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
Biotechnology & Applied Microbiology
Liang Zong, Yabing Zhu, Yuan Jiang, Ying Xia, Qun Liu, Sanjie Jiang
Summary: RNA-Seq analysis of FFPE samples is a highly effective approach but degradation of RNAs limits its application. A new RNA-Seq method has been developed to overcome this limitation. This study compares and evaluates three commercially available exome capture kits, providing valuable guidance for obtaining high-quality data from FFPE samples.
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
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
Chemistry, Analytical
Hao Chen, Yuefei Zhang, Haichao Zhou, Weiran Chen, Jiayi Peng, Yang Feng, Linyuan Fan, Jun Li, Jin Zi, Yan Ren, Qidan Li, Siqi Liu
Summary: Spatial proteomics plays an important role in the era of single-cell biology. In this study, a new routine workflow was developed for proteomic analysis of micro-FFPE tissues, allowing the construction of a spatial proteomic atlas of mouse brain, which exhibited typical characteristics of spatial-dependent protein abundance and functional enrichment.
ANALYTICAL CHEMISTRY
(2023)
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)
Review
Oncology
Amin Talebi, Jean Paul Thiery, Mohammad Amin Kerachian
Summary: Chimeric transcripts are important for diagnosis and prognosis, but their identification from FFPE tissues is limited due to the reduced quality and quantity of RNA. Strategies need to be developed to overcome these limitations and maximize the potential of FFPE tissues as a source for fusion transcript identification.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(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
Samar Ijaz Gul, Aqsa Ayoub, Syed Aoun Ali, Sharoon Hanook, Deeba Noreen Baig
Summary: The study revealed significant dysregulation in the transcriptional pattern of Pfn3 in brain tumors, suggesting a potential correlation between molecular variations in Pfn3 and the malignancy of brain tumors, similar to the role of tumor suppressor genes in other types of cancer.
Article
Biochemistry & Molecular Biology
Allison K. Miller, Cara L. Brosnahan, Anjali Pande, Cindy F. Baker, Jemma L. Geoghegan, Jane Kitson, Neil J. Gemmell, Edwina J. Dowle
Summary: Infectious diseases have a significant impact on various organisms, and understanding the interactions between hosts and pathogens is crucial for their conservation and management. The use of genomic approaches has made it easier to obtain this knowledge quickly, however, many species still face challenges in accessing appropriate samples and data. Archival materials, such as formalin-fixed paraffin-embedded tissue samples, may provide a valuable resource for studying pathogen emergence and host responses over long periods of time.
MOLECULAR ECOLOGY RESOURCES
(2023)
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)
Article
Multidisciplinary Sciences
Harim Oh, Chul Hwan Kim, Yoo Jin Lee
Summary: The study evaluated the diagnostic value of immunohistochemical staining for bullous pemphigoid (BP) detection, showing that IHC staining has high sensitivity and specificity, being helpful for the diagnosis of DIF-confirmed BP cases and clinically suspected BP cases.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Shen Yin, Xiaowei Zhan, Bo Yao, Guanghua Xiao, Xinlei Wang, Yang Xie
Summary: RNA-seq provides comprehensive quantification of transcriptomic activities in biological samples. This study introduces a new normalization method, SMIXnorm, for FFPE RNA-seq data, which simplifies the computational process, improves efficiency, and maintains superior performance compared to existing methods. Furthermore, a web-based tool, RSeqNorm, is developed to compute normalized RNA-seq data for both FFPE and FF samples, offering users a simple workflow for downstream analysis.
FRONTIERS IN GENETICS
(2021)