Interacting Protein Research Articles

Interactome Analysis Reveals a Link of the Novel ALMS1-CEP70 Complex to Centrosomal Clusters

Alström syndrome (ALMS) is a very rare autosomal-recessive disorder, causing a broad range of clinical defects most notably retinal degeneration, type 2 diabetes, and truncal obesity. The ALMS1 gene encodes a complex and huge ∼0.5MDa protein, which has hampered analysis in the past. The ALMS1 protein is localized to the centrioles and the basal body of cilia and is involved in signaling processes, for example, TGF-β signaling. However, the exact molecular function of ALMS1 at the basal body remains elusive and controversial. We recently demonstrated that protein complex analysis utilizing endogenously tagged cells provides an excellent tool to investigate protein interactions of ciliary proteins. Here, CRISPR/Cas9-mediated endogenously tagged ALMS1 cells were used for affinity-based protein complex analysis. Centrosomal and microtubule-associated proteins were identified, which are potential regulators of ALMS1 function, such as the centrosomal protein 70kDa (CEP70). Candidate proteins were further investigated in ALMS1-deficient hTERT-RPE1 cells. Loss of ALMS1 led to shortened cilia with no change in structural protein localization, for example, acetylated and ɣ-tubulin, Centrin-3, or the novel interactor CEP70. Conversely, reduction of CEP70 resulted in decreased ALMS1 at the ciliary basal body. Complex analysis of CEP70 revealed domain-specific ALMS1 interaction involving the TPR-containing C-terminal (TRP-CT) fragment of CEP70. In addition to ALMS1, several ciliary proteins, including CEP135, were found to specifically bind to the TPR-CT domain. Data are available via ProteomeXchange with the identifier PXD046401. Protein interactors identified in this study provide candidate lists that help to understand ALMS1 and CEP70 function in cilia-related protein modification, cell death, and disease-related mechanisms.

Structure-guided screening of protein-protein interaction for the identification of Myc-Max heterodimer complex modulators

De-regulation of oncogenic myelocytomatosis (c-Myc or Myc) transcription factor is one of the most common molecular anomalies encountered in human cancers, and it is typically linked to many aggressive malignancies including breast, lung, cervix, colon glioblastomas, and other haematological organs. The Myc belongs to the basic helix-loop-helix zipper protein family (bHLH-ZIP), and its dimerization with another principal interactor protein partner Myc-associated factor X (Max) is essentially required for cellular transformation, cell growth and proliferation, and transcriptional activation. Intermolecular interactions have been evaluated between hetero-dimer Myc-Max protein, which identified protein-protein interaction (PPI) specific modulators using highly précised molecular docking study followed by long-range interaction stability analyzed through molecular dynamic (MD) simulation. Moreover, ADME profile analyses have been estimated for screened hit compounds. MM-GBSA-based binding free energy (ΔG) estimations have been performed for all screened hit compounds obtained from multi-step molecular docking-based virtual screening technique. According to the employed various rigorous multi-chemometric techniques, four identified inhibitors/modulators appear to have a considerable number of intermolecular contacts with hotspot residues in the hetero-dimer interface region of the Myc-Max PPI complex. However, identified hit compounds might need further structural optimization or extensive biophysical analyses for better understanding of the molecular mechanism for exhibiting the Myc-Max PPI interface binding stability. Communicated by Ramaswamy H. Sarma

Defining Distinct RNA-Protein Interactomes of SARS-CoV-2 Genomic and Subgenomic RNAs.

Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different aspects of viral replication. Here, for the first time, we demonstrate the successful isolation of SARS-CoV-2 genomic RNA and three distinct sgRNAs (N, S, and ORF8) from a single population of infected cells and characterize their protein interactomes. Over 500 protein interactors (including 260 previously unknown) were identified as associated with one or more target RNA. These included protein interactors unique to a single RNA pool and others present in multiple pools, highlighting our ability to discriminate between distinct viral RNA interactomes despite high sequence similarity. Individual interactomes indicated viral associations with cell response pathways, including regulation of cytoplasmic ribonucleoprotein granules and posttranscriptional gene silencing. We tested the significance of three protein interactors in these pathways (APOBEC3F, PPP1CC, and MSI2) using siRNA knockdowns, with several knockdowns affecting viral gene expression, most consistently PPP1CC. This study describes a new technology for high-resolution studies of SARS-CoV-2 RNA regulation and reveals a wealth of new viral RNA-associated host factors of potential functional significance to infection.

Proteome landscape and interactome of voltage-gated potassium channel 1.6 (Kv1.6) of the murine ophthalmic artery and neuroretina

The voltage-gated potassium channel 1.6 (Kv1.6) plays a vital role in ocular neurovascular beds and exerts its modulatory functions via interaction with other proteins. However, the interactome and their potential roles remain unknown. Here, the global proteome landscape of the ophthalmic artery (OA) and neuroretina was mapped, followed by the determination of Kv1.6 interactome and validation of its functionality and cellular localization. Microfluorimetric analysis of intracellular [K+] and Western blot validated the native functionality and cellular expression of the recombinant Kv1.6 channel protein. A total of 54, 9 and 28 Kv1.6-interacting proteins were identified in the mouse OA and, retina of mouse and rat, respectively. The Kv1.6-protein partners in the OA, namely actin cytoplasmic 2, alpha-2-macroglobulin and apolipoprotein A-I, were implicated in the maintenance of blood vessel integrity by regulating integrin-mediated adhesion to extracellular matrix and Ca2+ flux. Many retinal protein interactors, particularly the ADP/ATP translocase 2 and cytoskeleton protein tubulin, were involved in endoplasmic reticulum stress response and cell viability. Three common interactors were found in all samples comprising heat shock cognate 71 kDa protein, Ig heavy constant gamma 1 and Kv1.6 channel. This foremost in-depth investigation enriched and identified the elusive Kv1.6 channel and, elucidated its complex interactome.

Interactome‐guided machine learning modeling reveals information embedded in blood plasma protein‐protein interactions in Alzheimer’s Disease patients treated by the complex plasma fraction GRF6019

AbstractBackgroundThe relevance of plasma fraction treatment to reverse age‐related conditions was underlined by our previous pre‐clinical results. In two Phase 2 clinical trials (GRF6019‐201 and GRF6019‐202), patients with Alzheimer’s Disease (AD) were treated with the complex plasma fraction GRF6019, which was determined to be safe and well‐tolerated. Interestingly, no cognitive decline and minimal functional decline were observed. While GRF6019 treatment was associated with a quick and widespread proteomics response, lasting molecular changes were more subtle. Here, we developed new machine learning models guided by protein‐protein interaction (PPI) information to deeper understand the molecular effects of GRF6019 plasma fraction treatment.MethodMore than 7k proteins were measured in 120 plasma samples from treated subjects enrolled in the GRF6019‐201 and GRF6019‐202 trials (n = 21 and 18, respectively) using the Somascan assay. Interacting protein pairs were curated from STRING and OmniPath PPI databases. For each protein‐protein interaction, linear Support Vector Machine (SVM) models were trained to separate before and after treatment samples based on measured protein levels and compared to single‐protein models. Proteins were ranked based on their individual performance and their gain of performance when combined with interaction partnersResultProteasome‐associated elements were overrepresented among proteins with top individual performance. Interaction models provided more details about related processes involving ubiquitination. Furthermore, various other immune, hormonal, and neuronal terms found to be enriched among the top interactors.ConclusionComplex biological functions can be mapped into pathways which are composed of and regulated by PPIs. Biological functionality can be encoded in concentrations of individual proteins, also in relative concentrations of interacting proteins. Our results indicate that the latter aspect may contain a significant amount of complementary information, not accessible with traditional approaches analyzing proteins as independent entities. Consequently, the development and the application of novel system biology tools on blood plasma proteomics will help to better understand patients’ responses to treatment in clinical trials.

The cytoskeletal protein Plectin regulates Tau‐induced neurotoxicity in Alzheimer’s Disease

AbstractBackgroundThe genetic causes for most cases of Alzheimer’s disease (AD) and the underlying biology of pathogenesis remain unknown. Recent large scale proteomics studies on AD patient brains have identified novel protein networks and targets that are highly correlated with AD diagnosis and neuropathology. The most significantly AD‐correlated protein network identified contains the cytoskeletal protein Plectin (PLEC) as a network hub. PLEC functions to crosslink different cytoskeletal components and plays a role in axonal transport of synaptic proteins. Considering that microtubule associated protein‐Tau (MAPT) dysfunction is an AD hallmark, we hypothesize that PLEC dysfunction increases AD susceptibility by disrupting cytoskeletal homeostasis and synaptic function.MethodUtilizing a combination of genetic and proteomic analyses, we validate Plectin as a potential AD risk factor. We assessed the role of PLEC in Tau‐induced neurotoxicity in the animal model Drosophila melanogaster and human neuronal cell culture. Furthermore, we have also elucidated PLEC mutant neurodegenerative phenotypes independent of Tau overexpression in the fly. Immunoprecipitation‐mass spectrometry (IP‐MS) analysis was performed to define a Drosophila Plectin protein‐protein interaction network in adult brains. This network will serve as the basis for cross‐species analysis of protein networks.ResultThe Drosophila homolog of Plectin (dPLEC) is ubiquitously expressed within the adult brain with strong enrichment in neuronal rich tissues. Using Drosophila models of human tauopathy, dPLEC regulates age dependent Tau‐induced neurotoxicity and locomotor dysfunction. Plus, altering levels dPLEC regulates Tau‐phosphorylation in both adult Drosophila brains and human neurons. In the absence of Tau overexpression, dPLEC functions in light‐induced neuronal transmission confirming its role in normal neuronal function. Continued mechanistic analysis in both Drosophila and human neuronal cultures will determine PLEC’s role in AD neuropathogenesis and elucidate the underlying role of the cytoskeleton in AD susceptibility. To that end, we generated an endogenous GFP‐tagged dPLEC (dPLEC‐GFP) and performed immunoprecipitation‐mass spectrometry (IP‐MS) analysis to identify dPLEC protein interactors. Several cytoskeletal and synaptic proteins were identified and are currently being tested for their role in Tau‐induced neurodegeneration and synaptic dysfunction.ConclusionWe functionally validate the AD target PLEC as a regulator of Tau‐induced neurodegeneration and identify PLEC as a regulator of Tau dynamics and neuronal function.

Target prioritization using human genetics – anchored protein – protein interactions network for Parkinson’s Disease

AbstractBackgroundAdvancements in genome‐wide association studies (GWAS) have provided pivotal information about genes that are genetically associated to disease conditions. For example, Parkinson’s Disease GWAS studies and GWAS meta‐analysis has provided many candidate genes representing various pathways associated with Parkinson’s Disease, e.g., Lysosomes, mitochondrial dysfunction, Syn‐aggregation, etc. Amongst them, Leucine‐rich repeat kinase 2 (LRRK2) is one of the strongest candidates for PD therapeutic and many compounds targeting LRRK2 are already under clinical trials. To optimize therapeutic effects, protein interactors of LRRK2 could be targeted. We hypothesized that instead of selecting GWAS candidate itself, e.g., LRRK2, exploring a network of interacting proteins to GWAS candidates could give us better understanding of the genetic link to disease biology and hence better targets for therapeutic success.MethodWe created genetically anchored protein‐protein interaction network for Parkinson’s Disease from genes having strong genetic link to PD (seed genes) and all proteins interacting with any of the seed genes. These networks were uploaded and visualized on our in‐house tool – PDNet, a network‐based visual analytics prototype to analyze the network modules and propose candidates for potential therapeutic target prioritization in PD. Published and internally generated gene expression data is used to identify differentially expressed genes that fit in pathways implicated in PD.ResultPathway crosstalk were observed amongst different pathways and hub‐genes were identified that could be potential key drivers of the network in the disease progression and help in understanding the disease pathology. Multiple parameters were computed for the prioritization of the candidate genes, that have the highest score of an indirect genetic link to PD and could be good target for consideration based on other OMICS evidence. The experimental target evaluation of these candidates has narrowed down targets for further screening for drug discovery.ConclusionOur GWAS‐based network analysis framework provides a new way of identifying targets that are genetically involved in the disease but doesn’t show strong signal in GWAS analysis.

Computational identification of precision therapeutics for Alzheimer’s disease specific to endocrine and APOE genotype status

AbstractBackgroundAlzheimer’s disease (AD) affects 6.5 million people in the US, two‐thirds of which are women. Despite extensive research, there are currently no highly effective treatments for AD. The greatest risk factors for AD are age, chromosomal female sex and APOEε4 genotype. A key driver of chronological and endocrinological aging is the activation of innate and adaptive immune systems occurring in midlife female brain. To effectively prevent and treat AD, it is crucial to develop computational methods that take into account these factors and screen for personalized therapeutics.MethodRNAseq data of 15‐month acyclic vs 9‐month regular APOEε3/ε3 and APOEε4/ε4 female mouse models were analyzed to identify APOE‐specific Differentially Expressed Genes (DEGs, pvalue<.01). STRING Protein‐Protein Interaction (PPI) database was used to extract protein interactors for the two APOEε3/ε3 and APOEε4/ε4 DEG lists and construct two APOE‐specific AD PPI networks. Target Proteins (TPs) candidates in each network were identified using the DrugBank database by selecting only proteins targeted by at least one FDA‐approved drug. A score of drug synergy was developed to rank FDA‐approved drugs based on the number of target proteins in‐ vs out‐ of the APOE‐AD specific networks and their distance to DEG nodes.ResultFrom RNAseq analyses, we identified a total of 265 DEGs for APOEε3/ε3 and 452 DEGs for APOEε4/ε4 genotype. The APOE‐AD‐specific PPI networks resulted in 1,711 nodes (proteins) and 21,445 edges (PPIs) for the APOEε3/ε3 genotype and 2,841 nodes and 35,493 edges for APOEε4/ε4 genotype. Using the DrugBank database, 342 and 568 potential therapeutic targets were identified in the APOEε3/ε3 and APOEε4/ε4 networks, respectively. Finally, drug synergy score enabled ranking 99 therapeutics for APOEε3/ε3 network and 102 drugs for APOEε4/ε4 network, of which 19 resulted in both lists.ConclusionThis study presents a network‐based approach for identifying personalized therapeutics for AD based on endocrine transition changes and APOE genotype. The results suggest that there is greater transcriptomic dysregulation in female APOEε4/ε4 brains compared to APOEε3/ε3 brains. The proposed computational approach has the potential to advance precision medicine for the prevention and treatment of AD, and future research will focus on identifying the most effective combinations of therapeutics.

Abstract A108: Metabolic oriented treatment: efficacy of sr59230a 𝜷3-adrenergic receptor antagonist, and sr plus buformin® in Ewing sarcoma

Abstract Purpose of study: Metabolic targeted therapies may represent an innovative strategy in Ewing sarcoma (ES). Introduction: Ewing sarcoma (ES) is highly aggressive round cell mesenchymal neoplasm, most often occurring in children and young adults. Metabolic peculiarities of ES cells are indeed involved in tumor growth, survival and resistance to therapy. We have further investigated apoptotic role of 𝜷3-adrenergic receptor (𝜷3-AR) SR59230A (SR) antagonist for its ability to reduce cells viability due increased oxidative stress, now we underline the metabolic role of SR. Materials & Methods: The metabolic profile after SR administration in A673 ES cell model was studied using the Seahorse XF Analyzer. Viability was evaluated with MTS. Changes in gene expression was evaluated with RNA sequencing. Western blot analysis and Immunofluorescence was performed for redox signature and metabolic alteration. Ros production was assessed by flow cytometry. Results: Quantification of transcript abundance using Salmon in A673 after SR treatment showed decrease in response to reactive oxygen species, increase of Thioredoxin Interacting Protein (TXNIP) inhibits the antioxidative function of thioredoxin, moreover reduced glucose uptake, consequently decrease NADPH/NADP resulting in the accumulation of ROS coincident with a decrease of GLUT1, SOD2, TrDX an increase of LC3IIA protein expression. SR enhances A673 pyruvate dependency, and decrease glyco and mito ATP production rate, more over observed under glucose deprivation. To inibite mitochondrial ATP production rate we proposed the metabolic oriented treatment with Buformin® (BUF) an oral antidiabetic drug of the biguanide class. BUF completely shut down mitochondrial respiration acted on complex I of electron transport chain (ETC). Buf combined with SR decrease ATP production and up-regulated ROS production in ES cells. Conclusion: SR antagonist of 𝜷3-AR and combination of SR with BUF could be an innovative therapeutic option to raise awareness ES. Citation Format: Cristina Banella, Laura Zocca, Alessia Boaretto, Gianluca Mattei, Marina Mola, Lara Ballerini, Lorito Nicla, Annalisa Tondo, Maura Calvani. Metabolic oriented treatment: efficacy of sr59230a 𝜷3-adrenergic receptor antagonist, and sr plus buformin® in Ewing sarcoma [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A108.

Integrative Analysis of PAIP2B to Identify a Novel Biomarker for Pancreatic Ductal Adenocarcinoma.

The aim of the study was to evaluate the potential diagnostic and prognostic value of gene, Poly A-Binding Protein Interacting Protein 2B ( PAIP2B ) in pancreatic cancer. We used the gene expression data and clinical information of pancreatic adenocarcinoma patients from The Cancer Genome Atlas database and Gene Expression Omnibus database to analyze the expression of PAIP2B in pancreatic cancer samples, and validated the expression of PAIP2B in tumor tissue, using bioinformatics technology to explore the prognostic value of PAIP2B and its possible biological function. A significantly lower level of PAIP2B was observed in pancreatic cancer patients than in controls, and validated by immunohistochemistry. PAIP2B reduced the proliferation and invasion of cancer cells and had a significantly high expression in early stage. Patients with lower levels of PAIP2B had a significantly shorter median survival time than those with higher levels. DNA demethylation played an important role in PAIP2B expression. In addition, PAIP2B expression was significantly associated with the tumor-infiltrating immune cells, especially T cells CD8, T cells CD4 memory resting, macrophages M0, and dendritic cells resting. Our study also found that PAIP2B regulated miRNA function leading to disease progression in pancreatic cancer patients. Our study explored the potential value of PAIP2B as a biological link between prognosis and pancreatic cancer, and provided reference for the follow-up study on the role of PAIP2B in pancreatic cancer.

Biological Function of Rab11-Family Interacting Protein 4 in the Development of Preeclampsia and Their Underlying Mechanism

To elucidate the biological function of Rab11-FIP4 in the development of preeclampsia, as well as its clinical significance and underlying mechanism. Relative levels of Rab11-FIP4, IL-6 and TNF-α in placental tissues of PE pregnant women and healthy pregnant women were detected by qRT-PCR. The correlation between Rab11-FIP4 and IL-6 or TNF-α was assessed by Pearson correlation test. After constructing overexpression lentivirus targeting Rab11-FIP4, its influences on biological characteristics of HTR-8/SVneo cells and expression levels of inflammatory cytokines were examined. Rab11-FIP4 was highly expressed in placental tissues of PE pregnant women. Overexpression of Rab11-FIP4 enhanced migratory and invasive capacities of trophoblasts, and upregulated inflammatory proteins. Rab11-FIP4 aggravates the development of PE by upregulating inflammatory proteins, and stimulating migratory and invasive capacities of trophoblasts.

Peptide-Mediated Cyclic Nucleotide Signaling in Plants: Identification and Characterization of Interactor Proteins with Nucleotide Cyclase Activity.

During the last decades, an increasing number of plant signaling peptides have been discovered and it appears that many of them are specific ligands for interacting receptor molecules. These receptors can enable the formation of second messengers which in turn transmit the ligand-induced stimuli into complex and tunable downstream responses. In order to perform such complex tasks, receptor proteins often contain several distinct domains such as a kinase and/or adenylate cyclase (AC) or guanylate cyclase (GC) domains. ACs catalyze the conversion of ATP to 3',5'-cyclic adenosine monophosphate (cAMP) while GCs catalyze the reaction of GTP to 3',5'-cyclic guanosine monophosphate (cGMP). Both cAMP and cGMP are now recognized as essential components of many plant responses, including responses to peptidic hormones. Here we describe the approach that led to the discovery of the Plant Natriuretic Peptide Receptor (PNP receptor), including a protocol for the identification of currently undiscovered peptidic interactions, and the subsequent application of computational methods for the identification of AC and/or GC domains in such interacting receptor candidates.

Identification and characterization of ARID1A-interacting proteins in renal tubular cells and their molecular regulation of angiogenesis

BackgroundDefects and deficiency of AT-rich interactive domain-containing protein 1A (ARID1A) encoded by a tumor suppressor gene ARID1A have recently been suggested to get involved in angiogenesis, a crucial process in carcinogenesis. However, molecular mechanisms of ARID1A deficiency to induce angiogenesis in kidney cancer remain underinvestigated.MethodsWe performed large-scale identification of ARID1A protein interactors in renal tubular epithelial cells (RTECs) using immunoprecipitation (IP) followed by nanoLC-ESI-LTQ-Orbitrap tandem mass spectrometry (MS/MS). Their roles in angiogenesis were investigated using various assays.ResultsA total of 74 ARID1A-interacting proteins were identified. Protein–protein interactions analysis revealed that these identified proteins interacted directly or indirectly with ARID1A. Among them, the direct interaction between ARID1A and β-actin was validated by IP and reciprocal IP followed by Western blotting. Small interfering RNA (siRNA) was used for single and double knockdowns of ARID1A and ACTB. Semi-quantitative RT-PCR demonstrated that deficiency of ARID1A, but not ACTB, significantly affected expression of angiogenesis-related genes in RTECs (VEGF and FGF2 were increased, whereas PDGF and EGF were decreased). However, the knockdowns did not affect TGFB1 and FGF1 levels. The quantitative mRNA expression data of VEGF and TGFB1 were consistent with the secreted levels of their protein products as measured by ELISA. Only secreted products derived from ARID1A-deficient RTECs significantly increased endothelial cells (ECs) migration and tube formation. Some of the other carcinogenic features could also be confirmed in the ARID1A-deficient RTECs, including increased cell migration and chemoresistance. Double knockdowns of both ARID1A and ACTB did not enhance the effects of single ARID1A knockdown in all assays.ConclusionsWe report herein a large dataset of the ARID1A-interacting proteins in RTECs using an IP-MS/MS approach and confirm the direct interaction between ARID1A and β-actin. However, the role of ARID1A deficiency in angiogenesis is independent of β-actin.

Mitochondrial protein BNIP3 regulates Chikungunya virus replication in the early stages of infection.

Chikungunya virus (CHIKV) is a human pathogen causing outbreaks of febrile illness for which vaccines and specific treatments remain unavailable. Autophagy-related (ATG) proteins and autophagy receptors are a set of host factors that participate in autophagy, but have also shown to function in other unrelated cellular pathways. Although autophagy is reported to both inhibit and enhance CHIKV replication, the specific role of individual ATG proteins remains largely unknown. Here, a siRNA screen was performed to evaluate the importance of the ATG proteome and autophagy receptors in controlling CHIKV infection. We observed that 7 out of 50 ATG proteins impact the replication of CHIKV. Among those, depletion of the mitochondrial protein and autophagy receptor BCL2 Interacting Protein 3 (BNIP3) increased CHIKV infection. Interestingly, BNIP3 controls CHIKV independently of autophagy and cell death. Detailed analysis of the CHIKV viral cycle revealed that BNIP3 interferes with the early stages of infection. Moreover, the antiviral role of BNIP3 was found conserved across two distinct CHIKV genotypes and the closely related Semliki Forest virus. Altogether, this study describes a novel and previously unknown function of the mitochondrial protein BNIP3 in the control of the early stages of the alphavirus viral cycle.

Blockage of CacyBP inhibits macrophage recruitment and improves anti-PD-1 therapy in hepatocellular carcinoma

BackgroundDespite remarkable advancements in cancer immunotherapy, the overall response rate to anti-programmed cell death-1 (anti-PD-1) therapy in hepatocellular carcinoma (HCC) patients remains low. Our previous study has demonstrated the critical role of CacyBP/SIP (Calcyclin-Binding Protein and Siah-1 Interacting Protein) as a regulator of HCC development and progression. However, the possible impact of CacyBP on the tumor immune microenvironment has not yet been clarified.MethodsThe expressions of CacyBP and Myd88 in HCC cell lines and tissues was detected by bioinformatics analysis, real-time quantitative PCR, western blotting and immunohistochemistry. The interaction between CacyBP and Myd88 was measured using co-immunoprecipitation and immunofluorescence. In vitro and in vivo assays were used to investigate the regulation of CacyBP on tumor-associated macrophages (TAMs).ResultsWe identified that CacyBP was positively correlated with Myd88, a master regulator of innate immunity, and Myd88 was a novel binding substrate downstream of CacyBP in HCC. Additionally, CacyBP protected Myd88 from Siah-1-mediated proteasome-dependent degradation by competitively binding to its Toll/interleukin-1 receptor (TIR) domain. Inhibition of CacyBP-Myd88 signaling subsequently diminished HDAC1-mediated H3K9ac and H3K27ac modifications on the CX3CL1 promoter and reduced its transcription and secretion in HCC cells. Moreover, by using in vitro and in vivo strategies, we demonstrated that depletion of CacyBP impaired the infiltration of TAMs and the immunosuppressive state of the tumor microenvironment, further sensitizing HCC-bearing anti-PD-1 therapy.ConclusionsOur findings suggest that targeting CacyBP may be a novel treatment strategy for improving the efficacy of anti-PD-1 immunotherapy in HCC.

Ergolide mediates anti-cancer effects on metastatic uveal melanoma cells and modulates their cellular and extracellular vesicle proteomes.

Uveal melanoma is a poor prognosis cancer. Ergolide, a sesquiterpene lactone isolated from Inula Brittanica, exerts anti-cancer properties. The objective of this study was to 1) evaluate whether ergolide reduced metastatic uveal melanoma (MUM) cell survival/viability in vitro and in vivo; and 2) to understand the molecular mechanism of ergolide action. Ergolide bioactivity was screened via long-term proliferation assay in UM/MUM cells and in zebrafish MUM xenograft models. Mass spectrometry profiled proteins modulated by ergolide within whole cell or extracellular vesicle (EVs) lysates of the OMM2.5 MUM cell line. Protein expression was analyzed by immunoblots and correlation analyses to UM patient survival used The Cancer Genome Atlas (TCGA) data. Ergolide treatment resulted in significant, dose-dependent reductions (48.5 to 99.9%; p<0.0001) in OMM2.5 cell survival in vitro and of normalized primary zebrafish xenograft fluorescence (56%; p<0.0001) in vivo, compared to vehicle controls. Proteome-profiling of ergolide-treated OMM2.5 cells, identified 5023 proteins, with 52 and 55 proteins significantly altered at 4 and 24 hours, respectively ( p<0.05; fold-change >1.2). Immunoblotting of heme oxygenase 1 (HMOX1) and growth/differentiation factor 15 (GDF15) corroborated the proteomic data. Additional proteomics of EVs isolated from OMM2.5 cells treated with ergolide, detected 2931 proteins. There was a large overlap with EV proteins annotated within the Vesiclepedia compendium. Within the differentially expressed proteins, the proteasomal pathway was primarily altered. Interestingly, BRCA2 and CDKN1A Interacting Protein (BCCIP) and Chitinase Domain Containing 1 (CHID1), were the only proteins significantly differentially expressed by ergolide in both the OMM2.5 cellular and EV isolates and they displayed inverse differential expression in the cells versus the EVs. Ergolide is a novel, promising anti-proliferative agent for UM/MUM. Proteomic profiling of OMM2.5 cellular/EV lysates identified candidate pathways elucidating the action of ergolide and putative biomarkers of UM, that require further examination.

Spatial Mechano-Signaling Regulation of GTPases through Non-Degradative Ubiquitination.

Blood flow produces shear stress exerted on the endothelial layer of the vessels. Spatial characterization of the endothelial proteome is required to uncover the mechanisms of endothelial activation by shear stress, as blood flow varies in the vasculature. An integrative ubiquitinome and proteome analysis of shear-stressed endothelial cells demonstrated that the non-degradative ubiquitination of several GTPases is regulated by mechano-signaling. Spatial analysis reveals increased ubiquitination of the small GTPase RAP1 in the descending aorta, a region exposed to laminar shear stress. The ubiquitin ligase WWP2is identified as a novel regulator of RAP1 ubiquitination during shear stress response. Non-degradative ubiquitination fine-tunes the function of GTPases by modifying their interacting network. Specifically, WWP2-mediated RAP1 ubiquitination at lysine 31 switches the balance from the RAP1/ Talin 1 (TLN1)toward RAP1/ Afadin (AFDN) or RAP1/ RAS Interacting Protein 1 (RASIP1) complex formation, which is essential to suppress shear stress-induced reactive oxygen species (ROS) production and maintain endothelial barrier integrity. Increased ROS production in endothelial cells in the descending aorta of endothelial-specific Wwp2-knockout mice leads to increased levels of oxidized lipids and inflammation. These results highlight the importance of the spatially regulated non-degradative ubiquitination of GTPases in endothelial mechano-activation.

Abstract 13959: A Role for Striated Muscle Nuclear Receptor Co-Regulator RIP140 ( Nrip1 ) in the Control of Endurance Fitness

During the development of heart failure (HF), the capacity for myocardial fatty acid oxidation (FAO) and oxidative phosphorylation is reduced, leading to an energy-starved state. Similar metabolic derangements occur in skeletal muscle during HF and with physical inactivity associated with chronic disease states. Receptor Interacting Protein 140 (RIP140) is a nuclear receptor co-regulator that has been shown to repress the transcription of genes involved in mitochondrial energy transduction in highly metabolic tissues. We recently demonstrated that striated muscle-specific RIP140 KO mice (str-RIP140 -/- ) were protected against the development of HF and had an adaptive form of cardiac hypertrophy (PMID: 36927960). To assess the impact of RIP140 deficiency on skeletal muscle function, we conducted physiological and genomic interrogation of str-RIP140 -/- mice. We found that the str-RIP140 -/- mice display an endurance performance phenotype. Specifically, str-RIP140 -/- mice run significantly longer on an endurance treadmill regimen (str-RIP140 -/- = 118.0 min, WT= 73.38 min; p= &lt;0.0001) with increased VO 2max compared to controls (str-RIP140 -/- = 9779 ml/kg/hr, WT= 7748 ml/kg/hr; p= &lt;0.0001). Respiratory Exchange Ratio (RER) was maintained at a decreased level during exercise in str-RIP140 -/- mice vs controls, indicative of increased utilization and capacity for FAO. The response of str-RIP140 -/- mice to endurance exercise training was also assessed. str-RIP140 -/- mice achieved a greater VO 2max following 8 weeks of training compared to control trained mice (str-RIP140 -/- = 9589 ml/kg/hr, WT= 8366 ml/kg/hr; p= 0.002). RNA-sequence analysis comparing RIP140 -/- and control fast-twitch muscle (EDL) prior to and following exercise training identified differentially upregulated genes involved in an array of pathways activated with endurance training including mitochondrial FAO, triglyceride turnover, the slow-twitch fiber program, angiogenesis, and components of the neuromuscular junction. We conclude that RIP140 serves as a co-repressor of a network of genes involved in skeletal muscle endurance. These results suggest that RIP140 could prove to be a target for novel metabolic therapies aimed at cardiac and skeletal muscle diseases.

Canagliflozin Inhibits Hedgehog Interacting Protein (Hhip)-Mediated Renal Tubular Cell Senescence in Type 1 Akita Mice

Canagliflozin Inhibits Hedgehog Interacting Protein (Hhip)-Mediated Renal Tubular Cell Senescence in Type 1 Akita Mice

Prognostic Value of Immunohistochemical Expression of MTAP and AKIP1 in IDH1 Mutant Astrocytoma.

Definite treatment for glioma is not exist, and with increased drug resistance, more effort should be paid to identify new prognostic biomarkers and molecular targets for therapy for glioma patients. The current study aimed to evaluate the immunohistochemical (IHC) expression of MTAP and A-Kinase Interacting Protein 1 (AKIP1) in astrocytoma and to investigate their association with the clinicopathological characters of these cases. Totally 66 cases of astrocytoma patients involved in this study. Cases underwent tumor resection and tissue sections were stained with MTAP, AKIP1 and IDH1 by IHC and evaluated in different grades of astrocytoma and their association with survival and response to therapy was investigated. High AKIP1 expression was positively correlated with treatment resistance and progressive disease. Positive IDH and retained MTAP expressions had shown better treatment response rather than negative IDH and lost MTAP. High AKIP, negative IDH and loss of MTAP expressions were significantly associated with poor survival outcome. Irrespective to grade and IDH status, the loss of MTAP immunoreactivity and high AKIP1 expression are predictive factors in astrocytoma, and they may be used as a biomarker for guiding astrocytoma management and prognosis surveillance.