Deep Learning in Pancreatic Tissue: Identification of Anatomical Structures, Pancreatic Intraepithelial Neoplasia, and Ductal Adenocarcinoma

Topographic analysis of pancreatic cancer by TMA and digital spatial profiling reveals biological complexity with potential therapeutic implications

Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal human malignancies. Tissue microarrays (TMA) are an established method of high throughput biomarker interrogation in tissues but may not capture histological features of cancer with potential biological relevance. Topographic TMAs (T-TMAs) representing pathophysiological hallmarks of cancer were constructed from representative, retrospective PDAC diagnostic material, including 72 individual core tissue samples. The T-TMA was interrogated with tissue hybridization-based experiments to confirm the accuracy of the topographic sampling, expression of pro-tumourigenic and immune mediators of cancer, totalling more than 750 individual biomarker analyses. A custom designed Next Generation Sequencing (NGS) panel and a spatial distribution-specific transcriptomic evaluation were also employed. The morphological choice of the pathophysiological hallmarks of cancer was confirmed by protein-specific expression. Quantitative analysis identified topography-specific patterns of expression in the IDO/TGF-β axis; with a heterogeneous relationship of inflammation and desmoplasia across hallmark areas and a general but variable protein and gene expression of c-MET. NGS results highlighted underlying genetic heterogeneity within samples, which may have a confounding influence on the expression of a particular biomarker. T-TMAs, integrated with quantitative biomarker digital scoring, are useful tools to identify hallmark specific expression of biomarkers in pancreatic cancer.

BEYOND TRADITIONAL TOOLS: EXPLORING CONVOLUTIONAL NEURAL NETWORKS AS INNOVATIVE PROGNOSTIC MODELS IN PANCREATIC DUCTAL ADENOCARCINOMA

BACKGROUND

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive and lethal form of cancer with limited prognostic accuracy using traditional factors. This has led to the exploration of innovative prognostic models, including convolutional neural networks (CNNs), in PDAC. CNNs, a type of artificial intelligence algorithm, have shown promise in various medical applications, including image analysis and pattern recognition. Their ability to extract complex features from medical images makes them suitable for improving prognostication in PDAC. However, implementing CNNs in clinical practice poses challenges, such as data availability and interpretability. Future research should focus on multi-center studies, integrating multiple data modalities, and combining CNN outputs with biomarker panels. Collaborative efforts and patient autonomy should be considered to ensure the ethical implementation of CNN-based prognostic models. Further validation and optimisation of CNN-based models are necessary to enhance their reliability and clinical utility in PDAC prognostication.

BACKGROUND

•Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with limited prognostic accuracy through traditional methods.

BACKGROUND

•Convolutional neural networks (CNNs) are being explored for prognostic models in PDAC.

BACKGROUND

•They can extract complex features from images, aiding PDAC prognostication.

BACKGROUND

•Further validation and optimization of CNN-based models are needed for better reliability and clinical utility in PDAC.

Role of artificial intelligence in the characterization of indeterminate pancreatic head mass and its usefulness in preoperative diagnosis

Artificial intelligence (AI) has been used in various fields of day-to-day life and its role in medicine is immense. Understanding of oncology has been improved with the introduction of AI which helps in diagnosis, treatment planning, management, prognosis, and follow-up. It also helps to identify high-risk groups who can be subjected to timely screening for early detection of malignant conditions. It is more important in pancreatic cancer as it is one of the major causes of cancer-related deaths worldwide and there are no specific early features (clinical and radiological) for diagnosis. With improvement in imaging modalities (computed tomography, magnetic resonance imaging, endoscopic ultrasound), most often clinicians were being challenged with lesions that were difficult to diagnose with human competence. AI has been used in various other branches of medicine to differentiate such indeterminate lesions including the thyroid gland, breast, lungs, liver, adrenal gland, kidney, etc. In the case of pancreatic cancer, the role of AI has been explored and is still ongoing. This review article will focus on how AI can be used to diagnose pancreatic cancer early or differentiate it from benign pancreatic lesions, therefore, management can be planned at an earlier stage.

Computer image analysis with artificial intelligence: a practical introduction to convolutional neural networks for medical professionals

Artificial intelligence tools, particularly convolutional neural networks (CNNs), are transforming healthcare by enhancing predictive, diagnostic, and decision-making capabilities. This review provides an accessible and practical explanation of CNNs for clinicians and highlights their relevance in medical image analysis. CNNs have shown themselves to be exceptionally useful in computer vision, a field that enables machines to 'see' and interpret visual data. Understanding how these models work can help clinicians leverage their full potential, especially as artificial intelligence continues to evolve and integrate into healthcare. CNNs have already demonstrated their efficacy in diverse medical fields, including radiology, histopathology, and medical photography. In radiology, CNNs have been used to automate the assessment of conditions such as pneumonia, pulmonary embolism, and rectal cancer. In histopathology, CNNs have been used to assess and classify colorectal polyps, gastric epithelial tumours, as well as assist in the assessment of multiple malignancies. In medical photography, CNNs have been used to assess retinal diseases and skin conditions, and to detect gastric and colorectal polyps during endoscopic procedures. In surgical laparoscopy, they may provide intraoperative assistance to surgeons, helping interpret surgical anatomy and demonstrate safe dissection zones. The integration of CNNs into medical image analysis promises to enhance diagnostic accuracy, streamline workflow efficiency, and expand access to expert-level image analysis, contributing to the ultimate goal of delivering further improvements in patient and healthcare outcomes.

Identifying Effective Biomarkers for Accurate Pancreatic Cancer Prognosis Using Statistical Machine Learning

Pancreatic cancer (PC) has one of the lowest survival rates among all major types of cancer. Consequently, it is one of the leading causes of mortality worldwide. Serum biomarkers historically correlate well with the early prognosis of post-surgical complications of PC. However, attempts to identify an effective biomarker panel for the successful prognosis of PC were almost non-existent in the current literature. The current study investigated the roles of various serum biomarkers including carbohydrate antigen 19-9 (CA19-9), chemokine (C-X-C motif) ligand 8 (CXCL-8), procalcitonin (PCT), and other relevant clinical data for identifying PC progression, classified into sepsis, recurrence, and other post-surgical complications, among PC patients. The most relevant biochemical and clinical markers for PC prognosis were identified using a random-forest-powered feature elimination method. Using this informative biomarker panel, the selected machine-learning (ML) classification models demonstrated highly accurate results for classifying PC patients into three complication groups on independent test data. The superiority of the combined biomarker panel (Max AUC-ROC = 100%) was further established over using CA19-9 features exclusively (Max AUC-ROC = 75%) for the task of classifying PC progression. This novel study demonstrates the effectiveness of the combined biomarker panel in successfully diagnosing PC progression and other relevant complications among Egyptian PC survivors.

Implementation of deep learning in liver pathology optimizes diagnosis of benign lesions and adenocarcinoma metastasis

INTRODUCTION

Differentiation of histologically similar structures in the liver, including anatomical structures, benign bile duct lesions, or common types of liver metastases, can be challenging with conventional histological tissue sections alone. Accurate histopathological classification is paramount for the diagnosis and adequate treatment of the disease. Deep learning algorithms have been proposed for objective and consistent assessment of digital histopathological images.

MATERIALS AND METHODS

In the present study, we trained and evaluated deep learning algorithms based on the EfficientNetV2 and ResNetRS architectures to discriminate between different histopathological classes. For the required dataset, specialized surgical pathologists annotated seven different histological classes, including different non-neoplastic anatomical structures, benign bile duct lesions, and liver metastases from colorectal and pancreatic adenocarcinoma in a large patient cohort. Annotation resulted in a total of 204.159 image patches, followed by discrimination analysis using our deep learning models. Model performance was evaluated on validation and test data using confusion matrices.

RESULTS

Evaluation of the test set based on tiles and cases revealed overall highly satisfactory prediction capability of our algorithm for the different histological classes, resulting in a tile accuracy of 89% (38 413/43 059) and case accuracy of 94% (198/211). Importantly, the separation of metastasis versus benign lesions was certainly confident on case level, confirming the classification model performed with high diagnostic accuracy. Moreover, the whole curated raw data set is made publically available.

CONCLUSIONS

Deep learning is a promising approach in surgical liver pathology supporting decision making in personalized medicine.

Lymphoma Recognition in Histology Image of Gastric Mucosal Biopsy with Prototype Learning

Lymphomas are a group of malignant tumors developed from lymphocytes, which may occur in many organs. Therefore, accurately distinguishing lymphoma from solid tumors is of great clinical significance. Due to the strong ability of graph structure to capture the topology of the micro-environment of cells, graph convolutional networks (GCNs) have been widely used in pathological image processing. Nevertheless, the softmax classification layer of the graph convolutional models cannot drive learned representations compact enough to distinguish some types of lymphomas and solid tumors with strong morphological analogies on H&E-stained images. To alleviate this problem, a prototype learning based model is proposed, namely graph convolutional prototype network (GCPNet). Specifically, the method follows the patch-to-slide architecture first to perform patch-level classification and obtain image-level results by fusing patch-level predictions. The classification model is assembled with a graph convolutional feature extractor and prototype-based classification layer to build more robust feature representations for classification. For model training, a dynamic prototype loss is proposed to give the model different optimization priorities at different stages of training. Besides, a prototype reassignment operation is designed to prevent the model from getting stuck in local minima during optimization. Experiments are conducted on a dataset of 183 Whole slide images (WSI) of gastric mucosa biopsy. The proposed method achieved superior performance than existing methods.Clinical relevance- The work proposed a new deep learning framework tailored to lymphoma recognition on pathological image of gastric mucosal biopsy to differentiate lymphoma, adenocarcinoma and inflammation.

Explainable AI in medical imaging: An overview for clinical practitioners – Saliency-based XAI approaches

Since recent achievements of Artificial Intelligence (AI) have proven significant success and promising results throughout many fields of application during the last decade, AI has also become an essential part of medical research. The improving data availability, coupled with advances in high-performance computing and innovative algorithms, has increased AI's potential in various aspects. Because AI rapidly reshapes research and promotes the development of personalized clinical care, alongside its implementation arises an urgent need for a deep understanding of its inner workings, especially in high-stake domains. However, such systems can be highly complex and opaque, limiting the possibility of an immediate understanding of the system's decisions. Regarding the medical field, a high impact is attributed to these decisions as physicians and patients can only fully trust AI systems when reasonably communicating the origin of their results, simultaneously enabling the identification of errors and biases. Explainable AI (XAI), becoming an increasingly important field of research in recent years, promotes the formulation of explainability methods and provides a rationale allowing users to comprehend the results generated by AI systems. In this paper, we investigate the application of XAI in medical imaging, addressing a broad audience, especially healthcare professionals. The content focuses on definitions and taxonomies, standard methods and approaches, advantages, limitations, and examples representing the current state of research regarding XAI in medical imaging. This paper focuses on saliency-based XAI methods, where the explanation can be provided directly on the input data (image) and which naturally are of special importance in medical imaging.

Artificial Intelligence in the Diagnosis and Treatment of Pancreatic Cystic Lesions and Adenocarcinoma

Pancreatic cancer is projected to become the second leading cause of cancer-related mortality in the United States by 2030. This is in part due to the paucity of reliable screening and diagnostic options for early detection. Amongst known pre-malignant pancreatic lesions, pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasms (IPMNs) are the most prevalent. The current standard of care for the diagnosis and classification of pancreatic cystic lesions (PCLs) involves cross-sectional imaging studies and endoscopic ultrasound (EUS) and, when indicated, EUS-guided fine needle aspiration and cyst fluid analysis. However, this is suboptimal for the identification and risk stratification of PCLs, with accuracy of only 65-75% for detecting mucinous PCLs. Artificial intelligence (AI) is a promising tool that has been applied to improve accuracy in screening for solid tumors, including breast, lung, cervical, and colon cancer. More recently, it has shown promise in diagnosing pancreatic cancer by identifying high-risk populations, risk-stratifying premalignant lesions, and predicting the progression of IPMNs to adenocarcinoma. This review summarizes the available literature on artificial intelligence in the screening and prognostication of precancerous lesions in the pancreas, and streamlining the diagnosis of pancreatic cancer.

Applications of Deep Learning in Endocrine Neoplasms

Machine learning methods have been growing in prominence across all areas of medicine. In pathology, recent advances in deep learning (DL) have enabled computational analysis of histological samples, aiding in diagnosis and characterization in multiple disease areas. In cancer, and particularly endocrine cancer, DL approaches have been shown to be useful in tasks ranging from tumor grading to gene expression prediction. This review summarizes the current state of DL research in endocrine cancer histopathology with an emphasis on experimental design, significant findings, and key limitations.

Deep learning for the detection of anatomical tissue structures and neoplasms of the skin on scanned histopathological tissue sections

Basal cell carcinoma (BCC), squamous cell carcinoma (SqCC) and melanoma are among the most common cancer types. Correct diagnosis based on histological evaluation after biopsy or excision is paramount for adequate therapy stratification. Deep learning on histological slides has been suggested to complement and improve routine diagnostics, but publicly available curated and annotated data and usable models trained to distinguish common skin tumors are rare and often lack heterogeneous non-tumor categories. A total of 16 classes from 386 cases were manually annotated on scanned histological slides, 129,364 100 x 100 µm (~395 x 395 px) image tiles were extracted and split into a training, validation and test set. An EfficientV2 neuronal network was trained and optimized to classify image categories. Cross entropy loss, balanced accuracy and Matthews correlation coefficient were used for model evaluation. Image and patient data were assessed with confusion matrices. Application of the model to an external set of whole slides facilitated localization of melanoma and non-tumor tissue. Automated differentiation of BCC, SqCC, melanoma, naevi and non-tumor tissue structures was possible, and a high diagnostic accuracy was achieved in the validation (98%) and test (97%) set. In summary, we provide a curated dataset including the most common neoplasms of the skin and various anatomical compartments to enable researchers to train, validate and improve deep learning models. Automated classification of skin tumors by deep learning techniques is possible with high accuracy, facilitates tumor localization and has the potential to support and improve routine diagnostics.

Artificial intelligence in pancreatic cancer

Pancreatic cancer is the deadliest disease, with a five-year overall survival rate of just 11%. The pancreatic cancer patients diagnosed with early screening have a median overall survival of nearly ten years, compared with 1.5 years for those not diagnosed with early screening. Therefore, early diagnosis and early treatment of pancreatic cancer are particularly critical. However, as a rare disease, the general screening cost of pancreatic cancer is high, the accuracy of existing tumor markers is not enough, and the efficacy of treatment methods is not exact. In terms of early diagnosis, artificial intelligence technology can quickly locate high-risk groups through medical images, pathological examination, biomarkers, and other aspects, then screening pancreatic cancer lesions early. At the same time, the artificial intelligence algorithm can also be used to predict the survival time, recurrence risk, metastasis, and therapy response which could affect the prognosis. In addition, artificial intelligence is widely used in pancreatic cancer health records, estimating medical imaging parameters, developing computer-aided diagnosis systems, etc. Advances in AI applications for pancreatic cancer will require a concerted effort among clinicians, basic scientists, statisticians, and engineers. Although it has some limitations, it will play an essential role in overcoming pancreatic cancer in the foreseeable future due to its mighty computing power.

MALDI-MSI: A Powerful Approach to Understand Primary Pancreatic Ductal Adenocarcinoma and Metastases

Cancer-related deaths are very commonly attributed to complications from metastases to neighboring as well as distant organs. Dissociate response in the treatment of pancreatic adenocarcinoma is one of the main causes of low treatment success and low survival rates. This behavior could not be explained by transcriptomics or genomics; however, differences in the composition at the protein level could be observed. We have characterized the proteomic composition of primary pancreatic adenocarcinoma and distant metastasis directly in human tissue samples, utilizing mass spectrometry imaging. The mass spectrometry data was used to train and validate machine learning models that could distinguish both tissue entities with an accuracy above 90%. Model validation on samples from another collection yielded a correct classification of both entities. Tentative identification of the discriminative molecular features showed that collagen fragments (COL1A1, COL1A2, and COL3A1) play a fundamental role in tumor development. From the analysis of the receiver operating characteristic, we could further advance some potential targets, such as histone and histone variations, that could provide a better understanding of tumor development, and consequently, more effective treatments.

Setting the Research Agenda for Clinical Artificial Intelligence in Pancreatic Adenocarcinoma Imaging

Simple Summary

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers worldwide, associated with a 98% loss of life expectancy and a 30% increase in disability-adjusted life years. Image-based artificial intelligence (AI) can help improve outcomes for PDAC given that current clinical guidelines are non-uniform and lack evidence-based consensus. However, research on image-based AI for PDAC is too scattered and lacking in sufficient quality to be incorporated into clinical workflows. In this review, an international, multi-disciplinary team of the world’s leading experts in pancreatic cancer breaks down the patient pathway and pinpoints the current clinical touchpoints in each stage. The available PDAC imaging AI literature addressing each pathway stage is then rigorously analyzed, and current performance and pitfalls are identified in a comprehensive overview. Finally, the future research agenda for clinically relevant, image-driven AI in PDAC is proposed.

Abstract

Pancreatic ductal adenocarcinoma (PDAC), estimated to become the second leading cause of cancer deaths in western societies by 2030, was flagged as a neglected cancer by the European Commission and the United States Congress. Due to lack of investment in research and development, combined with a complex and aggressive tumour biology, PDAC overall survival has not significantly improved the past decades. Cross-sectional imaging and histopathology play a crucial role throughout the patient pathway. However, current clinical guidelines for diagnostic workup, patient stratification, treatment response assessment, and follow-up are non-uniform and lack evidence-based consensus. Artificial Intelligence (AI) can leverage multimodal data to improve patient outcomes, but PDAC AI research is too scattered and lacking in quality to be incorporated into clinical workflows. This review describes the patient pathway and derives touchpoints for image-based AI research in collaboration with a multi-disciplinary, multi-institutional expert panel. The literature exploring AI to address these touchpoints is thoroughly retrieved and analysed to identify the existing trends and knowledge gaps. The results show absence of multi-institutional, well-curated datasets, an essential building block for robust AI applications. Furthermore, most research is unimodal, does not use state-of-the-art AI techniques, and lacks reliable ground truth. Based on this, the future research agenda for clinically relevant, image-driven AI in PDAC is proposed.

Tumour Size and T-Stage in Pancreatic Cancer Resection Specimens Depend on the Pathology Examination Approach

In the eighth edition of the TNM classification for pancreatic ductal adenocarcinoma (PDAC), stages T1 to T3 are defined by tumour size, size measurement being deemed objective and accurate. This study investigated whether various, currently used approaches to tumour measurement result in different tumour sizes and differences in T-stage assignment. In a series of 315 resected PDAC, tumour sizes were measured as follows: macroscopically in a single or in two perpendicular planes and with or without microscopic corroboration. Comparison of the resulting tumour sizes showed that both macroscopic measurement in two planes and microscopic corroboration gave significantly different results (p < 0.001). Compared to the most simple approach (macroscopic measurement in one plane), the comprehensive approach (macroscopic measurement in two planes with microscopic corroboration) resulted in a larger tumour size in 263 (83%) cases (mean absolute size difference: 10 mm; mean relative size change: 36%). T-stage assignment differed in 142 (45%) cases between the simple and comprehensive approach and affected 87%, 38% and 48% of the cases deemed to be stage T1, T2 and T3, respectively. In conclusion, tumour size and T-stage are highly approach-dependent. Consensus on an accurate method is required to ensure comparability of these basic data.

Assessment of glomerular morphological patterns by deep learning algorithms

Background

Compilation of different morphological lesion signatures is characteristic of renal pathology. Previous studies have documented the potential value of artificial intelligence (AI) in recognizing relatively clear-cut glomerular structures and patterns, such as segmental or global sclerosis or mesangial hypercellularity. This study aimed to test the capacity of deep learning algorithms to recognize complex glomerular structural changes that reflect common diagnostic dilemmas in nephropathology.

Methods

For this purpose, we defined nine classes of glomerular morphological patterns and trained twelve convolutional neuronal network (CNN) models on these. The two-step training process was done on a first dataset defined by an expert nephropathologist (12,253 images) and a second consensus dataset (11,142 images) defined by three experts in the field.

Results

The efficacy of CNN training was evaluated using another set with 180 consensus images, showing convincingly good classification results (kappa-values 0.838–0.938).

Furthermore, we elucidated the image areas decisive for CNN-based decision making by class activation maps. Finally, we demonstrated that the algorithm could decipher glomerular disease patterns coinciding in a single glomerulus (e.g. necrosis along with mesangial and endocapillary hypercellularity).

Conclusions

In summary, our model, focusing on glomerular lesions detectable by conventional microscopy, is the first sui generis to deploy deep learning as a reliable and promising tool in recognition of even discrete and/or overlapping morphological changes. Our results provide a stimulus for ongoing projects that integrate further input levels next to morphology (such as immunohistochemistry, electron microscopy, and clinical information) to develop a novel tool applicable for routine diagnostic nephropathology.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40620-021-01221-9.

Robust deep learning model for prognostic stratification of pancreatic ductal adenocarcinoma patients

A major challenge for treating patients with pancreatic ductal adenocarcinoma (PDAC) is the unpredictability of their prognoses due to high heterogeneity. We present Multi-Omics DEep Learning for Prognosis-correlated subtyping (MODEL-P) to identify PDAC subtypes and to predict prognoses of new patients. MODEL-P was trained on autoencoder integrated multi-omics of 146 patients with PDAC together with their survival outcome. Using MODEL-P, we identified two PDAC subtypes with distinct survival outcomes (median survival 10.1 and 22.7 months, respectively, log rank p = 1 × 10⁻⁶), which correspond to DNA damage repair and immune response. We rigorously validated MODEL-P by stratifying patients in five independent datasets into these two survival groups and achieved significant survival difference, which is superior to current practice and other subtyping schemas. We believe the subtype-specific signatures would facilitate PDAC pathogenesis discovery, and MODEL-P can provide clinicians the prognoses information in the treatment decision-making to better gauge the benefits versus the risks.

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We developed DL-based MODEL-P to identify prognosis-correlated PDAC subtypes

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The identified subtypes related to DNA damage repair and immune response processes

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MODEL-P stratified patients from independent datasets into distinct survival groups

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MODEL-P could be used in clinics to aid treatment decision-making