1
|
Jeroch J, Riedlinger T, Schmitt C, Ebner S, Winkelmann R, Wild PJ, Demes M. A Comparison of Two Different FFPE Tissue Dissection Methods for Routine Diagnostics in Molecular Pathology: Manual Macrodissection versus Automated Microdissection Using the Roche "AVENIO Millisect" System. Cancers (Basel) 2023; 15:3249. [PMID: 37370864 DOI: 10.3390/cancers15123249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/31/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Currently, in routine diagnostics, most molecular testing is performed on formalin-fixed, paraffin-embedded tissue after a histomorphological assessment. In order to find the best possible and targeted individual therapy, knowing the mutational status of the tumour is crucial. The "AVENIO Millisect" system Roche introduced an automation solution for the dissection of tissue on slides. This technology allows the precise and fully automated dissection of the tumour area without wasting limited and valuable patient material. In this study, the digitally guided microdissection was directly compared to the manual macrodissection regarding the precision and duration of the procedure, their DNA concentrations as well as DNA qualities, and the overall costs in 24 FFPE samples. In 21 of 24 cases (87.5%), the DNA yields of the manually dissected samples were higher in comparison to the automatically dissected samples. Shorter execution times and lower costs were also benefits of the manual scraping process. Nevertheless, the DNA quality achieved with both methods was comparable, which is essential for further molecular testing. Therefore, it could be used as an additional tool for precise tumour enrichment.
Collapse
Affiliation(s)
- Jan Jeroch
- Wildlab, University Hospital Frankfurt MVZ GmbH, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Tobias Riedlinger
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Christina Schmitt
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Silvana Ebner
- Wildlab, University Hospital Frankfurt MVZ GmbH, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Ria Winkelmann
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Peter J Wild
- Wildlab, University Hospital Frankfurt MVZ GmbH, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Melanie Demes
- Wildlab, University Hospital Frankfurt MVZ GmbH, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| |
Collapse
|
2
|
Jeong SH, Park M, Park SY, Park J, Kim TH, Lee YJ, Jung EJ, Ju YT, Jeong CY, Kim JY, Ko GH, Kim M, Nam KT, Goldenring JR. Transcriptome Analysis and the Prognostic Role of NUDC in Diffuse and Intestinal Gastric Cancer. Technol Cancer Res Treat 2021; 20:15330338211019501. [PMID: 34060350 PMCID: PMC8173992 DOI: 10.1177/15330338211019501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/05/2021] [Accepted: 04/19/2021] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION There have been few studies about gene differences between patients with diffuse-type gastric cancer and those with intestinal-type gastric cancer. The aim of this study was to compare the transcriptomes of signet ring cell gastric cancer (worst prognosis in diffuse-type) and well-differentiated gastric cancer (best prognosis in intestinal-type); NUDC was identified, and its prognostic role was studied. MATERIALS AND METHODS We performed next-generation sequencing with 5 well-differentiated gastric cancers and 3 of signet ring cell gastric cancer surgical samples. We performed gene enrichment and functional annotation analysis using the Database for Annotation, Visualization and Integrated Discovery bioinformatics resources. Immunohistochemistry was used to validate NUDC expression. RESULTS Overall, 900 genes showed significantly higher expression, 644 genes showed lower expression in signet ring cell gastric cancer than in well-differentiated gastric cancers, and there was a large difference in adhesion, vascular development, and cell-to-cell junction components between the 2 subtypes. We performed variant analysis and found 52 variants and 30 cancer driver genes, including NUDC. We analyzed NUDC expression in gastric cancer tissue and its relationship with prognosis. Cox proportional hazard analysis identified T stage, N stage, and NUDC expression as independent risk factors for survival (P < 0.05). The overall survival of the NUDC-positive group was significantly higher (53.2 ± 0.92 months) than that of the NUDC-negative group (44.6 ± 3.7 months) (P = 0.001) in Kaplan-Meier survival analysis. CONCLUSION We found 30 cancer driver gene candidates and found that the NUDC-positive group showed significantly better survival than the NUDC-negative group via variant analysis.
Collapse
Affiliation(s)
- Sang-Ho Jeong
- Department of Surgery, School of Medicine, Gyeongsang National University, Jinju, South Korea
- Department of Surgery, Gyeongsang National University, Changwon Hospital, Changwon, South Korea
| | - Miyeong Park
- Department of Anesthesiology, Gyeongsang National University, Changwon Hospital, Changwon, South Korea
| | - Sun Yi Park
- Department of Surgery, School of Medicine, Gyeongsang National University, Jinju, South Korea
| | - Jiho Park
- Department of Surgery, School of Medicine, Gyeongsang National University, Jinju, South Korea
| | - Tae-Han Kim
- Department of Surgery, Gyeongsang National University, Changwon Hospital, Changwon, South Korea
| | - Young-Joon Lee
- Department of Surgery, School of Medicine, Gyeongsang National University, Jinju, South Korea
| | - Eun-Jung Jung
- Department of Surgery, School of Medicine, Gyeongsang National University, Jinju, South Korea
- Department of Surgery, Gyeongsang National University, Changwon Hospital, Changwon, South Korea
| | - Young-tae Ju
- Department of Surgery, School of Medicine, Gyeongsang National University, Jinju, South Korea
| | - Chi-Young Jeong
- Department of Surgery, School of Medicine, Gyeongsang National University, Jinju, South Korea
| | - Ju-Yeon Kim
- Department of Surgery, School of Medicine, Gyeongsang National University, Jinju, South Korea
| | - Gyung Hyuck Ko
- Department of Pathology, School of Medicine, Gyeongsang National University, Jinju, South Korea
| | - Minhye Kim
- Department of Pathology, School of Medicine, Gyeongsang National University, Jinju, South Korea
| | - Ki Taek Nam
- Severance Biomedical Science, Yonsei University College of Medicine, Seodaemun-gu, South Korea
| | | |
Collapse
|
3
|
Qi P, Bai QM, Yao QL, Yang WT, Zhou XY. Performance of Automated Dissection on Formalin-Fixed Paraffin-Embedded Tissue Sections for the 21-Gene Recurrence Score Assay. Technol Cancer Res Treat 2020; 19:1533033820960760. [PMID: 33073677 PMCID: PMC7592317 DOI: 10.1177/1533033820960760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
This study aimed to compare the performance of MilliSect dissection and manual dissection. Twenty-five formalin-fixed paraffin-embedded (FFPE) breast cancer tissue blocks were selected for comparison. Specific areas of interest (AOIs) in invasive carcinoma on tissue sections were transferred to dissection slides by manual macrodissection or the MilliSect instrument. The comparison criteria were 1) the time required for dissection; 2) RNA concentration and purity; 3) RNA quantity of 5 housekeeping genes (by RT-qPCR); and 4) ER, PR, HER2, Ki-67 and recurrence score (RS) values (by the 21-gene assay). Then, tumor-adjacent tissues, including fibrocollagenous and epithelial tissues, from the same selected tissue blocks of 8 of 25 patients were scraped using the mesodissection method, and their RS values were assessed to evaluate the influence of tumor-adjacent tissues on the target AOIs. Ultimately, 4 AOIs of invasive ductal carcinoma (IDC) from 1 tissue block of another 4 patients with lymph node (LN) metastases each, LN tissue and a mixture of IDC and LN tissue from the other tissue block of the same 4 patients were mesodissected to evaluate the influence of infiltrating lymphocyte levels on the RS values of AOIs. In our experience, the MilliSect instrument, which provides process management documentation, required more time than manual macrodissection (on average, approximately 9.1 min per sample versus 5.8 min per sample, respectively). The RNA yield and quality of the dissected tissues were comparable for the 2 methods. However, the tumor-adjacent tissues of the AOIs may influence the RS to some extent. Tumor-infiltrating lymphocytes (TILs) can dramatically increase RSs, far exceeding the influence of tumor-adjacent fibrocollagenous and epithelial tissues. In conclusion, MilliSect mesodissection is comparable to manual dissection. This mesodissection tool may facilitate AOI alignment and the dissection process for the 21-gene RS assay. Samples whose adjacent tissues are intermixed with TILs warrant special attention.
Collapse
Affiliation(s)
- Peng Qi
- Department of Pathology, 89667Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, 89667Fudan University, Shanghai, China.,Institute of Pathology, 89667Fudan University, Shanghai, China
| | - Qian-Ming Bai
- Department of Pathology, 89667Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, 89667Fudan University, Shanghai, China.,Institute of Pathology, 89667Fudan University, Shanghai, China
| | - Qian-Lan Yao
- Department of Pathology, 89667Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, 89667Fudan University, Shanghai, China.,Institute of Pathology, 89667Fudan University, Shanghai, China
| | - Wen-Tao Yang
- Department of Pathology, 89667Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, 89667Fudan University, Shanghai, China.,Institute of Pathology, 89667Fudan University, Shanghai, China
| | - Xiao-Yan Zhou
- Department of Pathology, 89667Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, 89667Fudan University, Shanghai, China.,Institute of Pathology, 89667Fudan University, Shanghai, China
| |
Collapse
|
4
|
Nienhüser H, Crnovrsanin N, Nerz D, Heckler M, Sisic L, Lasitschka F, Schneider M, Schmidt T. Expression of Angiogenic Proteins in Tumor and Stroma Affects Survival in Patients With Gastric Cancer. J Surg Res 2020; 255:172-180. [PMID: 32563757 DOI: 10.1016/j.jss.2020.05.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 04/20/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Gastric cancer is one of the most frequent malignancies worldwide. Angiogenic growth factors play a crucial role in mediating the crosstalk between cancer cells and the surrounding microenvironment. In this exploratory study, we investigate the impact of angiogenic proteins within the tumor cell or stroma compartment on survival of patients with gastric cancer. MATERIALS AND METHODS In 29 patients, tumor and stromal compartments were separated using laser capture microdissection. Angiogenic protein expression was measured using a bead-based immunoassay and correlated with tumor stage and overall survival. RESULTS Overall survival was significantly shorter in patients with a high stroma concentration of vascular endothelial growth factor (VEGF)-A (23.5 (±17.6) versus 33.6 (±21.0) mo; P = 0.009) and stem cell factor (22.2 (±18.5) versus 33.6 (±21.8) mo; P = 0.01) compared with patients with a low stroma concentration. High stromal VEGF-D showed a trend toward worse survival (26.8 (±22.0) versus 37.2 (±19.0) mo; P = 0.09). We did not observe any significant correlation between tumor-specific expression of angiogenic cytokines and survival. CONCLUSIONS This translational study highlights the difference in clinical impact between tumor and stromal expression of angiogenic proteins. Compartment-specific concentrations of VEGF-A and stem cell factor affect the clinical prognosis and help to identify the best therapy for patients with gastric cancer.
Collapse
Affiliation(s)
- Henrik Nienhüser
- Department of General, Visceral and Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Nerma Crnovrsanin
- Department of General, Visceral and Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Daniel Nerz
- Department of General, Visceral and Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Max Heckler
- Department of General, Visceral and Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Leila Sisic
- Department of General, Visceral and Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | | | - Martin Schneider
- Department of General, Visceral and Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Thomas Schmidt
- Department of General, Visceral and Transplant Surgery, University of Heidelberg, Heidelberg, Germany.
| |
Collapse
|
5
|
Transcriptional Response of Ovine Lung to Infection with Jaagsiekte Sheep Retrovirus. J Virol 2019; 93:JVI.00876-19. [PMID: 31434729 PMCID: PMC6803282 DOI: 10.1128/jvi.00876-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/10/2019] [Indexed: 02/06/2023] Open
Abstract
Jaagsiekte sheep retrovirus (JSRV) is the etiologic agent of ovine pulmonary adenocarcinoma (OPA), a neoplastic lung disease of sheep. OPA is an important economic and welfare issue for sheep farmers and a valuable naturally occurring animal model for human lung adenocarcinoma. Here, we used RNA sequencing to study the transcriptional response of ovine lung tissue to infection by JSRV. We identified 1,971 ovine genes differentially expressed in JSRV-infected lung compared to noninfected lung, including many genes with roles in carcinogenesis and immunomodulation. The differential expression of selected genes was confirmed using immunohistochemistry and reverse transcription-quantitative PCR. A key finding was the activation of anterior gradient 2, yes-associated protein 1, and amphiregulin in OPA tumor cells, indicating a role for this oncogenic pathway in OPA. In addition, there was differential expression of genes related to innate immunity, including genes encoding cytokines, chemokines, and complement system proteins. In contrast, there was little evidence for the upregulation of genes involved in T-cell immunity. Many genes related to macrophage function were also differentially expressed, reflecting the increased abundance of these cells in OPA-affected lung tissue. Comparison of the genes differentially regulated in OPA with the transcriptional changes occurring in human lung cancer revealed important similarities and differences between OPA and human lung adenocarcinoma. This study provides valuable new information on the pathogenesis of OPA and strengthens the use of this naturally occurring animal model for human lung adenocarcinoma.IMPORTANCE Ovine pulmonary adenocarcinoma is a chronic respiratory disease of sheep caused by jaagsiekte sheep retrovirus (JSRV). OPA is a significant economic problem for sheep farmers in many countries and is a valuable animal model for some forms of human lung cancer. Here, we examined the changes in host gene expression that occur in the lung in response to JSRV infection. We identified a large number of genes with altered expression in infected lung, including factors with roles in cancer and immune system function. We also compared the data from OPA to previously published data from human lung adenocarcinoma and found a large degree of overlap in the genes that were dysregulated. The results of this study provide exciting new avenues for future studies of OPA and may have comparative relevance for understanding human lung cancer.
Collapse
|
6
|
Hipp JD, Johann DJ, Chen Y, Madabhushi A, Monaco J, Cheng J, Rodriguez-Canales J, Stumpe MC, Riedlinger G, Rosenberg AZ, Hanson JC, Kunju LP, Emmert-Buck MR, Balis UJ, Tangrea MA. Computer-Aided Laser Dissection: A Microdissection Workflow Leveraging Image Analysis Tools. J Pathol Inform 2018; 9:45. [PMID: 30622835 PMCID: PMC6298131 DOI: 10.4103/jpi.jpi_60_18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/16/2018] [Indexed: 01/05/2023] Open
Abstract
Introduction The development and application of new molecular diagnostic assays based on next-generation sequencing and proteomics require improved methodologies for procurement of target cells from histological sections. Laser microdissection can successfully isolate distinct cells from tissue specimens based on visual selection for many research and clinical applications. However, this can be a daunting task when a large number of cells are required for molecular analysis or when a sizeable number of specimens need to be evaluated. Materials and Methods To improve the efficiency of the cellular identification process, we describe a microdissection workflow that leverages recently developed and open source image analysis algorithms referred to as computer-aided laser dissection (CALD). CALD permits a computer algorithm to identify the cells of interest and drive the dissection process. Results We describe several "use cases" that demonstrate the integration of image analytic tools probabilistic pairwise Markov model, ImageJ, spatially invariant vector quantization (SIVQ), and eSeg onto the ThermoFisher Scientific ArcturusXT and Leica LMD7000 microdissection platforms. Conclusions The CALD methodology demonstrates the integration of image analysis tools with the microdissection workflow and shows the potential impact to clinical and life science applications.
Collapse
Affiliation(s)
- Jason D Hipp
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Google Inc., Mountain View, CA, USA
| | - Donald J Johann
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yun Chen
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Anant Madabhushi
- Department of Biomedical Engineering, Center for Computational Imaging and Personalized Diagnostics, Case Western Reserve University, Cleveland, OH, USA
| | | | - Jerome Cheng
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jaime Rodriguez-Canales
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Medimmune, LLC, Gaithersburg, MD, USA
| | | | - Greg Riedlinger
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Division of Translational Pathology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Avi Z Rosenberg
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jeffrey C Hanson
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Lakshmi P Kunju
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Michael R Emmert-Buck
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Avoneaux Medical Institute, LLC, Baltimore, MD, USA
| | - Ulysses J Balis
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Michael A Tangrea
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Alvin and Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA
| |
Collapse
|
7
|
Xi T, Zhang G. Integrated analysis of tumor differentiation genes in pancreatic adenocarcinoma. PLoS One 2018; 13:e0193427. [PMID: 29596435 PMCID: PMC5875763 DOI: 10.1371/journal.pone.0193427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 02/09/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Tumor differentiation is an important process in the development of cancer. It is valuable to identify key differentiation related genes in the prognosis and therapy of pancreatic adenocarcinoma. METHODS The mRNA expression data were downloaded from the Cancer Genome Atlas database. Then, differentially expressed tumor differentiation related genes were identified. Additionally, Gene Ontology functional categories and Kyoto Encyclopedia of Genes and Genomes biochemical pathway was used to explore the function. In addition, receiver operating characteristic and survival analysis were carried out to assess the diagnosis and prognosis value. Finally, the electronic validation of selected tumor differentiation related genes was performed. RESULTS A total of 932 genes were identified. Among which, 8 genes including JUB, ERLIN1, HMGA2, FAM110B, EGFR, MCM2, TCTA and SSTR1 were differentially expressed in all different tumor differentiation grades. Functional analysis revealed those genes between highly differentiated and other differentiation were remarkably enriched in pancreatic adenocarcinoma and cell cycle pathway. Finally, ERLIN1, HMGA2, FAM110B, EGFR, MCM2, BCL2L1, E2F1 and RAC1 were associated with the survival time of pancreatic adenocarcinoma patient. Among these genes, JUB, ERLIN1, FAM110B, MCM2 and BCL2L1 also had a diagnosis value for pancreatic adenocarcinoma. Additionally, the expression trend of JUB, HMGA2 and MCM2 was increased along with the tumor differentiation grades. And the expression trend of FAM110B was decreased along with the tumor differentiation grades. The electronic validation result was consistent with the bioinformatics analysis. CONCLUSIONS 12 tumor differentiation related genes including JUB, ERLIN1, HMGA2, FAM110B, EGFR, MCM2, TCTA, SSTR1, BCL2L1, E2F1, RAC1 and STAT1 played crucial roles in the differentiation of pancreatic adenocarcinoma.
Collapse
Affiliation(s)
- Ting Xi
- Department of Gastroenterology, First People’s Hospital of Liaocheng, Liaocheng, Shandong Province, China
- * E-mail:
| | - Guizhi Zhang
- Department of Gastroenterology, Second People’s Hospital of Liaocheng, Liaocheng, Shandong Province, China
| |
Collapse
|
8
|
Abstract
Supplemental Digital Content is available in the text. Sampling of formalin-fixed paraffin-embedded (FFPE) tissue blocks is a critical initial step in molecular pathology. Image-guided coring (IGC) is a new method for using digital pathology images to guide tissue block coring for molecular analyses. The goal of our study is to evaluate the use of IGC for both tissue-based and nucleic acid–based projects in molecular pathology. First, we used IGC to construct a tissue microarray (TMA); second, we used IGC for FFPE block sampling followed by RNA extraction; and third, we assessed the correlation between nuclear counts quantitated from the IGC images and RNA yields. We used IGC to construct a TMA containing 198 normal and breast cancer cores. Histopathologic analysis showed high accuracy for obtaining tumor and normal breast tissue. Next, we used IGC to obtain normal and tumor breast samples before RNA extraction. We selected a random subset of tumor and normal samples to perform computational image analysis to quantify nuclear density, and we built regression models to estimate RNA yields from nuclear count, age of the block, and core diameter. Number of nuclei and core diameter were the strongest predictors of RNA yields in both normal and tumor tissue. IGC is an effective method for sampling FFPE tissue blocks for TMA construction and nucleic acid extraction. We identify significant associations between quantitative nuclear counts obtained from IGC images and RNA yields, suggesting that the integration of computational image analysis with IGC may be an effective approach for tumor sampling in large-scale molecular studies.
Collapse
|
9
|
Rao VT, Ludwin SK, Fuh SC, Sawaya R, Moore CS, Ho MK, Bedell BJ, Sarnat HB, Bar-Or A, Antel JP. MicroRNA Expression Patterns in Human Astrocytes in Relation to Anatomical Location and Age. J Neuropathol Exp Neurol 2016; 75:156-66. [DOI: 10.1093/jnen/nlv016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
|
10
|
Digitally guided microdissection aids somatic mutation detection in difficult to dissect tumors. Cancer Genet 2015; 209:42-9. [PMID: 26767919 DOI: 10.1016/j.cancergen.2015.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/02/2015] [Accepted: 12/09/2015] [Indexed: 01/03/2023]
Abstract
Molecular genetic testing on formalin fixed, paraffin embedded (FFPE) tumors frequently requires dissection of tumor from tissue sections mounted on glass slides. In a process referred to as "manual macrodissection," the pathologist reviews an H&E stained slide at the light microscope and marks areas for dissection, and then the laboratory performs manual dissection from adjacent sections without the aid of a microscope, using the marked reference H&E slide as a guide. Manual macrodissection may be inadequate for tissue sections with low tumor content. We compared manual macrodissection to a new method, digitally guided microdissection, on a series of 32 FFPE pancreatic cancer samples. KRAS hotspot mutation profiling was performed using the Sequenom MassARRAY system (Agena Bioscience). Digitally guided microdissection was performed on multiple smaller areas of high tumor content selected from within the larger areas marked for manual macrodissection. The KRAS mutant allele fraction and estimated neoplastic cellularity were significantly higher in samples obtained by digitally guided microdissection (p < 0.01), and 7 of the 32 samples (22%) showed a detectable mutation only with digitally guided microdissection. DNA quality and yield per cubic millimeter of dissected tissue were similar for both dissection methods. These results indicate a significant improvement in tumor content achievable with digitally guided microdissection.
Collapse
|
11
|
Discovery and validation of an INflammatory PROtein-driven GAstric cancer Signature (INPROGAS) using antibody microarray-based oncoproteomics. Oncotarget 2015; 5:1942-54. [PMID: 24722433 PMCID: PMC4039123 DOI: 10.18632/oncotarget.1879] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
This study aimed to improve gastric cancer (GC) diagnosis by identifying and validating an INflammatory PROtein-driven GAstric cancer Signature (hereafter INPROGAS) using low-cost affinity proteomics. The detection of 120 cytokines, 43 angiogenic factors, 41 growth factors, 40 inflammatory factors and 10 metalloproteinases was performed using commercially available human antibody microarray-based arrays. We identified 21 inflammation-related proteins (INPROGAS) with significant differences in expression between GC tissues and normal gastric mucosa in a discovery cohort of matched pairs (n=10) of tumor/normal gastric tissues. Ingenuity pathway analysis confirmed the "inflammatory response", "cellular movement" and "immune cell trafficking" as the most overrepresented biofunctions within INPROGAS. Using an expanded independent validation cohort (n = 22), INPROGAS classified gastric samples as "GC" or "non-GC" with a sensitivity of 82% (95% CI 59-94) and a specificity of 73% (95% CI 49-89). The positive predictive value and negative predictive value in this validation cohort were 75% (95% CI 53-90) and 80% (95% CI 56-94), respectively. The positive predictive value and negative predictive value in this validation cohort were 75% (95% CI 53-90) and 80% (95% CI 56-94), respectively. Antibody microarray analyses of the GC-associated inflammatory proteome identified a 21-protein INPROGAS that accurately discriminated GC from noncancerous gastric mucosa.
Collapse
|
12
|
Hipp JD, Cheng J, Hanson JC, Rosenberg AZ, Emmert-Buck MR, Tangrea MA, Balis UJ. SIVQ-LCM protocol for the ArcturusXT instrument. J Vis Exp 2014. [PMID: 25078867 DOI: 10.3791/51662] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
SIVQ-LCM is a new methodology that automates and streamlines the more traditional, user-dependent laser dissection process. It aims to create an advanced, rapidly customizable laser dissection platform technology. In this report, we describe the integration of the image analysis software Spatially Invariant Vector Quantization (SIVQ) onto the ArcturusXT instrument. The ArcturusXT system contains both an infrared (IR) and ultraviolet (UV) laser, allowing for specific cell or large area dissections. The principal goal is to improve the speed, accuracy, and reproducibility of the laser dissection to increase sample throughput. This novel approach facilitates microdissection of both animal and human tissues in research and clinical workflows.
Collapse
Affiliation(s)
- Jason D Hipp
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health
| | | | - Jeffrey C Hanson
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health
| | - Avi Z Rosenberg
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health
| | | | - Michael A Tangrea
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health;
| | | |
Collapse
|
13
|
Leung CON, Deng W, Ye TM, Ngan HYS, Tsao SW, Cheung ANY, Pang RTK, Yeung WSB. miR-135a leads to cervical cancer cell transformation through regulation of β-catenin via a SIAH1-dependent ubiquitin proteosomal pathway. Carcinogenesis 2014; 35:1931-40. [PMID: 24503442 DOI: 10.1093/carcin/bgu032] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Human papillomaviruses (HPVs) is the principal etiological agent of cervical cancer (CC). However, exposure to the high-risk type HPV alone is insufficient for tumor formation, and additional factors are required for the HPV-infected cells to become tumorigenic. Dysregulated microRNAs (miRNAs) expression is frequently observed in cancer but their roles in the formation of CC have not been fully revealed. In this study, we compared the expression of miR-135a in laser capture microdissected cervical specimens and confirmed overexpression of the miRNA in malignant cervical squamous cell carcinoma compared with precancerous lesions. Transient force-expression of miR-135a induced growth in low-density culture, anchorage-independent growth, proliferation and invasion of a HPV-16 E6/E7-immortalized cervical epithelial cell line, NC104-E6/E7. The observed effects were due to the inhibitory action of miR-135a on its direct target seven in absentia homolog 1 (SIAH1) leading to upregulation of β-catenin/T cell factor signaling. miR-135a force-expression enhanced the growth of HeLa- and NC104-E6/E7-derived tumor in vivo. The effect of miR-135a could be partially nullified by SIAH1 force-expression. More importantly, the expression of SIAH1 and β-catenin correlated with that of miR-135a in precancerous and cancerous lesions of cervical biopsies. By comparing the tumorigenic activities of miR-135a in E6/E7 positive/negative cell lines and in NC104-E6/E7 with or without E6/E7 knockdown, we demonstrated that HPV E6/E7 proteins are prerequisite for miR-135a as an oncomiR. Taken together, miR-135a/SIAH1/β-catenin signaling is important in the transformation and progression of cervical carcinoma.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Ronald T K Pang
- Department of Obstetrics and Gynaecology, Centre for Reproduction, Development and Growth, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - William S B Yeung
- Department of Obstetrics and Gynaecology, Centre for Reproduction, Development and Growth, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| |
Collapse
|
14
|
Kim K, Lee KH, Lee J, Choi J. Overview of current standpoints in profiling of circulating tumor cells. Arch Pharm Res 2013; 37:88-95. [PMID: 24214218 DOI: 10.1007/s12272-013-0285-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 10/29/2013] [Indexed: 12/27/2022]
Abstract
The goal of this review is summarizing current technologies developed as the in vitro prognostic/diagnostic systems that can rapidly separate and detect circulating tumor cells (CTCs) from cancer patient's blood (1-10 CTCs of 1 billion red blood cells) by labeled and non-labeled method. The review is focused on three major areas of CTC research (1) Summary of previous research on capturing of CTCs, (2) New development of the in vitro prognostic diagnosis system of cancer that is capable of rapid separation of CTCs, (3) Future direction on development of new technologies for CTC profiling. Current CTC researches have helped on identifying patients who may benefit from chemotherapy before treatment, patients who may benefit from continued chemotherapy, and leading to clinical development of CTC-guided chemotherapy strategies. We analyze the feasibility of clinical application of these current CTC research for the ultimate goal of increasing the survivability of cancer patient. The biomolecular assays of viable CTCs from cancer patient may elucidate the mechanism of metastasis and tumor initiating cells and also may have high impact on the development of personalized medicine to overcome the incurable diseases.
Collapse
Affiliation(s)
- Kyobum Kim
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | | |
Collapse
|
15
|
Adey N, Emery D, Bosh D, Callahan S, Schreiner J, Chen Y, Greig A, Geiersbach K, Parry R. A mill based instrument and software system for dissecting slide-mounted tissue that provides digital guidance and documentation. BMC Clin Pathol 2013; 13:29. [PMID: 24188417 PMCID: PMC3826833 DOI: 10.1186/1472-6890-13-29] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 10/28/2013] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Dissection of specific Areas Of Interest (AOIs) of slide-mounted tumor samples is often used to enrich for cancer cells in order to generate better signal to noise ratios in subsequent biochemical characterization. Most clinical laboratories utilize manual dissection for practical reasons and to avoid the expense and difficulties of laser microdissection systems. Unfortunately, manual methods often lack resolution and process documentation. The goal of this project was to design a dissection system for slide-mounted tissue with better precision than manual methods that also provides digital image guidance and electronic process documentation. METHODS An instrument that is essentially a micro tissue mill was developed. It employs a specialized disposable mill bit that simultaneously dispenses liquid, cuts tissue from the slide surface, and aspirates the liquid along with the displaced tissue fragments. A software package was also developed that is capable of transferring digitally annotated AOIs between images of serially cut tissue sections to guide dissection and generate an electronic record of the process. RESULTS The performance of this "meso" dissection system was tested using post dissection visual examination for resolution and accuracy, fluorescence based DNA quantitation for recovery efficiency, and dissection of closely situated mouse-human tissue sections followed by PCR amplification for purity determination. The minimum resolution is a dissected circle smaller than 200 microns in diameter, edge dissection accuracy is tighter than 100 microns, recovery efficiency appears greater than 95%, and recovery purity is greater than 99% relative to a different tissue located 100 microns from the dissection boundary. The system can dissect from both paraffinized and deparaffinized FFPE tissue sections that are mounted on plain glass slides, and it is compatible with DNA, RNA, and protein isolation. CONCLUSIONS The mesodissection system is an effective alternative to manual dissection methods and is applicable for biomarker analysis of anatomical pathology samples, where enrichment of AOIs from the tissue section is helpful, but pure cell populations are not required.
Collapse
Affiliation(s)
- Nils Adey
- AvanSci Bio, LLC, 1290 West 2320 South, Suite D, Salt Lake City, UT 84119-1476, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Leong KJ, James J, Wen K, Taniere P, Morton DG, Bach SP, Matthews GM. Impact of tissue processing, archiving and enrichment techniques on DNA methylation yield in rectal carcinoma. Exp Mol Pathol 2013; 95:343-9. [PMID: 24161956 DOI: 10.1016/j.yexmp.2013.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 10/15/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND Formalin fixation, duration of tissue storage and tissue enrichment techniques can affect DNA methylation yield but these effects have not been quantitatively measured. The aim is to investigate the relative impact of these conditions on DNA methylation in rectal cancer. METHODS 10 rectal cancers with matched undissected fresh frozen tissues, laser capture microdissected (LCM) formalin-fixed paraffin-embedded (FFPE) tissues, manual macrodissected FFPE tissues, adjacent normal mucosa and stromal tissues were analysed for APC and LINE-1 methylation using bisulphite pyrosequencing. RESULTS FFPE cancer tissues, which had been stored for at least 4 years showed similar APC and LINE-1 methylation changes to matched fresh frozen cancer tissues. Laser capture microdissection did not increase the degree of methylation detected compared to manual macrodissection. Analysis of stromal tissues showed that they had undergone significant methylation changes compared to adjacent macroscopically normal mucosa, but not to the same extent as cancer tissues. CONCLUSION Reliable DNA methylation results can be obtained from FFPE rectal cancer tissues, which have been in long-term storage. Because only minor differences in methylation between macrodissected and LCM cancer tissues were found, our results do not support the routine use of LCM to enrich for cancer cells for DNA methylation studies.
Collapse
Affiliation(s)
- Kai Juen Leong
- School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom.
| | | | | | | | | | | | | |
Collapse
|
17
|
Tang W, Morgan DR, Meyers MO, Dominguez RL, Martinez E, Kakudo K, Kuan PF, Banet N, Muallem H, Woodward K, Speck O, Gulley ML. Epstein-barr virus infected gastric adenocarcinoma expresses latent and lytic viral transcripts and has a distinct human gene expression profile. Infect Agent Cancer 2012; 7:21. [PMID: 22929309 PMCID: PMC3598565 DOI: 10.1186/1750-9378-7-21] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Accepted: 08/22/2012] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND EBV DNA is found within the malignant cells of 10% of gastric cancers. Modern molecular technology facilitates identification of virus-related biochemical effects that could assist in early diagnosis and disease management. METHODS In this study, RNA expression profiling was performed on 326 macrodissected paraffin-embedded tissues including 204 cancers and, when available, adjacent non-malignant mucosa. Nanostring nCounter probes targeted 96 RNAs (20 viral, 73 human, and 3 spiked RNAs). RESULTS In 182 tissues with adequate housekeeper RNAs, distinct profiles were found in infected versus uninfected cancers, and in malignant versus adjacent benign mucosa. EBV-infected gastric cancers expressed nearly all of the 18 latent and lytic EBV RNAs in the test panel. Levels of EBER1 and EBER2 RNA were highest and were proportional to the quantity of EBV genomes as measured by Q-PCR. Among protein coding EBV RNAs, EBNA1 from the Q promoter and BRLF1 were highly expressed while EBNA2 levels were low positive in only 6/14 infected cancers. Concomitant upregulation of cellular factors implies that virus is not an innocent bystander but rather is linked to NFKB signaling (FCER2, TRAF1) and immune response (TNFSF9, CXCL11, IFITM1, FCRL3, MS4A1 and PLUNC), with PPARG expression implicating altered cellular metabolism. Compared to adjacent non-malignant mucosa, gastric cancers consistently expressed INHBA, SPP1, THY1, SERPINH1, CXCL1, FSCN1, PTGS2 (COX2), BBC3, ICAM1, TNFSF9, SULF1, SLC2A1, TYMS, three collagens, the cell proliferation markers MYC and PCNA, and EBV BLLF1 while they lacked CDH1 (E-cadherin), CLDN18, PTEN, SDC1 (CD138), GAST (gastrin) and its downstream effector CHGA (chromogranin). Compared to lymphoepithelioma-like carcinoma of the uterine cervix, gastric cancers expressed CLDN18, EPCAM, REG4, BBC3, OLFM4, PPARG, and CDH17 while they had diminished levels of IFITM1 and HIF1A. The druggable targets ERBB2 (Her2), MET, and the HIF pathway, as well as several other potential pharmacogenetic indicators (including EBV infection itself, as well as SPARC, TYMS, FCGR2B and REG4) were identified in some tumor specimens. CONCLUSION This study shows how modern molecular technology applied to archival fixed tissues yields novel insights into viral oncogenesis that could be useful in managing affected patients.
Collapse
Affiliation(s)
- Weihua Tang
- Department of Pathology & Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, 913 Brinkhous-Bullitt Building, Chapel Hill, NC, 27599-7525, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Guo T, Fan L, Ng WH, Zhu Y, Ho M, Wan WK, Lim KH, Ong WS, Lee SS, Huang S, Kon OL, Sze SK. Multidimensional Identification of Tissue Biomarkers of Gastric Cancer. J Proteome Res 2012; 11:3405-13. [DOI: 10.1021/pr300212g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tiannan Guo
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
| | - Lingling Fan
- Center for Stem Cell Research & Application, Union Hospital, Huazhong University of Science and Technology, Wuhan, P.R. China 430022
| | | | - Yi Zhu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
| | | | - Wei Keat Wan
- Pathology Department, Singapore General Hospital, Outram Road, Singapore
169608
| | - Kiat Hon Lim
- Pathology Department, Singapore General Hospital, Outram Road, Singapore
169608
| | | | | | - Shiang Huang
- Center for Stem Cell Research & Application, Union Hospital, Huazhong University of Science and Technology, Wuhan, P.R. China 430022
| | | | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
| |
Collapse
|