Ubiquitin Pathway Research Articles

Comprehensive analysis of pyroptotic gene prognostic signatures associated with tumor immune microenvironment and genomic mutation in breast cancer.

BackgroundBreast cancer is becoming a tumor with the highest morbidity rate, and inflammation-induced cell death namely pyroptosis reportedly plays dual roles in cancers. However, the specific mechanism between pyroptosis and the clinical prognosis of breast cancer patients is indistinct. Hence, novel pyroptosis-related biomarkers and their contributing factors deserve further exploration to predict the prognosis in breast cancer.MethodsPearson’s correlation analysis, and univariate and multivariate Cox regression analysis were utilized to obtain six optimal pyroptosis-related gene prognostic signatures (Pyro-GPS). The risk score of each breast cancer patient was calculated. Next, a Pyro-GPS risk model was constructed and verified in TCGA cohort (n=1,089) and GSE20711 cohort (n=88). Then analyses of immune microenvironment, genomic variation, functional enrichment, drug response and clinicopathologic feature stratification associated with the risk score of Pyro-GPS were performed. Subsequently, a nomogram based on the risk score and several significant clinicopathologic features was established. Ultimately, we further investigated the role of CCL5 in the biological behavior of MDA-MB-231 cell line.ResultsThe low-risk breast cancer patients have better survival outcomes than the high-risk patients. The low-risk patients also show higher immune cell infiltration levels and immune-oncology target expression levels. There is no significant difference in genetic variation between the two risk groups, but the frequency of gene mutations varies. Functional enrichment analysis shows that the low-risk patients are prominently correlated with immune-related pathways, whereas the high-risk patients are enriched in cell cycle, ubiquitination, mismatch repair, homologous recombination and biosynthesis-related pathways. Pyro-GPS is positively correlated with the IC50 of anti-tumor drugs. Furthermore, comprehensive analyses based on risk score and clinicopathological features were performed to predict the prognosis of breast cancer patients. Additionally, in vitro experiments confirmed that breast cancer cells with high expression of CCL5 had weaker proliferation, invasion and metastasis abilities as well as stronger apoptosis and cell cycle arrest abilities.ConclusionsThe risk score of Pyro-GPS can serve as a promising hallmark to predict the prognosis of BRCA patients. Risk score evaluation may assist to acquire relevant information of tumor immune microenvironment, genomic mutation status, functional pathways and drug sensitivity, and thus provide more effective personalized strategies.

Structural basis for the dual catalytic activity of the Legionella pneumophila ovarian tumor (OTU) domain deubiquitinase LotA

Legionella pneumophila, a bacterial pathogen that causes a severe pneumonia known as Legionnaires’ disease, extensively exploits the ubiquitin (Ub) pathway in the infected host cells through certain virulence effectors excreted by the Dot/Icm system. To date, several Dot/Icm effectors have been found to act as Ub ligases, and four effectors, including LotA, LotB, LotC, and Ceg7, have been identified as deubiquitinases (DUBs) from the ovarian tumor (OTU) domain family. LotA is unique among other OTU DUBs because it possesses two distinct DUB domains and exclusively exhibits catalytic activity against K6-linked diUb and polyUb chains. However, the structure of LotA and the molecular mechanism for the dual DUB activity remains elusive. In this study, we solved the structure of LotA in complex with proximally bound Ub and distal covalently bound Ub. Both Ub molecules are bound to the DUB1 domain and mimic a K6-linked diUb. Structural analysis reveals that the DUB1 domain utilizes a distinct mechanism for recognition of the K6-linked diUb within a large S1′ binding site that is uncommon to OTU DUBs. Structural fold of the LotA DUB2 domain closely resembles LotB and LotC, similarly containing an extra α-helix lobe that has been demonstrated to play an important role in Ub binding. Collectively, our study uncovers the structural basis for the dual catalytic activity of the unique OTU family DUB LotA.

ADHD-associated PARK2 copy number variants: A pilot study on gene expression and effects of supplementary deprivation in patient-derived cell lines.

Recent studies show an association of Parkin RBR E3 ubiquitin protein ligase (PARK2) copy number variations (CNVs) with attention deficit hyperactivity disorder (ADHD). The aim of our pilot study to investigate gene expression associated with PARK2 CNVs in human-derived cellular models. We investigated gene expression in fibroblasts, hiPSC and dopaminergic neurons (DNs) of ADHD PARK2 deletion and duplication carriers by qRT PCR compared with healthy and ADHD cell lines without PARK2 CNVs. The selected 10genes of interest were associated with oxidative stress response (TP53, NQO1, and NFE2L2), ubiquitin pathway (UBE3A, UBB, UBC, and ATXN3) and with a function in mitochondrial quality control (PINK1, MFN2, and ATG5). Additionally, an exploratory RNA bulk sequencing analysis in DNs was conducted. Nutrient deprivation as a supplementary deprivation stress paradigm was used to enhance potential genotype effects. At baseline, in fibroblasts, hiPSC, and DNs, there was no significant difference in gene expression after correction for multiple testing. After nutrient deprivation in fibroblasts NAD(P)H-quinone-dehydrogenase 1 (NQO1) expression was significantly increased in PARK2 CNV carriers. In a multivariate analysis, ubiquitin C (UBC) was significantly upregulated in fibroblasts of PARK2 CNV carriers. RNA sequencing analysis of DNs showed the strongest significant differential regulation in Neurontin (NNAT) at baseline and after nutrient deprivation. Our preliminary results suggest differential gene expression in pathways associated with oxidative stress, ubiquitine-proteasome, immunity, inflammation, cell growth, and differentiation, excitation/inhibition modulation, and energy metabolism in PARK2 CNV carriers compared to wildtype healthy controls and ADHD patients.

Integrated Analyses of miRNome and Transcriptome Reveal the Critical Role of miRNAs Toward Heat Stress Response in Isochrysis galbana.

Isochrysis galbana is widely used in aquaculture as a bait microalgal species. High temperature (HT) can severely impair the development of I. galbana, exerting adverse effects on its yield. MicroRNAs (miRNAs) play an essential role in modulating stress-responsive genes. However, the role of miRNAs in response to HT in microalgae remains largely unexplored. In the present study, we identified several conserved and novel miRNAs in I. galbana through miRNome sequencing. Among these identified miRNAs, 22 miRNAs were differentially expressed in response to heat stress, and their target genes were predicted accordingly. Moreover, a comprehensive and integrated analysis of miRNome and transcriptome was performed. We found that six potential reversely correlated differentially expressed miRNA (DEM) and differentially expressed gene (DEG) pairs were associated with heat stress response (HSR) in I. galbana. The expressions of DEMs and DEGs were further verified using real-time quantitative PCR (RT-qPCR). Integrated analyses showed that miRNAs played fundamental roles in the regulatory network of HSR in I. galbana mainly by regulating some heat-responsive genes, including heat shock proteins (HSPs), reactive oxygen species (ROS) signaling-related genes, and specific key genes in the ubiquitination pathway. Our current study identified the first set of heat-responsive miRNAs from I. galbana and helped elucidate the miRNA-mediated HSR and resistance mechanisms in I. galbana. This new knowledge could provide ways to enhance its heat stress tolerance.

Ubiquitination pathway model for the barber’s pole worm – Haemonchus contortus

The ubiquitin-mediated pathway has been comprehensively explored in the free-living nematode Caenorhabditis elegans, but very little is known about this pathway in parasitic nematodes. Here, we inferred the ubiquitination pathway for an economically significant and pathogenic nematode – Haemonchus contortus – using abundant resources available for C. elegans. We identified 215 genes encoding ubiquitin (Ub; n = 3 genes), ubiquitin-activating enzyme (E1; one), -conjugating enzymes (E2s; 21), ligases (E3s; 157) and deubiquitinating enzymes (DUBs; 33). With reference to C. elegans, Ub, E1 and E2 were relatively conserved in sequence and structure, and E3s and DUBs were divergent, likely reflecting functional and biological uniqueness in H. contortus. Most genes encoding ubiquitination pathway components exhibit high transcription in the egg compared with other stages, indicating marked protein homeostasis in this early developmental stage. The ubiquitination pathway model constructed for H. contortus provides a foundation to explore the ubiquitin–proteasome system, crosstalk between autophagy and the proteasome system, and the parasite-host interactions. Selected E3 and DUB proteins which are very divergent in sequence and structure from host homologues or entirely unique to H. contortus and related parasitic nematodes may represent possible anthelmintic targets.

Emerging Role of Deubiquitinating Enzymes (DUBs) in Melanoma Pathogenesis.

Simple SummaryMetastatic melanoma is one of the most aggressive skin tumors with a poor prognosis. Despite the efficacy of immunotherapy and targeted therapies, advanced melanoma patients are often refractory to treatments and have high rates of relapse and death. A major challenge is to identify and understand the mechanisms associated with melanoma development and resistance to gold-standard therapies. Thus, new therapeutic strategies are needed. Ubiquitination is a post-translational modification that plays a crucial role in various cellular biological activities and participates in cancer pathogenesis, including melanoma. Here, we report on the deubiquitination enzymes (DUBs) and their ubiquitin-modified substrates and signaling pathways involved in melanoma progression.Metastatic melanoma is the leading cause of death from skin cancer. Therapies targeting the BRAF oncogenic pathway and immunotherapies show remarkable clinical efficacy. However, these treatments are limited to subgroups of patients and relapse is common. Overall, the majority of patients require additional treatments, justifying the development of new therapeutic strategies. Non-genetic and genetic alterations are considered to be important drivers of cellular adaptation mechanisms to current therapies and disease relapse. Importantly, modification of the overall proteome in response to non-genetic and genetic events supports major cellular changes that are required for the survival, proliferation, and migration of melanoma cells. However, the mechanisms underlying these adaptive responses remain to be investigated. The major contributor to proteome remodeling involves the ubiquitin pathway, ubiquitinating enzymes, and ubiquitin-specific proteases also known as DeUBiquitinases (DUBs). In this review, we summarize the current knowledge regarding the nature and roles of the DUBs recently identified in melanoma progression and therapeutic resistance and discuss their potential as novel sources of vulnerability for melanoma therapy.

The Ubiquitin-Proteasome System in Apoptosis and Apoptotic Cell Clearance.

Ubiquitination, a critical post-translational modification of proteins, refers to the covalent attachment of ubiquitin to the substrate and is involved in various biological processes such as protein stability regulation, DNA damage repair, and apoptosis, among others. E3 ubiquitin ligases are essential enzymes of the ubiquitin pathway with high substrate specificity and precisely regulate specific proteins’ turnover. As one of the most well-studied forms of programmed cell death, apoptosis is substantially conserved across the evolutionary tree. The final critical stage in apoptosis is the removal of apoptotic cells by professional and non-professional phagocytes. Apoptosis and apoptotic cell clearance are crucial for the normal development, differentiation, and growth of multicellular organisms, as well as their association with a variety of inflammatory and immune diseases. In this review, we discuss the role of ubiquitination and deubiquitination in apoptosis and apoptotic cell clearance.

Emerging Roles of Non-proteolytic Ubiquitination in Tumorigenesis.

Ubiquitination is a critical type of protein post-translational modification playing an essential role in many cellular processes. To date, more than eight types of ubiquitination exist, all of which are involved in distinct cellular processes based on their structural differences. Studies have indicated that activation of the ubiquitination pathway is tightly connected with inflammation-related diseases as well as cancer, especially in the non-proteolytic canonical pathway, highlighting the vital roles of ubiquitination in metabolic programming. Studies relating degradable ubiquitination through lys48 or lys11-linked pathways to cellular signaling have been well-characterized. However, emerging evidence shows that non-degradable ubiquitination (linked to lys6, lys27, lys29, lys33, lys63, and Met1) remains to be defined. In this review, we summarize the non-proteolytic ubiquitination involved in tumorigenesis and related signaling pathways, with the aim of providing a reference for future exploration of ubiquitination and the potential targets for cancer therapies.

Discovery of Potent Small-Molecule USP8 Inhibitors for the Treatment of Breast Cancer through Regulating ERα Expression.

Ubiquitin-specific protease 8 (USP8), belonging to the deubiquitinase family, has been implicated to be closely related to the occurrence of many malignant tumors, but only a few USP8-targeting inhibitors have been reported to date. In this study, we present virtual screening to discover novel hit candidates that inhibit the catalytic activity of USP8. Exploration of the structure-activity relationship led to the identification of compound DC-U4106, which binds to USP8 with a KD value of 4.7 μM and is selective over USP2 and USP7. Western blotting and immunoprecipitation showed that DC-U4106 could target the ubiquitin pathway and facilitate the degradation of ERα. In a xenograft tumor model, DC-U4106 also significantly inhibited tumor growth with minimal toxicity. Overall, our findings suggest that DC-U4106 is a promising drug candidate and targeting the USP8-ERα complex could be a new approach to treat ER-positive or drug-resistant breast cancer.

Proteomic Analysis Identifies p62/SQSTM1 as a Critical Player in PARP Inhibitor Resistance.

Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPis) are currently being used for treating breast cancer patients with deleterious or suspected deleterious germline BRCA-mutated, HER2-negative locally advanced or metastatic diseases. Despite durable responses, almost all patients receiving PARPis ultimately develop resistance and succumb to their illness, but the mechanism of PARPi resistance is not fully understood. To better understand the mechanism of PARPi resistance, we established two olaparib-resistant SUM159 and MDA468 cells by chronically exposing olaparib-sensitive SUM159 and MDA468 cells to olaparib. Olaparib-resistant SUM159 and MDA468 cells displayed 5-fold and 7-fold more resistance over their corresponding counterparts. Despite defects in PARPi-induced DNA damage, these olaparib-resistant cells are sensitive to cisplatin-induced cell death. Using an unbiased proteomic approach, we identified 6 447 proteins, of which 107 proteins were differentially expressed between olaparib-sensitive and -resistant cells. Ingenuity pathway analysis (IPA) revealed a number of pathways that are significantly altered, including mTOR and ubiquitin pathways. Among these differentially expressed proteins, p62/SQSTM1 (thereafter p62), a scaffold protein, plays a critical role in binding to and delivering the ubiquitinated proteins to the autophagosome membrane for autophagic degradation, was significantly downregulated in olaparib-resistant cells. We found that autophagy inducers rapamycin and everolimus synergistically sensitize olaparib-resistant cells to olaparib. Moreover, p62 protein expression was correlated with better overall survival in estrogen receptor-negative breast cancer. Thus, these findings suggest that PARPi-sensitive TNBC cells hyperactivate autophagy as they develop acquired resistance and that pharmacological stimulation of excessive autophagy could lead to cell death and thus overcome PARPi resistance.

The role of ubiquitin signaling pathway on liver regeneration in rats.

The ubiquitin signalling pathway is a large system associated with numerous intracellular mechanisms. However, its function in the liver regeneration process remains unknown. This particular study investigates the intracellular effect mechanisms of the ubiquitin signalling pathway. It also determines the differences in the expression of 88 genes belonging to the ubiquitin pathway using the RT-PCR array method. To conduct this research, three genes-that differed in the expression analysis were selected. Moreover, their proteins were analysed by western blot analysis while using Ki67 immunohistochemical analysis that determines proliferation rates by hour. It was determined that BRCA1 and BARD1, which are effective in DNA repair, play an active role at PH24. Similarly, Ube2t expression, which belongs to the Fanconi anaemia pathway associated with DNA repair, was also found to be high at PH12-72h. In addition, it was revealed that the expressions of Anapc2, Anapc11, Cdc20 belonging to the APC/CCdc20 complex, which participate in cell cycle regulation, differed at different hours after PH. Expression of Mul1, which is involved in mitochondrial biogenesis and mitophagy mechanisms, peaked at PH12 under the observation. Considering the Mul1 gene expression difference, MUL1-mediated mitophagy and mitochondrial fission mechanism may be associated with liver regeneration. It was also determined that PARKIN-mediated mitophagy mechanisms are not active in 0-72h of liver regeneration since PARKIN expression did not show a significant change in PH groups.

Abstract 3923: Ubiquitin ligases implicated as predictive biomarkers for poor outcome to immunotherapy in melanoma patients

Abstract Background From a medical standpoint, melanoma is considered the most serious form of skin cancer. Immunotherapy treatment regimes frequently target the PD1 pathway and can be highly effective. Despite successes some patients remain unresponsive and a better understanding of what underlies these non-responders could enable better patient treatment stratification and an overall higher positive response rate. Here using unbiased mass spectrometry (LC-MS) proteomics profiling, we sought to identify protein biomarker signatures in patients with metastatic melanoma that correlate with the patients’ intervention responses. Via this discovery-based approach we identify a panel of protein biomarkers that correlate with an improved treatment response and could serve as a panel for patient stratification prior to commencement of immunotherapy regimes. Methods Formalin-fixed paraffin-embedded (FFPE) tumor samples were used for unbiased quantification of proteins using data-independent acquisition (DIA) LC-MS technology and Biognosys’ Spectronaut software. Patient samples were analyzed at the start of treatment (PD1 inhibitor) and classified as responders (n = 9) or non-responders (n = 15) at 3 months post-treatment. Significant protein expression changes between the two groups was determined by t-test (p < 0.01, log2 fold-change > 0.58) and further machine learning-assisted analysis was conducted. Additionally, patient’s tumor mutational burden (TMB) was analyzed. Results Analysis of the FFPE samples from anti-PD1-treated metastatic melanoma patients resulted in the identification and quantification of more than 9,000 proteins in total with an average of nearly 8,000 proteins per sample. Stratification of the patients into responders and non-responders led to the identification of 103 proteins that are significantly up- or down-regulated between the groups. Interestingly, proteins associated with ubiquitination pathways were significantly enriched among the identified regulated proteins with 7 proteins having significantly lower abundance in responders when compared to non-responders including various members of the ubiquitin ligase family. Further, a proteomic signature was identified that characterizes the responder and non-responder groups. Conclusions In this study we demonstrate the power of unbiased proteomic profiling for the characterization of melanoma patients and their responses to PD1-targeted immunotherapy. We identify a set of biomarkers associated with ubiquitination pathways that correlate with treatment outcome although these findings need to further be confirmed in orthogonal cohorts. Citation Format: Nigel Beaton, Tobias Treiber, Anna Juncker-Jensen, Xin-Xing Tan, Julia Martinez Gomez, Mitchell Levesque, Jakob Vowinkel. Ubiquitin ligases implicated as predictive biomarkers for poor outcome to immunotherapy in melanoma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3923.

Abstract 678: Identification of an E3 ligase regulating the catalytic subunit of RNA polymerase I

Abstract RNA polymerase I (Pol I) is responsible for the transcription of ribosomal DNA (rDNA), the first and rate-limiting step of ribosome biogenesis. Pol I is the most active RNA polymerase, and it comprises over 60% of transcriptional activity in cancer cells. The robust transcriptional activity, coupled with the high density of elongating Pol I transcription complexes on the rDNA, renders Pol I vulnerable to transcriptional blocks. In healthy cells, this type of transcriptional stress activates inhibitory downstream cascades such as the p53 pathway. However, cancer cells elude this regulatory mechanism to sustain high levels of growth. Further, oncogenic drivers upregulate Pol I activity and achieve abnormally high rates of ribosome biogenesis. This makes Pol I a highly relevant target for cancer therapeutics. Yet little is known about the stability and regulation of the enzyme complex and whether this knowledge can be used for therapeutic purposes. Our lab recently discovered a first-in-class small molecule, BMH-21, that inhibits Pol I transcription and induces the degradation of the catalytic subunit of Pol I, RPA194. We showed that the inducible degradation of RPA194 is cancer cell-specific, correlated with cell death, and is mediated by the proteasome system. A detailed understanding of the degradation process will provide essential knowledge about the stability of the Pol I complex and benefit therapeutic implementation of Pol I inhibitory strategies. To identify the E3 ligases involved, we conducted a cell-based RNAi screen for ubiquitin pathway genes associated with RPA194 degradation. This screen identified a Skp-Cullin-F-box (SCF) complex as a promising candidate E3 ligase. We focused on validating the role of the identified F-box protein, FBXL14, in RPA194 degradation. To do this, we conducted knockout, knockdown, and overexpression analyses of FBXL14 in melanoma, osteosarcoma, breast cancer and chronic myelogenous leukemia cancer cell lines. We show here that both the basal expression of RPA194 and the BMH-21-induced degradation depend on FBXL14. The expression of FBXL14 significantly affected the half-life of RPA194. Knockdown of FBXL14 increases RPA194 turnover upon BMH-21 treatment, while its overexpression reduces RPA194 half-life. Using co-immunoprecipitation analyses, we demonstrate that FBXL14 interacts with RPA194 both in cell lines and in vitro. To investigate the correlation between RPA194 degradation and cell death, we analyzed how the expression of FBXL14 affects sensitivity to BMH-21 using cell growth, viability, and colony formation assays. We found that FBXL14 overexpression increased the sensitivity to the drug. Our results have revealed novel regulatory aspects of Pol I, showing that the stability of the catalytic subunit is controlled by the F-box protein FBXL14. We discuss the implications of these findings on Pol I transcription activity and its regulation. Citation Format: Stephanie Pitts, Hester Liu, Wenjun Fan, Brittany Ford, Ronald Hay, Marikki Laiho. Identification of an E3 ligase regulating the catalytic subunit of RNA polymerase I [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 678.

Ubiquitinating the way to T cell metabolism.

In this issue, Harris et al. (2022. J. Cell Biol.https://doi.org/10.1083/jcb.202203095) show that phosphofructokinase is a substrate for ubiquitination by Fbxo7, a key protein in the ubiquitination pathway. Their findings point to a new interplay between metabolic enzyme degradation in the regulation of T cells.

Proteomic analysis of adipose tissue revealing differentially abundant proteins in highly efficient mid-lactating dairy cows

The improvement of nutrient utilization efficiency in dairy cows represents an important task in view of the current rising demand for animal products and sustainable resource usage. In this perspective, the identification of appropriate markers to identify the most efficient animals for dairy production becomes a crucial factor. Residual feed intake (RFI), which represents the difference between predicted and actual intake, is used to define the efficiency of cows. In this study, subcutaneous adipose tissue (AT) was collected from five high efficient (HEF) and five low efficient (LEF) mid-lactation Holstein dairy cows, that represented subgroups of the 20% lowest RFI values (HEF) and highest 20% RFI values (LEF), out of a cohort of 155 cows that were examined for feed efficiency at the individual dairy barn at Volcani Institute, Israel. Adipose samples were examined for proteomic analysis by nano-LC/MS–MS and gene expression by RT-PCR. A total of 101 differential proteins (P ≤ 0.05 and fold change ± 1.5) and two protein networks related to feed efficiency were found between HEF and LEF cows. Among the enriched top canonical pathways, FAT10 signaling, EIF2 signaling, Sirtuin signaling, Acute phase response signaling, Protein ubiquitination and mTOR signaling pathways were related to feed efficiency in AT. Furthermore, abundance of transferrin (TF; FC = 78.35, P = 0.02) enriched pathways, including mTOR signaling, LXR/RXR and FXR/RXR activation was found in AT of HEF cows. Relative mRNA expression of RBM39, which is involved in energy metabolism, was decreased in AT of HEF versus LEF. The relationship found between the AT proteins and/or metabolic pathways and the feed efficiency demonstrates that AT may reflect metabolic adaptations to high efficiency, and suggests that these proteins together with their metabolic mechanisms are suitable candidates as biomarkers to identify efficient cows for dairy production.

Cartilage debris and osteoarthritis risk factors influence gene expression in the synovium in end stage osteoarthritis

BackgroundGene expression in healthy synovium remains poorly characterised. Thus, synovial functional activity changes associated with osteoarthritis (OA) are difficult to define. This study sought to identify differentially expressed genes (DEG) of end-stage OA and assess the influence of OA risk factors on these DEG. MethodsAnonymised patient clinical data and x-ray images were analysed. Osteoarthritic and non-osteoarthritic patients with soft tissue or traumatic knee injuries were matched for body mass index (BMI) and sex. Tissue samples were partitioned for immunocytochemistry (IHC) and microarray analysis. Multiple bioinformatics applications were utilised to determine changes in functional and canonical pathway activation. ResultsAge, disease-modifying injections and hypertension were confounding factors between patient groups. Inflammation was present in all tissues. Cartilage debris and inflammatory aggregates were noted in many osteoarthritic patient tissues. IHC and expression analyses revealed upregulation of synoviolin 1 (SYVN1) in osteoarthritic synovium. Significant differential expression was noted in 2084 genes. Osteoarthritic synovium displayed a significant upregulation of 95% of DEG coding for proteins, relative to non-osteoarthritic synovium tissues. Unfolded protein response (UPR)-related genes were upregulated in osteoarthritic synovium; gene expression of molecules within many canonical pathways including protein ubiquitination and UPR pathways was modified by BMI and sex. ConclusionsThe synovium of all three pathologies exhibited elements of an inflammatory response. Cartilage debris, age, BMI and sex influence DEG of osteoarthritic synovium. UPR pathway is the top deregulated canonical pathway identified in osteoarthritic synovium regardless of BMI and sex, while typical OA-associated inflammatory and matrix gene responses were minimal.

Ubiquitin Mediated Degradation of EGFR by 17 β-estradiol in Triple Negative MDA-MB-231 (TNBC) Breast Cancer Cells Line.

Triple Negative Breast Cancer (TNBC) commonly displays Epidermal growth factor receptor (EGFR). Effective EGFR degradation results in the suppression of tumor in various models. Studies have addressed the relevance of this strategy in the treatment of TNBC. In the present study, we examined the effect of 17 β- estradiol on EGFR expression in MDA-MB-231 (TNBC) cell line and assessed whether 17 β-estradiol degrades EGFR by ubiquitination pathway. The objective of this study is to treat MDA-MB-231 cell lines with Cycloheximide with or without 17β-estrdiol to observe whether 17β-estradiol leads to EGFR degradation and to treat with MG-132 to assess whether degradation occurs through ubiquitination pathway. MDA-MB-231 cells were treated with 17β-estradiol (E2) and EGFR expression was studied by western blotting at different intervals by using Cycloheximide chase. To assess ubiquitination pathway of degradation of EGFR in MDA-MB-231 cell line, MG-132 was used. EGFR expression was reduced with β-estradiol treatment in MDA-MB-231 cell line with Cycloheximide chase. Upon Treatment with MG-132 and E2, EGFR expression did not reduce, suggesting that Estrogen degrades EGFR by ubiquitination pathway. Estrogen degrades EGFR in MDA-MB-231 cells and this degradation occurs by ubiquitination.

Proteomic analysis of ubiquitinated proteins in ‘Xiangshui’ lemon [Citrus limon (L.)] pistils after self- and cross-pollination

‘Xiangshui’ lemon exhibits gametophyte self-incompatibility: after self-pollination, the growth of a pollen tube in the style is inhibited. The aim of this work was to study the effect of pollination on the ubiquitylome and proteome in ‘Xiangshui’ lemon pistil. Here, by using label-free quantification, enrichment by anti-diglycine lysine antibody conjugated agarose beads, high-resolution liquid chromatography tandem mass spectrometry (LC-MS/MS) and the method of shotgun proteomics, we investigated the quantitative proteome, ubiquitylome, and crosstalk between the two datasets in the ‘Xiangshui’ lemon pistil after pollination. In total, 4682 protein species, 1956 ubiquitinated protein species and 6922 ubiquitination sites were quantified. A principal component analysis revealed that there were some differences in the ubiquitylome and proteome of CK, self-pollination and cross-pollination. The results of the crosstalk showed that the proteome and ubiquitylome were negatively correlated. After self-pollination, the abundance of the ubiquitinated protein species related to programmed cell death, cell aging and sphingolipid metabolic pathways was changed. Furthermore, we analyzed the proteasome pathway in the pistil after self-pollination and further discussed the mechanism by which ubiquitination events affect S-RNase in the style. Overall, pollination greatly changed the ubiquitinated protein species abundance in the pistils of ‘Xiangshui’ lemon. Accordingly, our work provides a systematic analysis of the proteome and ubiquitylome in ‘Xiangshui’ lemon pistils under self-incompatibility and sheds light for future studies on the function and mechanism of ubiquitination during self-incompatibility in ‘Xiangshui’ lemon. SignificanceAs a mechanism to prevent self-pollination, self-incompatibility (SI) exists widely in plant species. Although a large number of SI-related genes have been found in fruit trees, there are few studies on the PTMs that affect and are involved in fruit tree responses to SI. This study highlights the fact that the effects of pollination on proteome and ubiquitylome in the ‘Xiangshui’ lemon pistil, we discussed the correlation between transcriptome and proteome, ubiquitylome and proteome, and we analyzed the expression and the changes of ubiquitination levels of SI related proteins and pathway after self- and cross pollination, and the changes of ubiquitination level of 26S proteasome pathway after cross-pollination. This study provides new insights into the ubiquitination pathway of SI in ‘Xiangshui’ lemon.

MDM2-Mediated Ubiquitination of RXRβ Contributes to Mitochondrial Damage and Related Inflammation in Atherosclerosis.

A novel function of retinoid X receptor beta (RXRβ) in endothelial cells has been reported by us during the formation of atherosclerosis. Here, we extended the study to explore the cellular mechanisms of RXRβ protein stability regulation. In this study, we discovered that murine double minute-2 (MDM2) acts as an E3 ubiquitin ligase to target RXRβ for degradation. The result showed that MDM2 directly interacted with and regulated RXRβ protein stability. MDM2 promoted RXRβ poly-ubiquitination and degradation by proteasomes. Moreover, mutated MDM2 RING domain (C464A) or treatment with an MDM2 inhibitor targeting the RING domain of MDM2 lost the ability of MDM2 to regulate RXRβ protein expression and ubiquitination. Furthermore, treatment with MDM2 inhibitor alleviated oxidized low-density lipoprotein-induced mitochondrial damage, activation of TLR9/NF-κB and NLRP3/caspase-1 pathway and production of pro-inflammatory cytokines in endothelial cells. However, all these beneficial effects were reduced by the transfection of RXRβ siRNA. Moreover, pharmacological inhibition of MDM2 attenuated the development of atherosclerosis and reversed mitochondrial damage and related inflammation in the atherosclerotic process in LDLr-/- mice, along with the increased RXRβ protein expression in the aorta. Therefore, our study uncovers a previously unknown ubiquitination pathway and suggests MDM2-mediated RXRβ ubiquitination as a new therapeutic target in atherosclerosis.

Silencing suppressors of rice black-streaked dwarf virus and rice stripe virus hijack the 26S proteasome of Laodelphax striatellus to facilitate virus accumulation and transmission.

Rice black-streaked dwarf virus (RBSDV) is transmitted by small brown planthopper (Laodelphax striatellus [L. striatellus]) and causes devastating disease in rice. P9-1 has silencing suppression activity and is the key protein for viroplasm formation in RBSDV-infected plants and insects; however, its exact function is poorly understood. In this study, the P9-1 of RBSDV interacted with L. striatellus 26S proteasome subunit RPN8. RBSDV accumulation in L. striatellus increased after the 26S proteasome was disrupted by silencing the RPN8 expression. This finding indicated that L. striatellus 26S proteasome played a defense role against RBSDV infection by regulating RBSDV accumulation. Further investigations revealed that P9-1 could competitively bind to RPN8 with RPN7, thereby disrupting the assembly of 26S proteasome in L. striatellus and promoting the infection of RBSDV in insect vectors, and further affecting the transmission of the virus to rice by insect vectors. Similar to P9-1, rice stripe virus (RSV) NS2, a weak silencing suppressor, regulated virus accumulation and transmission by hijacking RPN8 to interfere with the function of 26S proteasome in L. striatellus. These results suggest that viruses promote their own infection via interfering with ubiquitination pathway of insect vectors, and this mechanism might be of universal importance. These findings provide a new insight into the mechanism of virus transmission in insect vectors. © 2022 Society of Chemical Industry.