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Tan L, Qu J, Wang J. Development of novel lysosome-related signatures and their potential target drugs based on bulk RNA-seq and scRNA-seq for diabetic foot ulcers. Hum Genomics 2024; 18:62. [PMID: 38862997 PMCID: PMC11165785 DOI: 10.1186/s40246-024-00629-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/27/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Diabetic foot ulcers (DFU) is the most serious complication of diabetes mellitus, which has become a global health problem due to its high morbidity and disability rates and the poor efficacy of conventional treatments. Thus, it is urgent to identify novel molecular targets to improve the prognosis and reduce disability rate in DFU patients. RESULTS In the present study, bulk RNA-seq and scRNA-seq associated with DFU were downloaded from the GEO database. We identified 1393 DFU-related DEGs by differential analysis and WGCNA analysis together, and GO/KEGG analysis showed that these genes were associated with lysosomal and immune/inflammatory responses. Immediately thereafter, we identified CLU, RABGEF1 and ENPEP as DLGs for DFU using three machine learning algorithms (Randomforest, SVM-RFE and LASSO) and validated their diagnostic performance in a validation cohort independent of this study. Subsequently, we constructed a novel artificial neural network model for molecular diagnosis of DFU based on DLGs, and the diagnostic performance in the training and validation cohorts was sound. In single-cell sequencing, the heterogeneous expression of DLGs also provided favorable evidence for them to be potential diagnostic targets. In addition, the results of immune infiltration analysis showed that the abundance of mainstream immune cells, including B/T cells, was down-regulated in DFUs and significantly correlated with the expression of DLGs. Finally, we found latamoxef, parthenolide, meclofenoxate, and lomustine to be promising anti-DFU drugs by targeting DLGs. CONCLUSIONS CLU, RABGEF1 and ENPEP can be used as novel lysosomal molecular signatures of DFU, and by targeting them, latamoxef, parthenolide, meclofenoxate and lomustine were identified as promising anti-DFU drugs. The present study provides new perspectives for the diagnosis and treatment of DFU and for improving the prognosis of DFU patients.
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Affiliation(s)
- Longhai Tan
- Department of Dermatology, Tianjin Beichen Hospital, Tianjin, 300400, China.
| | - Junjun Qu
- Zhu Xianyi Memorial Hospital of Tianjin Medical University, Tianjin, 300134, China
| | - Junxia Wang
- Department of Dermatology, Tianjin Beichen Hospital, Tianjin, 300400, China
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Yu D, Zhang J, Li X, Xiao S, Xing J, Li J. Developing the novel diagnostic model and potential drugs by integrating bioinformatics and machine learning for aldosterone-producing adenomas. Front Mol Biosci 2024; 10:1308754. [PMID: 38239411 PMCID: PMC10794617 DOI: 10.3389/fmolb.2023.1308754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/08/2023] [Indexed: 01/22/2024] Open
Abstract
Background: Aldosterone-producing adenomas (APA) are a common cause of primary aldosteronism (PA), a clinical syndrome characterized by hypertension and electrolyte disturbances. If untreated, it may lead to serious cardiovascular complications. Therefore, there is an urgent need for potential biomarkers and targeted drugs for the diagnosis and treatment of aldosteronism. Methods: We downloaded two datasets (GSE156931 and GSE60042) from the GEO database and merged them by de-batch effect, then screened the top50 of differential genes using PPI and enriched them, followed by screening the Aldosterone adenoma-related genes (ARGs) in the top50 using three machine learning algorithms. We performed GSEA analysis on the ARGs separately and constructed artificial neural networks based on the ARGs. Finally, the Enrich platform was utilized to identify drugs with potential therapeutic effects on APA by tARGseting the ARGs. Results: We identified 190 differential genes by differential analysis, and then identified the top50 genes by PPI, and the enrichment analysis showed that they were mainly enriched in amino acid metabolic pathways. Then three machine learning algorithms identified five ARGs, namely, SST, RAB3C, PPY, CYP3A4, CDH10, and the ANN constructed on the basis of these five ARGs had better diagnostic effect on APA, in which the AUC of the training set is 1 and the AUC of the validation set is 0.755. And then the Enrich platform identified drugs tARGseting the ARGs with potential therapeutic effects on APA. Conclusion: We identified five ARGs for APA through bioinformatic analysis and constructed Artificial neural network (ANN) based on them with better diagnostic effects, and identified drugs with potential therapeutic effects on APA by tARGseting these ARGs. Our study provides more options for the diagnosis and treatment of APA.
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Affiliation(s)
- Deshui Yu
- Department of Urology, Air Force Medical Center, Beijing, China
- China Medical University, Shenyang, China
| | - Jinxuan Zhang
- Department of Urology, Air Force Medical Center, Beijing, China
- China Medical University, Shenyang, China
| | - Xintao Li
- Department of Urology, Air Force Medical Center, Beijing, China
| | - Shuwei Xiao
- Department of Urology, Air Force Medical Center, Beijing, China
| | - Jizhang Xing
- Department of Urology, Air Force Medical Center, Beijing, China
| | - Jianye Li
- Department of Urology, Air Force Medical Center, Beijing, China
- China Medical University, Shenyang, China
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3
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Sobral-Leite M, Castillo S, Vonk S, Melillo X, Lam N, de Bruijn B, Hagos Y, Sanders J, Almekinders M, Visser L, Groen E, Kristel P, Ercan C, Azarang L, Yuan Y, Menezes R, Lips E, Wesseling J. Artificial intelligence-based morphometric signature to identify ductal carcinoma in situ with low risk of progression to invasive breast cancer. RESEARCH SQUARE 2023:rs.3.rs-3639521. [PMID: 38168198 PMCID: PMC10760295 DOI: 10.21203/rs.3.rs-3639521/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Ductal carcinoma in situ (DCIS) may progress to ipsilateral invasive breast cancer (iIBC), but often never will. Because DCIS is treated as early breast cancer, many women with harmless DCIS face overtreatment. To identify these women that may forego treatment, we hypothesized that DCIS morphometric features relate to the risk of subsequent iIBC. We developed an artificial intelligence-based DCIS morphometric analysis pipeline (AIDmap) to detect DCIS as a pathologist and measure morphological structures in hematoxylin-eosin-stained (H&E) tissue sections. These were from a case-control study of patients diagnosed with primary DCIS, treated by breast-conserving surgery without radiotherapy. We analyzed 689 WSIs of DCIS of which 226 were diagnosed with subsequent iIBC (cases) and 463 were not (controls). The distribution of 15 duct morphological measurements in each H&E was summarized in 55 morphometric variables. A ridge regression classifier with cross validation predicted 5-years-free of iIBC with an area-under the curve of 0.65 (95% CI 0.55-0.76). A morphometric signature based on the 30 variables most associated with outcome, identified lesions containing small-sized ducts, low number of cells and low DCIS/stroma area ratio. This signature was associated with lower iIBC risk in a multivariate regression model including grade, ER, HER2 and COX-2 expression (HR = 0.56; 95% CI 0.28-0.78). AIDmap has potential to identify harmless DCIS that may not need treatment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Caner Ercan
- The University of Texas MD Anderson Cancer Center
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Alrowais F, Alotaibi FA, Hassan AQA, Marzouk R, Alnfiai MM, Sayed A. Enhanced Pelican Optimization Algorithm with Deep Learning-Driven Mitotic Nuclei Classification on Breast Histopathology Images. Biomimetics (Basel) 2023; 8:538. [PMID: 37999179 PMCID: PMC10669319 DOI: 10.3390/biomimetics8070538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
Breast cancer (BC) is a prevalent disease worldwide, and accurate diagnoses are vital for successful treatment. Histopathological (HI) inspection, particularly the detection of mitotic nuclei, has played a pivotal function in the prognosis and diagnosis of BC. It includes the detection and classification of mitotic nuclei within breast tissue samples. Conventionally, the detection of mitotic nuclei has been a subjective task and is time-consuming for pathologists to perform manually. Automatic classification using computer algorithms, especially deep learning (DL) algorithms, has been developed as a beneficial alternative. DL and CNNs particularly have shown outstanding performance in different image classification tasks, including mitotic nuclei classification. CNNs can learn intricate hierarchical features from HI images, making them suitable for detecting subtle patterns related to the mitotic nuclei. In this article, we present an Enhanced Pelican Optimization Algorithm with a Deep Learning-Driven Mitotic Nuclei Classification (EPOADL-MNC) technique on Breast HI. This developed EPOADL-MNC system examines the histopathology images for the classification of mitotic and non-mitotic cells. In this presented EPOADL-MNC technique, the ShuffleNet model can be employed for the feature extraction method. In the hyperparameter tuning procedure, the EPOADL-MNC algorithm makes use of the EPOA system to alter the hyperparameters of the ShuffleNet model. Finally, we used an adaptive neuro-fuzzy inference system (ANFIS) for the classification and detection of mitotic cell nuclei on histopathology images. A series of simulations took place to validate the improved detection performance of the EPOADL-MNC technique. The comprehensive outcomes highlighted the better outcomes of the EPOADL-MNC algorithm compared to existing DL techniques with a maximum accuracy of 97.83%.
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Affiliation(s)
- Fadwa Alrowais
- Department of Computer Sciences, College of Computer and Information Sciences, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Faiz Abdullah Alotaibi
- Department of Information Science, College of Humanities and Social Sciences, King Saud University, P.O. Box 28095, Riyadh 11437, Saudi Arabia
| | - Abdulkhaleq Q. A. Hassan
- Department of English, College of Science and Arts at Mahayil, King Khalid University, Abha 62529, Saudi Arabia
| | - Radwa Marzouk
- Department of Information Systems, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Mrim M. Alnfiai
- Department of Information Technology, College of Computers and Information Technology, Taif University, Taif P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed Sayed
- Research Center, Future University in Egypt, New Cairo 11835, Egypt
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Verghese G, Lennerz JK, Ruta D, Ng W, Thavaraj S, Siziopikou KP, Naidoo T, Rane S, Salgado R, Pinder SE, Grigoriadis A. Computational pathology in cancer diagnosis, prognosis, and prediction - present day and prospects. J Pathol 2023; 260:551-563. [PMID: 37580849 PMCID: PMC10785705 DOI: 10.1002/path.6163] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/12/2023] [Accepted: 06/17/2023] [Indexed: 08/16/2023]
Abstract
Computational pathology refers to applying deep learning techniques and algorithms to analyse and interpret histopathology images. Advances in artificial intelligence (AI) have led to an explosion in innovation in computational pathology, ranging from the prospect of automation of routine diagnostic tasks to the discovery of new prognostic and predictive biomarkers from tissue morphology. Despite the promising potential of computational pathology, its integration in clinical settings has been limited by a range of obstacles including operational, technical, regulatory, ethical, financial, and cultural challenges. Here, we focus on the pathologists' perspective of computational pathology: we map its current translational research landscape, evaluate its clinical utility, and address the more common challenges slowing clinical adoption and implementation. We conclude by describing contemporary approaches to drive forward these techniques. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Gregory Verghese
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
- The Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
| | - Jochen K Lennerz
- Center for Integrated Diagnostics, Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Danny Ruta
- Guy's CancerGuy's and St Thomas’ NHS Foundation TrustLondonUK
| | - Wen Ng
- Department of Cellular PathologyGuy's and St Thomas NHS Foundation TrustLondonUK
| | - Selvam Thavaraj
- Head & Neck PathologyGuy's and St Thomas NHS Foundation TrustLondonUK
- Centre for Clinical, Oral & Translational Science, Faculty of Dentistry, Oral & Craniofacial SciencesKing's College LondonLondonUK
| | - Kalliopi P Siziopikou
- Department of Pathology, Section of Breast PathologyNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Threnesan Naidoo
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha, Eastern CapeSouth Africa and Africa Health Research InstituteDurbanSouth Africa
| | - Swapnil Rane
- Department of PathologyTata Memorial Centre – ACTRECHBNINavi MumbaiIndia
- Computational Pathology, AI & Imaging LaboratoryTata Memorial Centre – ACTREC, HBNINavi MumbaiIndia
| | - Roberto Salgado
- Department of PathologyGZA–ZNA ZiekenhuizenAntwerpBelgium
- Division of ResearchPeter MacCallum Cancer CentreMelbourneVictoriaAustralia
| | - Sarah E Pinder
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
- Department of Cellular PathologyGuy's and St Thomas NHS Foundation TrustLondonUK
| | - Anita Grigoriadis
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
- The Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
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Restrepo JC, Dueñas D, Corredor Z, Liscano Y. Advances in Genomic Data and Biomarkers: Revolutionizing NSCLC Diagnosis and Treatment. Cancers (Basel) 2023; 15:3474. [PMID: 37444584 DOI: 10.3390/cancers15133474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is a significant public health concern with high mortality rates. Recent advancements in genomic data, bioinformatics tools, and the utilization of biomarkers have improved the possibilities for early diagnosis, effective treatment, and follow-up in NSCLC. Biomarkers play a crucial role in precision medicine by providing measurable indicators of disease characteristics, enabling tailored treatment strategies. The integration of big data and artificial intelligence (AI) further enhances the potential for personalized medicine through advanced biomarker analysis. However, challenges remain in the impact of new biomarkers on mortality and treatment efficacy due to limited evidence. Data analysis, interpretation, and the adoption of precision medicine approaches in clinical practice pose additional challenges and emphasize the integration of biomarkers with advanced technologies such as genomic data analysis and artificial intelligence (AI), which enhance the potential of precision medicine in NSCLC. Despite these obstacles, the integration of biomarkers into precision medicine has shown promising results in NSCLC, improving patient outcomes and enabling targeted therapies. Continued research and advancements in biomarker discovery, utilization, and evidence generation are necessary to overcome these challenges and further enhance the efficacy of precision medicine. Addressing these obstacles will contribute to the continued improvement of patient outcomes in non-small cell lung cancer.
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Affiliation(s)
- Juan Carlos Restrepo
- Grupo de Investigación en Salud Integral (GISI), Departamento Facultad de Salud, Universidad Santiago de Cali, Cali 760035, Colombia
| | - Diana Dueñas
- Grupo de Investigación en Salud Integral (GISI), Departamento Facultad de Salud, Universidad Santiago de Cali, Cali 760035, Colombia
| | - Zuray Corredor
- Grupo de Investigaciones en Odontología (GIOD), Facultad de Odontología, Universidad Cooperativa de Colombia, Pasto 520002, Colombia
- Facultad de Salud, Departamento de Ciencias Básicas, Universidad Libre, Cali 760026, Colombia
| | - Yamil Liscano
- Grupo de Investigación en Salud Integral (GISI), Departamento Facultad de Salud, Universidad Santiago de Cali, Cali 760035, Colombia
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