Article
Medical Laboratory Technology
Ramanath Majumdar, Julie A. Vrana, Justin W. Koepplin, Dragana Milosevic, Anja C. Roden, Joaquin J. Garcia, Benjamin R. Kipp, Ann M. Moyer
Summary: This study developed a qualitative test for detecting SARS-CoV-2 in formalin-fixed paraffin-embedded (FFPE) tissues using droplet digital PCR (ddPCR). The results showed reliable detection of SARS-CoV-2, and the assay has broad clinical utility in various applications, including evaluation of pregnancy loss and liver transplant rejection.
CLINICA CHIMICA ACTA
(2022)
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
Biochemical Research Methods
Patcharaporn Boottanun, Chiaki Nagai-Okatani, Misugi Nagai, Umbhorn Ungkulpasvich, Shinjiro Yamane, Masao Yamada, Atsushi Kuno
Summary: The researchers evaluated the sensitivity of a new scanner for analyzing glycans attached to glycoproteins in biological samples. The scanner showed fourfold higher sensitivity compared to the previous scanner and allowed glycomic profiling with only three cells. It also enabled high-resolution spatial analysis in tissue glycome mapping.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Rory T. Steven, Marcel Niehaus, Adam J. Taylor, Ammar Nasif, Efstathios Elia, Richard J. A. Goodwin, Zoltan Takats, Josephine Bunch
Summary: Mass spectrometry imaging (MSI) is a powerful technique for providing spatially resolved atomic and molecular information from almost any sample type. Optimizing MSI methods for analysis of FFPE tissue is necessary due to the prevalence and importance of FFPE tissue storage.
ANALYTICAL CHEMISTRY
(2022)
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
Chemistry, Analytical
Warda Boutegrabet, Dominique Guenot, Olivier Bouche, Camille Boulagnon-Rombi, Aude Marchal Bressenot, Olivier Piot, Cyril Gobinet
Summary: A new automatic and multivariate methodology utilizing EMSC regression coefficients, validity indices, and KMeans clustering was proposed to separate paraffin and tissue pixels in infrared spectral images. Validation on simulated and real images showed high effectiveness of the method.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Jie Pu, Chao Xue, Shihan Huo, Qingqing Shen, Yang Qu, Xinxin Yang, Bo An, Thomas E. Angel, Zhuo Chen, John T. Mehl, Huaping Tang, Eric Yang, Timothy W. Sikorski, Jun Qu
Summary: This study extensively investigated the challenges of accurate quantification of target proteins in formalin-fixed paraffin-embedded (FFPE) tissues using liquid chromatography-mass spectrometry (LC-MS) and developed a strategy enabling precise quantification. The study demonstrated efficient recovery of target signature peptides from FFPE tissues, indicated that FFPE tissue storage mainly causes decreased immunoreactivity but not chemical degradation of proteins, and proposed a novel calibration approach for accurate quantification. The pipeline was successfully applied to measure the pharmacokinetics of monoclonal antibody (mAb) and its target in FFPE tissues, showing excellent correlation with fresh tissues.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Magdalena Kuras, Nicole Woldmar, Yonghyo Kim, Max Hefner, Johan Malm, Judit Moldvay, Balazs Dome, Janos Fillinger, Luciana Pizzatti, Jeovanis Gil, Gyorgy Marko-Varga, Melinda Rezeli
Summary: Efficient sample preparation workflow optimized for FFPE tissues can effectively tackle proteomic challenges. Through the use of S-Trap technology and TMTpro 16plex labeling, thousands of proteins were successfully identified, including those related to clinical outcomes. Additionally, a rapid acetylation protocol enabled the study of endogenous lysine acetylation in FFPE tissues.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Pathology
Giuseppa Zannini, Gaetano Facchini, Marco De Sio, Ferdinando De Vita, Andrea Ronchi, Michele Orditura, Maria Teresa Vietri, Fortunato Ciardiello, Renato Franco, Marina Accardo, Federica Zito Marino
Summary: BRCA1 and BRCA2 are genes involved in DNA repair mechanism and their mutations increase the risk of several cancer types. FDA has approved PARP inhibitors for treating BRCA1/2 mutated ovarian, breast, pancreatic, and prostate cancer patients. Guidelines for BRCA testing vary between tumor types, and there is limited data on detecting BRCA1/2 somatic mutations in FFPE samples. This review provides an overview of BRCA mutations, testing guidelines, molecular assays, and approved PARP inhibitors for various cancers, including breast, ovarian, fallopian tube, primary peritoneal, prostate, and pancreatic cancer.
PATHOLOGY RESEARCH AND PRACTICE
(2023)
Article
Multidisciplinary Sciences
Rochelle Hockney, Caroline H. Orr, Gareth J. Waring, Inge Christiaens, Gillian Taylor, Stephen P. Cummings, Stephen C. Robson, Andrew Nelson
Summary: This study investigated the feasibility of using FFPE fetal membrane samples for microbiota research. The results showed differences in bacterial composition between FFPE and frozen samples, as well as lower DNA quality in FFPE samples. Additionally, the microbiota of FFPE samples was influenced by processing methods and could not differentiate between tissue samples and surrounding wax blocks. Therefore, contamination prevention and detection methods should be considered when using FFPE samples for microbiota research.
Article
Chemistry, Analytical
Tae Hee Lee, Young Jun Kim, Woo Sun Rou, Hyuk Soo Eun
Summary: CTCs, rare circulating tumor cells, are promising diagnostic biomarkers but their analysis is often limited due to rarity and short-term presence. This study introduces a new method combining hydrogel core-mediated CTC accumulation and FFPE technology to prepare CTC blocks, showing great potential in cytopathological CTC studies.
Article
Oncology
Chia-Jung Busch, Christian Hagel, Benjamin Becker, Agnes Oetting, Nikolaus Moeckelmann, Conrad Droste, Christina Moeller-Koop, Melanie Witt, Markus Blaurock, Sonja Loges, Kai Rothkamm, Christian Betz, Adrian Muenscher, Till S. Clauditz, Thorsten Rieckmann
Summary: This study investigated the expression of Axl and Gas6 in head and neck squamous cell carcinoma, finding that high expression of Axl indicates a need for adjuvant radiotherapy after surgery. Gas6 expression was found to be a positive predictor of survival in patients receiving radiotherapy.
Article
Biochemistry & Molecular Biology
Georgia Mitsa, Qianyu Guo, Christophe Goncalves, Samuel E. J. Preston, Vincent Lacasse, Adriana Aguilar-Mahecha, Naciba Benlimame, Mark Basik, Alan Spatz, Gerald Batist, Wilson H. Miller, Sonia del Rincon, Rene P. Zahedi, Christoph H. Borchers
Summary: The article presents a 'green' xylene-free protocol for accelerated sample preparation of FFPE tissues, enabling streamlined and reproducible quantitative proteomic profiling.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(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
Kiyoshi Misawa, Daiki Mochizuki, Shiori Endo, Masato Mima, Yuki Misawa, Atsushi Imai, Kazuya Shinmura, Takeharu Kanazawa, Thomas E. Carey, Hiroyuki Mineta
MOLECULAR CARCINOGENESIS
(2017)
Article
Biochemistry & Molecular Biology
Kazuya Shinmura, Hisami Kato, Yuichi Kawanishi, Kimio Yoshimura, Hisaki Igarashi, Masanori Goto, Hong Tao, Yusuke Inoue, Takayuki Sugiyama, Hiroshi Furuse, Seiichiro Ozono, Haruhiko Sugimura
MOLECULAR CARCINOGENESIS
(2017)
Article
Oncology
Kazuya Shinmura, Hisami Kato, Yuichi Kawanishi, Takaharu Kamo, Yusuke Inoue, Katsuhiro Yoshimura, Kenta Sugiyama, Kiyoshi Misawa, Seiji Hosokawa, Hiroyuki Mineta, Haruhiko Sugimura
PATHOLOGY & ONCOLOGY RESEARCH
(2018)
Article
Oncology
Kiyoshi Misawa, Atsushi Imai, Daiki Mochizuki, Yuki Misawa, Shiori Endo, Seiji Hosokawa, Ryuji Ishikawa, Masato Mima, Kazuya Shinmura, Takeharu Kanazawa, Hiroyuki Mineta
Article
Oncology
Yusuke Inoue, Katsuhiro Yoshimura, Nobuya Kurabe, Tomoaki Kahyo, Akikazu Kawase, Masayuki Tanahashi, Hiroshi Ogawa, Naoki Inui, Kazuhito Funai, Kazuya Shinmura, Hiroshi Niwa, Takafumi Suda, Haruhiko Sugimura
Letter
Pathology
Haruna Yagi, Seishiro Takahashi, Kazuya Shinmura, Toshihide Iwashita, Hiroshi Ogawa
PATHOLOGY INTERNATIONAL
(2018)
Article
Oncology
Tomohiro Yamasaki, Naoto Sakai, Kazuya Shinmura, Hiroshi Kawaji, Shinichiro Koizumi, Tetsuro Samashima, Hiroki Namba
BRAIN TUMOR PATHOLOGY
(2018)
Review
Pathology
Takeharu Kanazawa, Kiyoshi Misawa, Kazuya Shinmura, Yuki Misawa, Gen Kusaka, Mikiko Maruta, Toru Sasaki, Yusuke Watanabe, Thomas E. Carey
EXPERT REVIEW OF MOLECULAR DIAGNOSTICS
(2019)
Article
Medicine, General & Internal
Seiji Hosokawa, Satoru Takebayashi, Yutaka Sasaki, Yuuki Nakamura, Kazuya Shinmura, Goro Takahashi, Hiroyuki Mineta
POSTGRADUATE MEDICINE
(2019)
Article
Biochemistry & Molecular Biology
Kazuya Shinmura, Hisami Kato, Yuichi Kawanishi, Masanori Goto, Hong Tao, Katsuhiro Yoshimura, Satoki Nakamura, Kiyoshi Misawa, Haruhiko Sugimura
FREE RADICAL BIOLOGY AND MEDICINE
(2019)
Article
Oncology
Kiyoshi Misawa, Takeharu Kanazawa, Daiki Mochizuki, Atsushi Imai, Masato Mima, Satoshi Yamada, Kotaro Morita, Yuki Misawa, Kazuya Shinmura, Hiroyuki Mineta
Article
Oncology
Kazuya Shinmura, Hisami Kato, Yuichi Kawanishi, Katsuhiro Yoshimura, Kazuo Tsuchiya, Yoshiyuki Takahara, Seiji Hosokawa, Akikazu Kawase, Kazuhito Funai, Haruhiko Sugimura
Article
Oncology
Katsuhiro Yoshimura, Yusuke Inoue, Masato Karayama, Kazuo Tsuchiya, Kazutaka Mori, Yuzo Suzuki, Yuji Iwashita, Tomoaki Kahyo, Akikazu Kawase, Masayuki Tanahashi, Hiroshi Ogawa, Koushi Yokomura, Naoki Inui, Kazuhito Funai, Kazuya Shinmura, Hiroshi Niwa, Takafumi Suda, Haruhiko Sugimura
Article
Oncology
Kazuya Shinmura, Kimihide Kusafuka, Hideya Kawasaki, Hisami Kato, Takahiko Hariyama, Kazuo Tsuchiya, Yuichi Kawanishi, Kazuhito Funai, Kiyoshi Misawa, Hiroyuki Mineta, Haruhiko Sugimura
Summary: The study found that primary cilia (PC) were present in salivary gland tumors (SGTs) with basaloid/myoepithelial differentiation components, but absent in those without. PC-positive SGTs exhibited longer PC than normal, a characteristic distribution pattern, activation of the Hedgehog pathway, and association with TTBK2 upregulation, indicating a significant link between SGT tumorigenesis and PC.
JOURNAL OF PATHOLOGY
(2021)
Article
Oncology
Yusuke Inoue, Shun Matsuura, Katsuhiro Yoshimura, Yuji Iwashita, Tomoaki Kahyo, Akikazu Kawase, Masayuki Tanahashi, Matsuyoshi Maeda, Hiroshi Ogawa, Naoki Inui, Kazuhito Funai, Kazuya Shinmura, Hiroshi Niwa, Takafumi Suda, Haruhiko Sugimura
