OUP accepted manuscript

Predicting Microwave Ablation Early Efficacy in Pulmonary Malignancies via Δ Radiomics Models

OBJECTIVE

This study aimed to explore the value of preoperative and postoperative computed tomography (CT)-based radiomic signatures and Δ radiomic signatures for evaluating the early efficacy of microwave ablation (MWA) for pulmonary malignancies.

METHODS

In total, 115 patients with pulmonary malignancies who underwent MWA treatment were categorized into response and nonresponse groups according to relevant guidelines and consensus. Quantitative image features of the largest pulmonary malignancies were extracted from CT noncontrast scan images preoperatively (time point 0, TP0) and immediately postoperatively (time point 1, TP1). Critical features were selected from TP0 and TP1 and as Δ radiomics signatures for building radiomics models. In addition, a combined radiomics model (C-RO) was developed by integrating radiomics parameters with clinical risk factors. Prediction performance was assessed using the area under the receiver operating characteristic curve (AUC) and decision curve analysis (DCA).

RESULTS

The radiomics model using Δ features outperformed the radiomics model using TP0 and TP1 features, with training and validation AUCs of 0.892, 0.808, and 0.787, and 0.705, 0.825, and 0.778, respectively. By combining the TP0, TP1, and Δ features, the logistic regression model exhibited the best performance, with training and validation AUCs of 0.945 and 0.744, respectively. The DCA confirmed the clinical utility of the Δ radiomics model.

CONCLUSIONS

A combined prediction model, including TP0, TP1, and Δ radiometric features, can be used to evaluate the early efficacy of MWA in pulmonary malignancies.

Enhancing Immunotherapy Response Prediction in Metastatic Lung Adenocarcinoma: Leveraging Shallow and Deep Learning with CT-Based Radiomics across Single and Multiple Tumor Sites

This study aimed to evaluate the potential of pre-treatment CT-based radiomics features (RFs) derived from single and multiple tumor sites, and state-of-the-art machine-learning survival algorithms, in predicting progression-free survival (PFS) for patients with metastatic lung adenocarcinoma (MLUAD) receiving first-line treatment including immune checkpoint inhibitors (CPIs). To do so, all adults with newly diagnosed MLUAD, pre-treatment contrast-enhanced CT scan, and performance status ≤ 2 who were treated at our cancer center with first-line CPI between November 2016 and November 2022 were included. RFs were extracted from all measurable lesions with a volume ≥ 1 cm3 on the CT scan. To capture intra- and inter-tumor heterogeneity, RFs from the largest tumor of each patient, as well as lowest, highest, and average RF values over all lesions per patient were collected. Intra-patient inter-tumor heterogeneity metrics were calculated to measure the similarity between each patient lesions. After filtering predictors with univariable Cox p < 0.100 and analyzing their correlations, five survival machine-learning algorithms (stepwise Cox regression [SCR], LASSO Cox regression, random survival forests, gradient boosted machine [GBM], and deep learning [Deepsurv]) were trained in 100-times repeated 5-fold cross-validation (rCV) to predict PFS on three inputs: (i) clinicopathological variables, (ii) all radiomics-based and clinicopathological (full input), and (iii) uncorrelated radiomics-based and clinicopathological variables (uncorrelated input). The Models' performances were evaluated using the concordance index (c-index). Overall, 140 patients were included (median age: 62.5 years, 36.4% women). In rCV, the highest c-index was reached with Deepsurv (c-index = 0.631, 95%CI = 0.625-0.647), followed by GBM (c-index = 0.603, 95%CI = 0.557-0.646), significantly outperforming standard SCR whatever its input (c-index range: 0.560-0.570, all p < 0.0001). Thus, single- and multi-site pre-treatment radiomics data provide valuable prognostic information for predicting PFS in MLUAD patients undergoing first-line CPI treatment when analyzed with advanced machine-learning survival algorithms.

Just how transformative will AI/ML be for immuno-oncology?

Immuno-oncology involves the study of approaches which harness the patient's immune system to fight malignancies. Immuno-oncology, as with every other biomedical and clinical research field as well as clinical operations, is in the midst of technological revolutions, which vastly increase the amount of available data. Recent advances in artificial intelligence and machine learning (AI/ML) have received much attention in terms of their potential to harness available data to improve insights and outcomes in many areas including immuno-oncology. In this review, we discuss important aspects to consider when evaluating the potential impact of AI/ML applications in the clinic. We highlight four clinical/biomedical challenges relevant to immuno-oncology and how they may be able to be addressed by the latest advancements in AI/ML. These challenges include (1) efficiency in clinical workflows, (2) curation of high-quality image data, (3) finding, extracting and synthesizing text knowledge as well as addressing, and (4) small cohort size in immunotherapeutic evaluation cohorts. Finally, we outline how advancements in reinforcement and federated learning, as well as the development of best practices for ethical and unbiased data generation, are likely to drive future innovations.

Adaptive Cancer Therapy in the Age of Generative Artificial Intelligence

Therapeutic resistance is a major challenge facing the design of effective cancer treatments. Adaptive cancer therapy is in principle the most viable approach to manage cancer's adaptive dynamics through drug combinations with dose timing and modulation. However, there are numerous open issues facing the clinical success of adaptive therapy. Chief among these issues is the feasibility of real-time predictions of treatment response which represent a bedrock requirement of adaptive therapy. Generative artificial intelligence has the potential to learn prediction models of treatment response from clinical, molecular, and radiomics data about patients and their treatments. The article explores this potential through a proposed integration model of Generative Pre-Trained Transformers (GPTs) in a closed loop with adaptive treatments to predict the trajectories of disease progression. The conceptual model and the challenges facing its realization are discussed in the broader context of artificial intelligence integration in oncology.

Cancer immunotherapy efficacy and machine learning

INTRODUCTION

Immunotherapy is one of the major breakthroughs in the treatment of cancer, and it has become a powerful clinical strategy, however, not all patients respond to immune checkpoint blockade and other immunotherapy strategies. Applying machine learning (ML) techniques to predict the efficacy of cancer immunotherapy is useful for clinical decision-making.

AREAS COVERED

Applying ML including deep learning (DL) in radiomics, pathomics, tumor microenvironment (TME) and immune-related genes analysis to predict immunotherapy efficacy. The studies in this review were searched from PubMed and ClinicalTrials.gov (January 2023).

EXPERT OPINION

An increasing number of studies indicate that ML has been applied to various aspects of oncology research, with the potential to provide more effective individualized immunotherapy strategies and enhance treatment decisions. With advances in ML technology, more efficient methods of predicting the efficacy of immunotherapy may become available in the future.

Recent Advances in the Field of Artificial Intelligence for Precision Medicine in Patients with a Diagnosis of Metastatic Cutaneous Melanoma

Standard-of-care medical imaging techniques such as CT, MRI, and PET play a critical role in managing patients diagnosed with metastatic cutaneous melanoma. Advancements in artificial intelligence (AI) techniques, such as radiomics, machine learning, and deep learning, could revolutionize the use of medical imaging by enhancing individualized image-guided precision medicine approaches. In the present article, we will decipher how AI/radiomics could mine information from medical images, such as tumor volume, heterogeneity, and shape, to provide insights into cancer biology that can be leveraged by clinicians to improve patient care both in the clinic and in clinical trials. More specifically, we will detail the potential role of AI in enhancing detection/diagnosis, staging, treatment planning, treatment delivery, response assessment, treatment toxicity assessment, and monitoring of patients diagnosed with metastatic cutaneous melanoma. Finally, we will explore how these proof-of-concept results can be translated from bench to bedside by describing how the implementation of AI techniques can be standardized for routine adoption in clinical settings worldwide to predict outcomes with great accuracy, reproducibility, and generalizability in patients diagnosed with metastatic cutaneous melanoma.

A Radiomics Approach to Identify Immunologically Active Tumor in Patients with Head and Neck Squamous Cell Carcinomas

BACKGROUND

We recently developed a gene-expression-based HOT score to identify the hot/cold phenotype of head and neck squamous cell carcinomas (HNSCCs), which is associated with the response to immunotherapy. Our goal was to determine whether radiomic profiling from computed tomography (CT) scans can distinguish hot and cold HNSCC.

METHOD

We included 113 patients from The Cancer Genome Atlas (TCGA) and 20 patients from the Groupe Hospitalier Pitié-Salpêtrière (GHPS) with HNSCC, all with available pre-treatment CT scans. The hot/cold phenotype was computed for all patients using the HOT score. The IBEX software (version 4.11.9, accessed on 30 march 2020) was used to extract radiomic features from the delineated tumor region in both datasets, and the intraclass correlation coefficient (ICC) was computed to select robust features. Machine learning classifier models were trained and tested in the TCGA dataset and validated using the area under the receiver operator characteristic curve (AUC) in the GHPS cohort.

RESULTS

A total of 144 radiomic features with an ICC >0.9 was selected. An XGBoost model including these selected features showed the best performance prediction of the hot/cold phenotype with AUC = 0.86 in the GHPS validation dataset.

CONCLUSIONS AND RELEVANCE

We identified a relevant radiomic model to capture the overall hot/cold phenotype of HNSCC. This non-invasive approach could help with the identification of patients with HNSCC who may benefit from immunotherapy.

New Challenges for Anatomists in the Era of Omics

Anatomic studies have traditionally relied on macroscopic, microscopic, and histological techniques to investigate the structure of tissues and organs. Anatomic studies are essential in many fields, including medicine, biology, and veterinary science. Advances in technology, such as imaging techniques and molecular biology, continue to provide new insights into the anatomy of living organisms. Therefore, anatomy remains an active and important area in the scientific field. The consolidation in recent years of some omics technologies such as genomics, transcriptomics, proteomics, and metabolomics allows for a more complete and detailed understanding of the structure and function of cells, tissues, and organs. These have been joined more recently by "omics" such as radiomics, pathomics, and connectomics, supported by computer-assisted technologies such as neural networks, 3D bioprinting, and artificial intelligence. All these new tools, although some are still in the early stages of development, have the potential to strongly contribute to the macroscopic and microscopic characterization in medicine. For anatomists, it is time to hitch a ride and get on board omics technologies to sail to new frontiers and to explore novel scenarios in anatomy.

Radiomics Correlation to CD68+ Tumor-Associated Macrophages in Clear Cell Renal Cell Carcinoma

INTRODUCTION

Renal cell carcinoma (RCC) is the ninth most common cancer worldwide, with clear cell RCC (ccRCC) being the most frequent histological subtype. The tumor immune microenvironment (TIME) of ccRCC is an important factor to guide treatment, but current assessments are tissue-based, which can be time-consuming and resource-intensive. In this study, we used radiomics extracted from clinically performed computed tomography (CT) as a noninvasive surrogate for CD68 tumor-associated macrophages (TAMs), a significant component of ccRCC TIME.

METHODS

TAM population was measured by CD68+/PanCK+ ratio and tumor-TAM clustering was measured by normalized K function calculated from multiplex immunofluorescence (mIF). A total of 1,076 regions on mIF slides from 78 patients were included. Radiomic features were extracted from multiphase CT of the ccRCC tumor. Statistical machine learning models, including random forest, Adaptive Boosting, and ElasticNet, were used to predict TAM population and tumor-TAM clustering.

RESULTS

The best models achieved an area under the ROC curve of 0.81 (95% CI: [0.69, 0.92]) for TAM population and 0.77 (95% CI: [0.66, 0.88]) for tumor-TAM clustering, respectively.

CONCLUSION

Our study demonstrates the potential of using CT radiomics-derived imaging markers as a surrogate for assessment of TAM in ccRCC for real-time treatment response monitoring and patient selection for targeted therapies and immunotherapies.

Radiomics using computed tomography to predict CD73 expression and prognosis of colorectal cancer liver metastases

BACKGROUND

Finding a noninvasive radiomic surrogate of tumor immune features could help identify patients more likely to respond to novel immune checkpoint inhibitors. Particularly, CD73 is an ectonucleotidase that catalyzes the breakdown of extracellular AMP into immunosuppressive adenosine, which can be blocked by therapeutic antibodies. High CD73 expression in colorectal cancer liver metastasis (CRLM) resected with curative intent is associated with early recurrence and shorter patient survival. The aim of this study was hence to evaluate whether machine learning analysis of preoperative liver CT-scan could estimate high vs low CD73 expression in CRLM and whether such radiomic score would have a prognostic significance.

METHODS

We trained an Attentive Interpretable Tabular Learning (TabNet) model to predict, from preoperative CT images, stratified expression levels of CD73 (CD73^High vs. CD73^Low) assessed by immunofluorescence (IF) on tissue microarrays. Radiomic features were extracted from 160 segmented CRLM of 122 patients with matched IF data, preprocessed and used to train the predictive model. We applied a five-fold cross-validation and validated the performance on a hold-out test set.

RESULTS

TabNet provided areas under the receiver operating characteristic curve of 0.95 (95% CI 0.87 to 1.0) and 0.79 (0.65 to 0.92) on the training and hold-out test sets respectively, and outperformed other machine learning models. The TabNet-derived score, termed rad-CD73, was positively correlated with CD73 histological expression in matched CRLM (Spearman's ρ = 0.6004; P < 0.0001). The median time to recurrence (TTR) and disease-specific survival (DSS) after CRLM resection in rad-CD73^High vs rad-CD73^Low patients was 13.0 vs 23.6 months (P = 0.0098) and 53.4 vs 126.0 months (P = 0.0222), respectively. The prognostic value of rad-CD73 was independent of the standard clinical risk score, for both TTR (HR = 2.11, 95% CI 1.30 to 3.45, P < 0.005) and DSS (HR = 1.88, 95% CI 1.11 to 3.18, P = 0.020).

CONCLUSIONS

Our findings reveal promising results for non-invasive CT-scan-based prediction of CD73 expression in CRLM and warrant further validation as to whether rad-CD73 could assist oncologists as a biomarker of prognosis and response to immunotherapies targeting the adenosine pathway.

The tumor immune microenvironment in pancreatic cancer and its potential in the identification of immunotherapy biomarkers

INTRODUCTION

Pancreatic cancer (PC) has an extremely poor prognosis, even with surgical resection and triplet chemotherapy treatment. Cancer immunotherapy has been recently approved for tumor-agnostic treatment with genome analysis, including in PC. However, it has limited efficacy.

AREAS COVERED

In addition to the low tumor mutation burden, one of the difficulties of immunotherapy in PC is the presence of abundant stromal cells in its microenvironment. Among stromal cells, cancer-associated fibroblasts (CAFs) play a major role in immunotherapy resistance, and CAF-targeted therapies are currently under development, including those in combination with immunotherapies. Meanwhile, microbiomes and tumor-derived exosomes (TDEs) have been shown to alter the behavior of distant receptor cells in PC. This review discusses the role of CAFs, microbiomes, and TDEs in PC tumor immunity.

EXPERT OPINION

Elucidating the mechanisms by which CAFs, microbiomes, and TDEs are involved in the tumorigenesis of PC will be helpful for developing novel immunotherapeutic strategies and identifying companion biomarkers for immunotherapy. Spatial single-cell analysis of the tumor microenvironment will be useful for identifying biomarkers of PC immunity. Furthermore, given the complexity of immune mechanisms, artificial intelligence models will be beneficial for predicting the efficacy of immunotherapy.

Artificial intelligence in cancer immunotherapy: Applications in neoantigen recognition, antibody design and immunotherapy response prediction

Cancer immunotherapy is a method of controlling and eliminating tumors by reactivating the body's cancer-immunity cycle and restoring its antitumor immune response. The increased availability of data, combined with advancements in high-performance computing and innovative artificial intelligence (AI) technology, has resulted in a rise in the use of AI in oncology research. State-of-the-art AI models for functional classification and prediction in immunotherapy research are increasingly used to support laboratory-based experiments. This review offers a glimpse of the current AI applications in immunotherapy, including neoantigen recognition, antibody design, and prediction of immunotherapy response. Advancing in this direction will result in more robust predictive models for developing better targets, drugs, and treatments, and these advancements will eventually make their way into the clinical setting, pushing AI forward in the field of precision oncology.

Skin Cancer Pathobiology at a Glance: A Focus on Imaging Techniques and Their Potential for Improved Diagnosis and Surveillance in Clinical Cohorts

Early diagnosis is essential for completely eradicating skin cancer and maximizing patients' clinical benefits. Emerging optical imaging modalities such as reflectance confocal microscopy (RCM), optical coherence tomography (OCT), magnetic resonance imaging (MRI), near-infrared (NIR) bioimaging, positron emission tomography (PET), and their combinations provide non-invasive imaging data that may help in the early detection of cutaneous tumors and surgical planning. Hence, they seem appropriate for observing dynamic processes such as blood flow, immune cell activation, and tumor energy metabolism, which may be relevant for disease evolution. This review discusses the latest technological and methodological advances in imaging techniques that may be applied for skin cancer detection and monitoring. In the first instance, we will describe the principle and prospective clinical applications of the most commonly used imaging techniques, highlighting the challenges and opportunities of their implementation in the clinical setting. We will also highlight how imaging techniques may complement the molecular and histological approaches in sharpening the non-invasive skin characterization, laying the ground for more personalized approaches in skin cancer patients.

Imaging assessment of toxicity related to immune checkpoint inhibitors

In recent years, a wide range of cancer immunotherapies have been developed and have become increasingly important in cancer treatment across multiple oncologic diseases. In particular, immune checkpoint inhibitors (ICIs) offer promising options to improve patient outcomes. However, a major limitation of these treatments consists in the development of immune-related adverse events (irAEs) occurring in potentially any organ system and affecting up to 76% of the patients. The most frequent toxicities involve the skin, gastrointestinal tract, and endocrine system. Although mostly manageable, potentially life-threatening events, particularly due to neuro-, cardiac, and pulmonary toxicity, occur in up to 30% and 55% of the patients treated with ICI-monotherapy or -combination therapy, respectively. Imaging, in particular computed tomography (CT), magnetic resonance imaging (MRI), and 2-deoxy-2-[¹⁸F]fluoro-D-glucose positron emission tomography/computed tomography (¹⁸F-FDG-PET/CT), plays an important role in the detection and characterization of these irAEs. In some patients, irAEs can even be detected on imaging before the onset of clinical symptoms. In this context, it is particularly important to distinguish irAEs from true disease progression and specific immunotherapy related response patterns, such as pseudoprogression. In addition, there are irAEs which might be easily confused with other pathologies such as infection or metastasis. However, many imaging findings, such as in immune-related pneumonitis, are nonspecific. Thus, accurate diagnosis may be delayed underling the importance for adequate imaging features characterization in the appropriate clinical setting in order to provide timely and efficient patient management. ¹⁸F-FDG-PET/CT and radiomics have demonstrated to reliably detect these toxicities and potentially have predictive value for identifying patients at risk of developing irAEs. The purpose of this article is to provide a review of the main immunotherapy-related toxicities and discuss their characteristics on imaging.

Tumor response assessment on imaging following immunotherapy

In recent years, various systemic immunotherapies have been developed for cancer treatment, such as monoclonal antibodies (mABs) directed against immune checkpoints (immune checkpoint inhibitors, ICIs), oncolytic viruses, cytokines, cancer vaccines, and adoptive cell transfer. While being estimated to be eligible in 38.5% of patients with metastatic solid or hematological tumors, ICIs, in particular, demonstrate durable disease control across many oncologic diseases (e.g., in melanoma, lung, bladder, renal, head, and neck cancers) and overall survival benefits. Due to their unique mechanisms of action based on T-cell activation, response to immunotherapies is characterized by different patterns, such as progression prior to treatment response (pseudoprogression), hyperprogression, and dissociated responses following treatment. Because these features are not encountered in the Response Evaluation Criteria in Solid Tumors version 1.1 (RECIST 1.1), which is the standard for response assessment in oncology, new criteria were defined for immunotherapies. The most important changes in these new morphologic criteria are, firstly, the requirement for confirmatory imaging examinations in case of progression, and secondly, the appearance of new lesions is not necessarily considered a progressive disease. Until today, five morphologic (immune-related response criteria (irRC), immune-related RECIST (irRECIST), immune RECIST (iRECIST), immune-modified RECIST (imRECIST), and intra-tumoral RECIST (itRECIST)) criteria have been developed to accurately assess changes in target lesion sizes, taking into account the specific response patterns after immunotherapy. In addition to morphologic response criteria, 2-deoxy-2-[18F]fluoro-D-glucose positron emission tomography/computed tomography (18F-FDG-PET/CT) is a promising option for metabolic response assessment and four metabolic criteria are used (PET/CT Criteria for Early Prediction of Response to Immune Checkpoint Inhibitor Therapy (PECRIT), PET Response Evaluation Criteria for Immunotherapy (PERCIMT), immunotherapy-modified PET Response Criteria in Solid Tumors (imPERCIST5), and immune PERCIST (iPERCIST)). Besides, there is evidence that parameters on 18F-FDG-PET/CT, such as the standardized uptake value (SUV)max and several radiotracers, e.g., directed against PD-L1, may be potential imaging biomarkers of response. Moreover, the emerge of human intratumoral immunotherapy (HIT-IT), characterized by the direct injection of immunostimulatory agents into a tumor lesion, has given new importance to imaging assessment. This article reviews the specific imaging patterns of tumor response and progression and available imaging response criteria following immunotherapy.

Prognostic Value and Quantitative CT Analysis in RANKL Expression of Spinal GCTB in the Denosumab Era: A Machine Learning Approach

The receptor activator of the nuclear factor kappa B ligand (RANKL) is the therapeutic target of denosumab. In this study, we evaluated whether radiomics signature and machine learning analysis can predict RANKL status in spinal giant cell tumors of bone (GCTB). This retrospective study consisted of 107 patients, including a training set (n = 82) and a validation set (n = 25). Kaplan-Meier survival analysis was used to validate the prognostic value of RANKL status. Radiomic feature extraction of three heterogeneous regions (VOIentire, VOIedge, and VOIcore) from pretreatment CT were performed. Followed by feature selection using Selected K Best and least absolute shrinkage and selection operator (LASSO) analysis, three classifiers (random forest (RF), support vector machine, and logistic regression) were used to build models. The area under the curve (AUC), accuracy, F1 score, recall, precision, sensitivity, and specificity were used to evaluate the models' performance. Classification of 75 patients with eligible follow-up based on RANKL status resulted in a significant difference in progression-free survival (p = 0.035). VOIcore-based RF classifier performs best. Using this model, the AUCs for the training and validation cohorts were 0.880 and 0.766, respectively. In conclusion, a machine learning approach based on CT radiomic features could discriminate prognostically significant RANKL status in spinal GCTB, which may ultimately aid clinical decision-making.

Unlocking the Potential of the Human Microbiome for Identifying Disease Diagnostic Biomarkers

The human microbiome encodes more than three million genes, outnumbering human genes by more than 100 times, while microbial cells in the human microbiota outnumber human cells by 10 times. Thus, the human microbiota and related microbiome constitute a vast source for identifying disease biomarkers and therapeutic drug targets. Herein, we review the evidence backing the exploitation of the human microbiome for identifying diagnostic biomarkers for human disease. We describe the importance of the human microbiome in health and disease and detail the use of the human microbiome and microbiota metabolites as potential diagnostic biomarkers for multiple diseases, including cancer, as well as inflammatory, neurological, and metabolic diseases. Thus, the human microbiota has enormous potential to pave the road for a new era in biomarker research for diagnostic and therapeutic purposes. The scientific community needs to collaborate to overcome current challenges in microbiome research concerning the lack of standardization of research methods and the lack of understanding of causal relationships between microbiota and human disease.