Article
Oncology
Leena Liljedahl, Johan Malmstrom, Bjorg Kristjansdottir, Sofia Waldemarson, Karin Sundfeldt
Summary: Ovarian cancer is a lethal disease often discovered late. A targeted assay has shown success in identifying different subtypes of ovarian cancer, potentially leading to improved early diagnostics and survival rates.
Article
Urology & Nephrology
Yuan Li, Ying Zhang, Xinjin Zhou, Xinli Xue, Muxi Wang, Dedong Kang, Yali Zhou, Ruimin Hu, Songxia Quan, Guolan Xing, Jinghua Yang
Summary: The study developed a PRM-based targeted proteomics method for the early diagnosis and typing of renal amyloidosis, which showed high sensitivity and reliability.
Review
Immunology
Shengman Yu, Xiaoyan Li, Zhuoyuan Xin, Liyuan Sun, Jingwei Shi
Summary: In this review, the proteomic studies of SARS-CoV-2 infection are summarized, providing insights into viral particles and host entry factors from a protein perspective, as well as analyzing protein pathological changes following host infection.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Saicharan Ghantasala, Medha Gayathri J. Pai, Deeptarup Biswas, Nikita Gahoi, Shuvolina Mukherjee, K. P. Manubhai, Mehar Un Nissa, Alisha Srivastava, Sridhar Epari, Prakash Shetty, Aliasgar Moiyadi, Sanjeeva Srivastava
Summary: Proteomics technologies, including Multiple reaction monitoring, show promise in quantifying proteins in brain cancers, potentially offering alternative strategies with increased accuracy and sensitivity for classifying and grading tumors. Future studies involving a large cohort of samples could lead to a panel of proteins showing ability to accurately detect and quantify peptides with roles in brain malignancies, ultimately making them translatable to clinical settings.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemical Research Methods
Natalia Pinto de Almeida, Domingos Ferreira Melo Neto, Gabriel Reis Alves Carneiro, Andreza Raquel Barbosa de Farias, Gilberto Barbosa Domont, Francisco de Assis de Paiva Campos, Fabio Cesar Sousa Nogueira
Summary: Research on Jatropha curcas is focused on understanding the biosynthesis and synthesis site of phorbol esters (PE), in order to develop genotypes unable to synthesize PE in seeds.
Review
Cell Biology
Jia-Mei Dong, Rui-Qi Wang, Ning-Ning Yuan, Jia-Hao Guo, Xin-Yang Yu, Ang-Hui Peng, Jia-Yi Cai, Lei Xue, Zhi-Ling Zhou, Yi-Hao Sun, Ying-Yin Chen
Summary: Hepatocellular carcinoma (HCC), accounting for 90% of all primary liver cancers, is a major malignancy globally. Aptasensors, known for their high sensitivity, excellent selectivity, and low production costs, have attracted attention for the diagnosis and surveillance of HCC. Optical aptasensors, offering advantages of a wide range of targets, rapid response, and simple instrumentation, show great potential in early diagnosis and prognosis monitoring of HCC. This review summarizes recent progress in various types of optical aptasensors for biomarkers in HCC, evaluates their strengths and limitations, and discusses the challenges and future perspectives for their use in HCC diagnosis and surveillance.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Environmental Sciences
Stephanie Chaousis, Frederic D. L. Leusch, Colin J. Limpus, Amanda Nouwens, Liesbeth J. Weijs, Antonia Weltmeyer, Adrian Covaci, Jason P. van de Merwe
Summary: All seven species of sea turtle are facing increasing pressures from human activities that are impacting their health. Changes in blood proteins can indicate adverse health outcomes. This study examines the protein abundance in sea turtle plasma, compares protein expression between different populations, and investigates markers of contaminant exposure.
ENVIRONMENTAL RESEARCH
(2023)
Article
Medicine, Research & Experimental
Ankit P. Jain, Janani Sambath, Gajanan Sathe, Irene A. George, Akhilesh Pandey, Erik W. Thompson, Prashant Kumar
Summary: This study developed a targeted proteomics method to accurately measure the abundance of EMT-associated proteins in cancer cell lines, and revealed discrepancies between proteomic and transcriptomic data. The study also found that changes in the EMT proteome may play a role in tumor transformation across different types of cancer.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Environmental Sciences
Maxime Lepretre, Arnaud Chaumot, Rayan Aboud, Nicolas Delorme, Anabelle Espeyte, Arnaud Salvador, Sophie Ayciriex, Jean Armengaud, Marina Coquery, Olivier Geffard, Davide Degli-Esposti
Summary: Mass spectrometry in multiple reaction monitoring (MRM) mode enables selective and multiplexed quantification of peptides derived from proteins. This study evaluates the feasibility of using dynamic MRM (dMRM) tools to investigate proteomes in sentinel species and demonstrates their potential for discovering new protein biomarkers. A dMRM assay was developed to capture the functional proteome of a freshwater crustacean and assess the effects of metal exposure. Metal-specific signatures were identified as potential biomarkers for tracking metal levels in freshwater ecosystems. This study highlights the potential of dMRM for identifying and developing biomarkers in sentinel species.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Chemistry, Applied
Kaizhi Zheng, Yuyang Yin, Yang Cao, Liangyong Guo, Peng Li, Junfang Jiang, Xin Huang, Yongqing Jiang, Jianliang Wu
Summary: The study found that mutton from intensively fattened sheep was more tender than that from traditionally raised sheep. Proteomic analysis revealed 49 differentially expressed proteins in the longissimus dorsi muscle, and after bioinformatics analysis, 5 cytoskeletal proteins, 3 protein binding proteins, and 7 metabolic enzymes were identified as potential biomarkers for mutton tenderness. The expression of these proteins was verified using parallel reaction monitoring (PRM). Cytoskeletal proteins and metabolic enzymes play a central role in determining mutton tenderness.
Article
Cell Biology
Ling Wang, Zhen Zhang, Yuan Li, Yanyan Wan, Baocai Xing
Summary: RBPs are aberrantly expressed in a tissue-specific manner in tumors. A risk score model based on RBPs was established to estimate prognosis in HCC, revealing 11 RBPs associated with overall survival of patients, potentially serving as drug targets.
Article
Biochemical Research Methods
Rong Chen, Hannah Marie Brown, R. Graham Cooks
Summary: DESI-MS is a suitable method for intraoperative tissue analysis due to its minimal sample preparation and quick molecular diagnostics. Combining multiple metabolites, such as GABA, creatine, carnitine, and hexol, with the established biomarker NAA, allows for improved accuracy in distinguishing brain parenchyma from glioma. The implementation of diagnostic ion abundance ratios based on these metabolites can enhance method robustness and strengthen discriminatory power, leading to an improved DESI-MS method for glioma diagnosis.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Medical Laboratory Technology
Ximeng Chen, Jianan Wang, Jinyang Wang, Jingyun Ye, Ping Di, Chang Dong, Hong Lei, Chengbin Wang
Summary: This study utilized proteomics to analyze serum proteins and identify potential biomarkers for the diagnosis of osteoarticular tuberculosis. ITIH2, CFHR2, CFHR3, and CFHR5 were found to be potential biomarkers, with CFHR2 and CFHR3 showing good diagnostic efficacy when combined in a diagnostic model.
CLINICA CHIMICA ACTA
(2023)
Review
Biochemistry & Molecular Biology
Yiwu Yan, Su Yeon Yeon, Chen Qian, Sungyong You, Wei Yang
Summary: Prostate cancer is a leading cause of morbidity and mortality among men worldwide, and advancements in multiple protein biomarkers offer hope for its diagnosis and prognosis. The identification of multi-protein biomarkers with high sensitivity and specificity, as well as their integration with clinicopathologic parameters, imaging, and other molecular biomarkers, can help achieve optimal personalized management for PC patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Oncology
Yu Wang, Baocheng Deng
Summary: Hepatocellular carcinoma (HCC) is a common malignancy and leading cause of cancer-related death. The complex biological process of HCC involves the imbalance of tumor suppressor genes and oncogenes, abnormal activation of signaling pathways, HCC cell differentiation, and angiogenesis regulation. Systematic antitumor therapy is crucial for middle-advanced HCC patients, yet survival rates remain low. Researchers are exploring biomolecular targeted therapeutics and biomarkers for HCC treatment. Understanding the molecular mechanisms of HCC occurrence and developing targeted therapies are key in improving outcomes for HCC patients.
CANCER AND METASTASIS REVIEWS
(2023)
Article
Endocrinology & Metabolism
Andreas Machens, Kerstin Lorenz, Frank Weber, Henning Dralle
Summary: The study suggests an association between Hashimoto thyroiditis and differentiated thyroid cancer (papillary and follicular), but not with medullary thyroid cancer. No significant associations were found between Graves' disease and thyroid cancer.
EXPERIMENTAL AND CLINICAL ENDOCRINOLOGY & DIABETES
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Manuel Weber, Jochen Schmitz, Ines Maric, Kim Pabst, Lale Umutlu, Martin Walz, Ken Herrmann, Christoph Rischpler, Frank Weber, Walter Jentzen, Sarah Theurer, Thorsten D. Poeppel, Nicole Unger, Wolfgang P. Fendler
Summary: The study found that I-124-MIBG PET has high sensitivity and specificity in patients with suspected pheochromocytoma, and it has a high accuracy for initial staging and restaging.
JOURNAL OF NUCLEAR MEDICINE
(2022)
Article
Endocrinology & Metabolism
Andreas Machens, Kerstin Lorenz, Frank Weber, Henning Dralle
Summary: This study aimed to determine the clinical penetrance and expression of RET missense mutations associated with MEN2A in an age-dependent manner based on parental inheritance. The results showed that offspring who inherited the trait from the father developed tumors at a significantly younger age. Parental inheritance was consistently associated with MEN2A-associated tumors, highlighting the importance of considering parental inheritance in screening and early detection of these tumors.
EUROPEAN JOURNAL OF ENDOCRINOLOGY
(2022)
Article
Oncology
Andreas Machens, Kerstin Lorenz, Frank Weber, Henning Dralle
Summary: This study found parent-of-origin and offspring gender effects on the risk and disease phenotype in MEN2A, suggesting a more significant association between fathers and sons in disease inheritance and manifestation.
Article
Multidisciplinary Sciences
Julian Uszkoreit, Katalin Barkovits, Sandra Pacharra, Kathy Pfeiffer, Simone Steinbach, Katrin Marcus, Martin Eisenacher
Summary: In this article, a data dependent acquisition (DDA) dataset is presented, which serves as a reference and ground truth quantitative dataset. The dataset can be used as a benchmark reference for any workflows working on DDA data and has the potential to be valuable in comparing samples measured with DDA and data independent acquisition (DIA). The dataset consists of 15 LC-MS/MS measurements with five distinct spike-in states, each with three replicates.
Article
Biochemistry & Molecular Biology
Thilo Bracht, Daniel Kleefisch, Karin Schork, Kathrin E. Witzke, Weiqiang Chen, Malte Bayer, Jan Hovanec, Georg Johnen, Swetlana Meier, Yon-Dschun Ko, Thomas Behrens, Thomas Bruning, Jana Fassunke, Reinhard Buettner, Julian Uszkoreit, Michael Adamzik, Martin Eisenacher, Barbara Sitek
Summary: Chronic obstructive pulmonary disease (COPD) is a major risk factor for the development of lung adenocarcinoma (AC). In this study, mass-spectrometry-based proteomics analysis and machine learning algorithms were used to identify potential biomarkers for differentiation between AC and COPD. The results showed promising performance for distinguishing AC from COPD and AC with COPD from COPD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Karin Schork, Michael Turewicz, Julian Uszkoreit, Jorg Rahnenfuhrer, Martin Eisenacher
Summary: In this study, we conducted a comprehensive analysis of bipartite graphs representing the relationship between proteins and peptides in bottom-up proteomics. We compared graphs using quantified peptides from measured data sets and theoretical peptides from in-silico digestion. The results showed that the accepted minimum peptide length during in-silico digestion had a significant influence on the graph structures. When using measured peptides, the graphs were smaller and less complex compared to theoretical peptides, but there was a higher proportion of protein nodes without unique peptides. The structure of bipartite peptide-protein graphs varied between database and quantitative level as well as between different species, highlighting the need for novel methods to quantify proteins without unique peptides.
Article
Multidisciplinary Sciences
Jasjot Singh, Hadeer Elhabashy, Pathma Muthukottiappan, Markus Stepath, Martin Eisenacher, Oliver Kohlbacher, Volkmar Gieselmann, Dominic Winter
Summary: Lysosomes are crucial organelles for degradation and metabolism regulation. Protein complexes play a decisive role in lysosomal function. This study investigates lysosomes and early endosomes using cross-linking mass spectrometry, revealing protein interactions, structures, and cargo of flotillin-mediated endocytosis.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Vu Thuy Khanh Le-Trilling, Sofia Banchenko, Darius Paydar, Pia Madeleine Leipe, Lukas Binting, Simon Lauer, Andrea Graziadei, Robin Klingen, Christine Gotthold, Joerg Buerger, Thilo Bracht, Barbara Sitek, Robert Jan Lebbink, Anna Malyshkina, Thorsten Mielke, Juri Rappsilber, Christian M. T. Spahn, Sebastian Voigt, Mirko Trilling, David Schwefel
Summary: This study revealed that rat cytomegalovirus infection induces the loss of transcription factor STAT2, which is crucial for antiviral interferon signaling. It was found that viral protein E27 exploits the host-cell CRL4 complexes to degrade STAT2 through poly-ubiquitylation. Furthermore, structural analyses showed that E27 recruits STAT2 through a bipartite binding interface, partially overlapping with the IRF9 binding site.
Article
Biochemistry & Molecular Biology
Svitlana Rozanova, Julian Uszkoreit, Karin Schork, Bettina Serschnitzki, Martin Eisenacher, Lars Toenges, Katalin Barkovits-Boeddinghaus, Katrin Marcus
Summary: Proteomic studies using mass spectrometry (MS)-based quantification are important for discovering new biomarkers, but the accuracy of the outcomes can be affected by various analytical conditions. Therefore, it is crucial to assess the quality of the acquired data, including raw data, identification, and quantification levels. This study demonstrates the assessment of four independent datasets from cerebrospinal fluid, highlighting the impact of sample processing-based differences on the quality of quantitative data. Additionally, a free and open source quality control tool called MaCProQC is provided for systematic and rapid data comparison.
Article
Biochemistry & Molecular Biology
Robert Hardt, Alireza Dehghani, Carmen Schoor, Markus Goedderz, Nur Cengiz Winter, Shiva Ahmadi, Ramesh Sharma, Karin Schork, Martin Eisenacher, Volkmar Gieselmann, Dominic Winter
Summary: In this study, we used mass spectrometry to investigate the differentiation of pluripotent neural stem cells (NSCs) into oligodendrocytes. We identified Dclk1 as one of the key proteins involved in this process and found that it undergoes a gradual transition between its short and long isoforms during NSC to OPC differentiation. Through interactome analyses, we characterized the interaction partners and substrates of different Dclk1 isoforms. The data from this study are available on ProteomeXchange with identifier PXD040652.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Endocrinology & Metabolism
Andreas Machens, Kerstin Lorenz, Frank Weber, Henning Dralle
Summary: Little is known about axillary node metastasis of medullary thyroid cancer (MTC). This study compared patients with and without axillary node metastases of MTC and found that patients with axillary node metastases had more node metastases, were more likely to develop distant metastases (especially to bone and brain), and had a higher cancer-specific death rate. Additionally, patients with axillary node metastases of MTC also had more lymph node metastases in the ipsilateral lateral and central neck. The cancer-specific survival of patients with axillary node metastases was significantly shorter compared to patients without axillary node metastases.
HORMONE AND METABOLIC RESEARCH
(2023)
Article
Cell Biology
Simon Ullrich, Susanne Leidescher, Yana Feodorova, Katharina Thanisch, Jean-Baptiste Fini, Bernd Kaspers, Frank Weber, Boyka Markova, Dagmar Fuehrer, Mirian Romitti, Stefan Krebs, Helmut Blum, Heinrich Leonhardt, Sabine Costagliola, Heike Heuer, Irina Solovei
Summary: Abnormalities play a crucial role in studying normal biological processes, and this study focuses on the remarkable phenomenon of the continuously and robustly upregulated thyroglobulin gene. The research demonstrates that this upregulation is common in various vertebrate groups and provides a unique model for studying the maintenance of high transcriptional upregulation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Meeting Abstract
Cell Biology
Pietro Crivello, Thilo Bracht, Sophia Layer, Joana Peters, Barbara Sitek, Katharina Fleischhauer
