USP14 is crucial for proteostasis regulation and α-synuclein degradation in human SH-SY5Y dopaminergic cells by Vignesh Srinivasan, Rabah Soliymani, Larisa Ivanova, Ove Eriksson, Nina Peitsaro, Maciej Lalowski, Mati Karelson, Dan Lindholm

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Genetic context modulates aging and degeneration in the murine retina by Olivia J. Marola, Michael MacLean, Travis L. Cossette, Cory A. Diemler, Amanda A. Hewes, Alaina M. Reagan, Jonathan Nyandu Kanyinda, Daniel A. Skelly, Gareth R. Howell

“…Methods Transcriptomics and proteomics were employed to elucidate retinal aging signatures in nine genetically diverse mouse strains (C57BL/6J, 129S1/SvlmJ, NZO/HlLtJ, WSB/EiJ, CAST/EiJ, PWK/PhK, NOD/ShiLtJ, A/J, and BALB/cJ) across lifespan. …”
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Gut bacterium Intestinimonas butyriciproducens improves host metabolic health: evidence from cohort and animal intervention studies by Elena Rampanelli, Nadia Romp, Antonio Dario Troise, Jakshana Ananthasabesan, Hao Wu, Ismail Sahin Gül, Sabrina De Pascale, Andrea Scaloni, Fredrik Bäckhed, Vincenzo Fogliano, Max Nieuwdorp, Thi Phuong Nam Bui

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APOE Christchurch enhances a disease-associated microglial response to plaque but suppresses response to tau pathology by Kristine M. Tran, Nellie E. Kwang, Claire A. Butler, Angela Gomez-Arboledas, Shimako Kawauchi, Cassandra Mar, Donna Chao, Rocio A. Barahona, Celia Da Cunha, Kate I. Tsourmas, Zechuan Shi, Shuling Wang, Sherilyn Collins, Amber Walker, Kai-Xuan Shi, Joshua A. Alcantara, Jonathan Neumann, Duc M. Duong, Nicholas T. Seyfried, Andrea J. Tenner, Frank M. LaFerla, Lindsay A. Hohsfield, Vivek Swarup, Grant R. MacGregor, Kim N. Green

“…We used immunohistochemical and biochemical analysis along with single-cell spatial omics and bulk proteomics to explore the impact of the ApoeCh variant on AD pathological development and the brain’s response to plaques and tau. …”
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Trojan-horse silk fibroin nanocarriers loaded with a re-call antigen to redirect immunity against cancer by Luca Mastracci, Patrizio Castagnola, Elia Bari, Francesca Ferrera, Tiziana Altosole, Sara Perteghella, Pierluigi Mauri, Rossana Rossi, Giulia Passignani, Martina Galati, Giuseppina Iliana Astone, Maddalena Mastrogiacomo, Daniela Fenoglio, Dario Di Silvestre, Maria Luisa Torre, Gilberto Filaci

“…Cancer dimensions/survival time were monitored, while, at the molecular level, system biology approaches based on graph theory and experimental proteomic data were performed.Results SFNs were efficiently in vitro uptaken by cancer and dendritic cells. …”
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NEAT1 regulates BMSCs aging through disruption of FGF2 nuclear transport by Zifei Wang, Wenyu Zhen, Qing Wang, Yuqiang Sun, Siyu Jin, Sensen Yu, Xing Wu, Wenhao Zhang, Yulong Zhang, Fei Xu, Rui Wang, Yuxuan Xie, Wansu Sun, Jianguang Xu, Hengguo Zhang

“…Subsequent RNA pulldown and proteomic analyses, along with single-cell analysis, immunofluorescence, RNA immunoprecipitation (RIP), and co-immunoprecipitation (Co-IP), were conducted to investigate that NEAT1 impairs the nuclear transport of mitotic FGF2 and contributes to BMSCs aging. …”
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Two-Component Signal Transduction System SaeRS Positively Regulates Staphylococcus epidermidis Glucose Metabolism by Qiang Lou, Yijun Qi, Yuanfang Ma, Di Qu

“…In this study, we performed a proteomic analysis of differences in expression between the S. epidermidis 1457 wild-type and saeRS mutant to identify candidates regulated by saeRS using two-dimensional gel electrophoresis (2-DE) combined with matrix-assisted laser desorption/lonization mass spectrometry (MALDI-TOF-MS). …”
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Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink by Lejla Gul, Anna Julia Elias, Tanvi Tambaku, Marton Olbei, Emily Watters, Balazs Bohar, Dezso Modos, Matthew Madgwick, Tamas Korcsmaros

“…We describe steps for setting up the environment, installing software, and preparing human transcriptomic and bacterial proteomic data. The protocol outlines procedures for predicting protein-protein interactions through domain-motif interactions, integrating multi-omic datasets to map downstream effects, performing network analyses to identify key regulatory pathways, and visualizing multi-layered networks for systems-level data interpretation.For complete details on the use and execution of this protocol, please refer to Gul et al.1 and Poletti et al.2 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.…”
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Role of New Biomarkers: Functional and Structural Damage by Evdoxia Tsigou, Vasiliki Psallida, Christos Demponeras, Eleni Boutzouka, George Baltopoulos

“…Innovative technologies such as genomics and proteomics have contributed to the discovery of new biomarkers, such as neutrophil gelatinase-associated lipocalin (NGAL), cystatin C (Cys C), kidney injury molecule-1 (KIM-1), interleukin-18 (IL-18), and liver-type fatty acid binding protein (L-FABP). …”
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Characterization of extracellular vesicles by capillary zone electrophoresis: A novel concept for characterization of a next-generation drug delivery platform by Aleksandra Steć, Andrea Heinz, Szymon Dziomba

“…According to current recommendations, quantification of EVs, confirmation of their identity, and purity assessment require the use of several analytical techniques, including particle-size distribution analysis, proteomics, and electron microscopy, making the characterization process demanding. …”
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The Problem of Abnormal Body Weight and Dyslipidemia as Risk Factors for Cardiovascular Diseases in Children and Adolescents with Type 1 Diabetes by Katarzyna Noras, Ewa Rusak, Przemysława Jarosz-Chobot

“…Recently, a new look at the vasoprotective effect of HDL has appeared, which due to its dysfunctional form in type 1 diabetes may not protect against cardiovascular risk. The HDL proteome in type 1 diabetes has an altered protein composition compared to the healthy population. …”
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Amyloids in bladder cancer hijack cancer-related proteins and are positive correlated to tumor stage by Diego Alem, César X. García-Laviña, Francisco Garagorry, Dardo Centurión, Joaquina Farias, Hany Pazos-Espinosa, María Noel Cuitiño-Mendiberry, Carolina Villadóniga, Susana Castro-Sowinski, Martín Fló, Federico Carrión, Brenda Iglesias, Kevin Madauss, Lucía Canclini

“…Subsequently, the amyloid proteome of the RT4 non-invasive and HT1197 invasive bladder cancer cell lines was identified and included oncogenes, tumor suppressors, and highly expressed cancer-related proteins. …”
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Joint fluid multi-omics improves diagnostic confidence during evaluation of children with presumed septic arthritis by Yolanda Peña-López, Naureen G. Tareen, Bo Zhang, Indu Raman, Carlos A. Arana, Chengsong Zhu, Yang Liu, Pratibha Selvakumar, Nicolai S. C. van Oers, Simrat Morris, Lora V. Hooper, Lawson A. B. Copley, Prithvi Raj

“…A multi-omics strategy comprising metagenomic and proteomic technologies were undertaken for children diagnosed with presumed septic arthritis to advance clinical diagnoses and care for affected individuals. …”
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Transient lymphocyte count decrease correlates with oncolytic adenovirus efficacy in humans: mechanistic and biomarker findings from TUNIMO phase I trial by Tuomo Alanko, Akseli Hemminki, Víctor Cervera-Carrascón, Riikka Havunen, Kristian Taipale, Dafne C A Quixabeira, Jorma Sormunen, Katriina Peltola, Suvi Sorsa, Santeri A Pakola, Elise Jirovec, Lyna Haybout, Claudia Kistler, Tatiana V Kudling, Victor Arias, James H A Clubb, Mirte van der Heijden, Teijo Pellinen, Joao M Santos

“…More substantial lymphocyte count change was linked to stronger immune activation in plasma proteome after intravenous TILT-123 and the presence of TILT-123 mRNA in tumors. …”
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Multilevel plasticity and altered glycosylation drive aggressiveness in hypoxic and glucose-deprived bladder cancer cells by Andreia Peixoto, Dylan Ferreira, Andreia Miranda, Marta Relvas-Santos, Rui Freitas, Tim S. Veth, Andreia Brandão, Eduardo Ferreira, Paula Paulo, Marta Cardoso, Cristiana Gaiteiro, Sofia Cotton, Janine Soares, Luís Lima, Filipe Teixeira, Rita Ferreira, Carlos Palmeira, Albert J.R. Heck, Maria José Oliveira, André M.N. Silva, Lúcio Lara Santos, José Alexandre Ferreira

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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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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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