Article
Biochemistry & Molecular Biology
Juan Manuel Velazquez-Enriquez, Alma Aurora Ramirez-Hernandez, Luis Manuel Sanchez Navarro, Itayetzi Reyes-Avendano, Karina Gonzalez-Garcia, Cristian Jimenez-Martinez, Luis Castro-Sanchez, Xariss Miryam Sanchez-Chino, Veronica Rocio Vasquez-Garzon, Rafael Baltierrez-Hoyos
Summary: Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease with unknown causes. This study identified differentially expressed proteins (DEPs) related to IPF pathogenesis by comparing IPF lung fibroblast cell lines with normal lung fibroblast cell lines. The results provide valuable information on the role of DEPs in IPF.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Juan Manuel Velazquez-Enriquez, Jovito Cesar Santos-Alvarez, Alma Aurora Ramirez-Hernandez, Edilburga Reyes-Jimenez, Armando Lopez-Martinez, Socorro Pina-Canseco, Sergio Roberto Aguilar-Ruiz, Maria De Los Angeles Romero-Tlalolini, Luis Castro-Sanchez, Jaime Arellanes-Robledo, Veronica Rocio Vasquez-Garzon, Rafael Baltierrez-Hoyos
Summary: IPF is a chronic, progressive, irreversible, and highly fatal disease characterized by the dysregulation of fibroblast and myofibroblast activation. Proteins contained within EVs cargo derived from IPF cell lines play key roles in the pathogenesis of the disease, as revealed by proteomic analysis. These findings suggest a potential therapeutic target for IPF treatment.
Article
Multidisciplinary Sciences
Jiangnan Zheng, Zhendong Zheng, Changying Fu, Yicheng Weng, An He, Xueting Ye, Weina Gao, Ruijun Tian
Summary: The authors developed a chemical proteomics method, termed interaction-guided crosslinking (IGC), to systematically identify ligand-receptor complexes formed between cell surface receptors and secreted proteins from neighboring cells. This approach successfully captures receptors from as few as 0.1 million living cells using only 10 ng of secreted ligand. It allows unbiased and all-to-all identification of ligand-receptor interactions and discovery of critical intercellular signaling events.
NATURE COMMUNICATIONS
(2023)
Review
Multidisciplinary Sciences
Lloyd M. Smith, Jeffrey N. Agar, Julia Chamot-Rooke, Paul O. Danis, Ying Ge, Joseph A. Loo, Ljiljana Pasa-Tolic, Yury O. Tsybin, Neil L. Kelleher
Summary: Understanding the structure and properties of proteins is crucial in deciphering biological functions. The concept of defining the human proteome as a reference set of proteoforms is proposed, with a call for improved technologies in a two-pronged strategy.
Article
Biochemical Research Methods
Florian A. Rosenberger, Marvin Thielert, Maximilian T. Strauss, Lisa Schweizer, Constantin Ammar, Sophia C. Maedler, Andreas Metousis, Patricia Skowronek, Maria Wahle, Katherine Madden, Janine Gote-Schniering, Anna Semenova, Herbert B. Schiller, Edwin Rodriguez, Thierry M. Nordmann, Andreas Mund, Matthias Mann
Summary: Single-cell proteomics by mass spectrometry is a powerful method for studying biological heterogeneity, and single-cell Deep Visual Proteomics (scDVP) is a technology that integrates high-content imaging, laser microdissection, and multiplexed mass spectrometry to analyze the spatial proteome of tissues. It can identify thousands of proteins and reveal differential regulation in spatially distinct regions.
Article
Chemistry, Analytical
Xiaoxue Wu, Zhen Li, Jinian Shu, Zhongbing Lu, Junling Gao, Bo Yang, Kui Jiang, Yedong Guo, Jingyun Huang
Summary: By analyzing the exhaled breath of mice using a newly developed AI-TOFMS method, it was found that acrolein, ethanol, nitric oxide, and ammonia are potential exhaled biomarkers for pulmonary fibrosis.
Article
Multidisciplinary Sciences
V. Dumrongprechachan, R. B. Salisbury, G. Soto, M. Kumar, M. L. MacDonald, Y. Kozorovitskiy
Summary: This study employed a genetically targeted APEX2-based proximity labeling approach to uncover proteome dynamics in two classes of striatal spiny projection neurons in the mouse brain. The findings were validated using imaging, electron microscopy, and mass spectrometry, providing important insights for understanding the development and functional organization of neural circuits in the brain.
NATURE COMMUNICATIONS
(2021)
Article
Immunology
Yang Miao, Xiaohe Li, Yue Yang, Jianwei Zhang, Li Chen, Qianyi Zhang, Wenqi Li, Ying Liu, Xianfeng Zhang, Ruimin Gu, Cheng Yang
Summary: In this study, it was found that Entrectinib effectively inhibits the development of pulmonary fibrosis by blocking TGF-β1 signaling, both in vitro and in vivo.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Anissa A. Widjaja, Sivakumar Viswanathan, Dong Jinrui, Brijesh K. Singh, Jessie Tan, Joyce Goh Wei Ting, David Lamb, Shamini G. Shekeran, Benjamin L. George, Sebastian Schafer, David Carling, Eleonora Adami, Stuart A. Cook
Summary: This study elucidates the translation-specific signaling pathways downstream of IL11, intersects immune and metabolic signaling, and reveals unappreciated effects of nintedanib.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Yuanyuan Li, Chaoshuang Xia, Hongxian Zhao, Yuping Xie, Yangjun Zhang, Wanjun Zhang, Yongliang Yu, Jianhua Wang, Weijie Qin
Summary: The cell surface membrane proteome, a class of proteins that mediate communication between cells and their environment, is challenging to purify and study. This study developed a new photolabeling probe for efficient tagging and enrichment of cell surface membrane proteins, enabling a deeper understanding of their structure and function.
CHINESE CHEMICAL LETTERS
(2023)
Article
Biochemistry & Molecular Biology
P. Bernhard, T. Feilen, M. Rogg, K. Froehlich, M. Cosenza-Contreras, F. Hause, C. Schell, O. Schilling
Summary: Clonal isolation is a crucial step in genome editing and cell engineering, impacting the cellular proteome in a cell line specific manner. The effects of clonal isolation on different biological processes vary and depend on the isolation method. Understanding the impact of clonal isolation is important when interpreting experimental data in these fields.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Cardiac & Cardiovascular Systems
Rosemary E. Maher, Emma Barrett, Robert J. Beynon, Victoria M. Harman, Andrew M. Jones, Paul S. McNamara, Jaclyn A. Smith, Robert W. Lord
Summary: This study aimed to investigate differences in the CF sputum proteome associated with disease severity and identify potential markers of disease with translational potential. Predictable changes in the CF sputum proteome occurred associated with progressive lung function impairment, which might have value as markers of disease severity.
RESPIRATORY MEDICINE
(2022)
Review
Immunology
Laura A. Solt
Summary: T cells transition from a quiescent state to active proliferation and effector function upon exposure to cognate antigen, a process tightly controlled by signal transduction pathways. Dysregulation of these events can mediate disease, and recent sequencing advances at the single-cell level have improved our understanding of T cell biology.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Chemistry, Analytical
Yuming Jiang, Alexandre Hutton, Caleb W. Cranney, Jesse G. Meyer
Summary: This article introduces an improved direct infusion and ion mobility method for proteome analysis, and proposes a label-free quantification method DISPA-LFQ, which can rapidly identify and quantify proteins in complex mixtures. This technology has important applications in drug screening, biomarker discovery, and clinical analysis.
ANALYTICAL CHEMISTRY
(2022)
Article
Cardiac & Cardiovascular Systems
Daniel Soetkamp, Romain Gallet, Sarah J. Parker, Ronald Holewinski, Vidya Venkatraman, Kiel Peck, Joshua Goldhaber, Eduardo Marban, Jennifer E. Van Eyk
Summary: The study suggests that the phosphorylation of sarcomeric proteins is associated with heart failure with preserved ejection fraction, and treatment with cardiosphere-derived cells can partially reverse this process, with PKC beta identified as a potential therapeutic target in HFpEF.
CIRCULATION RESEARCH
(2021)
Article
Surgery
Martin Eichhorn, Andre Rotarmel, Johannes Haag, Philip Baum, Hauke Winter
Summary: This study analyzed the learning curve and safety of establishing a RATS program at a high-volume thoracic surgery center, and quantified the costs of the surgical procedure in Germany. The results showed that RATS can be safely established, performed, and trained, with low complication rates and acceptable costs for consumables.
ZENTRALBLATT FUR CHIRURGIE
(2023)
Article
Endocrinology & Metabolism
Haifa Maalmi, Alexander Strom, Agnese Petrera, Stefanie M. Hauck, Klaus Strassburger, Oliver Kuss, Oana-Patricia Zaharia, Gidon J. Boenhof, Wolfgang Rathmann, Sandra Trenkamp, Volker Burkart, Julia Szendroedi, Dan Ziegler, Michael Roden, Christian Herder
Summary: No established blood-based biomarker exists for monitoring diabetic sensorimotor polyneuropathy (DSPN) and evaluating treatment response. This study found that higher serum levels of neurofilament light chain (NFL) were associated with prevalent DSPN and nerve dysfunction in individuals recently diagnosed with diabetes. The findings suggest that NFL could be a potential biomarker for DSPN.
Article
Neurosciences
Lew Kaplan, Corinne Drexler, Anna M. Pfaller, Santra Brenna, Kirsten A. Wunderlich, Andrea Dimitracopoulos, Juliane Merl-Pham, Maria-Theresa Perez, Ursula Schloetzer-Schrehardt, Volker Enzmann, Marijana Samardzija, Berta Puig, Peter Fuchs, Kristian Franze, Stefanie M. Hauck, Antje Grosche
Summary: This study revealed the expression profiles of cone- and rod-associated Muller cells in the human macula and identified pathways related to extracellular matrix and cell adhesion. EPPK1 was highly expressed in macular Muller cells and played a role in intermediate filament organization. Knockout of EPPK1 in a human Muller cell-derived cell line resulted in changes in cell size, shape, and filopodia characteristics. Therefore, EPPK1 is a central molecular player in the region-specific architecture of the human retina, enabling specific functions under mechanical loads in vivo.
Article
Biochemistry & Molecular Biology
Lena Molitor, Melina Klostermann, Sabrina Bacher, Juliane Merl-Pham, Nadine Spranger, Sandra Burczyk, Carolin Ketteler, Ejona Rusha, Daniel Tews, Anna Pertek, Marcel Proske, Anke Busch, Sarah Reschke, Regina Feederle, Stefanie M. Hauck, Helmut Blum, Micha Drukker, Pamela Fischer-Posovszky, Julian Koenig, Kathi Zarnack, Dierk Niessing
Summary: The RNA-binding protein PURA is predominantly located in the cytoplasm, where it binds to thousands of mRNAs. Reduced levels of PURA affect the formation and composition of P-bodies, leading to dysregulation of RNA processing. This study proposes PURA Syndrome as a new model for studying the connection between P-body-associated RNA regulation and neurodevelopmental disorders.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Misako Nakayama, Hannah Marchi, Anna M. Dmitrieva, Ashesh Chakraborty, Juliane Merl-Pham, Elisabeth Hennen, Ronan Le Gleut, Clemens Ruppert, Andreas Guenther, Kathrin Kahnert, Juergen Behr, Anne Hilgendorff, Stefanie M. Hauck, Heiko Adler, Claudia A. Staab-Weijnitz
Summary: This study compared the susceptibility and response of airway epithelium in patients with chronic obstructive pulmonary disease (COPD) and healthy individuals to influenza virus infection. Quantitative proteomics was used to assess protein changes during influenza virus infection. The results showed no significant differences between COPD and control airway epithelial cells in terms of cell type composition, susceptibility to influenza virus infection, and proteomes pre- and post-infection. Additionally, several novel influenza A virus-regulated proteins were identified in bronchial epithelial cells, which might serve as potential targets for modulating the pathogenicity of infection and acute exacerbations.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Oncology
Julia Walter, Diego Kauffmann-Guerrero, Thomas Muley, Martin Reck, Jan Fuge, Andreas Guenther, Raphael W. Majeed, Rajkumar Savai, Ina Koch, Julien Dinkel, Christian Schneider, Karsten Senghas, Sonja Kobinger, Farkhad Manapov, Michael Thomas, Kathrin Kahnert, Hauke Winter, Juergen Behr, Martin Tammemagi, Amanda Tufman
Summary: Using risk-based selection score can improve the sensitivity of lung cancer screening, but there are gender disparities that need to be addressed to close the gender gap in implementing a large-scale screening program.
Article
Oncology
Tanja Eichkorn, Jonathan W. Lischalk, Cedric Stuewe, Eric Tonndorf-Martini, Kai Schubert, Lisa-Antonia Dinges, Sebastian Regnery, Farastuk Bozorgmehr, Laila Koenig, Petros Christopoulos, Juliane Hoerner-Rieber, Sebastian Adeberg, Klaus Herfarth, Hauke Winter, Michael Thomas, Stefan Rieken, Juergen Debus, Rami A. El Shafie
Summary: This study investigates the feasibility of combining stereotactic body radiation therapy (SBRT) with volumetric arc therapy (VMAT) for the treatment of high-risk patients with inoperable locally advanced non-small cell lung cancer (NSCLC). The results show that SBRT+MLN significantly improves treatment outcomes and reduces the risk of side effects.
FRONTIERS IN ONCOLOGY
(2023)
Article
Endocrinology & Metabolism
Hong Luo, Alina Bauer, Jana Nano, Agnese Petrera, Wolfgang Rathmann, Christian Herder, Stefanie M. Hauck, Benjamin B. Sun, Annika Hoyer, Annette Peters, Barbara Thorand
Summary: This study aimed to investigate the role of plasma proteins in glucose metabolism and type 2 diabetes development. The study identified several novel proteins associated with glucose metabolism abnormalities and type 2 diabetes, as well as confirming previously reported proteins. These findings highlight the importance of proteins in the pathogenesis of type 2 diabetes and suggest potential targets for diabetes treatment and prevention.
Article
Allergy
Mauricius Marques dos Santos, Vadim Pivniouk, Bettina Rankl, Alesia Walker, Giulia Pagani, Norbert Hertkorn, Philippe Schmitt-Kopplin, Christoph Mueller, Franz Bracher, Juliane Merl-Pham, Stefanie M. Hauck, Michael Schloter, Ashley N. Michael, Dayna Anderson, Linnea Honeker, Justyna Gozdz, Oksana Pivniouk, Carole Ober, Mark Holbreich, Fernando D. Martinez, Shane A. Snyder, Erika Von Mutius, Donata Vercelli
Summary: This study identifies proteins from animals and plants on traditional farms that can transport microbial and plant metabolites, thereby providing protection against asthma.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Marie-Christin Schilloks, Isabella-Maria Giese, Arne Hinrichs, Lucia Korbonits, Stefanie M. Hauck, Eckhard Wolf, Cornelia A. Deeg
Summary: This study investigated the effects of impaired GHR signaling on immune functions and immunometabolism in GHR-KO pigs. The results showed significant differences in the relative proportion of the CD4(+)CD8a(-) subpopulation and IFN-a levels between GHR-KO pigs and WT controls. However, no significant difference was found in the respiratory capacity and the capacity for polyclonal stimulation in PBMCs between the two groups. Proteome analysis revealed multiple significant protein abundance differences related to amino acid metabolism, beta-oxidation of fatty acids, insulin secretion signaling, and oxidative phosphorylation between GHR-KO pigs and WT pigs.
Article
Oncology
Omid Azimzadeh, Juliane Merl-Pham, Vikram Subramanian, Kateryna Oleksenko, Franziska Krumm, Mariateresa Mancuso, Emanuela Pasquali, Ignacia B. Tanaka III, Satoshi Tanaka, Michael J. Atkinson, Soile Tapio, Simone Moertl
Summary: Recent epidemiologic studies have found an association between chronic low-dose radiation exposure and cardiovascular disease. However, the molecular mechanisms underlying this adverse effect are not fully understood. This study investigated changes in the heart proteome of ApoE deficient mice exposed to low dose radiation for 300 days. The analysis revealed persistent alterations in the cardiac proteome, especially at higher dose rates, and these changes were involved in energy metabolism, ECM remodelling, oxidative stress, and ageing signalling pathways.
Article
Biochemical Research Methods
Oliver Kardell, Stephan Breimann, Stefanie M. Hauck
Summary: mpwR is an R package designed for standardized comparison of mass spectrometry-based proteomic label-free workflows. It allows easy access to compare the impact of sample preparation procedures, combinations of liquid chromatography-MS setups, and software differences on critical performance measures across multiple analyses. mpwR supports outputs of commonly used software for bottom-up proteomics like ProteomeDiscoverer, Spectronaut, MaxQuant, and DIA-NN.
Article
Surgery
Martin Eichhorn, Andre Rotarmel, Johannes Haag, Philip Baum, Hauke Winter
Summary: The study analyzed the learning curve and safety of establishing a RATS program at a high-volume thoracic surgery center and quantified the costs of the surgical procedure in Germany. It found that RATS can be safely performed with low complication rates and acceptable costs.
ZENTRALBLATT FUR CHIRURGIE
(2023)
Article
Biochemistry & Molecular Biology
Kun He, Mengyi Xie, Weifeng Hong, Yonghe Li, Yaolin Yin, Xiaojin Gao, Yi He, Yu Chen, Chuan You, Jingdong Li
Summary: Centromere protein L (CENPL) is overexpressed in hepatocellular carcinoma (HCC) and is associated with poor patient prognosis. Upregulation of CENPL promotes tumor proliferation and glycolysis in HCC cells by activating the MEK1/2-ERK1/2 signaling pathway.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
(2024)
Article
Biochemistry & Molecular Biology
Yingzi Wang, Haozhong Huang, Huimin Weng, Chunsen Jia, Bin Liao, Yang Long, Fengxu Yu, Yongmei Nie
Summary: Talin protein plays a crucial role in transmitting mechanical forces by connecting the extracellular matrix to the cytoskeleton. It converts mechanical signals into biochemical signals and serves as diagnostic, therapeutic, and prognostic indicators in diseases.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
(2024)
Review
Biochemistry & Molecular Biology
Hema Saranya Ilamathi, Marc Germain
Summary: Mitochondria are the central metabolic hubs in cells, relying on proteins encoded by nuclear DNA and mitochondrial DNA (mtDNA) for their function. The maintenance and distribution of mtDNA are crucial for proper mitochondrial function and are associated with mitochondrial diseases. mtDNA is organized into nucleoids that dynamically move and interact with each other. The replication and distribution of mtDNA nucleoids are regulated by the complex interplay of mitochondrial dynamics, ER-mitochondria contact sites, and cytoskeletal networks.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
(2024)
Article
Biochemistry & Molecular Biology
K. K. Sruthi, Sirisha Natani, Ramesh Ummanni
Summary: The overexpression of TPD52 is associated with the emergence of neuroendocrine prostate cancer (NEPC). TPD52 activates the NF-kappa B - STAT3 axis to induce neuroendocrine differentiation (NED) of prostate cancer cells. Therapeutic targeting of TPD52 is important for the treatment of prostate cancer.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
(2024)
Article
Biochemistry & Molecular Biology
Cui Li, Feifan Xiang, Yuqi Gong, Yi Fu, Ge Chen, Zhi Wang, Zhong Li, Daiqing Wei
Summary: Our study demonstrates the significant role of tumor-derived microparticles (T-MPs) in osteosarcoma metastasis and immune response. T-MPs promote macrophage polarization and stimulate migration and chemoresistance of osteosarcoma cells, thereby affecting the progression of osteosarcoma.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
(2024)
