Article
Cell Biology
Konstantinos Venetis, Francesco Pepe, Elisabetta Munzone, Elham Sajjadi, Gianluca Russo, Pasquale Pisapia, Mariia Ivanova, Giuseppina Bonizzi, Davide Vacirca, Alessandra Rappa, Alberto Ranghiero, Sergio Vincenzo Taormina, Giuseppe Viale, Giancarlo Troncone, Massimo Barberis, Elena Guerini-Rocco, Umberto Malapelle, Nicola Fusco
Summary: This study evaluated the performance of next-generation sequencing (NGS) and RT-PCR for PIK3CA testing in breast cancer tissue and metastasis. The results showed that NGS detected mutations in all samples, while RT-PCR accuracy depended on the quality and quantity of DNA. Therefore, the choice of PIK3CA testing strategy and sample analysis should be personalized based on technical parameters.
Article
Biochemistry & Molecular Biology
Hua Zhang, Vamsi Krishna Polavarapu, Pengwei Xing, Miao Zhao, Lucy Mathot, Linxuan Zhao, Gabriela Rosen, Fredrik J. Swartling, Tobias Sjoblom, Xingqi Chen
Summary: Archived FFPE samples are widely used for cancer research, and we developed a highly sensitive method (FFPE-ATAC) to decode chromatin accessibility in FFPE tissues. This method generates high-quality chromatin accessibility profiles and allows analysis of chromatin profiles in regions of interest from a single FFPE tissue section.
Article
Multidisciplinary Sciences
Ziye Xu, Tianyu Zhang, Hongyu Chen, Yuyi Zhu, Yuexiao Lv, Shunji Zhang, Jiaye Chen, Haide Chen, Lili Yang, Weiqin Jiang, Shengyu Ni, Fangru Lu, Zhaolun Wang, Hao Yang, Ling Dong, Feng Chen, Hong Zhang, Yu Chen, Jiong Liu, Dandan Zhang, Longjiang Fan, Guoji Guo, Yongcheng Wang
Summary: The authors developed a droplet-based method (snRandom-seq) for high-throughput and sensitive snRNA sequencing of FFPE tissues, which captures full-length total RNAs and detects more non-coding RNAs and nascent RNAs. The method shows promise in biomedical research based on its application on a clinical FFPE liver cancer specimen.
NATURE COMMUNICATIONS
(2023)
Review
Genetics & Heredity
Gerardo Cazzato, Concetta Caporusso, Francesca Arezzo, Antonietta Cimmino, Anna Colagrande, Vera Loizzi, Gennaro Cormio, Teresa Lettini, Eugenio Maiorano, Vincenza Sara Scarcella, Paola Tarantino, Maricla Marrone, Alessandra Stellacci, Paola Parente, Paolo Romita, Aurora De Marco, Vincenzo Venerito, Caterina Foti, Giuseppe Ingravallo, Roberta Rossi, Leonardo Resta
Summary: Advancements in pathology have shifted towards molecular and genetic studies, allowing for the implementation of targeted therapies; however, issues may arise in NGS due to damage to genetic material in fixed samples.
Article
Veterinary Sciences
Nelly O. Elshafie, Jessica Hanlon, Mays Malkawi, Ekramy E. Sayedahmed, Lynn F. Guptill, Yava L. Jones-Hall, Andrea P. Santos
Summary: Pythium insidiosum is a waterborne fungus-like organism that can cause a disease called pythiosis in dogs and other animals. This disease can lead to inflammatory lesions on the skin and gastrointestinal tract, which can be fatal if left untreated. The development of a molecular technique called nested PCR can aid in the diagnosis of this organism by specifically detecting P. insidiosum DNA in biopsy specimens. The combination of this technique with microscopic examination can increase the sensitivity of diagnosing pythiosis in dogs.
VETERINARY SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Katarina Vitosevic, Danijela Todorovic, Zivana Slovic, Tatjana Varljen, Ivana Radakovic, Dusan Radojevic, Vanja Canovic, Milos Todorovic
Summary: This study compared the quality of DNA isolated from fixed tissues and tissues embedded in paraffin blocks after fixation, finding that the fixation time and embedding time have an impact on DNA yield and integrity.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Chemistry, Analytical
Kenneth Weke, Sachin Kote, Jakub Faktor, Sofian Al Shboul, Naomi Uwugiaren, Paul M. Brennan, David R. Goodlett, Ted R. Hupp, Irena Dapic
Summary: Developments in quantitative proteomics and DIA methodology have enabled protein quantification in biological samples, including formalin-fixed paraffin-embedded (FFPE) tissues. In this study, a simple and precise DIA-MS workflow was established to detect and quantify immune- and glioblastoma (GBM)-relevant proteins in FFPE patient materials. The results showed successful detection and quantification of more than 1700 proteins, including GBM-relevant proteins and immune-related proteins. This strategy has great potential for routine protein quantification in FFPE tissue samples.
ANALYTICA CHIMICA ACTA
(2022)
Article
Infectious Diseases
Shawn T. Clark, Yvonne C. W. Yau, Aaron Campigotto, Farhad Gharabaghi, Susan E. Richardson, Manal Tadros
Summary: In this study, we evaluated the performance of a DNA-based test for detecting fungal DNA in archived human biopsy tissues. Our results indicate that the best performance can be achieved when fungi are observed under a microscope before testing, suggesting that this test should only be used under these conditions.
Review
Biochemistry & Molecular Biology
Ekenedirichukwu N. Obi, Daniel A. Tellock, Gabriel J. Thomas, Timothy D. Veenstra
Summary: The recent developments in mass spectrometry (MS) have provided new opportunities in biomarker discovery and diagnostics, particularly in analyzing clinical samples at a deeper level. While most developments have focused on blood, there is potential in utilizing archived formalin-fixed paraffin-embedded (FFPE) tissues, which were previously considered difficult to analyze using proteomics techniques. Researchers have developed methods to extract proteins from FFPE tissues, allowing for their analysis using state-of-the-art technologies like MS and protein arrays. This review discusses the history of these developments and their current applications in identifying biomarkers and diagnosing diseases such as cancer.
Article
Biology
Masachika Ikegami, Shinji Kohsaka, Takeshi Hirose, Toshihide Ueno, Satoshi Inoue, Naoki Kanomata, Hideko Yamauchi, Taisuke Mori, Shigeki Sekine, Yoshihiro Inamoto, Yasushi Yatabe, Hiroshi Kobayashi, Sakae Tanaka, Hiroyuki Mano
Summary: The researchers developed MicroSEC, a filtering pipeline to remove sequencing artifacts from archival formalin-fixed and paraffin-embedded samples. The sensitivity and specificity of MicroSEC were confirmed to be 97% and 96% respectively using amplicon-based sequencing with 97 mutations. This tool may improve the reliability of clinical sequencing and advance cancer research using formalin-fixed, paraffin-embedded samples, which are of great interest for genomic analysis.
COMMUNICATIONS BIOLOGY
(2021)
Article
Pathology
Rebecca Sparks, Catriona L. Halliday, Wendy Green, Sharon C-A Chen
Summary: The performance of panfungal PCR-DNA sequencing assays for diagnosing invasive fungal disease on FFPE tissue is influenced by various factors. Interpretation of positive results is challenging due to the need to differentiate colonisers and contaminants from clinically significant pathogens. A retrospective audit was conducted on 248 FFPE tissue specimens, comparing panfungal PCR results between samples with and without visualised fungal elements on histopathology. The study found limited clinical utility of panfungal PCR in FFPE tissue without visible fungal elements, suggesting that restricting the assay to histopathology positive samples aids interpretation of PCR results and conserves resources.
Article
Multidisciplinary Sciences
Shirong Zhang, Shutao He, Xin Zhu, Yunfei Wang, Qionghuan Xie, Xianrang Song, Chunwei Xu, Wenxian Wang, Ligang Xing, Chengqing Xia, Qian Wang, Wenfeng Li, Xiaochen Zhang, Jinming Yu, Shenglin Ma, Jiantao Shi, Hongcang Gu
Summary: The authors developed a DNA methylation profiling assay and a machine learning classifier to predict the origin of metastatic tumours in CUP patients using formalin-fixed, paraffin embedded samples.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Monica Hepker, Griffin Clabaugh, Huajun Jin, Anumantha G. Kanthasamy
Summary: The real-time quaking-induced conversion (RT-QuIC) alpha-synuclein (aSyn) protein kinetic seeding assay has proven to be useful for detecting pathological aggregates in synucleinopathies including Parkinson's disease (PD). This study developed a protocol called kinetic assay seeding ability recovery (KASAR) to recover the seeding activity in formalin-fixed paraffin-embedded (FFPE) tissues, which are widely archived. The KASAR protocol successfully recovered the seeding activity in positive samples and demonstrated the potential for utilizing FFPE tissues in biomarker protein aggregate amplification.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Chemistry, Analytical
Yunxia Guo, Junjie Ma, Zhengyue Li, Kaitong Dang, Qinyu Ge, Yan Huang, Guang-zhong Wang, Xiangwei Zhao
Summary: This study investigates the effects of fixation and storage time on the nuclear transcriptome signatures of the brain. The fixation time has a greater impact on the transcriptomic profiles than the retention time of FFPE samples. The findings will guide the preparation of FFPE samples for single-nucleus RNA-seq, especially in transcriptomic studies of brain diseases.
ANALYTICA CHIMICA ACTA
(2023)
Article
Agriculture, Dairy & Animal Science
Jessica Maria Abbate, Alessia Giannetto, Francesca Arfuso, Barbara Brunetti, Giovanni Lanteri
Summary: This study found that the expression of certain MiRNAs is dysregulated in canine mammary tumors, and these MiRNAs may serve as candidate biomarkers to predict prognosis, as their dysregulation may lead to alterations in key pathways involved in cancer development.
