Article
Multidisciplinary Sciences
Jingbo Qie, Yang Liu, Yunzhi Wang, Fan Zhang, Zhaoyu Qin, Sha Tian, Mingwei Liu, Kai Li, Wenhao Shi, Lei Song, Mingjun Sun, Yexin Tong, Ping Hu, Tao Gong, Xiaqiong Wang, Yi Huang, Bolong Lin, Xuesen Zheng, Rongbin Zhou, Jie Lv, Changsheng Du, Yi Wang, Jun Qin, Wenjun Yang, Fuchu He, Chen Ding
Summary: Macrophages play important roles in tissue homeostasis and innate immune responses. This study investigated the proteomic and transcriptomic patterns of different macrophage populations in mice. The results showed distinct differences in protein expression and copy numbers between tissue-resident and recruited macrophages. Additionally, specific transcription factors were identified as markers for different macrophage subsets. The study also validated the importance of Il18 in distinguishing molecular signatures and cellular functions between tissue-resident and recruited macrophages in the lung and liver. The deposited datasets and the open proteome server provided valuable resources for future studies on the functional and mechanistic aspects of mouse macrophages.
NATURE COMMUNICATIONS
(2022)
Article
Environmental Sciences
Su Wen, Fei Yin, Chunmao Liu, Yan Dang, Dezhi Sun, Pengsong Li
Summary: Bacteria have developed mechanisms to resist Cd toxicity, which are important for Cd detoxication and bioremediation. Through integrated analysis of transcriptomic and protein-protein interaction data, the global view of mRNA changes in Cd-induced cellular processes was revealed in Geobacter sulfurreducens. Differentially expressed genes were identified, and gene ontology and KEGG enrichment analyses showed significant effects on sulfur compound metabolic processes. Hub genes related to molecular chaperones were found to play important roles through PPI network analysis. A Cd-responsive transcriptional regulator ArsR2 was also identified, and its function in Escherichia coli was verified. This study provides new insights into Cd stress response and identifies a potential sensor element for Cd detection.
ENVIRONMENTAL RESEARCH
(2023)
Article
Plant Sciences
Chong Zhang, Jiaxue Zhang, Yadi Liu, Xiatong Liu, Xiaorui Guo, Hui Li, Di Liu, Hai Lu
Summary: Xylem development in plants involves a rapid thickening process, characterized by initial rapid increases followed by stabilization. Transcriptome analysis revealed upregulation of xylan and lignin biosynthetic pathways in the second month. Multiple transcription factors and post-transcriptional modifications play key roles in the regulation of cell wall biosynthesis and programmed cell death during xylem development in Populus tomentosa.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Environmental Sciences
Jing Yu, Tao Han, Yingying Hou, Jinjin Zhao, Haiguang Zhang, Xinjie Wang, Shidong Ge
Summary: The aim of this study was to provide a comprehensive view of plant response to tetracycline stress by conducting transcriptomic, proteomic, and metabolomic analysis. The study found that tetracycline inhibited excessive growth in pumpkin roots, but not in cotyledons. The abundance of metabolites related to flavonoid biosynthesis and amino acid metabolism was affected by tetracycline.
ENVIRONMENTAL POLLUTION
(2024)
Article
Medicine, General & Internal
Laura Madrid, Sandra C. Labrador, Antonio Gonzalez-Perez, Maria E. Saez
Summary: The identification of reliable blood-based biomarkers for Alzheimer's disease has proven to be more difficult than expected, but utilizing high-throughput multi-omics data has opened up new possibilities. By analyzing candidate SNPs and gene expression quantitative trait loci, potential susceptibility factors and biomarkers for AD have been identified for further experimental validation.
Article
Food Science & Technology
Ning Zhao, Lingxia Jiao, Junnan Xu, Jie Zhang, Yiman Qi, Mengzhen Qiu, Xinyuan Wei, Mingtao Fan
Summary: Alicyclobacillus acidoterrestris can survive pasteurization and cause spoilage in pasteurized fruit juice. The response mechanisms to heat stress in A. acidoterrestris involve modulating peptidoglycan and fatty acid composition, reducing energy consumption, and activating oxidative stress and DNA/protein damage repair systems.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Plant Sciences
Dagang Wang, Yanan Wang, Lei Zhang, Yong Yang, Qian Wu, Guoyu Hu, Weihu Wang, Jiekun Li, Zhiping Huang
Summary: This study investigates the molecular mechanism underlying cytoplasmic male sterility (CMS) in soybean by comparing the transcriptomic and proteomic changes in pollen from a CMS line and its maintainer line. The results reveal that the deformations and degradation of pollen in the CMS line are likely regulated through changes in gene and protein expression. These findings enhance our understanding of CMS in soybean and can contribute to future research and improvement in soybean breeding efficiency.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Pathology
Josepmaria Argemi, Komal Kedia, Marina A. Gritsenko, Ana Clemente-Sanchez, Aliya Asghar, Jose M. Herranz, Zhang-Xu Liu, Stephen R. Atkinson, Richard D. Smith, Trina M. Norden-Krichmar, Le Z. Day, Andrew Stolz, John A. Tayek, Ramon Bataller, Timothy R. Morgan, Jon M. Jacobs
Summary: This study identified plasma protein signatures for patients with alcohol-associated hepatitis (AH) using an integrative analysis of hepatic RNA sequencing and liquid chromatography-tandem mass spectrometry. The identified protein markers were associated with hepatocellular function and disease severity, providing potential diagnostic assessment for AH.
AMERICAN JOURNAL OF PATHOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jiao Li, Tinashe Zenda, Songtao Liu, Anyi Dong, Yafei Wang, Xinyue Liu, Nan Wang, Huijun Duan
Summary: Maize requires nitrogen for its growth and development, but excessive nitrogen fertilizer application leads to land and water pollution. Cultivating low-N-tolerant maize varieties is crucial for minimizing nitrate pollution. In this study, we identified differentially expressed genes and proteins related to low-N tolerance through transcriptome and proteome analysis of maize leaves. The results showed that the low-N-tolerant variety XY335 exhibited better sensing and signaling, protein phosphorylation and stress response, and photosynthesis efficiency compared to the low-N-sensitive variety HN138. Additionally, glutathione transferase 42 gene was found to be associated with low-N tolerance.
Article
Oncology
Nathalia Cristina Campanella, Izabela Natalia Faria Gomes, Ana Laura Vieira Alves, Leticia Ferro Leal, Adriane Feijo Evangelista, Marcela Nunes Rosa, Matias Eliseo Melendez, Viviane Aline Oliveira Silva, Richard Lucas Konichi Dias, Lucas Faria Abrahao-Machado, Iara Santana, Olga Martinho, Denise Peixoto Guimaraes, Vitor Marcel Faca, Rui Manuel Reis
Summary: The study confirmed the prognostic significance of RKIP in GIST and found that RKIP knockout increased invasion and migration potential of GIST cells. Additionally, RKIP knockout cells showed reduced responsiveness to Imatinib treatment and higher cellular viability in 2D and 3D in vitro models.
CANCER CELL INTERNATIONAL
(2023)
Article
Biochemistry & Molecular Biology
Rebeka Popovic, Ivana Celardo, Yizhou Yu, Ana C. Costa, Samantha H. Y. Loh, L. Miguel Martins
Summary: In Drosophila, activation of dPerk by ER stress or defective mitochondria plays a role in neurodegenerative disorders. The study showed that dPerk activation leads to translational repression of mitochondrial proteins associated with various metabolic and signaling pathways. Further enhancing translation of these targets may offer protection against Perk toxicity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Aisajan Mamat, Kuerban Tusong, Juan Xu, Peng Yan, Chuang Mei, Jixun Wang
Summary: Korla pear fruit stone cells are mainly composed of cellulose, hemicellulose, lignin, and a small amount of polysaccharides. The differentiation and apoptosis of stone cells primarily occur between 20 and 50 days after flowering. Transcriptomic and proteomic analysis identified numerous genes and proteins related to secondary cell wall formation, with most being expressed at the prime stage of stone cell differentiation.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Kelsy C. Cotto, Yang-Yang Feng, Avinash Ramu, Megan Richters, Sharon L. Freshour, Zachary L. Skidmore, Huiming Xia, Joshua F. McMichael, Jason Kunisaki, Katie M. Campbell, Timothy Hung-Po Chen, Emily B. Rozycki, Douglas Adkins, Siddhartha Devarakonda, Sumithra Sankararaman, Yiing Lin, William C. Chapman, Christopher A. Maher, Vivek Arora, Gavin P. Dunn, Ravindra Uppaluri, Ramaswamy Govindan, Obi L. Griffith, Malachi Griffith
Summary: RegTools is a software package that integrates genomic data with transcriptomic data to identify somatic variants that may cause aberrant splicing. It has been applied to over 9000 tumor samples and discovered numerous splice-associated variants.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Rui Yang, Zhifen Yang, Ze Peng, Fang He, Luxi Shi, Yabing Dong, Mingjian Ren, Qingqin Zhang, Guangdong Geng, Suqin Zhang
Summary: Using proteomics techniques, crucial proteins and pathways were identified in Tritipyrum 'Y1805' under salt-stress and recovery conditions, revealing its salt-tolerance mechanism. 'Y1805' showed similar expression patterns of specific proteins under both conditions, along with recovery-specific pathways and unique proteins compared to salt-sensitive wheat 'Chinese Spring'. The strong salt tolerance of 'Y1805' can be attributed to various factors such as strengthened cell walls and enhanced respiration.
Article
Agricultural Engineering
Yuping Li, Ziyan Xie, Yun Huang, Jiangyi Zeng, Chao Yang, Ling Yuan, Ying Wang, Yongqing Li
Summary: In this study, the characteristic flavonoids (CFs) of three licorice species were identified through integrated metabolic and transcriptomic analysis. The key regulators of CF biosynthesis were also identified. These findings provide valuable information for understanding the biosynthesis of CFs and future breeding of Glycyrrhiza varieties.
INDUSTRIAL CROPS AND PRODUCTS
(2024)
Review
Oncology
Anton Buzdin, Maxim Sorokin, Andrew Garazha, Alexander Glusker, Alex Aleshin, Elena Poddubskaya, Marina Sekacheva, Ella Kim, Nurshat Gaifullin, Alf Giese, Alexander Seryakov, Pavel Rumiantsev, Sergey Moshkovskii, Alexey Moiseev
SEMINARS IN CANCER BIOLOGY
(2020)
Article
Oncology
Irina A. Krivosheeva, Alexandra Yu Filatova, Sergei A. Moshkovskii, Ancha Baranova, Mikhail Yu Skoblov
CANCER CELL INTERNATIONAL
(2020)
Article
Biochemical Research Methods
Anna A. Kliuchnikova, Anton O. Goncharov, Lev Levitsky, Mikhail A. Pyatnitskiy, Svetlana E. Novikova, Ksenia G. Kuznetsova, Mark Ivanov, Irina Y. Ilina, Tatyana E. Farafonova, Victor G. Zgoda, Mikhail Gorshkov, Sergei A. Moshkovskii
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Biochemical Research Methods
Ksenia G. Kuznetsova, Lev Levitsky, Mikhail A. Pyatnitskiy, Irina Y. Ilina, Julia A. Bubis, Elizaveta M. Solovyeva, Victor G. Zgoda, Mikhail Gorshkov, Sergei A. Moshkovskii
Summary: The study aimed to compare the effects of different cysteine alkylating agents on proteome analysis. Results showed that chloroacetamide outperformed other reagents in terms of identified peptides and off-site reactions. Additionally, iodoacetamide was found to increase the rate of methionine-to-isothreonine conversion, especially in gel-prepared samples.
JOURNAL OF PROTEOMICS
(2021)
Article
Oncology
Anastasiya V. Lipatova, Alesya V. Soboleva, Vladimir A. Gorshkov, Julia A. Bubis, Elizaveta M. Solovyeva, George S. Krasnov, Dmitry V. Kochetkov, Pavel O. Vorobyev, Irina Y. Ilina, Sergei A. Moshkovskii, Frank Kjeldsen, Mikhail V. Gorshkov, Peter M. Chumakov, Irina A. Tarasova
Summary: Studies have shown that interferon-induced resistance may affect the sensitivity of tumor cells to viruses, but inhibiting a single ISG may not necessarily increase sensitivity. Silencing specific genes may negatively impact the internalization of certain viruses.
Review
Biochemistry & Molecular Biology
Anton O. Goncharov, Victoria O. Shender, Ksenia G. Kuznetsova, Anna A. Kliuchnikova, Sergei A. Moshkovskii
Summary: Adenosine-to-inosine RNA editing is a widespread post-transcriptional modification system catalyzed by ADAR enzymes, which mainly occurs in dsRNA before splicing. This review focuses on the interconnections between RNA editing and splicing in human cancer. Dysregulated RNA splicing in cancer can lead to the release of excess dsRNA into the cytosol, triggering antiviral-like responses and potentially inhibiting tumor growth. Inhibiting ADAR may enhance the effects of spliceosome inhibitors and could be a promising approach in cancer therapies targeting RNA splicing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Anastasia S. Nikitina, Anastasia V. Lipatova, Anton O. Goncharov, Anna A. Kliuchnikova, Mikhail A. Pyatnitskiy, Ksenia G. Kuznetsova, Azzam Hamad, Pavel O. Vorobyev, Olga N. Alekseeva, Marah Mahmoud, Yasmin Shakiba, Ksenia S. Anufrieva, Georgy P. Arapidi, Mark V. Ivanov, Irina A. Tarasova, Mikhail V. Gorshkov, Peter M. Chumakov, Sergei A. Moshkovskii
Summary: This study compared the response of different cancer cell lines to type I interferon treatment in oncolytic therapy using vesicular stomatitis virus (VSV). The study identified differential effects and molecular factors by integrating analysis of transcriptome, proteome, and RNA editome. The results showed that inflammatory proteins and overexpression of EGFR and HER2 genes were associated with resistance and sensitivity to VSV, respectively. Furthermore, the protein expression level of HER2 in tumor cells might serve as a predictive biomarker for resistance to oncolytic viral therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Lev Levitsky, Ksenia G. Kuznetsova, Anna A. Kliuchnikova, Irina Y. Ilina, Anton O. Goncharov, Anna A. Lobas, Mark Ivanov, Vassili N. Lazarev, Rustam H. Ziganshin, Mikhail Gorshkov, Sergei A. Moshkovskii
Summary: This study proposes a method for interpreting proteomics data by determining the protein sequence coverage using multiple reads. The approach improves the reliability of peptide variant identification and reveals single amino acid variants in the HEK-293 cell line.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biology
Ksenia G. Kuznetsova, Sofia S. Zvonareva, Rustam Ziganshin, Elena S. Mekhova, Polina Dgebuadze, Dinh T. H. Yen, Thanh H. T. Nguyen, Sergei A. Moshkovskii, Alexander E. Fedosov
Summary: This study focuses on the venom of the Vexillum genus, which produces complex venoms dominated by diversified short cysteine-rich peptides called vexitoxins. Vexitoxins show similarities to conotoxins and provide insights into venom evolution. The findings support the hypothesis of lower divergence between vexitoxin genes and their ancestral counterparts compared to that in conotoxins, and discuss the importance of further studies on vexitoxins for understanding the origin of conotoxins and addressing outstanding questions in venom evolution.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Shamsudin S. Nasaev, Anna S. Kopeykina, Ksenia G. Kuznetsova, Lev I. Levitsky, Sergei A. Moshkovskii
Summary: RNA editing can lead to protein recoding, and recoding sites were identified in zebrafish proteins for the first time. This could have functional consequences for the proteins in the zebrafish.
BIOCHEMISTRY-MOSCOW
(2022)
Article
Biochemistry & Molecular Biology
Anna A. Kliuchnikova, Svetlana E. Novikova, Ekaterina V. Ilgisonis, Olga I. Kiseleva, Ekaterina V. Poverennaya, Victor G. Zgoda, Sergei A. Moshkovskii, Vladimir V. Poroikov, Andrey V. Lisitsa, Alexander I. Archakov, Elena A. Ponomarenko
Summary: A meta-analysis was conducted to create a reference standard kit for health analytics by conducting targeted quantitative screening of human blood plasma. The kit includes 53 proteins that are stably present in the proteome of a healthy individual and found in at least 70% of samples, with an interindividual coefficient of variation <40%. These proteins, with concentration range of 10(-10)-10(-3) M, were associated with rare familial diseases based on enrichment analysis. The study also identified specific protein concentration changes in patients with neurological disorders and lung adenocarcinoma compared to healthy volunteers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Anna A. Lobas, Elizaveta M. Solovyeva, Lev I. Levitsky, Anton O. Goncharov, Elena Y. Lyssuk, Sergey S. Larin, Sergei A. Moshkovskii, Mikhail V. Gorshkov
Summary: This study developed new algorithms for the identification and validation of protein splice isoforms in proteomic data without the need for RNA sequencing. The bioinformatic approaches were tested on proteome analysis of human melanoma cell lines. The identified splicing events were further validated at the mRNA level by quantitative PCR.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Lev I. Levitsky, Mark V. Ivanov, Anton O. Goncharov, Anna A. Kliuchnikova, Julia A. Bubis, Anna A. Lobas, Elizaveta M. Solovyeva, Mikhail A. Pyatnitskiy, Ruslan K. Ovchinnikov, Michail S. Kukharsky, Tatiana E. Farafonova, Svetlana E. Novikova, Victor G. Zgoda, Irina A. Tarasova, Mikhail V. Gorshkov, Sergei A. Moshkovskii
Summary: The proteogenomic search pipeline was used to reanalyze 40 publicly available shotgun proteomic datasets from various human tissues. A total of 5442 .raw data files were processed, identifying 33 recoded protein sites in 21 datasets. The study demonstrated that neural and cancer tissues were enriched with recoded proteins and the recoding rate was regulated by the interaction of enzymes with mRNA.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Elizaveta M. Solovyeva, Sergei A. Moshkovskii, Mikhail Gorshkov
Summary: Selecting a precursor ion from a peptide isotopic cluster to obtain a fragmentation mass spectrum is crucial in data-dependent proteome analysis using hybrid Orbitrap FTMS; considering the isotope error during the search can significantly impact the number of identified peptides; predictive metrics for this effect can be integrated into data quality control software to improve analysis efficiency.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemistry & Molecular Biology
K. G. Kuznetsova, E. M. Solovyeva, A. V. Kuzikov, M. V. Gorshkov, S. A. Moshkovskii
BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY
(2020)
