Application of digital pathology‐based advanced analytics of tumour microenvironment organisation to predict prognosis and therapeutic response

In recent years, the application of advanced analytics, especially artificial intelligence (AI), to digital H&E images, and other histological image types, has begun to radically change how histological images are used in the clinic. Alongside the recognition that the tumour microenvironment (TME) has a profound impact on tumour phenotype, the technical development of highly multiplexed immunofluorescence platforms has enhanced the biological complexity that can be captured in the TME with high precision. AI has an increasingly powerful role in the recognition and quantitation of image features and the association of such features with clinically important outcomes, as occurs in distinct stages in conventional machine learning. Deep‐learning algorithms are able to elucidate TME patterns inherent in the input data with minimum levels of human intelligence and, hence, have the potential to achieve clinically relevant predictions and discovery of important TME features. Furthermore, the diverse repertoire of deep‐learning algorithms able to interrogate TME patterns extends beyond convolutional neural networks to include attention‐based models, graph neural networks, and multimodal models. To date, AI models have largely been evaluated retrospectively, outside the well‐established rigour of prospective clinical trials, in part because traditional clinical trial methodology may not always be suitable for the assessment of AI technology. However, to enable digital pathology‐based advanced analytics to meaningfully impact clinical care, specific measures of ‘added benefit’ to the current standard of care and validation in a prospective setting are important. This will need to be accompanied by adequate measures of explainability and interpretability. Despite such challenges, the combination of expanding datasets, increased computational power, and the possibility of integration of pre‐clinical experimental insights into model development means there is exciting potential for the future progress of these AI applications. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

[1]  P. Siegel,et al.  Single-cell spatial landscapes of the lung tumour immune microenvironment , 2023, Nature.

[2]  P. Siegel,et al.  Single-cell spatial immune landscapes of primary and metastatic brain tumours , 2023, Nature.

[3]  S. Ather,et al.  DECIDE-AI: a new reporting guideline and its relevance to artificial intelligence studies in radiology. , 2023, Clinical radiology.

[4]  Jakob Nikolas Kather,et al.  Multistain deep learning for prediction of prognosis and therapy response in colorectal cancer , 2023, Nature Medicine.

[5]  Eric W. Tramel,et al.  Federated learning for predicting histological response to neoadjuvant chemotherapy in triple-negative breast cancer , 2023, Nature Medicine.

[6]  Thomas J. Fuchs,et al.  Clinical Validation of Artificial Intelligence-Augmented Pathology Diagnosis Demonstrates Significant Gains in Diagnostic Accuracy in Prostate Cancer Detection. , 2022, Archives of pathology & laboratory medicine.

[7]  Ming Y. Lu,et al.  A deep-learning model for transforming the style of tissue images from cryosectioned to formalin-fixed and paraffin-embedded , 2022, Nature Biomedical Engineering.

[8]  Alexandro E. Trevino,et al.  Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens , 2022, Nature Biomedical Engineering.

[9]  Michelle M. Li,et al.  Graph representation learning in biomedicine and healthcare , 2022, Nature Biomedical Engineering.

[10]  Zachary R. Lewis,et al.  High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. , 2022, Nature biotechnology.

[11]  Ming Y. Lu,et al.  Artificial intelligence for multimodal data integration in oncology. , 2022, Cancer cell.

[12]  Jakob Nikolas Kather,et al.  Artificial intelligence in histopathology: enhancing cancer research and clinical oncology , 2022, Nature Cancer.

[13]  D. Miklos,et al.  Tumor immune contexture is a determinant of anti-CD19 CAR T cell efficacy in large B cell lymphoma , 2022, Nature Medicine.

[14]  Ming Y. Lu,et al.  Pan-cancer integrative histology-genomic analysis via multimodal deep learning. , 2022, Cancer cell.

[15]  R. Socher,et al.  Prostate cancer therapy personalization via multi-modal deep learning on randomized phase III clinical trials , 2022, npj Digital Medicine.

[16]  Heather A. Harrington,et al.  Multiscale topology characterizes dynamic tumor vascular networks , 2022, Science advances.

[17]  Spiros C. Denaxas,et al.  Reporting guideline for the early stage clinical evaluation of decision support systems driven by artificial intelligence: DECIDE-AI , 2022, BMJ.

[18]  Spiros C. Denaxas,et al.  Reporting guideline for the early-stage clinical evaluation of decision support systems driven by artificial intelligence: DECIDE-AI , 2022, Nature Medicine.

[19]  I. Ellis,et al.  Breast tumor microenvironment structures are associated with genomic features and clinical outcome , 2022, Nature Genetics.

[20]  Nils Eling,et al.  Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy , 2022, Science Immunology.

[21]  H. Najafabadi,et al.  Spatially mapping the immune landscape of melanoma using imaging mass cytometry , 2022, Science Immunology.

[22]  O. Elemento,et al.  Unsupervised discovery of tissue architecture in multiplexed imaging , 2022, bioRxiv.

[23]  T. Kiehl,et al.  The explainability paradox: Challenges for xAI in digital pathology , 2022, Future Gener. Comput. Syst..

[24]  S. Ishikawa,et al.  Universal encoding of pan-cancer histology by deep texture representations. , 2022, Cell reports.

[25]  S. Devries,et al.  An AI-derived digital pathology-based biomarker to predict the benefit of androgen deprivation therapy in localized prostate cancer with validation in NRG/RTOG 9408. , 2022, Journal of Clinical Oncology.

[26]  Garry P. Nolan,et al.  Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA , 2022, Nature Methods.

[27]  Po-Hsuan Cameron Chen,et al.  Artificial intelligence for diagnosis and Gleason grading of prostate cancer: the PANDA challenge , 2022, Nature Medicine.

[28]  S. Tavaré,et al.  Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment , 2021, Nature Cancer.

[29]  Shujing Jane Lim,et al.  Guidelines for cellular and molecular pathology content in clinical trial protocols: the SPIRIT-Path extension. , 2021, The Lancet. Oncology.

[30]  W. Hahn,et al.  Biologically informed deep neural network for prostate cancer discovery , 2021, Nature.

[31]  J. Taube,et al.  Multi-institutional TSA-amplified Multiplexed Immunofluorescence Reproducibility Evaluation (MITRE) Study , 2021, Journal for ImmunoTherapy of Cancer.

[32]  B. Delahunt,et al.  ISUP Consensus Definition of Cribriform Pattern Prostate Cancer , 2021, The American journal of surgical pathology.

[33]  Cody N. Heiser,et al.  Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer , 2021, bioRxiv.

[34]  Andrew H. Beck,et al.  Human-interpretable image features derived from densely mapped cancer pathology slides predict diverse molecular phenotypes , 2021, Nature Communications.

[35]  D. Moher,et al.  Reporting guidelines for clinical trials of artificial intelligence interventions: the SPIRIT-AI and CONSORT-AI guidelines , 2021, Trials.

[36]  Salil S. Bhate,et al.  Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma , 2020, Nature Communications.

[37]  A. Kishan,et al.  A Systematic Review of the Evidence for the Decipher Genomic Classifier in Prostate Cancer. , 2020, European urology.

[38]  Jakob Nikolas Kather,et al.  Deep learning in cancer pathology: a new generation of clinical biomarkers , 2020, British Journal of Cancer.

[39]  Cecilia S. Lee,et al.  Reporting guidelines for clinical trial reports for interventions involving artificial intelligence: the CONSORT-AI extension. , 2020, The Lancet. Digital health.

[40]  Zhongping Zhang,et al.  Automatic Prediction of MGMT Status in Glioblastoma via Deep Learning-Based MR Image Analysis , 2020, BioMed research international.

[41]  Gary S Collins,et al.  Reporting guidelines for clinical trial reports for interventions involving artificial intelligence: the CONSORT-AI Extension , 2020, BMJ.

[42]  Cecilia S Lee,et al.  Reporting guidelines for clinical trial reports for interventions involving artificial intelligence: the CONSORT-AI extension , 2020, Nature Medicine.

[43]  Sangwoo Lee,et al.  Liver imaging features by convolutional neural network to predict the metachronous liver metastasis in stage I-III colorectal cancer patients based on preoperative abdominal CT scan , 2020, BMC Bioinformatics.

[44]  Gary S Collins,et al.  Guidelines for clinical trial protocols for interventions involving artificial intelligence: the SPIRIT-AI Extension , 2020, Nature Medicine.

[45]  J. Galon,et al.  The immune contexture and Immunoscore in cancer prognosis and therapeutic efficacy , 2020, Nature Reviews Cancer.

[46]  J. Galon,et al.  The immune contexture and Immunoscore in cancer prognosis and therapeutic efficacy , 2020, Nature Reviews Cancer.

[47]  Yuming Liu,et al.  Non-disruptive collagen characterization in clinical histopathology using cross-modality image synthesis , 2020, Communications Biology.

[48]  Salil S. Bhate,et al.  Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front , 2020, Cell.

[49]  K. Sirinukunwattana,et al.  Image-based consensus molecular subtype (imCMS) classification of colorectal cancer using deep learning , 2020, Gut.

[50]  M. Salto‐Tellez,et al.  A robust multiplex immunofluorescence and digital pathology workflow for the characterisation of the tumour immune microenvironment , 2020, Molecular oncology.

[51]  Ming Y. Lu,et al.  AI-based pathology predicts origins for cancers of unknown primary , 2020, Nature.

[52]  Stefano Trebeschi,et al.  Machine learning-based analysis of CT radiomics model for prediction of colorectal metachronous liver metastases , 2020, Abdominal Radiology.

[53]  James Y. Zou,et al.  Integrating spatial gene expression and breast tumour morphology via deep learning , 2020, Nature Biomedical Engineering.

[54]  A. Darzi,et al.  Developing specific reporting guidelines for diagnostic accuracy studies assessing AI interventions: The STARD-AI Steering Group , 2020, Nature Medicine.

[55]  Angela E. Leek,et al.  Geospatial immune variability illuminates differential evolution of lung adenocarcinoma , 2020, Nature Medicine.

[56]  Ming Y. Lu,et al.  Data-efficient and weakly supervised computational pathology on whole-slide images , 2020, Nature Biomedical Engineering.

[57]  Clinton J. V. Campbell,et al.  Pan-cancer diagnostic consensus through searching archival histopathology images using artificial intelligence. , 2020, NPJ digital medicine.

[58]  R. Jain,et al.  A framework for advancing our understanding of cancer-associated fibroblasts , 2020, Nature Reviews Cancer.

[59]  H. Moch,et al.  The single-cell pathology landscape of breast cancer , 2020, Nature.

[60]  Kimmo Kartasalo,et al.  Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study. , 2020, The Lancet. Oncology.

[61]  E. Sahai,et al.  Topological Tumor Graphs: a graph-based spatial model to infer stromal recruitment for immunosuppression in melanoma histology. , 2019, Cancer research.

[62]  Danielle Park,et al.  A FIJI macro for quantifying pattern in extracellular matrix , 2019, Life Science Alliance.

[63]  Morteza Babaie,et al.  Pan-cancer diagnostic consensus through searching archival histopathology images using artificial intelligence , 2019, npj Digital Medicine.

[64]  Jakob Nikolas Kather,et al.  Pan-cancer image-based detection of clinically actionable genetic alterations , 2019, Nature Cancer.

[65]  Ming Y. Lu,et al.  Weakly Supervised Prostate Tma Classification Via Graph Convolutional Networks , 2019, 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI).

[66]  Alexander W. Jung,et al.  Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis , 2019, Nature Cancer.

[67]  G. Wainrib,et al.  Deep learning-based classification of mesothelioma improves prediction of patient outcome , 2019, Nature Medicine.

[68]  Garry Nolan,et al.  MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure , 2019, Science Advances.

[69]  Honglak Lee,et al.  Near real-time intraoperative brain tumor diagnosis using stimulated Raman histology and deep neural networks , 2019, Nature Medicine.

[70]  Timo Kohlberger,et al.  An augmented reality microscope with real-time artificial intelligence integration for cancer diagnosis , 2019, Nature Medicine.

[71]  A. Madabhushi,et al.  Artificial intelligence in digital pathology — new tools for diagnosis and precision oncology , 2019, Nature reviews. Clinical oncology.

[72]  Thomas J. Fuchs,et al.  Clinical-grade computational pathology using weakly supervised deep learning on whole slide images , 2019, Nature Medicine.

[73]  Gary S. Collins,et al.  Reporting of artificial intelligence prediction models , 2019, The Lancet.

[74]  Jakob Nikolas Kather,et al.  Deep learning can predict microsatellite instability directly from histology in gastrointestinal cancer , 2019, Nature Medicine.

[75]  Constantino Carlos Reyes-Aldasoro,et al.  Predicting survival from colorectal cancer histology slides using deep learning: A retrospective multicenter study , 2019, PLoS medicine.

[76]  Jin Tae Kwak,et al.  Hover-Net: Simultaneous segmentation and classification of nuclei in multi-tissue histology images , 2018, Medical Image Anal..

[77]  Cynthia Rudin,et al.  Stop explaining black box machine learning models for high stakes decisions and use interpretable models instead , 2018, Nature Machine Intelligence.

[78]  Richard J. Chen,et al.  Deep Adversarial Training for Multi-Organ Nuclei Segmentation in Histopathology Images , 2018, IEEE Transactions on Medical Imaging.

[79]  N. Razavian,et al.  Classification and mutation prediction from non–small cell lung cancer histopathology images using deep learning , 2018, Nature Medicine.

[80]  Jakob Nikolas Kather,et al.  Topography of cancer-associated immune cells in human solid tumors , 2018, eLife.

[81]  Sean C. Bendall,et al.  A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging , 2018, Cell.

[82]  W. Sauerbrei,et al.  Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK): An Abridged Explanation and Elaboration , 2018, Journal of the National Cancer Institute.

[83]  Virginia G Kaklamani,et al.  Adjuvant Chemotherapy Guided by a 21‐Gene Expression Assay in Breast Cancer , 2018, The New England journal of medicine.

[84]  F. Marincola,et al.  International validation of the consensus Immunoscore for the classification of colon cancer: a prognostic and accuracy study , 2018, The Lancet.

[85]  Rajarsi R. Gupta,et al.  Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images. , 2018, Cell reports.

[86]  R. Figlin,et al.  A novel machine learning approach reveals latent vascular phenotypes predictive of renal cancer outcome , 2017, Scientific Reports.

[87]  D. Brat,et al.  Predicting cancer outcomes from histology and genomics using convolutional networks , 2017, Proceedings of the National Academy of Sciences.

[88]  A Harbias,et al.  Implications of Observer Variation in Gleason Scoring of Prostate Cancer on Clinical Management: A Collaborative Audit. , 2017, The Gulf journal of oncology.

[89]  Laurence Zitvogel,et al.  The immune contexture in cancer prognosis and treatment , 2017, Nature Reviews Clinical Oncology.

[90]  E. Sahai,et al.  Tumor Microenvironment and Differential Responses to Therapy. , 2017, Cold Spring Harbor perspectives in medicine.

[91]  Peter Bankhead,et al.  QuPath: Open source software for digital pathology image analysis , 2017, Scientific Reports.

[92]  B. Krishnamachary,et al.  Structure and Function of a Prostate Cancer Dissemination–Permissive Extracellular Matrix , 2016, Clinical Cancer Research.

[93]  Patricia D. Castro,et al.  Positive association of collagen type I with non-muscle invasive bladder cancer progression , 2016, Oncotarget.

[94]  Andrew J. Schaumberg,et al.  D R A F T H&E-stained Whole Slide Image Deep Learning Predicts SPOP Mutation State in Prostate Cancer , 2017 .

[95]  Holger Moch,et al.  The 2016 WHO Classification of Tumours of the Urinary System and Male Genital Organs-Part B: Prostate and Bladder Tumours. , 2016, European urology.

[96]  N. Rajpoot,et al.  Locality Sensitive Deep Learning for Detection and Classification of Nuclei in Routine Colon Cancer Histology Images , 2016, IEEE Trans. Medical Imaging.

[97]  Chris Bakal,et al.  Microenvironmental Heterogeneity Parallels Breast Cancer Progression: A Histology–Genomic Integration Analysis , 2016, PLoS medicine.

[98]  Angela E. Leek,et al.  Increased peri-ductal collagen micro-organization may contribute to raised mammographic density , 2016, Breast Cancer Research.

[99]  B. Delahunt,et al.  The 2014 International Society of Urological Pathology (ISUP) Consensus Conference on Gleason Grading of Prostatic Carcinoma: Definition of Grading Patterns and Proposal for a New Grading System , 2015, The American journal of surgical pathology.

[100]  Robert P. Jenkins,et al.  Dendritic Cells Control Fibroblastic Reticular Network Tension and Lymph Node Expansion , 2014, Nature.

[101]  J. Buhmann,et al.  Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry , 2014, Nature Methods.

[102]  Konradin Metze,et al.  Fractal dimension of chromatin: potential molecular diagnostic applications for cancer prognosis , 2013, Expert review of molecular diagnostics.

[103]  Jack Cuzick,et al.  Comparison of PAM50 risk of recurrence score with oncotype DX and IHC4 for predicting risk of distant recurrence after endocrine therapy. , 2013, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[104]  P. Royston,et al.  External validation of a Cox prognostic model: principles and methods , 2013, BMC Medical Research Methodology.

[105]  David Moher,et al.  SPIRIT 2013 explanation and elaboration: guidance for protocols of clinical trials , 2013, BMJ.

[106]  F. Markowetz,et al.  Quantitative Image Analysis of Cellular Heterogeneity in Breast Tumors Complements Genomic Profiling , 2012, Science Translational Medicine.

[107]  Douglas G Altman,et al.  Reporting recommendations for tumor marker prognostic studies (REMARK): explanation and elaboration , 2012, BMC Medicine.

[108]  C. Sautès-Fridman,et al.  The immune contexture in human tumours: impact on clinical outcome , 2012, Nature Reviews Cancer.

[109]  Pierre Validire,et al.  Matrix architecture defines the preferential localization and migration of T cells into the stroma of human lung tumors. , 2012, The Journal of clinical investigation.

[110]  Andrew H. Beck,et al.  Systematic Analysis of Breast Cancer Morphology Uncovers Stromal Features Associated with Survival , 2011, Science Translational Medicine.

[111]  D. Hanahan,et al.  Hallmarks of Cancer: The Next Generation , 2011, Cell.

[112]  K. Eliceiri,et al.  Aligned collagen is a prognostic signature for survival in human breast carcinoma. , 2011, The American journal of pathology.

[113]  Konradin Metze,et al.  Fractal dimension of chromatin is an independent prognostic factor for survival in melanoma , 2010, BMC Cancer.

[114]  D. Moher,et al.  CONSORT 2010 Explanation and Elaboration: updated guidelines for reporting parallel group randomised trials , 2010, BMJ : British Medical Journal.

[115]  D. Moher,et al.  CONSORT 2010 Explanation and Elaboration: updated guidelines for reporting parallel group randomised trials , 2011, BMJ : British Medical Journal.

[116]  Ian O Ellis,et al.  Prognostic significance of Nottingham histologic grade in invasive breast carcinoma. , 2008, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[117]  B. Ho,et al.  Preoperative and intraoperative diagnosis of low‐grade adenosquamous carcinoma of the breast: potential diagnostic pitfalls , 2006, Histopathology.

[118]  Douglas G Altman,et al.  REporting recommendations for tumour MARKer prognostic studies (REMARK). , 2005, European journal of cancer.

[119]  E. Sabo,et al.  Microscopic analysis and significance of vascular architectural complexity in renal cell carcinoma. , 2001, Clinical cancer research : an official journal of the American Association for Cancer Research.

[120]  J. Simpson,et al.  Metaplastic breast tumors with a dominant fibromatosis‐like phenotype have a high risk of local recurrence , 1999, Cancer.

[121]  F. Harrell,et al.  Prognostic/Clinical Prediction Models: Multivariable Prognostic Models: Issues in Developing Models, Evaluating Assumptions and Adequacy, and Measuring and Reducing Errors , 2005 .

[122]  I. Ellis,et al.  Histologic grading of breast cancer. Let's do it. , 1995, American journal of clinical pathology.

[123]  I. Ellis,et al.  Pathological prognostic factors in breast cancer. I. The value of histological grade in breast cancer: experience from a large study with long-term follow-up. , 2002, Histopathology.

[124]  Yuming Liu,et al.  Computational segmentation of collagen fibers from second-harmonic generation images of breast cancer , 2014, Journal of biomedical optics.

[125]  D. Sargent,et al.  Clinical Trial Designs for Prospective Validation of Biomarkers , 2005, American journal of pharmacogenomics : genomics-related research in drug development and clinical practice.

[126]  C. Redmond,et al.  Histologic grading of breast cancer. , 1980, Pathology annual.