Prediction of depression among patients with cardiovascular disease scheduled cardiac surgery using an AI-empowered pipeline

Introduction

Several studies have demonstrated, that one in three patients with cardiovascular disease (CVD) suffers from depression, and depression increases the likelihood for cardiac morbidity and mortality in the CVD population by 2–3-fold, independently of traditional risk factors or gender.

Purpose

The aim of this work is to predict depression in patients with CVD.

Methods

The clinical study was conducted in the cardiac surgical intensive care unit of The Central Clinical Hospital, the Medical University of Lodz in Poland, among patients scheduled for elective coronary artery bypass graft surgery (CABG). 224 patients signed an informed consent form, met the inclusion criteria and were enrolled in the study. All the patients had chronic coronary syndromes. The inclusion criteria were: consecutive adult patients scheduled for CABG surgery or CABG surgery with cardiac valve repair or replacement (CVR). The study population was examined by a psychiatrist the day prior to the scheduled operation, a diagnosis of major depressive disorder (MDD) was established on the basis of DSM-5 criteria.

A data curation pipeline was applied to automatically remove outliers and duplicated fields in the input dataset. An AI-empowered pipeline was developed to classify patients at higher risk for depression. Random downsampling with replacement was applied to deal with the increased class imbalance by taking into consideration two confound factors, namely the Mini Mental State Examination and Hemoglobin concentration <10mg/dl. The downsampling process was repeated K times. In each iteration, three bagging and boosting ML schemas were utilized for the classification task including the AdaBoost (adaptive boosting), Random Forests and Extreme Gradient boosting trees (XGBoost). To this end, a nested cross-validation process was applied for hyperparameter optimization and model validation, where: (i) a 3-fold cross-validation process was first applied to seek for the optimal set of hyperparameters based on the grid search approach by tuning core parameters, including the learning rate, number of estimators, and max depth, among others, and (ii) a stratified 5-fold cross-validation process was subsequently used to evaluate the performance of the best model from the previous stage by computing the classification accuracy, sensitivity, specificity, and area under the ROC curve (AUC). The performance evaluation results were averaged across the 5 folds and across the downsampling iterations. Shappley additive explanation analysis was finally applied to provide explainable risk factors for depression.

Results

sRAGE was significantly correlated with depression (r=0.32, p=0.038). The Random forests classifier presented the highest performance to predict depression (Accuracy: 0.71, Sensitivity: 0.71, Specificity: 0.75 and AUC: 0.74).

Conclusions

Depression can be predicted with 71% accuracy at patients with CVD and elevated sRAGE values.

Funding Acknowledgement

Type of funding sources: Public grant(s) – EU funding. Main funding source(s): HORIZON2020

Accumulation of copy number alterations and clinical progression across advanced prostate cancer

BACKGROUND

Genomic copy number alterations commonly occur in prostate cancer and are one measure of genomic instability. The clinical implication of copy number change in advanced prostate cancer, which defines a wide spectrum of disease from high-risk localised to metastatic, is unknown.

METHODS

We performed copy number profiling on 688 tumour regions from 300 patients, who presented with advanced prostate cancer prior to the start of long-term androgen deprivation therapy (ADT), in the control arm of the prospective randomised STAMPEDE trial. Patients were categorised into metastatic states as follows; high-risk non-metastatic with or without local lymph node involvement, or metastatic low/high volume. We followed up patients for a median of 7 years. Univariable and multivariable Cox survival models were fitted to estimate the association between the burden of copy number alteration as a continuous variable and the hazard of death or disease progression.

RESULTS

The burden of copy number alterations positively associated with radiologically evident distant metastases at diagnosis (P=0.00006) and showed a non-linear relationship with clinical outcome on univariable and multivariable analysis, characterised by a sharp increase in the relative risk of progression (P=0.003) and death (P=0.045) for each unit increase, stabilising into more modest increases with higher copy number burdens. This association between copy number burden and outcome was similar in each metastatic state. Copy number loss occurred significantly more frequently than gain at the lowest copy number burden quartile (q=4.1 × 10-6). Loss of segments in chromosome 5q21-22 and gains at 8q21-24, respectively including CHD1 and cMYC occurred more frequently in cases with higher copy number alteration (for either region: Kolmogorov-Smirnov distance, 0.5; adjusted P<0.0001). Copy number alterations showed variability across tumour regions in the same prostate. This variance associated with increased risk of distant metastases (Kruskal-Wallis test P=0.037).

CONCLUSIONS

Copy number alteration in advanced prostate cancer associates with increased risk of metastases at diagnosis. Accumulation of a limited number of copy number alterations associates with most of the increased risk of disease progression and death. The increased likelihood of involvement of specific segments in high copy number alteration burden cancers may suggest an order underlying the accumulation of copy number changes.

TRIAL REGISTRATION

ClinicalTrials.gov NCT00268476 , registered on December 22, 2005. EudraCT  2004-000193-31 , registered on October 4, 2004.

Abstract 401: Single-cell transcriptome and chromatin sequencing uncover gene expression and gene regulatory patterns associated with enzalutamide resistance

Resistance to androgen receptor-targeted therapy due to tumor heterogeneity and clonal evolution is a key challenge for improving prostate cancer outcomes. Despite this, the transcriptomic and chromatin accessibility changes contributing to the emergence of resistance remain incompletely understood at the level of individual cells. Using single-cell assays for transposase-accessible chromatin (ATAC) and RNA sequencing in models of early treatment response and resistance to enzalutamide, we previously identified pre-existing and persistent cell subpopulations that possess regenerative potential when subjected to treatment. Here we analyze the chromatin and transcriptomes of these single cells to characterize their gene regulation and gene expression trajectories. We present evidence of a model of enzalutamide resistance emergence in which the pre-existing and treatment-persistent cells regenerate the bulk of resistant cells. This process is underpinned by chromatin reprogramming that increases the overall relaxation of chromatin upon resistance. We show that the reprogramming of the chromatin further differentially contributes to transcription factor-mediated transcriptional reprogramming via DNA motif exposure in different cell subpopulations. For example, in the treatment-persistent cells, we identify chromatin configurations characterized by the exposure of DNA motifs for GATA2, RELA (a NFkB subunit), CREB1, and E2F1. Pre-existing and treatment-persistent cells consistently display transcriptional features of high developmental potential and RNA velocity analysis identifies them as precursors of cell populations that arise from enzalutamide treatment. We also analyze the pre-existing and treatment-persistent cells in spatial transcriptomics of prostate cancer patient specimens based on their characteristic gene expression profiles. We find these cells to be enriched in cancerous regions of the tissue but also detect them within apparent benign regions, which has potential implications for treatment choice. In summary, we show patterns of gene expression regulation in preclinical models and patient samples that uncover mechanisms of resistance to androgen receptor-targeted therapy in prostate cancer.

Citation Format: Sinja Taavitsainen, Nikolai Engedal, Shaolong Cao, Florian Handle, Andrew Erickson, Stefan Prekovic, Daniel Wetterskog, Teemu Tolonen, Elisa M. Vuorinen, Antti Kiviaho, Reetta Nätkin, Tomi Häkkinen, Wout Devlies, Sallamari Henttinen, Roosa Kaarijärvi, Mari Lahnalampi, Heidi Kaljunen, Karolina Nowakowska, Heimo Syvälä, Merja Bläuer, Paolo Cremaschi, Frank Claessens, Tapio Visakorpi, Teuvo L. Tammela, Teemu Murtola, Kirsi J. Granberg, Alastair D. Lamb, Kirsi Ketola, Ian G. Mills, Gerhardt Attard, Wenyi Wang, Matti Nykter, Alfonso Urbanucci. Single-cell transcriptome and chromatin sequencing uncover gene expression and gene regulatory patterns associated with enzalutamide resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 401.

Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse

Prostate cancer is heterogeneous and patients would benefit from methods that stratify those who are likely to respond to systemic therapy. Here, we employ single-cell assays for transposase-accessible chromatin (ATAC) and RNA sequencing in models of early treatment response and resistance to enzalutamide. In doing so, we identify pre-existing and treatment-persistent cell subpopulations that possess regenerative potential when subjected to treatment. We find distinct chromatin landscapes associated with enzalutamide treatment and resistance that are linked to alternative transcriptional programs. Transcriptional profiles characteristic of persistent cells are able to stratify the treatment response of patients. Ultimately, we show that defining changes in chromatin and gene expression in single-cell populations from pre-clinical models can reveal as yet unrecognized molecular predictors of treatment response. This suggests that the application of single-cell methods with high analytical resolution in pre-clinical models may powerfully inform clinical decision-making.

Basophil activation test in allergy diagnostics

The prevalence of allergic diseases in Poland and in the world continues to rise in recent years. The most commonly used methods for diagnosing IgE – dependent allergies are skin prick testing (SPT) and assessment of specific IgE (sIgE) directed against specific allergens. However, both methods have some disadvantages and the obtained results may be inconsistent. In particular, routine diagnostic tests are not always effective for some drugs and foods. Consequently, additional laboratory tools should be used. Basophil activation test (BAT) based on flow cytometry is a promising diagnostic method. The present paper demonstrates the usefulness and effectiveness of BAT protocols in allergy diagnosis in scientific research. In comparison to routinely used diagnostic methods, BAT is an expensive and complicated laboratory tool. However, it offers the possibility to efficiently and effectively recognize allergies. Introducing BAT into routine diagnostics in allergology is problematic because this method has not yet been standardized and validated. Therefore, there is a justified need to continue research in this field. If standardized and validated, BAT may offer a reasonable improvement in allergy diagnostics in the future.

Acute exposure of zebrafish (Danio rerio) larvae to environmental concentrations of selected antidepressants: Bioaccumulation, physiological and histological changes

Antidepressants have been detected in surface waters worldwide at ng-μg/L concentration. These compounds can exert adverse effects on fish even at low levels. But, all previous analyses have concentrated on adult fish. The aim of the study was to assess the effect of environmental concentrations of sertraline, paroxetine, fluoxetine and mianserin, and their mixtures on such unusual endpoints as physiological and histological changes of zebrafish (Danio rerio) larvae. We also determined the bioconcentration of the pharmaceuticals. Fish Embryo Toxicity test was used to analyze the influence on developmental progression. Histological sections were stained with hematoxylin and eosin. Proliferating cells in liver were determined immunohistochemically by detection of Proliferating Cell Nuclear Antigens. The bioconcentration factor was measured by liquid chromatography coupled to mass spectrometry. Pharmaceuticals were used at low, medium and high concentrations in mixtures and at medium concentration as single compound. Exposure to the analyzed pharmaceuticals increased the rate of abnormal embryo and larvae development, accelerated the hatching time and affected the total hatching rate. Three-times lower proliferation of hepatocytes was observed in larvae exposed to paroxetine, mianserin, sertraline and the mixture of the pharmaceuticals at the highest concentrations. The highest bioaccumulation factor (BCF) was obtained for sertraline. The BCF of the analyzed compounds was higher if the organisms were exposed to the mixtures than to single pharmaceuticals. To conclude, the exposure of zebrafish larvae to selected antidepressants and their mixtures may cause disturbances in the organogenesis of fish even at environmental concentrations.

Phase 1-2 study of progesterone receptor (PR) inhibition with extended-release (ER) onapristone (ONA) alone or in combination with abiraterone (AA) in patients (pts) with castration-resistant prostate cancer (CRPC) incorporating plasma DNA analysis to define androgen receptor (AR) status

5071

Background: An urgent need exists for new therapies after progression (PD) onAA and enzalutamide (ENZ). Increased PR expression or progesterone-activating AR mutations have been associated with resistance to AR targeting. We aimed to test ONA, a type I PR antagonist with clinical activity in PRpos cancers, in AA/enz-resistant CRPC. In a prospectively defined exploratory analysis, we aimed to report outcome by plasma AR status ( pAR). Methods: This was a multi-institution, open label phase I/II clinical trial in pts progressing after ENZ/AA. Pts were first treated with single agent (SA) ONA using a randomised dose escalation design. ONA at 2 doses was then combined with AA (1000mg od with pred 5mg bid) in pts progressing on AA. The primary end-points were safety, pharmacokinetics (PK) and anti-tumor activity split by p AR. Archival and metastatic biopsies were collected when possible and tested for PR status. p AR was studied using previous methods (Romanel STM 2015). Results: 21 pts received SA ONA (5 = 10mg/ 5 = 20mg/ 4 = 30mg/ 4 = 40mg /3 = 50mg BID) and 15 pts received ONA-AA combination (5 = 30mg ONA BID, 10 = 50mg ONA BID). There were not DLTs or significant LFT abnormalities and no G3/4 adverse events (AE), no treatment discontinuations due to AEs and no SAEs considered related to ONA. PK in SA ONA observed active plasma concentrations and no interaction with AA. Of 32 evaluated pts 15 had a 2105T > A (p.L702H) or 2632A > G (p.T878A) AR mutation detected in plasma pre-treatment and 1 had AR copy number gain. PSA declines were not observed with SA ONA but in 2 pts with combination (-30%, -7%) who were AR normal. The rPFS on SA ONA was 2.8 months for AR normal and 2.6 for AR aberrant (Hazard ratio (HR) 1.41; 95% CI, 0.62-3.72; P 0.48) and on combination was 4.4 months for AR normal (8/15) and 2.2 for AR aberrant (7/15) (HR 6.08; 95%CI, 6.32-221.9; P < 0.001). Conclusions: ONA is safe in CRPC as SA and in combination with AA. There was no difference in rPFS by p AR status for SA ONA but on the combination with AA, pts who were plasma AR normal had a significantly longer rPFS. Clinical trial information: NCT02049190.

Androgen receptor expression in circulating tumour cells from castration-resistant prostate cancer patients treated with novel endocrine agents

BACKGROUND

Abiraterone and enzalutamide are novel endocrine treatments that abrogate androgen receptor (AR) signalling in castration-resistant prostate cancer (CRPC). Here, we developed a circulating tumour cells (CTCs)-based assay to evaluate AR expression in real-time in CRPC and investigated nuclear AR expression in CTCs in patients treated with enzalutamide and abiraterone.

METHODS

CTCs were captured and characterised using the CellSearch system. An automated algorithm to identify CTCs and quantify AR expression was employed. The primary aim was to evaluate the association between CTC AR expression and prior treatment with abiraterone or enzalutamide.

RESULTS

AR expression in CTCs was evaluated in 94 samples from 48 metastatic CRPC patients. We observed large intra-patient heterogeneity of AR expression in CTCs. Prior exposure to abiraterone or enzalutamide was not associated with a change in CTCs AR expression (median intensity and distribution of AR-positive classes). In support of this, we also confirmed maintained nuclear AR expression in tissue samples collected after progression on abiraterone. AR staining also identified additional AR-positive CD45-negative circulating cells that were CK-negative/weak and therefore missed using standard protocols. The number of these events correlated with traditional CTCs and was associated with worse outcome on univariate analysis.

CONCLUSIONS

We developed a non-invasive method to monitor AR nuclear expression in CTCs. Our studies confirm nuclear AR expression in CRPC patients progressing on novel endocrine treatments. Owing to the significant heterogeneity of AR expression in CTCs, studies in larger cohorts of patients are required to identify associations with outcome.

Interactions of abiraterone, eplerenone, and prednisolone with wild-type and mutant androgen receptor: a rationale for increasing abiraterone exposure or combining with MDV3100

Prostate cancer progression can be associated with androgen receptor (AR) mutations acquired following treatment with castration and/or an antiandrogen. Abiraterone, a rationally designed inhibitor of CYP17A1 recently approved for the treatment of docetaxel-treated castration-resistant prostate cancer (CRPC), is often effective, but requires coadministration with glucocorticoids to curtail side effects. Here, we hypothesized that progressive disease on abiraterone may occur secondary to glucocorticoid-induced activation of mutated AR. We found that prednisolone plasma levels in patients with CRPC were sufficiently high to activate mutant AR. Mineralocorticoid receptor antagonists, such as spironolactone and eplerenone that are used to treat side effects related to mineralocorticoid excess, can also bind to and activate signaling through wild-type or mutant AR. Abiraterone inhibited in vitro proliferation and AR-regulated gene expression of AR-positive prostate cancer cells, which could be explained by AR antagonism in addition to inhibition of steroidogenesis. In fact, activation of mutant AR by eplerenone was inhibited by MDV3100, bicalutamide, or greater concentrations of abiraterone. Therefore, an increase in abiraterone exposure could reverse resistance secondary to activation of AR by residual ligands or coadministered drugs. Together, our findings provide a strong rationale for clinical evaluation of combined CYP17A1 inhibition and AR antagonism.

[Evaluation of treatment and preventive care for recurrent urolithiasis in children]

Among 425 children with urolithiasis treated in the Paediatric Clinical Department of the National Research Institute of Mother and Child in Warsaw between 1976-1997, 50 of them i.e. 11.7% (26 boys and 24 girls) had recurrent urolithiasis. Patients' age was from 10 months to 16 years and 5 months. The number of recurrences of uroliothiasis before treatment in the Institute was from 1 to 8. Most of the children had numerous surgical operations, some of them excreted stones spontaneously. The etiology was determined in all cases. A metabolic cause of urolithiasis was found in 34 cases, i.e. 68% of the analysed group. They were as follows: idiopathic hypercalcuria--24 cases, uric acid urolithiasis--5 cases, cystynuria--4 cases, and incomplete distal renal tubular acidosis--1 case. Other reasons for urolithiasis were: infection--7 cases, idiopathic urolithiasis--8 cases, ren spongiosum--1 case. Prevention of recurrences depending on the etiology was successful. In 45 cases no recurrences were found. Recurrent urolithiasis was observed in 4 cases of cystynuria and in one case of incomplete tubular acidosis. The observation period was from 3-19 years.

[Clinical evaluation of Uro-Vaxom in treatment of recurrent urinary tract infections in girls]

Uro-Vaxom was used in the treatment of recurrent urinary tract infections in 28 girls. Most of them (27/28) tolerated the drug very well, no side effects were observed. We stopped administration of the Uro-Vaxom in one girl during the first month of treatment because of vomiting. Uro-Vaxom efficiency was, therefore, evaluated in 27 girls. Uro-Vaxom was found to be a valuable drug, supplementing antibiotic therapy in recurrent urinary tract infections caused by E. coli.

[Bacterial flora in urinary tract infections of children and susceptibility to drugs]

The material consisted of 902 strains isolated from children with urinary tract infection with significant bacteriuria. Among isolated strains, Enterobacteriaceae consisted 67.4%, Gram-positive cocci 18.8% and non-fermenting Gram-negative bacilli (both against Gram-negative bacilli and Gram-positive cocci), appeared aminoglycosides and III generation cephalosporins (from 63 to 83% of susceptible strains). K. pneumoniae and P. aeruginosa were most resistant to antimicrobials tested. The authors point out that empiric antibiotic therapy of bacterial urinary tract infections in children which is not preceded by identification of the pathogen and determination of its drug susceptibility, can be ineffective in over 50% of cases.

Amino acid composition of cereal and oilseed

Quantitative amino acid composition of acid hydrolysates was determined for samples of some Polish varieties of cereal grain (wheat, rye, barley, oats, millet and buckwheat) and oilseed (rapeseed, sunflower, poppy and soybean). Comparison of investigated genera was done.