Article
Biochemistry & Molecular Biology
Jon I. Arellano, Yury M. Morozov, Nicola Micali, Pasko Rakic
Summary: Radial glial cells (RGC) play a crucial role in brain development in vertebrates, originating from neuroepithelial cells and becoming the main progenitor in the developing cerebrum. Questions remain regarding the transformation of NEC into RGC, the function of glial fibrillary acidic protein (GFAP) in RGCs, and the dynamic behavior of RGCs during neurogenesis.
NEUROCHEMICAL RESEARCH
(2021)
Article
Multidisciplinary Sciences
Christine Olander, Jesper Edvardsson Rasmussen, Per Olof Eriksson, Goran Laurell, Helge Rask-Andersen, Jonas Bergquist
Summary: This study analyzed the proteomics of the endolymphatic sac using a refined sampling technique, identifying a total of 1656 non-redundant proteins, with 110 proteins unique to the endolymphatic sac. The results validate a strategy for in vivo and in situ human sampling during surgery and may form a platform for further investigations into the function of this intriguing part of the inner ear.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Multidisciplinary
Jiaying Li, Jiahua Zhou, Kailu Tian, He Zhu, Yao Chen, Yangyu Huang, Guosheng Wang, Zhou Gong, Hongqiang Qin, Mingliang Ye, Hao Xu
Summary: The quantitative profiling of residue reactivity in proteins can help identify covalent druggable targets for precise therapy. In this study, a chemical proteomics platform was developed to analyze the reactivity of histidine (His) residues. Through this platform, the reactivity of His residues in the human proteome was characterized, and a large number of His residues with high reactivity were identified. The findings suggest that these highly reactive residues are less likely to be phosphorylation sites, which requires further research to understand the underlying mechanism. This comprehensive map of His residue reactivity provides potential bindable sites for disrupting protein activities and offers new opportunities for developing covalent inhibitors using acrolein derivatives as reactive warheads.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Review
Clinical Neurology
Lauren P. Giesler, Richelle Mychasiuk, Sandy R. Shultz, Stuart J. McDonald
Summary: Traumatic brain injury is a common health problem that affects millions of people every year. The Val66Met single-nucleotide polymorphism in BDNF has been studied for its impact on traumatic brain injury outcomes and its role in brain homeostasis. This review examines animal models and clinical studies investigating the effects of Val66Met on cognitive function, motor function, neuropsychiatric symptoms, and nociception in traumatic brain injury. It also reviews studies on the pathophysiology of traumatic brain injury and the use of circulating BDNF as a biomarker.
Article
Biochemistry & Molecular Biology
Lukasz Pawel Kozlowski
Summary: Proteome-pI 2.0 is an online database that predicts the isoelectric points and pKa values of proteins and peptides, catering to analytical biochemistry and proteomics techniques. The database includes over 61 million protein sequences and utilizes 21 methods to predict the isoelectric point of proteins and one method for inferring pKa values, facilitating bottom-up proteomics analysis.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Caroline Barbe, Jerome Salles, Christophe Chambon, Christophe Giraudet, Phelipe Sanchez, Veronique Patrac, Philippe Denis, Yves Boirie, Stephane Walrand, Marine Gueugneau
Summary: This study analyzed the proteome of undernourished aged skeletal muscle and found that undernutrition has profound effects on the muscle at a cellular and molecular level, which may vary depending on the muscle type.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Negin Nejatishahidein, Andrew L. Zydney
Summary: Depth filtration has a long history in bioprocessing and water treatment, with renewed interest driven by single-use manufacturing technologies and increased turbidity in products. The use of depth filtration for initial clarification and treatment of in process streams is growing, offering opportunities to reduce host cell proteins and remove key foulants for improved downstream process performance.
CURRENT OPINION IN CHEMICAL ENGINEERING
(2021)
Review
Plant Sciences
Chetana Tamadaddi, Amit K. Verma, Vyankatesh Zambare, Avanti Vairagkar, Danish Diwan, Chandan Sahi
Summary: J-like proteins (JLPs) are emerging as ancillaries to the cellular chaperone network, modulating the functions of Hsp70:J-domain protein (JDP) systems in plants. JLPs possess a structurally conserved J-like domain (JLD) but lack the HPD motif, which is crucial for interaction with Hsp70s. Some JLPs have been implicated in vital plant processes such as growth, development, and stress response.
PLANT CELL REPORTS
(2022)
Review
Cell Biology
Gregory L. Blatch
Summary: Plasmodium falciparum, the parasite causing severe malaria in humans, has developed sophisticated mechanisms, including heat shock proteins, to maintain protein homeostasis during its invasion of host erythrocytes. This review examines the contribution of major chaperones, particularly Hsp70 and Hsp40 families, to proteostasis in malaria parasite-infected erythrocytes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemical Research Methods
Gilbert S. Omenn
Summary: The HUPO Human Proteome Project celebrates its 10th anniversary by achieving the milestone of confident detection of proteins from 90% of predicted protein-coding genes. This global project has influenced data-sharing, quality assurance, and issued stringent guidelines for detecting missing proteins. The project's impact is highlighted in special issues of Nature Communications and Journal of Proteome Research.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Chemistry, Analytical
Guopan Liu, Ming Ho Choi, Haiying Ma, Xuejiao Guo, Pui-Chi Lo, Jinyong Kim, Liang Zhang
Summary: Surface biotinylation is widely used to analyze the cellular proteome associated with the plasma membrane. However, it is prone to interference from cytoplasmic biotin-associated proteins. This study established a new workflow (BCAP) that utilizes a bioorthogonal conjugation reaction to minimize interference and efficiently isolate surface proteins.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Shashi Gupta, Matthew J. Westacott, Deborah G. Ayers, Sophie J. Weiss, Penn Whitley, Christopher Mueller, Daniel C. Weaver, Daniel J. Schneider, Anis Karimpour-Fard, Lawrence E. Hunter, Daniel W. Drolet, Nebojsa Janjic
Summary: Early detection of cancer is crucial, but currently many cancers are diagnosed at an advanced stage. Researchers have studied the changes in the plasma proteome of mice with transplanted human tumors to gain insight into the value of protein biomarkers for early detection and stratification of cancer. They used an aptamer-based assay to measure around 5000 proteins and identified common markers as well as pathways among different types of cancer.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Piero Giansanti, Patroklos Samaras, Yangyang Bian, Chen Meng, Andrea Coluccio, Martin Frejno, Hannah Jakubowsky, Sophie Dobiasch, Rashmi R. Hazarika, Julia Rechenberger, Julia Calzada-Wack, Johannes Krumm, Sebastian Mueller, Chien-Yun Lee, Nicole Wimberger, Ludwig Lautenbacher, Zonera Hassan, Yun-Chien Chang, Chiara Falcomata, Florian P. Bayer, Stefanie Barthel, Tobias Schmidt, Roland Rad, Stephanie E. Combs, Matthew The, Frank Johannes, Dieter Saur, Martin Hrabe de Angelis, Mathias Wilhelm, Guenter Schneider, Bernhard Kuster
Summary: This study presents a quantitative draft of the mouse proteome and phosphoproteome constructed from 41 healthy tissues and 66 cell lines. The analysis reveals valuable insights into gene expression regulation and provides molecular markers for sensitivity and resistance in pancreatic ductal adenocarcinoma. The findings contribute to the understanding of biomedical research and can be accessed online for further exploration.
Article
Food Science & Technology
Veronica Sierra, Laura Gonzalez-Blanco, Yolanda Dineiro, Fernando Diaz, Maria Josefa Garcia-Espina, Ana Coto-Montes, Mohammed Gagaoua, Mamen Olivan
Summary: This study investigated the impact of various cattle management strategies on the myofibrillar subproteome of young bulls and its relationship with beef quality traits. Significant differences were found in multiple proteins among different factors, and correlations were identified between certain proteins and beef quality traits, suggesting their potential as biomarkers for meat quality.
Article
Multidisciplinary Sciences
Seda Koyuncu, Rute Loureiro, Hyun Ju Lee, Prerana Wagle, Marcus Krueger, David Vilchez
Summary: Ageing is driven by a loss of cellular integrity, with ubiquitin modifications playing a major role in cell function. Age-related remodelling of the ubiquitinated proteome is influenced by longevity paradigms like dietary restriction and reduced insulin signalling. The global loss of ubiquitination during ageing is linked to increased deubiquitinase activity, impacting the targeted degradation of structural and regulatory proteins which ultimately determine longevity.
Article
Immunology
Zoe Swank, Yasmeen Senussi, Zachary Manickas-Hill, Xu G. Yu, Jonathan Z. Li, Galit Alter, David R. Walt
Summary: This study analyzed plasma samples from PASC and COVID-19 patients and found that spike protein of SARS-CoV-2 can be detected predominantly in PASC patients for up to 12 months.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Dermatology
Paulene Sapao, Elisha D. O. Roberson, Bo Shi, Shervin Assassi, Brian Skaug, Fred Lee, Alexandra Naba, Bethany E. Perez White, Carlos Cerdova-Fletes, Pei-Suen Tsou, Amr H. Sawalha, Johann E. Gudjonsson, Feiyang Ma, Priyanka Verma, Dibyendu Bhattacharyya, Mary Carns, Jerome F. Strauss III, Delphine Sicard, Daniel J. Tschumperlin, Melissa I. Champer, Paul J. Campagnola, Maria E. Teves, John Varga
Summary: Systemic sclerosis (SSc) is a fibrotic disease with no effective treatment. This study found that SPAG17 expression was downregulated in SSc patients and negatively correlated with fibrotic gene expression. Further experiments revealed that reduced chromatin accessibility at the SPAG17 locus was observed in SSc fibroblasts and endothelial cells. Knock-down of SPAG17 resulted in myofibroblast transformation and increased sensitivity to profibrotic stimuli. These findings provide important insights into the pathogenesis of SSc and suggest SPAG17 as a potential target for developing innovative therapies for fibrotic conditions.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Article
Cardiac & Cardiovascular Systems
Lael M. Yonker, Zoe Swank, Yannic C. Bartsch, Madeleine D. Burns, Abigail Kane, Brittany P. Boribong, Jameson P. Davis, Maggie Loiselle, Tanya Novak, Yasmeen Senussi, Chi-An Cheng, Eleanor Burgess, Andrea G. Edlow, Janet Chou, Audrey Dionne, Duraisamy Balaguru, Manuella Lahoud-Rahme, Moshe Arditi, Boris Julg, Adrienne G. Randolph, Galit Alter, Alessio Fasano, David R. Walt
Summary: Blood samples from 16 patients who developed myocarditis after SARS-CoV-2 vaccination were analyzed for antibody and T-cell responses. The immune profiles of these patients were similar to those of vaccinated control subjects, except for the presence of free spike antigen in the blood of myocarditis patients.
Letter
Immunology
Zoe Swank, Yasmeen Senussi, Zachary Manickas-Hill, Xu G. Yu, Jonathan Z. Li, Galit Alter, David R. Walt
CLINICAL INFECTIOUS DISEASES
(2023)
Editorial Material
Biochemistry & Molecular Biology
Suneel S. Apte, Alexandra Naba
Article
Cell Biology
Alexandros Sountoulidis, Sergio Marco Salas, Emelie Braun, Christophe Avenel, Joseph Bergenstrahle, Jonas Theelke, Marco Vicari, Paulo Czarnewski, Andreas Liontos, Xesus Abalo, Zaneta Andrusivova, Reza Mirzazadeh, Michaela Asp, Xiaofei Li, Lijuan Hu, Sanem Sariyar, Anna Martinez Casals, Burcu Ayoglu, Alexandra Firsova, Jakob Michaelsson, Emma Lundberg, Carolina Waehlby, Erik Sundstroem, Sten Linnarsson, Joakim Lundeberg, Mats Nilsson, Christos Samakovlis
Summary: Sountoulidis et al. have created a spatial gene expression atlas of the human embryonic lung during the first trimester of gestation, identifying 83 cell states and developmental trajectories. They integrated single-cell RNA sequencing and spatially resolved transcriptomics, providing an open platform for interactive exploration. The atlas can serve as a reference for further research and understanding of pulmonary diseases.
NATURE CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Xinhao Shao, Clarissa D. Gomez, Nandini Kapoor, James M. Considine, Christopher Grams, Yu (Tom) Gao, Alexandra Naba
Summary: The extracellular matrix (ECM) is a complex assembly of proteins that provide structural support for cells, tissues, and organs. The use of mass-spectrometry-based proteomics has led to the development of MatrisomeDB, a comprehensive database that profiles the composition of ECM in various tissues. This recent update includes additional curated studies, enhanced data visualization, and an abstract-mining tool for enrichment analysis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biophysics
Graham T. Johnson, Eran Agmon, Matthew Akamatsu, Emma Lundberg, Blair Lyons, Wei Ouyang, Omar A. Quintero-Carmona, Megan Riel-Mehan, Susanne Rafelski, Rick Horwitz
Summary: Cell science faces challenges in integrating vast amounts of information and making data and methods more accessible. This paper proposes the concept of constructing next-generation virtual cells by integrating information from diverse sources, which can simulate real cells accurately, bridge the gap between theory and experiments, and facilitate collaboration among researchers across different fields.
BIOPHYSICAL JOURNAL
(2023)
Review
Biochemical Research Methods
Alexandra Naba
Summary: The extracellular matrix (ECM) is a complex assembly of proteins that form the structural scaffold of multicellular organisms and transmit signals regulating cellular phenotypes. Changes in ECM composition and structure are linked to diseases affecting all physiological systems. Proteomic approaches have been developed to decipher the ECM composition and identify disease biomarkers.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Oncology
Allison L. Hunt, Aratara Nutcharoen, Jamie Randall, Alyssa Papazian, John Deeken, G. Larry Maxwell, Nicholas W. Bateman, Emanuel F. Petricoin, Amin Benyounes, Thomas P. Conrads, Timothy L. Cannon
Summary: This case report underscores the importance of real-time integration of proteogenomic data from laser microdissected tumor specimens and dynamic biopsy testing in a molecular tumor board setting for improved precision oncology.
Article
Biology
Dmitry Ter-Ovanesyan, Tal Gilboa, Bogdan Budnik, Adele Nikitina, Sara Whiteman, Roey Lazarovits, Wendy Trieu, David Kalish, George M. Church, David R. Walt, Marcio L. Rodrigues
Summary: Extracellular vesicles (EVs) are challenging to separate from abundant free proteins and lipoproteins. We developed a digital ELISA assay to measure ApoB-100, a protein component of lipoproteins, and combined it with other assays to quantify the separation of EVs from lipoproteins and free proteins. We compared EV separation using different pore sizes in size exclusion chromatography and developed improved methods for EV isolation using multiple types of chromatography resins. Our approach allows quantitative measurement of impurities in EV isolation and enables novel methods for enriching EVs from human plasma.
Letter
Cardiac & Cardiovascular Systems
Lael M. Yonker, Alessio Fasano, David R. Walt
Article
Multidisciplinary Sciences
John P. McGee, Pei Su, Kenneth R. Durbin, Michael A. R. Hollas, Nicholas W. Bateman, G. Larry Maxwell, Thomas P. Conrads, Ryan T. Fellers, Rafael D. Melani, Jeannie M. Camarillo, Jared O. Kafader, Neil L. Kelleher
Summary: This study introduces a semi-automated single-ion mass spectrometry workflow for top-down tandem mass spectrometry analysis directly from tissue microenvironments. The results demonstrate that this method can identify multiple proteoforms in tumor samples within a short period of time, and effectively identify proteoform signatures in tumor and stromal regions.
NATURE COMMUNICATIONS
(2023)
Article
Hematology
Amy C. Sherman, Chi-An Cheng, Zoe Swank, Guohai Zhou, Xiaofang Li, Nicolas C. Issa, David R. Walt, Lindsey R. Baden, Robert J. Soiffer
Summary: This study evaluated the role of adoptive transfer of immunity in allogeneic hematopoietic stem cell transplantation recipients. The findings suggest that adoptive transfer of immunity may improve protection for this vulnerable population.
TRANSPLANTATION AND CELLULAR THERAPY
(2023)
Article
Oncology
Shaaron Ochoa-Rios, Calvin R. K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt, Stephane Elie Grauzam, David Lewin, Peggi Angel, Lewis R. Roberts, Richard Drake, Anand S. Mehta
Summary: There is a need to identify prognostic biomarkers for iCCA, and N-glycosylation alterations have shown potential for diagnostic strategies in various cancers. This study characterized N-glycan modifications in iCCA tissue and serum, and discovered that bisected fucosylated N-glycan structures were specific to iCCA tumor regions. These modifications were significantly upregulated in iCCA tissue and serum compared to HCC and bile duct disease. An algorithm based on these N-glycan modifications quadrupled the sensitivity of iCCA detection compared to the current biomarker CA19-9.
CANCER RESEARCH COMMUNICATIONS
(2023)
