Development of a method for generating SNP interaction-aware polygenic risk scores for radiotherapy toxicity

AIM

To identify the effect of single nucleotide polymorphism (SNP) interactions on the risk of toxicity following radiotherapy (RT) for prostate cancer (PCa) and propose a new method for polygenic risk score incorporating SNP-SNP interactions (PRSi).

MATERIALS AND METHODS

Analysis included the REQUITE PCa cohort that received external beam RT and was followed for 2 years. Late toxicity endpoints were: rectal bleeding, urinary frequency, haematuria, nocturia, decreased urinary stream. Among 43 literature-identified SNPs, the 30% most strongly associated with each toxicity were tested. SNP-SNP combinations (named SNP-allele sets) seen in ≥10% of the cohort were condensed into risk (RS) and protection (PS) scores, respectively indicating increased or decreased toxicity risk. Performance of RS and PS was evaluated by logistic regression. RS and PS were then combined into a single PRSi evaluated by area under the receiver operating characteristic curve (AUC).

RESULTS

Among 1,387 analysed patients, toxicity rates were 11.7% (rectal bleeding), 4.0% (urinary frequency), 5.5% (haematuria), 7.8% (nocturia) and 17.1% (decreased urinary stream). RS and PS combined 8 to 15 different SNP-allele sets, depending on the toxicity endpoint. Distributions of PRSi differed significantly in patients with/without toxicity with AUCs ranging from 0.61 to 0.78. PRSi was better than the classical summed PRS, particularly for the urinary frequency, haematuria and decreased urinary stream endpoints.

CONCLUSIONS

Our method incorporates SNP-SNP interactions when calculating PRS for radiotherapy toxicity. Our approach is better than classical summation in discriminating patients with toxicity and should enable incorporating genetic information to improve normal tissue complication probability models.

Treatment prescription, adherence, and persistence after the first hospitalization for heart failure: A population-based retrospective study on 100785 patients

BACKGROUND

This study evaluates, in a real-world setting, to what extent the recommended therapies by international guidelines, are prescribed after a first hospitalization for heart failure (HF), and to analyse adherence and persistence, and the effect of treatment adherence on mortality and re-hospitalization.

METHODS

From the Lombardy healthcare administrative database, we analysed patients discharged after their incident HF, from 2000 to 2012. Adherence was defined as the proportion of days covered (PDC) ≥80% adjusted for hospitalizations and persistence as the absence of discontinuation of therapy for >30 days. A logit model was used to determine the effect of patients' adherence on mortality and readmissions.

RESULTS

Of 100422 HF patients (52% males, age 75 ± 12 years), 86846 (87%) had a prescription for angiotensin-converting enzyme inhibitors/angiotensin II receptor blockers (ACE/ARBs), 64135 (64%) for beta-blockers (BB), and 36893 (37%) for mineralocorticoid receptor antagonists (MRAs), as mono-, bi- or tri-therapy. In patients on monotherapy, PDC was 78 ± 22% for ACE/ARBs, 69 ± 29% for BB and 54 ± 29% for MRAs; in those on bi-therapy, PDC was 63 ± 31% for ACEI/ARBs+BB, 41 ± 29% for ACEI/ARBs+MRAs, and 40 ± 26% for MRAs+BB; for patients on tri-therapy, PDC was 42 ± 28%. Medication persistence was present in 47% of patients treated with ACEI/ARBs, in 35% of patients treated with BB and in 14% of patients treated with MRAs. Re-hospitalizations and in mortality were significantly reduced in adherent patients (p < 0.000).

CONCLUSIONS

Polypharmacy is associated with an increased rate of non-adherence and non-persistence in incident HF. Non-adherence is associated with an increased risk of mortality and re-hospitalizations.

A Deep Learning Approach Validates Genetic Risk Factors for Late Toxicity After Prostate Cancer Radiotherapy in a REQUITE Multi-National Cohort

Background: REQUITE (validating pREdictive models and biomarkers of radiotherapy toxicity to reduce side effects and improve QUalITy of lifE in cancer survivors) is an international prospective cohort study. The purpose of this project was to analyse a cohort of patients recruited into REQUITE using a deep learning algorithm to identify patient-specific features associated with the development of toxicity, and test the approach by attempting to validate previously published genetic risk factors. Methods: The study involved REQUITE prostate cancer patients treated with external beam radiotherapy who had complete 2-year follow-up. We used five separate late toxicity endpoints: ≥grade 1 late rectal bleeding, ≥grade 2 urinary frequency, ≥grade 1 haematuria, ≥ grade 2 nocturia, ≥ grade 1 decreased urinary stream. Forty-three single nucleotide polymorphisms (SNPs) already reported in the literature to be associated with the toxicity endpoints were included in the analysis. No SNP had been studied before in the REQUITE cohort. Deep Sparse AutoEncoders (DSAE) were trained to recognize features (SNPs) identifying patients with no toxicity and tested on a different independent mixed population including patients without and with toxicity. Results: One thousand, four hundred and one patients were included, and toxicity rates were: rectal bleeding 11.7%, urinary frequency 4%, haematuria 5.5%, nocturia 7.8%, decreased urinary stream 17.1%. Twenty-four of the 43 SNPs that were associated with the toxicity endpoints were validated as identifying patients with toxicity. Twenty of the 24 SNPs were associated with the same toxicity endpoint as reported in the literature: 9 SNPs for urinary symptoms and 11 SNPs for overall toxicity. The other 4 SNPs were associated with a different endpoint. Conclusion: Deep learning algorithms can validate SNPs associated with toxicity after radiotherapy for prostate cancer. The method should be studied further to identify polygenic SNP risk signatures for radiotherapy toxicity. The signatures could then be included in integrated normal tissue complication probability models and tested for their ability to personalize radiotherapy treatment planning.

Non-parametric frailty Cox models for hierarchical time-to-event data

We propose a novel model for hierarchical time-to-event data, for example, healthcare data in which patients are grouped by their healthcare provider. The most common model for this kind of data is the Cox proportional hazard model, with frailties that are common to patients in the same group and given a parametric distribution. We relax the parametric frailty assumption in this class of models by using a non-parametric discrete distribution. This improves the flexibility of the model by allowing very general frailty distributions and enables the data to be clustered into groups of healthcare providers with a similar frailty. A tailored Expectation-Maximization algorithm is proposed for estimating the model parameters, methods of model selection are compared, and the code is assessed in simulation studies. This model is particularly useful for administrative data in which there are a limited number of covariates available to explain the heterogeneity associated with the risk of the event. We apply the model to a clinical administrative database recording times to hospital readmission, and related covariates, for patients previously admitted once to hospital for heart failure, and we explore latent clustering structures among healthcare providers.

Evaluating the effect of healthcare providers on the clinical path of heart failure patients through a semi-Markov, multi-state model

Background

Investigating similarities and differences among healthcare providers, on the basis of patient healthcare experience, is of interest for policy making. Availability of high quality, routine health databases allows a more detailed analysis of performance across multiple outcomes, but requires appropriate statistical methodology.

Methods

Motivated by analysis of a clinical administrative database of 42,871 Heart Failure patients, we develop a semi-Markov, illness-death, multi-state model of repeated admissions to hospital, subsequent discharge and death. Transition times between these health states each have a flexible baseline hazard, with proportional hazards for patient characteristics (case-mix adjustment) and a discrete distribution for frailty terms representing clusters of providers. Models were estimated using an Expectation-Maximization algorithm and the number of clusters was based on the Bayesian Information Criterion.

Results

We are able to identify clusters of providers for each transition, via the inclusion of a nonparametric discrete frailty. Specifically, we detect 5 latent populations (clusters of providers) for the discharge transition, 3 for the in-hospital to death transition and 4 for the readmission transition. Out of hospital death rates are similar across all providers in this dataset. Adjusting for case-mix, we could detect those providers that show extreme behaviour patterns across different transitions (readmission, discharge and death).

Conclusions

The proposed statistical method incorporates both multiple time-to-event outcomes and identification of clusters of providers with extreme behaviour simultaneously. In this way, the whole patient pathway can be considered, which should help healthcare managers to make a more comprehensive assessment of performance.

P1660Therapy treatment, adherence and persistence in chronic heart failure patients: a populaion study, from 2005 to TO 2012 in Lombardy

Background

The treatment with angiotensin-converting enzyme inhibitor (ACEI) or angiotensin receptor II blocker (ARB), beta blocker (BB), and aldosterone antagonist (AA), adherence and persistence to therapies, improve clinical status, prevent hospital admission and reduce mortality in patients with chronic heart failure (CHF).

Purpose

To analyze adherence and persistence to indicated therapies.

Methods

We analyzed, from the Lombardy healthcare system administrative database, the discharge forms of patients with HF-related diagnosis, recorded from 2000 to 2012. We evaluated the adherence using the proportion of days covered (PDC≥80%) method, adjusted for hospitalisations. Medication persistence was identified as a duration of time from initiation to discontinuation of therapy. Patient was considered non-persistent if does non-refill medication within a period of 30 days.

Results

We considered 100,784 HF patients, mean (SD) age 74.54 (11.73) years: of them 636 patients were lost from database, 71,166 were alive (71.06%) and 28,982 did not survive (28.94%) at the end of the study. The mean (SD) number of hospitalizations were 2.16 (1.48) per patient (217,422 in total) and drug prescriptions were 12.28 (7.56) per patient (1,237.784 in total). 77% of patients were treated with ACEI/ARB, 64% with BB and 37% with AA. In the table, we reported the results on adherence and persistence measures.

Prescribed Therapy Total pts, No (%) Days covered, mean (SD) Adherent pts, No (%) Persistent pts, No (%) PDC (%), mean (SD) ACEI/ARB+BB+AA 20,831 (21%) 148 (102) 2,649 (13%) 2,068 (10%) 41 (28) ACEI/ARB+BB 33,617 (33%) 237 (110) 14,528 (43%) 11,165 (33%) 65 (30) ACEI/ARB+AA 9,327 (9%) 157 (107) 1,469 (16%) 1,149 (12%) 43 (29) AA+BB 3,070 (3%) 166 (105) 518 (17%) 386 (13%) 45 (29) ACEI/ARB 23,398 (23%) 270 (103) 13,487 (58%) 10,882 (47%) 74 (28) BB 6,806 (7%) 259 (105) 3,567 (52%) 2,782 (41%) 71 (29) AA 3,735 (4%) 204 (113) 1,133 (30%) 922 (25%) 56 (31) pts, patients.

Conclusions

Findings of this database analysis suggests that while treatment with ACEI/ARB and BB is in line of European Guideline, treatment with AA is very low. Despite recommendations, treatment with a combination of two or three HF drug classes decreases further. Adherence and persistence were moderate across all HF therapies of interest, although around 70% for ACEIs, BBs alone and in combination. This analysis evidences the need to understand the reasons for a limited use of the therapeutic guidelines and the need for much more work to improve adherence and persistence to therapy in CHF patients.

Impact of in-hospital cardiac rehabilitation on mortality and readmissions in heart failure: A population study in Lombardy, Italy, from 2005 to 2012

Aims

The 2016 European guidelines for the diagnosis and treatment of heart failure classified cardiac rehabilitation as a mandatory class I intervention. We aimed to analyse in heart failure patients the impact of an in-hospital cardiac rehabilitation programme on all-cause mortality and readmissions.

Methods

From the Lombardy healthcare administrative database, we analysed in patients with incident heart failure, from 2005 to 2012, the number of all hospitalisations, cardiac rehabilitation admissions, post-discharge deaths, outpatient drug prescriptions and visits. We divided patients into hospitalised for heart failure in acute care only (group A) versus patients with one or more admission to cardiac rehabilitation for an in-hospital cardiac rehabilitation programme (group B).

Results

Of 140,552 incident cases, 100,843 (71%) were in group A and 39,709 (29%) in group B. Patients in group B had 3.26 ± 1.78 admissions to acute care before referral to an in-hospital cardiac rehabilitation programme. Male gender, age in women and comorbidities (more than two) were higher in group B ( P < 0.0001). Patients in group B had a higher number of interventional procedures ( P < 0.0001), drug prescription and outpatient visit rate ( P < 0.0001). Total mortality was 30% in group A versus 29% in group B. At Cox and logistic regression analyses, after adjustment for covariates, group B had a significantly lower risk of mortality (hazard ratio 0.5768, 95% confidence interval 0.5650–0.5888, P < 0.0001) and readmissions (0.7997, 0.7758–0.8244, P < 0.0001) than group A.

Conclusion

This study showed in a large population of heart failure patients that in-hospital cardiac rehabilitation is associated with a reduction of all-cause mortality and rehospitalisations in heart failure. Given its potential significant benefit, referral of heart failure patients to an in-hospital cardiac rehabilitation programme should be promoted.

Immunomodulatory Drugs in the Context of Autologous Hematopoietic Stem Cell Transplantation Associate With Reduced Pro-tumor T Cell Subsets in Multiple Myeloma

Immunomodulatory drugs (IMiDs) are effective therapeutics for multiple myeloma (MM), where in different clinical settings they exert their function both directly on MM cells and indirectly by modulating immune cell subsets, although with not completely defined mechanisms. Here we studied the role of IMiDs in the context of autologous hematopoietic stem cell transplantation on the T cell subset distribution in the bone marrow of newly diagnosed MM patients. We found that after transplantation pro-tumor Th17-Th1 and Th22 cells and their related cytokines were lower in patients treated with IMiDs during induction chemotherapy compared to untreated patients. Of note, lower levels of IL-17, IL-22, and related IL-6, TNF-α, IL-1β, and IL-23 in the bone marrow sera correlated with treatment with IMiDs and favorable clinical outcome. Collectively, our results suggest a novel anti-inflammatory role for IMiDs in MM.

Urn models for response-adaptive randomized designs: a simulation study based on a non-adaptive randomized trial

Recently, response-adaptive designs have been proposed in randomized clinical trials to achieve ethical and/or cost advantages by using sequential accrual information collected during the trial to dynamically update the probabilities of treatment assignments. In this context, urn models-where the probability to assign patients to treatments is interpreted as the proportion of balls of different colors available in a virtual urn-have been used as response-adaptive randomization rules. We propose the use of Randomly Reinforced Urn (RRU) models in a simulation study based on a published randomized clinical trial on the efficacy of home enteral nutrition in cancer patients after major gastrointestinal surgery. We compare results with the RRU design with those previously published with the non-adaptive approach. We also provide a code written with the R software to implement the RRU design in practice. In detail, we simulate 10,000 trials based on the RRU model in three set-ups of different total sample sizes. We report information on the number of patients allocated to the inferior treatment and on the empirical power of the t-test for the treatment coefficient in the ANOVA model. We carry out a sensitivity analysis to assess the effect of different urn compositions. For each sample size, in approximately 75% of the simulation runs, the number of patients allocated to the inferior treatment by the RRU design is lower, as compared to the non-adaptive design. The empirical power of the t-test for the treatment effect is similar in the two designs.

Randomly Reinforced Urn Designs with Prespecified Allocations

We construct a response adaptive design, described in terms of a two-color urn model, targeting fixed asymptotic allocations. We prove asymptotic results for the process of colors generated by the urn and for the process of its compositions. An application of the proposed urn model is presented in an estimation problem context.

Laparoscopic Retroperitoneal Lymph Node Dissection for Clinical Stage I Nonseminomatous Germ Cell Tumors of the Testis: Safety and Efficacy Analyses at a High Volume Center

PURPOSE

The prognosis of stage I nonseminomatous germ cell tumor of the testis is favorable. Early and late side effects of treatment may affect quality of life and survival. We determined the tolerability, safety and efficacy of laparoscopic retroperitoneal lymph node dissection in patients with stage I nonseminomatous germ cell tumor of the testis at a high volume center.

MATERIALS AND METHODS

Unilateral laparoscopic retroperitoneal lymph node dissection was prospectively recorded in 225 patients from 2000 to 2014. Since 2007, patients have been treated at a multidisciplinary clinic and were proposed surgery as an alternative to surveillance or adjuvant chemotherapy. The indication for adjuvant chemotherapy changed during the study period. Descriptive statistics and regression analyses were used to evaluate the domains of safety and oncologic outcomes.

RESULTS

A total of 221 patients were evaluable. Median operative time was 200 minutes. Conversion to open surgery was done in 20 cases (9%). A median of 14 nodes (IQR 11-20) was retrieved. Grade greater than 2 complications in 8 cases (3.6%) increased as the number of retrieved nodes increased. Antegrade ejaculation was maintained in 98.6% of patients. Nodal metastases were found in 29 patients (13%), of whom 7 underwent adjuvant chemotherapy. There were 14 recurrences (6.3%), including 8 of 192 (4.2%) associated with no nodal metastases and 6 of 22 (27.3%) associated with nodal metastases in patients not undergoing adjuvant chemotherapy. At regression analyses lymph node ratio was the only significant factor predictive of recurrence and of the administration of any chemotherapy (each p <0.001). Operative time, the number of retrieved nodes and conversions improved with time.

CONCLUSIONS

In the context of a high volume center laparoscopic retroperitoneal lymph node dissection was safe and its oncologic efficacy was comparable to that of open surgery. Select patients with stage I nonseminomatous germ cell tumor could be offered laparoscopic retroperitoneal lymph node dissection as an alternative to other options.

Trends in heart failure hospitalizations, patient characteristics, in-hospital and 1-year mortality: A population study, from 2000 to 2012 in Lombardy

BACKGROUND

This study was undertaken to evaluate trends in heat failure hospitalizations (HFHs) and 1-year mortality of HFH in Lombardy, the largest Italian region, from 2000 to 2012.

METHODS

Hospital discharge forms with HF-related ICD-9 CM codes collected from 2000 to 2012 by the regional healthcare service (n=699797 in 370538 adult patients), were analyzed with respect to in-hospital and 1-year mortality; Group (G) 1 included most acute HF episodes with primary cardiac diagnosis (70%); G2 included cardiomyopathies without acute HF codes (17%); and G3 included non-cardiac conditions with HF as secondary diagnosis (13%). Patients experiencing their first HFH since 2005 were analyzed as incident cases (n=216782).

RESULTS

Annual HFHs number (mean 53830) and in-hospital mortality (9.4%) did not change over the years, the latter being associated with increasing age (p<0.0001) and diagnosis Group (G1 9.1%, G2 5.6%, G3 15.9%, p<0.0001). Incidence of new cases decreased over the years (3.62 [CI 3.58-3.67] in 2005 to 3.13 [CI 3.09-3.17] in 2012, per 1000 adult inhabitants/year, p<0.0001), with an increasing proportion of patients aged ≥85y (22.3% to 31.4%, p<0.0001). Mortality lowered over time in <75y incident cases, both in-hospital (5.15% to 4.36%, p<0.0001) and at 1-year (14.8% to 12.9%, p=0.0006).

CONCLUSIONS

The overall burden and mortality of HFH appear stable for more than a decade. However, from 2005 to 2012, there was a reduction of new, incident cases, with increasing age at first hospitalization. Meanwhile, both in-hospital and 1-year mortality decreased in patients aged <75y, possibly due to improved prevention and treatment.

Functional regression models: Some directions of future research

We congratulate the authors for their excellent work that provides a clear overview of the large and now mature field of regression models for functional data. We here complement their discussion indicating some directions of further research that we deem particularly important.

Validation of the Italian Version of the Haemophilia Activities List

BACKGROUND

The aim of this study was to provide an Italian version of the Haemophilia Activities List (HAL) and check its reliability in Italian medical centers.

METHODS

The Italian version of this assessment was administered to 80 patients (aged 18-65 years) affected by haemophilia A and B (moderate or severe). The validation was accomplished by comparing it to the revised and expanded Arthritis Impact Measurement Scales (AIMS2).

RESULTS

The internal consistency of the Italian version of the HAL had statistically high results: Cronbach's α 0.957-0.579. The highest internal consistency was measured in the domains 'leg functionality' and in the overall points of the HAL questionnaire. The correlation between the AIMS2, which has been translated into Italian, and the version of the HAL questionnaire that we proposed, yielded good results for the following correlations: AIMS2 all and HAL overall (r = 0.64), AIMS2 physical function and HAL overall (r = 0.66), AIMS2 pain and HAL overall (r = 0.66).

CONCLUSION

The Italian version of the HAL questionnaire presents both internal coherence and convergent validity. It can be used in addition to other functional tests to measure outcomes in moderate and severe haemophiliac diseases or to determine the quality of life as observed in the everyday life of patients.

Methodological issues on the use of administrative data in healthcare research: the case of heart failure hospitalizations in Lombardy region, 2000 to 2012

BACKGROUND

Administrative data are increasingly used in healthcare research. However, in order to avoid biases, their use requires careful study planning. This paper describes the methodological principles and criteria used in a study on epidemiology, outcomes and process of care of patients hospitalized for heart failure (HF) in the largest Italian Region, from 2000 to 2012.

METHODS

Data were extracted from the administrative data warehouse of the healthcare system of Lombardy, Italy. Hospital discharge forms with HF-related diagnosis codes were the basis for identifying HF hospitalizations as clinical events, or episodes. In patients experiencing at least one HF event, hospitalizations for any cause, outpatient services utilization, and drug prescriptions were also analyzed.

RESULTS

Seven hundred one thousand, seven hundred one heart failure events involving 371,766 patients were recorded from 2000 to 2012. Once all the healthcare services provided to these patients after the first HF event had been joined together, the study database totalled about 91 million records. Principles, criteria and tips utilized in order to minimize errors and characterize some relevant subgroups are described.

CONCLUSIONS

The methodology of this study could represent the basis for future research and could be applied in similar studies concerning epidemiology, trend analysis, and healthcare resources utilization.

Interacting reinforced-urn systems

We introduce a class of discrete-time stochastic processes generated by interacting systems of reinforced urns. We show that such processes are asymptotically partially exchangeable and we prove a strong law of large numbers. Examples and the analysis of particular cases show that interacting reinforced-urn systems are very flexible representations for modelling countable collections of dependent and asymptotically exchangeable sequences of random variables.

Dynamic clustering of hazard functions: an application to disease progression in chronic heart failure

We analyse data collected from the administrative datawarehouse of an Italian regional district (Lombardia) concerning patients affected by Chronic Heart Failure. The longitudinal data gathering for each patient hospital readmissions in time, as well as patient-specific covariates, is studied as a realization of non homogeneous Poisson process. Since the aim behind this study is to identify groups of patients behaving similarly in terms of disease progression and then healthcare consumption, we conjectured the time segments between two consecutive hospitalizations to be Weibull distributed in each hidden cluster. Adding a frailty term to take into account the within subjects unknown variability, the corresponding patient-specific hazard functions are reconstructed. Therefore, the comprehensive distribution for each time to event variable is modelled as a Weibull Mixture. We are then able to easily interpret the related hidden groups as healthy, sick, and terminally ill subjects.

Use of Depth Measure for Multivariate Functional Data in Disease Prediction: An Application to Electrocardiograph Signals

In this paper we develop statistical methods to compare two independent samples of multivariate functional data that differ in terms of covariance operators. In particular we generalize the concept of depth measure to this kind of data, exploiting the role of the covariance operators in weighting the components that define the depth. Two simulation studies are carried out to validate the robustness of the proposed methods and to test their effectiveness in some settings of interest. We present an application to Electrocardiographic (ECG) signals aimed at comparing physiological subjects and patients affected by Left Bundle Branch Block. The proposed depth measures computed on data are then used to perform a nonparametric comparison test among these two populations. They are also introduced into a generalized regression model aimed at classifying the ECG signals.

Detecting and visualizing outliers in provider profiling via funnel plots and mixed effect models

In this work we propose the use of a graphical diagnostic tool (the funnel plot) to detect outliers among hospitals that treat patients affected by Acute Myocardial Infarction (AMI). We consider an application to data on AMI hospitalizations recorded in the administrative databases of our regional district. The outcome of interest is the in-hospital mortality, a variable indicating if the patient has been discharged dead or alive. We then compare the results obtained by graphical diagnostic tools with those arising from fitting parametric mixed effects models to the same data.

Optical identification of subjects at high risk for developing breast cancer

A time-domain multiwavelength (635 to 1060 nm) optical mammography was performed on 147 subjects with recent x-ray mammograms available, and average breast tissue composition (water, lipid, collagen, oxy- and deoxyhemoglobin) and scattering parameters (amplitude a and slope b) were estimated. Correlation was observed between optically derived parameters and mammographic density [Breast Imaging and Reporting Data System (BI-RADS) categories], which is a strong risk factor for breast cancer. A regression logistic model was obtained to best identify high-risk (BI-RADS 4) subjects, based on collagen content and scattering parameters. The model presents a total misclassification error of 12.3%, sensitivity of 69%, specificity of 94%, and simple kappa of 0.84, which compares favorably even with intraradiologist assignments of BI-RADS categories.

Estimating point and interval frequency of antigen-specific CD4+ T cells based on short in vitro expansion and improved poisson distribution analysis

BACKGROUND

Knowledge of antigen-specific CD4(+) T cells frequencies is pivotal to the choice of the antigen to be used in anti-viral and anti-tumor vaccination procedures and for monitoring of immune responses. Methods that employ small cell numbers from patient samples, are easy to perform and do not require complex techniques/instrumentations and therefore standardization are desirable.

METHODOLOGY/PRINCIPAL FINDINGS

Purified blood CD4(+) T cells from healthy donors were cultured with autologous antigen presenting cells in several replicate wells in equal numbers in the absence (un-stimulated wells) or in the presence of synthetic peptides corresponding to viral antigens promiscuous HLA-DR epitopes (antigen-stimulated wells). At day 7 of culture low dose IL-2 was added and at day 14 IFN-γ and IL-5 release in the supernatant was measured. A statistical analysis approach, based on Poisson distribution, was then implemented to calculate the frequency of viral-specific CD4(+) T cells. We first determined a patient-specific exceptionality threshold of cytokine release in the un-stimulated wells and then, based on this threshold, we counted the inactive/active wells within the antigen-stimulated wells. This number, along with the number of cells per well, allowed the point and interval estimates of frequencies. A ready-to-use Excel worksheet template with automatic calculations for frequencies estimate was developed and is provided as a supplemental file (Table S9).

CONCLUSIONS/SIGNIFICANCE

We report a simple experimental procedure combining short term in vitro cell culture with statistical analysis to calculate the frequency of antigen-specific CD4(+) T cells. The detailed experimental procedure along with the Excel applicative are a valuable tool for monitoring immune responses in the clinical practice.

CD4+ T cells against human papillomavirus-18 E7 in patients with high-grade cervical lesions associate with the absence of the virus in the cervix

Cervical neoplastic lesions are associated with infection by high-risk human papilloma-viruses (HPV). The two genotypes most frequently found in the lesions are HPV-16 and HPV-18 with a prevalence of 50-60% and 15-18%, respectively. The E6 and E7 viral oncoproteins are involved in the transformation process and represent foreign antigens for the host. We previously reported that anti-HPV-18 E6 CD4(+) T cells are present in patients with high-grade HPV-18-expressing cervical lesions but also in 50% of the total consecutive patients tested, independently of the HPV type carried. These results indicated that HPV-18 E6 is immunogenic and suggested that all responsive patients, irrespective of the HPV expressed, had encountered HPV-18 and cleared the infection. Here, we investigated anti-HPV-18 E7 CD4(+) T-cell immunity in a cohort of 23 HPV-18 E6-responsive patients. We found that, although E7-specific CD4(+) T cells were present in all women, a robust T helper type (Th1)/Th2 type response against E7 was associated with HPV-18-negative status, suggesting that indeed these patients might have cleared the virus. In agreement with this hypothesis, we found strong anti-E7 CD4(+) T-cell immunity in 20% of 24 healthy donors without evidence of disease. In contrast, a robust Th1/Th2 type response against E6 but not E7 correlated with a lack of disease relapse and/or infection recurrence but did not discriminate between HPV-18-positive and HPV-18-negative patients. Collectively, our data suggest different roles for anti-HPV-18 E6 and E7 CD4(+) T cells in anti-viral and anti-tumour immunity.

pT1 penile squamous cell carcinoma: a clinicopathologic study of 56 cases treated by CO2 laser therapy

OBJECTIVE

To evaluate the pathologic characteristics that are associated with outcomes in pT1 penile squamous cell carcinoma (SCC) treated with laser excision.

STUDY DESIGN

Peniscopic magnification and 5% acetic acid application were performed prior to CO2 laser excision. Specimens were reviewed to reassess stage, grade, invasion depth, carcinoma in situ, margins, tumor extension, lymphovascular invasion and human papillomavirus infection. Association between local recurrence (LR) and prognostic factors was established with Fisher exact test, chi2 test for categorical variables and Wilcoxon rank sum test for continuous variables.

RESULTS

After a median follow-up of 66 months, 53 of 56 patients were alive and disease free; 3 died of unrelated and intercurrent diseases. Thirteen had an LR, with 4 experiencing multiple recurrences and 1 needing a partial amputation. Two patients had inguinal nodal metastasis in 1 node. LR had a positive correlation with positive surgical margins and depth of invasion and a negative correlation with tumor extension.

CONCLUSION

Histopathologic parameters such as margin status, depth of invasion and tumor extension are predictors of LR in T1 penile SCC treated by CO2 laser excision. A logistic model could estimate each patient's risk of LR.

[Cardiological emergency network in Lombardy]

AIMS

To achieve a reduction of time to reperfusion through the organization of an interhospital network and the involvement of the Regional Health Authority.

METHODS

Four major endpoints were identified: institutional governance action, clinical management of acute ST-elevation myocardial infarction (STEMI), priority actions for cardiac arrest and early defibrillation, actions to avoid the delay related to decision-making, and logistic factors. Since 2001 in the urban area of Milan a network has been operating among 23 coronary care units, the 118 Dispatch Center (national free number for medical emergencies) and the Health Country Government Agency named Group for Prehospital Cardiac Emergency. In order to monitor the network activity and time to treatment and clinical outcomes a periodic monthly survey, called MOMI (One Month Monitoring Myocardial Infarction), was undertaken and repeated twice yearly. Data were evaluated according to hospital admission modality.

RESULTS

Global times are: symptom onset to first medical contact 116 min (interquartile range [IQR] 189), time to first ECG 7 min (IQR 12), door-to-balloon time 77 min (IQR 81.7). Non-parametric test showed that the modality of hospital admittance was the most critical determinant of door-to-balloon time. The shortest one (49.5 min) was that of patients transported by means of advanced rescue units with 12-lead ECG teletransmission and activation of a fast track directly to the cath lab.

CONCLUSIONS

Our data show how in a complex urban area the organization of an interhospital network and the availability of ECG teletransmission are effective in reducing time to reperfusion, in the treatment of major arrhythmias and in pre-alert of coronary care units and cath labs in case of confirmed STEMI. This experience also stimulated an improvement in technological equipment of rescue units with extension of 12-lead teletransmission to basic life support units. Through the Health Country Government Agency and the Scientific Societies we carry on with our job to create a regional network for cardiac emergency involving all the hospitals.

IFN-gamma produced by human papilloma virus-18 E6-specific CD4+ T cells predicts the clinical outcome after surgery in patients with high-grade cervical lesions

Cervical neoplastic lesions are associated with infection by high-risk human papilloma viruses (HPVs). HPV-16 and HPV-18 are the most common genotypes. It has been proposed that development of HPV-16-positive cervical lesions is associated with impaired CD4(+) T cell immunity against early Ags. The aim of the study was to evaluate whether this impairment also applies to HPV-18. We investigated the presence and the quality of anti-HPV-18 E6 CD4(+) T cell responses in the blood of 37 consecutive patients with high-grade cervical lesions, 25 normal donors, and 20 cord bloods. The immune infiltrate in the cervical lesions was also evaluated. The characteristics of the responses were correlated to the clinical outcome. We found that one or more HPV-18 E6 peptides, containing naturally processed epitopes, were able to induce a response in 40-50% of the patients, depending on the effector function tested. Importantly, these percentages rose to 80-100% when HPV-18-positive patients were considered. HPV-18 E6-specific CD4(+) T cells produced mixed Th1/Th2 responses and statistical analysis of the cytokines produced revealed that the amount of IFN-gamma released could predict infection persistence and/or disease relapse after surgery. Finally, we found that a higher number of infiltrating CD4(+) and T-bet(+) T cells in the lesions correlated with a favorable clinical outcome. Our results strongly suggest a relevant role for CD4(+) T cells in the control of the HPV-18 compared with HPV-16 infections in patients with high-grade cervical lesions and identify an immunologic parameter potentially useful for patients' stratification.