Editorial Material
Multidisciplinary Sciences
Roser Vento-Tormo, Roser Vilarrasa-Blasi
Summary: The HuBMAP consortium has created spatially resolved cell atlases for the human intestine, kidney, and placenta, providing unprecedented detail for analyzing tissue organization.
Article
Biochemical Research Methods
Gurjeet Kaur, Anne Poljak, Syed Azmal Ali, Ling Zhong, Mark J. Raftery, Perminder Sachdev
Summary: Human plasma is a commonly used tissue in clinical analysis, with plasma-based biomarkers essential for monitoring patient health status and response to treatment. Plasma proteomics faces challenges due to the complexity of the plasma proteome and the wide quantitative dynamic range. Different fractionation approaches can achieve high plasma proteome coverage, and one-dimensional gel-based prefractionation is effective for parallel sample processing and rapid analysis. Flexibility in method selection based on project-specific needs is crucial for accelerating plasma proteomics research to improve clinical diagnostics and research.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Adi L. Tarca, Roberto Romero, Gaurav Bhatti, Francesca Gotsch, Bogdan Done, Dereje W. Gudicha, Dahiana M. Gallo, Eunjung Jung, Roger Pique-Regi, Stanley M. Berry, Tinnakorn Chaiworapongsa, Nardhy Gomez-Lopez
Summary: The human plasma proteome was analyzed using an aptamer-based platform, revealing associations between gestational age and changes in proteins related to growth regulation, angiogenesis, immunity, and inflammation. Machine learning was able to accurately predict gestational age and time to term delivery, indicating the potential of the plasma proteome as a non-invasive tool for investigating obstetrical diseases.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Endocrinology & Metabolism
Isabel M. Diaz Lozano, Helena Sork, Virginia M. Stone, Maria Eldh, Xiaofang Cao, Maria Pernemalm, Susanne Gabrielsson, Malin Flodstrom-Tullberg
Summary: The mechanism by which pancreatic beta cells are destroyed in type 1 diabetes (T1D) is still not fully understood. Recent studies have shown that analyzing plasma samples and plasma-derived extracellular vesicles (EVs) can increase the identification of proteins and facilitate the discovery of tissue-enriched proteins. This method may be useful for the discovery of new and specific biomarkers in T1D.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Medicine, General & Internal
Shane Sakamaki-Ching, Suzaynn Schick, Gabriela Grigorean, Jun Li, Prue Talbot
Summary: The study found that acute dermal exposure to THS can alter the human plasma proteome, initiate mechanisms of skin inflammatory disease, and elevate urinary biomarkers of oxidative harm.
Article
Critical Care Medicine
Christopher J. Rhodes, John Wharton, Emilia M. Swietlik, Lars Harbaum, Barbara Girerd, J. Gerry Coghlan, James Lordan, Colin Church, Joanna Pepke-Zaba, Mark Toshner, Stephen J. Wort, David G. Kiely, Robin Condliffe, Allan Lawrie, Stefan Graf, David Montani, Athenais Boucly, Olivier Sitbon, Marc Humbert, Luke S. Howard, Nicholas W. Morrell, Martin R. Wilkins
Summary: In this study, an aptamer-based assay was used to identify prognostic proteins in patients with pulmonary arterial hypertension (PAH) that complement NT-proBNP and clinical risk scores. The results showed that these proteins could provide a more sensitive measure of therapeutic response and improved the prediction of 5-year outcomes in PAH patients.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2022)
Review
Biochemical Research Methods
Eric W. Deutsch, Gilbert S. Omenn, Zhi Sun, Michal Maes, Maria Pernemalm, Krishnan K. Palaniappan, Natasha Letunica, Yves Vandenbrouck, Virginie Brun, Sheng-ce Tao, Xiaobo Yu, Philipp E. Geyer, Vera Ignjatovic, Robert L. Moritz, Jochen M. Schwenk
Summary: The study of proteins circulating in blood presents significant opportunities for diagnosing, stratifying, or preventing diseases. Recent technological advancements have made the proteomic analysis of blood-derived serum and plasma increasingly important in understanding human biology and pathophysiology. By utilizing mass-spectrometry (MS) or affinity-based methods, valuable insights into SARS-CoV-2 infections, aging, and hemostasis have been gained, along with the potential to combine proteomics with genetic data for further insights. The ongoing challenges include translating plasma proteomics into precision medicine, with recent advances in the field providing impactful applications.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Multidisciplinary Sciences
Shaohua Lu, Hong Lu, Tingkai Zheng, Huiming Yuan, Hongli Du, Youhe Gao, Yongtao Liu, Xuanzhen Pan, Wenlu Zhang, Shuying Fu, Zhenghua Sun, Jingjie Jin, Qing-Yu He, Yang Chen, Gong Zhang
Summary: The development of high-throughput omics technology has greatly promoted the development of biomedicine, but its poor reproducibility limits its application. The use of standard reference materials is necessary to test and calibrate the accuracy and reproducibility of omics workflows. In this study, we demonstrated that the human hepatocellular cell line MHCC97H has a very stable transcriptome and proteome after 9 subculturing generations, providing a steady standard sample for industrial-scale production in the long term. Furthermore, this stability was consistent across labs and platforms.
Article
Cell Biology
Alina van Dieken, Hinrich Staecker, Heike Schmitt, Jennifer Harre, Andreas Pich, Willi Rossberg, Thomas Lenarz, Martin Durisin, Athanasia Warnecke
Summary: This study analyzes the perilymph proteome of cochlear implantation patients, identifying multiple proteins and patterns that can characterize patient subgroups. By predicting the protein composition of perilymph, the study helps understand the contribution of cochlear cells and proposes a human atlas of the cochlea. Additionally, druggable targets within the perilymph proteome are identified.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Yachen Liu, Yalan Lin, Wenxian Yang, Yuxiang Lin, Yujuan Wu, Zheyang Zhang, Nuoqi Lin, Xianlong Wang, Mengsha Tong, Rongshan Yu
Summary: This study systematically evaluated five individualized DEA algorithms for analyzing proteomic data in cancer research. The results showed that the relative expression orderings of protein pairs in normal tissues were highly stable, providing a basis for individualized DEA using these orderings. The individualized DEA algorithms demonstrated higher precision in detecting sample-specific deregulated proteins compared to population-level methods.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Gaurab Chatterjee, Bryn Ferris, Nikan Momenbeitollahi, Huiyan Li
Summary: A bioinformatic pipeline was established in this study to select plasma proteins overexpressed in specific types of cancer, by integrating information from both genetic and proteomic studies.
Article
Biochemical Research Methods
Jing Wei, Yuhang Huan, Ziqi Heng, Chenyang Zhao, Lulu Jia, Yuncui Yu, Youhe Gao
Summary: This study demonstrates that early muscle damage caused by simvastatin can be reflected in urinary proteins. The urine proteome also has the potential to reflect the pharmacology and toxicology of drugs in future clinical research.
JOURNAL OF PROTEOMICS
(2022)
Article
Environmental Sciences
Neeloffer Mookherjee, Min Hyung Ryu, Mahadevappa Hemshekhar, Juma Orach, Victor Spicer, Christopher Carlsten
Summary: This study details the impact of traffic-related air pollution on the human plasma proteome. It identifies specific proteins related to atherosclerosis that increase in concentration as the level of traffic-related air pollution increases.
ENVIRONMENTAL RESEARCH
(2022)
Article
Parasitology
Lin-Lin Cui, Chun-Xue Zhou, Bing Han, Sha-Sha Wang, Si-Ying Li, Shi-Chen Xie, Dong-Hui Zhou
Summary: The study analyzed urine samples from mice infected with T. gondii at different stages and identified significantly differentially expressed proteins. Gene ontology analysis revealed that proteins detected during acute infection were associated with biological binding activity and single-organism processes.
PARASITES & VECTORS
(2021)
Article
Biochemistry & Molecular Biology
Avgustina Danailova, Svetla Todinova, Lidia Gartcheva, Desislava Bogdanova, Elena Zlatareva, Nikolay Kalaydzhiev, Ivan Milanov, Sashka Krumova, Stefka G. Taneva
Summary: Discovery of diagnostic biomarkers for age-related neurodegenerative pathologies (NDDs) is crucial for accurate diagnosis, disease progression monitoring, and drug development. This study used differential scanning calorimetry to evaluate thermodynamic changes in the blood plasma proteome, aiming to identify new biomarkers for Parkinson's disease (PD) and amyotrophic lateral sclerosis (ALS). The thermodynamic behavior of plasma proteins reflected the complexity and heterogeneity of the two diseases, and the unfolding temperature of the protein albumin and the calorimetric profile center were identified as thermodynamic signatures. Stratification of PD and ALS patients based on these signatures was successful, except for a few cases with significantly different thermodynamic parameters. Additionally, capillary electrophoresis revealed altered globulin levels in PD and ALS patients' plasma. These findings highlight the potential of calorimetry and electrophoresis in indirectly identifying NDDs' biomarkers in blood plasma.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Urology & Nephrology
Tomoko Iida, Hidehiko Fujinaka, Bo Xu, Ying Zhang, Sameh Magdeldin, Masaaki Nameta, Zan Liu, Yutaka Yoshida, Eishin Yaoita, Shuichi Tomizawa, Akihiko Saito, Tadashi Yamamoto
CLINICAL AND EXPERIMENTAL NEPHROLOGY
(2014)
Article
Biochemical Research Methods
Sameh Magdeldin, Keiko Yamamoto, Yutaka Yoshida, Bo Xu, Ying Zhang, Hidehiko Fujinaka, Eishin Yaoita, John R. Yates, Tadashi Yamamoto
JOURNAL OF PROTEOME RESEARCH
(2014)
Article
Microbiology
Shymaa Enany, Yutaka Yoshida, Sameh Magdeldin, Xu Bo, Ying Zhang, Mohamed Enany, Tadashi Yamamoto
MICROBIOLOGICAL RESEARCH
(2013)
Article
Urology & Nephrology
Eishin Yaoita, Yutaka Yoshida, Masaaki Nameta, Ying Zhang, Hidehiko Fujinaka, Sameh Magdeldin, Bo Xu, Tadashi Yamamoto
Article
Biochemistry & Molecular Biology
Mahmoud Morsi, Firas Kobeissy, Sameh Magdeldin, Ahmed Maher, Omnia Aboelmagd, Dina Johar, Larry Bernstein
JOURNAL OF CELLULAR BIOCHEMISTRY
(2019)
Review
Biochemical Research Methods
Shand Ezzeldin, Aya El-Wazir, Shymaa Enany, Abdelrahman Muhammad, Dina Johar, Aya Osama, Eman Ahmed, Hassan Shikshaky, Sameh Magdeldin
JOURNAL OF PROTEOME RESEARCH
(2019)
Article
Biochemical Research Methods
Mohamed Soudy, Ali Mostafa Anwar, Eman Ali Ahmed, Aya Osama, Shahd Ezzeldin, Sebaey Mahgoub, Sameh Magdeldin
JOURNAL OF PROTEOMICS
(2020)
Article
Oncology
Mohamed E. Ashour, Walaa Allam, Waheba Elsayed, Reham Atteya, Menattallah Elserafy, Sameh Magdeldin, Mohamed K. Hassan, Sherif F. El-Khamisy
Summary: Research shows that hyperthermia can suppress the repair of DNA damage caused by topoisomerases, providing an explanation for the protective effect of hyperthermia on topoisomerase-targeting therapeutics, and paving the way for the use of controlled heat as a therapeutic adjunct.
Article
Medicine, Research & Experimental
Aya A. Ezzat, Salma N. Tammam, Rasha S. Hanafi, Omar Rashad, Aya Osama, Eman Abdelnaby, Sameh Magdeldin, Samar Mansour
Summary: The protein corona formed around nanoparticles plays a crucial role in their cellular interaction and biological fate. This study demonstrates that the composition of serum from different sources can result in completely different protein coronas around the same nanoparticles. Successful targeting of breast cancer cells was only observed when nanoparticles were incubated with target cells in the presence of serum from breast cancer patients.
MOLECULAR PHARMACEUTICS
(2022)
Article
Cell Biology
Mohamed A. A. Hussein, Hosni A. M. Hussein, Ali A. Thabet, Karim M. Selim, Mervat A. Dawood, Ahmed M. El-Adly, Ahmed A. Wardany, Ali Sobhy, Sameh Magdeldin, Aya Osama, Ali M. Anwar, Mohammed Abdel-Wahab, Hussam Askar, Elsayed K. Bakhiet, Serageldeen Sultan, Amgad A. Ezzat, Usama Abdel Raouf, Magdy M. Afifi
Summary: The study found that human Wharton's jelly MSC secretome (hWJ-MSC-S) has strong antiviral potential against SARS-CoV-2 and IBV infections, and revealed the mechanism by which it inhibits viral infection. These findings suggest that hWJ-MSC-S could be used in future research to develop effective therapeutic approaches.
Article
Chemistry, Medicinal
Nashwah G. M. Attallah, Fatma Alzahraa Mokhtar, Engy Elekhnawy, Selim Z. Heneidy, Eman Ahmed, Sameh Magdeldin, Walaa A. Negm, Aya H. El-Kadem
Summary: This study assessed the hepatoprotective effects of Salvinia auriculata methanol extract (SAME) against methotrexate (MTX)-induced hepatotoxicity and identified the possible mechanisms involved. The results showed that SAME effectively improved MTX-induced liver damage, suppressed inflammation, and decreased cellular apoptosis. Furthermore, SAME exhibited antibacterial activity.
Article
Biochemistry & Molecular Biology
Hassan Shikshaky, Eman Abdelnaby Ahmed, Ali Mostafa Anwar, Aya Osama, Shahd Ezzeldin, Antony Nasr, Sebaey Mahgoub, Sameh Magdeldin
Summary: This article aims to develop a novel SWATH platform for metabolite identification using accurate mass spectral library, providing new avenues for clinical diagnosis, molecular medicine, and therapeutic drug monitoring and development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Eman A. Ahmed, Marwa O. El-Derany, Ali Mostafa Anwar, Essa M. Saied, Sameh Magdeldin
Summary: This study compared the metabolic signatures between NASH and NASH-HCC patients, finding significantly higher levels of triacylglycerol, AFP, AST, and cancer antigen 19-9 in NASH-HCC patients than in NASH patients. Pathway analysis revealed the involvement of several metabolic pathways in HCC development from NASH. Metabolite-protein interaction network analysis identified key protein encoding genes that play important roles in cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Medicinal
Reem Binsuwaidan, Walaa A. Negm, Engy Elekhnawy, Nashwah G. M. Attallah, Eman Ahmed, Sameh Magdeldin, Ehssan Moglad, Sally Abdallah Mostafa, Suzy A. El-Sherbeni
Summary: Neuroinflammation is a complex disorder that causes neurological and somatic ailments. Salvadora persica extract (SPE) has been found to possess antioxidant and anti-inflammatory effects, and it also shows promising antiviral potential against herpes simplex virus type 2 (HSV-2). In addition, SPE has been shown to inhibit acetylcholinesterase, decrease oxidative stress, downregulate inflammatory gene expression, and protect against neurodegeneration in mice.
Article
Cell Biology
Maram Alaa, Nouran Al-Shehaby, Ali Mostafa Anwar, Nesma Farid, Mustafa Shaban Shawky, Manal Zamzam, Iman Zaky, Ahmed Elghounimy, Shahenda El-Naggar, Sameh Magdeldin
Summary: This study aimed to identify proteomic signatures that distinguish between different osteosarcoma subtypes, providing insights into their molecular heterogeneity and potential implications for personalized treatment approaches. The identified proteomics signature encompassed a diverse array of proteins involved in focal adhesion, ECM-receptor interaction, PI3K-Akt signaling pathways, and proteoglycans in cancer, among the top enriched pathways. By identifying subtype-specific proteomics signatures, clinicians may be able to tailor therapy regimens to individual patients, optimizing treatment efficacy and minimizing adverse effects.