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
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.
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
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
Medical Laboratory Technology
Feng-Ming Hsu, Yih-Leong Chang, Chung-Yung Chen, Shu-Rung Lin, Jason Chia-Hsien Cheng
Summary: HPR is an alternative RNA profiling approach with high sensitivity, reproducibility, robustness, and capability for molecular diagnostics in FFPE tumor biopsy specimens of lung and esophageal cancer.
CLINICAL 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)
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.
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
Gastroenterology & Hepatology
Kristina G. Hulten, Robert M. Genta, Ira N. Kalfus, Yi Zhou, Hongjun Zhang, David Y. Graham
Summary: This study compared the antimicrobial susceptibility testing of H. pylori using targeted next-generation sequencing (NGS) and culture-based methods. The results showed that NGS was reliable in predicting resistance to clarithromycin, levofloxacin, rifabutin, and tetracycline, while having fair consistency for metronidazole and amoxicillin. Culture-based testing can effectively predict treatment outcomes with clarithromycin and levofloxacin, and further studies are needed to compare the predictive ability of both methods for other antibiotics.
Article
Multidisciplinary Sciences
Sabine Bauer, Jessica Pauli, Jaroslav Pelisek
Summary: Extraction of DNA from formalin-fixed tissues poses challenges due to degradation, but an automated system established in the study shows promise in obtaining high-quality DNA for downstream analyses, especially for small FFPE tissue specimens.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
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
Medicine, Research & Experimental
Bradley L. Ackermann, Ryan D. Morrison, Salisha Hill, Matthew D. Westfall, Brent D. Butts, Michael D. Soper, Jeff A. Fill, Andrew E. Schade, Daniel C. Liebler, Aaron M. Gruver
Summary: MS analysis allows accurate protein quantification from stained paraffin-embedded tissue sections, providing valuable data for the assessment of clinical tissue specimens.
LABORATORY INVESTIGATION
(2023)
Article
Hematology
Elizabeth A. Middleton, Xue-Yan He, Frederik Denorme, Robert A. Campbell, David Ng, Steven P. Salvatore, Maria Mostyka, Amelia Baxter-Stoltzfus, Alain C. Borczuk, Massimo Loda, Mark J. Cody, Bhanu Kanth Manne, Irina Portier, Estelle S. Harris, Aaron C. Petrey, Ellen J. Beswick, Aleah F. Caulin, Anthony Iovino, Lisa M. Abegglen, Andrew S. Weyrich, Matthew T. Rondina, Mikala Egeblad, Joshua D. Schiffman, Christian Con Yost
Article
Oncology
Clifton G. Fulmer, Kyung Park, Thomas Dilcher, Mai Ho, Susanna Mirabelli, Susan Alperstein, Erika M. Hissong, Meredith Pittman, Momin Siddiqui, Jonas J. Heymann, Rhonda K. Yantiss, Alain C. Borczuk, Helen Fernandes, Carlie Sigel, Wei Song, Juan Miguel Mosquera, Rema Rao
CANCER CYTOPATHOLOGY
(2020)
Article
Cell & Tissue Engineering
Liuliu Yang, Yuling Han, Benjamin E. Nilsson-Payant, Vikas Gupta, Pengfei Wang, Xiaohua Duan, Xuming Tang, Jiajun Zhu, Zeping Zhao, Fabrice Jaffre, Tuo Zhang, Tae Wan Kim, Oliver Harschnitz, David Redmond, Sean Houghton, Chengyang Liu, Ali Naji, Gabriele Ciceri, Sudha Guttikonda, Yaron Bram, Duc-Huy T. Nguyen, Michele Cioffi, Vasuretha Chandar, Daisy A. Hoagland, Yaoxing Huang, Jenny Xiang, Hui Wang, David Lyden, Alain Borczuk, Huanhuan Joyce Chen, Lorenz Studer, Fong Cheng Pan, David D. Ho, Benjamin R. tenOever, Todd Evans, Robert E. Schwartz, Shuibing Chen
Review
Oncology
Lynette Sholl, Fred R. Hirsch, David Hwang, Johan Botling, Fernando Lopez-Rios, Lukas Bubendorf, Mari Mino-Kenudson, Anja C. Roden, Mary Beth Beasley, Alain Borczuk, Elisabeth Brambilla, Gang Chen, Teh-Ying Chou, Jin-Haeng Chung, Wendy A. Cooper, Sanja Dacic, Sylvie Lantuejoul, Deepali Jain, Dongmei Lin, Yuko Minami, Andre Moreira, Andrew G. Nicholson, Masayuki Noguchi, Mauro Papotti, Giuseppe Pelosi, Claudia Poleri, Natasha Rekhtman, Ming-Sound Tsao, Erik Thunnissen, William Travis, Yasushi Yatabe, Akihiko Yoshida, Jillian B. Daigneault, Ahmet Zehir, Solange Peters, Ignacio I. Wistuba, Keith M. Kerr, John W. Longshore
JOURNAL OF THORACIC ONCOLOGY
(2020)
Article
Oncology
Andre L. Moreira, Paolo S. S. Ocampo, Yuhe Xia, Hua Zhong, Prudence A. Russell, Yuko Minami, Wendy A. Cooper, Akihiko Yoshida, Lukas Bubendorf, Mauro Papotti, Giuseppe Pelosi, Fernando Lopez-Rios, Keiko Kunitoki, Dana Ferrari-Light, Lynette M. Sholl, Mary Beth Beasley, Alain Borczuk, Johan Botling, Elisabeth Brambilla, Gang Chen, Teh-Ying Chou, Jin-Haeng Chung, Sanja Dacic, Deepali Jain, Fred R. Hirsch, David Hwang, Sylvie Lantuejoul, Dongmei Lin, John W. Longshore, Noriko Motoi, Masayuki Noguchi, Claudia Poleri, Natasha Rekhtman, Ming-Sound Tsao, Erik Thunnissen, William D. Travis, Yasushi Yatabe, Anja C. Roden, Jillian B. Daigneault, Ignacio I. Wistuba, Keith M. Kerr, Harvey Pass, Andrew G. Nicholson, Mari Mino-Kenudson
JOURNAL OF THORACIC ONCOLOGY
(2020)
Editorial Material
Critical Care Medicine
Alain C. Borczuk
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2021)
Article
Cell Biology
Sarah S. Elsoukkary, Maria Mostyka, Alicia Dillard, Diana R. Berman, Lucy X. Ma, Amy Chadburn, Rhonda K. Yantiss, Jose Jessurun, Surya V. Seshan, Alain C. Borczuk, Steven P. Salvatore
Summary: This study reported the clinicopathologic findings from 32 autopsy studies conducted on patients who died of COVID-19, which revealed various pathological manifestations including pulmonary lesions, microthrombi, and liver injury. Most patients presented with symptoms like shortness of breath, cough, and low-grade fever, with comorbidities being common.
Editorial Material
Medical Laboratory Technology
Alain C. Borczuk
ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE
(2021)
Article
Cell Biology
Michael J. Corley, Alina P. S. Pang, Kush Dody, Philip A. Mudd, Bruce K. Patterson, Harish Seethamraju, Yaron Bram, Michael J. Peluso, Leonel Torres, Nikita S. Iyer, Thomas A. Premeaux, Stephen T. Yeung, Vasuretha Chandar, Alain Borczuk, Robert E. Schwartz, Timothy J. Henrich, Steven G. Deeks, Jonah B. Sacha, Lishomwa C. Ndhlovu
Summary: Severe COVID-19 patients show distinct epigenetic features in DNA methylation, including hypermethylation of IFN-related genes and hypomethylation of inflammatory genes. These results can help elucidate the pathogenic mechanisms, predict disease severity, and mortality risk.
JOURNAL OF LEUKOCYTE BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Yuling Han, Xiaohua Duan, Liuliu Yang, Benjamin E. Nilsson-Payant, Pengfei Wang, Fuyu Duan, Xuming Tang, Tomer M. Yaron, Tuo Zhang, Skyler Uhl, Yaron Bram, Chanel Richardson, Jiajun Zhu, Zeping Zhao, David Redmond, Sean Houghton, Duc-Huy T. Nguyen, Dong Xu, Xing Wang, Jose Jessurun, Alain Borczuk, Yaoxing Huang, Jared L. Johnson, Yuru Liu, Jenny Xiang, Hui Wang, Lewis C. Cantley, Benjamin R. TenOever, David D. Ho, Fong Cheng Pan, Todd Evans, Huanhuan Joyce Chen, Robert E. Schwartz, Shuibing Chen
Summary: Researchers have developed lung and colonic organoid models using human pluripotent stem cells, which demonstrate susceptibility to SARS-CoV-2 infection. These models are valuable for studying the infection of the virus and screening drugs, with potential therapeutic implications for COVID-19.
Meeting Abstract
Pathology
Mona Farahi, Alain Borczuk, Kartik Viswanathan, Michael Kluger, Hanina Hibshoosh
Meeting Abstract
Medicine, Research & Experimental
Amelia Baxter-Stoltzfus, Kartik Viswanathan, Michael Kluger, Hanina Hibshoosh, Alain Borczuk
LABORATORY INVESTIGATION
(2020)
Meeting Abstract
Pathology
Amelia Baxter-Stoltzfus, Kartik Viswanathan, Michael Kluger, Hanina Hibshoosh, Alain Borczuk
Meeting Abstract
Oncology
S. Mukherjee, E. Wennerberg, C. Hung, N. Saadallah, S. Kariyawasam, M. K. Hussein, N. Narula, P. Adusumilli, A. Borczuk, N. Altorki, T. McGraw, B. M. Stiles
JOURNAL OF THORACIC ONCOLOGY
(2020)
Meeting Abstract
Oncology
J. Qian, S. Zhao, Y. Zou, J. Rahman, M. Senosain, T. Stricker, C. Powell, A. Borczuk, P. Massion
JOURNAL OF THORACIC ONCOLOGY
(2020)