Article
Gastroenterology & Hepatology
Soo Young Cho, Heeyoun Hwang, Yun-Hee Kim, Byong Chul Yoo, Nayoung Han, Sun-Young Kong, Min-Jeong Baek, Kyung-Hee Kim, Mi Rim Lee, Jae Gwang Park, Sung-Sik Han, Woo Jin Lee, Charny Park, Jong Bae Park, Jin Young Kim, Sang-Jae Park, Sang Myung Woo
Summary: Through comprehensive analysis of genomic, transcriptomic, proteomic, and phosphoproteomic data from 102 iCC patients, three clinically supported subtypes were identified (stem-like, poorly immunogenic, and metabolism), and an organoid model was constructed for therapeutic testing. The ALDH1A1 inhibitor NCT-501 showed synergy with nanoparticle albumin-bound-paclitaxel in the organoid model for the stem-like subtype. Dysregulations in oncometabolites were associated with different clinical outcomes in the stem-like and metabolism subtypes. The poorly immunogenic subtype exhibited non-T-cell tumor infiltration. Integrated multiomics analysis reproduced the 3 subtypes and revealed heterogeneity in iCC.
Review
Biochemistry & Molecular Biology
Michal Levin, Falk Butter
Summary: Applications in omics research benefit from comprehensive high-quality annotation of coding genes. Transcriptome provides the optimal basis for identifying open reading frames, and the integration of proteomics data enriches for accurate gene models.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Medicine, Research & Experimental
Chang-Zhu Pei, Lan Jin, Kwang-Hyun Baek
Summary: PCOS is a common gynecological endocrine disease involving multiple genes and pathways, and cannot be explained by a single factor. Omics analysis plays a key role in studying the pathogenesis of PCOS, offering new perspectives for explaining new mechanisms and potential biomarkers discovery.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Article
Clinical Neurology
Dominique F. Leitner, Yik Siu, Aryeh Korman, Ziyan Lin, Evgeny Kanshin, Daniel Friedman, Sasha Devore, Beatrix Ueberheide, Aristotelis Tsirigos, Drew R. Jones, Thomas Wisniewski, Orrin Devinsky
Summary: High-fat and low-carbohydrate diets, such as the modified Atkins diet (MAD), can reduce seizure frequency in treatment-resistant epilepsy patients. These diets mimic fasting and induce high levels of ketone bodies, potentially shifting brain energy production and impacting neuronal and astrocyte metabolism.
Article
Immunology
Andrew D. Jerome, Jeffrey R. Atkinson, Arnetta L. Moffatt, Jesse A. Sepeda, Benjamin M. Segal, Andrew R. Sas
Summary: Recent studies have shown that neutrophils are more diverse than previously thought, with unique subsets identified in various conditions such as bacterial and parasitic infections, cancer, and tissue injury and repair. The characteristics of infiltrating neutrophils depend on the nature of the stimulus, the stage of inflammation, and the tissue microenvironment. This study used advanced techniques to analyze neutrophil populations following injection of a fungal cell wall extract, revealing distinct gene and protein expressions.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Plant Sciences
Xiangyu Xu, Cassio Flavio Fonseca de Lima, Lam Dai Vu, Ive De Smet
Summary: Changes in weather patterns, drought risks, and rising global temperature negatively impact crop growth and productivity. Plants are exposed to multiple stresses simultaneously, but most studies focus on individual stress conditions. This mini-review focuses on the combination of drought and heat, summarizing current research results, identifying knowledge gaps, and suggesting potential future focus areas.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Lei Li, Lin Huang, Chenyang Huang, Jia Xu, Yukai Huang, Haihua Luo, Xinya Lu, Shuyue He, Gang Yuan, Li Chen, Xue Han, Xusong Cao, Aolin Jiang, Cuiting Liu, Junmin Shi, Hong Yang, Yong Jiang
Summary: This study focused on the molecular dynamics profiles of exosomes in serum during the development of sepsis. High-performance liquid chromatography-tandem mass spectrometry and RNA-seq were used to detect the dynamic profiles of exosome proteins and RNAs. Integrative multiomics analyses revealed the association of exosome components with various biological processes and molecular pathways. Importantly, exosomes derived from septic serum showed potential therapeutic effects in septic mice.
JOURNAL OF ADVANCED RESEARCH
(2022)
Article
Clinical Neurology
Xin Lin, Yuanhao Yang, Melissa Gresle, Gabriel Cuellar-Partida, Xikun Han, Jim Stankovich, Steve Simpson-Yap, Valery Fuh-Ngwa, Jac Charlesworth, Kathryn P. Burdon, Helmut Butzkueven, Bruce Taylor, Yuan Zhou
Summary: This study identifies 39 novel plasma and brain proteins associated with multiple sclerosis onset risk and assesses their expression at tissue and cell level. Almost two-thirds of the identified candidates were also associated with disability progression.
Article
Microbiology
Lorena Alves Mesquita, Alexandre Melo Bailao, Juliana Santana de Curcio, Kassyo Lobato Potenciano da Silva, Gabriel da Rocha Fernandes, Mirelle Garcia Silva-Bailao, Evandro Novaes, Celia Maria de Almeida Soares
Summary: Zinc is an essential micronutrient for organisms and the host can sequester metals used in fungal metabolism as a defense mechanism. MicroRNAs play a role in the interaction between pathogens and hosts, influencing infection outcomes. This study focuses on Paracoccidioides brasiliensis, a fungus causing paracoccidioidomycosis, and investigates its adaptations during zinc deprivation using transcriptomic and proteomic analyses. The findings suggest that P. brasiliensis undergoes metabolic remodeling and miRNAs may be involved in the regulatory process.
Article
Nutrition & Dietetics
Federica Farabegoli, Francisco J. J. Santaclara, Daniel Costas, Mercedes Alonso, Ana G. G. Abril, Montserrat Espineira, Ignacio Ortea, Celina Costas
Summary: Inulin is a soluble fiber with prebiotic activity that can reduce inflammation by modulating gut microflora and their metabolites. This study used a macrophage cell model to evaluate the anti-inflammatory properties of inulin and investigated the immunomodulatory mechanism using omics technologies. The results identified two potential mechanisms responsible for the observed anti-inflammatory effects: inhibition of the NF-kappa B signaling pathway and promotion of the Nrf2 pathway. This research provides promising targets for immune modulation and improves the understanding of functional ingredients for personalized nutrition.
Article
Biochemical Research Methods
Nathaniel Kwok, Zita Aretz, Sumiko Takao, Zheng Ser, Paolo Cifani, Alex Kentsis
Summary: Recent advances in nucleic acid sequencing and mass spectrometry proteomics have enabled genome-scale analysis of genetic variation and transcription as well as whole proteome-scale studies of protein expression. However, most proteomic studies are limited to canonical protein sequences. Here, we develop ProteomeGenerator2 (PG2), which integrates genome and transcriptome sequencing to incorporate protein variants and other non-canonical features caused by genomic and transcriptomic variation. PG2 has been benchmarked using synthetic data and analysis of human leukemia cells and can be used with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms. It is open-source and available at https://github.com/kentsisresearchgroup/ProteomeGenerator2.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Agriculture, Dairy & Animal Science
Yang Liu, Xiaomin Wang, Xiaoping Luo, Rui Wang, Bintao Zhai, Penglong Wang, Junyan Li, Xiaoye Yang
Summary: In this study, transcriptomic and proteomic differences in ivermectin-resistant and -susceptible strains of H. contortus were examined before and after Ivermectin treatment. The results showed that genes such as UDP-glycosyltransferases (UGT), glutathione S-transferase (GST), cytochrome P450 (CYP), and p-glycoprotein (Pgp) play important roles in H. contortus drug resistance. The findings provide useful information for understanding the resistance response of H. contortus.
Article
Medicine, Research & Experimental
Tiago Oliveira, Mingfeng Zhang, Eun Ji Joo, Hisham Abdel-Azim, Chun-Wei Chen, Lu Yang, Chih-Hsing Chou, Xi Qin, Jianjun Chen, Kathirvel Alagesan, Andreia Almeida, Francis Jacob, Nicolle H. Packer, Mark von Itzstein, Nora Heisterkamp, Daniel Kolarich
Summary: This study integrated transcriptomics, proteomics and glycomics data to reveal extensive remodeling of glycocalyx in MLL-r cells, identifying potential therapeutic targets and previously unknown protein targets. The research demonstrated the importance of a systematic combined multi-omics approach in providing important diagnostic information that may be missed with a single omics technology.
Article
Cell Biology
Di Peng, Chen Ruan, Shanshan Fu, Chengwen He, Jingzhen Song, Hui Li, Yiran Tu, Dachao Tang, Lan Yao, Shaofeng Lin, Ying Shi, Weizhi Zhang, Hao Zhou, Le Zhu, Cong Ma, Cheng Chang, Jie Ma, Zhiping Xie, Chenwei Wang, Yu Xue
Summary: A multi-omic profiling revealed the influence of Atg9 on gene expression during autophagy and predicted 42 potential new Atg9-interacting proteins involved in autophagy. Two of these proteins, Glo3 and Scs7, were validated to be functional in autophagy, with Glo3 regulating the retrograde transport of Atg9. The study highlighted the importance of the Atg9 interactome and introduced a new method for analyzing multi-omics data.
Article
Oncology
Han Jin, Pieter Goossens, Peter Juhasz, Wouter Eijgelaar, Marco Manca, Joel M. H. Karel, Evgueni Smirnov, Cornelis J. J. M. Sikkink, Barend M. E. Mees, Olivia Waring, Kim van Kuijk, Gregorio E. Fazzi, Marion J. J. Gijbels, Martina Kutmon, Chris T. A. Evelo, Ulf Hedin, Mat J. A. P. Daemen, Judith C. Sluimer, Ljubica Matic, Erik A. L. Biessen
Summary: The study integrated multiple omics data and identified a protein-gene associated multiomics model with high predictive performance in distinguishing intraplaque hemorrhage and stable plaques, revealing cardiovascular disease features related to plaque vulnerability, and validated the findings in several independent cohorts.
CLINICAL AND TRANSLATIONAL MEDICINE
(2021)