Proteasome-mediated Protein Degradation Research Articles

The Proteasome and Cul3-Dependent Protein Ubiquitination Is Required for Gli Protein-Mediated Activation of Gene Expression in the Hedgehog Pathway.

Many cellular processes are regulated by proteasome-mediated protein degradation, including regulation of signaling pathways and gene expression. Among the pathways regulated by the ubiquitin-proteasome system is the Hedgehog pathway and its downstream effectors, the Gli transcription factors. Here we provide evidence that proteasomal activity is necessary for maintaining the activation of the Hedgehog pathway, and this crucial event takes place at the level of Gli proteins. We undertook extensive work to demonstrate the specificity of the observed phenomenon by ruling out the involvement of primary cilium, impaired nuclear import, failed dissociation from Sufu, microtubule stabilization, and stabilization of Gli repressor forms. Moreover, we showed that proteasomal-inhibition-mediated Hedgehog pathway downregulation is not restricted to the NIH-3T3 cell line. We demonstrated, using CRISPR/Ca9 mutagenesis, that neither Gli1, Gli2, nor Gli3 are solely responsible for the Hedgehog pathway downregulation upon proteasome inhibitor treatment, and that Cul3 KO renders the same phenotype. Finally, we report two novel E3 ubiquitin ligases, Btbd9 and Kctd3, known Cul3 interactors, as positive Hedgehog pathway regulators. Our data pave the way for a better understanding of the regulation of gene expression and the Hedgehog signaling pathway.

Synergistic induction of mitotic pyroptosis and tumor remission by inhibiting proteasome and WEE family kinases

Mitotic catastrophe (MC), which occurs under dysregulated mitosis, represents a fascinating tactic to specifically eradicate tumor cells. Whether pyroptosis can be a death form of MC remains unknown. Proteasome-mediated protein degradation is crucial for M-phase. Bortezomib (BTZ), which inhibits the 20S catalytic particle of proteasome, is approved to treat multiple myeloma and mantle cell lymphoma, but not solid tumors due to primary resistance. To date, whether and how proteasome inhibitor affected the fates of cells in M-phase remains unexplored. Here, we show that BTZ treatment, or silencing of PSMC5, a subunit of 19S regulatory particle of proteasome, causes G2- and M-phase arrest, multi-polar spindle formation, and consequent caspase-3/GSDME-mediated pyroptosis in M-phase (designated as mitotic pyroptosis). Further investigations reveal that inhibitor of WEE1/PKMYT1 (PD0166285), but not inhibitor of ATR, CHK1 or CHK2, abrogates the BTZ-induced G2-phase arrest, thus exacerbates the BTZ-induced mitotic arrest and pyroptosis. Combined BTZ and PD0166285 treatment (named BP-Combo) selectively kills various types of solid tumor cells, and significantly lessens the IC50 of both BTZ and PD0166285 compared to BTZ or PD0166285 monotreatment. Studies using various mouse models show that BP-Combo has much stronger inhibition on tumor growth and metastasis than BTZ or PD0166285 monotreatment, and no obvious toxicity is observed in BP-Combo-treated mice. These findings disclose the effect of proteasome inhibitors in inducing pyroptosis in M-phase, characterize pyroptosis as a new death form of mitotic catastrophe, and identify dual inhibition of proteasome and WEE family kinases as a promising anti-cancer strategy to selectively kill solid tumor cells.

Distinct Regulation of ASCL1 by the Cell Cycle and Chemotherapy in Small Cell Lung Cancer.

Small cell lung cancer (SCLC) is an aggressive and lethal malignancy. Achaete-scute homolog 1 (ASCL1) is essential for the initiation of SCLC in mice and the development of pulmonary neuroendocrine cells (PNEC), which are the major cells of origin for SCLC. However, the regulatory mechanism of ASCL1 in SCLC remains elusive. Here, we found that ASCL1 expression gradually increases as the tumors grow in a mouse SCLC model, and is regulated by the cell cycle. Mechanistically, CDK2-CyclinA2 complex phosphorylates ASCL1, which results in increased proteasome-mediated ASCL1 protein degradation by E3 ubiquitin ligase HUWE1 during mitosis. TCF3 promotes the multisite phosphorylation of ASCL1 through the CDK2-CyclinA2 complex and the interaction between ASCL1 and TCF3 protects ASCL1 from degradation. The dissociation of TCF3 from ASCL1 during mitosis accelerates the degradation of ASCL1. In addition, chemotherapy drugs greatly reduce the transcription of ASCL1 in SCLC cells. Depletion of ASCL1 sensitizes SCLC cells to chemotherapy drugs. Together, our study demonstrates that ASCL1 is a cell-cycle-regulated protein and provides a theoretical basis for applying cell-cycle-related antitumor drugs in SCLC treatment. Implications:Our study revealed a novel regulatory mechanism of ASCL1 by cell cycle and chemotherapy drugs in SCLC. Treating patients with SCLC with a combination of ASCL1-targeting therapy and chemotherapy drugs could potentially be beneficial.

Restorative effects of (+)-epicatechin in a rodent model of aging induced muscle atrophy: underlying mechanisms.

Sarcopenia is a progressive and generalized age-related skeletal muscle (SkM) disorder characterized by the accelerated loss of muscle mass (atrophy) and function. SkM atrophy is associated with increased incidence of falls, functional decline, frailty and mortality. In its early stage, SkM atrophy is associated with increased pro-inflammatory cytokine levels and proteasome-mediated protein degradation. These processes also link to the activation of atrophy associated factors and signaling pathways for which, there is a lack of approved pharmacotherapies. The objective of this study, was to characterize the capacity of the flavanol (+)-epicatechin (+Epi) to favorably modulate SkM mass and function in a rat model of aging induced sarcopenia and profile candidate mechanisms. Using 23 month old male Sprague-Dawley rats, an 8 weeks oral administration of the +Epi (1 mg per kg per day in water by gavage) was implemented while control rats only received water. SkM strength (grip), treadmill endurance, muscle mass, myofiber area, creatine kinase, lactate dehydrogenase, troponin, α-actin, tumor necrosis factor (TNF)-α and atrophy related endpoints (follistatin, myostatin, NFκB, MuRF 1, atrogin 1) were quantified in plasma and/or gastrocnemius. We also evaluated effects on insulin growth factor (IGF)-1 levels and downstream signaling (AKT/mTORC1). Treatment of aged rats with +Epi, led to significant increases in front paw grip strength, treadmill time and SkM mass vs. controls as well as beneficial changes in makers of myofiber integrity. Treatment significantly reversed adverse changes in plasma and/or SkM TNF-α, IGF-1, atrophy and protein synthesis related endpoints vs. controls. In conclusion, +Epi has the capacity to reverse sarcopenia associated detrimental changes in regulatory pathways leading to improved SkM mass and function. Given these results and its recognized safety and tolerance profile, +Epi warrants consideration for clinical trials.

Blockade of angiotensin II modulates insulin-like growth factor 1-mediated skeletal muscle homeostasis in experimental steatohepatitis

Sarcopenia is associated with mortality in patients with nonalcoholic steatohepatitis (NASH). Angiotensin II receptor blocker (ARB) has been suggested to prevent sarcopenia, but reports on its effect on NASH-derived skeletal muscle atrophy in conjunction with insulin-like growth factor 1 (IGF-1)-mediated muscle homeostasis are few. Our aim was to examine the combined effect of the ARB losartan and IGF-1 replacement on skeletal muscle atrophy in a methionine–choline deficient (MCD) diet-fed murine steatohepatitis model. The MCD-fed mice developed steatohepatitis and skeletal muscle atrophy, as indicated by the reduction of psoas muscle mass and attenuation of forelimb and hindlimb grip strength. Significantly suppressed steatohepatitis and skeletal muscle atrophy was observed after single treatment with ARB or IGF-1, and these effects were augmented after combination treatment. Treatment with ARB and IGF-1 effectively inhibited ubiquitin proteasome-mediated protein degradation by reducing forkhead box protein O1 (FOXO1) and FOXO3a transcriptional activity in the skeletal muscle. Combined ARB and IGF-1 decreased the intramuscular expression of proinflammatory cytokines (i.e., TNFα, IL6, and IL1β) and increased the Trolox equivalent antioxidant capacity and antioxidant enzymes (CAT, GPX1, SOD2, and CYTB). This antioxidant effect was based on downregulation of NADPH oxidase (NOX) 2, normalization of mitochondrial biogenesis and dynamics. Moreover, ARB increased the hepatic and plasma IGF-1 levels and improved steatohepatitis, leading to enhanced skeletal muscle protein synthesis mediated by IGF-1/ AKT/ mechanistic target of rapamycin signaling. Collectively, combined ARB and IGF-1 replacement could be a promising new therapeutic target for NASH-derived skeletal muscle wasting.

Ethanol extract of Herpetospermum caudigerum Wall ameliorates psoriasis-like skin inflammation and promotes degradation of keratinocyte-derived ICAM-1 and CXCL9

ObjectiveTo explore whether the ethanol extract of Herpetospermum caudigerum Wall (EHC), a Xizang medicinal plant traditionally used for treating liver diseases, can improve imiquimod-induced psoriasis-like skin inflammation. MethodsImmunohistochemistry and immunofluorescence staining were used to determine the effects of topical EHC use in vivo on the skin pathology of imiquimod-induced psoriasis in mice. The protein levels of interferon-γ (IFN-γ), tumor necrosis factor-α (TNF-α), and interleukin-17A (IL-17A) in mouse skin samples were examined using immunohistochemical staining. In vitro, IFN-γ-induced HaCaT cells with or without EHC treatment were used to evaluate the expression of keratinocyte-derived intercellular cell adhesion molecule-1 (ICAM-1) and chemokine CXC ligand 9 (CXCL9) using Western blotting and reverse transcription-quantitative polymerase chain reaction. The protein synthesis inhibitor cycloheximide and proteasome inhibitor MG132 were utilized to validate the EHC-mediated mechanism underlying degradation of ICAM-1 and CXCL9. ResultsEHC improved inflammation in the imiquimod-induced psoriasis mouse model and reduced the levels of IFN-γ, TNF-α, and IL-17A in psoriatic lesions. Treatment with EHC also suppressed ICAM-1 and CXCL9 in epidermal keratinocytes. Further mechanistic studies revealed that EHC suppressed keratinocyte-derived ICAM-1 and CXCL9 by promoting ubiquitin–proteasome-mediated protein degradation rather than transcriptional repression. Seven primary compounds including ehletianol C, dehydrodiconiferyl alcohol, herpetrione, herpetin, herpetotriol, herpetetrone and herpetetrol were identified from the EHC using ultra-performance liquid chromatography-quadrupole-time of flight-mass spectrometry. ConclusionTopical application of EHC ameliorates psoriasis-like skin symptoms and improves the inflammation at the lesion sites.Please cite this article as: Zhong Y, Zhang BW, Li JT, Zeng X, Pei JX, Zhang YM, Yang YX, Li FL, Deng Y, Zhao Q. Ethanol extract of Herpetospermum caudigerum Wall ameliorates psoriasis-like skin inflammation and promotes degradation of keratinocyte-derived ICAM-1 and CXCL9. J Integr Med. 2023; Epub ahead of print.

Selective Inhibition of mTORC1 Signaling Supports the Development and Maintenance of Pluripotency.

Insight into the molecular mechanisms governing the development and maintenance of pluripotency is important for understanding early development and the use of stem cells in regenerative medicine. We demonstrate the selective inhibition of mTORC1 signaling is important for developing the inner cell mass (ICM) and the self-renewal of human embryonic stem cells. S6K suppressed the expression and function of pluripotency-related transcription factors (PTFs) OCT4, SOX2, and KLF4 through phosphorylation and ubiquitin proteasome-mediated protein degradation, indicating that S6K inhibition is required for pluripotency. PTFs inhibited mTOR signaling. The phosphorylation of S6 was decreased in PTF-positive cells of the ICM in embryos. Activation of mTORC1 signaling blocked ICM formation and the selective inhibition of S6K by rapamycin increased the ICM size in mouse blastocysts. Thus, selective inhibition of mTORC1 signaling supports the development and maintenance of pluripotency.

1H, 15N, 13C resonance assignments for proteasome shuttle factor hHR23a.

hHR23a (human homolog of Rad23 a) functions in nucleotide excision repair and proteasome-mediated protein degradation. It contains an N-terminal ubiquitin-like (UBL) domain, an xeroderma pigmentosum C (XPC)-binding domain, and a ubiquitin-associated (UBA) domain preceding and following the XPC-binding domain. Each of the four structural domains are connected by flexible linker regions. We report in this NMR study, the 1H, 15N and 13C resonance assignments for the backbone and sidechain atoms of the hHR23a full-length protein with BioMagResBank accession number 52059. Assignments are 97% and 87% for the backbone (NH, N, C', Cα, and Hα) and sidechain atoms of the hHR23a structured regions. The secondary structural elements predicted from the NMR data fit well to the hHR23a NMR structure. The assignments described in this manuscript can be used to apply NMR for studies of hHR23a with its binding partners.

Wild-type and pathogenic forms of ubiquilin 2 differentially modulate components of the autophagy-lysosome pathways

Missense mutations of ubiquilin 2 (UBQLN2) have been identified to cause X-linked amyotrophic lateral sclerosis (ALS). Proteasome-mediated protein degradation is reported to be impaired by ALS-associated mutations of UBQLN2. However, it remains unknown how these mutations affect autophagy-lysosome protein degradation, which consists of macroautophagy (MA), microautophagy (mA), and chaperone-mediated autophagy (CMA). Using a CMA/mA fluorescence reporter we found that overexpression of wild-type UBQLN2 impairs CMA. Conversely, knockdown of endogenous UBQLN2 increases CMA activity, suggesting that normally UBQLN2 negatively regulates CMA. ALS-associated mutant forms of UBQLN2 exacerbate this impairment of CMA. Using cells stably transfected with wild-type or ALS-associated mutant UBQLN2, we further determined that wild-type UBQLN2 increased the ratio of LAMP2A (a CMA-related protein) to LAMP1 (a lysosomal protein). This could represent a compensatory reaction to the impairment of CMA by wild-type UBQLN2. However, ALS-associated mutant UBQLN2 failed to show this compensation, exacerbating the impairment of CMA by mutant UBQLN2. We further demonstrated that ALS-associated mutant forms of UBQLN2 also impair MA, but wild-type UBQLN2 does not. These results support the view that ALS-associated mutant forms of UBQLN2 impair both CMA and MA which may contribute to the neurodegeneration observed in patients with UBQLN2-mediated ALS.

1H, 15N, 13C backbone and Cβ resonance assignments for UBQLN1 UBA and UBAA domains

UBQLN1 functions in autophagy and proteasome-mediated protein degradation. It contains an N-terminal ubiquitin-like domain (UBL), a C-terminal ubiquitin-associated domain (UBA), and a flexible central region which functions as a chaperone to prevent protein aggregation. Here, we report the 1H, 15N, and 13C resonance assignments for the backbone (NH, N, C’, Cα, and Hα) and sidechain Cβ atoms of the UBQLN1 UBA and an N-terminally adjacent segment called the UBA-adjacent domain (UBAA). We find a subset of the resonances corresponding to the UBAA to have concentration-dependent chemical shifts, likely due to self-association. We also find the backbone amide nitrogen of T572 to be shifted upfield relative to the average value for a threonine amide nitrogen, a phenomenon likely caused by T572 Hγ1 engagement in a hydrogen bond with adjacent backbone carbonyl atoms. The assignments described in this manuscript can be used to study the protein dynamics of the UBQLN1 UBA and UBAA as well as the interaction of these domains with other proteins.

Neuronal and astrocytic protein degradation are critical for fear memory formation.

Strong evidence has implicated proteasome-mediated protein degradation in the memory consolidation process. However, due to the use of pharmacological approaches, the cell type specificity of this remains unknown. Here, we used neuron-specific and novel astrocyte-specific CRISPR-dCas9-KRAB-MECP2 plasmids to inhibit protein degradation in a cell type-specific manner in the amygdala of male rats. We found that while inhibition of neuronal, but not astrocytic, protein degradation impaired performance during the training session, both resulted in impaired contextual fear memory retention. Together, these data provide the first evidence of a cell type-specific role for protein degradation in the memory consolidation process.

USP41 Enhances Epithelial-Mesenchymal Transition of Breast Cancer Cells through Snail Stabilization.

Ubiquitination, one of many post-translational modifications, causes proteasome-mediated protein degradation by attaching ubiquitin to target proteins. Multiple deubiquitinases inhibit the ubiquitination pathway by removing the ubiquitin chain from protein, thus contributing to the stabilization of substrates. USP41 contributes to invasion, apoptosis and drug resistance in breast and lung cancer cells. However, the detailed mechanism and role of USP41 in breast cancer have not been elucidated. USP41 was overexpressed and showed poor prognosis according to the aggressive phenotype of breast cancer cells. Knockdown of USP41 inhibited migration and growth of breast cancer cells, whereas overexpression of USP41 increased cell growth and migration. In addition, depletion of USP41 downregulated Snail protein expression, an epithelial-mesenchymal transition marker, but not mRNA expression. Furthermore, USP41 interacted with and inhibited ubiquitination of Snail, resulting in the increase in Snail stabilization. Therefore, these data demonstrated that USP41 increases migration of breast cancer cells through Snail stabilization.

Inhibition of RNF182 mediated by Bap promotes non-small cell lung cancer progression.

Ubiquitylation that mediated by ubiquitin ligases plays multiple roles not only in proteasome-mediated protein degradation but also in various cellular process including DNA repair, signal transduction and endocytosis. RING finger (RNF) proteins form the majority of these ubiquitin ligases. Recent studies have demonstrated the important roles of RNF finger proteins in tumorigenesis and tumor progression. Benzo[a]pyrene (BaP) is one of the most common environmental carcinogens causing lung cancer. The molecular mechanism of Bap carcinogenesis remains elusive. Considering the critical roles of RNF proteins in tumorigenesis and tumor progression, we speculate on whether Bap regulates RNF proteins resulting in carcinogenesis. We used GEO analysis to identify the potential RING finger protein family member that contributes to Bap-induced NSCLC. We next used RT-qPCR, Western blot and ChIP assay to investigate the potential mechanism of Bap inhibits RNF182. BGS analyses were used to analyze the methylation level of RNF182. Here we reported that the carcinogen Bap suppresses the expression of ring finger protein 182 (RNF182) in non-small cell lung cancer (NSCLC) cells, which is mediated by abnormal hypermethylation in an AhR independent way and transcriptional regulation in an AhR dependent way. Furthermore, RNF182 exhibits low expression and hypermethylation in tumor tissues. RNF182 also significantly suppresses cell proliferation and induces cell cycle arrest in NSCLC cell lines. These results demonstrated that Bap inhibits RNF182 expression to promote lung cancer tumorigenesis through activating AhR and promoting abnormal methylation.

Proteomics to Metabolomics: A New Insight into the Pathogenesis of Hypertensive Nephropathy

Background: Hypertensive nephropathy (HN) is a high-burden disorder and a leading cause of end-stage renal disease. Despite huge investigations, the underlying mechanisms are yet largely unknown. Systems biology is a promising approach to providing a comprehensive insight into this complex disorder. Methods: Proteome profiles of kidney tubulointerstitium and outer and inner cortex from a rat model of HN were retrieved from the proteomics identification database, and the quality of the datasets was assessed. Proteins that exhibited differential expression were detected and their interactions were analyzed in the kidney sub-compartments. Furthermore, enzymes were linked to the attributed metabolites. Functional enrichment analyses were performed to identify key pathways and processes based on the differentially expressed proteins and predicted metabolites. Results: Proteasome-mediated protein degradation, actin cytoskeleton organization, and Rho GTPase signaling pathway are involved in the pathogenesis of HN. Furthermore, tissue hypoxia and dysregulated energy homeostasis are among the key underlying events. The metabolism of purine and amino acids is also affected in HN. Conclusion: Although the proposed pathogenic mechanisms remain to be further validated in experimental studies, this study contributes to the understanding of the molecular mechanisms of HN through a systematic unsupervised approach. Considering the significant alterations of metabolic pathways, HN can be viewed as an “acquired error of metabolism.”

EFFECTS OF FLAVANOL (+)-EPICATECHIN ON SKELETAL MUSCLE OF AGED RATS

Abstract Sarcopenia is a progressive and generalized age-related skeletal muscle (SkM) disorder characterized by the accelerated loss of muscle mass (atrophy) and function. SkM atrophy is associated with increased incidence of falls, functional decline, frailty and mortality. In its early stage, SkM atrophy is associated with oxidative stress, increased pro-inflammatory cytokine levels and proteasome-mediated protein degradation. These processes also link to the activation of atrophy associated factors and signaling pathways which lack any approved, targeted pharmacotherapy. We have characterized the capacity of flavanols specifically, epicatechin to favorably modulate SkM mass and function in animal models of SkM disease and in proof of concept studies in humans including muscular dystrophies. In this study we wished to evaluate the capacity of this flavanol to ameliorate aging associated sarcopenia. Using 24-month-old male rats a 4 week oral administration of the flavanol (+)-epicatechin (1mg/kg/day) was implemented while control rats only received vehicle (water). SkM strength (grip) and endurance (treadmill walk), muscle size, (muscle mass, cross sectional area of fibers), ubiquitin-proteasome atrophic pathway (including myostatin, Murf1 and Atrogin1 by Western blots) and markers of oxidative stress and inflammation in gastrocnemius were quantified. We also analyzed a relevant protein synthesis pathway (IGF/AKT/mTOR). The use of (+)-epicatechin in aged rats led to significant changes as follows: 1) improved SkM mass and function, 2) downregulation of atrophic pathway, 3) reduced levels of oxidative stress and proinflammatory cytokines and, 4) upregulation of protein synthesis pathway. Given its safety and tolerance profile this agent warrant its rigorous investigation in clinical trials.

HSP70-HSP90 Chaperone Networking in Protein-Misfolding Disease.

Molecular chaperones and their associated co-chaperones are essential in health and disease as they are key facilitators of protein-folding, quality control and function. In particular, the heat-shock protein (HSP) 70 and HSP90 molecular chaperone networks have been associated with neurodegenerative diseases caused by aberrant protein-folding. The pathogenesis of these disorders usually includes the formation of deposits of misfolded, aggregated protein. HSP70 and HSP90, plus their co-chaperones, have been recognised as potent modulators of misfolded protein toxicity, inclusion formation and cell survival in cellular and animal models of neurodegenerative disease. Moreover, these chaperone machines function not only in folding but also in proteasome-mediated degradation of neurodegenerative disease proteins. This chapter gives an overview of the HSP70 and HSP90 chaperones, and their respective regulatory co-chaperones, and explores how the HSP70 and HSP90 chaperone systems form a larger functional network and its relevance to counteracting neurodegenerative disease associated with misfolded proteins and disruption of proteostasis.

SNF1-related protein kinase 1 represses Arabidopsis growth through post-translational modification of E2Fa in response to energy stress.

Cellular sugar starvation and/or energy deprivation serves as an important signaling cue for the live cells to trigger the necessary stress adaptation response. When exposed to cellular energy stress (ES) conditions, the plants reconfigure metabolic pathways and rebalance energy status while restricting vegetative organ growth. Despite the vital importance of this ES-induced growth restriction, the regulatory mechanism underlying the response remains largely elusive in plants. Using plant cell- and whole plant-based functional analyses coupled with extended genetic validation, we show that cellular ES-activated SNF1-related protein kinase 1 (SnRK1.1) directly interacts with and phosphorylates E2Fa transcription factor, a critical cell cycle regulator. Phosphorylation of E2Fa by SnRK1.1 leads to its proteasome-mediated protein degradation, resulting in S-phase repression and organ growth restriction. Our findings show that ES-dependently activated SnRK1.1 adjusts cell proliferation and vegetative growth for plants to cope with constantly fluctuating environments.

UBI-XGB: IDENTIFICATION OF UBIQUITIN PROTEINS USING MACHINE LEARNING MODEL

A recent line of research has focused on Ubiquitination, a pervasive and proteasome-mediated protein degradation that controls apoptosis and is crucial in the breakdown of proteins and the development of cell disorders, is a major factor. The turnover of proteins and ubiquitination are two related processes. We predict ubiquitination sites; these attributes are lastly fed into the extreme gradient boosting (XGBoost) classifier. We develop reliable predictors computational tool using experimental identification of protein ubiquitination sites is typically labor- and time-intensive. First, we encoded protein sequence features into matrix data using Dipeptide Deviation from Expected Mean (DDE) features encoding techniques. We also proposed 2nd features extraction model named dipeptide composition (DPC) model. It is vital to develop reliable predictors since experimental identification of protein ubiquitination sites is typically labor- and time-intensive. In this paper, we proposed computational method as named Ubipro-XGBoost, a multi-view feature-based technique for predicting ubiquitination sites. Recent developments in proteomic technology have sparked renewed interest in the identification of ubiquitination sites in a number of human disorders, which have been studied experimentally and clinically. When more experimentally verified ubiquitination sites appear, we developed a predictive algorithm that can locate lysine ubiquitination sites in large-scale proteome data. This paper introduces Ubipro-XGBoost, a machine learning method. Ubipro-XGBoost had an AUC (area under the Receiver Operating Characteristic curve) of 0.914% accuracy, 0.836% Sensitivity, 0.992% Specificity, and 0.839% MCC on a 5-fold cross validation based on DPC model, and 2nd 0.909% accuracy, 0.839% Sensitivity, 0.979% Specificity, and 0. 0.829% MCC on a 5-fold cross validation based on DDE model. The findings demonstrate that the suggested technique, Ubipro-XGBoost, outperforms conventional ubiquitination prediction methods and offers fresh advice for ubiquitination site identification.

Exosome Mirnas Profiling in Serum and Prognostic Evaluation in Patients with Multiple Myeloma

Objective: Multiple Myeloma (MM) is a hematological malignancy characterized by the clonal expansion of malignant proliferation of plasma cells in the bone marrow. Moreover, the proliferation of MM cells is highly dependent on the BM microenvironment. MicroRNA (MiRNAs) are short, noncoding RNAs that regulate gene expression at the posttranscriptional level. MiRNAs carried by exosomes play pivotal roles in the crosstalk and signal transferring between malignant cells and non-malignant cells, which are involved in the pathogenesis of MM. Here, we investigated the exosome miRNA profiling in peripheral blood serum of MM patients and compared it with healthy donors. Bioinformatics analysis was utilized to clarify the molecular pathways associated with exosome miRNAs via their target genes. Furthermore, a prognostic model based on the top 20 hub genes was constructed in MM. Methods and materials: The serum samples including 19 newly diagnosed MM patients and 9 healthy donors were analyzed. Exosome in serum was isolated and miRNA profiling was investigated. Differential expression of miRNAs in exosomes was calculated between MM patients and HDs using the edgeR package. STRING and CytoHubba were applied to identify the hub miRNAs and core mRNAs. The exosomal miRNA-mRNA regulatory network was constructed. Functional enrichment of the core target genes was implemented using Metascape. The ESTIMATE immune scores were used to analyze the infiltration levels of immune cells in MM patients with GSE136324. The proportion of 22 tumor-infiltration immune cells in each MM patient was calculated using the CIBERSORT score. Multivariate Cox analysis of hub mRNAs was utilized to construct a novel prognostic model based on the top 20 hub genes. Results: In the present study, we found 353 differentially expressed exo-miRNAs between MM patients and healthy donors, and 9564 target mRNAs by 353 exo-miRNAs were predicted. GO and KEGG analysis of target mRNAs showed that they were involved in biological processes including proteasome-mediated ubiquitin-dependent protein degradation process. The exosomal miRNA-mRNA regulatory network was constructed and six hub miRNAs were identified. Target genes of these six hub miRNAs and the differential expressed genes (DEG) in Zhan Myeloma were intersected, and 513 DEGs targeted by hub miRNAs were identified. The protein-protein interaction (PPI) network was established in the STRING database. According to module analysis, the top 3 three modules were identified in the PPI network including mRNA splicing, cellular response to stress, and deubiquitination. Moreover, a module related to cytokine-related signaling pathways was enriched as well. Further analysis suggests that Interleukin 6 Signal Transducer (IL6ST), Tyrosine Kinase 2 (TYK2), and Adenosine Deaminase (ADAR) exhibited high correlations with immune scores in MM and were significantly associated with infiltration of CD4 T cell subtypes including follicular helper T cells and CD4 naïve T cells. Taken together, these findings suggested that IL6ST, TYK2, and ADAR might play pivotal roles in tumor immune escape. In addition, the top 20 hub genes were selected from the PPI network. Multivariate Cox regression analysis showed that the 20 hub genes-based signature could be utilized to construct a prognostic model. Conclusions: In conclusion, our study successfully depicted the exo-miRNA expression profiles in serum exosomes of MM patients and constructed the miRNA-mRNA regulatory network. A novel prognostic model based on 20 hub genes is constructed that facilitates the risk stratification of MM patients with distinct outcomes.

Identification of the Proteasome Subunits PSMB4 and PSMD4 As Novel Targets in Multiple Myeloma Patients Carrying 1q21 Amplification

Gain and/or amplification of the 1q21 (1q21+) region is one of the most frequent secondary cytogenetic abnormalities present in multiple myeloma (MM) patients. Interestingly, it has been reported that the incidence of the amplification of chromosome 1q (Amp1q) in patients with pre-malignant smoldering myeloma (SMM) is about 40%. Several data indicate that the presence of Amp1q is associated with a worse clinical outcome and a poor response to therapies including proteasome inhibitors (PIs). Recently, a study showed that newly diagnosed MM (NDMM) carrying Amp1q receiving carfilzomib-based treatment have an early disease progression and shorter overall survival, compared to those with 1q21 gain. The genes driving amplification of the 1q21 region have not been fully elucidated. This study aims to identify novel targets in the 1q21 region possibly correlated to PIs treatment. We purified CD138+ plasma cells (PCs) by immunomagnetic beads from bone marrow (BM) aspirates. We used a total cohort of 29 MM patients: 11 SMM and 18 NDMM. Fluorescent in situ hybridization analysis was performed on all the patients. 48% (14/29) patients carried 1q21+. A score indicating the number of 1q21 copies was calculated based on the FISH hybridization pattern of each patient. The expression profile of all 29 samples was generated using GeneChip ClariomD Arrays (Affymetrix Inc., Santa Clara, CA, USA). The smar package was used to identify differentially expressed genes between 1q21+ and control samples. The expression profile of our cohort showed that the expression of both proteasome subunits, PSMB4 and PSMD4 was significantly upregulated in MM patients Amp1q compared to control patients (PSMB4 p=0.0006; PSMD4p=<0.0001 respectively). Additionally, we found a strong positive correlation between gene expression levels and 1q21 copy number for the proteasome subunits PSMB4 (p=<0.0001, r=0.5631) and PSMD4 (p=<0.0001, r=0.6391). Interestingly, the PSMB4 and PSMD4 expression levels were independent of the disease stage (SMM vs MM) and the expression was driven exclusively by the 1q21 copy number. We evaluated PSMB4 and PSMD4 mRNA and protein expression levels in a 1q21 wild-type MM cell line (OCI-MY5) and a panel of MM cell lines carrying 1q21+. Our results showed that PSMB4 and PSMD4 expression levels were higher in cell lines with Amp1q, following a 1q21 copy number fashion. Subsequently, we assessed the role of PSMB4 and PSMD4 to the sensibility of PI bortezomib in two myeloma cell lines carrying 1q21+. Our results showed that bortezomib treatment downregulates the protein expression of PSMD4 while PSMB4 was unaffected. Moreover, the MTT viability test correlated with the anti-myeloma effect of bortezomib. Furthermore, we generated a JJN3 PSMB4 and PSMD4-knockdown MM cell line using short hairpin RNA (shRNA) lentivectors. An empty vector was used as a control plasmid. Cell viability and apoptosis assays were performed using MTT assay and Apo 2.7 staining. Our functional studies showed that shPSMB4 and shPSMD4 decreased MM cell viability when treated with PI. Moreover, both shPSMB4 and shPSMD4 knockdown cells showed elevated levels of polyubiquitylated proteins, indicating blockade of proteasome-mediated protein degradation. In conclusion, our study identified proteasome subunits PSMB4 and PSMD4 to be significantly upregulated in MM patients carrying 1q21+, correlated with 1q21 copy number but not with disease stage. Therefore, targeting PSMB4 and PSMD4 could be a strategy to treat MM patients with 1q21+.