Dataset Information

Particle uptake in cancer cells can predict malignancy and drug resistance using machine learning.

ABSTRACT: Tumor heterogeneity is a primary factor that contributes to treatment failure. Predictive tools, capable of classifying cancer cells based on their functions, may substantially enhance therapy and extend patient life span. The connection between cell biomechanics and cancer cell functions is used here to classify cells through mechanical measurements, via particle uptake. Machine learning (ML) was used to classify cells based on single-cell patterns of uptake of particles with diverse sizes. Three pairs of human cancer cell subpopulations, varied in their level of drug resistance or malignancy, were studied. Cells were allowed to interact with fluorescently labeled polystyrene particles ranging in size from 0.04 to 3.36 μm and analyzed for their uptake patterns using flow cytometry. ML algorithms accurately classified cancer cell subtypes with accuracy rates exceeding 95%. The uptake data were especially advantageous for morphologically similar cell subpopulations. Moreover, the uptake data were found to serve as a form of "normalization" that could reduce variation in repeated experiments.

SUBMITTER: Goldstein Y

PROVIDER: S-EPMC11314625 | biostudies-literature | 2024 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Particle uptake in cancer cells can predict malignancy and drug resistance using machine learning.

Goldstein Yoel Y Cohen Ora T OT Wald Ori O Bavli Danny D Kaplan Tommy T Benny Ofra O

Science advances 20240529 22

Tumor heterogeneity is a primary factor that contributes to treatment failure. Predictive tools, capable of classifying cancer cells based on their functions, may substantially enhance therapy and extend patient life span. The connection between cell biomechanics and cancer cell functions is used here to classify cells through mechanical measurements, via particle uptake. Machine learning (ML) was used to classify cells based on single-cell patterns of uptake of particles with diverse sizes. Thr ...[more]

PMID: 38809990

Similar Datasets

Project description:BackgroundVolume overload is a common complication encountered in hospitalized patients, and the mainstay of therapy is diuresis. Unfortunately, the diuretic response in some individuals is inadequate despite a typical dose of loop diuretics, a phenomenon called diuretic resistance. An accurate prediction model that predicts diuretic resistance using predosing variables could inform the right diuretic dose for a prospective patient.MethodsTwo large, deidentified, publicly available, and independent intensive care unit (ICU) databases from the United States were used-the Medical Information Mart for Intensive Care III (MIMIC) and the Philips eICU databases. Loop diuretic resistance was defined as <1400 ml of urine per 40 mg of diuretic dose in 24 hours. Using 24-hour windows throughout admission, commonly accessible variables were obtained and incorporated into the model. Data imputation was performed using a highly accurate machine learning method. Using XGBoost, several models were created using train and test datasets from the eICU database. These were then combined into an ensemble model optimized for increased specificity and then externally validated on the MIMIC database.ResultsThe final ensemble model was composed of four separate models, each using 21 commonly available variables. The ensemble model outperformed individual models during validation. Higher serum creatinine, lower systolic blood pressure, lower serum chloride, higher age, and female sex were the most important predictors of diuretic resistance (in that order). The specificity of the model on external validation was 92%, yielding a positive likelihood ratio of 3.46 while maintaining overall discrimination (C-statistic 0.69).ConclusionsA diuretic resistance prediction model was created using machine learning and was externally validated in ICU populations. The model is easy to use, would provide actionable information at the bedside, and would be ready for implementation in existing electronic medical records. This study also provides a framework for the development of future machine learning models.

Project description:Drug resistance mutations (DRMs) appear in HIV under treatment pressure. DRMs are commonly transmitted to naive patients. The standard approach to reveal new DRMs is to test for significant frequency differences of mutations between treated and naive patients. However, we then consider each mutation individually and cannot hope to study interactions between several mutations. Here, we aim to leverage the ever-growing quantity of high-quality sequence data and machine learning methods to study such interactions (i.e. epistasis), as well as try to find new DRMs. We trained classifiers to discriminate between Reverse Transcriptase Inhibitor (RTI)-experienced and RTI-naive samples on a large HIV-1 reverse transcriptase (RT) sequence dataset from the UK (n ≈ 55, 000), using all observed mutations as binary representation features. To assess the robustness of our findings, our classifiers were evaluated on independent data sets, both from the UK and Africa. Important representation features for each classifier were then extracted as potential DRMs. To find novel DRMs, we repeated this process by removing either features or samples associated to known DRMs. When keeping all known resistance signal, we detected sufficiently prevalent known DRMs, thus validating the approach. When removing features corresponding to known DRMs, our classifiers retained some prediction accuracy, and six new mutations significantly associated with resistance were identified. These six mutations have a low genetic barrier, are correlated to known DRMs, and are spatially close to either the RT active site or the regulatory binding pocket. When removing both known DRM features and sequences containing at least one known DRM, our classifiers lose all prediction accuracy. These results likely indicate that all mutations directly conferring resistance have been found, and that our newly discovered DRMs are accessory or compensatory mutations. Moreover, apart from the accessory nature of the relationships we found, we did not find any significant signal of further, more subtle epistasis combining several mutations which individually do not seem to confer any resistance.

Dataset Information

Particle uptake in cancer cells can predict malignancy and drug resistance using machine learning.

Publications

Particle uptake in cancer cells can predict malignancy and drug resistance using machine learning.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets