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Mirzakhel Z, Reddy GA, Boman J, Manns B, Veer ST, Katira P. "Patchiness" in mechanical stiffness across a tumor as an early-stage marker for malignancy. BMC Ecol Evol 2024; 24:33. [PMID: 38486161 PMCID: PMC10938681 DOI: 10.1186/s12862-024-02221-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 03/03/2024] [Indexed: 03/17/2024] Open
Abstract
Mechanical phenotyping of tumors, either at an individual cell level or tumor cell population level is gaining traction as a diagnostic tool. However, the extent of diagnostic and prognostic information that can be gained through these measurements is still unclear. In this work, we focus on the heterogeneity in mechanical properties of cells obtained from a single source such as a tissue or tumor as a potential novel biomarker. We believe that this heterogeneity is a conventionally overlooked source of information in mechanical phenotyping data. We use mechanics-based in-silico models of cell-cell interactions and cell population dynamics within 3D environments to probe how heterogeneity in cell mechanics drives tissue and tumor dynamics. Our simulations show that the initial heterogeneity in the mechanical properties of individual cells and the arrangement of these heterogenous sub-populations within the environment can dictate overall cell population dynamics and cause a shift towards the growth of malignant cell phenotypes within healthy tissue environments. The overall heterogeneity in the cellular mechanotype and their spatial distributions is quantified by a "patchiness" index, which is the ratio of the global to local heterogeneity in cell populations. We observe that there exists a threshold value of the patchiness index beyond which an overall healthy population of cells will show a steady shift towards a more malignant phenotype. Based on these results, we propose that the "patchiness" of a tumor or tissue sample, can be an early indicator for malignant transformation and cancer occurrence in benign tumors or healthy tissues. Additionally, we suggest that tissue patchiness, measured either by biochemical or biophysical markers, can become an important metric in predicting tissue health and disease likelihood just as landscape patchiness is an important metric in ecology.
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Affiliation(s)
- Zibah Mirzakhel
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, USA
| | - Gudur Ashrith Reddy
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, USA
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - Jennifer Boman
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, USA
| | - Brianna Manns
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, USA
| | - Savannah Ter Veer
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, USA
| | - Parag Katira
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, USA.
- Computational Science Research Center, San Diego State University, San Diego, CA, USA.
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2
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Shang Q, Jiang Y, Wan Z, Peng J, Xu Z, Li W, Yang D, Zhao H, Xu X, Zhou Y, Zeng X, Chen Q, Xu H. The clinical implication and translational research of OSCC differentiation. Br J Cancer 2024; 130:660-670. [PMID: 38177661 PMCID: PMC10876927 DOI: 10.1038/s41416-023-02566-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND The clinical value and molecular characteristics of tumor differentiation in oral squamous cell carcinoma (OSCC) remain unclear. There is a lack of a related molecular classification prediction system based on pathological images for precision medicine. METHODS Integration of epidemiology, genomics, experiments, and deep learning to clarify the clinical value and molecular characteristics, and develop a novel OSCC molecular classification prediction system. RESULTS Large-scale epidemiology data (n = 118,817) demonstrated OSCC differentiation was a significant prognosis indicator (p < 0.001), and well-differentiated OSCC was more chemo-resistant than poorly differentiated OSCC. These results were confirmed in the TCGA database and in vitro. Furthermore, we found chemo-resistant related pathways and cell cycle-related pathways were up-regulated in well- and poorly differentiated OSCC, respectively. Based on the characteristics of OSCC differentiation, a molecular grade of OSCC was obtained and combined with pathological images to establish a novel prediction system through deep learning, named ShuffleNetV2-based Molecular Grade of OSCC (SMGO). Importantly, our independent multi-center cohort of OSCC (n = 340) confirmed the high accuracy of SMGO. CONCLUSIONS OSCC differentiation was a significant indicator of prognosis and chemotherapy selection. Importantly, SMGO could be an indispensable reference for OSCC differentiation and assist the decision-making of chemotherapy.
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Affiliation(s)
- Qianhui Shang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Yuchen Jiang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Zixin Wan
- Department of Pathology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Jiakuan Peng
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Ziang Xu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Weiqi Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Dan Yang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Hang Zhao
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Xiaoping Xu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Yu Zhou
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Xin Zeng
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China.
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Affiliated Stomatology Hospital, Zhejiang University School of Stomatology, Hangzhou, Zhejiang, 310006, PR China.
| | - Hao Xu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China.
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Claes J, Agten A, Blázquez-Moreno A, Crabbe M, Tuefferd M, Goehlmann H, Geys H, Peng CY, Neyens T, Faes C. The influence of resolution on the predictive power of spatial heterogeneity measures as biomarkers of liver fibrosis. Comput Biol Med 2024; 171:108231. [PMID: 38422965 DOI: 10.1016/j.compbiomed.2024.108231] [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: 10/09/2023] [Revised: 01/23/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
Spatial heterogeneity of cells in liver biopsies can be used as biomarker for disease severity of patients. This heterogeneity can be quantified by non-parametric statistics of point pattern data, which make use of an aggregation of the point locations. The method and scale of aggregation are usually chosen ad hoc, despite values of the aforementioned statistics being heavily dependent on them. Moreover, in the context of measuring heterogeneity, increasing spatial resolution will not endlessly provide more accuracy. The question then becomes how changes in resolution influence heterogeneity indicators, and subsequently how they influence their predictive abilities. In this paper, cell level data of liver biopsy tissue taken from chronic Hepatitis B patients is used to analyze this issue. Firstly, Morisita-Horn indices, Shannon indices and Getis-Ord statistics were evaluated as heterogeneity indicators of different types of cells, using multiple resolutions. Secondly, the effect of resolution on the predictive performance of the indices in an ordinal regression model was investigated, as well as their importance in the model. A simulation study was subsequently performed to validate the aforementioned methods. In general, for specific heterogeneity indicators, a downward trend in predictive performance could be observed. While for local measures of heterogeneity a smaller grid-size is outperforming, global measures have a better performance with medium-sized grids. In addition, the use of both local and global measures of heterogeneity is recommended to improve the predictive performance.
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Affiliation(s)
- Jari Claes
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, Diepenbeek, 3590, Belgium.
| | - Annelies Agten
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, Diepenbeek, 3590, Belgium
| | - Alfonso Blázquez-Moreno
- Discovery Statistics, Global Development, Janssen Research and Development, Turnhoutseweg 30, Beerse, 2340, Belgium
| | - Marjolein Crabbe
- Discovery Statistics, Global Development, Janssen Research and Development, Turnhoutseweg 30, Beerse, 2340, Belgium
| | - Marianne Tuefferd
- Translational Biomarkers, Infectious Diseases, Janssen Research and Development, Turnhoutseweg 30, Beerse, 2340, Belgium
| | - Hinrich Goehlmann
- Translational Biomarkers, Infectious Diseases, Janssen Research and Development, Turnhoutseweg 30, Beerse, 2340, Belgium
| | - Helena Geys
- Discovery Statistics, Global Development, Janssen Research and Development, Turnhoutseweg 30, Beerse, 2340, Belgium
| | | | - Thomas Neyens
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, Diepenbeek, 3590, Belgium; L-BioStat, KU Leuven, Kapucijnenvoer 35, Leuven, 3000, Belgium
| | - Christel Faes
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, Diepenbeek, 3590, Belgium
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Chekhun V, Martynyuk О, Lukianova Y, Mushii O, Zadvornyi T, Lukianova N. FEATURES OF BREAST CANCER IN PATIENTS OF YOUNG AGE: SEARCH FOR DIAGNOSIS OPTIMIZATION AND PERSONALIZED TREATMENT. Exp Oncol 2023; 45:139-150. [PMID: 37824778 DOI: 10.15407/exp-oncology.2023.02.139] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Indexed: 10/14/2023]
Abstract
The statistical data of the recent decades demonstrate a rapid growth of breast cancer (BCa) incidence and a tendency toward its increase especially in young women. In the structure of morbidity of women in the age group of 18-29 years, BCa ranks first and in the age range of 15-39 years, BCa is one of the leading causes of mortality. According to the data of the epidemiological and clinical studies, the young age is an independent unfavorable prognostic factor of BCa that is associated with an unfavorable prognosis and low survival rates and is considered an important predictor of the disease aggressiveness, a high risk of metastasis and recurrence. The variability of clinicopathological and molecular-biological features of BCa in patients of different age groups as well as the varying course of the disease and different responses to the therapy are mediated by many factors. The analysis of the literature data on the factors and mechanisms of BCa initiation in patients of different age groups demonstrates that the pathogen- esis of BCa depends not only on the molecular-genetic alterations but also on the metabolic disorders caused by the current social and household rhythm of life and nutrition peculiarities. All these factors affect both the general con- dition of the body and the formation of an aggressive microenvironment of the tumor lesion. The identified features of transcriptome and the differential gene expression give evidence of different regulations of the immune response and the metabolic processes in BCa patients of different age groups. Association between the high expression of the components of the stromal microenvironment and the inflammatory immune infiltrate as well as the increased vascu- larization of the tumor lesion has been found in BCa tissue of young patients. Proving the nature of the formation of the landscape comprising molecular-genetic, cytokine, and immune factors of the tumor microenvironment will undoubtedly contribute to our understanding of the mechanisms of tumor growth allowing for the development of algorithms for delineating the groups at high risk of tumor progression, which requires more careful monitoring and personalized treatment approach. Th s will be helpful in the development of innovative technologies for complex BCa treatment.
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Affiliation(s)
- V Chekhun
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, NAS of Ukraine, 03022 Kyiv, Ukraine.
| | - О Martynyuk
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, NAS of Ukraine, 03022 Kyiv, Ukraine
| | - Ye Lukianova
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, NAS of Ukraine, 03022 Kyiv, Ukraine
| | - O Mushii
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, NAS of Ukraine, 03022 Kyiv, Ukraine
| | - T Zadvornyi
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, NAS of Ukraine, 03022 Kyiv, Ukraine
| | - N Lukianova
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, NAS of Ukraine, 03022 Kyiv, Ukraine
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Vu T, Seal S, Ghosh T, Ahmadian M, Wrobel J, Ghosh D. FunSpace: A functional and spatial analytic approach to cell imaging data using entropy measures. PLoS Comput Biol 2023; 19:e1011490. [PMID: 37756338 PMCID: PMC10561868 DOI: 10.1371/journal.pcbi.1011490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 10/09/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Spatial heterogeneity in the tumor microenvironment (TME) plays a critical role in gaining insights into tumor development and progression. Conventional metrics typically capture the spatial differential between TME cellular patterns by either exploring the cell distributions in a pairwise fashion or aggregating the heterogeneity across multiple cell distributions without considering the spatial contribution. As such, none of the existing approaches has fully accounted for the simultaneous heterogeneity caused by both cellular diversity and spatial configurations of multiple cell categories. In this article, we propose an approach to leverage spatial entropy measures at multiple distance ranges to account for the spatial heterogeneity across different cellular organizations. Functional principal component analysis (FPCA) is applied to estimate FPC scores which are then served as predictors in a Cox regression model to investigate the impact of spatial heterogeneity in the TME on survival outcome, potentially adjusting for other confounders. Using a non-small cell lung cancer dataset (n = 153) as a case study, we found that the spatial heterogeneity in the TME cellular composition of CD14+ cells, CD19+ B cells, CD4+ and CD8+ T cells, and CK+ tumor cells, had a significant non-zero effect on the overall survival (p = 0.027). Furthermore, using a publicly available multiplexed ion beam imaging (MIBI) triple-negative breast cancer dataset (n = 33), our proposed method identified a significant impact of cellular interactions between tumor and immune cells on the overall survival (p = 0.046). In simulation studies under different spatial configurations, the proposed method demonstrated a high predictive power by accounting for both clinical effect and the impact of spatial heterogeneity.
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Affiliation(s)
- Thao Vu
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Souvik Seal
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Tusharkanti Ghosh
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Mansooreh Ahmadian
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Julia Wrobel
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
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Wang Y, Ali MA, Vallon-Christersson J, Humphreys K, Hartman J, Rantalainen M. Transcriptional intra-tumour heterogeneity predicted by deep learning in routine breast histopathology slides provides independent prognostic information. Eur J Cancer 2023; 191:112953. [PMID: 37494846 DOI: 10.1016/j.ejca.2023.112953] [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: 01/11/2023] [Revised: 06/05/2023] [Accepted: 06/17/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Intra-tumour heterogeneity (ITH) causes diagnostic challenges and increases the risk for disease recurrence. Quantification of ITH is challenging and has not been demonstrated in large studies. It has previously been shown that deep learning can enable spatially resolved prediction of molecular phenotypes from digital histopathology whole slide images (WSIs). Here we propose a novel method (Deep-ITH) to predict and measure ITH, and we evaluate its prognostic performance in breast cancer. METHODS Deep convolutional neural networks were used to spatially predict gene-expression (PAM50 set) from WSIs. For each predicted transcript, 12 measures of heterogeneity were extracted in the training data set (N = 931). A prognostic score to dichotomise patients into Deep-ITH low- and high-risk groups was established using an elastic-net regularised Cox proportional hazards model (recurrence-free survival). Prognostic performance was evaluated in two independent data sets: SöS-BC-1 (N = 1358) and SCAN-B-Lund (N = 1262). RESULTS We observed an increase in risk of recurrence in the high-risk group with hazard ratio (HR) 2.11 (95%CI:1.22-3.60; p = 0.007) using nested cross-validation. Subgroup analyses confirmed the prognostic performance in oestrogen receptor (ER)-positive, human epidermal growth factor receptor 2 (HER2)-negative, grade 3, and large tumour subgroups. The prognostic value was confirmed in the independent SöS-BC-1 cohort (HR=1.84; 95%CI:1.03-3.3; p = 3.99 ×10-2). In the other external cohort, significant HR was observed in the subgroup of histological grade 2 patients, as well as in the subgroup of patients with small tumours (<20 mm). CONCLUSION We developed a novel method for an automated, scalable, and cost-efficient measure of ITH from WSIs that provides independent prognostic value for breast cancer. SIGNIFICANCE Transcriptional ITH predicted by deep learning models enables prediction of patient survival from routine histopathology WSIs in breast cancer.
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Affiliation(s)
- Yinxi Wang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Maya Alsheh Ali
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Hartman
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden; MedTechLabs, BioClinicum, Karolinska University Hospital, Solna, Sweden
| | - Mattias Rantalainen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; MedTechLabs, BioClinicum, Karolinska University Hospital, Solna, Sweden.
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Anderle N, Schäfer-Ruoff F, Staebler A, Kersten N, Koch A, Önder C, Keller AL, Liebscher S, Hartkopf A, Hahn M, Templin M, Brucker SY, Schenke-Layland K, Schmees C. Breast cancer patient-derived microtumors resemble tumor heterogeneity and enable protein-based stratification and functional validation of individualized drug treatment. J Exp Clin Cancer Res 2023; 42:210. [PMID: 37596623 PMCID: PMC10436441 DOI: 10.1186/s13046-023-02782-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/28/2023] [Indexed: 08/20/2023] Open
Abstract
Despite tremendous progress in deciphering breast cancer at the genomic level, the pronounced intra- and intertumoral heterogeneity remains a major obstacle to the advancement of novel and more effective treatment approaches. Frequent treatment failure and the development of treatment resistance highlight the need for patient-derived tumor models that reflect the individual tumors of breast cancer patients and allow a comprehensive analyses and parallel functional validation of individualized and therapeutically targetable vulnerabilities in protein signal transduction pathways. Here, we introduce the generation and application of breast cancer patient-derived 3D microtumors (BC-PDMs). Residual fresh tumor tissue specimens were collected from n = 102 patients diagnosed with breast cancer and subjected to BC-PDM isolation. BC-PDMs retained histopathological characteristics, and extracellular matrix (ECM) components together with key protein signaling pathway signatures of the corresponding primary tumor tissue. Accordingly, BC-PDMs reflect the inter- and intratumoral heterogeneity of breast cancer and its key signal transduction properties. DigiWest®-based protein expression profiling of identified treatment responder and non-responder BC-PDMs enabled the identification of potential resistance and sensitivity markers of individual drug treatments, including markers previously associated with treatment response and yet undescribed proteins. The combination of individualized drug testing with comprehensive protein profiling analyses of BC-PDMs may provide a valuable complement for personalized treatment stratification and response prediction for breast cancer.
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Affiliation(s)
- Nicole Anderle
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, 72770, Reutlingen, Germany.
| | - Felix Schäfer-Ruoff
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, 72770, Reutlingen, Germany
| | - Annette Staebler
- Institute of Pathology and Neuropathology, Eberhard Karls University Tuebingen, 72076, Tuebingen, Germany
| | - Nicolas Kersten
- Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karls University Tuebingen, Tuebingen, 72076, Germany
- FZI Research Center for Information Technology, 76131, Karlsruhe, Germany
| | - André Koch
- Department of Women's Health, University Women's Hospital, Eberhard Karls University Tuebingen, 72076, Tuebingen, Germany
| | - Cansu Önder
- Department of Women's Health, University Women's Hospital, Eberhard Karls University Tuebingen, 72076, Tuebingen, Germany
| | - Anna-Lena Keller
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, 72770, Reutlingen, Germany
| | - Simone Liebscher
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University Tuebingen, 72076, Tuebingen, Germany
| | - Andreas Hartkopf
- Department of Women's Health, University Women's Hospital, Eberhard Karls University Tuebingen, 72076, Tuebingen, Germany
- Department of Gynecology and Obstetrics, University Hospital of Ulm, 89081, Ulm, Germany
| | - Markus Hahn
- Department of Women's Health, University Women's Hospital, Eberhard Karls University Tuebingen, 72076, Tuebingen, Germany
| | - Markus Templin
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, 72770, Reutlingen, Germany
| | - Sara Y Brucker
- Department of Women's Health, University Women's Hospital, Eberhard Karls University Tuebingen, 72076, Tuebingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University Tuebingen, 72076, Tuebingen, Germany
| | - Katja Schenke-Layland
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, 72770, Reutlingen, Germany
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University Tuebingen, 72076, Tuebingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University Tuebingen, 72076, Tuebingen, Germany
| | - Christian Schmees
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, 72770, Reutlingen, Germany.
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Fu X, Sahai E, Wilkins A. Application of digital pathology-based advanced analytics of tumour microenvironment organisation to predict prognosis and therapeutic response. J Pathol 2023; 260:578-591. [PMID: 37551703 PMCID: PMC10952145 DOI: 10.1002/path.6153] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/25/2023] [Accepted: 06/07/2023] [Indexed: 08/09/2023]
Abstract
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.
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Affiliation(s)
- Xiao Fu
- Tumour Cell Biology LaboratoryThe Francis Crick InstituteLondonUK
- Biomolecular Modelling LaboratoryThe Francis Crick InstituteLondonUK
| | - Erik Sahai
- Tumour Cell Biology LaboratoryThe Francis Crick InstituteLondonUK
| | - Anna Wilkins
- Tumour Cell Biology LaboratoryThe Francis Crick InstituteLondonUK
- Division of Radiotherapy and ImagingInstitute of Cancer ResearchLondonUK
- Royal Marsden Hospitals NHS TrustLondonUK
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9
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Long F, Ma H, Hao Y, Tian L, Li Y, Li B, Chen J, Tang Y, Li J, Deng L, Xie G, Liu M. A novel exosome-derived prognostic signature and risk stratification for breast cancer based on multi-omics and systematic biological heterogeneity. Comput Struct Biotechnol J 2023; 21:3010-3023. [PMID: 37273850 PMCID: PMC10232662 DOI: 10.1016/j.csbj.2023.05.013] [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: 11/18/2022] [Revised: 04/29/2023] [Accepted: 05/11/2023] [Indexed: 06/06/2023] Open
Abstract
Tumor heterogeneity remains a major challenge for disease subtyping, risk stratification, and accurate clinical management. Exosome-based liquid biopsy can effectively overcome the limitations of tissue biopsy, achieving minimal invasion, multi-point dynamic monitoring, and good prognosis assessment, and has broad clinical prospects. However, there is still lacking comprehensive analysis of tumor-derived exosome (TDE)-based stratification of risk patients and prognostic assessment for breast cancer with systematic dissection of biological heterogeneity. In this study, the robust corroborative analysis for biomarker discovery (RCABD) strategy was used for the identification of exosome molecules, differential expression verification, risk prediction modeling, heterogenous dissection with multi-ome (6101 molecules), our ExoBCD database (306 molecules), and 53 independent studies (481 molecules). Our results showed that a 10-molecule exosome-derived signature (exoSIG) could successfully fulfill breast cancer risk stratification, making it a novel and accurate exosome prognostic indicator (Cox P = 9.9E-04, HR = 3.3, 95% CI 1.6-6.8). Interestingly, HLA-DQB2 and COL17A1, closely related to tumor metastasis, achieved high performance in prognosis prediction (86.35% contribution) and accuracy (Log-rank P = 0.028, AUC = 85.42%). With the combined information of patient age and tumor stage, they formed a bimolecular risk signature (Clinmin-exoSIG) and a convenient nomogram as operable tools for clinical applications. In conclusion, as an extension of ExoBCD, this study conducted systematic analyses to identify prognostic multi-molecular panel and risk signature, stratify patients and dissect biological heterogeneity based on breast cancer exosomes from a multi-omics perspective. Our results provide an important reference for in-depth exploration of the "biological heterogeneity - risk stratification - prognosis prediction".
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Affiliation(s)
- Fei Long
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Haodong Ma
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Youjin Hao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Luyao Tian
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Yinghong Li
- Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, PR China
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Juan Chen
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Ying Tang
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Jing Li
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Lili Deng
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Mingwei Liu
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
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10
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Mandair D, Reis-Filho JS, Ashworth A. Biological insights and novel biomarker discovery through deep learning approaches in breast cancer histopathology. NPJ Breast Cancer 2023; 9:21. [PMID: 37024522 PMCID: PMC10079681 DOI: 10.1038/s41523-023-00518-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/27/2023] [Indexed: 04/08/2023] Open
Abstract
Breast cancer remains a highly prevalent disease with considerable inter- and intra-tumoral heterogeneity complicating prognostication and treatment decisions. The utilization and depth of genomic, transcriptomic and proteomic data for cancer has exploded over recent times and the addition of spatial context to this information, by understanding the correlating morphologic and spatial patterns of cells in tissue samples, has created an exciting frontier of research, histo-genomics. At the same time, deep learning (DL), a class of machine learning algorithms employing artificial neural networks, has rapidly progressed in the last decade with a confluence of technical developments - including the advent of modern graphic processing units (GPU), allowing efficient implementation of increasingly complex architectures at scale; advances in the theoretical and practical design of network architectures; and access to larger datasets for training - all leading to sweeping advances in image classification and object detection. In this review, we examine recent developments in the application of DL in breast cancer histology with particular emphasis of those producing biologic insights or novel biomarkers, spanning the extraction of genomic information to the use of stroma to predict cancer recurrence, with the aim of suggesting avenues for further advancing this exciting field.
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Affiliation(s)
- Divneet Mandair
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, 94158, USA
| | | | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, 94158, USA.
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11
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Computational Pathology for Breast Cancer and Gynecologic Cancer. Cancers (Basel) 2023; 15:cancers15030942. [PMID: 36765900 PMCID: PMC9913809 DOI: 10.3390/cancers15030942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Advances in computation pathology have continued at an impressive pace in recent years [...].
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12
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Livesey M, Rossouw SC, Blignaut R, Christoffels A, Bendou H. Transforming RNA-Seq gene expression to track cancer progression in the multi-stage early to advanced-stage cancer development. PLoS One 2023; 18:e0284458. [PMID: 37093793 PMCID: PMC10124877 DOI: 10.1371/journal.pone.0284458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 03/31/2023] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Cancer progression can be tracked by gene expression changes that occur throughout early-stage to advanced-stage cancer development. The accumulated genetic changes can be detected when gene expression levels in advanced-stage are less variable but show high variability in early-stage. Normalizing advanced-stage expression samples with early-stage and clustering of the normalized expression samples can reveal cancers with similar or different progression and provide insight into clinical and phenotypic patterns of patient samples within the same cancer. OBJECTIVE This study aims to investigate cancer progression through RNA-Seq expression profiles across the multi-stage process of cancer development. METHODS RNA-sequenced gene expression of Diffuse Large B-cell Lymphoma, Lung cancer, Liver cancer, Cervical cancer, and Testicular cancer were downloaded from the UCSC Xena database. Advanced-stage samples were normalized with early-stage samples to consider heterogeneity differences in the multi-stage cancer progression. WGCNA was used to build a gene network and categorized normalized genes into different modules. A gene set enrichment analysis selected key gene modules related to cancer. The diagnostic capacity of the modules was evaluated after hierarchical clustering. RESULTS Unnormalized RNA-Seq gene expression failed to segregate advanced-stage samples based on selected cancer cohorts. Normalization with early-stage revealed the true heterogeneous gene expression that accumulates across the multi-stage cancer progression, this resulted in well segregated cancer samples. Cancer-specific pathways were enriched in the normalized WGCNA modules. The normalization method was further able to stratify patient samples based on phenotypic and clinical information. Additionally, the method allowed for patient survival analysis, with the Cox regression model selecting gene MAP4K1 in cervical cancer and Kaplan-Meier confirming that upregulation is favourable. CONCLUSION The application of the normalization method further enhanced the accuracy of clustering of cancer samples based on how they progressed. Additionally, genes responsible for cancer progression were discovered.
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Affiliation(s)
- Michelle Livesey
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Sophia Catherine Rossouw
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Renette Blignaut
- Department of Statistics and Population Studies, University of the Western Cape, Cape Town, South Africa
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Hocine Bendou
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
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13
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Failmezger H, Hessel H, Kapil A, Schmidt G, Harder N. Spatial heterogeneity of cancer associated protein expression in immunohistochemically stained images as an improved prognostic biomarker. Front Oncol 2022; 12:964716. [PMID: 36601480 PMCID: PMC9806230 DOI: 10.3389/fonc.2022.964716] [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: 06/08/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022] Open
Abstract
The identification of new tumor biomarkers for patient stratification before therapy, for monitoring of disease progression, and for characterization of tumor biology plays a crucial role in cancer research. The status of these biomarkers is mostly scored manually by a pathologist and such scores typically, do not consider the spatial heterogeneity of the protein's expression in the tissue. Using advanced image analysis methods, marker expression can be determined quantitatively with high accuracy and reproducibility on a per-cell level. To aggregate such per-cell marker expressions on a patient level, the expression values for single cells are usually averaged for the whole tissue. However, averaging neglects the spatial heterogeneity of the marker expression in the tissue. We present two novel approaches for quantitative scoring of spatial marker expression heterogeneity. The first approach is based on a co-occurrence analysis of the marker expression in neighboring cells. The second approach accounts for the local variability of the protein's expression by tiling the tissue with a regular grid and assigning local spatial heterogeneity phenotypes per tile. We apply our novel scores to quantify the spatial expression of four different membrane markers, i.e., HER2, CMET, CD44, and EGFR in immunohistochemically (IHC) stained tissue sections of colorectal cancer patients. We evaluate the prognostic relevance of our spatial scores in this cohort and show that the spatial heterogeneity scores clearly outperform the marker expression average as a prognostic factor (CMET: p-value=0.01 vs. p-value=0.3).
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14
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Intratumor graph neural network recovers hidden prognostic value of multi-biomarker spatial heterogeneity. Nat Commun 2022; 13:4250. [PMID: 35869055 PMCID: PMC9307796 DOI: 10.1038/s41467-022-31771-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/01/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractBiomarkers are indispensable for precision medicine. However, focused single-biomarker development using human tissue has been complicated by sample spatial heterogeneity. To address this challenge, we tested a representation of primary tumor that synergistically integrated multiple in situ biomarkers of extracellular matrix from multiple sampling regions into an intratumor graph neural network. Surprisingly, the differential prognostic value of this computational model over its conventional non-graph counterpart approximated that of combined routine prognostic biomarkers (tumor size, nodal status, histologic grade, molecular subtype, etc.) for 995 breast cancer patients under a retrospective study. This large prognostic value, originated from implicit but interpretable regional interactions among the graphically integrated in situ biomarkers, would otherwise be lost if they were separately developed into single conventional (spatially homogenized) biomarkers. Our study demonstrates an alternative route to cancer prognosis by taping the regional interactions among existing biomarkers rather than developing novel biomarkers.
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15
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Woodward AA, Urbanowicz RJ, Naj AC, Moore JH. Genetic heterogeneity: Challenges, impacts, and methods through an associative lens. Genet Epidemiol 2022; 46:555-571. [PMID: 35924480 PMCID: PMC9669229 DOI: 10.1002/gepi.22497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 01/07/2023]
Abstract
Genetic heterogeneity describes the occurrence of the same or similar phenotypes through different genetic mechanisms in different individuals. Robustly characterizing and accounting for genetic heterogeneity is crucial to pursuing the goals of precision medicine, for discovering novel disease biomarkers, and for identifying targets for treatments. Failure to account for genetic heterogeneity may lead to missed associations and incorrect inferences. Thus, it is critical to review the impact of genetic heterogeneity on the design and analysis of population level genetic studies, aspects that are often overlooked in the literature. In this review, we first contextualize our approach to genetic heterogeneity by proposing a high-level categorization of heterogeneity into "feature," "outcome," and "associative" heterogeneity, drawing on perspectives from epidemiology and machine learning to illustrate distinctions between them. We highlight the unique nature of genetic heterogeneity as a heterogeneous pattern of association that warrants specific methodological considerations. We then focus on the challenges that preclude effective detection and characterization of genetic heterogeneity across a variety of epidemiological contexts. Finally, we discuss systems heterogeneity as an integrated approach to using genetic and other high-dimensional multi-omic data in complex disease research.
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Affiliation(s)
- Alexa A. Woodward
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Ryan J. Urbanowicz
- Department of Computational BiomedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Adam C. Naj
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jason H. Moore
- Department of Computational BiomedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
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16
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Cruz-Gregorio A, Aranda-Rivera AK, Sciutto E, Fragoso G, Pedraza-Chaverri J. Redox state associated with antitumor and immunomodulatory peptides in cancer. Arch Biochem Biophys 2022; 730:109414. [PMID: 36174750 DOI: 10.1016/j.abb.2022.109414] [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: 06/28/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/27/2022]
Abstract
Cancer, a major public health problem, is the fourth cause of death in the world. While cancer mortality has decreased in recent decades due to more effective treatments, mostly based on improving antitumor immunity, some forms of cancer are resistant to these immunotherapies. A promising approach for cancer treatment involves the administration of antitumor and immunomodulatory peptides. Immunomodulatory peptides have been proved to exert antitumor and immunomodulatory effects by activating immune cells such as cytotoxic T cells, with fewer side-effects. A process closely related to the regulation of the immune system by immunomodulatory antitumor peptides is the modulation of the redox state, which has been poorly studied. This review focuses on the redox state regulated by antitumor and immunomodulatory peptides in cancer development, and on the potential of redox state as a therapy associated with these peptides in cancer treatment.
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Affiliation(s)
- Alfredo Cruz-Gregorio
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, 04510, Ciudad de México, Mexico.
| | - Ana Karina Aranda-Rivera
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, 04510, Ciudad de México, Mexico
| | - Edda Sciutto
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Gladis Fragoso
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - José Pedraza-Chaverri
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, 04510, Ciudad de México, Mexico.
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17
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Wu J, Mayer AT, Li R. Integrated imaging and molecular analysis to decipher tumor microenvironment in the era of immunotherapy. Semin Cancer Biol 2022; 84:310-328. [PMID: 33290844 PMCID: PMC8319834 DOI: 10.1016/j.semcancer.2020.12.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/29/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023]
Abstract
Radiological imaging is an integral component of cancer care, including diagnosis, staging, and treatment response monitoring. It contains rich information about tumor phenotypes that are governed not only by cancer cellintrinsic biological processes but also by the tumor microenvironment, such as the composition and function of tumor-infiltrating immune cells. By analyzing the radiological scans using a quantitative radiomics approach, robust relations between specific imaging and molecular phenotypes can be established. Indeed, a number of studies have demonstrated the feasibility of radiogenomics for predicting intrinsic molecular subtypes and gene expression signatures in breast cancer based on MRI. In parallel, promising results have been shown for inferring the amount of tumor-infiltrating lymphocytes, a key factor for the efficacy of cancer immunotherapy, from standard-of-care radiological images. Compared with the biopsy-based approach, radiogenomics offers a unique avenue to profile the molecular makeup of the tumor and immune microenvironment as well as its evolution in a noninvasive and holistic manner through longitudinal imaging scans. Here, we provide a systematic review of the state of the art radiogenomics studies in the era of immunotherapy and discuss emerging paradigms and opportunities in AI and deep learning approaches. These technical advances are expected to transform the radiogenomics field, leading to the discovery of reliable imaging biomarkers. This will pave the way for their clinical translation to guide precision cancer therapy.
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Affiliation(s)
- Jia Wu
- Department of Imaging Physics, MD Anderson Cancer Center, Texas, 77030, USA; Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Texas, 77030, USA.
| | - Aaron T Mayer
- Department of Bioengineering, Stanford University, Stanford, California, 94305, USA; Department of Radiology, Stanford University, Stanford, California, 94305, USA; Molecular Imaging Program at Stanford, Stanford University, Stanford, California, 94305, USA; BioX Program at Stanford, Stanford University, Stanford, California, 94305, USA
| | - Ruijiang Li
- Department of Radiation Oncology, Stanford University, Stanford, California, 94305, USA
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18
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Khawatmi M, Steux Y, Zourob S, Sailem HZ. ShapoGraphy: A User-Friendly Web Application for Creating Bespoke and Intuitive Visualisation of Biomedical Data. FRONTIERS IN BIOINFORMATICS 2022; 2:788607. [PMID: 36304310 PMCID: PMC9580894 DOI: 10.3389/fbinf.2022.788607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 05/23/2022] [Indexed: 12/05/2022] Open
Abstract
Effective visualisation of quantitative microscopy data is crucial for interpreting and discovering new patterns from complex bioimage data. Existing visualisation approaches, such as bar charts, scatter plots and heat maps, do not accommodate the complexity of visual information present in microscopy data. Here we develop ShapoGraphy, a first of its kind method accompanied by an interactive web-based application for creating customisable quantitative pictorial representations to facilitate the understanding and analysis of image datasets (www.shapography.com). ShapoGraphy enables the user to create a structure of interest as a set of shapes. Each shape can encode different variables that are mapped to the shape dimensions, colours, symbols, or outline. We illustrate the utility of ShapoGraphy using various image data, including high dimensional multiplexed data. Our results show that ShapoGraphy allows a better understanding of cellular phenotypes and relationships between variables. In conclusion, ShapoGraphy supports scientific discovery and communication by providing a rich vocabulary to create engaging and intuitive representations of diverse data types.
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Affiliation(s)
| | | | | | - Heba Z. Sailem
- Institute of Biomedical Engineering, Department of Engineering, University of Oxford, Oxford, United Kingdom
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19
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Schmidt ST, Akhave N, Knightly RE, Reuben A, Vokes N, Zhang J, Li J, Fujimoto J, Byers LA, Sanchez-Espiridion B, Diao L, Wang J, Federico L, Forget MA, McGrail DJ, Weissferdt A, Lin SY, Lee Y, Suzuki E, Kovacs JJ, Behrens C, Wistuba II, Futreal A, Vaporciyan A, Sepesi B, Heymach JV, Bernatchez C, Haymaker C, Cascone T, Zhang J, Bristow CA, Heffernan TP, Negrao MV, Gibbons DL. Shared Nearest Neighbors Approach and Interactive Browser for Network Analysis of a Comprehensive Non-Small-Cell Lung Cancer Data Set. JCO Clin Cancer Inform 2022; 6:e2200040. [PMID: 35944232 PMCID: PMC9470146 DOI: 10.1200/cci.22.00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/25/2022] [Accepted: 06/30/2022] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Advances in biological measurement technologies are enabling large-scale studies of patient cohorts across multiple omics platforms. Holistic analysis of these data can generate actionable insights for translational research and necessitate new approaches for data integration and mining. METHODS We present a novel approach for integrating data across platforms on the basis of the shared nearest neighbors algorithm and use it to create a network of multiplatform data from the immunogenomic profiling of non-small-cell lung cancer project. RESULTS Benchmarking demonstrates that the shared nearest neighbors-based network approach outperforms a traditional gene-gene network in capturing established interactions while providing new ones on the basis of the interplay between measurements from different platforms. When used to examine patient characteristics of interest, our approach provided signatures associated with and new leads related to recurrence and TP53 oncogenotype. CONCLUSION The network developed offers an unprecedented, holistic view into immunogenomic profiling of non-small-cell lung cancer, which can be explored through the accompanying interactive browser that we built.
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Affiliation(s)
- Stephanie T. Schmidt
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Neal Akhave
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ryan E. Knightly
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Natalie Vokes
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jun Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lauren A. Byers
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lorenzo Federico
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Marie-Andree Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Daniel J. McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Annikka Weissferdt
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Younghee Lee
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Erika Suzuki
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jeffrey J. Kovacs
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ignacio I. Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ara Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John V. Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chantale Bernatchez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Tina Cascone
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Christopher A. Bristow
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Timothy P. Heffernan
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Marcelo V. Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Don L. Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
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Qaiser T, Lee CY, Vandenberghe M, Yeh J, Gavrielides MA, Hipp J, Scott M, Reischl J. Usability of deep learning and H&E images predict disease outcome-emerging tool to optimize clinical trials. NPJ Precis Oncol 2022; 6:37. [PMID: 35705792 PMCID: PMC9200764 DOI: 10.1038/s41698-022-00275-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 04/27/2022] [Indexed: 11/24/2022] Open
Abstract
Understanding factors that impact prognosis for cancer patients have high clinical relevance for treatment decisions and monitoring of the disease outcome. Advances in artificial intelligence (AI) and digital pathology offer an exciting opportunity to capitalize on the use of whole slide images (WSIs) of hematoxylin and eosin (H&E) stained tumor tissue for objective prognosis and prediction of response to targeted therapies. AI models often require hand-delineated annotations for effective training which may not be readily available for larger data sets. In this study, we investigated whether AI models can be trained without region-level annotations and solely on patient-level survival data. We present a weakly supervised survival convolutional neural network (WSS-CNN) approach equipped with a visual attention mechanism for predicting overall survival. The inclusion of visual attention provides insights into regions of the tumor microenvironment with the pathological interpretation which may improve our understanding of the disease pathomechanism. We performed this analysis on two independent, multi-center patient data sets of lung (which is publicly available data) and bladder urothelial carcinoma. We perform univariable and multivariable analysis and show that WSS-CNN features are prognostic of overall survival in both tumor indications. The presented results highlight the significance of computational pathology algorithms for predicting prognosis using H&E stained images alone and underpin the use of computational methods to improve the efficiency of clinical trial studies.
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Affiliation(s)
- Talha Qaiser
- Precision Medicine and Biosamples, Oncology R&D, AstraZeneca, Cambridge, UK.
| | | | | | - Joe Yeh
- AetherAI, Taipei City, Taiwan
| | | | - Jason Hipp
- Early Oncology, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Marietta Scott
- Precision Medicine and Biosamples, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Joachim Reischl
- Precision Medicine and Biosamples, Oncology R&D, AstraZeneca, Cambridge, UK
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21
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He L, Li ZH, Yan LX, Chen X, Sanduleanu S, Zhong WZ, Lambin P, Ye ZX, Sun YS, Liu YL, Qu JR, Wu L, Tu CL, Scrivener M, Pieters T, Coche E, Yang Q, Yang M, Liang CH, Huang YQ, Liu ZY. Development and validation of a computed tomography-based immune ecosystem diversity index as an imaging biomarker in non-small cell lung cancer. Eur Radiol 2022; 32:8726-8736. [PMID: 35639145 DOI: 10.1007/s00330-022-08873-6] [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: 09/28/2021] [Revised: 04/22/2022] [Accepted: 05/11/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVES To date, there are no data on the noninvasive surrogate of intratumoural immune status that could be prognostic of survival outcomes in non-small cell lung cancer (NSCLC). We aimed to develop and validate the immune ecosystem diversity index (iEDI), an imaging biomarker, to indicate the intratumoural immune status in NSCLC. We further investigated the clinical relevance of the biomarker for survival prediction. METHODS In this retrospective study, two independent NSCLC cohorts (Resec1, n = 149; Resec2, n = 97) were included to develop and validate the iEDI to classify the intratumoural immune status. Paraffin-embedded resected specimens in Resec1 and Resec2 were stained by immunohistochemistry, and the density percentiles of CD3+, CD4+, and CD8+ T cells to all cells were quantified to estimate intratumoural immune status. Then, EDI features were extracted using preoperative computed tomography to develop an imaging biomarker, called iEDI, to determine the immune status. The prognostic value of iEDI was investigated on NSCLC patients receiving surgical resection (Resec1; Resec2; internal cohort Resec3, n = 419; external cohort Resec4, n = 96; and TCIA cohort Resec5, n = 55). RESULTS iEDI successfully classified immune status in Resec1 (AUC 0.771, 95% confidence interval [CI] 0.759-0.783; and 0.770 through internal validation) and Resec2 (0.669, 0.647-0.691). Patients with higher iEDI-score had longer overall survival (OS) in Resec3 (unadjusted hazard ratio 0.335, 95%CI 0.206-0.546, p < 0.001), Resec4 (0.199, 0.040-1.000, p < 0.001), and TCIA (0.303, 0.098-0.944, p = 0.001). CONCLUSIONS iEDI is a non-invasive surrogate of intratumoural immune status and prognostic of OS for NSCLC patients receiving surgical resection. KEY POINTS • Decoding tumour immune microenvironment enables advanced biomarkers identification. • Immune ecosystem diversity index characterises intratumoural immune status noninvasively. • Immune ecosystem diversity index is prognostic for NSCLC patients.
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Affiliation(s)
- Lan He
- Department of Radiology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, China
| | - Zhen-Hui Li
- Department of Radiology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, China.,Department of Radiology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | - Li-Xu Yan
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xin Chen
- Department of Radiology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Sebastian Sanduleanu
- The D-lab and the M-lab, Department of Precision Medicine, GROW-School for Oncology, Maastricht University, Maastricht, The Netherlands
| | - Wen-Zhao Zhong
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Phillippe Lambin
- The D-lab and the M-lab, Department of Precision Medicine, GROW-School for Oncology, Maastricht University, Maastricht, The Netherlands.,Department of Radiology and Nuclear Medicine, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Zhao-Xiang Ye
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Ying-Shi Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department Radiology, Peking University Cancer Hospital & Institute, Hai Dian District, Beijing, China
| | - Yu-Lin Liu
- Department of Radiology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jin-Rong Qu
- Department of Radiology, the Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Lin Wu
- Department of Pathology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | - Chang-Ling Tu
- Department of Cadres Medical Oncology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | - Madeleine Scrivener
- Department of Internal Medicine, Cliniques Universitaires St-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Thierry Pieters
- Departement of Pneumology, Cliniques Universitaires St-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Emmanuel Coche
- Department of Radiology, Cliniques Universitaires St-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Qian Yang
- Department of Radiology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mei Yang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chang-Hong Liang
- Department of Radiology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, China.,Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yan-Qi Huang
- Department of Radiology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, China. .,The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.
| | - Zai-Yi Liu
- Department of Radiology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, China. .,Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
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22
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Mohammad Mirzaei N, Tatarova Z, Hao W, Changizi N, Asadpoure A, Zervantonakis IK, Hu Y, Chang YH, Shahriyari L. A PDE Model of Breast Tumor Progression in MMTV-PyMT Mice. J Pers Med 2022; 12:807. [PMID: 35629230 PMCID: PMC9145520 DOI: 10.3390/jpm12050807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
The evolution of breast tumors greatly depends on the interaction network among different cell types, including immune cells and cancer cells in the tumor. This study takes advantage of newly collected rich spatio-temporal mouse data to develop a data-driven mathematical model of breast tumors that considers cells' location and key interactions in the tumor. The results show that cancer cells have a minor presence in the area with the most overall immune cells, and the number of activated immune cells in the tumor is depleted over time when there is no influx of immune cells. Interestingly, in the case of the influx of immune cells, the highest concentrations of both T cells and cancer cells are in the boundary of the tumor, as we use the Robin boundary condition to model the influx of immune cells. In other words, the influx of immune cells causes a dominant outward advection for cancer cells. We also investigate the effect of cells' diffusion and immune cells' influx rates in the dynamics of cells in the tumor micro-environment. Sensitivity analyses indicate that cancer cells and adipocytes' diffusion rates are the most sensitive parameters, followed by influx and diffusion rates of cytotoxic T cells, implying that targeting them is a possible treatment strategy for breast cancer.
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Affiliation(s)
- Navid Mohammad Mirzaei
- Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst, MA 01003, USA; (N.M.M.); (Y.H.)
| | - Zuzana Tatarova
- Department of Radiology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Wenrui Hao
- Department of Mathematics, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Navid Changizi
- Department of Civil and Environmental Engineering, University of Massachusetts, Dartmouth, MA 02747, USA; (N.C.); (A.A.)
| | - Alireza Asadpoure
- Department of Civil and Environmental Engineering, University of Massachusetts, Dartmouth, MA 02747, USA; (N.C.); (A.A.)
| | - Ioannis K. Zervantonakis
- Department of Bioengineering, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15219, USA;
| | - Yu Hu
- Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst, MA 01003, USA; (N.M.M.); (Y.H.)
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Leili Shahriyari
- Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst, MA 01003, USA; (N.M.M.); (Y.H.)
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23
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Alexandra T, Maria G, Charalampos T, Eleni Z, George ZC, Nikolaos MV. Exosomes in breast cancer management. Where do we stand? A literature review. Biol Cell 2022; 114:109-122. [PMID: 35080041 DOI: 10.1111/boc.202100081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/10/2022] [Accepted: 01/17/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Exosomes constitute cellular molecular fingertips that participate in intercellular communication both in health and disease states. Hence, exosomes emerge as critical mediators of cancer development and progression, as well as potential biomarkers and novel therapeutic targets. OBJECTIVE To review literature data regarding applications of circulating exosomes in breast cancer management. METHODS This is a literature review of relevant published studies until April 2020 in PubMed and Google Scholar databases. Original papers in the English language concerning exosome related studies were included. RESULTS Exosomes represent molecular miniatures of their parent cells. Several homeostatic mechanisms control exosomal secretion and synthesis. Exosomal exchange among cells creates an intricate intercellular crosstalk orchestrating almost every tissue process, as well as carcinogenesis. Available data highlight exosomes as major mediators of cancer development and progression. The secretion of specific exosomal molecules, particularly miRNAs, correlates with the underlying processes and can be used as a means of tumor detection and prognostic assessment. CONCLUSIONS Exosomal miRNAs expression profiles and levels closely relate to cancer extent, type and prognosis. Deep comprehension of such correlations and systematization of experimental outcomes will offer a novel approach in cancer detection and management. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Triantafyllou Alexandra
- 1st Propaedeutic Surgical Department, Hippocration General Hospital, National and Kapodistrian University of Athens, Greece
| | - Gazouli Maria
- Department of Biology, School of Medicine, National and Kapodistrian University of Athens, Greece
| | - Theodoropoulos Charalampos
- 1st Propaedeutic Surgical Department, Hippocration General Hospital, National and Kapodistrian University of Athens, Greece
| | - Zografos Eleni
- 1st Propaedeutic Surgical Department, Hippocration General Hospital, National and Kapodistrian University of Athens, Greece
| | - Zografos C George
- 1st Propaedeutic Surgical Department, Hippocration General Hospital, National and Kapodistrian University of Athens, Greece
| | - Michalopoulos V Nikolaos
- 1st Propaedeutic Surgical Department, Hippocration General Hospital, National and Kapodistrian University of Athens, Greece
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24
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Zhang J, Song C, Tian Y, Yang X. Single-Cell RNA Sequencing in Lung Cancer: Revealing Phenotype Shaping of Stromal Cells in the Microenvironment. Front Immunol 2022; 12:802080. [PMID: 35126365 PMCID: PMC8807562 DOI: 10.3389/fimmu.2021.802080] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
The lung tumor microenvironment, which is composed of heterogeneous cell populations, plays an important role in the progression of lung cancer and is closely related to therapeutic efficacy. Increasing evidence has shown that stromal components play a key role in regulating tumor invasion, metastasis and drug resistance. Therefore, a better understanding of stromal components in the tumor microenvironment is helpful for the diagnosis and treatment of lung cancer. Rapid advances in technology have brought our understanding of disease into the genetic era, and single-cell RNA sequencing has enabled us to describe gene expression profiles with unprecedented resolution, enabling quantitative analysis of gene expression at the single-cell level to reveal the correlations among heterogeneity, signaling pathways, drug resistance and microenvironment molding in lung cancer, which is important for the treatment of this disease. In this paper, several common single-cell RNA sequencing methods and their advantages and disadvantages are briefly introduced to provide a reference for selection of suitable methods. Furthermore, we review the latest progress of single-cell RNA sequencing in the study of stromal cells in the lung tumor microenvironment.
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25
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Wu L, Ye W, Liu Y, Chen D, Wang Y, Cui Y, Li Z, Li P, Li Z, Liu Z, Liu M, Liang C, Yang X, Xie Y, Wang Y. An integrated deep learning model for the prediction of pathological complete response to neoadjuvant chemotherapy with serial ultrasonography in breast cancer patients: a multicentre, retrospective study. Breast Cancer Res 2022; 24:81. [PMID: 36414984 PMCID: PMC9680135 DOI: 10.1186/s13058-022-01580-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/13/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The biological phenotype of tumours evolves during neoadjuvant chemotherapy (NAC). Accurate prediction of pathological complete response (pCR) to NAC in the early-stage or posttreatment can optimize treatment strategies or improve the breast-conserving rate. This study aimed to develop and validate an autosegmentation-based serial ultrasonography assessment system (SUAS) that incorporated serial ultrasonographic features throughout the NAC of breast cancer to predict pCR. METHODS A total of 801 patients with biopsy-proven breast cancer were retrospectively enrolled from three institutions and were split into a training cohort (242 patients), an internal validation cohort (197 patients), and two external test cohorts (212 and 150 patients). Three imaging signatures were constructed from the serial ultrasonographic features before (pretreatment signature), during the first-second cycle of (early-stage treatment signature), and after (posttreatment signature) NAC based on autosegmentation by U-net. The SUAS was constructed by subsequently integrating the pre, early-stage, and posttreatment signatures, and the incremental performance was analysed. RESULTS The SUAS yielded a favourable performance in predicting pCR, with areas under the receiver operating characteristic curve (AUCs) of 0.927 [95% confidence interval (CI) 0.891-0.963] and 0.914 (95% CI 0.853-0.976), compared with those of the clinicopathological prediction model [0.734 (95% CI 0.665-0.804) and 0.610 (95% CI 0.504-0.716)], and radiologist interpretation [0.632 (95% CI 0.570-0.693) and 0.724 (95% CI 0.644-0.804)] in the external test cohorts. Furthermore, similar results were also observed in the early-stage treatment of NAC [AUC 0.874 (0.793-0.955)-0.897 (0.851-0.943) in the external test cohorts]. CONCLUSIONS We demonstrate that autosegmentation-based SAUS integrating serial ultrasonographic features throughout NAC can predict pCR with favourable performance, which can facilitate individualized treatment strategies.
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Affiliation(s)
- Lei Wu
- grid.410643.4Department of Radiology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Road, Guangzhou, 510080 China ,grid.410643.4Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080 China ,grid.413352.20000 0004 1760 3705Guangdong Cardiovascular Institute, 106 Zhongshan 2nd Road, Guangzhou, 510080 China
| | - Weitao Ye
- grid.410643.4Department of Radiology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Road, Guangzhou, 510080 China ,grid.410643.4Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080 China
| | - Yu Liu
- grid.410643.4Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080 China ,grid.410643.4Department of Ultrasound, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Road, Guangzhou, 510080 China
| | - Dong Chen
- grid.452826.fDepartment of Medical Ultrasound, Yunnan Cancer Hospital, Yunnan Cancer Center, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118 China
| | - Yuxiang Wang
- grid.263452.40000 0004 1798 4018Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013 China
| | - Yanfen Cui
- grid.263452.40000 0004 1798 4018Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013 China
| | - Zhenhui Li
- grid.452826.fDepartment of Radiology, Yunnan Cancer Hospital, Yunnan Cancer Center, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118 China
| | - Pinxiong Li
- grid.410643.4Department of Radiology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Road, Guangzhou, 510080 China ,grid.410643.4Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080 China
| | - Zhen Li
- grid.452826.fDepartment of 3rd Breast Surgery, Yunnan Cancer Hospital, Yunnan Cancer Center, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118 China
| | - Zaiyi Liu
- grid.410643.4Department of Radiology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Road, Guangzhou, 510080 China ,grid.410643.4Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080 China
| | - Min Liu
- grid.488530.20000 0004 1803 6191Department of Ultrasound, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 China
| | - Changhong Liang
- grid.410643.4Department of Radiology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Road, Guangzhou, 510080 China ,grid.410643.4Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080 China
| | - Xiaotang Yang
- grid.263452.40000 0004 1798 4018Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013 China
| | - Yu Xie
- grid.452826.fDepartment of Radiology, Yunnan Cancer Hospital, Yunnan Cancer Center, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118 China
| | - Ying Wang
- grid.470124.4Department of Medical Ultrasonics, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang West Road, Guangzhou, 510120 China
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26
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Cancer immunoediting hypothesis: history, clinical implications and controversies. Cent Eur J Immunol 2022; 47:168-174. [PMID: 36751395 PMCID: PMC9894085 DOI: 10.5114/ceji.2022.117376] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
The main function of the immune system is to protect against infectious pathogens and to ensure tissue homeostasis. The latter function includes preventing autoimmune reactions, tolerizing cells to nonpathogenic environmental microorganisms, and eliminating apoptotic/damaged, transformed, or neoplastic cells. The process of carcinogenesis and tumor development and the role of the immune system in inhibiting progression of cancer have been the subject of intense research since the end of the 20th century and resulted in formulation of the cancer immunoediting hypothesis. The hypothesis postulates three steps in oncogenesis: 1) elimination - corresponding to immunosurveillance, 2) equilibrium in which the growth of transformed or neoplastic cells is efficiently controlled by immune effector mechanisms, and 3) escape in which cancer progresses due to an ineffective antitumor response. In parallel, a new field of science - immune-oncology - has arisen. Attempts are also being made to quantify intra-tumoral and peritumoral T cell infiltrations and to define optimal immunological parameters for prognostic/predictive purposes in several types of cancer. The knowledge of relationships between the tumor and the immune system has been and is practically exploited therapeutically in the clinic to treat cancer. Immunotherapy is a standard or supplementary treatment in various types of cancer.
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27
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Mavrommati I, Johnson F, Echeverria GV, Natrajan R. Subclonal heterogeneity and evolution in breast cancer. NPJ Breast Cancer 2021; 7:155. [PMID: 34934048 PMCID: PMC8692469 DOI: 10.1038/s41523-021-00363-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 11/26/2021] [Indexed: 12/11/2022] Open
Abstract
Subclonal heterogeneity and evolution are characteristics of breast cancer that play a fundamental role in tumour development, progression and resistance to current therapies. In this review, we focus on the recent advances in understanding the epigenetic and transcriptomic changes that occur within breast cancer and their importance in terms of cancer development, progression and therapy resistance with a particular focus on alterations at the single-cell level. Furthermore, we highlight the utility of using single-cell tracing and molecular barcoding methodologies in preclinical models to assess disease evolution and response to therapy. We discuss how the integration of single-cell profiling from patient samples can be used in conjunction with results from preclinical models to untangle the complexities of this disease and identify biomarkers of disease progression, including measures of intra-tumour heterogeneity themselves, and how enhancing this understanding has the potential to uncover new targetable vulnerabilities in breast cancer.
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Affiliation(s)
- Ioanna Mavrommati
- grid.18886.3fThe Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Flora Johnson
- grid.18886.3fThe Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Gloria V. Echeverria
- grid.39382.330000 0001 2160 926XLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX USA ,grid.39382.330000 0001 2160 926XDepartment of Medicine, Baylor College of Medicine, Houston, TX USA ,grid.39382.330000 0001 2160 926XDan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX USA ,grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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28
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Radziuviene G, Rasmusson A, Augulis R, Grineviciute RB, Zilenaite D, Laurinaviciene A, Ostapenko V, Laurinavicius A. Intratumoral Heterogeneity and Immune Response Indicators to Predict Overall Survival in a Retrospective Study of HER2-Borderline (IHC 2+) Breast Cancer Patients. Front Oncol 2021; 11:774088. [PMID: 34858854 PMCID: PMC8631965 DOI: 10.3389/fonc.2021.774088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
Breast cancer (BC) categorized as human epidermal growth factor receptor 2 (HER2) borderline [2+ by immunohistochemistry (IHC 2+)] presents challenges for the testing, frequently obscured by intratumoral heterogeneity (ITH). This leads to difficulties in therapy decisions. We aimed to establish prognostic models of overall survival (OS) of these patients, which take into account spatial aspects of ITH and tumor microenvironment by using hexagonal tiling analytics of digital image analysis (DIA). In particular, we assessed the prognostic value of Immunogradient indicators at the tumor–stroma interface zone (IZ) as a feature of antitumor immune response. Surgical excision samples stained for estrogen receptor (ER), progesterone receptor (PR), Ki67, HER2, and CD8 from 275 patients with HER2 IHC 2+ invasive ductal BC were used in the study. DIA outputs were subsampled by HexT for ITH quantification and tumor microenvironment extraction for Immunogradient indicators. Multiple Cox regression revealed HER2 membrane completeness (HER2 MC) (HR: 0.18, p = 0.0007), its spatial entropy (HR: 0.37, p = 0.0341), and ER contrast (HR: 0.21, p = 0.0449) as independent predictors of better OS, with worse OS predicted by pT status (HR: 6.04, p = 0.0014) in the HER2 non-amplified patients. In the HER2-amplified patients, HER2 MC contrast (HR: 0.35, p = 0.0367) and CEP17 copy number (HR: 0.19, p = 0.0035) were independent predictors of better OS along with worse OS predicted by pN status (HR: 4.75, p = 0.0018). In the non-amplified tumors, three Immunogradient indicators provided the independent prognostic value: CD8 density in the tumor aspect of the IZ and CD8 center of mass were associated with better OS (HR: 0.23, p = 0.0079 and 0.14, p = 0.0014, respectively), and CD8 density variance along the tumor edge predicted worse OS (HR: 9.45, p = 0.0002). Combining these three computational indicators of the CD8 cell spatial distribution within the tumor microenvironment augmented prognostic stratification of the patients. In the HER2-amplified group, CD8 cell density in the tumor aspect of the IZ was the only independent immune response feature to predict better OS (HR: 0.22, p = 0.0047). In conclusion, we present novel prognostic models, based on computational ITH and Immunogradient indicators of the IHC biomarkers, in HER2 IHC 2+ BC patients.
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Affiliation(s)
- Gedmante Radziuviene
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania.,Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Allan Rasmusson
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania.,Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Renaldas Augulis
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania.,Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Ruta Barbora Grineviciute
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
| | - Dovile Zilenaite
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania.,Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Aida Laurinaviciene
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania.,Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Valerijus Ostapenko
- Department of Breast Surgery and Oncology, National Cancer Institute, Vilnius, Lithuania
| | - Arvydas Laurinavicius
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania.,Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
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29
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Azzalini E, Barbazza R, Stanta G, Giorda G, Bortot L, Bartoletti M, Puglisi F, Canzonieri V, Bonin S. Histological patterns and intra-tumor heterogeneity as prognostication tools in high grade serous ovarian cancers. Gynecol Oncol 2021; 163:498-505. [PMID: 34602289 DOI: 10.1016/j.ygyno.2021.09.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 08/24/2021] [Accepted: 09/19/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVE High grade serous ovarian carcinoma (HGSOC) is the most common type of malignant ovarian neoplasm and the main cause of ovarian cancer related deaths worldwide. Although novel biomarkers such as homologous recombination deficiency testing have been implemented into the clinical decision-making algorithm since diagnosis, morphological classification and immunohistochemistry analysis are essential for diagnostic purpose. This study aims at identifying histologic and clinical features that can be predictive of patients' prognosis. METHODS Morphological and architectural characterization including SET (Solid-Endometroid-Transitional)/Classic features was carried out in a cohort of 234 patients analyzing 695 slides. From each slide tumor infiltrating lymphocyte (TILs), the presence of necrosis, the number of mitoses, the presence of psammoma bodies, giant cells and atypical mitoses were recorded. Morphological heterogeneity was quantified by the Shannon's diversity index (SDI) considering the percentage of each architectural pattern per patient's slide. RESULTS The frequency of architectural patterns and morphological variables varied with respect of the surgical strategy (primary debulking surgery vs interval surgery after neoadjuvant chemotherapy). HGSOCs exhibiting SET features had a longer overall as well as progression free survival. Among SET features, pseudo-endometrioid and transitional like patterns had the best outcome, while it was heterogenous for solid pattern, that had better outcome for BRCA 1 negative and less heterogeneous tumors. In patients submitted to neoadjuvant chemotherapy a higher intratumor heterogeneity as defined by SDI was a negative independent prognostic factor. CONCLUSIONS A comprehensive histological examination considering architectural patterns and their heterogeneity can help in prognostication of HGSOCs.
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Affiliation(s)
- Eros Azzalini
- DSM- Department of Medical Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy; IRCCS CRO Aviano-National Cancer Institute, Via Gallini 2, 33081 Aviano, Italy
| | - Renzo Barbazza
- DSM- Department of Medical Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
| | - Giorgio Stanta
- DSM- Department of Medical Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
| | - Giorgio Giorda
- IRCCS CRO Aviano-National Cancer Institute, Via Gallini 2, 33081 Aviano, Italy
| | - Lucia Bortot
- Unit of Medical Oncology and Cancer Prevention, Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, PN, Italy; DAME - Department of Medicine, University of Udine, Via Colugna 50, 33100 Udine, Italy
| | - Michele Bartoletti
- Unit of Medical Oncology and Cancer Prevention, Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, PN, Italy; DAME - Department of Medicine, University of Udine, Via Colugna 50, 33100 Udine, Italy
| | - Fabio Puglisi
- Unit of Medical Oncology and Cancer Prevention, Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, PN, Italy; DAME - Department of Medicine, University of Udine, Via Colugna 50, 33100 Udine, Italy
| | - Vincenzo Canzonieri
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, Via Gallini 2, 33081 Aviano, Italy; DSM- Department of Medical Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy.
| | - Serena Bonin
- DSM- Department of Medical Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy.
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Hao W, Li Y, Du B, Li X. Heterogeneity of estrogen receptor based on 18F-FES PET imaging in breast cancer patients. Clin Transl Imaging 2021. [DOI: 10.1007/s40336-021-00456-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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31
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Wortman JC, He TF, Solomon S, Zhang RZ, Rosario A, Wang R, Tu TY, Schmolze D, Yuan Y, Yost SE, Li X, Levine H, Atwal G, Lee PP, Yu CC. Spatial distribution of B cells and lymphocyte clusters as a predictor of triple-negative breast cancer outcome. NPJ Breast Cancer 2021; 7:84. [PMID: 34210991 PMCID: PMC8249408 DOI: 10.1038/s41523-021-00291-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
While tumor infiltration by CD8+ T cells is now widely accepted to predict outcomes, the clinical significance of intratumoral B cells is less clear. We hypothesized that spatial distribution rather than density of B cells within tumors may provide prognostic significance. We developed statistical techniques (fractal dimension differences and a box-counting method 'occupancy') to analyze the spatial distribution of tumor-infiltrating lymphocytes (TILs) in human triple-negative breast cancer (TNBC). Our results indicate that B cells in good outcome tumors (no recurrence within 5 years) are spatially dispersed, while B cells in poor outcome tumors (recurrence within 3 years) are more confined. While most TILs are located within the stroma, increased numbers of spatially dispersed lymphocytes within cancer cell islands are associated with a good prognosis. B cells and T cells often form lymphocyte clusters (LCs) identified via density-based clustering. LCs consist either of T cells only or heterotypic mixtures of B and T cells. Pure B cell LCs were negligible in number. Compared to tertiary lymphoid structures (TLS), LCs have fewer lymphocytes at lower densities. Both types of LCs are more abundant and more spatially dispersed in good outcomes compared to poor outcome tumors. Heterotypic LCs in good outcome tumors are smaller and more numerous compared to poor outcome. Heterotypic LCs are also closer to cancer islands in a good outcome, with LC size decreasing as they get closer to cancer cell islands. These results illuminate the significance of the spatial distribution of B cells and LCs within tumors.
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Affiliation(s)
- Juliana C Wortman
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, USA
| | - Ting-Fang He
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA, USA
| | - Shawn Solomon
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA, USA
| | - Robert Z Zhang
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA, USA
| | - Anthony Rosario
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA, USA
| | - Roger Wang
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA, USA
| | - Travis Y Tu
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA, USA
| | - Daniel Schmolze
- Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Yuan Yuan
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Susan E Yost
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Xuefei Li
- Department of Bioengineering and the Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Herbert Levine
- Department of Bioengineering and the Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Bioengineering and Department of Physics, Northeastern University, Boston, MA, USA
| | - Gurinder Atwal
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Peter P Lee
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA, USA.
| | - Clare C Yu
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, USA.
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Fitzgerald J, Higgins D, Mazo Vargas C, Watson W, Mooney C, Rahman A, Aspell N, Connolly A, Aura Gonzalez C, Gallagher W. Future of biomarker evaluation in the realm of artificial intelligence algorithms: application in improved therapeutic stratification of patients with breast and prostate cancer. J Clin Pathol 2021; 74:429-434. [PMID: 34117103 DOI: 10.1136/jclinpath-2020-207351] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 12/24/2022]
Abstract
Clinical workflows in oncology depend on predictive and prognostic biomarkers. However, the growing number of complex biomarkers contributes to costly and delayed decision-making in routine oncology care and treatment. As cancer is expected to rank as the leading cause of death and the single most important barrier to increasing life expectancy in the 21st century, there is a major emphasis on precision medicine, particularly individualisation of treatment through better prediction of patient outcome. Over the past few years, both surgical and pathology specialties have suffered cutbacks and a low uptake of pathology specialists means a solution is required to enable high-throughput screening and personalised treatment in this area to alleviate bottlenecks. Digital imaging in pathology has undergone an exponential period of growth. Deep-learning (DL) platforms for hematoxylin and eosin (H&E) image analysis, with preliminary artificial intelligence (AI)-based grading capabilities of specimens, can evaluate image characteristics which may not be visually apparent to a pathologist and offer new possibilities for better modelling of disease appearance and possibly improve the prediction of disease stage and patient outcome. Although digital pathology and AI are still emerging areas, they are the critical components for advancing personalised medicine. Integration of transcriptomic analysis, clinical information and AI-based image analysis is yet an uncultivated field by which healthcare professionals can make improved treatment decisions in cancer. This short review describes the potential application of integrative AI in offering better detection, quantification, classification, prognosis and prediction of breast and prostate cancer and also highlights the utilisation of machine learning systems in biomarker evaluation.
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Affiliation(s)
- Jenny Fitzgerald
- Invent Building, Deciphex Ltd, Dublin City University, Dublin, Ireland
| | - Debra Higgins
- OncoAssure, Nova UCD, Belfield Innovation Park, Dublin, Ireland
| | - Claudia Mazo Vargas
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - William Watson
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Catherine Mooney
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Arman Rahman
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Niamh Aspell
- Invent Building, Deciphex Ltd, Dublin City University, Dublin, Ireland
| | - Amy Connolly
- Invent Building, Deciphex Ltd, Dublin City University, Dublin, Ireland
| | - Claudia Aura Gonzalez
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - William Gallagher
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
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Abubakar M, Zhang J, Ahearn TU, Koka H, Guo C, Lawrence SM, Mutreja K, Figueroa JD, Ying J, Lissowska J, Lyu N, Garcia-Closas M, Yang XR. Tumor-Associated Stromal Cellular Density as a Predictor of Recurrence and Mortality in Breast Cancer: Results from Ethnically Diverse Study Populations. Cancer Epidemiol Biomarkers Prev 2021; 30:1397-1407. [PMID: 33952648 DOI: 10.1158/1055-9965.epi-21-0055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/08/2021] [Accepted: 04/26/2021] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Tumor-associated stroma is comprised of fibroblasts, tumor-infiltrating lymphocytes (TIL), macrophages, endothelial cells, and other cells that interactively influence tumor progression through inflammation and wound repair. Although gene-expression signatures reflecting wound repair predict breast cancer survival, it is unclear whether combined density of tumor-associated stromal cells, a morphologic proxy for inflammation and wound repair signatures on routine hematoxylin and eosin (H&E)-stained sections, is of prognostic relevance. METHODS By applying machine learning to digitized H&E-stained sections for 2,084 breast cancer patients from China (n = 596; 24-55 years), Poland (n = 810; 31-75 years), and the United States (n = 678; 55-78 years), we characterized tumor-associated stromal cellular density (SCD) as the percentage of tumor-stroma that is occupied by nucleated cells. Hazard ratios (HR) and 95% confidence intervals (CI) for associations between SCD and clinical outcomes [recurrence (China) and mortality (Poland and the United States)] were estimated using Cox proportional hazard regression, adjusted for clinical variables. RESULTS SCD was independently predictive of poor clinical outcomes in hormone receptor-positive (luminal) tumors from China [multivariable HR (95% CI)fourth(Q4) vs. first(Q1) quartile = 1.86 (1.06-3.26); P trend = 0.03], Poland [HR (95% CI)Q4 vs. Q1 = 1.80 (1.12-2.89); P trend = 0.01], and the United States [HR (95% CI)Q4 vs. Q1 = 2.42 (1.33-4.42); P trend = 0.002]. In general, SCD provided more prognostic information than most classic clinicopathologic factors, including grade, size, PR, HER2, IHC4, and TILs, predicting clinical outcomes irrespective of menopausal or lymph nodal status. SCD was not predictive of outcomes in hormone receptor-negative tumors. CONCLUSIONS Our findings support the independent prognostic value of tumor-associated SCD among ethnically diverse luminal breast cancer patients. IMPACT Assessment of tumor-associated SCD on standard H&E could help refine prognostic assessment and therapeutic decision making in luminal breast cancer.
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Affiliation(s)
- Mustapha Abubakar
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland.
| | - Jing Zhang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Thomas U Ahearn
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Hela Koka
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Changyuan Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Scott M Lawrence
- Molecular and Digital Pathology Laboratory, Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Karun Mutreja
- Molecular and Digital Pathology Laboratory, Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Jonine D Figueroa
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Scotland, UK
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jolanta Lissowska
- Epidemiology Unit, Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Ning Lyu
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Montserrat Garcia-Closas
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Xiaohong Rose Yang
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
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Li J, Kaneda MM, Ma J, Li M, Shepard RM, Patel K, Koga T, Sarver A, Furnari F, Xu B, Dhawan S, Ning J, Zhu H, Wu A, You G, Jiang T, Venteicher AS, Rich JN, Glass CK, Varner JA, Chen CC. PI3Kγ inhibition suppresses microglia/TAM accumulation in glioblastoma microenvironment to promote exceptional temozolomide response. Proc Natl Acad Sci U S A 2021; 118:e2009290118. [PMID: 33846242 PMCID: PMC8072253 DOI: 10.1073/pnas.2009290118] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Precision medicine in oncology leverages clinical observations of exceptional response. Toward an understanding of the molecular features that define this response, we applied an integrated, multiplatform analysis of RNA profiles derived from clinically annotated glioblastoma samples. This analysis suggested that specimens from exceptional responders are characterized by decreased accumulation of microglia/macrophages in the glioblastoma microenvironment. Glioblastoma-associated microglia/macrophages secreted interleukin 11 (IL11) to activate STAT3-MYC signaling in glioblastoma cells. This signaling induced stem cell states that confer enhanced tumorigenicity and resistance to the standard-of-care chemotherapy, temozolomide (TMZ). Targeting a myeloid cell restricted an isoform of phosphoinositide-3-kinase, phosphoinositide-3-kinase gamma isoform (PI3Kγ), by pharmacologic inhibition or genetic inactivation disrupted this signaling axis by reducing microglia/macrophage-associated IL11 secretion in the tumor microenvironment. Mirroring the clinical outcomes of exceptional responders, PI3Kγ inhibition synergistically enhanced the anti-neoplastic effects of TMZ in orthotopic murine glioblastoma models. Moreover, inhibition or genetic inactivation of PI3Kγ in murine glioblastoma models recapitulated expression profiles observed in clinical specimens isolated from exceptional responders. Our results suggest key contributions from tumor-associated microglia/macrophages in exceptional responses and highlight the translational potential for PI3Kγ inhibition as a glioblastoma therapy.
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Affiliation(s)
- Jie Li
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455
| | - Megan M Kaneda
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92037
| | - Jun Ma
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455
| | - Ming Li
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455
| | - Ryan M Shepard
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92037
| | - Kunal Patel
- Department of Neurosurgery, University of California, Los Angeles, CA 90095
| | - Tomoyuki Koga
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455
| | - Aaron Sarver
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455
| | - Frank Furnari
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA
| | - Beibei Xu
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455
| | - Sanjay Dhawan
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455
| | - Jianfang Ning
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455
| | - Hua Zhu
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455
- Department of Pediatrics, The First Hospital of China Medical University, Shenyang 110122, China
| | - Anhua Wu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang 110122, China
| | - Gan You
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Tao Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, China
| | | | - Jeremy N Rich
- Department of Medicine, Division of Regenerative Medicine, University of California San Diego, La Jolla, CA 92093
| | - Christopher K Glass
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Judith A Varner
- Department of Pathology, University of California San Diego, La Jolla, CA 92161
| | - Clark C Chen
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455;
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Baudoin NC, Bloomfield M. Karyotype Aberrations in Action: The Evolution of Cancer Genomes and the Tumor Microenvironment. Genes (Basel) 2021; 12:558. [PMID: 33921421 PMCID: PMC8068843 DOI: 10.3390/genes12040558] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/27/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer is a disease of cellular evolution. For this cellular evolution to take place, a population of cells must contain functional heterogeneity and an assessment of this heterogeneity in the form of natural selection. Cancer cells from advanced malignancies are genomically and functionally very different compared to the healthy cells from which they evolved. Genomic alterations include aneuploidy (numerical and structural changes in chromosome content) and polyploidy (e.g., whole genome doubling), which can have considerable effects on cell physiology and phenotype. Likewise, conditions in the tumor microenvironment are spatially heterogeneous and vastly different than in healthy tissues, resulting in a number of environmental niches that play important roles in driving the evolution of tumor cells. While a number of studies have documented abnormal conditions of the tumor microenvironment and the cellular consequences of aneuploidy and polyploidy, a thorough overview of the interplay between karyotypically abnormal cells and the tissue and tumor microenvironments is not available. Here, we examine the evidence for how this interaction may unfold during tumor evolution. We describe a bidirectional interplay in which aneuploid and polyploid cells alter and shape the microenvironment in which they and their progeny reside; in turn, this microenvironment modulates the rate of genesis for new karyotype aberrations and selects for cells that are most fit under a given condition. We conclude by discussing the importance of this interaction for tumor evolution and the possibility of leveraging our understanding of this interplay for cancer therapy.
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Affiliation(s)
- Nicolaas C. Baudoin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Biological Sciences and Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Mathew Bloomfield
- Department of Biological Sciences and Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
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Yu CC, Wortman JC, He TF, Solomon S, Zhang RZ, Rosario A, Wang R, Tu TY, Schmolze D, Yuan Y, Yost SE, Li X, Levine H, Atwal G, Lee PP. Physics approaches to the spatial distribution of immune cells in tumors. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2021; 84:022601. [PMID: 33232952 DOI: 10.1088/1361-6633/abcd7b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The goal of immunotherapy is to mobilize the immune system to kill cancer cells. Immunotherapy is more effective and, in general, the prognosis is better, when more immune cells infiltrate the tumor. We explore the question of whether the spatial distribution rather than just the density of immune cells in the tumor is important in forecasting whether cancer recurs. After reviewing previous work on this issue, we introduce a novel application of maximum entropy to quantify the spatial distribution of discrete point-like objects. We apply our approach to B and T cells in images of tumor tissue taken from triple negative breast cancer patients. We find that the immune cells are more spatially dispersed in good clinical outcome (no recurrence of cancer within at least 5 years of diagnosis) compared to poor clinical outcome (recurrence within 3 years of diagnosis). Our results highlight the importance of spatial distribution of immune cells within tumors with regard to clinical outcome, and raise new questions on their role in cancer recurrence.
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Affiliation(s)
- Clare C Yu
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697, United States of America
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Juliana C Wortman
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697, United States of America
| | - Ting-Fang He
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Shawn Solomon
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Robert Z Zhang
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Anthony Rosario
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Roger Wang
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Travis Y Tu
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Daniel Schmolze
- Department of Pathology, City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Yuan Yuan
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Susan E Yost
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Xuefei Li
- Department of Bioengineering and the Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, United States of America
| | - Herbert Levine
- Department of Bioengineering and the Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, United States of America
- Department of Bioengineering and Department of Physics, Northeastern University, Boston, MA 02115, United States of America
| | - Gurinder Atwal
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, United States of America
| | - Peter P Lee
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
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Desa DE, Strawderman RL, Wu W, Hill RL, Smid M, Martens JWM, Turner BM, Brown EB. Intratumoral heterogeneity of second-harmonic generation scattering from tumor collagen and its effects on metastatic risk prediction. BMC Cancer 2020; 20:1217. [PMID: 33302909 PMCID: PMC7731482 DOI: 10.1186/s12885-020-07713-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/06/2020] [Indexed: 12/21/2022] Open
Abstract
Background Metastases are the leading cause of breast cancer-related deaths. The tumor microenvironment impacts cancer progression and metastatic ability. Fibrillar collagen, a major extracellular matrix component, can be studied using the light scattering phenomenon known as second-harmonic generation (SHG). The ratio of forward- to backward-scattered SHG photons (F/B) is sensitive to collagen fiber internal structure and has been shown to be an independent prognostic indicator of metastasis-free survival time (MFS). Here we assess the effects of heterogeneity in the tumor matrix on the possible use of F/B as a prognostic tool. Methods SHG imaging was performed on sectioned primary tumor excisions from 95 untreated, estrogen receptor-positive, lymph node negative invasive ductal carcinoma patients. We identified two distinct regions whose collagen displayed different average F/B values, indicative of spatial heterogeneity: the cellular tumor bulk and surrounding tumor-stroma interface. To evaluate the impact of heterogeneity on F/B’s prognostic ability, we performed SHG imaging in the tumor bulk and tumor-stroma interface, calculated a 21-gene recurrence score (surrogate for OncotypeDX®, or S-ODX) for each patient and evaluated their combined prognostic ability. Results We found that F/B measured in tumor-stroma interface, but not tumor bulk, is prognostic of MFS using three methods to select pixels for analysis: an intensity threshold selected by a blinded observer, a histogram-based thresholding method, and an adaptive thresholding method. Using both regression trees and Random Survival Forests for MFS outcome, we obtained data-driven prediction rules that show F/B from tumor-stroma interface, but not tumor bulk, and S-ODX both contribute to predicting MFS in this patient cohort. We also separated patients into low-intermediate (S-ODX < 26) and high risk (S-ODX ≥26) groups. In the low-intermediate risk group, comprised of patients not typically recommended for adjuvant chemotherapy, we find that F/B from the tumor-stroma interface is prognostic of MFS and can identify a patient cohort with poor outcomes. Conclusions These data demonstrate that intratumoral heterogeneity in F/B values can play an important role in its possible use as a prognostic marker, and that F/B from tumor-stroma interface of primary tumor excisions may provide useful information to stratify patients by metastatic risk. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-020-07713-4.
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Affiliation(s)
- Danielle E Desa
- Department of Biomedical Engineering, Hajim School of Engineering and Applied Sciences, University of Rochester, Rochester, New York, USA
| | - Robert L Strawderman
- Department of Biostatistics and Computational Biology, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, New York, USA
| | - Wencheng Wu
- Goergen Institute for Data Science, University of Rochester, Rochester, New York, USA
| | | | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - J W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Bradley M Turner
- Department of Pathology and Laboratory Medicine, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, New York, USA
| | - Edward B Brown
- Department of Biomedical Engineering, Hajim School of Engineering and Applied Sciences, University of Rochester, Rochester, New York, USA.
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Valous NA, Moraleda RR, Jäger D, Zörnig I, Halama N. Interrogating the microenvironmental landscape of tumors with computational image analysis approaches. Semin Immunol 2020; 48:101411. [PMID: 33168423 DOI: 10.1016/j.smim.2020.101411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/13/2020] [Accepted: 09/04/2020] [Indexed: 02/07/2023]
Abstract
The tumor microenvironment is an interacting heterogeneous collection of cancer cells, resident as well as infiltrating host cells, secreted factors, and extracellular matrix proteins. With the growing importance of immunotherapies, it has become crucial to be able to characterize the composition and the functional orientation of the microenvironment. The development of novel computational image analysis methodologies may enable the robust quantification and localization of immune and related biomarker-expressing cells within the microenvironment. The aim of the review is to concisely highlight a selection of current and significant contributions pertinent to methodological advances coupled with biomedical or translational applications. A further aim is to concisely present computational advances that, to our knowledge, have currently very limited use for the assessment of the microenvironment but have the potential to enhance image analysis pipelines; on this basis, an example is shown for the detection and segmentation of cells of the microenvironment using a published pipeline and a public dataset. Finally, a general proposal is presented on the conceptual design of automation-optimized computational image analysis workflows in the biomedical and clinical domain.
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Affiliation(s)
- Nektarios A Valous
- Applied Tumor Immunity Clinical Cooperation Unit, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.
| | - Rodrigo Rojas Moraleda
- Applied Tumor Immunity Clinical Cooperation Unit, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.
| | - Dirk Jäger
- Applied Tumor Immunity Clinical Cooperation Unit, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Inka Zörnig
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Niels Halama
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; Division of Translational Immunotherapy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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Kantamneni H, Barkund S, Donzanti M, Martin D, Zhao X, He S, Riman RE, Tan MC, Pierce MC, Roth CM, Ganapathy V, Moghe PV. Shortwave infrared emitting multicolored nanoprobes for biomarker-specific cancer imaging in vivo. BMC Cancer 2020; 20:1082. [PMID: 33172421 PMCID: PMC7654009 DOI: 10.1186/s12885-020-07604-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 10/30/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The ability to detect tumor-specific biomarkers in real-time using optical imaging plays a critical role in preclinical studies aimed at evaluating drug safety and treatment response. In this study, we engineered an imaging platform capable of targeting different tumor biomarkers using a multi-colored library of nanoprobes. These probes contain rare-earth elements that emit light in the short-wave infrared (SWIR) wavelength region (900-1700 nm), which exhibits reduced absorption and scattering compared to visible and NIR, and are rendered biocompatible by encapsulation in human serum albumin. The spectrally distinct emissions of the holmium (Ho), erbium (Er), and thulium (Tm) cations that constitute the cores of these nanoprobes make them attractive candidates for optical molecular imaging of multiple disease biomarkers. METHODS SWIR-emitting rare-earth-doped albumin nanocomposites (ReANCs) were synthesized using controlled coacervation, with visible light-emitting fluorophores additionally incorporated during the crosslinking phase for validation purposes. Specifically, HoANCs, ErANCs, and TmANCs were co-labeled with rhodamine-B, FITC, and Alexa Fluor 647 dyes respectively. These Rh-HoANCs, FITC-ErANCs, and 647-TmANCs were further conjugated with the targeting ligands daidzein, AMD3100, and folic acid respectively. Binding specificities of each nanoprobe to distinct cellular subsets were established by in vitro uptake studies. Quantitative whole-body SWIR imaging of subcutaneous tumor bearing mice was used to validate the in vivo targeting ability of these nanoprobes. RESULTS Each of the three ligand-functionalized nanoprobes showed significantly higher uptake in the targeted cell line compared to untargeted probes. Increased accumulation of tumor-specific nanoprobes was also measured relative to untargeted probes in subcutaneous tumor models of breast (4175 and MCF-7) and ovarian cancer (SKOV3). Preferential accumulation of tumor-specific nanoprobes was also observed in tumors overexpressing targeted biomarkers in mice bearing molecularly-distinct bilateral subcutaneous tumors, as evidenced by significantly higher signal intensities on SWIR imaging. CONCLUSIONS The results from this study show that tumors can be detected in vivo using a set of targeted multispectral SWIR-emitting nanoprobes. Significantly, these nanoprobes enabled imaging of biomarkers in mice bearing bilateral tumors with distinct molecular phenotypes. The findings from this study provide a foundation for optical molecular imaging of heterogeneous tumors and for studying the response of these complex lesions to targeted therapy.
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Affiliation(s)
- Harini Kantamneni
- Department of Chemical & Biochemical Engineering, Rutgers University, 98 Brett Road, Piscataway, NJ, 08854, USA
| | - Shravani Barkund
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ, 08854, USA
| | - Michael Donzanti
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ, 08854, USA
| | - Daniel Martin
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ, 08854, USA
| | - Xinyu Zhao
- Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Rd, Singapore, 487372, Singapore
| | - Shuqing He
- Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Rd, Singapore, 487372, Singapore
| | - Richard E Riman
- Department of Materials Science and Engineering, Rutgers University, 607 Taylor Road, Piscataway, NJ, 08854, USA
| | - Mei Chee Tan
- Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Rd, Singapore, 487372, Singapore
| | - Mark C Pierce
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ, 08854, USA
| | - Charles M Roth
- Department of Chemical & Biochemical Engineering, Rutgers University, 98 Brett Road, Piscataway, NJ, 08854, USA.,Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ, 08854, USA
| | - Vidya Ganapathy
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ, 08854, USA.
| | - Prabhas V Moghe
- Department of Chemical & Biochemical Engineering, Rutgers University, 98 Brett Road, Piscataway, NJ, 08854, USA. .,Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ, 08854, USA.
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Wortman JC, He TF, Rosario A, Wang R, Schmolze D, Yuan Y, Yost SE, Li X, Levine H, Atwal G, Lee P, Yu CC. Occupancy and Fractal Dimension Analyses of the Spatial Distribution of Cytotoxic (CD8+) T Cells Infiltrating the Tumor Microenvironment in Triple Negative Breast Cancer. ACTA ACUST UNITED AC 2020. [DOI: 10.1142/s1793048020500022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Favorable outcomes have been associated with high densities of tumor infiltrating lymphocytes (TILs) such as cytotoxic ([Formula: see text]) T cells. However, the clinical significance of the spatial distribution of TILs is less well understood. We have developed novel statistical techniques to characterize the spatial distribution of TILs at various length scales. These include a box counting method that we call “occupancy” and novel applications of fractal dimensions. We apply these techniques to the spatial distribution of [Formula: see text] T cells in the tumor microenvironment of tissue resected from 35 triple negative breast cancer patients. We find that there is a distinct difference in the spatial distribution of [Formula: see text] T cells between good clinical outcome (no recurrence within at least 5 years of diagnosis) and poor clinical outcome (recurrence within 3 years of diagnosis). The statistical significance of the difference between good and poor outcome in the occupancy, fractal dimension (FD), and FD difference of [Formula: see text] T cells is comparable to that of the [Formula: see text] T cell density. Even when we randomly exclude some of the cells so that the images have the same cell density, we still find that the fractal dimension at short length scales is correlated with cancer recurrence, implying that the actual spatial distribution of [Formula: see text] cells, and not just the [Formula: see text] cell density, is associated with clinical outcome. The occupancy and FD difference indicate that the [Formula: see text] T cells are more spatially dispersed in good outcome and more aggregated in poor outcome. We discuss possible interpretations.
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Affiliation(s)
- Juliana C. Wortman
- Department of Physics and Astronomy, University of California, Irvine 92697, CA, USA
| | - Ting-Fang He
- Cancer Immunotherapeutics & Tumor Immunology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte 91010, CA, USA
| | - Anthony Rosario
- Cancer Immunotherapeutics & Tumor Immunology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte 91010, CA, USA
| | - Roger Wang
- Cancer Immunotherapeutics & Tumor Immunology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte 91010, CA, USA
| | - Daniel Schmolze
- Department of Pathology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte 91010, CA, USA
| | - Yuan Yuan
- Department of Medical Oncology and Molecular Therapeutics, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte 91010, CA, USA
| | - Susan E. Yost
- Department of Medical Oncology and Molecular Therapeutics, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte 91010, CA, USA
| | - Xuefei Li
- Department of Bioengineering and the Center for Theoretical Biological Physics, Rice University, Houston 77030, TX, USA
| | - Herbert Levine
- Department of Bioengineering and the Center for Theoretical Biological Physics, Rice University, Houston 77030, TX, USA
| | - Gurinder Atwal
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Peter Lee
- Cancer Immunotherapeutics & Tumor Immunology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte 91010, CA, USA
| | - Clare C. Yu
- Department of Physics and Astronomy, University of California, Irvine 92697, CA, USA
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Rahman A, Jahangir C, Lynch SM, Alattar N, Aura C, Russell N, Lanigan F, Gallagher WM. Advances in tissue-based imaging: impact on oncology research and clinical practice. Expert Rev Mol Diagn 2020; 20:1027-1037. [PMID: 32510287 DOI: 10.1080/14737159.2020.1770599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Tissue-based imaging has emerged as a critical tool in translational cancer research and is rapidly gaining traction within a clinical context. Significant progress has been made in the digital pathology arena, particularly in respect of brightfield and fluorescent imaging. Critically, the cellular context of molecular alterations occurring at DNA, RNA, or protein level within tumor tissue is now being more fully appreciated. Moreover, the emergence of novel multi-marker imaging approaches can now provide unprecedented insights into the tumor microenvironment, including the potential interplay between various cell types. AREAS COVERED This review summarizes the recent developments within the field of tissue-based imaging, centering on the application of these approaches in oncology research and clinical practice. EXPERT OPINION Significant advances have been made in digital pathology during the last 10 years. These include the use of quantitative image analysis algorithms, predictive artificial intelligence (AI) on large datasets of H&E images, and quantification of fluorescence multiplexed tissue imaging data. We believe that new methodologies that can integrate AI-derived histologic data with omic data, together with other forms of imaging data (such as radiologic image data), will enhance our ability to deliver better diagnostics and treatment decisions to the cancer patient.
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Affiliation(s)
- Arman Rahman
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin , Dublin, Ireland
| | - Chowdhury Jahangir
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin , Dublin, Ireland
| | - Seodhna M Lynch
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin , Dublin, Ireland
| | - Nebras Alattar
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin , Dublin, Ireland
| | - Claudia Aura
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin , Dublin, Ireland
| | - Niamh Russell
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin , Dublin, Ireland
| | - Fiona Lanigan
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin , Dublin, Ireland
| | - William M Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin , Dublin, Ireland.,OncoMark Limited , Dublin, Ireland
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Amgad M, Stovgaard ES, Balslev E, Thagaard J, Chen W, Dudgeon S, Sharma A, Kerner JK, Denkert C, Yuan Y, AbdulJabbar K, Wienert S, Savas P, Voorwerk L, Beck AH, Madabhushi A, Hartman J, Sebastian MM, Horlings HM, Hudeček J, Ciompi F, Moore DA, Singh R, Roblin E, Balancin ML, Mathieu MC, Lennerz JK, Kirtani P, Chen IC, Braybrooke JP, Pruneri G, Demaria S, Adams S, Schnitt SJ, Lakhani SR, Rojo F, Comerma L, Badve SS, Khojasteh M, Symmans WF, Sotiriou C, Gonzalez-Ericsson P, Pogue-Geile KL, Kim RS, Rimm DL, Viale G, Hewitt SM, Bartlett JMS, Penault-Llorca F, Goel S, Lien HC, Loibl S, Kos Z, Loi S, Hanna MG, Michiels S, Kok M, Nielsen TO, Lazar AJ, Bago-Horvath Z, Kooreman LFS, van der Laak JAWM, Saltz J, Gallas BD, Kurkure U, Barnes M, Salgado R, Cooper LAD. Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group. NPJ Breast Cancer 2020; 6:16. [PMID: 32411818 PMCID: PMC7217824 DOI: 10.1038/s41523-020-0154-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/18/2020] [Indexed: 02/07/2023] Open
Abstract
Assessment of tumor-infiltrating lymphocytes (TILs) is increasingly recognized as an integral part of the prognostic workflow in triple-negative (TNBC) and HER2-positive breast cancer, as well as many other solid tumors. This recognition has come about thanks to standardized visual reporting guidelines, which helped to reduce inter-reader variability. Now, there are ripe opportunities to employ computational methods that extract spatio-morphologic predictive features, enabling computer-aided diagnostics. We detail the benefits of computational TILs assessment, the readiness of TILs scoring for computational assessment, and outline considerations for overcoming key barriers to clinical translation in this arena. Specifically, we discuss: 1. ensuring computational workflows closely capture visual guidelines and standards; 2. challenges and thoughts standards for assessment of algorithms including training, preanalytical, analytical, and clinical validation; 3. perspectives on how to realize the potential of machine learning models and to overcome the perceptual and practical limits of visual scoring.
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Affiliation(s)
- Mohamed Amgad
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA USA
| | | | - Eva Balslev
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Herlev, Denmark
| | - Jeppe Thagaard
- DTU Compute, Department of Applied Mathematics, Technical University of Denmark, Lyngby, Denmark
- Visiopharm A/S, Hørsholm, Denmark
| | - Weijie Chen
- FDA/CDRH/OSEL/Division of Imaging, Diagnostics, and Software Reliability, Silver Spring, MD USA
| | - Sarah Dudgeon
- FDA/CDRH/OSEL/Division of Imaging, Diagnostics, and Software Reliability, Silver Spring, MD USA
| | - Ashish Sharma
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA USA
| | | | - Carsten Denkert
- Institut für Pathologie, Universitätsklinikum Gießen und Marburg GmbH, Standort Marburg, Philipps-Universität Marburg, Marburg, Germany
- Institute of Pathology, Philipps-University Marburg, Marburg, Germany
- German Cancer Consortium (DKTK), Partner Site Charité, Berlin, Germany
| | - Yinyin Yuan
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Khalid AbdulJabbar
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Stephan Wienert
- Institut für Pathologie, Universitätsklinikum Gießen und Marburg GmbH, Standort Marburg, Philipps-Universität Marburg, Marburg, Germany
| | - Peter Savas
- Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, University of Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | - Leonie Voorwerk
- Department of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Anant Madabhushi
- Case Western Reserve University, Department of Biomedical Engineering, Cleveland, OH USA
- Louis Stokes Cleveland Veterans Administration Medical Center, Cleveland, OH USA
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, Solna, Sweden
| | - Manu M. Sebastian
- Departments of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Hugo M. Horlings
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jan Hudeček
- Department of Research IT, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Francesco Ciompi
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - David A. Moore
- Department of Pathology, UCL Cancer Institute, London, UK
| | - Rajendra Singh
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Elvire Roblin
- Université Paris-Saclay, Univ. Paris-Sud, Villejuif, France
| | - Marcelo Luiz Balancin
- Department of Pathology, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Marie-Christine Mathieu
- Department of Medical Biology and Pathology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Jochen K. Lennerz
- Department of Pathology, Massachusetts General Hospital, Boston, MA USA
| | - Pawan Kirtani
- Department of Histopathology, Manipal Hospitals Dwarka, New Delhi, India
| | - I-Chun Chen
- Department of Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Jeremy P. Braybrooke
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Department of Medical Oncology, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Giancarlo Pruneri
- Pathology Department, Fondazione IRCCS Istituto Nazionale Tumori and University of Milan, School of Medicine, Milan, Italy
| | | | - Sylvia Adams
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY USA
| | - Stuart J. Schnitt
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA USA
| | - Sunil R. Lakhani
- The University of Queensland Centre for Clinical Research and Pathology Queensland, Brisbane, Australia
| | - Federico Rojo
- Pathology Department, CIBERONC-Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
- GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain
| | - Laura Comerma
- Pathology Department, CIBERONC-Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
- GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain
| | - Sunil S. Badve
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN USA
| | | | - W. Fraser Symmans
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium
- ULB-Cancer Research Center (U-CRC) Université Libre de Bruxelles, Brussels, Belgium
| | - Paula Gonzalez-Ericsson
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN USA
| | | | | | - David L. Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, CT USA
| | - Giuseppe Viale
- Department of Pathology, IEO, European Institute of Oncology IRCCS & State University of Milan, Milan, Italy
| | - Stephen M. Hewitt
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - John M. S. Bartlett
- Ontario Institute for Cancer Research, Toronto, ON Canada
- Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, UK
| | - Frédérique Penault-Llorca
- Department of Pathology and Molecular Pathology, Centre Jean Perrin, Clermont-Ferrand, France
- UMR INSERM 1240, Universite Clermont Auvergne, Clermont-Ferrand, France
| | - Shom Goel
- Victorian Comprehensive Cancer Centre building, Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Huang-Chun Lien
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Sibylle Loibl
- German Breast Group, c/o GBG-Forschungs GmbH, Neu-Isenburg, Germany
| | - Zuzana Kos
- Department of Pathology, BC Cancer, Vancouver, British Columbia Canada
| | - Sherene Loi
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Matthew G. Hanna
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Stefan Michiels
- Gustave Roussy, Universite Paris-Saclay, Villejuif, France
- Université Paris-Sud, Institut National de la Santé et de la Recherche Médicale, Villejuif, France
| | - Marleen Kok
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Alexander J. Lazar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | | | - Loes F. S. Kooreman
- GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
- Department of Pathology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Jeroen A. W. M. van der Laak
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
- Center for Medical Image Science and Visualization, Linköping University, Linköping, Sweden
| | - Joel Saltz
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY USA
| | - Brandon D. Gallas
- FDA/CDRH/OSEL/Division of Imaging, Diagnostics, and Software Reliability, Silver Spring, MD USA
| | - Uday Kurkure
- Roche Tissue Diagnostics, Digital Pathology, Santa Clara, CA USA
| | - Michael Barnes
- Roche Diagnostics Information Solutions, Belmont, CA USA
| | - Roberto Salgado
- Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, University of Melbourne, Victoria, Australia
- Department of Pathology, GZA-ZNA Ziekenhuizen, Antwerp, Belgium
| | - Lee A. D. Cooper
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL USA
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Lu Z, Xu S, Shao W, Wu Y, Zhang J, Han Z, Feng Q, Huang K. Deep-Learning-Based Characterization of Tumor-Infiltrating Lymphocytes in Breast Cancers From Histopathology Images and Multiomics Data. JCO Clin Cancer Inform 2020; 4:480-490. [PMID: 32453636 PMCID: PMC7265782 DOI: 10.1200/cci.19.00126] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2020] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Tumor-infiltrating lymphocytes (TILs) and their spatial characterizations on whole-slide images (WSIs) of histopathology sections have become crucial in diagnosis, prognosis, and treatment response prediction for different cancers. However, fully automatic assessment of TILs on WSIs currently remains a great challenge because of the heterogeneity and large size of WSIs. We present an automatic pipeline based on a cascade-training U-net to generate high-resolution TIL maps on WSIs. METHODS We present global cell-level TIL maps and 43 quantitative TIL spatial image features for 1,000 WSIs of The Cancer Genome Atlas patients with breast cancer. For more specific analysis, all the patients were divided into three subtypes, namely, estrogen receptor (ER)-positive, ER-negative, and triple-negative groups. The associations between TIL scores and gene expression and somatic mutation were examined separately in three breast cancer subtypes. Both univariate and multivariate survival analyses were performed on 43 TIL image features to examine the prognostic value of TIL spatial patterns in different breast cancer subtypes. RESULTS The TIL score was in strong association with immune response pathway and genes (eg, programmed death-1 and CLTA4). Different breast cancer subtypes showed TIL score in association with mutations from different genes suggesting that different genetic alterations may lead to similar phenotypes. Spatial TIL features that represent density and distribution of TIL clusters were important indicators of the patient outcomes. CONCLUSION Our pipeline can facilitate computational pathology-based discovery in cancer immunology and research on immunotherapy. Our analysis results are available for the research community to generate new hypotheses and insights on breast cancer immunology and development.
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Affiliation(s)
- Zixiao Lu
- Guangdong Provincial Key Laboratory of Medical Image Processing, School of Biomedical Engineering, Southern Medical University, Guangzhou, People’s Republic of China
| | - Siwen Xu
- Institute of Intelligent System and Bioinformatics, College of Automation, Harbin Engineering University, Harbin, Heilongjiang, People’s Republic of China
| | - Wei Shao
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Yi Wu
- Wormpex AI Research, Bellevue, WA
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Zhi Han
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Qianjin Feng
- Guangdong Provincial Key Laboratory of Medical Image Processing, School of Biomedical Engineering, Southern Medical University, Guangzhou, People’s Republic of China
| | - Kun Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
- Regenstrief Institute, Indianapolis, IN
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Computational analysis of pathological images enables a better diagnosis of TFE3 Xp11.2 translocation renal cell carcinoma. Nat Commun 2020; 11:1778. [PMID: 32286325 PMCID: PMC7156652 DOI: 10.1038/s41467-020-15671-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 03/23/2020] [Indexed: 12/17/2022] Open
Abstract
TFE3 Xp11.2 translocation renal cell carcinoma (TFE3-RCC) generally progresses more aggressively compared with other RCC subtypes, but it is challenging to diagnose TFE3-RCC by traditional visual inspection of pathological images. In this study, we collect hematoxylin and eosin- stained histopathology whole-slide images of 74 TFE3-RCC cases (the largest cohort to date) and 74 clear cell RCC cases (ccRCC, the most common RCC subtype) with matched gender and tumor grade. An automatic computational pipeline is implemented to extract image features. Comparative study identifies 52 image features with significant differences between TFE3-RCC and ccRCC. Machine learning models are built to distinguish TFE3-RCC from ccRCC. Tests of the classification models on an external validation set reveal high accuracy with areas under ROC curve ranging from 0.842 to 0.894. Our results suggest that automatically derived image features can capture subtle morphological differences between TFE3-RCC and ccRCC and contribute to a potential guideline for TFE3-RCC diagnosis. Translocation renal cell carcinoma is an aggressive form of renal cancer that is often misdiagnosed to other subtypes. Here the authors demonstrated that by using machine learning and H&E stained whole-slide images, an accurate diagnose of this particular type of renal cancer can be achieved.
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Zou MX, Zheng BW, Liu FS, Wang XB, Hu JR, Huang W, Dai ZH, Zhang QS, Liu FB, Zhong H, Jiang Y, She XL, Li XB, Lv GH, Li J. The Relationship Between Tumor-Stroma Ratio, the Immune Microenvironment, and Survival in Patients With Spinal Chordoma. Neurosurgery 2020; 85:E1095-E1110. [PMID: 31501892 DOI: 10.1093/neuros/nyz333] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/23/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Currently, little is known about the clinical relevance of tumor-stroma ratio (TSR) in chordoma and data discussing the relationship between TSR and immune status of chordoma are lacking. OBJECTIVE To characterize TSR distribution in spinal chordoma, and investigated its correlation with clinicopathologic or immunological features of patients and outcome. METHODS TSR was assessed visually on hematoxylin and eosin-stained sections from 54 tumor specimens by 2 independent pathologists. Multiplex immunofluorescence was used to quantify the expression levels of microvessel density, Ki-67, Brachyury, and tumor as well as stromal PD-L1. Tumor immunity status including the Immunoscore and densities of tumor-infiltrating lymphocytes (TILs) subtypes were obtained from our published data and reanalyzed. RESULTS Bland-Altman plot showed no difference between mean TSR derived from the two observers. TSR was positively associated with stromal PD-L1 expression, the Immunoscore and CD3+ as well as CD4+ TILs density, but negatively correlated with tumor microvessel density, Ki-67 index, surrounding muscle invasion by tumor and number of Foxp3+ and PD-1+ TILs. Low TSR independently predicted poor local recurrence-free survival and overall survival. Moreover, patients with low TSR and low Immunoscore chordoma phenotype were associated with the worst survival. More importantly, combined TSR and Immunoscore accurately reflected prognosis and enhanced the ability of TSR or Immunoscore alone for outcome prediction. CONCLUSION These data reveal the significant impact of TSR on tumor progression and immunological response of patients. Subsequent use of agents targeting the stroma compartment may be an effective strategy to treat chordoma especially in combination with immune-based drugs.
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Affiliation(s)
- Ming-Xiang Zou
- Department of Spine Surgery, The Second Xiangya Hospital, Central South, University, Changsha, China
| | - Bo-Wen Zheng
- Department of Spine Surgery, The Second Xiangya Hospital, Central South, University, Changsha, China
| | - Fu-Sheng Liu
- Department of Spine Surgery, The Second Xiangya Hospital, Central South, University, Changsha, China
| | - Xiao-Bin Wang
- Department of Spine Surgery, The Second Xiangya Hospital, Central South, University, Changsha, China
| | - Jia-Rui Hu
- Department of Spine Surgery, The Second Xiangya Hospital, Central South, University, Changsha, China
| | - Wei Huang
- Institute of Precision Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Zhe-Hao Dai
- Department of Spine Surgery, The Second Xiangya Hospital, Central South, University, Changsha, China
| | - Qian-Shi Zhang
- Department of Spine Surgery, The Second Xiangya Hospital, Central South, University, Changsha, China
| | - Fu-Bing Liu
- Department of Spine Surgery, The Second Xiangya Hospital, Central South, University, Changsha, China
| | - Hua Zhong
- Department of Orthopedics Surgery, Central Hospital of Yi Yang, Yiyang, China
| | - Yi Jiang
- Department of Pathology, The Second Xiangya Hospital, Central South, University, Changsha, China
| | - Xiao-Ling She
- Department of Pathology, The Second Xiangya Hospital, Central South, University, Changsha, China
| | - Xiao-Bing Li
- Department of Spine Surgery, The Second Xiangya Hospital, Central South, University, Changsha, China
| | - Guo-Hua Lv
- Department of Spine Surgery, The Second Xiangya Hospital, Central South, University, Changsha, China
| | - Jing Li
- Department of Spine Surgery, The Second Xiangya Hospital, Central South, University, Changsha, China
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Karami E, Ruschin M, Soliman H, Sahgal A, Stanisz GJ, Sadeghi-Naini A. An MR Radiomics Framework for Predicting the Outcome of Stereotactic Radiation Therapy in Brain Metastasis. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2020; 2019:1022-1025. [PMID: 31946067 DOI: 10.1109/embc.2019.8856558] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Despite recent advances in cancer treatment, patients with brain metastasis still suffer from poor overall survival (OS) after standard treatment. Predicting the treatment outcome before or early after the treatment can potentially assist the physicians in improving the therapy outcome by adjusting a standard treatment on an individual patient basis. In this study, a data-driven computational framework was proposed and investigated to predict the local control/failure (LC/LF) outcome in patients with brain metastasis treated with hypo-fractionated stereotactic radiation therapy (SRT). The framework extracted several geometrical and textural features from the magnetic resonance (MR) images of the tumour and edema regions acquired for 38 patients. Subsequent to a multi-step feature reduction/selection, a quantitative MR biomarker consisting of two features was constructed. A support vector machine classifier was used for outcome prediction using the constructed MR biomarker. The bootstrap .632+ and leave-one-patient-out cross-validation methods were used to assess the model's performance. The results indicated that the outcome of LF after SRT could be predicted with an area under the curve of 0.80 and a cross-validated accuracy of 82%. The results obtained implied a good potential of the proposed framework for local outcome prediction in patients with brain metastasis treated with SRT and encourage further investigations on a larger cohort of patients.
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Karami E, Soliman H, Ruschin M, Sahgal A, Myrehaug S, Tseng CL, Czarnota GJ, Jabehdar-Maralani P, Chugh B, Lau A, Stanisz GJ, Sadeghi-Naini A. Quantitative MRI Biomarkers of Stereotactic Radiotherapy Outcome in Brain Metastasis. Sci Rep 2019; 9:19830. [PMID: 31882597 PMCID: PMC6934477 DOI: 10.1038/s41598-019-56185-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 12/08/2019] [Indexed: 02/08/2023] Open
Abstract
About 20–40% of cancer patients develop brain metastases, causing significant morbidity and mortality. Stereotactic radiation treatment is an established option that delivers high dose radiation to the target while sparing the surrounding normal tissue. However, up to 20% of metastatic brain tumours progress despite stereotactic treatment, and it can take months before it is evident on follow-up imaging. An early predictor of radiation therapy outcome in terms of tumour local failure (LF) is crucial, and can facilitate treatment adjustments or allow for early salvage treatment. In this study, an MR-based radiomics framework was proposed to derive and investigate quantitative MRI (qMRI) biomarkers for the outcome of LF in brain metastasis patients treated with hypo-fractionated stereotactic radiation therapy (SRT). The qMRI biomarkers were constructed through a multi-step feature extraction/reduction/selection framework using the conventional MR imaging data acquired from 100 patients (133 lesions), and were applied in conjunction with machine learning techniques for outcome prediction and risk assessment. The results indicated that the majority of the features in the optimal qMRI biomarkers characterize the heterogeneity in the surrounding regions of tumour including edema and tumour/lesion margins. The optimal qMRI biomarker consisted of five features that predict the outcome of LF with an area under the curve (AUC) of 0.79, and a cross-validated sensitivity and specificity of 81% and 79%, respectively. The Kaplan-Meier analyses showed a statistically significant difference in local control (p-value < 0.0001) and overall survival (p = 0.01). Findings from this study are a step towards using qMRI for early prediction of local failure in brain metastasis patients treated with SRT. This may facilitate early adjustments in treatment, such as surgical resection or salvage radiation, that can potentially improve treatment outcomes. Investigations on larger cohorts of patients are, however, required for further validation of the technique.
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Affiliation(s)
- Elham Karami
- Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Hany Soliman
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Mark Ruschin
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Arjun Sahgal
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Sten Myrehaug
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Chia-Lin Tseng
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Gregory J Czarnota
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | | | - Brige Chugh
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Angus Lau
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Greg J Stanisz
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Neurosurgery and Pediatric Neurosurgery, Medical University, Lublin, Poland
| | - Ali Sadeghi-Naini
- Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, ON, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. .,Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada. .,Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.
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Polak KL, Chernosky NM, Smigiel JM, Tamagno I, Jackson MW. Balancing STAT Activity as a Therapeutic Strategy. Cancers (Basel) 2019; 11:cancers11111716. [PMID: 31684144 PMCID: PMC6895889 DOI: 10.3390/cancers11111716] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/23/2019] [Accepted: 10/31/2019] [Indexed: 12/13/2022] Open
Abstract
Driven by dysregulated IL-6 family member cytokine signaling in the tumor microenvironment (TME), aberrant signal transducer and activator of transcription (STAT3) and (STAT5) activation have been identified as key contributors to tumorigenesis. Following transformation, persistent STAT3 activation drives the emergence of mesenchymal/cancer-stem cell (CSC) properties, important determinants of metastatic potential and therapy failure. Moreover, STAT3 signaling within tumor-associated macrophages and neutrophils drives secretion of factors that facilitate metastasis and suppress immune cell function. Persistent STAT5 activation is responsible for cancer cell maintenance through suppression of apoptosis and tumor suppressor signaling. Furthermore, STAT5-mediated CD4+/CD25+ regulatory T cells (Tregs) have been implicated in suppression of immunosurveillance. We discuss these roles for STAT3 and STAT5, and weigh the attractiveness of different modes of targeting each cancer therapy. Moreover, we discuss how anti-tumorigenic STATs, including STAT1 and STAT2, may be leveraged to suppress the pro-tumorigenic functions of STAT3/STAT5 signaling.
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Affiliation(s)
- Kelsey L Polak
- Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA.
| | - Noah M Chernosky
- Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA.
| | - Jacob M Smigiel
- Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA.
| | - Ilaria Tamagno
- Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA.
| | - Mark W Jackson
- Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA.
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Besse HC, Barten-van Rijbroek AD, van der Wurff-Jacobs KMG, Bos C, Moonen CTW, Deckers R. Tumor Drug Distribution after Local Drug Delivery by Hyperthermia, In Vivo. Cancers (Basel) 2019; 11:cancers11101512. [PMID: 31600958 PMCID: PMC6826934 DOI: 10.3390/cancers11101512] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/27/2019] [Accepted: 10/02/2019] [Indexed: 02/02/2023] Open
Abstract
Tumor drug distribution and concentration are important factors for effective tumor treatment. A promising method to enhance the distribution and the concentration of the drug in the tumor is to encapsulate the drug in a temperature sensitive liposome. The aim of this study was to investigate the tumor drug distribution after treatment with various injected doses of different liposomal formulations of doxorubicin, ThermoDox (temperature sensitive liposomes) and DOXIL (non-temperature sensitive liposomes), and free doxorubicin at macroscopic and microscopic levels. Only ThermoDox treatment was combined with hyperthermia. Experiments were performed in mice bearing a human fibrosarcoma. At low and intermediate doses, the largest growth delay was obtained with ThermoDox, and at the largest dose, the largest growth delay was obtained with DOXIL. On histology, tumor areas with increased doxorubicin concentration correlated with decreased cell proliferation, and substantial variations in doxorubicin heterogeneity were observed. ThermoDox treatment resulted in higher tissue drug levels than DOXIL and free doxorubicin for the same dose. A relation with the distance to the vasculature was shown, but vessel perfusion was not always sufficient to determine doxorubicin delivery. Our results indicate that tumor drug distribution is an important factor for effective tumor treatment and that its dependence on delivery formulation merits further systemic investigation.
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Affiliation(s)
- Helena C Besse
- Center of Imaging Sciences, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands.
| | | | - Kim M G van der Wurff-Jacobs
- Center of Imaging Sciences, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Clemens Bos
- Center of Imaging Sciences, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands.
| | - Chrit T W Moonen
- Center of Imaging Sciences, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Roel Deckers
- Center of Imaging Sciences, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands.
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50
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de Santiago I, Yau C, Heij L, Middleton MR, Markowetz F, Grabsch HI, Dustin ML, Sivakumar S. Immunophenotypes of pancreatic ductal adenocarcinoma: Meta-analysis of transcriptional subtypes. Int J Cancer 2019; 145:1125-1137. [PMID: 30720864 PMCID: PMC6767191 DOI: 10.1002/ijc.32186] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 01/21/2019] [Indexed: 01/08/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common malignancy of the pancreas and has one of the highest mortality rates of any cancer type with a 5-year survival rate of <5%. Recent studies of PDAC have provided several transcriptomic classifications based on separate analyses of individual patient cohorts. There is a need to provide a unified transcriptomic PDAC classification driven by therapeutically relevant biologic rationale to inform future treatment strategies. Here, we used an integrative meta-analysis of 353 patients from four different studies to derive a PDAC classification based on immunologic parameters. This consensus clustering approach indicated transcriptomic signatures based on immune infiltrate classified as adaptive, innate and immune-exclusion subtypes. This reveals the existence of microenvironmental interpatient heterogeneity within PDAC and could serve to drive novel therapeutic strategies in PDAC including immune modulation approaches to treating this disease.
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Affiliation(s)
- Ines de Santiago
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Christopher Yau
- Centre for Computational Biology, Institute of Cancer and Genomic SciencesUniversity of BirminghamBirminghamUnited Kingdom
| | - Lara Heij
- GROW School for Oncology and Developmental Biology, Department of PathologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Department of Surgery and TransplantationUniversity Hospital RWTH AachenAachenGermany
| | - Mark R. Middleton
- Department of OncologyUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Florian Markowetz
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Heike I. Grabsch
- GROW School for Oncology and Developmental Biology, Department of PathologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Division of Pathology and Data Analytics, Leeds Institute of Medical Research at St James'sUniversity of LeedsLeedsUnited Kingdom
| | - Michael L. Dustin
- Kennedy Institute of RheumatologyUniversity of OxfordOxfordUnited Kingdom
- Department of PathologyNew York University School of MedicineNew YorkNY
| | - Shivan Sivakumar
- Department of OncologyUniversity of OxfordOxfordUnited Kingdom
- Kennedy Institute of RheumatologyUniversity of OxfordOxfordUnited Kingdom
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