Measurement of the Acetabular Cup Orientation after Total Hip Arthroplasty Based on Three-Dimensional Reconstruction from a Single X-ray Image Using Generative Adversarial Networks.

BACKGROUND: The purpose of this study was to reconstruct three-dimensional (3D) computed tomography (CT) images from single anteroposterior (AP) postoperative total hip arthroplasty (THA) X-ray images using a deep learning algorithm known as generative adversarial networks (GANs) and to validate the accuracy of cup angle measurement on GAN-generated CT. METHODS: We used two GAN-based models, CycleGAN and X2CT-GAN, to generate 3D CT images from X-ray images of 386 patients who underwent primary THAs using a cementless cup. The training dataset consisted of 522 CT images and 2,282 X-ray images. The image quality was validated using the peak signal-to-noise ratio (PSNR) and the structural similarity index measure (SSIM). The cup anteversion and inclination measurements on the GAN-generated CT images were compared with the actual CT measurements. Statistical analyses of absolute measurement errors were performed using Mann-Whitney U tests and nonlinear regression analyses. RESULTS: The study successfully achieved 3D reconstruction from single AP postoperative THA X-ray images using GANs, exhibiting excellent PSNR (37.40) and SSIM (0.74). The median absolute difference in radiographic anteversion (RA) was 3.45° and the median absolute difference in radiographic inclination (RI) was 3.25°, respectively. Absolute measurement errors tended to be larger in cases with cup malposition than in those with optimal cup orientation. CONCLUSION: This study demonstrates the potential of GANs for 3D reconstruction from single AP postoperative THA X-ray images to evaluate cup orientation. Further investigation and refinement of this model are required to improve its performance.

Decoding the specificity of m6A RNA methylation and its implication in cancer therapy.

N6-methyladenosine (m6A) is the most abundant endogenous modification in eukaryotic RNAs. It plays important roles in various biological processes and diseases, including cancers. More and more studies have revealed that the deposition of m6A is specifically regulated in a context-dependent manner. Here, we review the diverse mechanisms that determine the topology of m6A along RNAs and the cell-type-specific m6A methylomes. The exon junction complex (EJC) as well as histone modifications play important roles in determining the topological distribution of m6A along nascent RNAs, while the transcription factors and RNA-binding proteins, which usually bind specific DNAs and RNAs in a cell-type-specific manner, largely account for the cell-type-specific m6A methylomes. Due to the lack of specificity of m6A writers and readers, there are still challenges to target the core m6A machinery for cancer therapies. Therefore, understanding the mechanisms underlying the specificity of m6A modifications in cancers would be important for future cancer therapies through m6A intervention.

Development of interpretable machine learning models to predict in-hospital prognosis of acute heart failure patients.

AIMS: In recent years, there has been remarkable development in machine learning (ML) models, showing a trend towards high prediction performance. ML models with high prediction performance often become structurally complex and are frequently perceived as black boxes, hindering intuitive interpretation of the prediction results. We aimed to develop ML models with high prediction performance, interpretability, and superior risk stratification to predict in-hospital mortality and worsening heart failure (WHF) in patients with acute heart failure (AHF). METHODS AND RESULTS: Based on the Kyoto Congestive Heart Failure registry, which enrolled 4056 patients with AHF, we developed prediction models for in-hospital mortality and WHF using information obtained on the first day of admission (demographics, physical examination, blood test results, etc.). After excluding 16 patients who died on the first or second day of admission, the original dataset (n = 4040) was split 4:1 into training (n = 3232) and test datasets (n = 808). Based on the training dataset, we developed three types of prediction models: (i) the classification and regression trees (CART) model; (ii) the random forest (RF) model; and (iii) the extreme gradient boosting (XGBoost) model. The performance of each model was evaluated using the test dataset, based on metrics including sensitivity, specificity, area under the receiver operating characteristic curve (AUC), Brier score, and calibration slope. For the complex structure of the XGBoost model, we performed SHapley Additive exPlanations (SHAP) analysis, classifying patients into interpretable clusters. In the original dataset, the proportion of females was 44.8% (1809/4040), and the average age was 77.9 ± 12.0. The in-hospital mortality rate was 6.3% (255/4040) and the WHF rate was 22.3% (900/4040) in the total study population. In the in-hospital mortality prediction, the AUC for the XGBoost model was 0.816 [95% confidence interval (CI): 0.815-0.818], surpassing the AUC values for the CART model (0.683, 95% CI: 0.680-0.685) and the RF model (0.755, 95% CI: 0.753-0.757). Similarly, in the WHF prediction, the AUC for the XGBoost model was 0.766 (95% CI: 0.765-0.768), outperforming the AUC values for the CART model (0.688, 95% CI: 0.686-0.689) and the RF model (0.713, 95% CI: 0.711-0.714). In the XGBoost model, interpretable clusters were formed, and the rates of in-hospital mortality and WHF were similar among each cluster in both the training and test datasets. CONCLUSIONS: The XGBoost models with SHAP analysis provide high prediction performance, interpretability, and reproducible risk stratification for in-hospital mortality and WHF for patients with AHF.

Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking.

The cyclic peptide OS1 (amino acid sequence: CTERMALHNLC), which has a disulfide bond between both termini cysteine residues, inhibits complex formation between the platelet glycoprotein Ibα (GPIbα) and the von Willebrand factor (vWF) by forming a complex with GPIbα. To study the binding mechanism between GPIbα and OS1 and, therefore, the inhibition mechanism of the protein-protein GPIbα-vWF complex, we have applied our multicanonical molecular dynamics (McMD)-based dynamic docking protocol starting from the unbound state of the peptide. Our simulations have reproduced the experimental complex structure, although the top-ranking structure was an intermediary one, where the peptide was bound in the same location as in the experimental structure; however, the ß-switch of GPIbα attained a different conformation. Our analysis showed that subsequent refolding of the ß-switch results in a more stable binding configuration, although the transition to the native configuration appears to take some time, during which OS1 could dissociate. Our results show that conformational changes in the ß-switch are crucial for successful binding of OS1. Furthermore, we identified several allosteric binding sites of GPIbα that might also interfere with vWF binding, and optimization of the peptide to target these allosteric sites might lead to a more effective inhibitor, as these are not dependent on the ß-switch conformation.

LTK mutations responsible for resistance to lorlatinib in non-small cell lung cancer harboring CLIP1-LTK fusion.

The CLIP1-LTK fusion was recently discovered as a novel oncogenic driver in non-small cell lung cancer (NSCLC). Lorlatinib, a third-generation ALK inhibitor, exhibited a dramatic clinical response in a NSCLC patient harboring CLIP1-LTK fusion. However, it is expected that acquired resistance will inevitably develop, particularly by LTK mutations, as observed in NSCLC induced by oncogenic tyrosine kinases treated with corresponding tyrosine kinase inhibitors (TKIs). In this study, we evaluate eight LTK mutations corresponding to ALK mutations that lead to on-target resistance to lorlatinib. All LTK mutations show resistance to lorlatinib with the L650F mutation being the highest. In vitro and in vivo analyses demonstrate that gilteritinib can overcome the L650F-mediated resistance to lorlatinib. In silico analysis suggests that introduction of the L650F mutation may attenuate lorlatinib-LTK binding. Our study provides preclinical evaluations of potential on-target resistance mutations to lorlatinib, and a novel strategy to overcome the resistance.

Interpretable machine learning-based individual analysis of acute kidney injury in immune checkpoint inhibitor therapy.

BACKGROUND: Acute kidney injury (AKI) is a critical complication of immune checkpoint inhibitor therapy. Since the etiology of AKI in patients undergoing cancer therapy varies, clarifying underlying causes in individual cases is critical for optimal cancer treatment. Although it is essential to individually analyze immune checkpoint inhibitor-treated patients for underlying pathologies for each AKI episode, these analyses have not been realized. Herein, we aimed to individually clarify the underlying causes of AKI in immune checkpoint inhibitor-treated patients using a new clustering approach with Shapley Additive exPlanations (SHAP). METHODS: We developed a gradient-boosting decision tree-based machine learning model continuously predicting AKI within 7 days, using the medical records of 616 immune checkpoint inhibitor-treated patients. The temporal changes in individual predictive reasoning in AKI prediction models represented the key features contributing to each AKI prediction and clustered AKI patients based on the features with high predictive contribution quantified in time series by SHAP. We searched for common clinical backgrounds of AKI patients in each cluster, compared with annotation by three nephrologists. RESULTS: One hundred and twelve patients (18.2%) had at least one AKI episode. They were clustered per the key feature, and their SHAP value patterns, and the nephrologists assessed the clusters' clinical relevance. Receiver operating characteristic analysis revealed that the area under the curve was 0.880. Patients with AKI were categorized into four clusters with significant prognostic differences (p = 0.010). The leading causes of AKI for each cluster, such as hypovolemia, drug-related, and cancer cachexia, were all clinically interpretable, which conventional approaches cannot obtain. CONCLUSION: Our results suggest that the clustering method of individual predictive reasoning in machine learning models can be applied to infer clinically critical factors for developing each episode of AKI among patients with multiple AKI risk factors, such as immune checkpoint inhibitor-treated patients.

Developing a GNN-based AI model to predict mitochondrial toxicity using the bagging method.

Mitochondrial toxicity has been implicated in the development of various toxicities, including hepatotoxicity. Therefore, mitochondrial toxicity has become a major screening factor in the early discovery phase of drug development. Several models have been developed to predict mitochondrial toxicity based on chemical structures. However, they only provide a binary classification of positive or negative results and do not provide the substructures that contribute to a positive decision. Therefore, we developed an artificial intelligence (AI) model to predict mitochondrial toxicity and visualize structural alerts. To construct the model, we used the open-source software library kMoL, which employs a graph neural network approach that allows learning from chemical structure data. We also utilized the integrated gradient method, which enables the visualization of substructures that contribute to positive results. The dataset used to construct the AI model exhibited a significant imbalance, with significantly more negative than positive data. To address this, we employed the bagging method, which resulted in a model with high predictive performance, as evidenced by an F1 score of 0.839. This model can also be used to visualize substructures that contribute to mitochondrial toxicity using the integrated gradient method. Our AI model predicts mitochondrial toxicity based on chemical structures and may contribute to screening mitochondrial toxicity in the early stages of drug discovery.

Feature extraction of particle morphologies of pharmaceutical excipients from scanning electron microscope images using convolutional neural networks.

Scanning electron microscopy (SEM) images are the most widely used tool for evaluating particle morphology; however, quantitative evaluation using SEM images is time-consuming and often neglected. In this study, we aimed to extract features related to particle morphology of pharmaceutical excipients from SEM images using a convolutional neural network (CNN). SEM images of 67 excipients were acquired and used as models. A classification CNN model of the excipients was constructed based on the SEM images. Further, features were extracted from the middle layer of this CNN model, and the data was compressed to two dimensions using uniform manifold approximation and projection. Lastly, hierarchical clustering analysis (HCA) was performed to categorize the excipients into several clusters and identify similarities among the samples. The classification CNN model showed high accuracy, allowing each excipient to be identified with a high degree of accuracy. HCA revealed that the 67 excipients were classified into seven clusters. Additionally, the particle morphologies of excipients belonging to the same cluster were found to be very similar. These results suggest that CNN models are useful tools for extracting information and identifying similarities among the particle morphologies of excipients.

A macrocyclic kinase inhibitor overcomes triple resistant mutations in EGFR-positive lung cancer.

Brigatinib-based therapy was effective against osimertinib-resistant EGFR C797S mutants and is undergoing clinical studies. However, tumor relapse suggests additional resistance mutations might emerge. Here, we first demonstrated the binding mode of brigatinib to the EGFR-T790M/C797S mutant by crystal structure analysis and predicted brigatinib-resistant mutations through a cell-based assay including N-ethyl-N-nitrosourea (ENU) mutagenesis. We found that clinically reported L718 and G796 compound mutations appeared, consistent with their proximity to the binding site of brigatinib, and brigatinib-resistant quadruple mutants such as EGFR-activating mutation/T790M/C797S/L718M were resistant to all the clinically available EGFR-TKIs. BI-4020, a fourth-generation EGFR inhibitor with a macrocyclic structure, overcomes the quadruple and major EGFR-activating mutants but not the minor mutants, such as L747P or S768I. Molecular dynamics simulation revealed the binding mode and affinity between BI-4020 and EGFR mutants. This study identified potential therapeutic strategies using the new-generation macrocyclic EGFR inhibitor to overcome the emerging ultimate resistance mutants.

Recent developments in machine learning modeling methods for hypertension treatment.

Hypertension is the leading cause of cardiovascular complications. This review focuses on the advancements in medical artificial intelligence (AI) models aimed at individualized treatment for hypertension, with particular emphasis on the approach to time-series big data on blood pressure and the development of interpretable medical AI models. The digitalization of daily blood pressure records and the downsizing of measurement devices enable the accumulation and utilization of time-series data. As mainstream blood pressure data shift from snapshots to time series, the clinical significance of blood pressure variability will be clarified. The time-series blood pressure prediction model demonstrated the capability to forecast blood pressure variabilities with a reasonable degree of accuracy for up to four weeks in advance. In recent years, various explainable AI techniques have been proposed for different purposes of model interpretation. It is essential to select the appropriate technique based on the clinical aspects; for example, actionable path-planning techniques can present individualized intervention plans to efficiently improve outcomes such as hypertension. Despite considerable progress in this field, challenges remain, such as the need for the prospective validation of AI-driven interventions and the development of comprehensive systems that integrate multiple AI methods. Future research should focus on addressing these challenges and refining the AI models to ensure their practical applicability in real-world clinical settings. Furthermore, the implementation of interdisciplinary collaborations among AI experts, clinicians, and healthcare providers are crucial to further optimizing and validate AI-driven solutions for hypertension management.

Idiopathic pulmonary fibrosis-specific Bayesian network integrating extracellular vesicle proteome and clinical information.

Idiopathic pulmonary fibrosis (IPF) is a progressive disease characterized by severe lung fibrosis and a poor prognosis. Although the biomolecules related to IPF have been extensively studied, molecular mechanisms of the pathogenesis and their association with serum biomarkers and clinical findings have not been fully elucidated. We constructed a Bayesian network using multimodal data consisting of a proteome dataset from serum extracellular vesicles, laboratory examinations, and clinical findings from 206 patients with IPF and 36 controls. Differential protein expression analysis was also performed by edgeR and incorporated into the constructed network. We have successfully visualized the relationship between biomolecules and clinical findings with this approach. The IPF-specific network included modules associated with TGF-ß signaling (TGFB1 and LRC32), fibrosis-related (A2MG and PZP), myofibroblast and inflammation (LRP1 and ITIH4), complement-related (SAA1 and SAA2), as well as serum markers, and clinical symptoms (KL-6, SP-D and fine crackles). Notably, it identified SAA2 associated with lymphocyte counts and PSPB connected with the serum markers KL-6 and SP-D, along with fine crackles as clinical manifestations. These results contribute to the elucidation of the pathogenesis of IPF and potential therapeutic targets.

Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model.

In all-atom (AA) molecular dynamics (MD) simulations, the rugged energy profile of the force field makes it challenging to reproduce spontaneous structural changes in biomolecules within a reasonable calculation time. Existing coarse-grained (CG) models, in which the energy profile is set to a global minimum around the initial structure, are unsuitable to explore the structural dynamics between metastable states far away from the initial structure without any bias. In this study, we developed a new hybrid potential composed of an artificial intelligence (AI) potential and minimal CG potential related to the statistical bond length and excluded volume interactions to accelerate the transition dynamics while maintaining the protein character. The AI potential is trained by energy matching using a diverse structural ensemble sampled via multicanonical (Mc) MD simulation and the corresponding AA force field energy, profile of which is smoothed by energy minimization. By applying the new methodology to chignolin and TrpCage, we showed that the AI potential can predict the AA energy with significantly high accuracy, as indicated by a correlation coefficient (R-value) between the true and predicted energies exceeding 0.89. In addition, we successfully demonstrated that CGMD simulation based on the smoothed hybrid potential can significantly enhance the transition dynamics between various metastable states while preserving protein properties compared to those obtained with conventional CGMD and AAMD.

VGAE-MCTS: A New Molecular Generative Model Combining the Variational Graph Auto-Encoder and Monte Carlo Tree Search.

Molecular generation is crucial for advancing drug discovery, materials science, and chemical exploration. It expedites the search for new drug candidates, facilitates tailored material creation, and enhances our understanding of molecular diversity. By employing artificial intelligence techniques such as molecular generative models based on molecular graphs, researchers have tackled the challenge of identifying efficient molecules with desired properties. Here, we propose a new molecular generative model combining a graph-based deep neural network and a reinforcement learning technique. We evaluated the validity, novelty, and optimized physicochemical properties of the generated molecules. Importantly, the model explored uncharted regions of chemical space, allowing for the efficient discovery and design of new molecules. This innovative approach has considerable potential to revolutionize drug discovery, materials science, and chemical research for accelerating scientific innovation. By leveraging advanced techniques and exploring previously unexplored chemical spaces, this study offers promising prospects for the efficient discovery and design of new molecules in the field of drug development.

Network-based prediction approach for cancer-specific driver missense mutations using a graph neural network.

BACKGROUND: In cancer genomic medicine, finding driver mutations involved in cancer development and tumor growth is crucial. Machine-learning methods to predict driver missense mutations have been developed because variants are frequently detected by genomic sequencing. However, even though the abnormalities in molecular networks are associated with cancer, many of these methods focus on individual variants and do not consider molecular networks. Here we propose a new network-based method, Net-DMPred, to predict driver missense mutations considering molecular networks. Net-DMPred consists of the graph part and the prediction part. In the graph part, molecular networks are learned by a graph neural network (GNN). The prediction part learns whether variants are driver variants using features of individual variants combined with the graph features learned in the graph part. RESULTS: Net-DMPred, which considers molecular networks, performed better than conventional methods. Furthermore, the prediction performance differed by the molecular network structure used in learning, suggesting that it is important to consider not only the local network related to cancer but also the large-scale network in living organisms. CONCLUSIONS: We propose a network-based machine learning method, Net-DMPred, for predicting cancer driver missense mutations. Our method enables us to consider the entire graph architecture representing the molecular network because it uses GNN. Net-DMPred is expected to detect driver mutations from a lot of missense mutations that are not known to be associated with cancer.

Establishment of an MR1 Presentation Reporter Screening System and Identification of Phenylpropanoid Derivatives as MR1 Ligands.

Mucosal-associated invariant T (MAIT) cells are innate-like T cells that are modulated by ligands presented on MHC class I-related proteins (MR1). These cells have attracted attention as potential drug targets because of their involvement in the initial response to infection and various disorders. Herein, we have established the MR1 presentation reporter assay system employing split-luciferase, which enables the efficient exploration of MR1 ligands. Using our screening system, we identified phenylpropanoid derivatives as MR1 ligands, including coniferyl aldehyde, which have an ability to inhibit the MR1-MAIT cell axis. Further, the structure-activity relationship study of coniferyl aldehyde analogs revealed the key structural features of ligands required for MR1 recognition. These results will contribute to identifying a broad range of endogenous and exogenous MR1 ligands and to developing novel MAIT cell modulators.

Deep Learning-Based Differential Diagnosis of Follicular Thyroid Tumors Using Histopathological Images.

Deep learning systems (DLSs) have been developed for the histopathological assessment of various types of tumors, but none are suitable for differential diagnosis between follicular thyroid carcinoma (FTC) and follicular adenoma (FA). Furthermore, whether DLSs can identify the malignant characteristics of thyroid tumors based only on random views of tumor tissue histology has not been evaluated. In this study, we developed DLSs able to differentiate between FTC and FA based on 3 types of convolutional neural network architecture: EfficientNet, VGG16, and ResNet50. The performance of all 3 DLSs was excellent (area under the receiver operating characteristic curve = 0.91 ± 0.04; F1 score = 0.82 ± 0.06). Visual explanations using gradient-weighted class activation mapping suggested that the diagnosis of both FTC and FA was largely dependent on nuclear features. The DLSs were then trained with FTC images and linked information (presence or absence of recurrence within 10 years, vascular invasion, and wide capsular invasion). The ability of the DLSs to diagnose these characteristics was then determined. The results showed that, based on the random views of histology, the DLSs could predict the risk of FTC recurrence, vascular invasion, and wide capsular invasion with a certain level of accuracy (area under the receiver operating characteristic curve = 0.67 ± 0.13, 0.62 ± 0.11, and 0.65 ± 0.09, respectively). Further improvement of our DLSs could lead to the establishment of automated differential diagnosis systems requiring only biopsy specimens.

Ensemble-Learning and Feature Selection Techniques for Enhanced Antisense Oligonucleotide Efficacy Prediction in Exon Skipping.

Antisense oligonucleotide (ASO)-mediated exon skipping has become a valuable tool for investigating gene function and developing gene therapy. Machine-learning-based computational methods, such as eSkip-Finder, have been developed to predict the efficacy of ASOs via exon skipping. However, these methods are computationally demanding, and the accuracy of predictions remains suboptimal. In this study, we propose a new approach to reduce the computational burden and improve the prediction performance by using feature selection within machine-learning algorithms and ensemble-learning techniques. We evaluated our approach using a dataset of experimentally validated exon-skipping events, dividing it into training and testing sets. Our results demonstrate that using a three-way-voting approach with random forest, gradient boosting, and XGBoost can significantly reduce the computation time to under ten seconds while improving prediction performance, as measured by R2 for both 2'-O-methyl nucleotides (2OMe) and phosphorodiamidate morpholino oligomers (PMOs). Additionally, the feature importance ranking derived from our approach is in good agreement with previously published results. Our findings suggest that our approach has the potential to enhance the accuracy and efficiency of predicting ASO efficacy via exon skipping. It could also facilitate the development of novel therapeutic strategies. This study could contribute to the ongoing efforts to improve ASO design and optimize gene therapy approaches.

Improving Compound-Protein Interaction Prediction by Self-Training with Augmenting Negative Samples.

Identifying compound-protein interactions (CPIs) is crucial for drug discovery. Since experimentally validating CPIs is often time-consuming and costly, computational approaches are expected to facilitate the process. Rapid growths of available CPI databases have accelerated the development of many machine-learning methods for CPI predictions. However, their performance, particularly their generalizability against external data, often suffers from a data imbalance attributed to the lack of experimentally validated inactive (negative) samples. In this study, we developed a self-training method for augmenting both credible and informative negative samples to improve the performance of models impaired by data imbalances. The constructed model demonstrated higher performance than those constructed with other conventional methods for solving data imbalances, and the improvement was prominent for external datasets. Moreover, examination of the prediction score thresholds for pseudo-labeling during self-training revealed that augmenting the samples with ambiguous prediction scores is beneficial for constructing a model with high generalizability. The present study provides guidelines for improving CPI predictions on real-world data, thus facilitating drug discovery.

Individual health-disease phase diagrams for disease prevention based on machine learning.

Early disease detection and prevention methods based on effective interventions are gaining attention worldwide. Progress in precision medicine has revealed that substantial heterogeneity exists in health data at the individual level and that complex health factors are involved in chronic disease development. Machine-learning techniques have enabled precise personal-level disease prediction by capturing individual differences in multivariate data. However, it is challenging to identify what aspects should be improved for disease prevention based on future disease-onset prediction because of the complex relationships among multiple biomarkers. Here, we present a health-disease phase diagram (HDPD) that represents an individual's health state by visualizing the future-onset boundary values of multiple biomarkers that fluctuate early in the disease progression process. In HDPDs, future-onset predictions are represented by perturbing multiple biomarker values while accounting for dependencies among variables. We constructed HDPDs for 11 diseases using longitudinal health checkup cohort data of 3,238 individuals, comprising 3,215 measurement items and genetic data. The improvement of biomarker values to the non-onset region in HDPD remarkably prevented future disease onset in 7 out of 11 diseases. HDPDs can represent individual physiological states in the onset process and be used as intervention goals for disease prevention.

Exploring the mechanism of BK polyomavirus-associated nephropathy through consensus gene network approach.

BK polyomavirus-associated nephropathy occurs in kidney transplant recipients under immunosuppressive treatment. BK polyomavirus is implicated in cancer development and invasion, and case reports of renal cell carcinoma and urothelial carcinoma possibly associated with BK polyomavirus has been reported. Further, it has been suggested that the immune responses of KT-related diseases could play a role in the pathogenesis and progression of renal cell carcinoma. Thus, we thought to examine the relationship between BK polyomavirus-associated nephropathy and renal cell carcinoma in terms of gene expression. To identify the common and specific immune responses involved in kidney transplantation-related diseases with a specific focus on BK polyomavirus-associated nephropathy, we performed consensus weighted gene co-expression network analysis on gene profile datasets of renal biopsy samples from different institutions. After the identification of gene modules and validation of the obtained network by immunohistochemistry of the marker across kidney transplantation-related diseases, the relationship between prognosis of renal cell carcinoma and modules was assessed. We included the data from 248 patients and identified the 14 gene clusters across the datasets. We revealed that one cluster related to the translation regulating process and DNA damage response was specifically upregulated in BK polyomavirus-associated nephropathy. There was a significant association between the expression value of hub genes of the identified cluster including those related to cGAS-STING pathway and DNA damage response, and the prognosis of renal cell carcinoma. The study suggested the potential link between kidney transplantation-related diseases, especially specific transcriptomic signature of BK polyomavirus associated nephropathy and renal cell carcinoma.