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Alajaji SA, Khoury ZH, Jessri M, Sciubba JJ, Sultan AS. An Update on the Use of Artificial Intelligence in Digital Pathology for Oral Epithelial Dysplasia Research. Head Neck Pathol 2024; 18:38. [PMID: 38727841 PMCID: PMC11087425 DOI: 10.1007/s12105-024-01643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/30/2024] [Indexed: 05/13/2024]
Abstract
INTRODUCTION Oral epithelial dysplasia (OED) is a precancerous histopathological finding which is considered the most important prognostic indicator for determining the risk of malignant transformation into oral squamous cell carcinoma (OSCC). The gold standard for diagnosis and grading of OED is through histopathological examination, which is subject to inter- and intra-observer variability, impacting accurate diagnosis and prognosis. The aim of this review article is to examine the current advances in digital pathology for artificial intelligence (AI) applications used for OED diagnosis. MATERIALS AND METHODS We included studies that used AI for diagnosis, grading, or prognosis of OED on histopathology images or intraoral clinical images. Studies utilizing imaging modalities other than routine light microscopy (e.g., scanning electron microscopy), or immunohistochemistry-stained histology slides, or immunofluorescence were excluded from the study. Studies not focusing on oral dysplasia grading and diagnosis, e.g., to discriminate OSCC from normal epithelial tissue were also excluded. RESULTS A total of 24 studies were included in this review. Nineteen studies utilized deep learning (DL) convolutional neural networks for histopathological OED analysis, and 4 used machine learning (ML) models. Studies were summarized by AI method, main study outcomes, predictive value for malignant transformation, strengths, and limitations. CONCLUSION ML/DL studies for OED grading and prediction of malignant transformation are emerging as promising adjunctive tools in the field of digital pathology. These adjunctive objective tools can ultimately aid the pathologist in more accurate diagnosis and prognosis prediction. However, further supportive studies that focus on generalization, explainable decisions, and prognosis prediction are needed.
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Affiliation(s)
- Shahd A Alajaji
- Department of Oncology and Diagnostic Sciences, University of Maryland School of Dentistry, 650 W. Baltimore Street, 7 Floor, Baltimore, MD, 21201, USA
- Department of Oral Medicine and Diagnostic Sciences, College of Dentistry, King Saud University, Riyadh, Saudi Arabia
- Division of Artificial Intelligence Research, University of Maryland School of Dentistry, Baltimore, MD, USA
| | - Zaid H Khoury
- Department of Oral Diagnostic Sciences and Research, Meharry Medical College School of Dentistry, Nashville, TN, USA
| | - Maryam Jessri
- Oral Medicine and Pathology Department, School of Dentistry, University of Queensland, Herston, QLD, Australia
- Oral Medicine Department, Metro North Hospital and Health Services, Queensland Health, Brisbane, QLD, Australia
| | - James J Sciubba
- Department of Otolaryngology, Head & Neck Surgery, The Johns Hopkins University, Baltimore, MD, USA
| | - Ahmed S Sultan
- Department of Oncology and Diagnostic Sciences, University of Maryland School of Dentistry, 650 W. Baltimore Street, 7 Floor, Baltimore, MD, 21201, USA.
- Division of Artificial Intelligence Research, University of Maryland School of Dentistry, Baltimore, MD, USA.
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA.
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Carlson ER, Kademani D, Ward B, Oreadi D. American Association of Oral and Maxillofacial Surgeon's Position Paper on Oral Mucosal Dysplasia R2. J Oral Maxillofac Surg 2023:S0278-2391(23)00397-X. [PMID: 37244288 DOI: 10.1016/j.joms.2023.04.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 04/27/2023] [Accepted: 04/29/2023] [Indexed: 05/29/2023]
Abstract
Oral potentially malignant disorders (OPMDs) of the oral mucosa include leukoplakia, erythroplakia, erythroleukoplakia, lichen planus, and oral lichenoid lesions, each with varying incidences of dysplastic disease at the time of presentation and each with observed incidences of malignant transformation over time. The primary goal of the management of dysplasia, therefore, includes their early detection and treatment prior to malignant transformation. The recognition and management of these OPMDs and an understanding of their potential progression to oral squamous cell carcinoma will reduce the morbidity and mortality associated with these lesions with expedient and properly executed treatment strategies that will have a positive effect on patient survival. It is the purpose of this position paper to discuss oral mucosal dysplasia in terms of its nomenclature, epidemiology, types, natural history, and treatment to acquaint clinicians regarding the timing of biopsy, type of biopsy, and follow-up of patients with these lesions of the oral mucosa. This position paper represents a synthesis of existing literature on this topic with the intention of closing gaps in our understanding of oral mucosal dysplasia while also stimulating new thinking to guide clinicians in the proper diagnosis and management of OPMDs. The fifth edition of the World Health Organization classification of head and neck tumors published in 2022 represents new information regarding this topic and a construct for this position paper.
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Affiliation(s)
- Eric R Carlson
- Professor and Kelly L. Krahwinkel Endowed Chairman, Department of Oral and Maxillofacial Surgery, University of Tennessee Graduate School of Medicine, Knoxville, TN.
| | - Deepak Kademani
- President, Minnesota Oral and Facial/Head and Neck Surgery, Fellowship Director, Oral/Head and Neck Oncologic and Reconstructive Surgery
| | - Brent Ward
- Professor and Chairman, Department of Oral and Maxillofacial Surgery, University of Michigan
| | - Daniel Oreadi
- Associate Professor, Department of Oral and Maxillofacial Surgery, Tufts University School of Dental Medicine
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On the Cutting Edge of Oral Cancer Prevention: Finding Risk-Predictive Markers in Precancerous Lesions by Longitudinal Studies. Cells 2022; 11:cells11061033. [PMID: 35326482 PMCID: PMC8947091 DOI: 10.3390/cells11061033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 02/06/2023] Open
Abstract
Early identification and management of precancerous lesions at high risk of developing cancers is the most effective and economical way to reduce the incidence, mortality, and morbidity of cancers as well as minimizing treatment-related complications, including pain, impaired functions, and disfiguration. Reliable cancer-risk-predictive markers play an important role in enabling evidence-based decision making as well as providing mechanistic insight into the malignant conversion of precancerous lesions. The focus of this article is to review updates on markers that may predict the risk of oral premalignant lesions (OPLs) in developing into oral squamous cell carcinomas (OSCCs), which can logically be discovered only by prospective or retrospective longitudinal studies that analyze pre-progression OPL samples with long-term follow-up outcomes. These risk-predictive markers are different from those that prognosticate the survival outcome of cancers after they have been diagnosed and treated, or those that differentiate between different lesion types and stages. Up-to-date knowledge on cancer-risk-predictive markers discovered by longitudinally followed studies will be reviewed. The goal of this endeavor is to use this information as a starting point to address some key challenges limiting our progress in this area in the hope of achieving effective translation of research discoveries into new clinical interventions.
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Liu KYP, Zhu SY, Harrison A, Chen ZY, Guillaud M, Poh CF. Quantitative nuclear phenotype signatures predict nodal disease in oral squamous cell carcinoma. PLoS One 2021; 16:e0259529. [PMID: 34735529 PMCID: PMC8568158 DOI: 10.1371/journal.pone.0259529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/18/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Early-stage oral squamous cell carcinoma (OSCC) patients have a one-in-four risk of regional metastasis (LN+), which is also the most significant prognostic factor for survival. As there are no validated biomarkers for predicting LN+ in early-stage OSCC, elective neck dissection often leads to over-treatment and under-treatment. We present a machine-learning-based model using the quantitative nuclear phenotype of cancer cells from the primary tumor to predict the risk of nodal disease. METHODS AND FINDINGS Tumor specimens were obtained from 35 patients diagnosed with primary OSCC and received surgery with curative intent. Of the 35 patients, 29 had well (G1) or moderately (G2) differentiated tumors, and six had poorly differentiated tumors. From each, two consecutive sections were stained for hematoxylin & eosin and Feulgen-thionin staining. The slides were scanned, and images were processed to curate nuclear morphometric features for each nucleus, measuring nuclear morphology, DNA amount, and chromatin texture/organization. The nuclei (n = 384,041) from 15 G1 and 14 G2 tumors were randomly split into 80% training and 20% test set to build the predictive model by using Random Forest (RF) analysis which give each tumor cell a score, NRS. The area under ROC curve (AUC) was 99.6% and 90.7% for the training and test sets, respectively. At the cutoff score of 0.5 as the median NRS of each region of interest (n = 481), the AUC was 95.1%. We then developed a patient-level model based on the percentage of cells with an NRS ≥ 0.5. The prediction performance showed AUC of 97.7% among the 80% (n = 23 patient) training set and with the cutoff of 61% positive cells achieved 100% sensitivity and 91.7% specificity. When applying the 61% cutoff to the 20% test set patients, the model achieved 100% accuracy. CONCLUSIONS Our findings may have a clinical impact with an easy, accurate, and objective biomarker from routine pathology tissue, providing an unprecedented opportunity to improve neck management decisions in early-stage OSCC patients.
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Affiliation(s)
- Kelly Yi Ping Liu
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Sarah Yuqi Zhu
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Alan Harrison
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Zhao Yang Chen
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Martial Guillaud
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Catherine F. Poh
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
- * E-mail:
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Datta M, Laronde DM, Rosin MP, Zhang L, Chan B, Guillaud M. Predicting progression of low-grade oral dysplasia using brushing based DNA ploidy and Chromatin Organization analysis. Cancer Prev Res (Phila) 2021; 14:1111-1118. [PMID: 34376461 DOI: 10.1158/1940-6207.capr-21-0134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/28/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022]
Abstract
Most oral cancers arise from oral potentially malignant lesions, which show varying grades of dysplasia. Risk of progression increases with increasing grade of dysplasia, however risk prediction among oral low-grade dysplasia (LGDs) i.e., mild and moderate dysplasia can be challenging as only 5-15% transform. Moreover, grading of dysplasia is subjective and varies with the area of the lesion being biopsied. To date, no biomarkers or tools are used clinically to triage oral LGDs. This study utilizes a combination of DNA ploidy and chromatin organization (CO) scores from cells obtained from lesion brushings to identify oral LGDs at high-risk of progression. A total of 130 lesion brushings from patients with oral LGDs were selected of which 16 (12.3%) lesions progressed to severe dysplasia or cancer. DNA ploidy and CO scores were analyzed from nuclear features measured by our in-house DNA image cytometry (DNA-ICM) system and used to classify brushings into low risk and high risk. A total of 57 samples were classified as high-risk of which 13 were progressors. High-risk DNA brushing was significant for progression (P = 0.001) and grade of dysplasia (P = 0.004). Multivariate analysis showed high-risk DNA brushing showed 5.1 to 8-fold increased risk of progression, a stronger predictor than dysplasia grading and lesion clinical features. DNA-ICM can serve as a non-invasive, high throughput tool to identify high-risk lesions several years prior to transformation. This will help clinicians focus on such lesions while low-risk lesions may be spared from unnecessary biopsies.
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Affiliation(s)
- Madhurima Datta
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia
| | - Denise M Laronde
- Oral Biological and Medical Sciences, University of British Columbia
| | | | | | - Bertrand Chan
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia
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Durham JS, Brasher P, Anderson DW, Yoo J, Hart R, Dort JC, Seikaly H, Kerr P, Rosin MP, Poh CF. Effect of Fluorescence Visualization-Guided Surgery on Local Recurrence of Oral Squamous Cell Carcinoma: A Randomized Clinical Trial. JAMA Otolaryngol Head Neck Surg 2021; 146:1149-1155. [PMID: 33034628 PMCID: PMC7545352 DOI: 10.1001/jamaoto.2020.3147] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance High local recurrence rates with aggressive disease remain the main concern in oral cancer survival. Use of a translational device using fluorescence visualization (FV) approved by the US Food and Drug Administration and Health Canada, has shown a marked reduction in the 3-year local recurrence rate of high-grade oral lesions in a single-center observational study. Objective To determine whether FV- guided surgery can improve local control rates in the treatment of in situ or T1 to T2 category oral squamous cell carcinoma (OSCC). Design, Setting, and Participants A multicenter randomized clinical trial was conducted in a surgical setting. A total of 457 patients were enrolled between January 18, 2010, and April 30, 2015. Data analysis of the intention-to-treat population was performed from April 3, 2019, to March 20, 2020. Patients with histologically confirmed high-grade dysplasia/carcinoma in situ or T1 to T2 category OSCC were randomized to receive traditional peroral surgery or FV-guided surgery. Intervention Fluorescence visualization during surgery. Main Outcomes and Measures The primary outcome was local recurrence of OSCC. Secondary outcomes were failure of the first-pass margin, defined as a histologically confirmed positive margin for severe dysplasia or greater histologic change of the main specimen (ie, not the margins taken from the resection bed), regional or distant metastasis, and death due to disease. Results Of the 457 patients enrolled in the study, 443 patients (264 [59.6%] men; mean [SD] age, 61.5 [13.3] years) completed the randomized treatment: 227 FV-guided and 216 non-FV guided surgery. The median follow-up was 52 (range, 0.29-90.8) months. In total, 45 patients (10.2%) experienced local recurrence. The 3-year local recurrence rate was 9.4% in the FV-guided group and 7.2% in the non-FV group (difference, 2.2%; 95% CI, -3.2% to 7.4%). Other similarities between the FV vs non-FV groups included failure of first-pass margin (68/227 [30.0%]) vs 65/216 [30.1%]), regional failure (39/227 [17.2%] vs 37/216 [17.1%]), disease-specific survival (23/227 [10.1%] vs 19/26 [8.8%]), and overall survival (41/227 [18.1%] vs 38/216 [17.6%]) were also similar between groups. No adverse events were judged to be related to the intervention. Conclusions and Relevance In this randomized clinical trial, FV-guided surgery did not improve local control rates in the treatment of patients with in situ or T1 to T2 category oral cancer. Under a controlled environment, FV-guided surgery did not have an evident effect in reduction of local recurrence for localized OSCC. This result suggests that attention be directed to strategies other than improving definitions of nonapparent disease at clinical margins to identify the sources of local recurrence. Trial Registration ClinicalTrial.gov Identifier: NCT01039298.
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Affiliation(s)
- J Scott Durham
- Department of Surgery, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Penelope Brasher
- Department of Statistics, Faculty of Science, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Donald W Anderson
- Department of Surgery, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - John Yoo
- Department of Otolaryngology-Head and Neck Surgery and Oncology, London Health Sciences Center, London, Ontario, Canada
| | - Rob Hart
- Division of Otolaryngology-Head and Neck Surgery, University of Calgary, Calgary, Alberta, Canada
| | - Joseph C Dort
- Division of Otolaryngology-Head and Neck Surgery, University of Calgary, Calgary, Alberta, Canada
| | - Hadi Seikaly
- Division of Otolaryngology, Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Paul Kerr
- Department of Otolaryngology-Head & Neck Surgery, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Miriam P Rosin
- School of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Catherine F Poh
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, The University of British Columbia, Vancouver, British Columbia, Canada
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Oral potentially malignant disorders: A scoping review of prognostic biomarkers. Crit Rev Oncol Hematol 2020; 153:102986. [PMID: 32682268 DOI: 10.1016/j.critrevonc.2020.102986] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 02/08/2023] Open
Abstract
This scoping review aimed to map evidence regarding biomarkers for malignant transformation of oral potentially malignant disorders (OPMD). Seventy-three longitudinal studies investigating prognostic biomarkers for OPMD malignant transformation were included, encompassing 5612 disorders and 108 biomarkers, of which 72 were investigated by immunohistochemistry. Most biomarkers were assessed in one or two studies, while five (p53, Ki-67, podoplanin, p16, and DNA ploidy) were analyzed in five or more studies. All studies investigating podoplanin (n = 8) reported a significant association between positive/high immunoexpression and malignant transformation. Similarly, all studies assessing DNA ploidy (n = 5) found that aneuploidy or gross genomic aberrations were significantly associated with malignant transformation. Included studies often presented mixed data from different OPMD subtypes, inadequate description of population characteristics, and lack of adjusted analysis for confounding factors. One hundred and eight biomarkers were identified and, from these, podoplanin immunoexpression and DNA ploidy were considered promising candidates for future long-term clinical research.
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Identification of Malignancy-Associated Changes in Histologically Normal Tumor-Adjacent Epithelium of Patients with HPV-Positive Oropharyngeal Cancer. Anal Cell Pathol (Amst) 2018; 2018:1607814. [PMID: 29713583 PMCID: PMC5866869 DOI: 10.1155/2018/1607814] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/08/2018] [Accepted: 01/11/2018] [Indexed: 12/28/2022] Open
Abstract
The incidence of HPV-positive oropharyngeal cancer (HPV+ OPC) is increasing, thus presenting new challenges for disease detection and management. Noninvasive methods involving brush biopsies of diseased tissues were recently reported as insufficient for tumor detection in HPV+ OPC patients, likely due to differences between the site of tumor initiation at the base of involuted crypts and the site of brush biopsy at the crypt surface. We hypothesized that histologically normal surface epithelial cells in the oropharynx contain changes in nuclear morphology that arise due to tumor proximity. We analyzed the nuclear phenotype of matched tumor, tumor-adjacent normal, and contralateral normal tissues from biopsies of nine HPV+ OPC patients. Measurements of 89 nuclear features were used to train a random forest-based classifier to discriminate between normal and tumor nuclei. We then extracted voting scores from the trained classifier, which classify nuclei on a continuous scale from zero (“normal-like”) to one (“tumor-like”). In each case, the average score of the adjacent normal nuclei was intermediate between the tumor and contralateral normal nuclei. These results provide evidence for the existence of phenotypic changes in histologically normal, tumor-adjacent surface epithelial cells, which could be used as brush biopsy-based biomarkers for HPV+ OPC detection.
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Guillaud M, MacAulay CE, Berean KW, Bullock M, Guggisberg K, Klieb H, Puttagunta L, Penner C, Kwan K, Rosin MP, Poh CF. Using quantitative tissue phenotype to assess the margins of surgical samples from a pan-Canadian surgery study. Head Neck 2018; 40:1263-1270. [DOI: 10.1002/hed.25106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 10/19/2017] [Accepted: 01/18/2018] [Indexed: 11/06/2022] Open
Affiliation(s)
- Martial Guillaud
- Department of Integrative Oncology; BC Cancer Agency; Vancouver British Columbia Canada
| | - Calum E. MacAulay
- Department of Integrative Oncology; BC Cancer Agency; Vancouver British Columbia Canada
| | - Kenneth W. Berean
- Department of Pathology and Laboratory Medicine; the University of British Columbia; Vancouver British Columbia Canada
| | - Martin Bullock
- Department of Pathology; Dalhousie University; Halifax Nova Scotia Canada
| | - Kelly Guggisberg
- Department of Pathology and Laboratory Medicine; University of Calgary; Calgary Alberta Canada
| | - Hagen Klieb
- Department of Pathology; Sunnybrook Health Sciences Centre; Toronto Ontario Canada
| | - Lakshmi Puttagunta
- Department of Laboratory Medicine and Pathology; University of Alberta; Edmonton Alberta Canada
| | - Carla Penner
- Department of Pathology; University of Manitoba; Winnipeg Manitoba Canada
| | - Keith Kwan
- Department of Pathology and Laboratory Medicine; University of Western; London Ontario Canada
| | - Miriam P. Rosin
- Department of Pathology and Laboratory Medicine; the University of British Columbia; Vancouver British Columbia Canada
- Department of Cancer Control Research; BC Cancer Agency; Vancouver British Columbia Canada
- Biomedical Physiology and Kinesiology; Simon Fraser University; Burnaby British Columbia Canada
| | - Catherine F. Poh
- Department of Integrative Oncology; BC Cancer Agency; Vancouver British Columbia Canada
- Department of Pathology and Laboratory Medicine; the University of British Columbia; Vancouver British Columbia Canada
- Faculty of Dentistry; the University of British Columbia; Vancouver British Columbia Canada
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Large-scale DNA organization is a prognostic marker of breast cancer survival. Med Oncol 2017; 35:9. [PMID: 29214466 DOI: 10.1007/s12032-017-1068-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 11/30/2017] [Indexed: 01/22/2023]
Abstract
Breast cancer is the leading cause of cancer-related deaths among women worldwide. We investigated whether changes in large-scale DNA organization (LDO) of tumor epithelial nuclei are an indicator of the aggressiveness of the tumor. We tested our algorithm on a set of 172 duplicates TMA cores samples coming from 95 breast cancer patients. Thirty-five patients died of breast cancer, and 60 were still alive 10 years after surgery. Duplicates cores were used to create training and test set. The TMA slides were stained with Feulgen-thionin and imaged using our in-house high-resolution Imaging system. Automated segmentation of cell nuclei followed by manual selection of intact, in-focus nuclei resulted in an average of 50 cell nuclei per sample available for analysis. Using forward stepwise linear discriminant analysis, a combination of six features that combined linearly gave the best discrimination between the two groups of cells: cells collected from 'deceased' patients TMA specimens and cells collected from "survivors" patients TMA specimens. Five of these features measure the spatial organization of DNA chromatin. The resulting canonical score is named cell LDO score. A patient LDO score, percentage of cell nuclei with a cell LDO score higher than a predefined cutoff value, was processed for the specimens in the test set, and a cutoff value was defined to classify patients with a low or a high LDO score. Using this binary test, 82.1% of patients were correctly classified are "deceased" or "survivors," with a specificity of 79% and a sensitivity of 88%. The relative risk of death of an individual with a high LDO score was nine times higher than for a patient with a low LDO score. When testing the combination of LDO score, node status, histological grade, and tumor grade to predict breast cancer survival, LDO was the most significant predictor. LDO classification was also highly associated with survival for only grade 1 and 2 patients as well as for only grade 3 patients. Our result confirms the potential of LDO to measure phenotypic changes associated with more aggressive disease and could be evaluated to identify patients more likely to benefit from adjuvant therapies.
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MacAulay C, Keyes M, Hayes M, Lo A, Wang G, Guillaud M, Gleave M, Fazli L, Korbelik J, Collins C, Keyes S, Palcic B. Quantification of large scale DNA organization for predicting prostate cancer recurrence. Cytometry A 2017; 91:1164-1174. [PMID: 29194951 DOI: 10.1002/cyto.a.23287] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 10/06/2017] [Accepted: 10/31/2017] [Indexed: 11/09/2022]
Abstract
This study investigates whether Genomic Organization at Large Scales (which we propose to call GOALS) as quantified via nuclear phenotype characteristics and cell sociology features (describing cell organization within tissue) collected from prostate tissue microarrays (TMAs) can separate biochemical failure from biochemical nonevidence of disease (BNED) after radical prostatectomy (RP). Of the 78 prostate cancer tissue cores collected from patients treated with RP, 16 who developed biochemical relapse (failure group) and 16 who were BNED patients (nonfailure group) were included in the analyses (36 cores from 32 patients). A section from this TMA was stained stoichiometrically for DNA using the Feulgen-Thionin methodology, and scanned with a Pannoramic MIDI scanner. Approximately 110 nuclear phenotypic features, predominately quantifying large scale DNA organization (GOALS), were extracted from each segmented nuclei. In addition, the centers of these segmented nuclei defined a Voronoi tessellation and subsequent architectural analysis. Prostate TMA core classification as biochemical failure or BNED after RP using GOALS features was conducted (a) based on cell type and cell position within the epithelium (all cells, all epithelial cells, epithelial >2 cell layers away from basement membrane) from all cores, and (b) based on epithelial cells more than two cell layers from the basement membrane using a Classifier trained on Gleason 6, 8, 9 (16 cores) only and applied to a Test set consisting of the Gleason 7 cores (20 cores). Successful core classification as biochemical failure or BNED after RP by a linear classifier was 75% using all cells, 83% using all epithelial cells, and 86% using epithelial >2 layers. Overall success of predicted classification by the linear Classifier of (b) was 87.5% using the Training Set and 80% using the Test Set. Overall success of predicted progression using Gleason score alone was 75% for Gleason >7 as failures and 69% for Gleason >6 as failures. © 2017 International Society for Advancement of Cytometry.
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Affiliation(s)
- Calum MacAulay
- BC Cancer Research Centre, Department of Integrative Oncology, Vancouver, BC, Canada
| | - Mira Keyes
- BC Cancer Agency, Department of Radiation Oncology, Vancouver, BC, Canada
| | - Malcolm Hayes
- BC Cancer Agency, Department of Pathology, Vancouver, BC, Canada
| | - Andrea Lo
- BC Cancer Agency, Department of Radiation Oncology, Vancouver, BC, Canada
| | - Gang Wang
- BC Cancer Agency, Department of Pathology, Vancouver, BC, Canada
| | - Martial Guillaud
- BC Cancer Research Centre, Department of Integrative Oncology, Vancouver, BC, Canada
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urology, Vancouver, BC, Canada
| | - Laden Fazli
- Vancouver Prostate Centre, Department of Pathology, Vancouver, BC, Canada
| | - Jagoda Korbelik
- BC Cancer Research Centre, Department of Integrative Oncology, Vancouver, BC, Canada
| | - Colin Collins
- Vancouver Prostate Centre, Department of Urology, Vancouver, BC, Canada
| | - Sarah Keyes
- BC Cancer Research Centre, Department of Integrative Oncology, Vancouver, BC, Canada
| | - Branko Palcic
- BC Cancer Research Centre, Department of Integrative Oncology, Vancouver, BC, Canada
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Bag S, Dutta D, Chaudhary A, Sing BC, Pal M, Ray AK, Banerjee R, Paul RR, Basak A, Das AK, Chatterjee J. Identification of α-enolase as a prognostic and diagnostic precancer biomarker in oral submucous fibrosis. J Clin Pathol 2017; 71:228-238. [PMID: 28821582 DOI: 10.1136/jclinpath-2017-204430] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/30/2017] [Accepted: 07/03/2017] [Indexed: 11/03/2022]
Abstract
AIMS Diagnostic ambiguities regarding the malignant potentiality of oral submucous fibrosis (OSF), an oral precancerous condition having dysplastic and non-dysplastic isoforms are the major failure for early intervention of oral squamous cell carcinoma (OSCC) patients. Our goal is to identify proteomic signatures from biopsies that can be used as precancer diagnostic marker for patient suffering from OSF. METHODS The high throughput techniques adopting de novo peptide sequencing (1D SDS-PAGE coupled nanoLC MALDI tandem mass spectrometry (MS/MS)-based peptide mass fingerprint), immunohistochemistry (IHC), Western blot (WB) and real-time PCR (RT-PCR) analysis are considered for such biomarker identification and multilevel validations. RESULTS Alpha-enolase is identified as an overexpressed protein in biopsies of oral submucous fibrosis with dysplasia (OSFWD) compared with oral submucous fibrosis without dysplasia (OSFWT) and normal oral mucosa (NOM). Total proteome analysis of an overexpressed protein band around 47 kDa of OSFWD identifies 334 peptides corresponding to 61 human proteins. Among them α-enolase is identified as a prime protein with highest number of peptides (44 out of 334 peptides) and sequence coverage (66.4%). Furthermore, RT-PCR, WB and IHC analysis also show mRNA and tissue level upregulation of α-enolase in OSFWD validating α-enolase as precancer marker. CONCLUSIONS This study for the first time identifies and validates α-enolase as a novel biomarker for early diagnosis of malignant potentiality of OSF. Hence, the identified protein marker, α-enolase can help in early therapeutic intervention of OSF patients leading to the reduction of patient's pain, treatment cost and enhancement of patient's quality of life.
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Affiliation(s)
- Swarnendu Bag
- Department of Biotechnology, National Institute of Technology Sikkim, South Sikkim, India
| | - Debabrata Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Amrita Chaudhary
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Bidhan Chandra Sing
- Department of Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Mousumi Pal
- Department of Oral and Maxillofacial Pathology, Guru Nanak Institute of Dental Sciences and Research, Kolkata, India
| | - Ajoy Kumar Ray
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, India
| | - Rita Banerjee
- Department of Science and Technology, New Delhi, India
| | - Ranjan Rashmi Paul
- Department of Oral and Maxillofacial Pathology, Guru Nanak Institute of Dental Sciences and Research, Kolkata, India
| | - Amit Basak
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Jyotirmoy Chatterjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
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Pilati SFM, Bianco BC, Vieira DSC, Modolo F. Histopathologic features in actinic cheilitis by the comparison of grading dysplasia systems. Oral Dis 2016; 23:219-224. [DOI: 10.1111/odi.12597] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/03/2016] [Accepted: 10/13/2016] [Indexed: 11/29/2022]
Affiliation(s)
- SFM Pilati
- Odontology; Health Sciences Center; Vale do Itajaí University; Itajaí Brazil
| | - BC Bianco
- Odontology; Health Sciences Center; Vale do Itajaí University; Itajaí Brazil
| | - DSC Vieira
- Anatomical Pathology Service; Department of Pathology; Federal University of Santa Catarina; Florianopolis Brazil
| | - F Modolo
- Oral Pathology Laboratory; Department of Pathology; Federal University of Santa Catarina; Florianopolis Brazil
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14
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Lee H, Baek TH, Park M, Lee SY, Son HJ, Kang DW, Kim JH, Kim SY. Difference of the Nuclear Green Light Intensity between Papillary Carcinoma Cells Showing Clear Nuclei and Non-neoplastic Follicular Epithelia in Papillary Thyroid Carcinoma. J Pathol Transl Med 2016; 50:355-60. [PMID: 27550048 PMCID: PMC5042896 DOI: 10.4132/jptm.2016.05.19] [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: 03/11/2016] [Revised: 05/03/2016] [Accepted: 05/19/2016] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND There is subjective disagreement regarding nuclear clearing in papillary thyroid carcinoma. In this study, using digital instruments, we were able to quantify many ambiguous pathologic features and use numeric data to express our findings. METHODS We examined 30 papillary thyroid carcinomas. For each case, we selected representative cancer cells showing clear nuclei and surrounding non-neoplastic follicular epithelial cells and evaluated objective values of green light intensity (GLI) for quantitative analysis of nuclear clearing in papillary thyroid carcinoma. RESULTS From 16,274 GLI values from 600 cancer cell nuclei and 13,752 GLI values from 596 non-neoplastic follicular epithelial nuclei, we found a high correlation of 94.9% between GLI and clear nuclei. GLI between the cancer group showing clear nuclei and non-neoplastic follicular epithelia was statistically significant. The overall average level of GLI in the cancer group was over two times higher than the non-neoplastic group despite a wide range of GLI. On a polygonal line graph, there was a fluctuating unique difference between both the cancer and non-neoplastic groups in each patient, which was comparable to the microscopic findings. CONCLUSIONS Nuclear GLI could be a useful factor for discriminating between carcinoma cells showing clear nuclei and non-neoplastic follicular epithelia in papillary thyroid carcinoma.
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Affiliation(s)
- Hyekyung Lee
- Department of Pathology, Eulji University Hospital, Eulji University School of Medicine, Daejeon, Korea
| | - Tae Hwa Baek
- Medical Examiner's Office, National Forensic Service, Wonju, Korea
| | - Meeja Park
- Department of Pathology, Eulji University Hospital, Eulji University School of Medicine, Daejeon, Korea
| | - Seung Yun Lee
- Department of Pathology, Eulji University Hospital, Eulji University School of Medicine, Daejeon, Korea
| | - Hyun Jin Son
- Department of Pathology, Eulji University Hospital, Eulji University School of Medicine, Daejeon, Korea
| | - Dong Wook Kang
- Department of Pathology, Eulji University Hospital, Eulji University School of Medicine, Daejeon, Korea
| | - Joo Heon Kim
- Department of Pathology, Eulji University Hospital, Eulji University School of Medicine, Daejeon, Korea
| | - Soo Young Kim
- Department of Occupational Medicine, Eulji University Hospital, Eulji University School of Medicine, Daejeon, Korea
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15
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El Hallani S, Guillaud M, Korbelik J, Marginean EC. Evaluation of Quantitative Digital Pathology in the Assessment of Barrett Esophagus-Associated Dysplasia. Am J Clin Pathol 2015; 144:151-64. [PMID: 26071473 DOI: 10.1309/ajcpk0y1mmfsjdku] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVES Barrett esophagus (BE) is a precursor lesion that confers an increased risk of esophageal adenocarcinoma. Two issues confront the diagnosis of patients with BE: (1) sampling error at the time of endoscopy and (2) variability among pathologists in grading dysplasia. The purpose of our study was to evaluate quantitative digital pathology (QDP) as a marker of dysplasia and stratification from low-grade to high-grade dysplasia to intramucosal adenocarcinoma in BE. METHODS Sixty-one esophageal biopsy specimens with BE were selected and divided into six groups according to the dysplasia grade. QDP image analysis was carried out by an in-house automated quantitative system on sections. The values of 110 nuclear features that analyze the morphology and chromatin texture were generated for each nucleus. RESULTS A progressive correlation was found between nuclear morphometric features and chromatin features with BE dysplasia. The chromatin texture was the best discriminator of the class diagnosis. There was a significant difference between the chromatin features of isolated low-grade dysplasia vs low-grade dysplasia that was associated with higher grade lesions in other biopsy tissue fragments. CONCLUSIONS QDP is a promising tool in the new era of digital pathology. Pending clinical validation studies, analysis of chromatin texture could contribute to the differential diagnosis of BE class and the detection of concomitant high-grade lesions if not sampled.
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16
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Martinez VD, MacAulay CE, Guillaud M, Lam WL, Zhang L, Corbett KK, Rosin MP. Targeting of chemoprevention to high-risk potentially malignant oral lesions: challenges and opportunities. Oral Oncol 2014; 50:1123-30. [PMID: 25240917 PMCID: PMC4539364 DOI: 10.1016/j.oraloncology.2014.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 08/11/2014] [Accepted: 08/20/2014] [Indexed: 12/11/2022]
Abstract
Worldwide, oral cancer is responsible for 170,000 deaths per year. Intervention to prevent this disease is a long sought after goal. Chemoprevention studies have focused on clinicopathological features of potentially malignant lesions (PML) in an effort to prevent their progression to cancer. However, prediction of future behavior for such lesions is difficult and remains a major challenge to such intervention. Different approaches to this problem have been tested in the past 20years. Early genetic progression models identified critical regions of allelic imbalance at 3p and 9p, and provided the basis for molecular markers to identify progressing PMLs. Subsequently, technological advances, such as genome-wide high-throughput array platforms, computer imaging, visualization technology and next generation sequencing, have broadened the scope for marker development and have the potential of further improving our ability to identify high-risk lesions in the near future either alone or in combination. In this article, we examine the milestones in the development of markers for PML progression. We emphasize the critical importance of networks among scientists, health professionals and community to facilitate the validation and application of putative markers into clinical practice. With a growing number of new agents to validate, it is necessary to coordinate the design and implementation of strategies for patient recruitment, integration of marker assessment, and the final translation of such approaches into clinical use.
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Affiliation(s)
- Victor D Martinez
- BC Cancer Research Centre, Department of Integrative Oncology, Vancouver, Canada
| | - Calum E MacAulay
- BC Cancer Research Centre, Department of Integrative Oncology, Vancouver, Canada
| | - Martial Guillaud
- BC Cancer Research Centre, Department of Integrative Oncology, Vancouver, Canada
| | - Wan L Lam
- BC Cancer Research Centre, Department of Integrative Oncology, Vancouver, Canada
| | - Lewei Zhang
- Faculty of Dentistry, Departments of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Kitty K Corbett
- School of Public Health and Health Systems, University of Waterloo, Ontario, Canada
| | - Miriam P Rosin
- BC Cancer Research Centre, Department of Cancer Control Research, Vancouver, Canada; Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada.
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17
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Automated classification of oral premalignant lesions using image cytometry and Random Forests-based algorithms. Cell Oncol (Dordr) 2014; 37:193-202. [PMID: 24817187 DOI: 10.1007/s13402-014-0172-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2014] [Indexed: 10/25/2022] Open
Abstract
PURPOSE A major challenge for the early diagnosis of oral cancer is the ability to differentiate oral premalignant lesions (OPL) at high risk of progressing into invasive squamous cell carcinoma (SCC) from those at low risk. Our group has previously used high-resolution image analysis algorithms to quantify the nuclear phenotypic changes occurring in OPLs. This approach, however, requires a manual selection of nuclei images. Here, we investigated a new, semi-automated algorithm to identify OPLs at high risk of progressing into invasive SCC from those at low risk using Random Forests, a tree-based ensemble classifier. METHODS We trained a sequence of classifiers using morphometric data calculated on nuclei from 29 normal, 5 carcinoma in situ (CIS) and 28 SCC specimens. After automated discrimination of nuclei from other objects (i.e., debris, clusters, etc.), a nuclei classifier was trained to discriminate abnormal nuclei (8,841) from normal nuclei (5,762). We extracted voting scores from this trained classifier and created an automated nuclear phenotypic score (aNPS) to identify OPLs at high risk of progression. RESULTS The new algorithm showed a correct classification rate of 80% (80.6% sensitivity, 79.3% specificity) at the cellular level for the test set, and a correct classification rate of 75% (77.8% sensitivity, 71.4% specificity) at the tissue level with a negative predictive value of 76% and a positive predictive value of 74% for predicting progression among 71 OPLs, performed on par with the manual method in our previous study. CONCLUSIONS We conclude that the newly developed aNPS algorithm serves as a crucial asset in the implementation of high-resolution image analysis in routine clinical pathology practice to identify lesions that require molecular evaluation or more frequent follow-up.
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18
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Csikász-Nagy A, Escudero LM, Guillaud M, Sedwards S, Baum B, Cavaliere M. Cooperation and competition in the dynamics of tissue architecture during homeostasis and tumorigenesis. Semin Cancer Biol 2013; 23:293-8. [PMID: 23751796 DOI: 10.1016/j.semcancer.2013.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 05/28/2013] [Accepted: 05/30/2013] [Indexed: 01/26/2023]
Abstract
The construction of a network of cell-to-cell contacts makes it possible to characterize the patterns and spatial organization of tissues. Such networks are highly dynamic, depending on the changes of the tissue architecture caused by cell division, death and migration. Local competitive and cooperative cell-to-cell interactions influence the choices cells make. We review the literature on quantitative data of epithelial tissue topology and present a dynamical network model that can be used to explore the evolutionary dynamics of a two dimensional tissue architecture with arbitrary cell-to-cell interactions. In particular, we show that various forms of experimentally observed types of interactions can be modelled using game theory. We discuss a model of cooperative and non-cooperative cell-to-cell communication that can capture the interplay between cellular competition and tissue dynamics. We conclude with an outlook on the possible uses of this approach in modelling tumorigenesis and tissue homeostasis.
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Affiliation(s)
- Attila Csikász-Nagy
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige 38010, Italy.
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19
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Messadi DV. Diagnostic aids for detection of oral precancerous conditions. Int J Oral Sci 2013; 5:59-65. [PMID: 23743617 PMCID: PMC3707069 DOI: 10.1038/ijos.2013.24] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 03/17/2013] [Indexed: 02/07/2023] Open
Abstract
Oral cancer has a tendency to be detected at late stage which is detrimental to the patients because of its high mortality and morbidity rates. Early detection of oral cancer is therefore important to reduce the burden of this devastating disease. In this review article, the most common oral precancerous lesions are discussed and the importance of early diagnosis is emphasized. In addition, the most common non-invasive oral cancer devices that can aid the general practitioners in early diagnosis are also discussed.
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20
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El Hallani S, Poh CF, Macaulay CE, Follen M, Guillaud M, Lane P. Ex vivo confocal imaging with contrast agents for the detection of oral potentially malignant lesions. Oral Oncol 2013; 49:582-90. [PMID: 23415144 DOI: 10.1016/j.oraloncology.2013.01.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/25/2013] [Accepted: 01/26/2013] [Indexed: 12/15/2022]
Abstract
OBJECTIVES We investigated the potential use of real-time confocal microscopy in the non-invasive detection of occult oral potentially malignant lesions. Our objectives were to select the best fluorescence contrast agent for cellular morphology enhancement, to build an atlas of confocal microscopic images of normal human oral mucosa, and to determine the accuracy of confocal microscopy to recognize oral high-grade dysplasia lesions on live human tissue. MATERIALS AND METHODS Five clinically used fluorescent contrast agents were tested in vitro on cultured human cells and validated ex vivo on human oral mucosa. Images acquired ex vivo from normal and diseased human oral biopsies with bench-top fluorescent confocal microscope were compared to conventional histology. Image analyzer software was used as an adjunct tool to objectively compare high-grade dysplasia versus low-grade dysplasia and normal epithelium. RESULTS Acriflavine Hydrochloride provided the best cellular contrast by preferentially staining the nuclei of the epithelium. Using topical application of Acriflavine Hydrochloride followed by confocal microscopy, we could define morphological characteristics of each cellular layer of the normal human oral mucosa, building an atlas of histology-like images. Applying this technique to diseased oral tissue specimen, we were also able to accurately diagnose the presence of high-grade dysplasia through the increased cellularity and changes in nuclear morphological features. Objective measurement of cellular density by quantitative image analysis was a strong discriminant to differentiate between high-grade dysplasia and low-grade dysplasia lesions. CONCLUSIONS Pending clinical investigation, real-time confocal microscopy may become a useful adjunct to detect precancerous lesions that are at high risk of cancer progression, direct biopsy and delineate excision margins.
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Affiliation(s)
- S El Hallani
- British Columbia Cancer Research Centre, Integrative Oncology Department and Cancer Imaging Unit, Vancouver, BC, Canada V5Z 1L3.
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21
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Abstract
Deregulation of gene expression, a hallmark of cancer, is caused by both genetic and epigenetic mechanisms. The rapid accumulation of epigenome maps of various cancers suggests a new avenue of research, namely integrating epigenomic data with other types of omic data for cancer diagnosis, prognosis, and biomarker discovery. We introduce the MAPIT algorithm (Multi Analyte Pathway Inference Tool), to enable principled integration of epigenomic, transcriptomic, and protein interactome data. As a proof-of-principle, we apply MAPIT to glioblastoma multiforme (GBM), the most common and aggressive form of brain tumor. Few predictive markers were reported for the prognosis of GBM patients. By integrating mRNA transcriptome, promoter DNA methylome and protein-protein physical interactome, we find ten expression- and three methylation-based network markers, involving 118 genes. When tested on additional GBM patient samples, the prognostic accuracy of the multi-analyte network markers (73.5%) is 9.7% and 8.6% higher than previous prognostic signatures built on gene expression or DNA methylation alone. Our results highlight the critical role of two novel pathways in the prognosis of GBM patients, small GTPase-mediated protein trafficking and ubiquitination-dependent protein degradation. A better understanding of these two pathways could lead to personalized therapies for subgroups of GBM patients. Our study demonstrates that integrating epigenomic, transcriptomic, and interactomic data can improve the accuracy network-based prognosis markers and lead to novel mechanistic understanding of cancer.
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Affiliation(s)
- Jongkwang Kim
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Long Gao
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, United States of America
| | - Kai Tan
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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Macaulay C, Poh CF, Guillaud M, Michele Williams P, Laronde DM, Zhang L, Rosin MP. High throughput image cytometry for detection of suspicious lesions in the oral cavity. JOURNAL OF BIOMEDICAL OPTICS 2012; 17:086004-1. [PMID: 23224191 DOI: 10.1117/1.jbo.17.8.086004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The successful management of oral cancer depends upon early detection, which relies heavily on the clinician's ability to discriminate sometimes subtle alterations of the infrequent premalignant lesions from the more common reactive and inflammatory conditions in the oral mucosa. Even among experienced oral specialists this can be challenging, particularly when using new wide field-of-view direct fluorescence visualization devices clinically introduced for the recognition of at-risk tissue. The objective of this study is to examine if quantitative cytometric analysis of oral brushing samples could facilitate the assessment of the risk of visually ambiguous lesions. About 369 cytological samples were collected and analyzed: (1) 148 samples from pathology-proven sites of SCC, carcinoma in situ or severe dysplasia; (2) 77 samples from sites with inflammation, infection, or trauma, and (3) 144 samples from normal sites. These were randomly separated into training and test sets. The best algorithm correctly recognized 92.5% of the normal samples, 89.4% of the abnormal samples, 86.2% of the confounders in the training set as well as 100% of the normal samples, and 94.4% of the abnormal samples in the test set. These data suggest that quantitative cytology could reduce by more than 85% the number of visually suspect lesions requiring further assessment by biopsy.
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Affiliation(s)
- Calum Macaulay
- BC Cancer Agency, Integrative Oncology Department, 675 West 10th Avenue, Vancouver, B.C., Canada V5Z1L3.
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Pierce MC, Schwarz RA, Bhattar VS, Mondrik S, Williams MD, Lee JJ, Richards-Kortum R, Gillenwater AM. Accuracy of in vivo multimodal optical imaging for detection of oral neoplasia. Cancer Prev Res (Phila) 2012; 5:801-9. [PMID: 22551901 DOI: 10.1158/1940-6207.capr-11-0555] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
If detected early, oral cancer is eminently curable. However, survival rates for oral cancer patients remain low, largely due to late-stage diagnosis and subsequent difficulty of treatment. To improve clinicians' ability to detect early disease and to treat advanced cancers, we developed a multimodal optical imaging system (MMIS) to evaluate tissue in situ, at macroscopic and microscopic scales. The MMIS was used to measure 100 anatomic sites in 30 patients, correctly classifying 98% of pathologically confirmed normal tissue sites, and 95% of sites graded as moderate dysplasia, severe dysplasia, or cancer. When used alone, MMIS classification accuracy was 35% for sites determined by pathology as mild dysplasia. However, MMIS measurements correlated with expression of candidate molecular markers in 87% of sites with mild dysplasia. These findings support the ability of noninvasive multimodal optical imaging to accurately identify neoplastic tissue and premalignant lesions. This in turn may have considerable impact on detection and treatment of patients with oral cancer and other epithelial malignancies.
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Affiliation(s)
- Mark C Pierce
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
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Poh CF, MacAulay CE, Laronde DM, Williams PM, Zhang L, Rosin MP. Squamous cell carcinoma and precursor lesions: diagnosis and screening in a technical era. Periodontol 2000 2011; 57:73-88. [PMID: 21781180 DOI: 10.1111/j.1600-0757.2011.00386.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Nandakumar V, Kelbauskas L, Johnson R, Meldrum D. Quantitative characterization of preneoplastic progression using single-cell computed tomography and three-dimensional karyometry. Cytometry A 2011; 79:25-34. [PMID: 21182180 DOI: 10.1002/cyto.a.20997] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The development of morphological biosignatures to precisely characterize preneoplastic progression necessitates high-resolution three-dimensional (3D) cell imagery and robust image processing algorithms. We report on the quantitative characterization of nuclear structure alterations associated with preneoplastic progression in human esophageal epithelial cells using single-cell optical tomography and fully automated 3D karyometry. We stained cultured cells with hematoxylin and generated 3D images of individual cells by mathematically reconstructing 500 projection images acquired using optical absorption tomographic imaging. For 3D karyometry, we developed novel, fully automated algorithms to robustly segment the cellular, nuclear, and subnuclear components in the acquired cell images, and computed 41 quantitative morphological descriptors from these segmented volumes. In addition, we developed algorithms to quantify the spatial distribution and texture of the nuclear DNA. We applied our methods to normal, metaplastic, and dysplastic human esophageal epithelial cell lines, analyzing 100 cells per line. The 3D karyometric descriptors elucidated quantitative differences in morphology and enabled robust discrimination between cell lines on the basis of extracted morphological features. The morphometric hallmarks of cancer progression such as increased nuclear size, elevated nuclear content, and anomalous chromatin texture and distribution correlated with this preneoplastic progression model, pointing to the clinical use of our method for early cancer detection.
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Affiliation(s)
- Vivek Nandakumar
- School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe, Arizona, USA
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Guillaud M, Clem C, MacAulay C. An in silico platform for the study of epithelial pre-invasive neoplastic development. Biosystems 2010; 102:22-31. [DOI: 10.1016/j.biosystems.2010.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 07/15/2010] [Indexed: 11/29/2022]
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Abnormal DNA content in oral epithelial dysplasia is associated with increased risk of progression to carcinoma. Br J Cancer 2010; 103:1432-42. [PMID: 20859287 PMCID: PMC2990600 DOI: 10.1038/sj.bjc.6605905] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background: Oral epithelial dysplasia (OED) is a histologically detectable lesion that may progress to carcinoma but there are no accurate markers that predict progression. This study examined the development of carcinoma from oral dysplastic lesions, and the association between abnormal DNA content and progression to carcinoma. Methods: Epithelial dysplasias from the Oral Pathology Diagnostic Service were matched against the Ontario Cancer Registry database to identify cases that progressed to carcinoma. A case–control study was conducted to compare DNA image cytometry of dysplasias that progressed with those that have not progressed. For a subset of the progressed dysplasias, DNA content of the carcinoma was also analysed. Results: A total of 8% of epithelial dysplasias progressed to carcinoma after 6–131 months. In all, 28 of 99 dysplasias showed abnormal DNA content by image cytometry. In multivariate analysis of time to progression, abnormal DNA content was a significant predictor with hazard ratio of 3.3 (95% confidence interval: 1.5–7.4) corrected for site and grade of dysplasia. Analysis of sequential samples of dysplasia and carcinoma suggested that epithelial cell populations with grossly abnormal DNA content were transient intermediates during oral cancer development. Conclusions: Abnormal DNA content is a significant biomarker of a subset of OED that progress to carcinoma.
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Ogbureke KUE, Abdelsayed RA, Kushner H, Li L, Fisher LW. Two members of the SIBLING family of proteins, DSPP and BSP, may predict the transition of oral epithelial dysplasia to oral squamous cell carcinoma. Cancer 2010; 116:1709-17. [PMID: 20186700 DOI: 10.1002/cncr.24938] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND : Patients with oral premalignant lesions (OPL) present with oral squamous cell carcinomas (OSCC) at a much higher rate than the general population. There are currently no useful markers that indicate specifically which OPLs are most likely to progress. Three small integrin binding ligands N-linked glycoprotein (SIBLING) family proteins, bone sialoprotein (BSP), osteopontin (OPN), and dentin sialophosphoprotein (DSPP), have been shown to be up-regulated in many cancers, including OSCC. The status of SIBLING expression in OPLs and their correlation to transition to oral cancer are unknown. METHODS : Sixty archival surgical biopsies of dysplastic OPLs were evaluated by immunohistochemistry for expression of BSP, DSPP, and OPN and correlated with local transformation to OSCC at sites adjacent to surgically removed dysplastic OPL. RESULTS : The OPL patient population was representative of previous studies with 20% progressing to OSCC, and no correlation between degree of dysplasia and progression. Eighty-seven percent were positive for at least 1 SIBLING protein. OPN expression had no correlation with progression. The BSP+/DSPP- expression pattern however correlated with decreased transformation to OSCC (point prevalence = 0%; 95% confidence interval [CI], 0-20.6), whereas the BSP-/DSPP+ pattern was associated with more frequent progression (point prevalence = 77.8%; 95%CI, 47.8-95.4). Incrementally higher expression scores (0 to 3) of BSP and DSPP were also associated with increased predictive values (odds ratio, 25.53; 95% CI, 2.14-304.7 and 10.13; 95% CI, 2.0-50.0, respectively, for each increment). CONCLUSIONS : BSP and DSPP are excellent candidate markers for successful OPL surgical intervention and may be predictors of OPL-OSCC progression. Cancer 2010. (c) 2010 American Cancer Society.
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Affiliation(s)
- Kalu U E Ogbureke
- School of Dentistry, Medical College of Georgia, Augusta, Georgia, USA.
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29
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Tsui IFL, Poh CF, Garnis C, Rosin MP, Zhang L, Lam WL. Multiple pathways in the FGF signaling network are frequently deregulated by gene amplification in oral dysplasias. Int J Cancer 2009; 125:2219-28. [PMID: 19623652 DOI: 10.1002/ijc.24611] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Genetic alteration in oral premalignant lesions (OPLs), the precursors of oral squamous cell carcinomas (OSCCs), may represent key changes in disease initiation and development. We ask if DNA amplification occurs at this early stage of cancer development and which oncogenic pathways are disrupted in OPLs. Here, we evaluated 50 high-grade dysplasias and low-grade dysplasias that later progressed to cancer for gene dosage aberrations using tiling-path DNA microarrays. Early occurrences of DNA amplification and homozygous deletion were frequently detected, with 40% (20/50) of these early lesions exhibiting such features. Expression for 88 genes in 7 recurrent amplicons were evaluated in 5 independent head and neck cancer datasets, with 40 candidates found to be overexpressed relative to normal tissues. These genes were significantly enriched in the canonical ERK/MAPK, FGF, p53, PTEN and PI3K/AKT signaling pathways (p = 8.95 x 10(-3) to 3.18 x 10(-2)). These identified pathways share interactions in one signaling network, and amplification-mediated deregulation of this network was found in 30.0% of these preinvasive lesions. No such alterations were found in 14 low-grade dysplasias that did not progress, whereas 43.5% (10/23) of OSCCs were found to have altered genes within the pathways with DNA amplification. Multitarget FISH showed that amplification of EGFR and CCND1 can coexist in single cells of an oral dysplasia, suggesting the dependence on multiple oncogenes for OPL progression. Taken together, these findings identify a critical biological network that is frequently disrupted in high-risk OPLs, with different specific genes disrupted in different individuals.
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Affiliation(s)
- Ivy F L Tsui
- Department of Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
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30
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Kissel HD, Galipeau PC, Li X, Reid BJ. Translation of an STR-based biomarker into a clinically compatible SNP-based platform for loss of heterozygosity. Cancer Biomark 2009; 5:143-58. [PMID: 19407369 DOI: 10.3233/cbm-2009-0618] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Loss of heterozygosity (LOH) has been shown to be a promising biomarker of cancer risk in patients with premalignant conditions. In this study we describe analytical validation in clinical biopsy samples of a SNP-based pyrosequencing panel targeting regions of LOH on chromosomes 17p and 9p including TP53 and CDKN2A tumor suppressor genes. Assays were tested for analytic specificity, sensitivity, efficiency, and reproducibility. Accuracy was evaluated by comparing SNP-based LOH results to those obtained by previously well-studied short tandem repeat polymorphisms (STRs) in DNA derived from different tissue sources including fresh-frozen endoscopic biopsies, samples from surgical resections, and formalin-fixed paraffin-embedded sections. A 17p/9p LOH panel comprised of 43 SNPs was designed to amplify with universal assay conditions in a two-step PCR and sequence-by-synthesis reaction that can be completed in two hours and 10 minutes. The methods presented can be a model for developing a SNP-based LOH approach targeted to any chromosomal region of interest for other premalignant conditions and this panel could be incorporated as part of a biomarker for cancer risk prediction, early detection, or as entry criteria for randomized trials.
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Affiliation(s)
- Heather D Kissel
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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31
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Abstract
Dysplasia of the oral, laryngeal and oropharyngeal stratified squamous epithelia is a microscopically defined change that may occur in clinically identifiable lesions including erythroplakia, leukoplakia and erythroleukoplakia, lesions that convey a heightened risk for carcinomatous progression. Dysplastic lesions have been classified microscopically according to degree of cytologic atypia and changes in architectural patterns, usually on a three part or four part gradation scale. Vocal cord epithelial lesions are graded according to either the Ljubljana or the World Health Organization (WHO) system whereas oral dysplasias are generally classified according to WHO criteria. Cytologically atypical cells are considered to represent precancerous changes predicting an increase risk for carcinomatous transformation. Inter- and intra-rater reliability studies among pathologists have disclosed low correlation coefficients for four part grading systems, whereas improved agreement is achieved (kappa correlation values) using the Ljubljana systems. Evidence forwarded by some studies supports the prognostic value of progressively severe dysplastic changes for carcinomatous transformation; however, some studies indicate that the presence of a clinically defined lesion without microscopic evidence of dysplasia also connotes increased risk for carcinomatous transformation. Loss of heterozygosity (LOH) at 3p and 9p microsatellite domains, DNA ploidy analysis and nuclear image analyses may have predictive value as molecular and histomorphological biomarkers.
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Affiliation(s)
- Lewis Roy Eversole
- Oral Pathology Diagnostic Services, 4945 Mercury Street, San Diego, CA 92111, USA.
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32
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Rosin MP, Poh CF, Elwood JM, Williams PM, Gallagher R, MacAulay C, Lam WW, Auluck A, Zhang L, Hislop TG. New hope for an oral cancer solution: together we can make a difference. JOURNAL (CANADIAN DENTAL ASSOCIATION) 2008; 74:261-266. [PMID: 18387266 PMCID: PMC2387224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Oral cancer is associated with high mortality and morbidity rates, largely as a result of late diagnosis. Although dental practitioners are trained to identify premalignant and malignant lesions, an organized system is needed to offer guidance and to improve access to experts in diagnosis and management of these lesions. In this article, we describe the many ways in which the British Columbia Oral Cancer Prevention Program (BC OCPP) is addressing this challenge: by linking community dental practices and referral centres, by creating partnerships between scientists and clinicians that already have resulted in new technologies to enhance early diagnosis, by involving a broad range of stakeholders to ensure population-based screening and by engaging in provincial, national and international outreach.
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Affiliation(s)
- Miriam P Rosin
- Simon Fraser University, and BC Oral Cancer Prevention Program, BC Cancer Agency/Cancer Research Centre, Vancouver, British Columbia
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