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Zheng J, Wang T, Wang H, Yan B, Lai J, Qiu K, Zhou X, Tan J, Wang S, Ji H, Feng M, Jiang W, Wang H, Yan J. Use of a Pathomics Nomogram to Predict Postoperative Liver Metastasis in Patients with Stage III Colorectal Cancer. Ann Surg Oncol 2024:10.1245/s10434-024-16519-8. [PMID: 39614006 DOI: 10.1245/s10434-024-16519-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 10/30/2024] [Indexed: 12/01/2024]
Abstract
BACKGROUND Approximately 25% of patients with stage III colorectal cancer experience liver metastasis after radical resection; however, there is currently a lack of methods to predict liver metastasis. This study aims to develop and validate a pathomics nomogram to predict liver metastasis in patients with stage III colorectal cancer. METHODS A total of 318 enrolled patients were divided into three cohorts: a training cohort (n = 139), a validation cohort (n = 69), and an external cohort (n = 110). A competitive risk nomogram was established by the pathomics signature and clinicopathological characteristics and assessed by calibration, discrimination, and clinical usefulness. RESULTS A significant correlation between the pathomics signature and liver metastasis in stage III colorectal cancer was found. Multivariate Fine-Gray analysis indicated that preoperative carcinoembryonic antigen level, postoperative chemotherapy, and pathomics signature were independent predictors of liver metastasis. A competitive risk nomogram was developed to predict liver metastasis in patients with stage III colorectal cancer. The predicting nomogram shows good discrimination and calibration, with C-indexes of 0.811 (95% confidence interval [CI] 0.651-0.971), 0.759 (95% CI 0.531-0.987), and 0.845 (95% CI 0.641-0.999), with area under the receiver operating characteristic (AUROC) curves at 5 years of 0.833 (95% CI 0.742-0.925), 0.760 (95% CI 0.652-0.893), and 0.812 (95% CI 0.692-0.931) in the training, validation, and external cohorts, respectively. Compared with the clinicopathological nomogram, the nomogram combined with the pathomics signature had better performance (AUROC 0.823 [95% CI 0.764-0.881] vs. 0.678 [95% CI 0.606-0.751]; p < 0.001). CONCLUSIONS The pathomics signature is a predictive indicator for liver metastasis in patients with stage III colorectal cancer, and the integrated nomogram can be used to predict liver metastasis better than the clinicopathological nomogram alone.
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Affiliation(s)
- Jixiang Zheng
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, People's Republic of China
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Ting Wang
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, People's Republic of China
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Huaiming Wang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, People's Republic of China
| | - Botao Yan
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, People's Republic of China
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Jianbo Lai
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Kemao Qiu
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Xinyi Zhou
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Jie Tan
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Shijie Wang
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Hongli Ji
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, People's Republic of China
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Mingyuan Feng
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Wei Jiang
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, People's Republic of China.
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China.
| | - Hui Wang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, People's Republic of China.
| | - Jun Yan
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, People's Republic of China.
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China.
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Yli-Hallila A, Bankhead P, Arends MJ, Lehenkari P, Palosaari S. QuPath Edu and OpenMicroanatomy: Open-source virtual microscopy tools for medical education. J Anat 2024. [PMID: 39555994 DOI: 10.1111/joa.14172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 10/22/2024] [Accepted: 10/23/2024] [Indexed: 11/19/2024] Open
Abstract
Virtual microscopy is becoming increasingly common in both medical education and routine clinical practice. Virtual microscopy software is typically designed either for (1) training students in anatomy, histology, and histopathology, or (2) quantitative analysis-but not both simultaneously. QuPath is one of the most widely used software applications for histopathology image analysis in research and provides a comprehensive set of computational tools to evaluate histology slides. We have enhanced QuPath by developing a new extension, QuPath Edu, which adapts the software to function as an intuitive microanatomy learning environment. Additionally, we have created an entirely new, complementary software platform called OpenMicroanatomy, which provides an alternative way to access QuPath Edu teaching content through a web interface. These tools have been used in teaching of first year medical and dentistry students at the University of Oulu Medical Faculty, and we conducted a user survey for the Class of 2023 to assess the usability and student experience. In general, the introduced annotation and quiz features were appreciated by the students and the system usability of OpenMicroanatomy was considered excellent (SUS score 84.8). Together, these freely available tools enable teachers to develop and deploy innovative training material for anatomy, histopathology, quantitative analysis, and artificial intelligence in a wide range of contexts. This unique combination can provide the next generation of students with essential multidisciplinary skills.
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Affiliation(s)
- Aaron Yli-Hallila
- Translational Medicine Research Unit, Medical Faculty, University of Oulu, Oulu, Finland
| | - Peter Bankhead
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Edinburgh Pathology and CRUK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Mark J Arends
- Edinburgh Pathology and CRUK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Petri Lehenkari
- Translational Medicine Research Unit, Medical Faculty, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Sanna Palosaari
- Translational Medicine Research Unit, Medical Faculty, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland
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Köhne M, Diel E, Packeiser EM, Böttcher D, Tönissen A, Unruh C, Goericke-Pesch S, Ulrich R, Sieme H. Analysis of gene and protein expression in the endometrium for validation of an ex vivo model of the equine uterus using PCR, digital and visual histopathology. Theriogenology 2024; 221:38-46. [PMID: 38537320 DOI: 10.1016/j.theriogenology.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/09/2024]
Abstract
In the past, most research in equine reproduction has been performed in vivo but the use of in vitro and ex vivo models has recently increased. This study aimed to evaluate the functional stability of an ex vivo hemoperfused model for equine uteri with molecular characterization of marker genes and their proteins. In addition, the study validated the respective protein expression and the aptness of the software QuPath for identifying and scoring immunohistochemically stained equine endometrium. After collection, uteri (n = 12) were flushed with preservation solution, transported to the laboratory on ice, and perfused with autologous blood for 6 h. Cycle stage was determined by examination of the ovaries for presence of Graafian follicles or corpora lutea and analysis of plasma progesterone concentration (estrus: n = 4; diestrus: n = 4; anestrus: n = 4). Samples were obtained directly after slaughter, after transportation, and during perfusion (240, 300, 360 min). mRNA expression levels of progesterone (PGR), estrogen (ESR1) and oxytocin (OXTR) receptor as well as of MKI67 (marker of cell growth) and CASP3 (marker of apoptosis) were analyzed by RT-qPCR, and correlation to protein abundance was validated by immunohistochemical staining. Endometrial samples were analyzed by visual and computer-assisted evaluation of stained antigens via QuPath. For PGR, effects of the perfusion and cycle stage on expression were found (P < 0.05), while ESR1 was affected only by cycle stage (P < 0.05) and OXTR was unaffected by perfusion and cycle stage. MKI67 was lower after 360 min of perfusion as compared to samples collected before perfusion (P < 0.05). For CASP3, differences in gene expression were found after transport and samples taken after 240 min (P < 0.05). Immunohistochemical staining revealed effects of perfusion on stromal and glandular cells for steroid hormone receptors, but not for Ki-67 and active Caspase 3. OXTR was visualized in all layers of the endometrium and was unaffected by perfusion. Comparison of QuPath and visual analysis resulted in similar results. For most cell types and stained antigens, the correlation coefficient was r > 0.5. In conclusion, the isolated hemoperfused model of the equine uterus was successfully validated at the molecular level, demonstrating stability of key marker gene expression. The utility of computer-assisted immunohistochemical analysis of equine endometrial samples was also confirmed.
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Affiliation(s)
- Martin Köhne
- Unit for Reproductive Medicine, Clinic for Horses, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany.
| | - Emilia Diel
- Unit for Reproductive Medicine, Clinic for Horses, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany
| | - Eva-Maria Packeiser
- Unit for Reproductive Medicine, Clinic for Small Animals, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany
| | - Denny Böttcher
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, 04103, Leipzig, Germany
| | - Anna Tönissen
- Unit for Reproductive Medicine, Clinic for Horses, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany
| | - Christin Unruh
- Unit for Reproductive Medicine, Clinic for Horses, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany
| | - Sandra Goericke-Pesch
- Unit for Reproductive Medicine, Clinic for Small Animals, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany
| | - Reiner Ulrich
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, 04103, Leipzig, Germany
| | - Harald Sieme
- Unit for Reproductive Medicine, Clinic for Horses, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany
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Kashimura A, Nishikawa S, Ozawa Y, Hibino Y, Tateoka T, Mizukawa M, Nishina H, Sakairi T, Shiga T, Aihara N, Kamiie J. Combination of pathological, biochemical and behavioral evaluations for peripheral neurotoxicity assessment in isoniazid-treated rats. J Toxicol Pathol 2024; 37:69-82. [PMID: 38584972 PMCID: PMC10995436 DOI: 10.1293/tox.2023-0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/08/2023] [Indexed: 04/09/2024] Open
Abstract
In drug development, assessment of non-clinical peripheral neurotoxicity is important to ensure human safety. Clarifying the pathological features and mechanisms of toxicity enables the management of safety risks in humans by estimating the degree of risk and proposing monitoring strategies. Published guidelines for peripheral neurotoxicity assessment do not provide detailed information on which endpoints should be monitored preferentially and how the results should be integrated and discussed. To identify an optimal assessment method for the characterization of peripheral neurotoxicity, we conducted pathological, biochemical (biomaterials contributing to mechanistic considerations and biomarkers), and behavioral evaluations of isoniazid-treated rats. We found a discrepancy between the days on which marked pathological changes were noted and those on which biochemical and behavioral changes were noted, suggesting the importance of combining these evaluations. Although pathological evaluation is essential for pathological characterization, the results of biochemical and behavioral assessments at the same time points as the pathological evaluation are also important for discussion. In this study, since the measurement of serum neurofilament light chain could detect changes earlier than pathological examination, it could be useful as a biomarker for peripheral neurotoxicity. Moreover, examination of semi-thin specimens and choline acetyltransferase immunostaining were useful for characterizing morphological neurotoxicity, and image analysis of semi-thin specimens enabled us to objectively show the pathological features.
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Affiliation(s)
- Akane Kashimura
- Safety Research Laboratories, Sohyaku, Innovative Research
Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1
Muraoka-Higashi, Fujisawa-shi, Kanagawa 251-8555, Japan
- Laboratory of Veterinary Pathology, School of Veterinary
Medicine, Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa 252-5201,
Japan
| | - Satomi Nishikawa
- Safety Research Laboratories, Sohyaku, Innovative Research
Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1
Muraoka-Higashi, Fujisawa-shi, Kanagawa 251-8555, Japan
| | - Yuhei Ozawa
- Safety Research Laboratories, Sohyaku, Innovative Research
Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1
Muraoka-Higashi, Fujisawa-shi, Kanagawa 251-8555, Japan
| | - Yui Hibino
- Safety Research Laboratories, Sohyaku, Innovative Research
Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1
Muraoka-Higashi, Fujisawa-shi, Kanagawa 251-8555, Japan
| | - Takashi Tateoka
- Safety Research Laboratories, Sohyaku, Innovative Research
Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1
Muraoka-Higashi, Fujisawa-shi, Kanagawa 251-8555, Japan
| | - Mao Mizukawa
- Safety Research Laboratories, Sohyaku, Innovative Research
Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1
Muraoka-Higashi, Fujisawa-shi, Kanagawa 251-8555, Japan
- Laboratory of Veterinary Pathology, School of Veterinary
Medicine, Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa 252-5201,
Japan
| | - Hironobu Nishina
- Safety Research Laboratories, Sohyaku, Innovative Research
Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1
Muraoka-Higashi, Fujisawa-shi, Kanagawa 251-8555, Japan
| | - Tetsuya Sakairi
- Safety Research Laboratories, Sohyaku, Innovative Research
Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1
Muraoka-Higashi, Fujisawa-shi, Kanagawa 251-8555, Japan
| | - Takanori Shiga
- Laboratory of Veterinary Pathology, School of Veterinary
Medicine, Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa 252-5201,
Japan
| | - Naoyuki Aihara
- Laboratory of Veterinary Pathology, School of Veterinary
Medicine, Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa 252-5201,
Japan
| | - Junichi Kamiie
- Laboratory of Veterinary Pathology, School of Veterinary
Medicine, Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa 252-5201,
Japan
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Despotovic V, Kim SY, Hau AC, Kakoichankava A, Klamminger GG, Borgmann FBK, Frauenknecht KB, Mittelbronn M, Nazarov PV. Glioma subtype classification from histopathological images using in-domain and out-of-domain transfer learning: An experimental study. Heliyon 2024; 10:e27515. [PMID: 38562501 PMCID: PMC10982966 DOI: 10.1016/j.heliyon.2024.e27515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
We provide in this paper a comprehensive comparison of various transfer learning strategies and deep learning architectures for computer-aided classification of adult-type diffuse gliomas. We evaluate the generalizability of out-of-domain ImageNet representations for a target domain of histopathological images, and study the impact of in-domain adaptation using self-supervised and multi-task learning approaches for pretraining the models using the medium-to-large scale datasets of histopathological images. A semi-supervised learning approach is furthermore proposed, where the fine-tuned models are utilized to predict the labels of unannotated regions of the whole slide images (WSI). The models are subsequently retrained using the ground-truth labels and weak labels determined in the previous step, providing superior performance in comparison to standard in-domain transfer learning with balanced accuracy of 96.91% and F1-score 97.07%, and minimizing the pathologist's efforts for annotation. Finally, we provide a visualization tool working at WSI level which generates heatmaps that highlight tumor areas; thus, providing insights to pathologists concerning the most informative parts of the WSI.
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Affiliation(s)
- Vladimir Despotovic
- Bioinformatics Platform, Department of Medical Informatics, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Sang-Yoon Kim
- Bioinformatics Platform, Department of Medical Informatics, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Ann-Christin Hau
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Frankfurt am Main, Germany
- Edinger Institute, Institute of Neurology, Goethe University, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- University Cancer Center Frankfurt, Frankfurt am Main, Germany
- University Hospital, Goethe University, Frankfurt am Main, Germany
- Laboratoire national de santé, National Center of Pathology, Dudelange, Luxembourg
| | - Aliaksandra Kakoichankava
- Multi-Omics Data Science group, Department of Cancer Research, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Gilbert Georg Klamminger
- Luxembourg Centre of Neuropathology, Dudelange, Luxembourg
- Klinik für Frauenheilkunde, Geburtshilfe und Reproduktionsmedizin, Saarland University, Homburg, Germany
| | - Felix Bruno Kleine Borgmann
- Luxembourg Centre of Neuropathology, Dudelange, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, Strassen, Luxembourg
- Haupitaux Robert Schumann, Kirchberg, Luxembourg
| | - Katrin B.M. Frauenknecht
- Laboratoire national de santé, National Center of Pathology, Dudelange, Luxembourg
- Luxembourg Centre of Neuropathology, Dudelange, Luxembourg
| | - Michel Mittelbronn
- Laboratoire national de santé, National Center of Pathology, Dudelange, Luxembourg
- Luxembourg Centre of Neuropathology, Dudelange, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, Strassen, Luxembourg
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg
- Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Petr V. Nazarov
- Bioinformatics Platform, Department of Medical Informatics, Luxembourg Institute of Health, Strassen, Luxembourg
- Multi-Omics Data Science group, Department of Cancer Research, Luxembourg Institute of Health, Strassen, Luxembourg
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Chauveau B, Merville P. Segment Anything by Meta as a foundation model for image segmentation: a new era for histopathological images. Pathology 2023; 55:1017-1020. [PMID: 37813761 DOI: 10.1016/j.pathol.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/16/2023] [Accepted: 09/17/2023] [Indexed: 10/11/2023]
Affiliation(s)
- Bertrand Chauveau
- CHU de Bordeaux, Service de Pathologie, Hôpital Pellegrin, Bordeaux, France; ImmunoConcEpT, CNRS, Université Bordeaux, UMR 5164, Bordeaux, France.
| | - Pierre Merville
- ImmunoConcEpT, CNRS, Université Bordeaux, UMR 5164, Bordeaux, France; CHU de Bordeaux, Service de Néphrologie-Transplantation-Dialyse-Aphéréses, Hôpital Pellegrin, Bordeaux, France
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7
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Sun X, Li W, Fu B, Peng Y, He J, Wang L, Yang T, Meng X, Li J, Wang J, Huang P, Wang R. TGMIL: A hybrid multi-instance learning model based on the Transformer and the Graph Attention Network for whole-slide images classification of renal cell carcinoma. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023; 242:107789. [PMID: 37722310 DOI: 10.1016/j.cmpb.2023.107789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/20/2023]
Abstract
BACKGROUND AND OBJECTIVES The pathological diagnosis of renal cell carcinoma is crucial for treatment. Currently, the multi-instance learning method is commonly used for whole-slide image classification of renal cell carcinoma, which is mainly based on the assumption of independent identical distribution. But this is inconsistent with the need to consider the correlation between different instances in the diagnosis process. Furthermore, the problem of high resource consumption of pathology images is still urgent to be solved. Therefore, we propose a new multi-instance learning method to solve this problem. METHODS In this study, we proposed a hybrid multi-instance learning model based on the Transformer and the Graph Attention Network, called TGMIL, to achieve whole-slide image of renal cell carcinoma classification without pixel-level annotation or region of interest extraction. Our approach is divided into three steps. First, we designed a feature pyramid with the multiple low magnifications of whole-slide image named MMFP. It makes the model incorporates richer information, and reduces memory consumption as well as training time compared to the highest magnification. Second, TGMIL amalgamates the Transformer and the Graph Attention's capabilities, adeptly addressing the loss of instance contextual and spatial. Within the Graph Attention network stream, an easy and efficient approach employing max pooling and mean pooling yields the graph adjacency matrix, devoid of extra memory consumption. Finally, the outputs of two streams of TGMIL are aggregated to achieve the classification of renal cell carcinoma. RESULTS On the TCGA-RCC validation set, a public dataset for renal cell carcinoma, the area under a receiver operating characteristic (ROC) curve (AUC) and accuracy of TGMIL were 0.98±0.0015,0.9191±0.0062, respectively. It showcased remarkable proficiency on the private validation set of renal cell carcinoma pathology images, attaining AUC of 0.9386±0.0162 and ACC of 0.9197±0.0124. Furthermore, on the public breast cancer whole-slide image test dataset, CAMELYON 16, our model showed good classification performance with an accuracy of 0.8792. CONCLUSIONS TGMIL models the diagnostic process of pathologists and shows good classification performance on multiple datasets. Concurrently, the MMFP module efficiently diminishes resource requirements, offering a novel angle for exploring computational pathology images.
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Affiliation(s)
- Xinhuan Sun
- Engineering Research Center of Text Computing & Cognitive Intelligence, Ministry of Education, Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province, State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China; Department of Radiology, International Exemplary Cooperation Base of Precision Imaging for Diagnosis and Treatment, Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Wuchao Li
- Department of Radiology, International Exemplary Cooperation Base of Precision Imaging for Diagnosis and Treatment, Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Bangkang Fu
- Department of Radiology, International Exemplary Cooperation Base of Precision Imaging for Diagnosis and Treatment, Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Yunsong Peng
- Department of Radiology, International Exemplary Cooperation Base of Precision Imaging for Diagnosis and Treatment, Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Junjie He
- Engineering Research Center of Text Computing & Cognitive Intelligence, Ministry of Education, Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province, State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China; Department of Radiology, International Exemplary Cooperation Base of Precision Imaging for Diagnosis and Treatment, Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Lihui Wang
- Engineering Research Center of Text Computing & Cognitive Intelligence, Ministry of Education, Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province, State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China
| | - Tongyin Yang
- Department of Pathology, Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Xue Meng
- Department of Pathology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Jin Li
- Department of Pathology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Jinjing Wang
- Department of Pathology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Ping Huang
- Department of Pathology, Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Rongpin Wang
- Department of Radiology, International Exemplary Cooperation Base of Precision Imaging for Diagnosis and Treatment, Guizhou Provincial People's Hospital, Guiyang, 550002, China.
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Aliar K, Waterhouse HR, Vyas F, Krebs N, Zhang B, Poulton E, Chan N, Gonzalez R, Jang GH, Bronsert P, Fischer SE, Gallinger S, Grünwald BT, Khokha R. Hourglass, a rapid analysis framework for heterogeneous bioimaging data, identifies sex disparity in IL-6/STAT3-associated immune phenotypes in pancreatic cancer. J Pathol 2023; 261:413-426. [PMID: 37768107 DOI: 10.1002/path.6199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/06/2023] [Accepted: 08/11/2023] [Indexed: 09/29/2023]
Abstract
Integration and mining of bioimaging data remains a challenge and lags behind the rapidly expanding digital pathology field. We introduce Hourglass, an open-access analytical framework that streamlines biology-driven visualization, interrogation, and statistical assessment of multiparametric datasets. Cognizant of tissue and clinical heterogeneity, Hourglass systematically organizes observations across spatial and global levels and within patient subgroups. Applied to an extensive bioimaging dataset, Hourglass promptly consolidated a breadth of known interleukin-6 (IL-6) functions via its downstream effector STAT3 and uncovered a so-far unknown sexual dimorphism in the IL-6/STAT3-linked intratumoral T-cell response in human pancreatic cancer. As an R package and cross-platform application, Hourglass facilitates knowledge extraction from multi-layered bioimaging datasets for users with or without computational proficiency and provides unique and widely accessible analytical means to harness insights hidden within heterogeneous tissues at the sample and patient level. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Kazeera Aliar
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Henry R Waterhouse
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Foram Vyas
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Niklas Krebs
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, Göttingen, Germany
| | - Bowen Zhang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Emily Poulton
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Nathan Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ricardo Gonzalez
- Department of Laboratory Medicine and Pathology, Division of Computational Pathology and Artificial Intelligence, Mayo Clinic, Rochester, MN, USA
| | - Gun Ho Jang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Peter Bronsert
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Sandra E Fischer
- Department of Laboratory Medicine and Pathobiology, University of Toronto, University Health Network, Toronto, ON, Canada
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Surgery, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, ON, Canada
| | - Barbara T Grünwald
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Rama Khokha
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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9
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Khozeymeh F, Ariamanesh M, Roshan NM, Jafarian A, Farzanehfar M, Majd HM, Sedghian A, Dehghani M. Comparison of FNA-based conventional cytology specimens and digital image analysis in assessment of pancreatic lesions. Cytojournal 2023; 20:39. [PMID: 37942305 PMCID: PMC10629281 DOI: 10.25259/cytojournal_61_2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/05/2023] [Indexed: 11/10/2023] Open
Abstract
Objectives Endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) is one of the most important diagnostic tools for investigation of suspected pancreatic masses, although the interpretation of the results is controversial. In recent decades, digital image analysis (DIA) has been considered in pathology. The aim of this study was to assess the DIA in the evaluation of EUS-FNA based cytopathological specimens of pancreatic masses and comparing it with conventional cytology analysis by pathologist. Material and Methods This study was performed using cytological slides related to EUS-FNA samples of pancreatic lesions. The digital images were prepared and then analyzed by ImageJ software. Factors such as perimeter, circularity, area, minimum, maximum, mean, median of gray value, and integrated chromatin density of cell nucleus were extracted by software ImageJ and sensitivity, specificity, and cutoff point were evaluated in the diagnosis of malignant and benign lesions. Results In this retrospective study, 115 cytology samples were examined. Each specimen was reviewed by a pathologist and 150 images were prepared from the benign and malignant lesions and then analyzed by ImageJ software and a cut point was established by SPSS 26. The cutoff points for perimeter, integrated density, and the sum of three factors of perimeter, integrated density, and circularity to differentiate between malignant and benign lesions were reported to be 204.56, 131953, and 24643077, respectively. At this cutting point, the accuracy of estimation is based on the factors of perimeter, integrated density, and the sum of the three factors of perimeter, integrated density, and circularity were 92%, 92%, and 94%, respectively. Conclusion The results of this study showed that digital analysis of images has a high accuracy in diagnosing malignant and benign lesions in the cytology of EUS-FNA in patients with suspected pancreatic malignancy and by obtaining cutoff points by software output factors; digital imaging can be used to differentiate between benign and malignant pancreatic tumors.
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Affiliation(s)
- Farzaneh Khozeymeh
- Department of Pathology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Ariamanesh
- Department of Pathology, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | | | | | | | - Hassan Mehrad Majd
- Clinical Research Development Unit, Ghaem Hospital, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Sedghian
- Department of Computer, Ferdowsi University of Engineering, Mashhad, Iran
| | - Mansoureh Dehghani
- Department of Oncology, Mashhad University of Medical Sciences, Mashhad, Iran
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10
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Parra ER, Ilié M, Wistuba II, Hofman P. Quantitative multiplexed imaging technologies for single-cell analysis to assess predictive markers for immunotherapy in thoracic immuno-oncology: promises and challenges. Br J Cancer 2023; 129:1417-1431. [PMID: 37391504 PMCID: PMC10628288 DOI: 10.1038/s41416-023-02318-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/05/2023] [Accepted: 06/12/2023] [Indexed: 07/02/2023] Open
Abstract
The past decade has witnessed a revolution in cancer treatment by the shift from conventional drugs (chemotherapies) towards targeted molecular therapies and immune-based therapies, in particular the immune-checkpoint inhibitors (ICIs). These immunotherapies selectively release the host immune system against the tumour and have shown unprecedented durable remission for patients with cancers that were thought incurable such as advanced non-small cell lung cancer (aNSCLC). The prediction of therapy response is based since the first anti-PD-1/PD-L1 molecules FDA and EMA approvals on the level of PD-L1 tumour cells expression evaluated by immunohistochemistry, and recently more or less on tumour mutation burden in the USA. However, not all aNSCLC patients benefit from immunotherapy equally, since only around 30% of them received ICIs and among them 30% have an initial response to these treatments. Conversely, a few aNSCLC patients could have an efficacy ICIs response despite low PD-L1 tumour cells expression. In this context, there is an urgent need to look for additional robust predictive markers for ICIs efficacy in thoracic oncology. Understanding of the mechanisms that enable cancer cells to adapt to and eventually overcome therapy and identifying such mechanisms can help circumvent resistance and improve treatment. However, more than a unique universal marker, the evaluation of several molecules in the tumour at the same time, particularly by using multiplex immunostaining is a promising open room to optimise the selection of patients who benefit from ICIs. Therefore, urgent further efforts are needed to optimise to individualise immunotherapy based on both patient-specific and tumour-specific characteristics. This review aims to rethink the role of multiplex immunostaining in immuno-thoracic oncology, with the current advantages and limitations in the near-daily practice use.
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Affiliation(s)
- Edwin Roger Parra
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Biobank Côte d'Azur BB-0033-00025, FHU OncoAge, IHU RespirERA, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Biobank Côte d'Azur BB-0033-00025, FHU OncoAge, IHU RespirERA, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France.
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11
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Abstract
Multiplex imaging has emerged as an invaluable tool for immune-oncologists and translational researchers, enabling them to examine intricate interactions among immune cells, stroma, matrix, and malignant cells within the tumor microenvironment (TME). It holds significant promise in the quest to discover improved biomarkers for treatment stratification and identify novel therapeutic targets. Nonetheless, several challenges exist in the realms of study design, experiment optimization, and data analysis. In this review, our aim is to present an overview of the utilization of multiplex imaging in immuno-oncology studies and inform novice researchers about the fundamental principles at each stage of the imaging and analysis process.
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Affiliation(s)
- Chen Zhao
- Thoracic and GI Malignancies Branch, CCR, NCI, Bethesda, Maryland, USA
- Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, Bethesda, Maryland, USA
| | - Ronald N Germain
- Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, Bethesda, Maryland, USA
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12
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Brunel B, Prada P, Slimano F, Boulagnon-Rombi C, Bouché O, Piot O. Deep learning for the prediction of the chemotherapy response of metastatic colorectal cancer: comparing and combining H&E staining histopathology and infrared spectral histopathology. Analyst 2023; 148:3909-3917. [PMID: 37466305 DOI: 10.1039/d3an00627a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Colorectal cancer is a global public health problem with one of the highest death rates. It is the second most deadly type of cancer and the third most frequently diagnosed in the world. The present study focused on metastatic colorectal cancer (mCRC) patients who had been treated with chemotherapy-based regimen for which it remains uncertainty about the efficacy for all eligible patients. This is a major problem, as it is not yet possible to test different therapies in view of the consequences on the health of the patients and the risk of progression. Here, we propose a method to predict the efficacy of an anticancer treatment in an individualized way, using a deep learning model constructed on the retrospective analysis of the primary tumor of several patients. Histological sections from tumors were imaged by standard hematoxylin and eosin (HE) staining and infrared spectroscopy (IR). Images obtained were then processed by a convolutional neural network (CNN) to extract features and correlate them with the subsequent progression-free survival (PFS) of each patient. Separately, HE and IR imaging resulted in a PFS prediction with an error of 6.6 and 6.3 months respectively (28% and 26% of the average PFS). Combining both modalities allowed to decrease the error to 5.0 months (21%). The inflammatory state of the stroma seemed to be one of the main features detected by the CNN. Our pilot study suggests that multimodal imaging analyzed with deep learning methods allow to give an indication of the effectiveness of a treatment when choosing.
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Affiliation(s)
- Benjamin Brunel
- Université de Reims Champagne-Ardenne, EA7506-BioSpectroscopie Translationnelle (BioSpecT), Reims, France
- Université de Franche-Comté, CNRS, institut FEMTO-ST, F-25000 Besançon, France
| | - Pierre Prada
- Université de Reims Champagne-Ardenne, EA7506-BioSpectroscopie Translationnelle (BioSpecT), Reims, France
| | - Florian Slimano
- Université de Reims Champagne-Ardenne, EA7506-BioSpectroscopie Translationnelle (BioSpecT), Reims, France
| | | | - Olivier Bouché
- Université de Reims Champagne-Ardenne, EA7506-BioSpectroscopie Translationnelle (BioSpecT), Reims, France
- Service d'Oncologie Digestive, CHU Reims, 51100 Reims, France
| | - Olivier Piot
- Université de Reims Champagne-Ardenne, EA7506-BioSpectroscopie Translationnelle (BioSpecT), Reims, France
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13
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Asif A, Rajpoot K, Graham S, Snead D, Minhas F, Rajpoot N. Unleashing the potential of AI for pathology: challenges and recommendations. J Pathol 2023; 260:564-577. [PMID: 37550878 PMCID: PMC10952719 DOI: 10.1002/path.6168] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 08/09/2023]
Abstract
Computational pathology is currently witnessing a surge in the development of AI techniques, offering promise for achieving breakthroughs and significantly impacting the practices of pathology and oncology. These AI methods bring with them the potential to revolutionize diagnostic pipelines as well as treatment planning and overall patient care. Numerous peer-reviewed studies reporting remarkable performance across diverse tasks serve as a testimony to the potential of AI in the field. However, widespread adoption of these methods in clinical and pre-clinical settings still remains a challenge. In this review article, we present a detailed analysis of the major obstacles encountered during the development of effective models and their deployment in practice. We aim to provide readers with an overview of the latest developments, assist them with insights into identifying some specific challenges that may require resolution, and suggest recommendations and potential future research directions. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Amina Asif
- Tissue Image Analytics Centre, Department of Computer ScienceUniversity of WarwickCoventryUK
| | - Kashif Rajpoot
- School of Computer ScienceUniversity of BirminghamBirminghamUK
| | - Simon Graham
- Histofy Ltd, Birmingham Business ParkBirminghamUK
| | - David Snead
- Histofy Ltd, Birmingham Business ParkBirminghamUK
- Department of PathologyUniversity Hospitals Coventry & Warwickshire NHS TrustCoventryUK
| | - Fayyaz Minhas
- Tissue Image Analytics Centre, Department of Computer ScienceUniversity of WarwickCoventryUK
- Cancer Research CentreUniversity of WarwickCoventryUK
| | - Nasir Rajpoot
- Tissue Image Analytics Centre, Department of Computer ScienceUniversity of WarwickCoventryUK
- Histofy Ltd, Birmingham Business ParkBirminghamUK
- Cancer Research CentreUniversity of WarwickCoventryUK
- The Alan Turing InstituteLondonUK
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14
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TCNN: A Transformer Convolutional Neural Network for artifact classification in whole slide images. Biomed Signal Process Control 2023. [DOI: 10.1016/j.bspc.2023.104812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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15
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Chen D, Lai J, Cheng J, Fu M, Lin L, Chen F, Huang R, Chen J, Lu J, Chen Y, Huang G, Yan M, Ma X, Li G, Chen G, Yan J. Predicting peritoneal recurrence in gastric cancer with serosal invasion using a pathomics nomogram. iScience 2023; 26:106246. [PMID: 36994190 PMCID: PMC10040964 DOI: 10.1016/j.isci.2023.106246] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/29/2023] [Accepted: 02/16/2023] [Indexed: 03/06/2023] Open
Abstract
Peritoneal recurrence is the most frequent and lethal recurrence pattern in gastric cancer (GC) with serosal invasion after radical surgery. However, current evaluation methods are not adequate for predicting peritoneal recurrence in GC with serosal invasion. Emerging evidence shows that pathomics analyses could be advantageous for risk stratification and outcome prediction. Herein, we propose a pathomics signature composed of multiple pathomics features extracted from digital hematoxylin and eosin-stained images. We found that the pathomics signature was significantly associated with peritoneal recurrence. A competing-risk pathomics nomogram including carbohydrate antigen 19-9 level, depth of invasion, lymph node metastasis, and pathomics signature was developed for predicting peritoneal recurrence. The pathomics nomogram had favorable discrimination and calibration. Thus, the pathomics signature is a predictive indicator of peritoneal recurrence, and the pathomics nomogram may provide a helpful reference for predicting an individual's risk in peritoneal recurrence of GC with serosal invasion.
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Affiliation(s)
- Dexin Chen
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
- Corresponding author
| | - Jianbo Lai
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Jiaxin Cheng
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Meiting Fu
- Department of Gastroenterology, Guangdong Provincial Key Laboratory of Gastroenterology, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Liyan Lin
- Department of Pathology, Fujian Provincial Key Laboratory of Translational Cancer Medicine, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, P.R. China
| | - Feng Chen
- Department of Oncological Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362000, P.R. China
| | - Rong Huang
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Jun Chen
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Jianping Lu
- Department of Gastroenterology, Guangdong Provincial Key Laboratory of Gastroenterology, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Yuning Chen
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Guangyao Huang
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Miaojia Yan
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Xiaodan Ma
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Guoxin Li
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
- Corresponding author
| | - Gang Chen
- Department of Pathology, Fujian Provincial Key Laboratory of Translational Cancer Medicine, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, P.R. China
- Corresponding author
| | - Jun Yan
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
- Corresponding author
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16
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Stergar J, Hren R, Milanič M. Design and Validation of a Custom-Made Hyperspectral Microscope Imaging System for Biomedical Applications. SENSORS (BASEL, SWITZERLAND) 2023; 23:2374. [PMID: 36904578 PMCID: PMC10007032 DOI: 10.3390/s23052374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/10/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Hyperspectral microscope imaging (HMI) is an emerging modality that integrates spatial information collected by standard laboratory microscopy and the spectral-based contrast obtained by hyperspectral imaging and may be instrumental in establishing novel quantitative diagnostic methodologies, particularly in histopathology. Further expansion of HMI capabilities hinges upon the modularity and versatility of systems and their proper standardization. In this report, we describe the design, calibration, characterization, and validation of the custom-made laboratory HMI system based on a Zeiss Axiotron fully motorized microscope and a custom-developed Czerny-Turner-type monochromator. For these important steps, we rely on a previously designed calibration protocol. Validation of the system demonstrates a performance comparable to classic spectrometry laboratory systems. We further demonstrate validation against a laboratory hyperspectral imaging system for macroscopic samples, enabling future comparison of spectral imaging results across length scales. An example of the utility of our custom-made HMI system on a standard hematoxylin and eosin-stained histology slide is also shown.
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Affiliation(s)
- Jošt Stergar
- Jožef Stefan Institute, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska ulica 19, SI-1000 Ljubljana, Slovenia
| | - Rok Hren
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska ulica 19, SI-1000 Ljubljana, Slovenia
| | - Matija Milanič
- Jožef Stefan Institute, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska ulica 19, SI-1000 Ljubljana, Slovenia
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17
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Annotating for Artificial Intelligence Applications in Digital Pathology: A Practical Guide for Pathologists and Researchers. Mod Pathol 2023; 36:100086. [PMID: 36788085 DOI: 10.1016/j.modpat.2022.100086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/24/2022] [Accepted: 12/14/2022] [Indexed: 01/13/2023]
Abstract
Training machine learning models for artificial intelligence (AI) applications in pathology often requires extensive annotation by human experts, but there is little guidance on the subject. In this work, we aimed to describe our experience and provide a simple, useful, and practical guide addressing annotation strategies for AI development in computational pathology. Annotation methodology will vary significantly depending on the specific study's objectives, but common difficulties will be present across different settings. We summarize key aspects and issue guiding principles regarding team interaction, ground-truth quality assessment, different annotation types, and available software and hardware options and address common difficulties while annotating. This guide was specifically designed for pathology annotation, intending to help pathologists, other researchers, and AI developers with this process.
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18
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McNamara MC, Hosios AM, Torrence ME, Zhao T, Fraser C, Wilkinson M, Kwiatkowski DJ, Henske EP, Wu CL, Sarosiek KA, Valvezan AJ, Manning BD. Reciprocal effects of mTOR inhibitors on pro-survival proteins dictate therapeutic responses in tuberous sclerosis complex. iScience 2022; 25:105458. [PMID: 36388985 PMCID: PMC9663903 DOI: 10.1016/j.isci.2022.105458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/30/2022] [Accepted: 10/23/2022] [Indexed: 11/13/2022] Open
Abstract
mTORC1 is aberrantly activated in cancer and in the genetic tumor syndrome tuberous sclerosis complex (TSC), which is caused by loss-of-function mutations in the TSC complex, a negative regulator of mTORC1. Clinically approved mTORC1 inhibitors, such as rapamycin, elicit a cytostatic effect that fails to eliminate tumors and is rapidly reversible. We sought to determine the effects of mTORC1 on the core regulators of intrinsic apoptosis. In TSC2-deficient cells and tumors, we find that mTORC1 inhibitors shift cellular dependence from MCL-1 to BCL-2 and BCL-XL for survival, thereby altering susceptibility to BH3 mimetics that target specific pro-survival BCL-2 proteins. The BCL-2/BCL-XL inhibitor ABT-263 synergizes with rapamycin to induce apoptosis in TSC-deficient cells and in a mouse tumor model of TSC, resulting in a more complete and durable response. These data expose a therapeutic vulnerability in regulation of the apoptotic machinery downstream of mTORC1 that promotes a cytotoxic response to rapamycin.
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Affiliation(s)
- Molly C. McNamara
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Aaron M. Hosios
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Margaret E. Torrence
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - Ting Zhao
- Department of Urology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Cameron Fraser
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02215, USA
| | - Meghan Wilkinson
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - David J. Kwiatkowski
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth P. Henske
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Chin-Lee Wu
- Department of Urology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Kristopher A. Sarosiek
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02215, USA
| | - Alexander J. Valvezan
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - Brendan D. Manning
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
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19
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Evaluation of MetaSystems Automated Fluorescent Microscopy System for the Machine-Assisted Detection of Acid-Fast Bacilli in Clinical Samples. J Clin Microbiol 2022; 60:e0113122. [PMID: 36121216 PMCID: PMC9580351 DOI: 10.1128/jcm.01131-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Manual reading of fluorescent acid-fast bacilli (AFB) microscopy slides is time-intensive and technically demanding. The aim of this study was to evaluate the accuracy of MetaSystems' automated fluorescent AFB slide scanner and analyzer. Auramine O-stained slides corresponding to 133 culture-positive and 363 culture-negative respiratory (n = 284), tissue (n = 120), body fluid (n = 81), and other (n = 11) sources were evaluated with the MetaSystems Mycobacteria Scanner running the NEON Metafer AFB Module. The sensitivity and specificity of the MetaSystems platform was measured as a standalone diagnostic and as an assistant to technologists to review positive images. Culture results were used as the reference method. The MetaSystems platform failed to scan 57 (11.5%) slides. The MetaSystems platform used as a standalone had a sensitivity of 97.0% (129/133; 95% CI 92.5 to 99.2) and specificity of 12.7% (46/363; 95% CI 9.4 to 16.5). When positive scans were used to assist technologists, the MetaSystems platform had a sensitivity of 70.7% (94/133; 95% CI 62.2 to 78.3) and specificity of 89.0% (323/363; 95% CI 85.3 to 92.0). The manual microscopy method had a sensitivity of 79.7% (106/133; 95% CI 71.9 to 86.2) and specificity of 98.6% (358/363; 95% CI 96.8 to 99.6). The sensitivity of the MetaSystems platform was not impacted by smear grade or mycobacterial species. The majority (70.3%) of false positive smears had ≥2+ smear results with the MetaSystems platform. Further performance improvements are needed before the MetaSystems' automated fluorescent AFB slide reader can be used to assist microscopist in the clinical laboratory.
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20
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The area of residual tumor predicts esophageal squamous cell carcinoma prognosis following neoadjuvant chemotherapy. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04366-7. [PMID: 36201027 DOI: 10.1007/s00432-022-04366-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/16/2022] [Indexed: 10/10/2022]
Abstract
PURPOSE To clarify the utility of the area of residual tumor for patients with esophageal squamous cell cancer treated with neoadjuvant chemotherapy. METHODS We enrolled 186 patients with esophageal squamous cell cancer who underwent surgical resection following neoadjuvant chemotherapy at our hospital. Using digital images, we measured the area of residual tumor at the maximum plane of the specimen and divided the patient into three groups as follows: 0 (area = 0 mm2), low (area = 0-40 mm2), and high (area ≥ 40 mm2). The clinicopathological factors and prognosis were compared among these groups. RESULTS The median area of the residual tumor was 15.0 mm2 (range 0-1,448.8 mm2). Compared with the 0 and low group, the high group was significantly associated with poorer recurrence-free survival (all P < .001) and overall survival (P < .001 [vs. 0] and P = .017 [vs low]). The area of residual tumor, ypN, tumor regression grade, and lymphovascular invasion were independent predictors of recurrence-free survival. By dividing the patients using a combination of the area of residual tumor and lymphovascular invasion, the high and/or lymphovascular invasion ( +) group displayed significantly poor recurrence-free survival than the 0 group and low/lymphovascular invasion ( -) group. However, there was no significant difference in the recurrence-free survival between the 0 group and low/lymphovascular invasion ( -) group. CONCLUSION The area of residual tumor is a promising histopathological prognostic factor for patients with esophageal squamous cell cancer treated with neoadjuvant chemotherapy. Moreover, it is a possible candidate histopathological factor for postoperative chemotherapy selection.
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Sauter D, Lodde G, Nensa F, Schadendorf D, Livingstone E, Kukuk M. Validating Automatic Concept-Based Explanations for AI-Based Digital Histopathology. SENSORS (BASEL, SWITZERLAND) 2022; 22:s22145346. [PMID: 35891026 PMCID: PMC9319808 DOI: 10.3390/s22145346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/01/2022] [Accepted: 07/15/2022] [Indexed: 05/06/2023]
Abstract
Digital histopathology poses several challenges such as label noise, class imbalance, limited availability of labelled data, and several latent biases to deep learning, negatively influencing transparency, reproducibility, and classification performance. In particular, biases are well known to cause poor generalization. Proposed tools from explainable artificial intelligence (XAI), bias detection, and bias discovery suffer from technical challenges, complexity, unintuitive usage, inherent biases, or a semantic gap. A promising XAI method, not studied in the context of digital histopathology is automated concept-based explanation (ACE). It automatically extracts visual concepts from image data. Our objective is to evaluate ACE's technical validity following design science principals and to compare it to Guided Gradient-weighted Class Activation Mapping (Grad-CAM), a conventional pixel-wise explanation method. To that extent, we created and studied five convolutional neural networks (CNNs) in four different skin cancer settings. Our results demonstrate that ACE is a valid tool for gaining insights into the decision process of histopathological CNNs that can go beyond explanations from the control method. ACE validly visualized a class sampling ratio bias, measurement bias, sampling bias, and class-correlated bias. Furthermore, the complementary use with Guided Grad-CAM offers several benefits. Finally, we propose practical solutions for several technical challenges. In contradiction to results from the literature, we noticed lower intuitiveness in some dermatopathology scenarios as compared to concept-based explanations on real-world images.
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Affiliation(s)
- Daniel Sauter
- Department of Computer Science, Fachhochschule Dortmund, 44227 Dortmund, Germany;
- Correspondence:
| | - Georg Lodde
- Department of Dermatology, University Hospital Essen, 45147 Essen, Germany; (G.L.); (D.S.); (E.L.)
| | - Felix Nensa
- Institute for AI in Medicine (IKIM), University Hospital Essen, 45131 Essen, Germany;
- Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, 45147 Essen, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, 45147 Essen, Germany; (G.L.); (D.S.); (E.L.)
| | - Elisabeth Livingstone
- Department of Dermatology, University Hospital Essen, 45147 Essen, Germany; (G.L.); (D.S.); (E.L.)
| | - Markus Kukuk
- Department of Computer Science, Fachhochschule Dortmund, 44227 Dortmund, Germany;
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