scholarly journals Ovarian Cancer Translational Activity of the Multicenter Italian Trial in Ovarian Cancer (MITO) Group: Lessons Learned in 10 Years of Experience

Cells ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 903
Author(s):  
Daniela Califano ◽  
Daniela Russo ◽  
Giosuè Scognamiglio ◽  
Nunzia Simona Losito ◽  
Anna Spina ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Clinical Trials ◽  
Clinical Data ◽  
Gynecologic Cancer ◽  
Years Of Experience ◽  
Web Based ◽  
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Embedded Blocks ◽  
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Ovarian cancer is the most lethal gynecological cancer, and despite years of research, with the exception of a BRCA mutation driving the use of PARP inhibitors, no new prognostic/predictive biomarkers are clinically available. Improvement in biomarker selection and validation may derive from the systematic inclusion of translational analyses into the design of clinical trials. In the era of personalized medicine, the prospective centralized collection of high-quality biological material, expert pathological revision, and association to well-controlled clinical data are important or even essential added values to clinical trials. Here, we present the academic experience of the MITO (Multicenter Italian Trial in Ovarian Cancer) group, including gynecologists, pathologists, oncologists, biostatisticians, and translational researchers, whose effort is dedicated to the care and basic/translational research of gynecologic cancer. In our ten years of experience, we have been able to collect and process, for translational analyses, formalin-fixed, paraffin-embedded blocks from more than one thousand ovarian cancer patients. Standard operating procedures for collection, shipping, and processing were developed and made available to MITO researchers through the coordinating center’s web-based platform. Clinical data were collected through dedicated electronic case report forms hosted in a web-based electronic platform and stored in a central database at the trial’s coordinating center, which performed all the analyses related to the proposed translational researches. During this time, we improved our strategies of block management from retrospective to prospective collection, up to the design of a prospective collection with a quality check for sample eligibility before patients’ accrual. The final aim of our work is to share our experience by suggesting a guideline for the process of centralized collection, revision processing, and storing of formalin-fixed, paraffin-embedded blocks for translational purposes.

scholarly journals miRNA expression profiling in formalin-fixed paraffin-embedded endometriosis and ovarian cancer samples

2017 ◽  
Vol Volume 10 ◽  
pp. 4225-4238 ◽  
Author(s):  
Ovidiu-Leonard Braicu ◽  
Liviuta Budisan ◽  
Rares Buiga ◽  
Ancuta Jurj ◽  
Patriciu Achimas-Cadariu ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Mirna Expression ◽  
Expression Profiling ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Mirna Expression Profiling ◽  
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scholarly journals Genetic Diversity of Hepatic/Non-Hepatic Cystic Echinococ-cosis in Baqiyatallah Hospital, Tehran, Iran

2020 ◽  
Author(s):  
Hamidreza NEYSI ◽  
Tahereh MOHAMMADZADEH ◽  
Seyed Mahmoud SADJJADI ◽  
Jamal AKHAVANMOGHADDAM ◽  
Alireza SHAMSAEI
Keyword(s):  
Sensu Stricto ◽  
Sequence Alignments ◽  
Oxidase Gene ◽  
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Formalin Fixed Paraffin Embedded ◽  
Embedded Blocks ◽  
Related Genotype ◽  
Polymerase Chain ◽  
Organ Tropism ◽  
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Background: Cystic echinococcosis (CE) is a worldwide zoonotic helminthic disease caused by the larval stage of Echinococcus granulosus. The infection is particularly important in terms of economic and medico-veterinary aspects in endemic areas including Iran. Considering the possibility of organ-tropism in E. granulosus strains, the present study was aimed to identify the genotypes of E. granulosus in different organs involved in patients, undergone surgery in Baqiyatallah Hospital, Tehran, Iran from 2005-2015. Methods: Overall, 29 formalin-fixed paraffin-embedded tissues (FFPT) from patients with histologically confirmed CE including liver (N: 14) lungs (N: 6) abdomen (N: 2), pancreas (N: 2) and each of spleen, gallbladder and, muscles (N: 1) plus unknown organs (N: 2) were used and genetically characterized using polymerase chain reaction, followed by partial sequencing of mitochondrial cytochrome c oxidase gene subunit 1(cox1) and analyzed. Results: Nineteen out of 29 isolates including liver (N: 6) lungs (N: 4) abdomen (N: 2), pancreas (N: 2) and each of spleen, gallbladder, and muscle (N: 1), unknown organs (N: 2) obtained from paraffin-embedded blocks of human CE created an acceptable sequence in two directions. All 19 isolates regardless of the organ involved were recognized as E. granulosus sensu stricto (G1). Conclusion: The sequence alignments of the isolates displayed two profiles. All sequenced samples showed E. granulosus sensu stricto (G1) with no organ-related genotype.

scholarly journals SMIXnorm: Fast and Accurate RNA-Seq Data Normalization for Formalin-Fixed Paraffin-Embedded Samples

2021 ◽  
Vol 12 ◽  
Author(s):  
Shen Yin ◽  
Xiaowei Zhan ◽  
Bo Yao ◽  
Guanghua Xiao ◽  
Xinlei Wang ◽  
...  
Keyword(s):  
Mixture Model ◽  
Normalization Method ◽  
Superior Performance ◽  
Rna Seq ◽  
Web Based ◽  
Normalization Methods ◽  
Formalin Fixed Paraffin ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded ◽  
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RNA-sequencing (RNA-seq) provides a comprehensive quantification of transcriptomic activities in biological samples. Formalin-Fixed Paraffin-Embedded (FFPE) samples are collected as part of routine clinical procedure, and are the most widely available biological sample format in medical research and patient care. Normalization is an essential step in RNA-seq data analysis. A number of normalization methods, though developed for RNA-seq data from fresh frozen (FF) samples, can be used with FFPE samples as well. The only extant normalization method specifically designed for FFPE RNA-seq data, MIXnorm, which has been shown to outperform the normalization methods, but at the cost of a complex mixture model and a high computational burden. It is therefore important to adapt MIXnorm for simplicity and computational efficiency while maintaining superior performance. Furthermore, it is critical to develop an integrated tool that performs commonly used normalization methods for both FF and FFPE RNA-seq data. We developed a new normalization method for FFPE RNA-seq data, named SMIXnorm, based on a simplified two-component mixture model compared to MIXnorm to facilitate computation. The expression levels of expressed genes are modeled by normal distributions without truncation, and those of non-expressed genes are modeled by zero-inflated Poisson distributions. The maximum likelihood estimates of the model parameters are obtained by a nested Expectation-Maximization algorithm with a less complicated latent variable structure, and closed-form updates are available within each iteration. Real data applications and simulation studies show that SMIXnorm greatly reduces computing time compared to MIXnorm, without sacrificing the performance. More importantly, we developed a web-based tool, RNA-seq Normalization (RSeqNorm), that offers a simple workflow to compute normalized RNA-seq data for both FFPE and FF samples. It includes SMIXnorm and MIXnorm for FFPE RNA-seq data, together with five commonly used normalization methods for FF RNA-seq data. Users can easily upload a raw RNA-seq count matrix and select one of the seven normalization methods to produce a downloadable normalized expression matrix for any downstream analysis. The R package is available at https://github.com/S-YIN/RSEQNORM. The web-based tool, RSeqNorm is available at http://lce.biohpc.swmed.edu/rseqnorm with no restriction to use or redistribute.

scholarly journals In-House Packed Porous Graphitic Carbon Columns for Liquid Chromatography-Mass Spectrometry Analysis of N-Glycans

2021 ◽  
Vol 9 ◽  
Author(s):  
Clifford Young ◽  
Mark R. Condina ◽  
Matthew T. Briggs ◽  
Edward S. X. Moh ◽  
Gurjeet Kaur ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Ovarian Cancer ◽  
Liquid Chromatography ◽  
Late Stage ◽  
Porous Graphitic Carbon ◽  
Graphitic Carbon ◽  
Liquid Chromatography Mass Spectrometry ◽  
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Protein glycosylation is a common post-translational modification that modulates biological processes such as the immune response and protein trafficking. Altered glycosylation profiles are associated with cancer and inflammatory diseases, as well as impacting the efficacy of therapeutic monoclonal antibodies. Consisting of oligosaccharides attached to asparagine residues, enzymatically released N-linked glycans are analytically challenging due to the diversity of isomeric structures that exist. A commonly used technique for quantitative N-glycan analysis is liquid chromatography-mass spectrometry (LC-MS), which performs glycan separation and characterization. Although many reversed and normal stationary phases have been utilized for the separation of N-glycans, porous graphitic carbon (PGC) chromatography has become desirable because of its higher resolving capability, but is difficult to implement in a robust and reproducible manner. Herein, we demonstrate the analytical properties of a 15 cm fused silica capillary (75 µm i.d., 360 µm o.d.) packed in-house with Hypercarb PGC (3 µm) coupled to an Agilent 6550 Q-TOF mass spectrometer for N-glycan analysis in positive ion mode. In repeatability and intermediate precision measurements conducted on released N-glycans from a glycoprotein standard mixture, the majority of N-glycans reported low coefficients of variation with respect to retention times (≤4.2%) and peak areas (≤14.4%). N-glycans released from complex samples were also examined by PGC LC-MS. A total of 120 N-glycan structural and compositional isomers were obtained from formalin-fixed paraffin-embedded ovarian cancer tissue sections. Finally, a comparison between early- and late-stage formalin-fixed paraffin-embedded ovarian cancer tissues revealed qualitative changes in the α2,3- and α2,6-sialic acid linkage of a fucosylated bi-antennary complex N-glycan. Although the α2,3-linkage was predominant in late-stage ovarian cancer, the alternate α2,6-linkage was more prevalent in early-stage ovarian cancer. This study establishes the utility of in-house packed PGC columns for the robust and reproducible LC-MS analysis of N-glycans.

scholarly journals Immunohistochemical expression of Cyclin D1 among Sudanese patients diagnosed with benign and malignant prostatic lesions

2019 ◽  
Author(s):  
Eiman Siddig Ahmed ◽  
Lubna S. Elnour ◽  
Rowa Hassan ◽  
Emmanuel Edwar Siddig ◽  
Mintu Elsa Chacko ◽  
...  
Keyword(s):  
Family History ◽  
Cyclin D1 ◽  
P Value ◽  
Low Grade ◽  
High Grade ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Embedded Blocks ◽  
History Of ◽  
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Abstract Objectives: Prostate cancer (PC) is common cancer worldwide. Several markers have been developed to differentiate between benign prostatic hyperplasia (BPH) from PC. A descriptive retrospective hospital-based study aimed at determining the expression of Cyclin D1 in BPH and PC. the study took place at different histopathology laboratories in Khartoum state, Sudan, from December 2016 to January 2019. Formalin-fixed paraffin-embedded blocks were sectioned and fixed in 3-aminopropyltriethoxysilane coated slides incubated into primary antibody for Cyclin D1. The assessment of immunoreactivity of Cyclin D1 of each section was done using the Gleason scoring system. Results: A total of 153 males’ prostate sections included in this study, of them, 120 (78.4%) were PC, and 33 (21.6%) were BPH. Their age ranged from 45 to 88 years, mean age was 66.19 ± 8.599. 142 (92.8%) did not have a family history of PC, while 11 (7.2%) patients reported having a family history. The Gleason scoring showed a total of 81 (52.9%) patients with high-grade and 39 (25.5%) with low-grade. 118 (97.5%) patients had PC showed positive results for Cyclin D1, while BPH was 3 (2.5%). P value < 0.001. Cyclin D1 staining was associated with high-grade Gleason score and perineural invasion, P value 0.001.

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