tests that the observed correlations go beyond what would be observed by simple synchronous activity, to reflect a preferential choice of closely located testing booths. The use of automatized cognitive testing therefore presents a new way of obtaining a large and regular amount of social information that is necessary to develop social network analysis. It also opens the possibility of studying dynamic changes in network structure with time and in relation to the cognitive performance of individuals.

Relative index of inequality and slope index of inequality: a structured regression framework for estimation.

BACKGROUND: The relative index of inequality and the slope index of inequality are the two major indices used in epidemiologic studies for the measurement of socioeconomic inequalities in health. Yet the current definitions of these indices are not adapted to their main purpose, which is to provide summary measures of the linear association between socioeconomic status and health in a way that enables valid between-population comparisons. The lack of appropriate definitions has dissuaded the application of suitable regression methods for estimating the slope index of inequality. METHODS: We suggest formally defining the relative and slope indices of inequality as so-called least false parameters, or more precisely, as the parameters that provide the best approximation of the relation between socioeconomic status and the health outcome by log-linear and linear models, respectively. From this standpoint, we establish a structured regression framework for inference on these indices. Guidelines for implementation of the methods, including R and SAS codes, are provided. RESULTS: The new definitions yield appropriate summary measures of the linear association across the entire socioeconomic scale, suitable for comparative studies in epidemiology. Our regression-based approach for estimation of the slope index of inequality contributes to an advancement of the current methodology, which mainly consists of a heuristic formula relying on restrictive assumptions. A study of the educational inequalities in all-cause and cause-specific mortality in France is used for illustration. CONCLUSION: The proposed definitions and methods should guide the use and estimation of these indices in future studies.

Direct likelihood inference and sensitivity analysis for competing risks regression with missing causes of failure.

Competing risks arise in the analysis of failure times when there is a distinction between different causes of failure. In many studies, it is difficult to obtain complete cause of failure information for all individuals. Thus, several authors have proposed strategies for semi-parametric modeling of competing risks when some causes of failure are missing under the missing at random (MAR) assumption. As many authors have stressed, while semi-parametric models are convenient, fully-parametric regression modeling of the cause-specific hazards (CSH) and cumulative incidence functions (CIF) may be of interest for prediction and is likely to contribute towards a fuller understanding of the time-dynamics of the competing risks mechanism. We propose a so-called "direct likelihood" approach for fitting fully-parametric regression models for these two functionals under MAR. The MAR assumption not being verifiable from the observed data, we propose an approach for performing sensitivity analyses to assess the robustness of inferences to departures from this assumption. The method relies on so-called "pattern-mixture models" from the missing data literature and was evaluated in a simulation study. This sensitivity analysis approach is applicable to various competing risks regression models (fully-parametric or semi-parametric, for the CSH or the CIF). We illustrate the proposed methods with the analysis of a breast cancer clinical trial, including suggestions for ad hoc graphical goodness-of-fit assessments under MAR.

A competing risks approach for nonparametric estimation of transition probabilities in a non-Markov illness-death model.

Competing risks model time to first event and type of first event. An example from hospital epidemiology is the incidence of hospital-acquired infection, which has to account for hospital discharge of non-infected patients as a competing risk. An illness-death model would allow to further study hospital outcomes of infected patients. Such a model typically relies on a Markov assumption. However, it is conceivable that the future course of an infected patient does not only depend on the time since hospital admission and current infection status but also on the time since infection. We demonstrate how a modified competing risks model can be used for nonparametric estimation of transition probabilities when the Markov assumption is violated.

Systematic assessment of tumor necrosis at baseline in cervical cancer - An independent factor associated with poor outcome.

Cervical cancer (CC) is a leading challenge in oncology worldwide, with high prevalence and mortality rates in young adults, most prominent in low to middle-income countries with marginal screening facilities. From the prospectively collected BioRAIDS (NCT02428842) cohort of primary squamous CC conducted in 7 European countries, a central pathology review was carried out on 294 patients' tumors. The focus was on identification of tumor-stromal characteristics such as CD8+, CD45+, CD68+ staining cells, PD-L1 expression, tumor infiltrating lymphocytes (TILs) together with the degree of tumor necrosis. Both (FIGO-2018) stage (I-II/III-IV) as well as tumor necrosis were highly significantly associated with Progression-free Survival (PFS); with tumor necrosis scoring as most potent independent factor in a multivariable analysis (p < 0.001). Tumor necrosis can be assessed in the very first diagnostic biopsyand our data suggest that this rapid, simple and cost-effective biomarker, should be routinely assessed prior to treatment decisions.

Early morning immune checkpoint blockade and overall survival of patients with metastatic cancer: An In-depth chronotherapeutic study.

INTRODUCTION: Recent retrospective studies suggest potential large patient's benefit through proper timing of immune checkpoint blockers (ICB). The association between ICB treatment timing and patient survival, neoplastic response and toxicities was investigated, together with interactions with performance status (PS) and sex. METHODS: A cohort of patients with metastatic or locally advanced solid tumors, who received pembrolizumab, nivolumab, atezolizumab, durvalumab, or avelumab, alone or with concomitant chemotherapy, between November 2015 and March 2021, at the Centre Leon Bérard (France), was retrospectively studied. RESULTS: 361 patients were investigated (80% non-small cell lung cancer patients, mean [SD] age: 63 [11] years, 39% of women, 83% PS0-1 at first infusion, 19% received concomitant chemotherapy). ICB were administered from 07:25 to 17:21 and optimal morning/afternoon cut-off was 11:37. Morning infusions were associated with increased OS as compared to afternoon (median 30.3 vs 15.9 months, p = 0.0024; HR 1.56 [1.17-2.1], p = 0.003). A strong PS-timing interaction was found (PS0-1 patients, HR=1.53 [1.10-2.12], p = 0.011; PS2-3 patients, HR=0.50 [0.25-0.97], p = 0.042). Morning PS0-1 patients displayed increased OS (median 36.7 vs 21.3 months, p = 0.023), partial/complete response rate (58% vs 41%, p = 0.027), and grade1-3 toxicities (49% vs 34%, p = 0.028). Mortality risk ratio between infusions at worst time-of-day, estimated at 13:36 [12:48-14:23], and in early morning was equal to 4.8 ([2.3-10.1], p = 0.008). Timing differences in toxicities resulted significant only in female patients (women vs men: p < 0.001 vs 0.4). CONCLUSIONS: Early morning ICB infusion was associated with increased OS, response, and toxicities in patients with PS0-1 as compared to later infusions within the day. Prospective randomized trials are needed to confirm this retrospective study.

Concomitant medication, comorbidity and survival in patients with breast cancer.

Between 30% and 70% of patients with breast cancer have pre-existing chronic conditions, and more than half are on long-term non-cancer medication at the time of diagnosis. Preliminary epidemiological evidence suggests that some non-cancer medications may affect breast cancer risk, recurrence, and survival. In this nationwide cohort study, we assessed the association between medication use at breast cancer diagnosis and survival. We included 235,368 French women with newly diagnosed non-metastatic breast cancer. In analyzes of 288 medications, we identified eight medications positively associated with either overall survival or disease-free survival: rabeprazole, alverine, atenolol, simvastatin, rosuvastatin, estriol (vaginal or transmucosal), nomegestrol, and hypromellose; and eight medications negatively associated with overall survival or disease-free survival: ferrous fumarate, prednisolone, carbimazole, pristinamycin, oxazepam, alprazolam, hydroxyzine, and mianserin. Full results are available online from an interactive platform ( https://adrenaline.curie.fr ). This resource provides hypotheses for drugs that may naturally influence breast cancer evolution.

Competing risks regression for clustered data.

A population average regression model is proposed to assess the marginal effects of covariates on the cumulative incidence function when there is dependence across individuals within a cluster in the competing risks setting. This method extends the Fine-Gray proportional hazards model for the subdistribution to situations, where individuals within a cluster may be correlated due to unobserved shared factors. Estimators of the regression parameters in the marginal model are developed under an independence working assumption where the correlation across individuals within a cluster is completely unspecified. The estimators are consistent and asymptotically normal, and variance estimation may be achieved without specifying the form of the dependence across individuals. A simulation study evidences that the inferential procedures perform well with realistic sample sizes. The practical utility of the methods is illustrated with data from the European Bone Marrow Transplant Registry.