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Xiao Y, Zhang G, Wang L, Liang M. Exploration and validation of a combined immune and metabolism gene signature for prognosis prediction of colorectal cancer. Front Endocrinol (Lausanne) 2022; 13:1069528. [PMID: 36518242 PMCID: PMC9742469 DOI: 10.3389/fendo.2022.1069528] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/14/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is still one of the most frequently diagnosed malignancy around the world. The complex etiology and high heterogeneity of CRC necessitates the identification of new reliable signature to identify different tumor prognosis, which may help more precise understanding of the molecular properties of CRC and identify the appropriate treatment for CRC patients. In this study, we aimed to identify a combined immune and metabolism gene signature for prognosis prediction of CRC from large volume of CRC transcriptional data. METHODS Gene expression profiling and clinical data of HCC samples was retrieved from the from public datasets. IRGs and MRGs were identified from differential expression analysis. Univariate and multivariate Cox regression analysis were applied to establish the prognostic metabolism-immune status-related signature. Kaplan-Meier survival and receiver operating characteristic (ROC) curves were generated for diagnostic efficacy estimation. Real-time polymerase chain reaction (RT-PCR), Western blot and immunohistochemistry (IHC) was conducted to verified the expression of key genes in CRC cells and tissues. RESULTS A gene signature comprising four genes (including two IRGs and two MRGs) were identified and verified, with superior predictive performance in discriminating the overall survival (OS) of high-risk and low-risk compared to existing signatures. A prognostic nomogram based on the four-gene signature exhibited a best predictive performance, which enabled the prognosis prediction of CRC patients. The hub gene ESM1 related to CRC were selected via the machine learning and prognostic analysis. RT-PCR, Western blot and IHC indicated that ESM1 was high expressed in tumor than normal with superior predictive performance of CRC survival. CONCLUSIONS A novel combined MRGs and IRGs-related prognostic signature that could stratify CRC patients into low-and high- risk groups of unfavorable outcomes for survival, was identified and verified. This might help, to some extent, to individualized treatment and prognosis assessment of CRC patients. Similarly, the mining of key genes provides a new perspective to explore the molecular mechanisms and targeted therapies of CRC.
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Affiliation(s)
- Yitai Xiao
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
- *Correspondence: Yitai Xiao, ; Mingzhu Liang,
| | - Guixiong Zhang
- Department of Interventional Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lizhu Wang
- Department of Radiology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Mingzhu Liang
- Department of Radiology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
- *Correspondence: Yitai Xiao, ; Mingzhu Liang,
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3
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Pan LJ, Chen JL, Wu ZX, Wu YM. Exportin-T: A Novel Prognostic Predictor and Potential Therapeutic Target for Neuroblastoma. Technol Cancer Res Treat 2021; 20:15330338211039132. [PMID: 34469238 PMCID: PMC8414936 DOI: 10.1177/15330338211039132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 07/22/2021] [Indexed: 01/06/2023] Open
Abstract
Exportins as the key mediators of nucleocytoplasmic transport have been identified as the controllers of the passage of numerous types of crucial cancer-related proteins. Targeting exportins in cancer cells might represent an emerging strategy in cancer intervention with the potential to affect clinical outcomes. Here, we focused on the prognostic and therapeutic values of Exportin-T (XPOT) in neuroblastoma. The correlation between the expression and prognostic values of XPOT in patients with neuroblastoma was investigated based on both published transcriptome data and our clinical data. Then, decision curve analysis (DCA) was implemented to identify a XPOT risk prediction model. In addition, RNA inference was performed to silence the expression of XPOT to further investigate the specific roles of XPOT in the progression of neuroblastoma in vitro. Overexpression of XPOT mRNA was associated with poor clinical characteristics, such as age at diagnosis more than 18 months, amplification of MYCN, and advanced International Neuroblastoma Staging System (INSS) stage, and XPOT expression was identified as an independent poor prognosis factor for neuroblastoma using Cox proportional hazards model (P < .001). DCA suggested that neuroblastoma patients could benefit from XPOT risk prediction model-guided interventions (status of MYCN + INSS stage + XPOT). Experimentally, knockdown of XPOT by small interfering RNA inhibited the proliferation and migration in neuroblastoma cells. XPOT is identified as a novel prognostic predictor and potential therapeutic target for neuroblastoma patients. Further investigation should focus on the profound molecular mechanism underlying the tumor inhibition activity of XPOT inhibitors.
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Affiliation(s)
- Li-Jia Pan
- Xinhua Hospital Affiliated to Shanghai
Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Pediatric Research, Shanghai, China
| | - Jian-Lei Chen
- Children’s Hospital of Soochow
University, Suzhou, China
| | - Zhi-Xiang Wu
- Xinhua Hospital Affiliated to Shanghai
Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Pediatric Research, Shanghai, China
- Children’s Hospital of Soochow
University, Suzhou, China
| | - Ye-Ming Wu
- Xinhua Hospital Affiliated to Shanghai
Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Pediatric Research, Shanghai, China
- Children’s Hospital of Soochow
University, Suzhou, China
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5
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Wei BR, Halsey CH, Hoover SB, Puri M, Yang HH, Gallas BD, Lee MP, Chen W, Durham AC, Dwyer JE, Sánchez MD, Traslavina RP, Frank C, Bradley C, McGill LD, Esplin DG, Schaffer PA, Cramer SD, Lyle LT, Beck J, Buza E, Gong Q, Hewitt SM, Simpson RM. Agreement in Histological Assessment of Mitotic Activity Between Microscopy and Digital Whole Slide Images Informs Conversion for Clinical Diagnosis. Acad Pathol 2019; 6:2374289519859841. [PMID: 31321298 PMCID: PMC6628521 DOI: 10.1177/2374289519859841] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/15/2019] [Accepted: 05/19/2019] [Indexed: 01/27/2023] Open
Abstract
Validating digital pathology as substitute for conventional microscopy in diagnosis
remains a priority to assure effectiveness. Intermodality concordance studies typically
focus on achieving the same diagnosis by digital display of whole slide images and
conventional microscopy. Assessment of discrete histological features in whole slide
images, such as mitotic figures, has not been thoroughly evaluated in diagnostic practice.
To further gauge the interchangeability of conventional microscopy with digital display
for primary diagnosis, 12 pathologists examined 113 canine naturally occurring mucosal
melanomas exhibiting a wide range of mitotic activity. Design reflected diverse diagnostic
settings and investigated independent location, interpretation, and enumeration of mitotic
figures. Intermodality agreement was assessed employing conventional microscopy (CM40×),
and whole slide image specimens scanned at 20× (WSI20×) and at 40× (WSI40×) objective
magnifications. An aggregate 1647 mitotic figure count observations were available from
conventional microscopy and whole slide images for comparison. The intraobserver
concordance rate of paired observations was 0.785 to 0.801; interobserver rate was 0.784
to 0.794. Correlation coefficients between the 2 digital modes, and as compared to
conventional microscopy, were similar and suggest noninferiority among modalities,
including whole slide image acquired at lower 20× resolution. As mitotic figure counts
serve for prognostic grading of several tumor types, including melanoma, 6 of 8
pathologists retrospectively predicted survival prognosis using whole slide images,
compared to 9 of 10 by conventional microscopy, a first evaluation of whole slide image
for mitotic figure prognostic grading. This study demonstrated agreement of replicate
reads obtained across conventional microscopy and whole slide images. Hence, quantifying
mitotic figures served as surrogate histological feature with which to further credential
the interchangeability of whole slide images for primary diagnosis.
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Affiliation(s)
- Bih-Rong Wei
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Charles H Halsey
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shelley B Hoover
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Munish Puri
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Howard H Yang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brandon D Gallas
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, USA
| | - Maxwell P Lee
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Weijie Chen
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, USA
| | - Amy C Durham
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer E Dwyer
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Melissa D Sánchez
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan P Traslavina
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Chad Frank
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Charles Bradley
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Paula A Schaffer
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Sarah D Cramer
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - L Tiffany Lyle
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jessica Beck
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth Buza
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Qi Gong
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, USA
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - R Mark Simpson
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Villa I, Mathieu MC, Bosq J, Auperin A, Pomerol JF, Lacroix-Triki M, Scoazec JY, Dartigues P. Daily Biopsy Diagnosis in Surgical Pathology: Concordance Between Light Microscopy and Whole-Slide Imaging in Real-Life Conditions. Am J Clin Pathol 2018; 149:344-351. [PMID: 29452345 DOI: 10.1093/ajcp/aqx161] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVES The current challenge for the various digital whole-slide imaging (WSI) systems is to be definitively validated for diagnostic purposes. We designed a concordance study between glass slide and digital slide diagnosis in real-life conditions, coupled with an ergonomic study. METHODS Three senior pathologists evaluated, first in glass slides and then in digital slides, 119 biopsy cases, including 749 slides, with 332 H&E saffron stains and 417 additional techniques, mainly immunohistochemistry. RESULTS All digital slides, including specially stained slides, were interpretable. Concordance between glass slides and digital slides was observed in 87.4% of cases. Minor discordances were observed in 12 (10.1%) cases and major discordances, with therapeutic impact, in three (2.5%), including one related to WSI. The satisfaction of participants was high and increased with time. CONCLUSIONS Our study confirms the feasibility and accuracy of WSI diagnosis, even for cases having multiple samples and requiring special staining techniques, such as immunohistochemistry and in situ hybridization.
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Affiliation(s)
- Irène Villa
- Département de Biologie et Pathologie Médicales, Service de Pathologie Morphologique, Villejuif, France
| | - Marie-Christine Mathieu
- Département de Biologie et Pathologie Médicales, Service de Pathologie Morphologique, Villejuif, France
| | - Jacques Bosq
- Département de Biologie et Pathologie Médicales, Service de Pathologie Morphologique, Villejuif, France
| | - Anne Auperin
- Service de Biostatistique et d’Epidémiologie, Gustave Roussy Cancer Campus, Villejuif, France
| | | | - Magali Lacroix-Triki
- Département de Biologie et Pathologie Médicales, Service de Pathologie Morphologique, Villejuif, France
| | - Jean-Yves Scoazec
- Département de Biologie et Pathologie Médicales, Service de Pathologie Morphologique, Villejuif, France
- Faculté de Médecine de Bicêtre, Université Paris Saclay, Université Paris Sud XI, Le Kremlin-Bicêtre, France
| | - Peggy Dartigues
- Département de Biologie et Pathologie Médicales, Service de Pathologie Morphologique, Villejuif, France
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Abstract
Whole-slide imaging revolutionizes the field of pathology especially in the areas of facilitation of research, long-term storages, exchange of information, and image analysis. In this process, a scanning equipment (scanner) scans the whole glass slide into a digital file. In research in esophageal adenocarcinoma or other cancers, whole-slide imaging could help in production of high-resolution images for studying and sharing of research information, assessment of tissue microarray slides as well as allowing digital image analysis of the tissue information such as level of staining (e.g., HER2) in a more efficient and objective manner. In this chapter, we will elaborate the concepts, advantages, barriers, and the operations of whole-slide imaging scanning.
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Affiliation(s)
- Alfred K Lam
- Cancer Molecular Pathology of School of Medicine, Griffith University, Gold Coast, Australia.
| | - Melissa Leung
- Cancer Molecular Pathology of School of Medicine, Griffith University, Gold Coast, Australia
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8
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Whole Slide Imaging Versus Microscopy for Primary Diagnosis in Surgical Pathology: A Multicenter Blinded Randomized Noninferiority Study of 1992 Cases (Pivotal Study). Am J Surg Pathol 2017; 42:39-52. [PMID: 28961557 PMCID: PMC5737464 DOI: 10.1097/pas.0000000000000948] [Citation(s) in RCA: 228] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Most prior studies of primary diagnosis in surgical pathology using whole slide imaging (WSI) versus microscopy have focused on specific organ systems or included relatively few cases. The objective of this study was to demonstrate that WSI is noninferior to microscopy for primary diagnosis in surgical pathology. A blinded randomized noninferiority study was conducted across the entire range of surgical pathology cases (biopsies and resections, including hematoxylin and eosin, immunohistochemistry, and special stains) from 4 institutions using the original sign-out diagnosis (baseline diagnosis) as the reference standard. Cases were scanned, converted to WSI and randomized. Sixteen pathologists interpreted cases by microscopy or WSI, followed by a wash-out period of ≥4 weeks, after which cases were read by the same observers using the other modality. Major discordances were identified by an adjudication panel, and the differences between major discordance rates for both microscopy (against the reference standard) and WSI (against the reference standard) were calculated. A total of 1992 cases were included, resulting in 15,925 reads. The major discordance rate with the reference standard diagnosis was 4.9% for WSI and 4.6% for microscopy. The difference between major discordance rates for microscopy and WSI was 0.4% (95% confidence interval, -0.30% to 1.01%). The difference in major discordance rates for WSI and microscopy was highest in endocrine pathology (1.8%), neoplastic kidney pathology (1.5%), urinary bladder pathology (1.3%), and gynecologic pathology (1.2%). Detailed analysis of these cases revealed no instances where interpretation by WSI was consistently inaccurate compared with microscopy for multiple observers. We conclude that WSI is noninferior to microscopy for primary diagnosis in surgical pathology, including biopsies and resections stained with hematoxylin and eosin, immunohistochemistry and special stains. This conclusion is valid across a wide variety of organ systems and specimen types.
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