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. 2024 Oct 12;17(10):1364.
doi: 10.3390/ph17101364.

A Machine Learning Approach to Gene Expression in Hypertrophic Cardiomyopathy

Jelena Pavić  1   2 , Marko Živanović  1 , Irena Tanasković  3 , Ognjen Pavić  1 , Vesna Stanković  4 , Katarina Virijević  1   2 , Tamara Mladenović  1   2 , Jelena Košarić  1 , Bogdan Milićević  1   5 , Safi Ur Rehman Qamar  2   5 , Lazar Velicki  6   7 , Ivana Novaković  8 , Andrej Preveden  6   7 , Dejana Popović  9 , Milorad Tesić  8   10 , Stefan Seman  11 , Nenad Filipović  2   5
Affiliations

A Machine Learning Approach to Gene Expression in Hypertrophic Cardiomyopathy

Jelena Pavić et al. Pharmaceuticals (Basel). .

Abstract

Background/objectives: Hypertrophic cardiomyopathy (HCM) is a common heart disorder characterized by the thickening of the heart muscle, particularly in the left ventricle, which increases the risk of cardiac complications. This study aims to analyze the expression of apoptosis-regulating genes (CASP8, CASP9, CASP3, BAX, and BCL2) in blood samples from HCM patients, to better understand their potential as biomarkers for disease progression.

Methods: Quantitative real-time PCR (qPCR) was used to evaluate gene expression in blood samples from 93 HCM patients. The correlation between apoptosis-regulating genes was conducted and clinical parameters were integrated for feature importance and clustering analysis.

Results: Most patients exhibited significant downregulation of CASP8, CASP9, and CASP3. In contrast, BAX expression was elevated in 71 out of 93 patients, while BCL2 was increased in 55 out of 93 patients. Correlation analysis revealed weak negative correlations between the BAX/BCL2 ratio and CASP gene expression.

Conclusions: These findings suggest that reduced expression of apoptotic genes may indicate a protective cellular mechanism, which could serve as a biomarker for disease progression. Further studies are needed to investigate the potential for therapeutic modulation of these pathways to improve patient outcomes.

Keywords: BCL2; CASP3; apoptosis; gene expression; hypertrophic cardiomyopathy.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 2
Figure 2
Correlation between the BAX/BCL2 ratio and CASP genes.
Figure 1
Figure 1
Heatmap showing expression of selected genes across patient samples. The color intensity represents the level of gene expression: bright red indicates high expression; white indicates average expression; light-blue indicates low expression. Rows correspond to individual patients and columns represent specific genes (CASP8, CASP9, CASP3, BAX, and BCL2).
Figure 3
Figure 3
Ground truth state of HCM patients expressed by apoptotic genes (the red points represent high-risk patients, while the green points represent low-risk patients).
Figure 4
Figure 4
K-means clustered HCM patients expressed by apoptotic genes (the red points represent high-risk patients, while the green points represent low-risk patients).
See this image and copyright information in PMC

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