Article
Plant Sciences
Juanjuan Yu, Juan M. Gonzalez, Zhiping Dong, Qianru Shan, Bowen Tan, Jin Koh, Tong Zhang, Ning Zhu, Craig Dufresne, Gregory B. Martin, Sixue Chen
Summary: Plants have developed a two-layered immune system consisting of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). Through integrative proteomic and phosphoproteomic analyses of the tomato-Pseudomonas syringae (Pst) pathosystem, it was found that ETI response is stronger than PTI response. Protein abundance and phosphorylation changes revealed key regulators involved in signaling, oxidative stress, transport, cell remodeling, hormone signaling, and implicated potential markers for PTI and ETI.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Gastroenterology & Hepatology
Soo Young Cho, Heeyoun Hwang, Yun-Hee Kim, Byong Chul Yoo, Nayoung Han, Sun-Young Kong, Min-Jeong Baek, Kyung-Hee Kim, Mi Rim Lee, Jae Gwang Park, Sung-Sik Han, Woo Jin Lee, Charny Park, Jong Bae Park, Jin Young Kim, Sang-Jae Park, Sang Myung Woo
Summary: Through comprehensive analysis of genomic, transcriptomic, proteomic, and phosphoproteomic data from 102 iCC patients, three clinically supported subtypes were identified (stem-like, poorly immunogenic, and metabolism), and an organoid model was constructed for therapeutic testing. The ALDH1A1 inhibitor NCT-501 showed synergy with nanoparticle albumin-bound-paclitaxel in the organoid model for the stem-like subtype. Dysregulations in oncometabolites were associated with different clinical outcomes in the stem-like and metabolism subtypes. The poorly immunogenic subtype exhibited non-T-cell tumor infiltration. Integrated multiomics analysis reproduced the 3 subtypes and revealed heterogeneity in iCC.
Review
Immunology
Gertraud Orend, Richard P. Tucker
Summary: Tenascin-C plays important roles in immunity, interacting with Toll-like receptor 4, integrin alpha 9 beta 1, and chemokines. While tenascins predate the appearance of adaptive immunity, the first tenascin-C appears to have evolved in early chordate lineages. Adaptive immunity evolved independently in jawless and jawed vertebrates, with the former using variable lymphocyte receptors and the latter using immunoglobulins.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Environmental Sciences
Juan Wang, Xiaojuan Wang, Conghui Zhang, Xiao Zhou
Summary: The study reveals the potential harm of microplastics to the human immune system. Microplastics in drinking water cause spleen damage and immune suppression in mice, potentially through modulation of protein expression and signaling pathways.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Article
Multidisciplinary Sciences
Hannah Huckstep, Liam G. Fearnley, Melissa J. Davis
Summary: Protein phosphorylation is a well-known post-translational mechanism that plays a key role in cellular processes. While data-driven approaches have had limited success in revealing phosphosite functionality, using prior knowledge from literature-derived databases is a more suitable alternative. This study analyzed seven widely used databases to assess their suitability in providing functional insights into phosphoproteomics data, highlighting their relative strengths and weaknesses and providing guidance on how to best identify biological mechanisms in phosphoproteomic data.
Article
Biochemistry & Molecular Biology
Lianzhen Mao, Yunhua Dai, Yu Huang, Sha Yang, Hao Sun, Yao Zhou, Ying Sun, Bozhi Yang, Xuexiao Zou, Zhoubin Liu
Summary: The leaf is a vital plant organ linked to agricultural yields, and understanding leaf photosynthesis regulation can improve crop yield. This study analyzed the photosynthetic changes of pepper leaves under different light intensities, revealing significant effects on chlorophyll fluorescence and photosynthetic parameters. Proteins involved in photosynthesis and carbon fixation were differentially expressed, and phosphorylation levels varied under different light conditions. These findings provide new insights into studying pepper photosynthesis mechanisms under varying light intensities.
Article
Biochemistry & Molecular Biology
Tian Wang, Hao-Qi Wang, Bao Yuan, Guo-Kun Zhao, Yi-Ran Ma, Pei-Sen Zhao, Wen-Yin Xie, Fei Gao, Wei Gao, Wen-Zhi Ren
Summary: Proteomic and phosphoproteomic analyses were performed to investigate the changes in rat adenohypophysis after GnRH treatment. The results revealed proteins and phosphorylation sites related to FSH synthesis and secretion, providing valuable insights into the complex molecular mechanisms of GnRH-FSH regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Vincent Danna, Hugh Mitchell, Lindsey Anderson, Iobani Godinez, Sara J. C. Gosline, Justin Teeguarden, Jason E. McDermott
Summary: The goal of high-throughput data studies is to identify functional mechanisms underlying biological phenomena, which requires time-consuming evaluation of various statistical methods. The leapR package allows rapid assessment of biological pathway activity, facilitating integration of multisource data.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Ye Hong, Dani Flinkman, Tomi Suomi, Sami Pietila, Peter James, Eleanor Coffey, Laura L. Elo
Summary: This article introduces an integrated pipeline that utilizes multiple R packages to extract high-level biological understanding from large-scale phosphoproteomic data. The pipeline includes data clean-up, statistical analysis, differential expression analysis, phosphosite annotation and translation, enrichment analysis, proteome-wide kinase activity and substrate mapping, and network hub analysis.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Plant Sciences
Yaxiu Xu, Jiaojiao Liu, Nannan Zang, Zepeng Yin, Aide Wang
Summary: This study identifies the mechanisms by which calcium regulates fruit ripening in apple fruit. It reveals that calcium affects multiple pathways involved in cell wall degradation, signaling and transport, protein degradation, and primary and secondary metabolisms. Phosphorylation and ubiquitination play important roles in these processes.
HORTICULTURAL PLANT JOURNAL
(2022)
Article
Plant Sciences
Sadegh Balotf, Calum R. Wilson, Robert S. Tegg, David S. Nichols, Richard Wilson
Summary: Potato is an important food crop, and infection by the pathogen S. subterranea causes economic losses. This study used proteomics and phosphoproteomics to investigate potato's response to S. subterranea infection. The results showed differential responses in resistant and susceptible cultivars, including changes in oxidoreductase activity, electron transfer, photosynthesis, signal transduction, and defense response.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Ya Zheng, Bin Mao, Qian Wang, Xin Duan, Meng-Yan Chen, Wei Shen, Chao Li, Yu-Feng Wang
Summary: Knockdown of ocn gene in Drosophila testes resulted in smaller testis without germ cells. Through proteomics sequencing, 606 proteins were identified as significantly changed in expression after ocn knockdown. The down-regulation of ocn disturbed key signaling pathways related to cell survival and differentiation.
Article
Biochemistry & Molecular Biology
Liting Ma, Yuran Hao, Xiaorong Liu, Leilei Shao, Hairong Wang, Hao Zhou, Dazhong Zhang, Ting Zhu, Qin Ding, Lingjian Ma
Summary: This study used proteomic and phosphoproteomic analyses to investigate the binucleate anther of a thermosensitive sterile wheat line. It revealed the importance of energy metabolism in male fertility and predicted potential kinase-substrate pairs involved in fertility regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Lili Blumenberg, Emily A. Kawaler, MacIntosh Cornwell, Shaleigh Smith, Kelly Ruggles, David Fenyo
Summary: Researchers use BlackSheep, a nonparametric description and differential analysis tool, to analyze molecules aberrantly enriched in small sample cohorts, complementing other differential expression analysis methods.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Yanfang Chen, Severine Roselli, Nikita Panicker, Joshua S. Brzozowski, David A. Skerrett-Byrne, Heather C. Murray, Nicole M. Verrills
Summary: This article provides a comprehensive characterization of the proteome and phosphoproteome of wild-type primary MEFs from C57BL/6 mice. The study identifies abundant EIF2/4 and MTOR signaling pathways, as well as extracellular matrix and cytoskeleton associated pathways. Kinase enrichment analysis reveals the activation of P38A, P90RSK, P70S6K, and MTOR. This dataset serves as a valuable resource for future research in the field.
Article
Microbiology
Nabil Hanna, Hendrik Koliwer-Brandl, Louise H. Lefrancois, Vera Kalinina, Elena Cardenal-Munoz, Joddy Appiah, Florence Leuba, Aurelie Gueho, Hubert Hilbi, Thierry Soldati, Caroline Barisch
Summary: This study investigates the role of zinc ions in Mycobacterium marinum infection, revealing that the bacterium can sense toxic levels of zinc ions and respond by upregulating a specific isoform of a zinc efflux transporter. The interplay of zinc ion transporters ZntA and ZntB affects bacterial growth, with deletion of these transporters leading to different levels of zinc accumulation in Mycobacterium-containing vacuoles. Overall, zinc poisoning plays a crucial role in restricting mycobacterial infections by impacting zinc ion homeostasis.
Article
Biochemical Research Methods
Kevin A. Kovalchik, Qing Ma, Laura Wessling, Frederic Saab, Jerome D. Duquette, Peter Kubiniok, David J. Hamelin, Pouya Faridi, Chen Li, Anthony W. Purcell, Anne Jang, Eustache Paramithiotis, Marco Tognetti, Lukas Reiter, Roland Bruderer, Joel Lanoix, Mathieu Courcelles, Pierre Thibault, Etienne Caron, Isabelle Sirois
Summary: Researchers have developed a semi-automated quality control software tool called MhcVizPipe (MVP) for rapid assessment of multiple MHC class I and II immunopeptidomic datasets generated by mass spectrometry. MVP provides a quick and comprehensive view of sample quality, composition, and MHC specificity to accelerate the decision-making process for data interpretation.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemical Research Methods
Jenna Cleyle, Marie-Pierre Hardy, Robin Minati, Mathieu Courcelles, Chantal Durette, Joel Lanoix, Jean-Philippe Laverdure, Krystel Vincent, Claude Perreault, Pierre Thibault
Summary: This study identified tumor-specific antigens in colorectal cancer using a novel proteogenomic approach. The researchers found that many of these antigens originated from noncoding regions and could have therapeutic potential in various tumors. These findings are significant for the development of T cell-based vaccines and could improve treatment efficacy across subtypes of colorectal cancer when used in combination with existing immune checkpoint inhibition therapies.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Cell Biology
Anca Apavaloaei, Leslie Hesnard, Marie-Pierre Hardy, Basma Benabdallah, Gregory Ehx, Catherine Theriault, Jean-Philippe Laverdure, Chantal Durette, Joel Lanoix, Mathieu Courcelles, Nandita Noronha, Kapil Dev Chauhan, Sebastien Lemieux, Christian Beausejour, Mick Bhatia, Pierre Thibault, Claude Perreault
Summary: This study characterizes the MHC I-associated peptide (MAP) repertoire of human induced pluripotent stem cells (iPSCs) and identifies a set of pluripotency-associated MAPs (paMAPs). These paMAPs are absent in normal tissues and adult stem cells but are expressed in iPSCs and multiple adult cancers. Some of these paMAPs are immunogenic, but their expression in tumors is associated with activation of immune evasion pathways. The authors propose that inhibiting these pathways in combination with immune targeting of paMAPs could be a potential treatment strategy for poorly differentiated cancers.
Article
Chemistry, Analytical
Zhaoguan Wu, Eric Bonneil, Michael Belford, Cornelia Boeser, Maria Virginia Ruiz Cuevas, Sebastien Lemieux, Jean-Jacques Dunyach, Pierre Thibault
Summary: The integration of ion mobility with segmented ion fractionation (SIFT) enhances the comprehensiveness of proteomic analyses and improves the identification of low abundance peptides.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Jose Luis Marin-Rubio, Laura Vela-Martin, Jack Gudgeon, Eduardo Perez-Gomez, Frances R. Sidgwick, Matthias Trost, Debbie L. Cunningham, Javier Santos, Jose Fernandez-Piqueras, Maria Villa-Morales
Summary: A reduction in FADD levels has been found in precursor T-cell neoplasms, which may affect tumor cell apoptosis and lead to poor clinical outcomes. FADD is involved in both apoptotic and non-apoptotic functions, and its expression could serve as a prognostic marker and guide targeted therapeutic strategies in these tumors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Chongyang Li, Alison Boutet, Cristina Mirela Pascariu, Trent Nelson, Mathieu Courcelles, Zhaoguan Wu, Simon Comtois-Marotte, Gregory Emery, Pierre Thibault
Summary: Protein inhibitor of activated STAT (PIAS) proteins are E3 SUMO ligases that play important roles in protein stability and signaling transduction pathways. In this study, quantitative SUMO proteomics was used to investigate the regulatory role of PIAS SUMO E3 ligases in cell proliferation and cell cycle. The results reveal novel insights into both the redundant and specific regulatory mechanisms of PIAS SUMO E3 ligases.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Oncology
Douglas G. G. Millar, S. Y. Cindy Yang, Azin Sayad, Qingchuan Zhao, Linh T. T. Nguyen, Kathrin Warner, Ami G. G. Sangster, Munehide Nakatsugawa, Kenji Murata, Ben X. X. Wang, Patricia Shaw, Blaise Clarke, Marcus Q. Q. Bernardini, Trevor Pugh, Pierre Thibault, Naoto Hirano, Claude Perreault, Pamela S. S. Ohashi
Summary: Immunotherapeutic strategies can enhance tumor cell killing by tumor-specific T cells, thus reducing tumor burden and prolonging survival of cancer patients. By analyzing the tumor transcriptome, serum, and proteome of HGSC patients, we identified potential tumor antigens that can be recognized by the patient's T cells. These antigens are processed and presented by tumor cells, indicating an ongoing autoimmune response against self-antigens by HGSC T cells.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2023)
Article
Biochemical Research Methods
Noe Guilloy, Marie A. Brunet, Sebastien Leblanc, Jean-Francois Jacques, Marie-Pierre Hardy, Gregory Ehx, Joel Lanoix, Pierre Thibault, Claude Perreault, Xavier Roucou
Summary: Proteomic diversity in biological samples can be characterized using mass spectrometry (MS)-based proteomics and customized protein databases generated from RNA-seq data. The recent discovery of translated alternative open reading frames in mRNAs and ncRNAs has increased this diversity. To fill the gap in current computational workflows, OpenCustomDB is a bioinformatics tool that identifies genomic variants in both canonical and alternative open reading frames using sample-specific RNA-seq data. It has been shown to detect a significant number of peptides from alternative proteins in a cohort of acute myeloid leukemia patients.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biology
Lyudmil Raykov, Manon Mottet, Jahn Nitschke, Thierry Soldati
Summary: Cells have mechanisms to repair or remove damaged membranes, but little is known about how the damage is sensed and how damaged organelles are marked. In this study using Dictyostelium discoideum, a conserved E3 ligase called TrafE was found to be recruited to intracellular compartments that were disrupted after infection or damage. TrafE plays a crucial role in recruiting ESCRT subunits to the damaged sites, and its absence impairs xenophagy restriction and membrane damage repair, leading to cell death.
Article
Cell Biology
James H. Vines, Hannes Maib, Catherine M. Buckley, Aurelie Gueho, Zhou Zhu, Thierry Soldati, David H. Murray, Jason S. King
Summary: The authors introduce a new biosensor for PI(3,5)P-2, a phosphoinositide signaling lipid, and demonstrate its effectiveness in studying PI(3,5)P-2 dynamics in both amoebae and mammalian cells. Through their research, they uncover new details about the regulation of PI(3,5)P-2 during phagosome maturation. This work is significant as it enhances our understanding of the roles and regulation of PI(3,5)P-2, an important lipid in various cellular processes.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Biochemical Research Methods
Charles Homsi, Roshan Elizabeth Rajan, Robin Minati, Edlie St-Hilaire, Eric Bonneil, Simon F. Dufresne, Hugo Wurtele, Alain Verreault, Pierre Thibault
Summary: This article describes a simple filter-aided sample preparation method for extracting and purifying histones, which eliminates tedious steps and is particularly suitable for yeast cells. The method not only improves extraction efficiency, but also inactivates histone-modifying enzymes. The authors demonstrate that the method prevents the common artifact of N-terminal clipping of H3 in yeast cells. It is scalable and enables efficient histone recovery from as few as two million yeast cells, and can be used for analyzing histone modifications in limited fungal clinical isolates.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Virginie Emond-Fraser, Myreille Larouche, Peter Kubiniok, Eric Bonneil, Jingjing Li, Mohammed Bourouh, Laura Frizzi, Pierre Thibault, Vincent Archambault
Summary: Mitotic exit necessitates dephosphorylation of proteins previously phosphorylated during mitosis. PP2A-B55 regulates the dephosphorylation of emerin in Drosophila, which in turn determines the timing of nuclear envelope reformation. This regulation is essential for embryonic development and may be conserved across species.
Article
Multidisciplinary Sciences
Edgar Pinedo-Carpio, Julien Dessapt, Adele Beneyton, Lauralicia Sacre, Marie-Anne Berube, Romain Villot, Elise G. Lavoie, Yan Coulombe, Andreanne Blondeau, Jonathan Boulais, Abba Malina, Vincent M. Luo, Anna-Maria Lazaratos, Jean-Francois Cote, Frederick A. Mallette, Alba Guarne, Jean-Yves Masson, Amelie Fradet-Turcotte, Alexandre Orthwein
Summary: Using CRISPR-based genomics, we identified FIRRM as a sensitizer of the ICL-inducing agent mafosfamide, highlighting its crucial role in resolving ICL-induced DSBs.
Article
Biochemical Research Methods
Charlotte Stutzmann, Jiaxi Peng, Zhaoguan Wu, Christopher Savoie, Isabelle Sirois, Pierre Thibault, Aaron R. Wheeler, Etienne Caron
Summary: The identification of tumor-specific antigens (TSAs) is crucial for effective cancer immunotherapies. However, current immunopeptidomics platforms face challenges in measuring low-abundance TSAs in a precise manner. Microfluidics technology offers a promising solution by providing improved isolation of peptides with higher sensitivity. This article highlights the challenges in sample preparation and the rationale for developing microfluidics technology in immunopeptidomics, and discusses the latest research on its application in MS-based immunopeptidomics and single-cell proteomics.
CELL REPORTS METHODS
(2023)