Machine learning-based prediction of the post-thrombotic syndrome: Model development and validation study

Integration of bulk RNA-seq and scRNA-seq reveals transcriptomic signatures associated with deep vein thrombosis

Background

Deep vein thrombosis (DVT) is a prevalent peripheral vascular disease. The intricate and multifaceted nature of the associated mechanisms hinders a comprehensive understanding of disease-relevant targets. This study aimed to identify and examine the most distinctive genes linked to DVT.

Methods

In this study, the bulk RNA sequencing (bulk RNA-seq) analysis was conducted on whole blood samples from 11 DVT patients and six control groups. Topology analysis was performed using seven protein-protein interaction (PPI) network algorithms. The combination of weighted correlation network analysis (WGCNA) and clinical prediction models was employed to validate hub DEGs. Furthermore, single-cell RNA sequencing (scRNA-seq) was performed on peripheral blood samples from 3 DVT patients and three control groups to probe the cellular localization of target genes. Based on the same methodology as the internal test set, 12 DVT patients and six control groups were collected to construct an external test set and validated using machine learning (ML) algorithms and immunofluorescence (IF). Concurrently, the examination of the pathways in disparate cell populations was conducted on the basis of the CellChat pathway.

Results

A total of 193 DEGs were identified in the internal test set. Additionally, a total of eight highly characteristic genes (including TLR1, TLR7, TLR8, CXCR4, DDX58, TNFSF10, FCGR1A and CD36) were identified by the PPI network algorithm. In accordance with the WGCNA model, the aforementioned genes were all situated within the blue core module, exhibiting a correlation coefficient of 0.84. The model demonstrated notable disparities in TLR8 (P = 0.018, AUC = 0.847), CXCR4 (P = 0.00088, AUC = 1.000), TNFSF10 (P = 0.00075, AUC = 0.958), and FCGR1A (P = 0.00022, AUC = 0.986). Furthermore, scRNA-seq demonstrated that B cells, T cells and monocytes play an active role in DVT. In the external validation set, CXCR4 was validated as a potential target by the ML algorithm and IF. In the context of the CellChat pathway, it indicated that MIF - (CD74 + CXCR4) plays a potential role.

Conclusion

The findings of this study indicate that CXCR4 may serve as a potential genetic marker for DVT, with MIF - (CD74 + CXCR4) potentially implicated in the regulatory mechanisms underlying DVT.

Artificial Intelligence in Vascular Diseases: From Clinical Practice to Medical Research and Education

Artificial Intelligence (AI) has brought new opportunities in medicine, with a great potential to improve care provided to patients. Given the technical complexity and continuously evolving field, it can be challenging for vascular specialists to anticipate and foresee how AI will shape their practice. The aim of this review is to provide an overview of the current landscape of applications of AI in clinical practice for the management of non-cardiac vascular diseases including aortic aneurysm, peripheral artery disease, carotid stenosis, and venous diseases. The review describes and highlights how AI has the potential to shape the three pillars in the management of vascular diseases including clinical practice, medical research and education. In the limelight of these results, we show how AI should be considered and developed within a responsible ecosystem favoring transdisciplinary collaboration, where multiple stake holders can work together to face current challenges and move forward future directions.

Machine Learning-Based Predictive Models for Patients with Venous Thromboembolism: A Systematic Review

BACKGROUND

 Venous thromboembolism (VTE) is a chronic disorder with a significant health and economic burden. Several VTE-specific clinical prediction models (CPMs) have been used to assist physicians in decision-making but have several limitations. This systematic review explores if machine learning (ML) can enhance CPMs by analyzing extensive patient data derived from electronic health records. We aimed to explore ML-CPMs' applications in VTE for risk stratification, outcome prediction, diagnosis, and treatment.

METHODS

 Three databases were searched: PubMed, Google Scholar, and IEEE electronic library. Inclusion criteria focused on studies using structured data, excluding non-English publications, studies on non-humans, and certain data types such as natural language processing and image processing. Studies involving pregnant women, cancer patients, and children were also excluded. After excluding irrelevant studies, a total of 77 studies were included.

RESULTS

 Most studies report that ML-CPMs outperformed traditional CPMs in terms of receiver operating area under the curve in the four clinical domains that were explored. However, the majority of the studies were retrospective, monocentric, and lacked detailed model architecture description and external validation, which are essential for quality audit. This review identified research gaps and highlighted challenges related to standardized reporting, reproducibility, and model comparison.

CONCLUSION

 ML-CPMs show promise in improving risk assessment and individualized treatment recommendations in VTE. Apparently, there is an urgent need for standardized reporting and methodology for ML models, external validation, prospective and real-world data studies, as well as interventional studies to evaluate the impact of artificial intelligence in VTE.

Machine learning models for predicting risks of MACEs for myocardial infarction patients with different VEGFR2 genotypes

Background

The development of prognostic models for the identification of high-risk myocardial infarction (MI) patients is a crucial step toward personalized medicine. Genetic factors are known to be associated with an increased risk of cardiovascular diseases; however, little is known about whether they can be used to predict major adverse cardiac events (MACEs) for MI patients. This study aimed to build a machine learning (ML) model to predict MACEs in MI patients based on clinical, imaging, laboratory, and genetic features and to assess the influence of genetics on the prognostic power of the model.

Methods

We analyzed the data from 218 MI patients admitted to the emergency department at the Surgut District Center for Diagnostics and Cardiovascular Surgery, Russia. Upon admission, standard clinical measurements and imaging data were collected for each patient. Additionally, patients were genotyped for VEGFR-2 variation rs2305948 (C/C, C/T, T/T genotypes with T being the minor risk allele). The study included a 9-year follow-up period during which major ischemic events were recorded. We trained and evaluated various ML models, including Gradient Boosting, Random Forest, Logistic Regression, and AutoML. For feature importance analysis, we applied the sequential feature selection (SFS) and Shapley's scheme of additive explanation (SHAP) methods.

Results

The CatBoost algorithm, with features selected using the SFS method, showed the best performance on the test cohort, achieving a ROC AUC of 0.813. Feature importance analysis identified the dose of statins as the most important factor, with the VEGFR-2 genotype among the top 5. The other important features are coronary artery lesions (coronary artery stenoses ≥70%), left ventricular (LV) parameters such as lateral LV wall and LV mass, diabetes, type of revascularization (CABG or PCI), and age. We also showed that contributions are additive and that high risk can be determined by cumulative negative effects from different prognostic factors.

Conclusion

Our ML-based approach demonstrated that the VEGFR-2 genotype is associated with an increased risk of MACEs in MI patients. However, the risk can be significantly reduced by high-dose statins and positive factors such as the absence of coronary artery lesions, absence of diabetes, and younger age.

Development and validation of a risk prediction model and prediction tools for post-thrombotic syndrome in patients with lower limb deep vein thrombosis

PURPOSE

Our research aims to compare the predictive performance of decision tree algorithms (DT) and logistic regression analysis (LR) in constructing models, and develop a Post-Thrombotic Syndrome (PTS) risk stratification tool.

METHODS

We retrospectively collected and analyzed relevant case information of 618 patients diagnosed with DVT from January 2012 to December 2021 in three different tertiary hospitals in Jiangxi Province as the modeling group. Additionally, we used the case information of 212 patients diagnosed with DVT from January 2022 to January 2023 in two tertiary hospitals in Hubei Province and Guangdong Province as the validation group. We extracted electronic medical record information including general patient data, medical history, laboratory test indicators, and treatment data for analysis. We established DT and LR models and compared their predictive performance using receiver operating characteristic (ROC) curves and confusion matrices. Internal and external validations were conducted. Additionally, we utilized LR to generate nomogram charts, calibration curves, and decision curves analysis (DCA) to assess its predictive accuracy.

RESULTS

Both DT and LR models indicate that Year, Residence, Cancer, Varicose Vein Operation History, DM, and Chronic VTE are risk factors for PTS occurrence. In internal validation, DT outperforms LR (0.962 vs 0.925, z = 3.379, P < 0.001). However, in external validation, there is no significant difference in the area under the ROC curve between the two models (0.963 vs 0.949, z = 0.412, P = 0.680). The validation results of calibration curves and DCA demonstrate that LR exhibits good predictive accuracy and clinical effectiveness. A web-based calculator software of nomogram (https://sunxiaoxuan.shinyapps.io/dynnomapp/) was utilized to visualize the logistic regression model.

CONCLUSIONS

The combination of decision tree and logistic regression models, along with the web-based calculator software of nomogram, can assist healthcare professionals in accurately assessing the risk of PTS occurrence in individual patients with lower limb DVT.

A systematic review and meta-analysis of risk prediction models for post-thrombotic syndrome in patients with deep vein thrombosis

Objective

This systematic review and meta-analysis aimed to systematically evaluate the prediction models for the risk of post-thrombotic syndrome (PTS) in deep vein thrombosis (DVT) patients.

Methods

This systematic review and meta-analysis was guided by the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA). A systematic search on the following electronic database: PubMed/MEDLINE, EMBASE, and Cochrane Library, and Chinese databases such as WANFANG and CNKI was conducted to look for relevant articles based on the research question. The risk of bias for each studies included was carried out based on Prediction Model Risk of Bias Assessment Tool (PROBAST).

Results

We identified 10 studies that developed a total of 13 clinical prediction models for PTS risk in DVT patients, 3 models were externally validated, 2 models were temporally validated. The top 5 predictors were: BMI (N = 9), Varicose vein (N = 6), Baseline Villalta Score (N = 6), Iliofemoral thrombosis (N = 5), and Age (N = 4). The high risk of bias was from the analysis domain, which the number of participants and selection of predictors often did not meet the requirements of PROBAST. A random-effects meta-analysis of C-statistics was conducted, the pooled discrimination was C-statistic 0.75, 95%CI (0.69, 0.81).

Conclusion

Among the 13 PTS risk prediction models reported in this study, no prediction model has been applied to clinical practice due to the lack of external validation. In the development of prediction models, most models were not standardized in data analysis. It is recommended that future studies on the design and implementation of prediction models refer to Transparent reporting of a multivariable prediction model for individual prognosis or diagnosis (TRIPOD) and PROBAST.

A systematic evaluation and meta-analysis of early prediction of post-thrombotic syndrome

Objective

Post-thrombotic syndrome (PTS) is the most common long-term complication in patients with deep venous thrombosis, and the prevention of PTS remains a major challenge in clinical practice. Some studies have explored early predictors and constructed corresponding prediction models, whereas their specific application and predictive value are controversial. Therefore, we conducted this systematic evaluation and meta-analysis to investigate the incidence of PTS and the feasibility of early prediction.

Methods

We systematically searched databases of PubMed, Embase, Cochrane and Web of Science up to April 7, 2023. Newcastle-Ottawa Scale (NOS) was used to evaluate the quality of the included articles, and the OR values of the predictors in multi-factor logistic regression were pooled to assess whether they could be used as effective independent predictors.

Results

We systematically included 20 articles involving 8,512 subjects, with a predominant onset of PTS between 6 and 72 months, with a 2-year incidence of 37.5% (95% CI: 27.8-47.7%). The results for the early predictors were as follows: old age OR = 1.840 (95% CI: 1.410-2.402), obesity or overweight OR = 1.721 (95% CI: 1.245-2.378), proximal deep vein thrombosis OR = 2.335 (95% CI: 1.855-2.938), history of venous thromboembolism OR = 3.593 (95% CI: 1.738-7.240), history of smoking OR = 2.051 (95% CI: 1.305-3.224), varicose veins OR = 2.405 (95% CI: 1.344-4.304), and baseline Villalta score OR = 1.095(95% CI: 1.056-1.135). Meanwhile, gender, unprovoked DVT and insufficient anticoagulation were not independent predictors. Seven studies constructed risk prediction models. In the training set, the c-index of the prediction models was 0.77 (95% CI: 0.74-0.80) with a sensitivity of 0.75 (95% CI: 0.68-0.81) and specificity of 0.69 (95% CI: 0.60-0.77). In the validation set, the c-index, sensitivity and specificity of the prediction models were 0.74(95% CI: 0.69-0.79), 0.71(95% CI: 0.64-0.78) and 0.72(95% CI: 0.67-0.76), respectively.

Conclusions

With a high incidence after venous thrombosis, PTS is a complication that cannot be ignored in patients with venous thrombosis. Risk prediction scoring based on early model construction is a feasible option, which helps to identify the patient's condition and develop an individualized prevention program to reduce the risk of PTS.

Performance and Head-to-Head Comparison of Three Clinical Models to Predict Occurrence of Postthrombotic Syndrome: A Validation Study

OBJECTIVE

 The SOX-PTS, Amin, and Méan models are three different clinical prediction scores stratifying the risk for postthrombotic syndrome (PTS) development in patients with acute deep vein thrombosis (DVT) of the lower limbs. Herein, we aimed to assess and compare these scores in the same cohort of patients.

METHODS

 We retrospectively applied the three scores in a cohort of 181 patients (196 limbs) who participated in the SAVER pilot trial for an acute DVT. Patients were stratified into PTS risk groups using positivity thresholds for high-risk patients as proposed in the derivation studies. All patients were assessed for PTS 6 months after index DVT using the Villalta scale. We calculated the predictive accuracy for PTS and area under receiver operating characteristic (AUROC) curve for each model.

RESULTS

 The Méan model was the most sensitive (sensitivity 87.7%; 95% confidence interval [CI]: 77.2-94.5) with the highest negative predictive value (87.5%; 95% CI: 76.8-94.4) for PTS. The SOX-PTS was the most specific score (specificity 97.5%; 95% CI: 92.7-99.5) with the highest positive predictive value (72.7%; 95% CI: 39.0-94.0). The SOX-PTS and Méan models performed well for PTS prediction (AUROC: 0.72; 95% CI: 0.65-0.80 and 0.74; 95% CI: 0.67-0.82), whereas the Amin model did not (AUROC: 0.58; 95% CI: 0.49-0.67).

CONCLUSION

 Our data support that the SOX-PTS and Méan models have good accuracy to stratify the risk for PTS.