Machine learning based personalized drug response prediction for lung cancer patients

Research progress of HIF-1a on immunotherapy outcomes in immune vascular microenvironment

The hypoxia-inducible factor-1α (HIF-1α) plays a key role in facilitating the adaptation of cells to hypoxia, profoundly influencing the immune vascular microenvironment (IVM) and immunotherapy outcomes. HIF-1α-mediated tumor hypoxia drives angiogenesis, immune suppression, and extracellular matrix remodeling, creating an environment that promotes tumor progression and resistance to immunotherapies. HIF-1α regulates critical pathways, including the expression of vascular endothelial growth factor and immune checkpoint upregulation, leading to tumor-infiltrating lymphocyte dysfunction and recruitment of immunosuppressive cells like regulatory T cells and myeloid-derived suppressor cells. These alterations reduce the efficacy of checkpoint inhibitors and other immunotherapies. Recent studies highlight therapeutic strategies that target HIF-1α, such as the use of pharmacological inhibitors, gene editing techniques, and hypoxia-modulating treatments, which show promise in enhancing responses to immunotherapy. This review explores the molecular mechanisms of action of HIF-1α in IVM, its impact on immunotherapy resistance, as well as potential interventions, emphasizing the need for innovative approaches to circumvent hypoxia-driven immunosuppression in cancer therapy.

Predicting the hub interactome of COVID-19 and oral squamous cell carcinoma: uncovering ALDH-mediated Wnt/β-catenin pathway activation via salivary inflammatory proteins

Understanding shared pathways and mechanisms involved in the pathogenesis of diseases like oral squamous cell carcinoma (OSCC) and COVID-19 could lead to the development of novel therapeutic strategies and diagnostic biomarkers. This study aims to predict the interactome of OSCC and COVID-19 based on salivary inflammatory proteins. Datasets for OSCC and COVID-19 were obtained from https://www.salivaryproteome.org/differential-expression and selected for differential gene expression analysis. Differential gene expression analysis was performed using log transformation and a fold change of two. Hub proteins were identified using Cytoscape and Cytohubba, and machine learning algorithms including naïve Bayes, neural networks, gradient boosting, and random forest were used to predict hub genes. Top hub genes identified included ALDH1A1, MT-CO2, SERPINC1, FGB, and TF. The random forest model achieved the highest accuracy (93%) and class accuracy (84%). The naive Bayes model had lower accuracy (63%) and class accuracy (66%), while the neural network model showed 55% accuracy and class accuracy, possibly due to data pre-processing issues. The gradient boosting model outperformed all models with an accuracy of 95% and class accuracy of 95%. Salivary proteomic interactome analysis revealed novel hub proteins as potential common biomarkers.

Explainable Machine Learning Predictions for the Benefit From Chemotherapy in Advanced Non-Small Cell Lung Cancer Without Available Targeted Mutations

BACKGROUND

Non-small cell lung cancer (NSCLC) is a global health challenge. Chemotherapy remains the standard therapy for advanced NSCLC without mutations, but drug resistance often reduces effectiveness. Developing more effective methods to predict and monitor chemotherapy benefits early is crucial.

METHODS

We carried out a retrospective cohort study of NSCLC patients without targeted mutations who received chemotherapy at West China Hospital from 2009 to 2013. We identified variables associated with chemotherapy outcomes and built four predictive models by machine learning. Shapley additive explanations (SHAP) interpreted the best model's predictions. The Kaplan-Meier method assessed key variables' impact on 5-year overall survival.

RESULTS

The study enrolled 461 NSCLC patients. Eight variables were selected for the model: differentiation, surgery history, neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), total bilirubin (TBIL), total protein (TP), alanine aminotransferase (ALT), and lactate dehydrogenase (LDH). The extreme gradient boosting (Xgboost) model exhibited superior discriminatory ability in predicting complete response (CR) probabilities to chemotherapy, with an AUC of 0.78. SHAP plots showed surgery history and high differentiation were related to CR benefits from chemotherapy. Absence of surgery, higher NLR, higher PLR, and higher LDH were all independent prognostic factors for poor survivals in NSCLC patients without mutations receiving chemotherapy.

CONCLUSIONS

By machine learning, we developed a predictive model to assess chemotherapy benefits in NSCLC patients without targeted mutations, utilizing eight readily available and non-invasive clinical indicators. Demonstrating satisfactory predictive performance and clinical practicability, this model may help clinicians identify patients' tendency to benefit from chemotherapy, potentially improving their prognosis.

Application of artificial intelligence in drug design: A review

Artificial intelligence (AI) is a field of computer science that involves acquiring information, developing rule bases, and mimicking human behaviour. The fundamental concept behind AI is to create intelligent computer systems that can operate with minimal human intervention or without any intervention at all. These rule-based systems are developed using various machine learning and deep learning models, enabling them to solve complex problems. AI is integrated with these models to learn, understand, and analyse provided data. The rapid advancement of Artificial Intelligence (AI) is reshaping numerous industries, with the pharmaceutical sector experiencing a notable transformation. AI is increasingly being employed to automate, optimize, and personalize various facets of the pharmaceutical industry, particularly in pharmacological research. Traditional drug development methods areknown for being time-consuming, expensive, and less efficient, often taking around a decade and costing billions of dollars. The integration of artificial intelligence (AI) techniques addresses these challenges by enabling the examination of compounds with desired properties from a vast pool of input drugs. Furthermore, it plays a crucial role in drug screening by predicting toxicity, bioactivity, ADME properties (absorption, distribution, metabolism, and excretion), physicochemical properties, and more. AI enhances the drug design process by improving the efficiency and accuracy of predicting drug behaviour, interactions, and properties. These approaches further significantly improve the precision of drug discovery processes and decrease clinical trial costs leading to the development of more effective drugs.

Performance of machine learning algorithms for lung cancer prediction: a comparative approach

Due to the excessive growth of PM 2.5 in aerosol, the cases of lung cancer are increasing rapidly and are most severe among other types as the highest mortality rate. In most of the cases, lung cancer is detected with least symptoms at its later stage. Hence, clinical records may play a vital role to diagnose this disease at the correct stage for suitable medication to cure it. To detect lung cancer an accurate prediction method is needed which is significantly reliable. In the digital clinical record era with advancement in computing algorithms including machine learning techniques opens an opportunity to ease the process. Various machine learning algorithms may be applied over realistic clinical data but the predictive power is yet to be comprehended for accurate results. This paper envisages to compare twelve potential machine learning algorithms over clinical data with eleven symptoms of lung cancer along with two major habits of patients to predict a positive case accurately. The result has been found based on classification and heat map correlation. K-Nearest Neighbor Model and Bernoulli Naive Bayes Model are found most significant methods for early lung cancer prediction.

scDrug+: predicting drug-responses using single-cell transcriptomics and molecular structure

Predicting drug responses based on individual transcriptomic profiles holds promise for refining prognosis and advancing precision medicine. Although many studies have endeavored to predict the responses of known drugs to novel transcriptomic profiles, research into predicting responses for newly discovered drugs remains sparse. In this study, we introduce scDrug+, a comprehensive pipeline that seamlessly integrates single-cell analysis with drug-response prediction. Importantly, scDrug+ is equipped to predict the response of new drugs by analyzing their molecular structures. The open-source tool is available as a Docker container, ensuring ease of deployment and reproducibility. It can be accessed at https://github.com/ailabstw/scDrugplus.

An extensive review on lung cancer therapeutics using machine learning techniques: state-of-the-art and perspectives

There are over 100 types of human cancer, accounting for millions of deaths every year. Lung cancer alone claims over 1.8 million lives per year and is expected to surpass 3.2 million by 2050, which underscores the urgent need for rapid drug development and repurposing initiatives. The application of AI emerges as a pivotal solution to developing anti-cancer therapeutics. This state-of-the-art review aims to explore the various applications of AI in lung cancer therapeutics. Predictive models can analyse large datasets, including clinical data, genetic information, and treatment outcomes, for novel drug design and to generate personalised treatment recommendations, potentially optimising therapeutic strategies, enhancing treatment efficacy, and minimising adverse effects. A thorough literature review study was conducted based on articles indexed in PubMed and Scopus. We compiled the use of various machine learning approaches, including CNN, RNN, GAN, VAEs, and other AI techniques, enhancing efficiency with accuracy exceeding 95%, which is validated through a computer-aided drug design process. AI can revolutionise lung cancer therapeutics, streamlining processes and saving biological scientists' time and effort-however, further research is needed to overcome challenges and fully unlock AI's potential in Lung Cancer Therapeutics.

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

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.

Uncovering the subtype-specific disease module and the development of drug response prediction models for glioma

The poor prognosis of glioma patients brought attention to the need for effective therapeutic approaches for precision therapy. Here, we deployed algorithms relying on network medicine and artificial intelligence to design the framework for subtype-specific target identification and drug response prediction in glioma. We identified the driver mutations that were differentially expressed in each subtype of lower-grade glioma and glioblastoma multiforme and were linked to cancer-specific processes. Driver mutations that were differentially expressed were also subjected to subtype-specific disease module identification. The drugs from the drug bank database were retrieved to target these disease modules. However, the efficacy of anticancer drugs depends on the molecular profile of the cancer and varies among cancer patients due to intratumor heterogeneity. Hence, we developed a deep-learning-based drug response prediction framework using the experimental drug screening data. Models for 30 drugs that can target the disease module were developed, where drug response measured by IC50 was considered a response and gene expression and mutation data were considered predictor variables. The model construction consists of three steps: feature selection, data integration, and classification. We observed the consistent performance of the models in training, test, and validation datasets. Drug responses were predicted for particular cell lines derived from distinct subtypes of gliomas. We found that subtypes of gliomas respond differently to the drug, highlighting the importance of subtype-specific drug response prediction. Therefore, the development of personalized therapy by integrating network medicine and a deep learning-based approach can lead to cancer-specific treatment and improved patient care.

Preclinical Anticipation of On- and Off-Target Resistance Mechanisms to Anti-Cancer Drugs: A Systematic Review

The advent of targeted therapies has led to tremendous improvements in treatment options and their outcomes in the field of oncology. Yet, many cancers outsmart precision drugs by developing on-target or off-target resistance mechanisms. Gaining the ability to resist treatment is the rule rather than the exception in tumors, and it remains a major healthcare challenge to achieve long-lasting remission in most cancer patients. Here, we discuss emerging strategies that take advantage of innovative high-throughput screening technologies to anticipate on- and off-target resistance mechanisms before they occur in treated cancer patients. We divide the methods into non-systematic approaches, such as random mutagenesis or long-term drug treatment, and systematic approaches, relying on the clustered regularly interspaced short palindromic repeats (CRISPR) system, saturated mutagenesis, or computational methods. All these new developments, especially genome-wide CRISPR-based screening platforms, have significantly accelerated the processes for identification of the mechanisms responsible for cancer drug resistance and opened up new avenues for future treatments.

In silico resources help combat cancer drug resistance mediated by target mutations

Drug resistance causes catastrophic cancer treatment failures. Mutations in target proteins with altered drug binding indicate a main mechanism of cancer drug resistance (CDR). Global research has generated considerable CDR-related data and well-established knowledge bases and predictive tools. Unfortunately, these resources are fragmented and underutilized. Here, we examine computational resources for exploring CDR caused by target mutations, analyzing these tools based on their functional characteristics, data capacity, data sources, methodologies and performance. We also discuss their disadvantages and provide examples of how potential inhibitors of CDR have been discovered using these resources. This toolkit is designed to help specialists explore resistance occurrence effectively and to explain resistance prediction to non-specialists easily.

AI in drug discovery and its clinical relevance

The COVID-19 pandemic has emphasized the need for novel drug discovery process. However, the journey from conceptualizing a drug to its eventual implementation in clinical settings is a long, complex, and expensive process, with many potential points of failure. Over the past decade, a vast growth in medical information has coincided with advances in computational hardware (cloud computing, GPUs, and TPUs) and the rise of deep learning. Medical data generated from large molecular screening profiles, personal health or pathology records, and public health organizations could benefit from analysis by Artificial Intelligence (AI) approaches to speed up and prevent failures in the drug discovery pipeline. We present applications of AI at various stages of drug discovery pipelines, including the inherently computational approaches of de novo design and prediction of a drug's likely properties. Open-source databases and AI-based software tools that facilitate drug design are discussed along with their associated problems of molecule representation, data collection, complexity, labeling, and disparities among labels. How contemporary AI methods, such as graph neural networks, reinforcement learning, and generated models, along with structure-based methods, (i.e., molecular dynamics simulations and molecular docking) can contribute to drug discovery applications and analysis of drug responses is also explored. Finally, recent developments and investments in AI-based start-up companies for biotechnology, drug design and their current progress, hopes and promotions are discussed in this article.