Microarray Profiling of DNA Extracted from FFPE Tissues Using SNP 6.0 Affymetrix Platform

Abstract Background Osteoarthritis (OA) is thought to be the most prevalent chronic joint disease, especially in Tibet of China. Here, we aimed to explore the integrative lncRNA and mRNA landscape between the OA patients of Tibet and Han. Methods The lncRNA and mRNA expression microarray profiling was performed by SurePrint G3 Human Gene Expression 8x60K v2 Microarray in articular cartilage samples from OA patients of Han nationality and Tibetans, followed by GO, KEGG, and trans-regulation and cis-regulation analysis of lncRNA and mRNA. Results We found a total of 117 lncRNAs and 297 mRNAs differently expressed in the cartilage tissues of Tibetans (n = 5) comparing with those of Chinese Han (n = 3), in which 49 lncRNAs and 158 mRNAs were upregulated, and 68 lncRNAs and 139 mRNAs were downregulated. GO and KEGG analysis showed that several unreported biological processes and signaling pathways were particularly identified. LncRNA-mRNA co-expression analysis revealed a remarkable lncRNA-mRNA relationship, in which OTOA may play a critical role in the different mechanisms of the OA progression between Tibetans and Chinese Han. Conclusion This study identified different lncRNA/mRNA expression profiling between OA patients of Tibetans and Han, which were involved in many characteristic biological processes and signaling pathways.

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Identification of candidate biomarkers of liver hydatid disease via microarray profiling, bioinformatics analysis, and machine learning

Journal of International Medical Research ◽

10.1177/0300060521993980 ◽

2021 ◽

Vol 49 (3) ◽

pp. 030006052199398

Author(s):

Jinwu Peng ◽

Zhili Duan ◽

Yamin Guo ◽

Xiaona Li ◽

Xiaoqin Luo ◽

...

Keyword(s):

Random Forest ◽

Hydatid Disease ◽

Characteristic Curve ◽

Receiver Operator Characteristic Curve ◽

Random Forest Model ◽

Hepatic Hydatid Disease ◽

Forest Model ◽

Protein Protein Interaction ◽

Ppi Networks ◽

Microarray Profiling

Objectives Liver echinococcosis is a severe zoonotic disease caused by Echinococcus (tapeworm) infection, which is epidemic in the Qinghai region of China. Here, we aimed to explore biomarkers and establish a predictive model for the diagnosis of liver echinococcosis. Methods Microarray profiling followed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis was performed in liver tissue from patients with liver hydatid disease and from healthy controls from the Qinghai region of China. A protein–protein interaction (PPI) network and random forest model were established to identify potential biomarkers and predict the occurrence of liver echinococcosis, respectively. Results Microarray profiling identified 1152 differentially expressed genes (DEGs), including 936 upregulated genes and 216 downregulated genes. Several previously unreported biological processes and signaling pathways were identified. The FCGR2B and CTLA4 proteins were identified by the PPI networks and random forest model. The random forest model based on FCGR2B and CTLA4 reliably predicted the occurrence of liver hydatid disease, with an area under the receiver operator characteristic curve of 0.921. Conclusion Our findings give new insight into gene expression in patients with liver echinococcosis from the Qinghai region of China, improving our understanding of hepatic hydatid disease.

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Multiplexed In Situ Protein Profiling with High-Performance Cleavable Fluorescent Tyramide

Molecules ◽

10.3390/molecules26082206 ◽

2021 ◽

Vol 26 (8) ◽

pp. 2206

Author(s):

Thai Pham ◽

Renjie Liao ◽

Joshua Labaer ◽

Jia Guo

Keyword(s):

High Performance ◽

Single Cells ◽

Protein Quantification ◽

Cellular Systems ◽

Protein Profiling ◽

High Signal ◽

Protein Targets ◽

Chemical Reagents ◽

Ffpe Tissues

Understanding the composition, function and regulation of complex cellular systems requires tools that quantify the expression of multiple proteins at their native cellular context. Here, we report a highly sensitive and accurate protein in situ profiling approach using off-the-shelf antibodies and cleavable fluorescent tyramide (CFT). In each cycle of this method, protein targets are stained with horseradish peroxidase (HRP) conjugated antibodies and CFT. Subsequently, the fluorophores are efficiently cleaved by mild chemical reagents, which simultaneously deactivate HRP. Through reiterative cycles of protein staining, fluorescence imaging, fluorophore cleavage, and HRP deactivation, multiplexed protein quantification in single cells in situ can be achieved. We designed and synthesized the high-performance CFT, and demonstrated that over 95% of the staining signals can be erased by mild chemical reagents while preserving the integrity of the epitopes on protein targets. Applying this method, we explored the protein expression heterogeneity and correlation in a group of genetically identical cells. With the high signal removal efficiency, this approach also enables us to accurately profile proteins in formalin-fixed paraffin-embedded (FFPE) tissues in the order of low to high and also high to low expression levels.

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Characterization of epididymal and testicular histologic lesions and use of immunohistochemistry and PCR on formalin-fixed tissues to detect Brucella canis in male dogs

Journal of Veterinary Diagnostic Investigation ◽

10.1177/1040638720986883 ◽

2021 ◽

pp. 104063872098688

Author(s):

Andrea M. Camargo-Castañeda ◽

Lauren W. Stranahan ◽

John F. Edwards ◽

Daniel G. Garcia-Gonzalez ◽

Leonardo Roa ◽

...

Keyword(s):

Accurate Diagnosis ◽

Testicular Atrophy ◽

Detection Techniques ◽

Formalin Fixed Paraffin ◽

Brucella Canis ◽

Formalin Fixed Paraffin Embedded ◽

Variable Sensitivity ◽

Ffpe Tissues ◽

Formalin Fixed

In male dogs, Brucella canis frequently causes epididymitis, ultimately resulting in testicular atrophy and infertility. Although B. canis predominantly affects the epididymis, the misleading term “orchitis” is still commonly used by clinicians. Of additional concern, diagnosis in dogs remains challenging because of variable sensitivity and specificity of serologic assays and fluctuations in bacteremia levels in infected dogs, reducing the sensitivity of blood culture. We describe here the histologic lesions in the scrotal contents of 8 dogs suspected of being infected with B. canis and clinically diagnosed with orchitis. We explored the possibility of using immunohistochemistry (IHC) and real-time PCR (rtPCR) in formalin-fixed, paraffin-embedded (FFPE) tissues to detect the presence of B. canis. Epididymitis of variable chronicity was identified in all 8 dogs, with only 3 also exhibiting orchitis. Using rtPCR, the presence of B. canis was identified in 4 of 8 dogs, with 3 of these 4 dogs also positive by IHC. These results suggest that rtPCR and IHC are promising techniques that can be used in FFPE tissues to detect B. canis when other detection techniques are unavailable. Additionally, accurate recognition of epididymitis rather than orchitis in suspect cases could aid in accurate diagnosis.

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LINC-25. BRAF ABERRATIONS IN PEDIATRIC PILOCYTIC ASTROCYTOMAS (PCAs): PREVALENCE AND IMPACT ON CLINICAL OUTCOME

Neuro-Oncology ◽

10.1093/neuonc/noaa222.459 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii383-iii383

Author(s):

Subramaniam Ramanathan ◽

Maya Prasad ◽

Tushar Vora ◽

Mamta Gurav ◽

Ayushi Sahay ◽

...

Keyword(s):

Clinical Outcome ◽

Statistical Significance ◽

Tumor Resection ◽

Brafv600e Mutation ◽

Therapeutic Implications ◽

Pilocytic Astrocytomas ◽

Ffpe Tissues ◽

Braf Fusion ◽

Poor Outcomes ◽

The Impact

Abstract BACKGROUND Increasing knowledge on pilocytic astrocytoma (PCA) biology now points towards an aberration in BRAF/MAPK/ERK pathway which has both diagnostic and therapeutic implications. This study was done to note the impact of BRAF aberrations on clinical outcome in childhood PCA. METHODS FFPE tissues of all childhood PCA diagnosed during 2011–2017 were evaluated for BRAFV600E mutation by Sanger sequencing and KIAA1549 fusion transcripts (16–9;15–9;16-11) by reverse transcriptase polymerase chain reaction. Children undergoing gross tumor resection received no adjuvant treatment. Unresectable tumors (only biopsy) and NF-1 associated PCAs, were treated if clinically indicated. Only patients with documented therapy details/followup were included for analysis. STUDY RESULTS Ninety-eight patients (median age-7.7yrs; boy:girl ratio-1.4) were included. Major sites were: Cerebellum-37(38%), 3rd Ventricle-26(27%), Cerebrum-15(15%). While BRAFV600E mutation was noted in 7/89(8%) specimens, BRAF-fusions were found in 34/85(40%). Following surgery/biopsy, 23(24%) and 21(22%) received adjuvant chemotherapy and radiotherapy respectively. The 1-year/3-year/5-year-EFS of the overall cohort was 90.7%/81.3%/67.4% respectively. Cerebellar tumors did better vis-à-vis other sites(5yr-EFS:74.3% v/s 66.4%;p=0.403). The 5yr-EFS of BRAF-fusion positive tumors (34), tumors without any BRAF aberration (40) and BRAFV600E mutant tumors (7) was 84.8%/ 69.6%/ 42.9% (p=0.215). CONCLUSIONS BRAF-fusion and BRAFV600E mutation were associated with good and poor outcomes respectively. Lack of statistical significance could be attributed to use of radiation as planned therapy in patients from earlier years. Data on BRAF aberrations in PCAs aids decision making regarding adjuvant therapy and choosing appropriate salvage-therapy especially in relapsed/refractory PCAs.

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Large-scale microarray profiling reveals four stages of immune escape in non-Hodgkin lymphomas

OncoImmunology ◽

10.1080/2162402x.2016.1188246 ◽

2016 ◽

Vol 5 (7) ◽

pp. e1188246 ◽

Cited By ~ 21

Author(s):

Marie Tosolini ◽

Christelle Algans ◽

Frédéric Pont ◽

Bernard Ycart ◽

Jean-Jacques Fournié

Keyword(s):

Large Scale ◽

Immune Escape ◽

Microarray Profiling

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Reactivation of BK Polyomavirus in Urine Cytology Is Not Associated with Urothelial Cell Carcinoma

Viruses ◽

10.3390/v12121412 ◽

2020 ◽

Vol 12 (12) ◽

pp. 1412

Author(s):

Faisal Klufah ◽

Ghalib Mobaraki ◽

Axel zur Hausen ◽

Iryna V. Samarska

Keyword(s):

Cell Carcinoma ◽

Urine Cytology ◽

Urothelial Cell ◽

The Other ◽

Urothelial Cell Carcinoma ◽

Tissue Samples ◽

Bk Polyomavirus ◽

Ffpe Tissues ◽

Immunosuppressed Patients ◽

History Of

BK polyomavirus (BKPyV) has been associated with some high-grade and special urothelial cell carcinoma (UCC) subtypes in immunosuppressed patients. Here, we evaluated the relationship of BKPyV-positive urine cytology specimens (UCS) with UCC. A large single-institution database was retrospectively searched for UCS positive for decoy cells, suggesting BKPyV infection. These were tested for the presence of BKPyV by PCR and immunohistochemistry (IHC) in urine sediments and formalin-fixed paraffin-embedded (FFPE) tissue samples of UCC. Decoy cells were reported in 30 patients out of the database with 22.867 UCS. Of these 30 patients, 16 (53.3%) had no history of UCC. Six patients out of these 16 had a history of transplantation, 4 had a history of severe chronic medical conditions, and 6 had no chronic disease. The other fourteen patients were diagnosed with either in situ or invasive UCC of the urinary bladder (14/30; 46.6%) prior to the detection of decoy cells in the urine. Nine of these UCC patients received intravesical treatment (BCG or mitomycin) after the first presentation with UCC. However, the clinical data on the treatment of the other five UCC patients was lacking. IHC identified BKPyV-positivity in the urine samples of non-UCC and UCC patients, while no BKPyV positivity was found in FFPE tissues of primary UCCs and metastases. In addition, BKPyV-PCR results revealed the presence of BKPyV DNA in the urine of the UCC cases, yet none in the UCC tissues itself. These data strongly indicate that BKPyV reactivation is not restricted to immunosuppression. It can be found in UCS of the immunocompetent patients and may be related to the intravesical BCG or mitomycin treatment of the UCC patients.

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