Article
Endocrinology & Metabolism
Norifusa Iwahashi, Hironobu Umakoshi, Masatoshi Ogata, Tazuru Fukumoto, Hiroki Kaneko, Eriko Terada, Shunsuke Katsuhara, Naohiro Uchida, Katsuhiko Sasaki, Maki Yokomoto-Umakoshi, Yayoi Matsuda, Ryuichi Sakamoto, Yoshihiro Ogawa
Summary: This study evaluated the utility of transcriptome data from formalin-fixed paraffin-embedded (FFPE) samples in adrenocortical tumor research. The results demonstrated that FFPE samples can serve as a reliable alternative to fresh frozen samples for whole transcriptome profiling of adrenocortical tumors, enabling distinction of tumor types and detection of marker genes.
FRONTIERS IN ENDOCRINOLOGY
(2022)
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
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
Pathology
Stephen Murphy, James Smadbeck, Bruce Eckloff, Yean Lee, Sarah Johnson, Giannoula Karagouga, Vishnu Serla, Anurag Sharma, Robert Sikkink, Jesse Voss, Faye Harris, Janet Schaefer Kline, Farhad Kosari, Andrew Feldman, Eric Wieben, Marie Christine Aubry, Benjamin Kipp, Jin Jen, John Cheville, George Vasmatzis
Summary: DNA junctions (DNAJs) in tumors impact clinically relevant genes, and their comprehensive detection is crucial for clinical genomics testing. Optimized whole-genome sequencing and specialized bioinformatics algorithms allow efficient detection of DNAJs, enabling comprehensive testing on formalin-fixed clinical specimens.
JOURNAL OF MOLECULAR DIAGNOSTICS
(2021)
Article
Biochemistry & Molecular Biology
Linxuan Zhao, Pengwei Xing, Vamsi Krishna Polavarapu, Miao Zhao, Blanca Valero-Martinez, Yonglong Dang, Nagaprathyusha Maturi, Lucy Mathot, Ines Neves, Irem Yildirim, Fredrik Johansson Swartling, Tobias Sjoblom, Lene Uhrbom, Xingqi Chen
Summary: The study introduces a new method (FACT-seq) for efficient analysis of histone modifications in archived FFPE tissues, significantly improving resolution. High-quality chromatin profiles can be generated using a small number of FFPE nuclei, offering insights into epigenetic regulation in cancer and human disease.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Kyrillus S. Shohdy, Rohan Bareja, Michael Sigouros, David C. Wilkes, Princesca Dorsaint, Jyothi Manohar, Daniel Bockelman, Jenny Z. Xiang, Rob Kim, Kentaro Ohara, Kenneth Eng, Juan Miguel Mosquera, Olivier Elemento, Andrea Sboner, Alicia Alonso, Bishoy M. Faltas
Summary: In this study, three exome capture-based methods were used to analyze 32 FFPE tumor samples, showing high correlation and reliable detection of key immune gene expression and outlier gene transcription. The Agilent assay demonstrated the highest molecular subtype concordance with FF-TruSeq in urothelial cancer samples.
NPJ GENOMIC MEDICINE
(2021)
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
Dymph Klay, Karin M. Kazemier, Joanne J. van der Vis, Hidde M. Smits, Jan C. Grutters, Coline H. M. van Moorsel
Summary: This study found differences between sporadic idiopathic pulmonary fibrosis, telomere mutation-induced pulmonary fibrosis, and surfactant related gene mutation-induced pulmonary fibrosis, as well as a significant association between high expression of a high number of endoplasmic reticulum stress genes and shorter survival time.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Stine Bottcher Jacobsen, Jacob Tfelt-Hansen, Morten Holdgaard Smerup, Jeppe Dyrberg Andersen, Niels Morling
Summary: The use of fresh tissue for molecular studies is preferred but often impossible. Frozen or formalin-fixed, paraffin-embedded (FFPE) tissues are widely used and valuable for retrospective studies. RNA extracted from FFPE tissues is highly degraded and yields different gene expression profiles compared to fresh and frozen tissues. However, protein-coding transcripts show high correlations among different storage conditions. Proper quality control and caution regarding technical variability are required when using frozen and FFPE tissues for gene expression analyses.
Article
Genetics & Heredity
Shandra Devi Balasubramaniam, Venugopal Balakrishnan, Chern Ein Oon, Gurjeet Kaur
Summary: By studying the various stages of cervical cancer development, we have identified the perturbed cellular pathways and changes in gene expression that contribute to the disease. These findings provide guidance for further investigation and validation of the molecular mechanisms involved in HPV-associated cervical cancer.
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)
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
Oncology
Alessandra Borgognone, Garazi Serna, Marc Noguera-Julian, Lidia Alonso, Mariona Parera, Francesc Catala-Moll, Lidia Sanchez, Roberta Fasani, Roger Paredes, Paolo Nuciforo
Summary: The comparison of fresh-frozen (FF) and FFPE colorectal cancer (CRC) tissues revealed differences in microbial diversity and composition, with FF samples enriched in representative CRC-associated bacteria and FFPE samples mainly enriched in typical contaminants. An internal quality index showed a correlation between the similarity within sample pairs and the dominance of contaminant taxa. These findings may provide useful indications for accurate and reproducible metagenomics analyses, especially in larger studies in human cancer genomics using FFPE specimens.
Article
Medicine, Research & Experimental
Lisa Kreutzer, Peter Weber, Theresa Heider, Mathias Heikenwaelder, Tobias Riedl, Philipp Baumeister, Frederick Klauschen, Claus Belka, Axel Walch, Horst Zitzelsberger, Julia Hess, Kristian Unger
Summary: This study presents a method for simultaneous measurement of the whole exome and the transcriptome from formalin-fixed paraffin-embedded tissue sections. The data demonstrate the feasibility and reproducibility of this approach, expanding the possibilities of multi-omics integration in cancer research.
LABORATORY INVESTIGATION
(2022)