[Prediction of cancer drug sensitivity based on genomic feature distribution alignment and drug structure information].

Sheng Wu Gong Cheng Xue Bao

College of Computer Science and Technology, Zhejiang University of Technology, Hangzhou 310023, Zhejiang, China.

Published: July 2024

In recent years, precision medicine has demonstrated wide applications in cancer therapy, and the focus of precision medicine lies in accurately predicting the responses of different patients to drug treatment. We propose a model for predicting cancer drug sensitivity based on genomic feature distribution alignment and drug structure information. This model initially aligns the genomic features from cell lines with those from patients and removes noise from gene expression data. Subsequently, it integrates drug structure features and employs multi-task learning to predict the drug sensitivity of patients. The experimental results on the genomics of drug sensitivity in cancer (GDSC) dataset indicates that this method achieved a reduced mean square error of 0.905 2, an increased correlation coefficient of 0.875 4, and an enhanced accuracy rate of 0.836 0 which significantly outperformed the recently published methods. On the cancer genome atlas (TCGA) dataset, this method demonstrates an improved average recall rate of 0.571 4 and an increased F1-score of 0.658 0 in predicting drug sensitivity, exhibiting excellent generalization performance. The result demonstrates the potential of this method to assist in the selection of clinical treatment plans in the future.

Download full-text PDF

Source
http://dx.doi.org/10.13345/j.cjb.230902DOI Listing

Publication Analysis

Top Keywords

drug sensitivity
20
drug structure
12
drug
9
cancer drug
8
sensitivity based
8
based genomic
8
genomic feature
8
feature distribution
8
distribution alignment
8
alignment drug
8

Similar Publications

Background: Pancreatic cancer is a highly aggressive neoplasm characterized by poor diagnosis. Amino acids play a prominent role in the occurrence and progression of pancreatic cancer as essential building blocks for protein synthesis and key regulators of cellular metabolism. Understanding the interplay between pancreatic cancer and amino acid metabolism offers potential avenues for improving patient clinical outcomes.

View Article and Find Full Text PDF

Multiomic characterization, immunological and prognostic potential of SMAD3 in pan-cancer and validation in LIHC.

Sci Rep

January 2025

Jiangxi Key Laboratory of Molecular Medicine, Jiangxi Medical College, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, China.

SMAD3, a protein-coding gene, assumes a pivotal role within the transforming growth factor-beta (TGF-β) signaling pathway. Notably, aberrant SMAD3 expression has been linked to various malignancies. Nevertheless, an extensive examination of the comprehensive pan-cancer impact on SMAD3's diagnostic, prognostic, and immunological predictive utility has yet to be undertaken.

View Article and Find Full Text PDF

Background: Patients with diffuse anaplastic Wilms tumor (DAWT) experience relatively poor oncologic outcomes. Previous work has described mechanisms of telomerase upregulation in DAWT, posing a potential therapeutic target.

Methods: We assessed in vitro sensitivity to vincristine, irinotecan, and telomerase-targeting drug 6-thio-2'-deoxyguanosine (6 dG) in DAWT cell lines WiT49 and PDM115 and in spheroids derived from cell lines and four DAWT patient-derived xenografts (PDX).

View Article and Find Full Text PDF

Applying AI to Structured Real-World Data for Pharmacovigilance Purposes: Scoping Review.

J Med Internet Res

December 2024

Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé - LIMICS, Inserm, Université Sorbonne Paris-Nord, Sorbonne Université, Paris, France.

Background: Artificial intelligence (AI) applied to real-world data (RWD; eg, electronic health care records) has been identified as a potentially promising technical paradigm for the pharmacovigilance field. There are several instances of AI approaches applied to RWD; however, most studies focus on unstructured RWD (conducting natural language processing on various data sources, eg, clinical notes, social media, and blogs). Hence, it is essential to investigate how AI is currently applied to structured RWD in pharmacovigilance and how new approaches could enrich the existing methodology.

View Article and Find Full Text PDF

Molecular basis of proton sensing by G protein-coupled receptors.

Cell

December 2024

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94148, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94115, USA. Electronic address:

Three proton-sensing G protein-coupled receptors (GPCRs)-GPR4, GPR65, and GPR68-respond to extracellular pH to regulate diverse physiology. How protons activate these receptors is poorly understood. We determined cryogenic-electron microscopy (cryo-EM) structures of each receptor to understand the spatial arrangement of proton-sensing residues.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!