Article
Oncology
Francesca Piaggio, Michela Croce, Francesco Reggiani, Paola Monti, Cinzia Bernardi, Marianna Ambrosio, Barbara Banelli, Mehmet Dogrusoez, Ralf Jockers, Domenico Bordo, Roberto Puzone, Silvia Viaggi, Domenico Coviello, Francesco B. Lanza, Martina Bartolucci, Andrea Petretto, Carlo Mosci, Rosaria Gangemi, Pieter A. van der Velden, Martine J. Jager, Ulrich Pfeffer, Adriana Amaro
Summary: This study investigated the impact of GNAQ and GNA11 gene mutations on the characteristics and prognosis of uveal melanoma. The results showed that GNA11 mutation was associated with worse prognosis and high-risk cytogenetic, mutational, and molecular tumor characteristics. Additionally, G-proteins encoded by GNAQ and GNA11 had different protein interaction partners, and differential DNA methylation might contribute to different progression risks.
EUROPEAN JOURNAL OF CANCER
(2022)
Article
Biochemical Research Methods
Smarajit Mondal, Muthukumar Ramanathan, Weili Miao, Robin M. Meyers, Deepti Rao, Vanessa Lopez-Pajares, Zurab Siprashvili, David L. Reynolds, Douglas F. Porter, Ian Ferguson, Poornima Neela, Yang Zhao, Lindsey M. Meservey, Margaret Guo, Yen-Yu Yang, Lin Li, Yinsheng Wang, Paul A. Khavari
Summary: DNA-protein interactions play a crucial role in gene regulation and can be affected by DNA variants associated with polygenic diseases. A new method called PROBER has been developed to rapidly identify and quantify proteins associated with specific DNA sequences in living cells. PROBER utilizes high-copy episomes and proximity proteomics to accurately identify transcription factors and gene regulators associated with target DNA sequences and single-nucleotide variants. The method has been used to study the impact of cancer hotspot mutations on regulator associations.
Article
Environmental Sciences
Ian J. Vander Meulen, Danna M. Schock, Fardausi Akhter, Lukas J. Mundy, Kristin M. Eccles, Catherine Soos, Kerry M. Peru, Dena W. McMartin, John V. Headley, Bruce D. Pauli
Summary: This study investigated the occurrence and characteristics of naphthenic acids (NAs) in boreal wetlands in the Athabasca oil sands region of Alberta, Canada. The results showed that NAs in surface waters were mainly derived from oil sands deposits, but similar patterns were also observed in undeveloped natural wetlands.
ENVIRONMENTAL POLLUTION
(2023)
Article
Biochemical Research Methods
Quynh-Trang Do, Ting-En Huang, Yi-Chen Liu, Jung-Hsiang Tai, Shu-Hui Chen
Summary: This study identified protein targets of CEs in estrogen-sensitive breast cancer cells using proteomics, revealing the mechanism of covalent adduct formation between CEs and proteins. The results suggest that CEs may downregulate proteins involved in metabolism or detoxification, indicating a negative correlation between CE-induced cellular damage and the expression of stress-alleviating proteins.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Chemistry, Analytical
Xiujun Cao, Yuan Luo, Xueli Liu, Chunqing Shang, Jun Lu, Guoxin Song, Chunhui Deng
Summary: Hirudin, a natural substance found in leeches, has both therapeutic and toxic effects. This study proposes a new method for detecting hirudin in serum using affinity magnetic microspheres. The method combines liquid chromatography and mass spectrometry analysis to achieve accurate detection. The method has a low limit of detection, good linearity, and acceptable precision.
Review
Biochemistry & Molecular Biology
Alicia L. Richards, Manon Eckhardt, Nevan J. Krogan
Summary: Quantitative mass spectrometry (MS) techniques have enabled unbiased mapping of global changes in protein-protein interactions mediated by diseases, which can reveal disease mechanisms and identify new therapeutic targets.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Review
Environmental Sciences
Carlos Castillo-Zacarias, Mario E. Barocio, Enrique Hidalgo-Vazquez, Juan Eduardo Sosa-Hernandez, Lizeth Parra-Arroyo, Itzel Y. Lopez-Pacheco, Damia Barcelo, Hafiz N. M. Iqbal, Roberto Parra-Saldivar
Summary: Antidepressants contaminate urban and non-urban water bodies, leading to bioaccumulation in aquatic animals. This contamination is expected to increase due to rising depression and anxiety levels during the COVID-19 pandemic.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Oncology
Madison T. Wright, Lars Plate
Summary: The endoplasmic reticulum (ER) plays a crucial role in processing the human proteome, with mass spectrometry technology being key in understanding protein quality control mechanisms. There are still unexplored areas in ER proteostasis where mass spectrometry can be utilized to expand our understanding of protein quality control processes in diverse diseases.
EXPERIMENTAL CELL RESEARCH
(2021)
Article
Engineering, Environmental
Yufeng Gong, Diwen Yang, Holly Barrett, Jianxian Sun, Hui Peng
Summary: Advancements in nontargeted analysis have allowed for the detection of multiple chemical contaminants. However, environmental toxicology approaches are lacking, impeding the transition to health risk assessment. A protein-guided approach called APNA has been developed to screen bioactive chemical contaminants at the exposome-wide level. This approach utilizes a tagged functional protein to isolate and identify contaminants, leading to the discovery of new ligands and protein targets. A proposed framework, eCPIN, aims to establish a comprehensive map of interactions between chemical contaminants and human proteins to facilitate screening and identification at a proteome-wide level.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Cell Biology
Devanarayanan Siva Sankar, Joern Dengjel
Summary: Autophagy is a crucial cellular degradation process that helps in maintaining cellular homeostasis through the clearance of damaged organelles and harmful substances. Protein-protein interaction networks play a key role in regulating autophagy, contributing to the degradation process and maintaining cellular function.
Article
Chemistry, Analytical
Benjamin J. Place, Elin M. Ulrich, Jonathan K. Challis, Alex Chao, Bowen Du, Kristin Favela, Yong-Lai Feng, Christine M. Fisher, Piero Gardinali, Alan Hood, Ann M. Knolhoff, Andrew D. McEachran, Sara L. Nason, Seth R. Newton, Brian Ng, Jamie Nunez, Katherine T. Peter, Allison L. Phillips, Natalia Quinete, Ryan Renslow, Jon R. Sobus, Eric M. Sussman, Benedikt Warth, Samanthi Wickramasekara, Antony J. Williams
Summary: Non-targeted analysis (NTA) is a rapidly evolving set of mass spectrometry techniques aimed at characterizing complex samples' chemical composition, identifying unknown compounds, and classifying samples. Recent advances are due to improved instrumentation and accessible data analysis tools, with a growing need for community-wide method reporting guidelines. This has led to the formation of the Benchmarking and Publications for Non-Targeted Analysis Working Group (BP4NTA) to address challenges and establish consensus in NTA-related terms and reporting practices.
ANALYTICAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Roberto Giambruno, Francesco Nicassio
Summary: Proximity ligation technologies are powerful tools for studying RNA-protein interactions in living cells. They use inducible enzymes to biotinylate molecules within a 20 nm range, allowing for easy purification and analysis. These methods have been widely used to map molecular interactions and can also be used to study post-transcriptional modifications.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Chemistry, Analytical
Adway O. Zacharias, Zixiang Fang, Aurchie Rahman, Akash Talukder, Sharel Cornelius, Saiful M. Chowdhury
Summary: Protein post-translational modifications and interactions are key research areas in mass spectrometry-based proteomics, but selective enrichment of modifications/interactions of interest during sample preparation remains a major bottleneck. Various strategies have been developed to target specific modifications/interactions based on physical or chemical properties, with only a few successful applications for systematic proteome-wide study.
JOURNAL OF SEPARATION SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Tyler L. Peterson, Gabe Nagy
Summary: The new high-throughput screening method based on cIMS-MS separation allows rapid resolution of alpha/beta anomers for carbohydrates and detection of their impurities at levels below 2%, demonstrating high-throughput nature with experiments completed in 1 minute. This methodology can also be extended to separate isomeric mixtures of protected disaccharides, illustrating its utility beyond monosaccharides.
Review
Agronomy
Rosalia Lopez-Ruiz, Jesus Marin-Saez, Antonia Garrido Frenich, Roberto Romero-Gonzalez
Summary: The cultivation of cannabis has been increasing in recent years due to its diverse applications, leading to a greater need for analysis of contaminants to ensure consumer safety. Chromatographic techniques, especially liquid chromatography-mass spectrometry, have been widely utilized for the determination of contaminants in cannabis products. New advances such as high-resolution mass spectrometry are also discussed for targeted and untargeted analyses in cannabis analysis.
PEST MANAGEMENT SCIENCE
(2022)
Article
Oncology
Johanna S. Rees, Lawrence C. C. Cheung, Samir W. Hamaia, Gareth Davies, Alan Sandercock, Kathryn S. Lilley, Natalie Tigue, Antony P. Jackson
INTERNATIONAL JOURNAL OF ONCOLOGY
(2020)
Article
Cell Biology
Iris K. Jarsch, Jonathan R. Gadsby, Annalisa Nuccitelli, Julia Mason, Hanae Shimo, Ludovic Pilloux, Bishara Marzook, Claire M. Mulvey, Ulrich Dobramysl, Charles R. Bradshaw, Kathryn S. Lilley, Richard D. Hayward, Tristan J. Vaughan, Claire L. Dobson, Jennifer L. Gallop
JOURNAL OF CELL BIOLOGY
(2020)
Article
Biochemical Research Methods
Alerie G. de la Fuente, Rayner M. L. Queiroz, Tanay Ghosh, Christopher E. McMurran, Juan F. Cubillos, Dwight E. Bergles, Denise C. Fitzgerald, Clare A. Jones, Kathryn S. Lilley, Colin P. Glover, Robin J. M. Franklin
MOLECULAR & CELLULAR PROTEOMICS
(2020)
Article
Multidisciplinary Sciences
Michael A. S. Thorne, Nina Kocevar Britovsek, Liam Hawkins, Kathryn S. Lilley, Kenneth Storey
Article
Biochemical Research Methods
Eneko Villanueva, Tom Smith, Rayner M. L. Queiroz, Mie Monti, Mariavittoria Pizzinga, Mohamed Elzek, Veronica Dezi, Robert F. Harvey, Manasa Ramakrishna, Anne E. Willis, Kathryn S. Lilley
Article
Biology
Siqi Fang, Paul D. W. Kirk, Marcus Bantscheff, Kathryn S. Lilley, Oliver M. Crook
Summary: Thermal proteome profiling is a method for monitoring protein thermal stability that can provide insights into protein function, drug targets, and off-targets. The use of Bayesian functional data analysis tools can improve sensitivity and identify new drug-protein associations.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Rayner M. L. Queiroz, Sian C. Piper, Johanna S. Rees, Sam Strickson, Emmanuel Briend, Choon Pei Low, G. John Ferguson, Kathryn S. Lilley, Antony P. Jackson, Donna K. Finch
Summary: The ability of the cellular immune system to distinguish self from foreign antigens depends on the calibration of the T cell receptor signaling threshold, which can be affected by interleukin 7 (IL-7). In this study, the researchers investigated the early signaling events triggered by IL-7 and discovered previously unknown transduction events. They found that IL-7 leads to dephosphorylation of cytohesin interacting protein (CYTIP) and alters the co-localization of cytohesin-1 with the TCR and LFA-1 integrin. This study provides insights into the molecular mechanisms underlying TCR activation thresholds and has implications for autoimmune disease therapy and cancer immunotherapy.
BIOCHEMICAL JOURNAL
(2022)
Review
Biochemical Research Methods
Josie A. Christopher, Aikaterini Geladaki, Charlotte S. Dawson, Owen L. Vennard, Kathryn S. Lilley
Summary: The internal environment of cells is crowded with molecules, requiring spatial organization through subcellular compartmentalization. These compartments provide specific conditions for molecules to carry out their biological functions, and molecules traffic between these compartments. Aberrant localization of proteins or RNA species is associated with various pathological conditions. Differential expression studies often overlook the importance of subcellular information, and subcellular transcriptomics and proteomics data do not always overlap, highlighting their complementary nature.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Letter
Biotechnology & Applied Microbiology
Georg Kustatscher, Tom Collins, Anne-Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S. Lilley, Emma Lundberg, Edward M. Marcotte, Markus Ralser, Juri Rappsilber
NATURE BIOTECHNOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Georg Kustatscher, Tom Collins, Anne-Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S. Lilley, Emma Lundberg, Edward M. Marcotte, Markus Ralser, Juri Rappsilber
Article
Multidisciplinary Sciences
Vadim Demichev, Lukasz Szyrwiel, Fengchao Yu, Guo Ci Teo, George Rosenberger, Agathe Niewienda, Daniela Ludwig, Jens Decker, Stephanie Kaspar-Schoenefeld, Kathryn S. Lilley, Michael Muelleder, Alexey Nesvizhskii, Markus Ralser
Summary: The dia-PASEF technology utilizes ion mobility separation to reduce signal interference and enhance sensitivity in proteomic experiments. This study introduces a novel algorithm and software solution that significantly improves proteomic depth in dia-PASEF experiments, particularly for fast experiments and those with limited sample sizes.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Clarissa Braccia, Josie A. Christopher, Oliver M. Crook, Lisa M. Breckels, Rayner M. L. Queiroz, Nara Liessi, Valeria Tomati, Valeria Capurro, Tiziano Bandiera, Simona Baldassari, Nicoletta Pedemonte, Kathryn S. Lilley, Andrea Armirotti
Summary: This study investigates the impact of pharmacological rescue treatment on the proteome of a CF model. The results suggest that VX-809 treatment induces extensive structural and functional remodeling of mitochondria and peroxisomes. These findings are important for further understanding the therapeutic mechanisms and drug research of CF.
Article
Multidisciplinary Sciences
Oliver M. Crook, Colin T. R. Davies, Lisa M. Breckels, Josie A. Christopher, Laurent Gatto, Paul D. W. Kirk, Kathryn S. Lilley
Summary: The steady-state localisation and re-localisation of proteins are crucial for understanding their function and cellular dynamics, with high-throughput methods like BANDLE using Bayesian principles to accurately compute differential protein localisation probabilities upon cellular perturbation, reducing errors compared to existing approaches.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Alistair R. Hines, Matthew Edgeworth, Paul W. A. Devine, Samuel Shepherd, Nicholas Chatterton, Claire Turner, Kathryn S. Lilley, Xiaoyu Chen, Nicholas J. Bond
Summary: Antibody-drug conjugates (ADCs) have been widely developed, leading to new approvals and improved standard of care for cancer patients. This study describes the development of a mass-spectrometry-based method that can simultaneously monitor four quality attributes of ADCs, providing new insights into their properties and manufacturing processes. The study identified variations in thiol state, N-linked glycosylation, reduction of disulfide bonds, and polypeptide fragmentation in ADCs. The method offers a high-throughput approach to support the development of engineered antibody scaffolds.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Multidisciplinary Sciences
Nicola M. Moloney, Konstantin Barylyuk, Eelco Tromer, Oliver M. Crook, Lisa M. Breckels, Kathryn S. Lilley, Ross F. Waller, Paula MacGregor
Summary: This study maps the spatial proteomes of two African trypanosome species, Trypanosoma brucei and Trypanosoma congolense, providing insights into the molecular basis for diversity within and between these pathogen species. Comparative analysis reveals key routes of parasitic adaptation to different biological niches.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
K. Ramki, G. Thiruppathi, Selva Kumar Ramasamy, P. Sundararaj, P. Sakthivel
Summary: A chromone-based ratiometric fluorescent probe L2 was developed for the selective detection of Hg(II) in a semiaqueous solution. The probe exhibited enhanced fluorescence in its aggregated state and even higher fluorescence when chelated with Hg(II). The probe demonstrated high sensitivity and specificity for Hg(II) detection and was successfully applied for imaging Hg(II) in a living model.
Article
Biochemical Research Methods
Qun Zhang, Rui Yang, Gang Liu, Shiyan Jiang, Jiarui Wang, Juqiang Lin, Tingyin Wang, Jing Wang, Zufang Huang
Summary: This research aims to develop a cost-effective and portable method for measuring creatinine levels using the enhanced Tyndall effect phenomenon. The method offers a promising solution for monitoring renal healthcare in resource-limited settings.