BoxCar and shotgun proteomic analyses reveal molecular networks regulated by UBR5 in prostate cancer

5hmC-profiles in Puerto Rican Hispanic/Latino men with aggressive prostate cancer

Introduction

Puerto Rican (PR) Hispanic/Latino (H/L) men are an understudied population that has the highest prostate cancer (PCa) specific mortality among other Hispanic populations. Little information is known about the higher mortality in PR H/L men. It is thought that epigenetic changes in key genes may play a critical role in aggressive tumors.

Methods

We aimed to identify key 5-hydroxymethylcytosine (5hmC) changes in PR H/L men with aggressive PCa. We performed sequencing analysis using the 5hmC-enriched DNA from 22 prostate tumors and 24 adjacent normal FFPE samples.

Results

We identified 808 differentially methylated genes (DMGs) in tumors compared to adjacent normal tissues. These genes suggest key mechanisms, including upregulated signatures of negative Androgen Receptor (AR) regulation, Wnt/β-catenin pathway activation, and downregulation of tumor suppressor genes. Pathway analysis of DMGs demonstrated that DNA repair pathway was most upregulated in tumors. Since 5hmC abundance positively correlates with gene expression levels, we further investigated 808 DMGs in TCGA PCa gene expression data. Further, we identified 59 DMGs with significant gene expression changes in the same direction. Additionally, we identified 111 aggressiveness-related DMGs, of which, two hypomethylated genes (CCDC122, NUDT15) and four hypermethylated genes (PVT1, RPL30, TRMT12, UBR5) were found to be altered at transcriptomic level in a concordant manner in PR H/L PCa patients. Aberrant 5hmC and GE changes in these six genes were also associated with progression-free survival in the mixed PCa population.

Discussion

The 5hmC modifications and associated gene expression changes in these six genes could be linked to the highest prostate cancer (PCa)-specific mortality in PR H/L men. In conclusion, our study identified 59 DMGs showing concordant epigenetic and transcriptomic changes in tumor tissues and 111 DMGs showing association with aggressive PCa among PR H/L men. Our findings have significant implications for understanding these key genes' molecular mechanisms, which may drive PCa progression and mortality in this population. This will help in developing potential biomarkers or therapeutic targets for personalized treatment strategies in this high-risk subgroup. Future research will explore how these genes contribute to PCa-specific mortality through molecular analyses, with plans to validate them in a larger validation cohort.

Enhanced Analysis of Low-Abundance Proteins in Soybean Seeds Using Advanced Mass Spectrometry

This study presents an advanced approach for the comprehensive analysis of low-abundance proteins in soybean seeds, addressing challenges posed by high-abundance storage proteins. We compared the effectiveness of Data-Dependent Acquisition (DDA), Data-Independent Acquisition (DIA), and BoxCar mass spectrometry techniques to identify low-abundance proteins in two types of soybean seeds: High-Oil and High-Protein seeds. The results indicate that the DIA method, and particularly the BoxCar methods, significantly improve the detection of low-abundance proteins compared to DDA, offering deeper insights into soybean seed biology. Specifically, BoxCar-based analysis revealed distinct proteomic differences between High-Oil and High-Protein seeds, highlighting more active metabolic processes in High-Oil seeds. Additionally, several key proteins were identified and annotated as uniquely expressed in either High-Oil or High-Protein seeds. These findings emphasize the importance of advanced proteomic techniques, such as BoxCar, in deepening our understanding of soybean seed biology and supporting breeding strategies to improve nutritional qualities.

Single-Cell Multi-Omics Analysis of In Vitro Post-Ovulatory-Aged Oocytes Revealed Aging-Dependent Protein Degradation

Once ovulated, the oocyte has to be fertilized in a short time window or it will undergo post-ovulation aging (POA), whose underlying mechanisms are still not elucidated. Here, we optimized single-cell proteomics methods and performed single-cell transcriptomic, proteomic, and phosphoproteomic analysis of fresh, POA, and melatonin-treated POA oocytes. POA oocytes showed downregulation of most differentially expressed proteins, with little correlation with mRNA expression, and the protein changes can be rescued by melatonin treatment. MG132 treatment rescued the decreased fertilization and polyspermy rates and upregulated fragmentation and parthenogenesis rates of POA oocytes. MG132-treated oocytes displayed health status at proteome, phosphoproteome, and fertilization ability similar to fresh oocytes, suggesting that protein stabilization might be the underlying mechanism for melatonin to rescue POA. The important roles of proteasome-mediated protein degradation during oocyte POA revealed by single-cell multi-omics analyses offer new perspectives for increasing oocyte quality during POA and improving assisted reproduction technologies.

A review: targeting UBR5 domains to mediate emerging roles and mechanisms - chance or necessity?

Ubiquitinases are known to catalyze ubiquitin chains on target proteins to regulate various physiological functions like cell proliferation, autophagy, apoptosis, and cell cycle progression. As a member of E3 ligase, ubiquitin protein ligase E3 component n-recognin 5 (UBR5) belongs to the HECT E3 ligase and has been reported to be correlated with various pathophysiological processes. In this review, the authors give a comprehensive insight into the structure and function of UBR5. The authors discuss the specific domains of UBR5 and explore their biological functions separately. Furthermore, the authors describe the involvement of UBR5 in different pathophysiological conditions, including immune response, virus infection, DNA damage response, and protein quality control. Moreover, the authors provide a thorough summary of the important roles and regulatory mechanisms of UBR5 in cancers and other diseases. On the whole, investigating the domains and functions of UBR5, elucidating the underlying mechanisms of UBR5 with various substrates in detail may provide new theoretical basis for the treatment of diseases, including cancers, which could improve future studies to construct novel UBR5-targeted therapy strategies.

The role of UBR5 in tumor proliferation and oncotherapy

Ubiquitin (Ub) protein ligase E3 component n-recognin 5 (UBR5), as a crucial Ub ligase, plays a pivotal role in the field of cell biology, attracting significant attention for its functions in regulating protein degradation and signaling pathways. This review delves into the fundamental characteristics and structure of UBR5. UBR5, through ubiquitination, regulates various key proteins, directly or indirectly participating in cell cycle control, thereby exerting a direct impact on the proliferation of tumor cells. Meanwhile, we comprehensively review the expression levels of UBR5 in different types of tumors and its relationship with tumor development, providing key clues for the role of UBR5 in cancer. Furthermore, we summarize the current research status of UBR5 in cancer treatment. Through literature review, we find that UBR5 may play a crucial role in the sensitivity of tumor cells to radiotherapy chemotherapy, and other anti-tumor treatment, providing new insights for optimizing cancer treatment strategies. Finally, we discuss the challenges faced by UBR5 in cancer treatment, and looks forward to the future research directions. With the continuous breakthroughs in technology and in-depth research, we hope to further study the biological functions of UBR5 and lay the foundation for its anti-tumor treatment.