Article
Multidisciplinary Sciences
Navratan Bagwan, Henrik H. El Ali, Alicia Lundby
Summary: Post translational modifications (PTMs) are covalent modifications of proteins that regulate protein function and increase proteome diversity. In human hearts, high-resolution mass spectrometry measurements and PTM identification algorithms identified over 150 different PTMs, highlighting the diversity of cardiac protein modifications.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Analytical
Pierre Sabatier, Christian M. Beusch, Zhaowei Meng, Roman A. Zubarev
Summary: The ResT-PISA assay enables quantification of the lifetime of drug-target interaction by monitoring temporal protein solubility profiles after drug removal. It combines affinity and residence time assessments into a single proteomic analysis and improves target prioritization with a combined scoring system. This method is valuable in drug development and precision medicine.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Lin Bai, Guojian Yang, Zhaoyu Qin, Jiacheng Lyu, Yunzhi Wang, Jinwen Feng, Mingwei Liu, Tongqing Gong, Xianju Li, Zhengyang Li, Jixi Li, Jun Qin, Wenjun Yang, Chen Ding
Summary: This study used a novel method to analyze the binding activity of transcription factors under DNA modifications and identified potential readers for 5fC-modified DNA. By quantifying the modified DNA-binding activity of 1039 TFs, it revealed the hierarchical networks between the transcriptional protein machinery and modified DNA.
Article
Biochemical Research Methods
Min Ma, Fabao Liu, Hannah N. Miles, Eui-Jun Kim, Lauren Fields, Wei Xu, Lingjun Li
Summary: Arginine methylation catalyzed by PRMTs is a prevalent PTM that regulates cellular processes. This study mapped ADMA in breast cancer PDX tumors and identified 403 methylated sites from 213 proteins, including novel sites. Peptide array validation confirmed methylated substrates by PRMT1, PRMT4, and PRMT6. The study provides a resource for PRMT and breast cancer research.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Chemistry, Analytical
Asad Ali Siyal, Eric Sheng-Wen Chen, Hsin-Ju Chan, Reta Birhanu Kitata, Jhih-Ci Yang, Hsiung-Lin Tu, Yu-Ju Chen
Summary: The study presents a sample size-comparable library-based DIA approach, achieving higher protein group identification from small-size library compared to medium-size, large-size, and lung cancer resource spectral library. The approach shows good generality across different instruments and data analysis methods.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Haizhu Zhang, Zhaoyu Qin, Xuetong Yue, Yang Liu, Xiaogang Sun, Jinwen Feng, Ziyan Xu, Jiangyan Zhao, Kai Li, Jiange Qiu, Wenjun Yang, Fuchu He, Chen Ding
Summary: ATAC-MS is a method to identify transcriptional protein complexes assembled on accessible chromatin, providing insight into the protein machinery in open chromatin. Combined with ATAC-seq, it allows for high-resolution profiling of chromatin-transcriptional machinery. Additionally, the fusion protein ctATAC-MS enables systematic pinpointing of the transcriptional machinery at specific open chromatin regions.
Review
Biochemical Research Methods
Lan Huang, Dan Shao, Yan Wang, Xueteng Cui, Yufei Li, Qian Chen, Juan Cui
Summary: Recent research on body-fluid proteomes has resulted in the discovery of novel disease biomarkers and therapeutic drugs, with over 15,000 different proteins detected in major human body fluids. Challenges remain in effectively handling the variety of protein modifications in these fluids. Computational efforts using statistical and machine-learning approaches have shown promise in identifying biomarker proteins in specific human diseases.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Chemistry, Analytical
Chengfei Ruan, Jiahua Zhou, Zhouxian Li, Kejia Li, Zheng Fang, Xiaolei Zhang, Mingliang Ye
Summary: This study developed a new lysine reactivity profiling method to identify drug targets and binding sites in complex proteomes, demonstrating high sensitivity and comparability with existing methods. The method also revealed drug-induced conformational changes of target proteins and showed the complementary nature of target identification by different methods. Further applications of the method in probing multiple events involving lysine reactivity changes in the proteome were envisioned.
ANALYTICAL CHEMISTRY
(2022)
Article
Biology
Kelsie M. Rodriguez, Sara C. Buch-Larsen, Ilsa T. Kirby, Ivan Rodriguez Siordia, David Hutin, Marit Rasmussen, Denis M. Grant, Larry L. David, Jason Matthews, Michael L. Nielsen, Michael S. Cohen
Summary: PARP-7 has been identified as an important regulator of the innate immune response, with a key target being the inactive PARP family member PARP-13. Specifically, PARP-7 preferentially MARylates cysteine residues in the RNA binding zinc finger domain of PARP-13, as revealed by proteome-wide ADP-ribosylation analysis.
Article
Medicine, Research & Experimental
Elze Rackaityte, Irina Proekt, Haleigh S. Miller, Akshaya Ramesh, Jeremy F. Brooks, Andrew F. Kung, Caleigh Mandel-Brehm, David Yu, Colin R. Zamecnik, Rebecca Bair, Sara E. Vazquez, Sara Sunshine, Clare L. Abram, Clifford A. Lowell, Gabrielle Rizzuto, Michael R. Wilson, Julie Zikherman, Mark S. Anderson, Joseph L. Derisi
Summary: Autoimmunity is a complex condition characterized by the loss of tolerance to tissue-specific and systemic antigens. This study introduces a new method called murine proteome-wide PhIP-seq, which allows for the profiling of mouse autoantibodies. The method was extensively validated using genetically distinct mouse lines and was used to study three different autoimmune disease models. The results demonstrate the potential of this method for antigenic profiling and autoantibody discovery in mouse models of autoimmunity.
Article
Multidisciplinary Sciences
Yangfan Zhou, Lixia Wang, Zhike Lu, Zhenxing Yu, Lijia Ma
Summary: Genome-wide CRISPR-based knockout screening is a powerful tool for analyzing cellular or molecular phenotypes, but is limited by the size of the sgRNA library. In this study, a minimal genome-wide human sgRNA library, H-mLib, was designed using a selection strategy, comprising 21,159 sgRNA pairs targeting all potential SpCas9/sgRNAs in the human genome. These sgRNA pairs were cloned into a dual-gRNA vector, resulting in a compact library size comparable to the number of human protein-coding genes. Benchmarking against other CRISPR libraries in a proliferation screening verified the high specificity and sensitivity of H-mLib. Furthermore, by comparing screening results from K562 and Jurkat cells, core essential genes and cell-type specific essential genes were identified. In conclusion, H-mLib demonstrates excellent performance in identifying essential genes while having minimal library complexity, making it advantageous and suitable for CRISPR screening with limited cell numbers.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Jiaming Li, Zhenying Cai, Laura Pontano Vaites, Ning Shen, Dylan C. Mitchell, Edward L. Huttlin, Joao A. Paulo, Brian L. Harry, Steven P. Gygi
Summary: By combining cycloheximide chase assays with advanced quantitative proteomics, this study mapped short-lived proteins under translational inhibition in four human cell lines. Short-lived proteins are less abundant, evolutionarily younger, and less thermally stable compared to other proteins, with 103 proteins showing different stabilities among cell lines. Truncated forms of certain proteins in U2OS and HCT116 cells were also identified, indicating lower stability than full-length counterparts. This research provides a large-scale resource for understanding human short-lived proteins and their potential for therapeutic interventions.
Article
Chemistry, Multidisciplinary
Jun Shi Chang, Alexander A. Vinogradov, Yue Zhang, Yuki Goto, Hiroaki Suga
Summary: A deep learning model was used to streamline the design of mRNA display libraries, leading to the discovery of potent thiopeptide ligands with favorable pharmacological properties against IRAK4 kinase and TLR10 cell surface receptor.
ACS CENTRAL SCIENCE
(2023)
Article
Biochemical Research Methods
Ashley Di Meo, Dorsa Sohaei, Ihor Batruch, Pantelis Alexandrou, Ioannis Prassas, Eleftherios P. Diamandis
Summary: The analysis utilized LC-MS/MS technology to profile the normal human proteome from 117 samples across 46 normal tissues and organs, quantifying 10,438 unique proteins. By combining data from biological fluid proteomics of healthy individuals, tandem mass spectra corresponding to 13,028 unique human protein-coding genes were generated, serving as an important complementary resource for future biomarker discovery.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Chemistry, Analytical
Guoli Wang, Yang Li, Ting Wang, Jun Wang, Jun Yao, Guoquan Yan, Ying Zhang, Haojie Lu
Summary: O-GlcNAcylation, a simple but essential protein post-translational modification, plays critical roles in cellular processes and is closely associated with various diseases. However, the low stoichiometry and reversibility properties of O-GlcNAcylation pose challenges for system-wide research. In this study, a novel method combining multi-comparative thermal proteome profiling was developed for O-GlcNAc transferase (OGT) substrate discovery. By profiling and comparing the melting curves of proteins under different treatments, proteins with significantly altered stabilities induced by OGT and uridine-5'-diphosphate N-acetylglucosamine were identified and new O-GlcNAcylated proteins were uncovered.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Nien-Ching Han, Tammy J. Bullwinkle, Kaeli F. Loeb, Kym F. Faull, Kyle Mohler, Jesse Rinehart, Michael Ibba
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Multidisciplinary Sciences
Hong Zhang, Zhihui Lyu, Yongqiang Fan, Christopher R. Evans, Karl W. Barber, Kinshuk Banerjee, Oleg A. Igoshin, Jesse Rinehart, Jiqiang Ling
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Nicolle A. Rosa-Mercado, Joshua T. Zimmer, Maria Apostolidi, Jesse Rinehart, Matthew D. Simon, Joan A. Steitz
Summary: This study reveals that stress-induced readthrough transcription leading to the synthesis of downstream-of-gene (DoG)-containing transcripts is independent of the transcriptional level of upstream genes. The redistribution of RNA polymerase (Pol) II under stress correlates with gene transcriptional output. Additionally, alterations in the Pol II interactome and dissociation of Integrator complex subunits from Pol II contribute to genome-wide loss of Integrator on DNA and production of stress-induced readthrough transcripts.
Article
Oncology
Pedro Torres-Ayuso, Elvira An, Katherine M. Nyswaner, Ryan C. Bensen, Daniel A. Ritt, Suzanne Specht, Sudipto Das, Thorkell Andresson, Raul E. Cachau, Roger J. Liang, Amy L. Ries, Christina M. Robinson, Simone Difilippantonio, Brad Gouker, Laura Bassel, Baktiar O. Karim, Chad J. Miller, Benjamin E. Turk, Deborah K. Morrison, John Brognard
Summary: Research identified TNIK as a potential therapeutic target in LSCC, with genetic depletion or pharmacologic inhibition showing efficacy in reducing the growth of LSCC cells. In preclinical models, TNIK inhibition displayed antitumor activity and increased apoptosis in LSCC patient-derived xenografts.
Article
Oncology
Maria Apostolidi, Ioannis A. Vathiotis, Viswanathan Muthusamy, Patricia Gaule, Brandon M. Gassaway, David L. Rimm, Jesse Rinehart
Summary: PKM2 phosphorylation is associated with aggressive breast cancer cell phenotypes in TNBC, and targeting PKM2pS37 could be an effective therapeutic approach for treating triple-negative breast cancer.
Article
Biochemistry & Molecular Biology
Karl W. Barber, Ellen Shrock, Stephen J. Elledge
Summary: CRISPR-inspired systems have been developed for genome editing and nucleic acid detection. The CRISPR-based peptide display technology introduced in this study allows for customized, high-throughput in vitro protein interaction studies by self-assembling bespoke peptide libraries on a DNA microarray surface for rapid, multiplexed binding assays. This platform shows promise for viral epitope mapping and multiplexed diagnostics.
Article
Multidisciplinary Sciences
M. Bryana Cassie, Gabriel J. Rocklin, Matthew J. Bick, Alex Ford, Sonia Majri-Morrison, Ashley V. Kroll, Chad J. Miller, Lauren Carter, Inna Goreshnik, Alex Kang, Frank DiMaio, Kristin V. Tarbell, David Baker
Summary: The PD-1 pathway plays a crucial role in regulating immune responses, and the computationally designed hyperstable PD-1 binding protein PD-MP1 acts as an agonist that strongly inhibits murine T cell activation, offering a new approach for the treatment of autoimmune and inflammatory diseases.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Paula Schiapparelli, Natasha L. Pirman, Kyle Mohler, Pierre A. Miranda-Herrera, Natanael Zarco, Onur Kilic, Chad Miller, Sagar R. Shah, Svetlana Rogulina, William Hungerford, Laura Abriola, Denton Hoyer, Benjamin E. Turk, Hugo Guerrero-Cazares, Farren J. Isaacs, Alfredo Quinones-Hinojosa, Andre Levchenko, Jesse Rinehart
Summary: Genetic code expansion has enabled the production of proteins with specific post-translational modifications, and in this study, a recoded bacterial strain was used to encode phosphoserine into human kinases. This synthetic activation of WNK kinase networks was shown to accurately model cellular systems and could be applied more broadly for research and discovery of phosphorylated protein networks.
Article
Oncology
Michal Marczyk, Vignesh Gunasekharan, David Casadevall, Tao Qing, Julia Foldi, Raghav Sehgal, Naing Lin Shan, Kim R. M. Blenman, Tess A. O'Meara, Sheila Umlauf, Yulia Surovtseva, Viswanathan Muthusamy, Jesse Rinehart, Rachel J. Perry, Richard Kibbey, Christos Hatzis, Lajos Pusztai
Summary: This study examines the expression patterns of isozymes in cancer and identifies potential therapeutic targets. It shows that the loss of isozyme diversity in cancer can be exploited for anticancer therapy.
Article
Biochemical Research Methods
Brandon M. Gassaway, Jiaming Li, Ramin Rad, Julian Mintseris, Kyle Mohler, Tyler Levy, Mike Aguiar, Sean A. Beausoleil, Joao A. Paulo, Jesse Rinehart, Edward L. Huttlin, Steven P. Gygi
Summary: Iterative Synthetically Phosphorylated Isomers (iSPI) is a proteome-scale library of human-derived phosphoserine-containing phosphopeptides with precisely known positions of phosphorylation. It serves as a valuable resource for optimization, standardization, and benchmarking in phosphoproteomics workflows, and addresses the lack of inexpensive and diverse phosphopeptides with ground-truth phosphorylation positions.
Article
Multidisciplinary Sciences
Jack M. Moen, Kyle Mohler, Svetlana Rogulina, Xiaojian Shi, Hongying Shen, Jesse Rinehart
Summary: Protein phosphorylation is a crucial post-translational modification that regulates cellular processes and protein-protein interactions. Traditional strategies for functional assignment of phosphorylation events have become inadequate in keeping up with the rapid identification pace through proteomic surveillance. However, the development of phospho-amino-acid-specific orthogonal translation systems offers a kinase-independent method to assess the physiological function of phosphorylation.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Felix Radford, Jesse Rinehart, Farren J. Isaacs
Summary: This study develops a method to map the nucleotides in the peptidyl transfer center and the resulting epistatic interactions.
Article
Biochemistry & Molecular Biology
Kyle Mohler, Jack M. Moen, Svetlana Rogulina, Jesse Rinehart
Summary: In the past two decades, synthetic biological systems have revolutionized the study of cellular physiology. The use of orthogonal translation systems (OTSs) to incorporate non-standard amino acids has provided unprecedented access to cellular mechanisms regulated by post-translational modifications. However, the systems-level biology of OTS development and utilization remains underexplored. This study investigates the global interactions between OTS components and the cellular environment, aiming to improve OTS performance and enhance orthogonality.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Pol Arranz-Gibert, Koen Vanderschuren, Adrian Haimovich, Anushka Halder, Kallol Gupta, Jesse Rinehart, Farren J. Isaacs
Summary: This study presents a pH-tunable diazotransfer reaction that efficiently converts para-amino-phenyl-alanine (pAF) to para-azido-phenylalanine (pAzF) in proteins. The method selectively modifies pAzF at multiple sites per protein without introducing off-target modifications.
CELL CHEMICAL BIOLOGY
(2022)
Article
Cell Biology
Abudukadier Abulizi, Rebecca L. Cardone, Romana Stark, Sophie L. Lewandowski, Xiaojian Zhao, Joelle Hillion, Lingjun Ma, Raghav Sehgal, Tiago C. Alves, Craig Thomas, Charles Kung, Bei Wang, Stephan Siebel, Zane B. Andrews, Graeme F. Mason, Jesse Rinehart, Matthew J. Merrins, Richard G. Kibbey