Article
Biochemical Research Methods
Souvik Seal, Debashis Ghosh
Summary: This study presents a new method for analyzing the interaction of proteins or markers in the tumor microenvironment of cancer patients, finding co-expression to be associated with disease risk and survival, and demonstrating the robustness of the method.
Article
Nanoscience & Nanotechnology
Rupsa Gupta, Yihao Wang, Ghinwa H. Darwish, Jade Poisson, Agnes Szwarczewski, Subin Kim, Christine Traaseth, Zachary M. Hudson, W. Russ Algar
Summary: Semiconducting polymer dots (Pdots) stabilized with bovine serum albumin (BSA) showed improved physical and colloidal stability compared to conventional stabilizing agents. The bioconjugation of BSA-stabilized Pdots allowed for selective fluorescent labeling of cells based on ligand-receptor and antibody-antigen binding. This research demonstrated the promising potential of BSA stabilization for Pdots in various bioanalytical and imaging applications.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Review
Biochemistry & Molecular Biology
Caddie Laberiano-Fernandez, Sharia Hernandez-Ruiz, Frank Rojas, Edwin Roger Parra
Summary: Multiplex immunofluorescence (mIF) with tyramide signal amplification is a valuable tool for cancer research, but requires careful attention to antibody selection, staining optimization, panel design, and data analysis strategies to ensure high reproducibility and address challenges.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Pathology
Paul W. Harms, Timothy L. Frankel, Myrto Moutafi, Arvind Rao, David L. Rimm, Janis M. Taube, Dafydd Thomas, May P. Chan, Liron Pantanowitz
Summary: Our understanding of human disease has evolved greatly in recent decades, particularly in the areas of immunology and cancer treatment. Advances in digital pathology have opened new avenues for studying the tumor microenvironment. Traditional tissue-based evaluations are limited in their ability to analyze complex quantitative data and multiple biomarkers, making multiplex staining techniques a promising alternative.
Article
Biochemical Research Methods
Ryan Cohen, Tracey Lee-Pullen, Timothy J. Miller, Katie Meehan, Kathy Fuller, Melanie J. McCoy
Summary: Exploring the tumour microenvironment provides insight into the unique interaction between the host and tumour. Immune biomarkers within the tumour microenvironment in colorectal cancer are more accurate in predicting disease recurrence than traditional histopathological staging. Multiplex immunofluorescence allows for simultaneous assessment of multiple markers to accurately classify immune cells and their spatial relationship to tumour tissue.
Article
Immunology
Haoxin Peng, Xiangrong Wu, Ran Zhong, Tao Yu, Xiuyu Cai, Jun Liu, Yaokai Wen, Yiyuan Ao, Jiana Chen, Yutian Li, Miao He, Caichen Li, Hongbo Zheng, Yanhui Chen, Zhenkui Pan, Jianxing He, Wenhua Liang
Summary: This study analyzed the tumor immune microenvironment (TIME) in non-small cell lung cancer (NSCLC) using multiplex immunofluorescence, identifying three immune subtypes correlated with distinct characteristics and prognosis for patients. Various immune cells were found to play different roles in NSCLC, offering potential prognostic biomarkers and risk stratification methods.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Rossana Lazcano, Frank Rojas, Caddie Laberiano, Sharia Hernandez, Edwin Roger Parra
Summary: The immune profiling of formalin-fixed, paraffin-embedded tissues using multiplex immunofluorescence staining allows for the study of multiple biomarkers on a single slide. Pathology quality control for tumor tissue immune profiling using digital image analysis of core needle biopsies is crucial to avoid wastage of time and materials. Lack of malignant cells is the most limiting sample characteristic for mIF image analysis, making quality control an important step to achieve accurate and reproducible data.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Sharia Hernandez, Frank Rojas, Caddie Laberiano, Rossana Lazcano, Ignacio Wistuba, Edwin Roger Parra
Summary: Multiplex immunofluorescence (mIF) is a powerful tool for phenotyping cells in the cancer immune microenvironment, providing extensive information about cell phenotypes composition and their spatial localization, which is critical for discovering novel cancer immunotherapies and related biomarkers.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Medicine, Research & Experimental
Omozojie P. Aigbogun, Christopher P. Phenix, Ed S. Krol, Eric W. Price
Summary: Small-molecule drugs have short in vivo half-lives, hindering their success as therapeutics. Chemically programmed antibodies (cPAbs) have been developed to address these limitations by augmenting small molecules with antibodies for effector functions and prolonged pharmacokinetic profiles. This review summarizes the different methods used to produce cPAbs and highlights their potential applications in antibody modification fields.
MOLECULAR PHARMACEUTICS
(2023)
Article
Oncology
Jiangchun Wu, Qinhao Guo, Jun Zhu, Yong Wu, Simin Wang, Siyuan Liang, Xingzhu Ju, Xiaohua Wu
Summary: This study utilizes multiplex immunofluorescence (mIF) to explore the potential mechanism of pelvic lymph node (pLN) metastasis in cervical cancer (CC) and develops a nomogram for preoperative prediction of pLN metastasis.
Review
Oncology
Frank Rojas, Sharia Hernandez, Rossana Lazcano, Caddie Laberiano-Fernandez, Edwin Roger Parra
Summary: A robust understanding of the tumor immune environment is crucial for cancer diagnosis, prognosis, research, and immunotherapy. Multiplexed imaging technologies allow for the simultaneous analysis of multiple parameters in a tissue section, enabling researchers to study different populations of immune cells within a single cell group. Image analysis software using machine learning approaches has significantly advanced digital pathology and provided the necessary data for translational research. Optimization and standardization of image analysis algorithms are essential for increasing the amount of data generated and their accuracy in a short time in cancer research.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Zarwa Yaseen, Tuba N. Gide, Jordan W. Conway, Alison J. Potter, Camelia Quek, Angela M. Hong, Georgina V. Long, Richard A. Scolyer, James S. Wilmott
Summary: This study validated the accuracy, precision, and reproducibility of multiplex immunofluorescence in characterizing the expression of immune and melanoma markers in the tumor and its microenvironment. The results showed significant positive correlations between multiplex immunofluorescence and immunohistochemistry, as well as single-plex immunofluorescence. The high reproducibility of multiplex immunofluorescence suggests its reliability and validity in accurately profiling the tumor and microenvironment.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Johnathan C. Maza, Derek M. Garcia-Almedina, Lydia E. Boike, Noah X. Hamlish, Daniel K. Nomura, Matthew B. Francis
Summary: A convenient enzymatic strategy is described for modifying cell surfaces using tyrosinase enzyme. The strategy involves introducing unique tyrosine residues at the C-termini of nanobodies, which can then be selectively oxidized to reactive o-quinones. These reactive intermediates readily react with thiol, amine, and imidazole residues present on cell surfaces, resulting in novel nanobody-cell conjugates that exhibit targeted antigen binding. The approach is further extended to the synthesis of nanobody-NK cell conjugates for targeted immunotherapy applications, which demonstrate targeted cell binding and induce targeted cell death.
ACS CENTRAL SCIENCE
(2022)
Article
Cell Biology
Nahla M. Badr, Jack L. McMurray, Irini Danial, Steven Hayward, Nancy Y. Asaad, Moshira M. Abd El-Wahed, Asmaa G. Abdou, Marwa Serag M. El-Dien, Nisha Sharma, Yoshiya Horimoto, Tapan Sircar, Raghavan Vidya, Fiona Hoar, Daniel Rea, J. Louise Jones, Andrea Stevens, David Spooner, Reena Merard, Paul Lewis, Kelly John Hunter, Fedor Berditchevski, Abeer M. Shaaban
Summary: This study examined the immune microenvironment profiling in inflammatory breast cancer (IBC), revealing different distributions of immune cell subtypes in lower grade tumors. The infiltration of CD20+ cells and CD4+ cells were associated with chemotherapy response and survival rates.
Review
Biochemistry & Molecular Biology
Keith A. Wharton, Douglas Wood, Mael Manesse, Kirsteen H. Maclean, Florian Leiss, Aleksandra Zuraw
Summary: Multiplex tissue analysis using immunofluorescence has the potential to enhance pathologic diagnosis by providing insights into tissue-level biology and single-cell phenotypes that traditional methods cannot address. Widespread implementation will require improved detection chemistry, greater standardization of workflows and data pipelines, and integration of multichannel images into digital pathology systems, with interpretation aided by AI. Adoption will also depend on evidence justifying clinical use, regulatory pathways, and adequate budgets and reimbursement.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Yong Woong Jun, Eddy Albarran, David L. Wilson, Jun Ding, Eric T. Kool
Summary: Mitochondrial function declines with aging and neurodegeneration, largely due to accumulated mutations in mtDNA from deficient DNA repair. A fluorescent probe, UBER, was used to visualize mitochondrial BER activity, showing increased repair under oxidative stress and time delay between stress onset and BER initiation. Cells lacking MTH1 exhibited elevated demand for BER activity during extended stress, while absence of OGG1 limited glycosylation capacity.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Biswarup Jash, Eric T. Kool
Summary: In this study, we investigated the acylation reactivity of RNA 2'-OH groups and identified the strong influence of steric and inductive effects on the reaction. These findings provide insights into new strategies for enhancing conjugation and mapping of RNA.
CHEMICAL COMMUNICATIONS
(2022)
Article
Microbiology
Mericien Venzon, Ritika Das, Daniel J. Luciano, Julia Burnett, Hyun Shin Park, Joseph Cooper Devlin, Eric T. Kool, Joel G. Belasco, E. Jane Albert Hubbard, Ken Cadwell
Summary: Microbial byproducts play a crucial role in the reproductive development of nematodes by affecting their fertility and hatching abilities through alterations in arginine and aldehyde levels.
CELL HOST & MICROBE
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Emily M. Harcourt, Yong Woong Jun, David L. Wilson, Emily D. Ledgerwood, Eric T. Kool
Article
Biochemistry & Molecular Biology
Yujeong Lee, Yoshiyuki Onishi, Lisa McPherson, Anna M. Kietrys, Marian Hebenbrock, Yong Woong Jun, Ishani Das, Shanthi Adimoolam, Debin Ji, Michael G. Mohsen, James M. Ford, Eric T. Kool
Summary: Impaired DNA repair activity is associated with increased cancer rates. This study found that certain tyrosine kinase inhibitors, such as nilotinib, can activate the repair enzyme MTH1, which cleanses oxidatively damaged nucleotides. Structural optimization resulted in compounds that strongly activate MTH1 and decrease mutagenic nucleotides in cellular DNA. These findings suggest that MTH1 activators may be a promising strategy to suppress tumorigenesis in individuals with elevated cancer risks.
ACS CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yong Woong Jun, Emily M. Harcourt, Lu Xiao, David L. Wilson, Eric T. Kool
Summary: This article presents a convenient and versatile method for general fluorescence labeling of DNAs. It utilizes deaminated DNA bases and aminooxy-substituted rotor dyes to mark label positions and trap AP sites, resulting in high emission intensities for fluorescence labeling of oligonucleotides and dsDNA.
NATURE COMMUNICATIONS
(2022)
Review
Chemistry, Multidisciplinary
Yong Woong Jun, Eric T. Kool
Summary: DNA repair enzymes play a significant role in protecting cellular DNA from damage and are closely associated with cancer and inflammation pathways. The development of new tools and methods has greatly contributed to the study of these enzymes and their potential applications in diagnostics and therapies. This article provides an overview of the development of chemical tools for studying DNA repair processes and discusses the insights gained from their application. The article also highlights the importance of future research in the field of biomedicine and human health.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Lu Xiao, Linglan Fang, Sayantan Chatterjee, Eric T. Kool
Summary: RNA 2'-OH acylation is widely used for structure mapping and conjugation, and depends on selective reactions with unpaired nucleotides. We prepared a range of structurally diverse acylimidazole reagents and used deep sequencing to study their reactivity and selectivity in a variety of RNA structures. Our results demonstrate that the reagent scaffold significantly affects reactivity profiles and highlight new acylating agents with altered selectivity, including compounds that show elevated selectivity within loops and reduced off-target reactivity in loop closing base pairs. We also discovered a simple reagent that is cell permeable and can map RNA structure in the presence of protein contacts, and describe reagents with elevated selectivity within small loops for site-selective labeling.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Sayantan Chatterjee, Ryuta Shioi, Eric T. Kool
Summary: The nucleophilic reactivity of RNA 2'-OH groups has been applied in various RNA-related processes. In this study, it is discovered that activated small-molecule sulfonyl species can retain their reactivity in water. Reactions with ribose 2'-OH show high yields, especially for aryl sulfonyltriazole species. Additionally, an azide-substituted sulfonyltriazole reagent is developed for labeling RNA via click chemistry.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Yong Woong Jun, Melis Kant, Erdem Coskun, Takamitsu A. A. Kato, Pawel Jaruga, Elizabeth Palafox, Miral Dizdaroglu, Eric T. T. Kool
Summary: High-temperature cooking damages DNA in food, which can then enter the cellular DNA and lead to genetic risks.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Linglan Fang, Lu Xiao, Yong Woong Jun, Yoshiyuki Onishi, Eric T. T. Kool
Summary: The presence of a hydroxyl group at the 2'-position in ribose makes RNA susceptible to hydrolysis. In this study, reversible 2'-OH acylation was presented as a general strategy to preserve RNA stability. High-yield polyacylation of 2'-hydroxyls effectively protected RNAs from degradation, and subsequent treatment with nucleophilic reagents removed acylation adducts and recovered a wide range of RNA functions.
Article
Chemistry, Multidisciplinary
Ryuta Shioi, Lu Xiao, Sayantan Chatterjee, Eric T. Kool
Summary: The reactivity of RNA 2'-OH groups with acylating agents has been studied for high-yield conjugation of RNA strands. This study focuses on the stereoselectivity of chiral acylimidazoles in RNA reactions. The results reveal that positional selectivity and reactivity vary greatly with local RNA macro-chirality, and the chirality of the reagents has a significant impact on their reactivity. This study demonstrates new chemical strategies for selective RNA modification and probing.
Article
Biochemical Research Methods
Reema Baskar, Amy F. Chen, Patricia Favaro, Warren Reynolds, Fabian Mueller, Luciene Borges, Sizun Jiang, Hyun Shin Park, Eric T. Kool, William J. Greenleaf, Sean C. Bendall
Summary: Master transcription factors regulate cell states by driving gene-expression programs, and their abundance affects cell fate at the chromatin level. InTAC-seq method allows the study of the relationship between protein abundance and gene regulation in cells.
CELL REPORTS METHODS
(2022)
Article
Biochemistry & Molecular Biology
Lu Xiao, Linglan Fang, Eric T. Kool
Summary: The reactivity of RNA 2'-OH acylation has been extensively studied in this research. The results show that there is a wide range of reactivity among single-stranded RNA sequences, with nearest neighbors playing a significant role. Interestingly, certain small loops exhibit much higher reactivity compared to single-stranded RNAs, which is attributed to conformational constraints.
CELL CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Sergio M. Marques, Michaela Slanska, Klaudia Chmelova, Radka Chaloupkova, Martin Marek, Spencer Clark, Jiri Damborsky, Eric T. Kool, David Bodnar, Zbynek Prokop
Summary: HaloTag labeling technology has revolutionized protein chemistry and cellular biology, and a systematic analysis of different ligands has led to the discovery of an optimal protein tag selection protocol, eliminating the need for expensive and complex protein engineering.