Genomic 8-oxoguanine modulates gene transcription independent of its repair by DNA glycosylases OGG1 and MUTYH by Tobias Obermann, Teri Sakshaug, Vishnu Vignesh Kanagaraj, Andreas Abentung, Mirta Mittelstedt Leal de Sousa, Lars Hagen, Antonio Sarno, Magnar Bjørås, Katja Scheffler

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A Systems Biology Overview on Human Diabetic Nephropathy: From Genetic Susceptibility to Post-Transcriptional and Post-Translational Modifications by Francesca Conserva, Loreto Gesualdo, Massimo Papale

“…We performed a systematic analysis of the most relevant studies investigating genetic susceptibility and specific transcriptomic, epigenetic, proteomic, and metabolomic patterns in order to summarize the most significant traits associated with the disease onset and progression. …”
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The Occurrence of Sequences Identical with Epitopes from the Allergen Pen a 1.0102 Among Food and Non-Food Proteins by Minkiewicz Piotr, Sokolowska Jolanta, Darewicz Malgorzata

“…The work presented is the first survey concerning global distribution of epitopes from Pen a 1.0102 in universal proteome. In the group of known tropomyosin epitopes, the fragment with the sequence ESKIVELEEEL was found in the sequence of channel catfish (Ictalurus punctatus) tropomyosin. …”
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Absence of MCJ/DnaJC15 promotes brown adipose tissue thermogenesis by Beatriz Cicuéndez, Alfonso Mora, Juan Antonio López, Andrea Curtabbi, Javier Pérez-García, Begoña Porteiro, Daniel Jimenez-Blasco, Pedro Latorre-Muro, Paula Vo, Madison Jerome, Beatriz Gómez-Santos, Rafael Romero-Becerra, Magdalena Leiva, Elena Rodríguez, Marta León, Luis Leiva-Vega, Noemi Gómez-Lado, Jorge L. Torres, Lourdes Hernández-Cosido, Pablo Aguiar, Miguel Marcos, Martin Jastroch, Andreas Daiber, Patricia Aspichueta, Juan Pedro Bolaños, Jessica B. Spinelli, Pere Puigserver, José Antonio Enriquez, Jesús Vázquez, Cintia Folgueira, Guadalupe Sabio

“…Electron microscopy unveils changes in mitochondrial morphology resembling BAT activation. Proteomic analysis confirms these findings and suggests involvement of the eIF2α mediated stress response. …”
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RNA structure in alternative splicing regulation: from mechanism to therapy by Bao Nengcheng, Wang Zhechao, Fu Jiayan, Dong Haiyang, Jin Yongfeng

“…Alternative splicing is a highly intricate process that plays a crucial role in post-transcriptional regulation and significantly expands the functional proteome of a limited number of coding genes in eukaryotes. …”
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Spatial transcriptomic analysis drives PET imaging of tight junction protein expression in pancreatic cancer theranostics by James Wang, Jai Woong Seo, Aris J. Kare, Martin Schneider, Mallesh Pandrala, Spencer K. Tumbale, Marina N. Raie, Gokce Engudar, Nisi Zhang, Yutong Guo, Xiaoxu Zhong, Sofia Ferreira, Bo Wu, Laura D. Attardi, Guillem Pratx, Andrei Iagaru, Ryan L. Brunsing, Gregory W. Charville, Walter G. Park, Katherine W. Ferrara

“…While cancer-associated fibroblasts and integrins have been proposed as targets for imaging of pancreatic ductal adenocarcinoma (PDAC), herein, spatial transcriptomics and proteomics of human surgical samples are applied to select PDAC targets. …”
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Machine learning and multi-omics in precision medicine for ME/CFS by Katherine Huang, Brett A. Lidbury, Natalie Thomas, Paul R. Gooley, Christopher W. Armstrong

“…In this review, we explore how machine learning and multi-omics (genomics, transcriptomics, proteomics, and metabolomics) can transform precision medicine in ME/CFS research and healthcare. …”
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Phenotypic alterations in articulating joint cells: Role of mechanically loaded MSC secretome by Yann D. Ladner, Ursula Menzel, Keith Thompson, Angela R. Armiento, Martin J. Stoddart

“…Previously, we employed a small-panel microarray to demonstrate differences within conditioned medium (CM) of MSCs that were mechanically stimulated within a joint-mimicking bioreactor and their unloaded controls.This study analyzed the proteomic content within CM from 4 week mechanically loaded MSCs with a larger protein microarray. …”
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3D‐Printed Bioceramic Scaffolds Reinforced by the In Situ Oriented Growth of Grains for Supercritical Bone Defect Reconstruction by Boqing Zhang, Kaixin Wang, Xingyu Gui, Wenzhao Wang, Ping Song, Lina Wu, Likun Guo, Changchun Zhou, Yujiang Fan, Xingdong Zhang

“…Calcium sulfate improves the release of active calcium ions from calcium phosphate ceramics, further enhancing their bioactivity and osteoinductivity in vivo. Transcriptome and proteome sequencing reveals that the in situ whisker‐reinforced ceramics increase the expression of proteins related to calcium ion binding and promote the expression of osteogenesis‐related proteins. …”
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Identification of Osteosarcoma-Related Specific Proteins in Serum Samples Using Surface-Enhanced Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry by Jianli Gu, Jitian Li, Manyu Huang, Zhiyong Zhang, Dongsheng Li, Guoying Song, Xingpo Ding, Wuyin Li

“…Two proteins showed a significantly different expression in OS serum samples from control groups. Proteomic profiles and external leave-one-out cross-validation analysis showed that the correct rate of allocation, the sensitivity, and the specificity of diagnosis were 100%. …”
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How the Knowledge of Interactions between Meningococcus and the Human Immune System Has Been Used to Prepare Effective Neisseria meningitidis Vaccines by R. Gasparini, D. Panatto, N. L. Bragazzi, P. L. Lai, A. Bechini, M. Levi, P. Durando, D. Amicizia

“…In the last decades, tremendous advancement in dissecting the mechanisms of pathogenicity of Neisseria meningitidis at a molecular level has been achieved, exploiting converging approaches of different disciplines, ranging from pathology to microbiology, immunology, and omics sciences (such as genomics and proteomics). Here, we review the molecular biology of the infectious agent and, in particular, its interactions with the immune system, focusing on both the innate and the adaptive responses. …”
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Colistin Resistance and Management of Drug Resistant Infections by Juhi Sharma, Divakar Sharma, Amit Singh, Kumari Sunita

“…Researchers focus on the most advanced genomics (whole genome sequencing), proteomics, and bioinformatics approaches to explore the question of colistin resistance. …”
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Classifications of triple-negative breast cancer: insights and current therapeutic approaches by Ziqi Chen, Yumeng Liu, Minchuan Lyu, Chi Ho Chan, Meiheng Sun, Xin Yang, Shuangying Qiao, Zheng Chen, Sifan Yu, Meishen Ren, Aiping Lu, Ge Zhang, Fangfei Li, Yuanyuan Yu

“…Additionally, TNBC exhibits significant heterogeneity at histopathological, proteomic, transcriptomic, and genomic levels, further complicating the development of effective treatments. …”
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<i>Pseudomonas aeruginosa pqs</i> Quorum Sensing Mediates Interaction with <i>Mycobacterium abscessus</i> In Vitro by Yun Long, Zhi Li, Menglu Li, Peiyi Lu, Yujia Deng, Pengyao Wu, Xue Li, Gangjian Qin, Jiamin Huang, Wenying Gao, Guobao Li, Tianyuan Jia, Liang Yang

“…In this study, we first demonstrated that <i>P. aeruginosa</i> inhibits the growth of <i>M. abscessus</i> by iron chelating via <i>pqs</i> quorum sensing. Next, through proteomic analysis, we discovered that the PQS molecule significantly changed a large amount of protein expression in <i>M. abscessus</i>, including proteins involved in the type VII secretion system and iron homeostasis. …”
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Psychrophilic Enzymes: From Folding to Function and Biotechnology by Georges Feller

“…Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. …”
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Assessment of Salivary Adipokines Resistin, Visfatin, and Ghrelin as Type 2 Diabetes Mellitus Biomarkers by Mythily Srinivasan, Melinda L. Meadows, Lisa Maxwell

“…Human saliva is an easily accessible biospecimen amenable for painless frequent collection and possesses nearly 50% of serum proteome. In this study, we measured the adipokines resistin, visfatin, TNF-α, and ghrelin as markers for T2DM in unstimulated whole saliva (UWS) using specific assay kits. …”
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Metabonomics Research Progress on Liver Diseases by Mengqian Yu, Ying Zhu, Qingwei Cong, Chunyan Wu

“…Metabolomics as the new omics technique develops after genomics, transcriptomics, and proteomics and has rapid development at present. Liver diseases are worldwide public health problems. …”
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SIRT5 Contributes to Colorectal Cancer Growth by Regulating T Cell Activity by Ke Wang, Zuojian Hu, Cuiping Zhang, Lujie Yang, Li Feng, Pengyuan Yang, Hongxiu Yu

“…In this work, we found that Sirt5 knockout mice were resistant to AOM and DSS-induced colitis-associated colorectal tumorigenesis and the level of IFN-γ in their tumor microenvironment was higher. Additionally, proteome and network analysis revealed that SIRT5 was important in the T cell receptor signaling pathway. …”
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Phytochemical Evaluation of Moth Bean (Vigna aconitifolia L.) Seeds and Their Divergence by Neha Gupta, Nidhi Shrivastava, Pramod Kumar Singh, Sameer S. Bhagyawant

“…Over 20 individual protein fractions were distributed over the gel as a series of spots in two moth bean accessions. Seed proteome accumulated spots of high intensity over a broad range of pI values of 3–10 in a molecular weight range of 11–170 kDa. …”
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Non-histone lactylation: unveiling its functional significance by Pusong Shi, Yongjie Ma, Yongjie Ma, Yongjie Ma, Yongjie Ma, Yongjie Ma, Shaolu Zhang, Shaolu Zhang, Shaolu Zhang, Shaolu Zhang, Shaolu Zhang

“…Recently, high-throughput proteomics studies have identified a large number of lactylated proteins and sites, revealing their global regulatory role in disease development. …”
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