Ribonucleoprotein Complex Biogenesis Research Articles

Construction of a miRNA-mRNA Network Related to Exosomes in Colon Cancer

Background The competing endogenous RNA (CeRNA) network plays important roles in the occurrence and development of colon cancer. This research is aimed at constructing a miRNA-mRNA network associated with exosomes in colon cancer. Methods We explored the GEO database and then analyzed the RNAs of 722 samples to obtain differentially expressed miRNAs (DEMs) and mRNAs (DEGs) alongside the progress of colon cancer. Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEM target genes and DEGs were performed. In addition, a miRNA-mRNA network related to exosomes in colon cancer was constructed based on DEMs and DEGs. Finally, the expression of miRNA and mRNA in the network was verified by GEPIA2 on the base of TCGA database. Results Through our analysis, 19 DEMs (17 up and 2 down) and 1672 DEGs (954 up and 718 down) were screened. The GO and KEGG results show that these DEGs were mainly enriched in ribonucleoprotein complex biogenesis, noncoding RNA metabolic process, cell-substrate junction, cadherin binding, transcription coregulator activity, and regulation of the human T-cell leukemia virus 1 infection-related pathway. Besides, a miRNA-mRNA network, including 4 miRNAs (hsa-miR-623, hsa-miR-320c, hsa-miR-486-5p, and hsa-miR-1290) and 7 mRNAs (GNAI1, CADM1, PGRMC2, etc.), was constructed. Three of these seven mRNAs were downregulated in colon cancer. Ultimately, the GNAI1, CADM1, and PGRMC2 expression levels were verified by TCGA database. Conclusions This study reveals the network relationship between colon cancer exosome-derived miRNA and targeted mRNA. It deepens our understanding of new molecular mechanisms and pathways that may play a role in the occurrence and metastasis of colon cancer.

Comprehensive Effects of Flowering Locus T-Mediated Stem Growth in Tobacco.

In flowering plants, Flowering locus T (FT) encodes a major florigen. It is a key flowering hormone in controlling flowering time and has a wide range of effects on plant development. Although the mechanism by which FT promotes flowering is currently clearly understood, comprehensive effects of the FT gene on plant growth have not been evaluated. Therefore, the effects of FT on vegetative growth need to be explored for a complete understanding of the molecular functions of the FT gene. In this study, the Jatropha curcas L. FT gene was overexpressed in tobacco (JcFTOE) in order to discover multiple aspects and related mechanisms of how the FT gene affects plant development. In JcFTOE plants, root, stem, and leaf development was strongly affected. Stem tissues were selected for further transcriptome analysis. In JcFTOE plants, stem growth was affected because of changes in the nucleus, cytoplasm, and cell wall. In the nucleus of JcFTOE plants, the primary effect was to weaken all aspects of DNA replication, which ultimately affected the cell cycle and cell division. The number of stem cells decreased significantly in JcFTOE plants, which decreased the thickness and height of tobacco stems. In the cell wall of JcFTOE plants, hemicellulose and cellulose contents increased, with the increase in hemicellulose associated with up-regulation of xylan synthase-related genes expression. In the cytoplasm of JcFTOE plants, the primary effects were on biogenesis of ribonucleoprotein complexes, photosynthesis, carbohydrate biosynthesis, and the cytoskeleton. In addition, in the cytoplasm of JcFTOE plants, there were changes in certain factors of the core oscillator, expression of many light-harvesting chlorophyll a/b binding proteins was down-regulated, and expression of fructose 1,6-bisphosphatase genes was up-regulated to increase starch content in tobacco stems. Changes in the xylem and phloem of JcFTOE plants were also identified, and in particular, xylem development was affected by significant increases in expression of irregular xylem genes.

The Role of RNA-Binding Protein HuR in Lung Cancer by RNA Sequencing Analysis.

Background: The overexpression of human antigen R (HuR) has been proven in various types of cancer and is associated with the poor survival lung cancer patients. HuR overexpression stabilizes the mRNA of tumor-promoting genes by binding with 3′-UTR AU-rich elements. However, the role of HuR in the proliferation of lung cancer is unclear. Methods: HuR expression was assessed using immunohistochemistry of tumor tissue samples from ten patients with lung cancer and ten patients with benign lung disease. Gene, protein, mRNA, and lncRNA changes in A549 HuR knockdown (KD) cells were assessed by single-cell RNA sequencing analysis. Furthermore, cell proliferation, migration, and invasion were determined by Cell Counting Kit-8 (CCK-8) assays and Transwell assays with or without Matrigel. The cell cycle was assessed by propidium iodide staining. The protein level, mRNA level and half-life of PLK1 were detected by western blotting and RT-qPCR. Results: In clinical patients, the expression of HuR was significantly higher in lung cancer patients than in patients with benign lung disease. RNA sequencing analysis of A549 HuR knockdown cells revealed that the main function of HuR was related to ribonucleoprotein complex biogenesis. HuR was found to regulate signaling pathways mainly related to the spliceosome, RNA transport and the cell cycle. HuR KD suppressed the proliferation, migration and invasion of A549 cells, indicating its promotive role in these processes. Conclusion: These results demonstrate that HuR plays an important role in the progression of lung cancer.

Systematic Screening of Penetratin's Protein Targets by Yeast Proteome Microarrays.

Cell-penetrating peptides (CPPs) have distinct properties to translocate across cell envelope. The key property of CPPs to translocation with attached molecules has been utilized as vehicles for the delivery of several potential drug candidates that illustrate the significant effect in in-vitro experiment but fail in in-vivo experiment due to selectively permeable nature of cell envelop. Penetratin, a well-known CPP identified from the third α-helix of Antennapedia homeodomain of Drosophila, has been widely used and studied for the delivery of bioactive molecules to treat cancers, stroke, and infections caused by pathogenic organisms. Few studies have demonstrated that penetratin directly possesses antimicrobial activities against bacterial and fungal pathogens; however, the mechanism is unknown. In this study, we have utilized the power of high-throughput Saccharomyces cerevisiae proteome microarrays to screen all the potential protein targets of penetratin. Saccharomyces cerevisiae proteome microarrays assays of penetratin followed by statistical analysis depicted 123 Saccharomyces cerevisiae proteins as the protein targets of penetratin out of ~5800 Saccharomyces cerevisiae proteins. To understand the target patterns of penetratin, enrichment analyses were conducted using 123 protein targets. In biological process: ribonucleoprotein complex biogenesis, nucleic acid metabolic process, actin filament-based process, transcription, DNA-templated, and negative regulation of gene expression are a few significantly enriched terms. Cytoplasm, nucleus, and cell-organelles are enriched terms for cellular component. Protein-protein interactions network depicted ribonucleoprotein complex biogenesis, cortical cytoskeleton, and histone binding, which represent the major enriched terms for the 123 protein targets of penetratin. We also compared the protein targets of penetratin and intracellular protein targets of antifungal AMPs (Lfcin B, Histatin-5, and Sub-5). The comparison results showed few unique proteins between penetratin and AMPs. Nucleic acid metabolic process and cellular component disassembly were the common enrichment terms for penetratin and three AMPs. Penetratin shows unique enrichment items that are related to DNA biological process. Moreover, motif enrichment analysis depicted different enriched motifs in the protein targets of penetratin, LfcinB, Histatin-5, and Sub-5.

A Novel Model of Tumor-Infiltrating B Lymphocyte Specific RNA-Binding Protein-Related Genes With Potential Prognostic Value and Therapeutic Targets in Multiple Myeloma.

Background: RNA-binding proteins (RBPs) act as important regulators in the progression of tumors. However, their role in the tumorigenesis and prognostic assessment in multiple myeloma (MM), a B-cell hematological cancer, remains elusive. Thus, the current study was designed to explore a novel prognostic B-cell-specific RBP signature and the underlying molecular mechanisms. Methods: Data used in the current study were obtained from the Gene Expression Omnibus (GEO) database. Significantly upregulated RBPs in B cells were defined as B cell-specific RBPs. The biological functions of B-cell-specific RBPs were analyzed by the cluster Profiler package. Univariate and multivariate regressions were performed to identify robust prognostic B-cell specific RBP signatures, followed by the construction of the risk classification model. Gene set enrichment analysis (GSEA)-identified pathways were enriched in stratified groups. The microenvironment of the low- and high-risk groups was analyzed by single-sample GSEA (ssGSEA). Moreover, the correlations among the risk score and differentially expressed immune checkpoints or differentially distributed immune cells were calculated. The drug sensitivity of the low- and high-risk groups was assessed via Genomics of Drug Sensitivity in Cancer by the pRRophetic algorithm. In addition, we utilized a GEO dataset involving patients with MM receiving bortezomib therapy to estimate the treatment response between different groups. Results: A total of 56 B-cell-specific RBPs were identified, which were mainly enriched in ribonucleoprotein complex biogenesis and the ribosome pathway. ADAR, FASTKD1 and SNRPD3 were identified as prognostic B-cell specific RBP signatures in MM. The risk model was constructed based on ADAR, FASTKD1 and SNRPD3. Receiver operating characteristic (ROC) curves revealed the good predictive capacity of the risk model. A nomogram based on the risk score and other independent prognostic factors exhibited excellent performance in predicting the overall survival of MM patients. GSEA showed enrichment of the Notch signaling pathway and mRNA cis-splicing via spliceosomes in the high-risk group. Moreover, we found that the infiltration of diverse immune cell subtypes and the expression of CD274, CD276, CTLA4 and VTCN1 were significantly different between the two groups. In addition, the IC50 values of 11 drugs were higher in the low-risk group. Patients in the low-risk group exhibited a higher complete response rate to bortezomib therapy. Conclusion: Our study identified novel prognostic B-cell-specific RBP biomarkers in MM and constructed a unique risk model for predicting MM outcomes. Moreover, we explored the immune-related mechanisms of B cell-specific RBPs in regulating MM. Our findings could pave the way for developing novel therapeutic strategies to improve the prognosis of MM patients.

Transcriptome Analysis of Chronic Myelogenous Leukemia Cell Line with Imatinib Resistance

To investigate the regulation of chronic myelogenous leukemia （CML） imatinib resistant genes, in order to improve the therapeutic effect of CML imatinib resistant patients. The human CML cell line K562 and imatinib-resistant K562 cells (K562/G01) were collected, and transcriptome of the cells were achieved by RNA-seq. The sequencing data were analyzed by using standard procedures. Compared with K562 cells, 464 genes were significantly changed in K562/G01 cells, including 163 up-regulated and 301 down-regulated genes. The GO function annotation analysis and KEGG pathway analysis results showed that the differentially expressed genes were mainly involved in biological processes such as oxidative phosphorylation, localization to protein organelle, ribonucleoprotein complex biogenesis and so on. Gene Set Enrichment Analysis (GSEA) plots showed that 5 gene-sets were up-regulated in K562/G01 significantly, including the pathway of TGF-beta, mTOR and CML. CML imatinib resistance is associated with oxidative phosphorylation, during which the pathway of TGF-beta and mTOR are significantly up-regulated.

OAB-028: FAM46C-dependent tuning of endoplasmic reticulum capacity in Multiple Myeloma

<h3>Background</h3> Protein secretion is a driving force in evolution and tissue specialization. Plasma cells (PC), responsible for intense antibody (Ab) production, are paradigmatic professional secretors whose differentiation entails rapid endoplasmic reticulum (ER) expansion and concerted expression of the protein translocation, folding and trafficking machinery. A novel player in PC differentiation, recently implicated in Ab immunity is the non-canonical poly(A) polymerase FAM46C/TENT5C. <h3>Methods</h3> In developing PCs, FAM46C is induced to polyadenylate and enhance the translation of a number of mRNAs encoding Igs and ER-targeted proteins [1,2]. Being deleted or mutated in up to 20% multiple myeloma (MM) patients, but intact in other cancers, the FAM46C gene is among the most frequent genomic hits in MM and a myeloma-specific onco-suppressor [3,4]. <h3>Results</h3> We have recently shown that the ER-specific action of FAM46C depends on its interaction with the ER transmembrane FNDC3 proteins. As a result, FAM46C concertedly boosts the expression of ER and Golgi proteins, potently upsizing the secretory apparatus and Ig secretion [5]. Our data suggest that in MM the FAM46C gene is under selective pressure to contain the proteosynthetic, oxidative and metabolic stress associated with Ig secretion, favoring myeloma cell survival and growth. In keeping with this, exogenous re-expression of FAM46C in mutated MM cells raised Ig secretory capacity beyond sustainability, causing ATP shortage, ROS accumulation and apoptosis. Interestingly, although able to increase the secretory capacity across different cell types, FAM46C overexpression induced apoptosis exclusively in MM cells, being well tolerated in non-professional secretors, suggesting a key role of the secretory cargo in FAM46C toxicity. Moreover, we discovered a broader function of FAM46C in ER homeostasis beyond mRNA stabilization. Indeed, we found that FAM46C is part of a novel integrated network coordinating the biogenesis of ribonucleoprotein complexes, ER protein translation and import, and ER expansion, to harmonize massive Ab production with protein homeostasis. Finally, our proteomic analysis unveiled a surprising opposite modulation of signal recognition particle (SRP) proteins mediated by FAM46C. Indeed, while 4 out of 6 SRP proteins were positively regulated by FAM46C, the heterodimeric members SRP9 and SRP14, mediating translational arrest, increased upon FAM46C loss. <h3>Conclusions</h3> We infer that PCs have the ability to sense FAM46C-induced ER expansion and modulate SRP composition to minimize translational pausing and maximize Ab manufacture. This novel integrated network offers a framework to identify unprecedented highly specific therapeutic targets against PC dyscrasias.

Interactome Analysis of the Nucleocapsid Protein of SARS-CoV-2 Virus.

SARS-CoV-2 infection has caused a global pandemic that has severely damaged both public health and the economy. The nucleocapsid protein of SARS-CoV-2 is multifunctional and plays an important role in ribonucleocapsid formation and viral genome replication. In order to elucidate its functions, interaction partners of the SARS-CoV-2 N protein in human cells were identified via affinity purification and mass spectrometry. We identified 160 cellular proteins as interaction partners of the SARS-CoV-2 N protein in HEK293T and/or Calu-3 cells. Functional analysis revealed strong enrichment for ribosome biogenesis and RNA-associated processes, including ribonucleoprotein complex biogenesis, ribosomal large and small subunits biogenesis, RNA binding, catalysis, translation and transcription. Proteins related to virus defence responses, including MOV10, EIF2AK2, TRIM25, G3BP1, ZC3HAV1 and ZCCHC3 were also identified in the N protein interactome. This study comprehensively profiled the viral–host interactome of the SARS-CoV-2 N protein in human cells, and the findings provide the basis for further studies on the pathogenesis and antiviral strategies for this emerging infection.

Integrative analysis of gut microbiome and host transcriptomes reveals associations between treatment outcomes and immunotherapy-induced colitis.

Immune checkpoint inhibitors (ICIs) are widely used to treat various malignancies. Although the gut microbiome is known to influence the efficacy of ICIs on epithelial tumors, the functional interactions between gut taxa and colonic mucosa remain poorly understood. Here we performed transcriptomic profiling and 16S rRNA sequencing to investigate the relationships between mucosal gene expression and microbial composition with ICI responses and gastrointestinal immune‐related adverse events (GI irAEs). In responders, genes related to DNA repair and cell cycle signatures were enriched in responders whereas signatures related to innate immune response, NFAT and IFN‐γ signaling pathways were enriched in nonresponders. Gut microbial composition revealed an association between moderate GI irAE and favorable response to ICI therapy. Favorable therapeutic responses to ICI and GI irAE treatments were associated with taxa classified as Enterobacteriaceae and were related to ribonucleoprotein complex biogenesis, cytokine‐mediated signaling pathway, tRNA metabolic process, and ribonucleoprotein complex assembly in the colon. These findings open new perspectives for improving the efficacy and safety of cancer immunotherapy.

1,25-Dihydroxyvitamin D3 inhibits porcine epidemic diarrhea virus replication by regulating cell cycle resumption in IPEC-J2 porcine epithelial cells

Porcine epidemic diarrhea virus (PEDV) infection causes heavy economic losses in the pig industry. Currently, the lack of effective treatments prompts new antiviral researches. We have shown that 25-hydroxyvitamin D3 supplementation alleviated PEDV infection in weaned pigs before. However, it is not clear whether vitamin D inhibits PEDV replication. In this study, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) inhibited PEDV induced mitochondria damage and cell apoptosis. In addition, 1,25(OH)2D3 treatment decreased PEDV nucleocapsid gene and protein levels in IPEC-J2 cells. Transcriptomic data showed that PEDV infection altered the expression of 5316 genes (2498 up, 2818 down) in IPEC-J2 cells. The differentially expressed genes were mainly involved in cell cycle process, ribonucleoprotein complex biogenesis, mitotic nuclear division, and other biological processes. Then we examined the effects of PEDV infection on cell cycle progression in IPEC-J2 cells, and the results showed that PEDV induced G0/G1 phase arrest. G0/G1-phase arrest was also conducive to PEDV replication. However, 1,25(OH)2D3 treatment decreased G0/G1 phase percentage induced by PEDV. Cyclin D and cyclin E mRNA expression were also increased by 1,25(OH)2D3 supplementation upon PEDV infection. Moreover, the regulation of 1,25(OH)2D3 on cell cycle progression was abrogated by ERK1/2 inhibitor, as well as the mRNA expression of cyclin D. The inhibition of 1,25(OH)2D3 on PEDV replication was also eliminated by ERK1/2 inhibitor. Taken together, these results demonstrated that 1,25(OH)2D3 supplementation inhibited PEDV replication, and the anti-virus effect of 1,25(OH)2D3 was mediated in part by regulating cell cycle progression through ERK1/2 signaling pathway.

Genes for RNA-binding proteins involved in neural-specific functions and diseases are downregulated in Rubinstein-Taybi iNeurons.

Taking advantage of the fast-growing knowledge of RNA-binding proteins (RBPs) we review the signature of downregulated genes for RBPs in the transcriptome of induced pluripotent stem cell neurons (iNeurons) modelling the neurodevelopmental Rubinstein Taybi Syndrome (RSTS) caused by mutations in the genes encoding CBP/p300 acetyltransferases. We discuss top and functionally connected downregulated genes sorted to “RNA processing” and “Ribonucleoprotein complex biogenesis” Gene Ontology clusters. The first set of downregulated RBPs includes members of hnRNHP (A1, A2B1, D, G, H2-H1, MAGOHB, PAPBC), core subunits of U small nuclear ribonucleoproteins and Serine-Arginine splicing regulators families, acting in precursor messenger RNA alternative splicing and processing. Consistent with literature findings on reduced transcript levels of serine/arginine repetitive matrix 4 (SRRM4) protein, the main regulator of the neural-specific microexons splicing program upon depletion of Ep300 and Crebbp in mouse neurons, RSTS iNeurons show downregulated genes for proteins impacting this network. We link downregulated genes to neurological disorders including the new HNRNPH1-related intellectual disability syndrome with clinical overlap to RSTS. The set of downregulated genes for Ribosome biogenesis includes several components of ribosomal subunits and nucleolar proteins, such NOP58 and fibrillarin that form complexes with snoRNAs with a central role in guiding post-transcriptional modifications needed for rRNA maturation. These nucleolar proteins are “dual” players as fibrillarin is also required for epigenetic regulation of ribosomal genes and conversely NOP58-associated snoRNA levels are under the control of NOP58 interactor BMAL1, a transcriptional regulator of the circadian rhythm. Additional downregulated genes for “dual specificity” RBPs such as RUVBL1 and METTL1 highlight the links between chromatin and the RBP-ome and the contribution of perturbations in their cross-talk to RSTS. We underline the hub position of CBP/p300 in chromatin regulation, the impact of its defect on neurons’ post-transcriptional regulation of gene expression and the potential use of epidrugs in therapeutics of RBP-caused neurodevelopmental disorders.

BZW2/5MP1 acts as a promising target in hepatocellular carcinoma.

Basic leucine zipper and W2 domain 2 (BZW2), also known as 5MP1, is a protein related to translation regulation. Evidence from previous studies indicates that BZW2 is involved in tumorigenesis in several cancers. However, little is known about the role of BZW2 in hepatocellular carcinoma (HCC). In this study, we first analyzed the gene expression profile of BZW2 in multiple HCC datasets. Next, we explored the biological effects of BZW2 in HCC cell lines. BZW2 was overexpressed in different HCC cohorts. Multivariate analysis confirmed that increased BZW2 expression is an independent prognostic indicator of shorter overall survival. BZW2 coexpressed genes were mainly enriched in the biological processes of ribonucleoprotein complex biogenesis, rRNA metabolism, translational initiation, and negative regulation of metabolic processes. BZW2 depletion reduced proliferation, clonality, and invasion and increased apoptosis in MHCC97-H cells. Furthermore, BZW2 overexpression or knockdown enhanced or impaired c-Myc expression, respectively. Overall, these findings identified BZW2 as a biomarker of HCC and provided novel insight that the effect of BZW2 on the translatome is a potential mechanism that promotes HCC progression via the c-Myc pathway.

ROLE OF R2TP COMPLEX IN LYMPHOMA AND ITS THERAPEUTIC POTENTIAL

The R2TP complex which comprises of RUVBL1, RUVBL2, PIH1D1 and RPAP3 in humans is known to be a specialized Co-chaperone of Hsp-90 protein. This multimeric-protein complex is involved in the assembly and maturation of several multi-subunit complexes including RNA polymerase II, small nucleolar ribonucleoproteins, and complexes containing phosphatidylinositol-3-kinase-like kinases. Since their discovery as a co-chaperone of Hsp90, the R2TP complex is involved in multitude of cellular processes including, chromatin remodelling, transcription regulation, ribonucleoprotein complex biogenesis, mitotic assembly, telomerase complex assembly, and apoptosis. Lymphoma arises from the abnormal proliferation of B-cells and the R2TP complex have been reported to play an important role in the activation of p53 and RB. Therefore, the inactivation in any of the tumor suppressor pathways can drive cells to malignancy.However, there are multiple factors which may contribute towards malignancy but the folding defects in these tumor suppressor pathways could be one of the reasons. R2TP is tightly linked with oncogenesis and its inhibition can decrease the proliferation activity of cancer cells. So, the multisubunit chaperone complex as well as its components could be promising candidates for cancer chemotherapy.

Carbohydrate Sulfotransferase 4 Inhibits the Progression of Hepatitis B Virus-Related Hepatocellular Carcinoma and Is a Potential Prognostic Marker in Several Tumors.

Carbohydrate sulfotransferase 4 (CHST4) plays an important role in lymphocyte homing and is abnormally expressed in several cancer types; however, its precise function in tumor development and progression is unknown. Here we confirm that CHST4 is aberrantly expressed in various tumor subtypes. In particular, we found that CHST4 expression was downregulated in hepatitis B virus-related hepatocellular carcinoma (HBV-HCC) tumors compared to paired normal tissue. We also showed that CHST4 overexpression inhibited the proliferation and metastasis of HCC cells in vitro. Clinically, CHST4 was identified as an independent prognostic factor for HBV-HCC patients. We further illuminated the anti-tumor role and mechanism of CHST4 in HBV-HCC by constructing a FENDRR–miR-10b-5p–CHST4 competing endogenous RNA network. We found that downregulation of CHST4 expression may promote HBV expression and regulate ribonucleoprotein complex biogenesis to promote malignant behaviors in HBV-HCC. CHST4 may also recruit CD4+ T cells, macrophages, dendritic cells, and neutrophils into the tumor microenvironment to inhibit the progression of HBV-HCC. Overall, our findings suggest that CHST4 acts as a tumor suppressor in HCC-HBV and represents a potential diagnostic and therapeutic target.

CD37 high expression as a potential biomarker and association with poor outcome in acute myeloid leukemia.

Background: CD37, a member of the transmembrane 4 superfamilies (TM4SF), has been proved to be abnormally expressed in a range of malignancies. Herein, we investigate the effects of CD37 expression and analyze its clinical outcome in acute myeloid leukemia (AML) patients.Methods: The RNA-seq and clinical data of AML patients were obtained from cBioPortal database. CD37 correlated genes, the expression prolife and survival curve of eight key genes were acquired from Gene Expression Profiling Interactive Analysis (GEPIA) and UALCAN. Pathway enrichment and protein–protein interaction (PPI) network analysis were performed based on metascape databases.Results: Our results showed that CD37 mRNA expression level was significantly up-regulated in patients with AML compared with healthy persons. Patients with high CD37 expression had shorter overall survival (OS) and disease-free survival (DFS). Pathway analysis data showed that CD37 is involved in DNA replication, RNA transport, Salmonella infection, ribonucleoprotein complex biogenesis, cell cycle phase transition and so on. Furthermore, we found eight genes correlated with CD37 are all highly expressed in AML patients, and high expression is associated with poor prognosis.Conclusion: Our study described systematical expression profiles and the prognostic values of CD37 in AML; our data suggested CD37 might be novel therapeutic target and promising prognostic biomarker in the patients.

Abstract P4-06-11: High immune response identified as a good prognostic factor by proteomic SWATH-MS approach in 157 ER+/HER2- early breast cancer

Abstract Background: Estrogen positive/HER2 negative (ER+/HER2-) early (e) breast carcinoma (BC) is an heterogeneous entity, on the prognostic and predictive plan. Several prognostic multigene tests have been developed to identify patients in whom chemotherapy could be safely avoided. Proteomic is a complementary approach as variations in mRNA expression only account for ≈40% of the tumor-encoded protein range and it is taking into account, as other OMICs the tumoral microenvironment Sequential Windowed Acquisition of All Theoretical fragment (SWATH-MS) proteomic approach let an accurate and reproducible label-free quantification of large proteome. To our knowledge, no study has been conducted in a large cohort of luminal BC by SWATH-MS. The aim of this study was to establish a proteomic cartography of ER+/HER2- eBC and identify prognostic biomarkers. Methods: Frozen primary tumors were collected from 157 ER+/HER2- eBC treated in the ICO cancer center between 2006 and 2009. Patients were included if they fulfilled the following criteria: 1) ductal carcinoma; 2) unilateral; 3) first occurrence; 4) have received adjuvant chemotherapy. Clinicopathologic characteristics as outcomes were collected. Each sample was analyzed using SWATH-MS acquisition method as previously described (Aebersold et al, 2012). Peak extraction of the SWATH data was performed using either the Spectronaut software (ver 8.0, Biognosys, Switzerland). Peptide identification results were filtered with a q-value of &amp;lt; 1%. We performed clustering analysis (fuzzy clustering method) based on the 15% of most variant proteins. Functional annotation of clusters based on GO biological process terms enrichment (GOEA) was performed by means of ToppGene and GORILLA web tools. Results: The median of follow-up was 8.34 years. Respectively 32, 4 and 7 patients presented a metastatic, locoregional and controlateral recurrence. 684 among 4555 proteins represented the 15% of most variants proteins.Two ER+/HER2- eBC clusters were identified (C1 [23%] and C2 [77%]) by means of fuzzy clustering and GOEA. Two significant clinicopathological differences were observed between the two subgroups: more unifocal tumors in C1 (P = 0.0415) and mostly a clear better outcome in term of Disease Free Survival (DFS), Distant DFS (DDFS) and Overall survival (OS) in patients belonging to C2 (cf table 1). Functional annotation found that C1 was characterized by mRNA processing and protein synthesis (GO:0006396: RNA processing; GO:0008380: RNA splicing; GO:0016071: mRNA metabolic process; GO:0022613: ribonucleoprotein complex biogenesis), and C2 by a high immune response (GO:0002757: immune response-activating signal transduction; GO:0050778: positive regulation of immune response; GO:0002253: activation of immune response; GO:0050776: regulation of immune response). Differential protein expression according to the C1-C2 clusters will be presented at the meeting. Conclusion: Proteomic cartography by SWATH-MS can clearly distinguish two ER+/HER2- eBC subgroups with clear different prognosis with a better outcome for C2 patients compared to C1 patients. High immune response observed in C2 could underlie this difference with results that must be confirmed on external cohort. Nevertheless this approach could be considered as a complementary approach, helpful for clinical decision for administration of adjuvant treatment. All (n=157)Cluster 1 (n = 36)Cluster 2 (n = 121)PDisease-free survival72%55.5%77.6%0.0016Distant disease-free survival79.6%66.6%83.4%0.0063Overall survival81%61%87%0.0009Specific overall survival86%69%91%0.0012 Citation Format: Anne Patsouris, Hamza Lasla, Pascal Jézéquel, Philippe Juin, Alice Boissard, Cécile Henry, Mario Campone, Catherine Guette. High immune response identified as a good prognostic factor by proteomic SWATH-MS approach in 157 ER+/HER2- early breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-06-11.

Monocytes affect bone mineral density in pre- and postmenopausal women through ribonucleoprotein complex biogenesis by integrative bioinformatics analysis

Osteoporosis is one of the most common metabolic bone disease among pre- and postmenopausal women. As the precursors of osteoclast cells, circulating monocytes play important role in bone destruction and remodeling. The aim of study is to identify potential key genes and pathways correlated with the pathogenesis of osteoporosis. Then we construct novel estimation model closely linked to the bone mineral density (BMD) with key genes. Weighted gene co-expression network analysis (WGCNA) were conducted by collecting gene data set with 80 samples from gene expression omnibus (GEO) database. Besides, hub genes were identified by series of bioinformatics and machine learning algorithms containing protein-protein interaction (PPI) network, receiver operating characteristic curve and Pearson correlation. The direction of correlation coefficient were performed to screen for gene signatures with high BMD and low BMD. A novel BMD score system was put forward based on gene set variation analysis and logistic regression, which was validated by independent data sets. We identified six modules correlated with BMD. Finally 100 genes were identified as the high bone mineral density signatures while 130 genes were identified as low BMD signatures. Besides, we identified the significant pathway in monocytes: ribonucleoprotein complex biogenesis. What's more, our score validated it successfully.

Identification of diagnostic markers for major depressive disorder by cross-validation of data from whole blood samples

BackgroundMajor depressive disorder (MDD) is a severe disease characterized by multiple pathological changes. However, there are no reliable diagnostic biomarkers for MDD. The aim of the current study was to investigate the gene network and biomarkers underlying the pathophysiology of MDD.MethodsIn this study, we conducted a comprehensive analysis of the mRNA expression profile of MDD using data from Gene Expression Omnibus (GEO). The MDD dataset (GSE98793) with 128 MDD and 64 control whole blood samples was divided randomly into two non-overlapping groups for cross-validated differential gene expression analysis. The gene ontology (GO) enrichment and gene set enrichment analysis (GSEA) were performed for annotation, visualization, and integrated discovery. Protein–protein interaction (PPI) network was constructed by STRING database and hub genes were identified by the CytoHubba plugin. The gene expression difference and the functional similarity of hub genes were investigated for further gene expression and function exploration. Moreover, the receiver operating characteristic curve was performed to verify the diagnostic value of the hub genes.ResultsWe identified 761 differentially expressed genes closely related to MDD. The Venn diagram and GO analyses indicated that changes in MDD are mainly enriched in ribonucleoprotein complex biogenesis, antigen receptor-mediated signaling pathway, catalytic activity (acting on RNA), structural constituent of ribosome, mitochondrial matrix, and mitochondrial protein complex. The GSEA suggested that tumor necrosis factor signaling pathway, Toll-like receptor signaling pathway, apoptosis pathway, and NF-kappa B signaling pathway are all crucial in the development of MDD. A total of 20 hub genes were selected via the PPI network. Additionally, the identified hub genes were downregulated and show high functional similarity and diagnostic value in MDD.ConclusionsOur findings may provide novel insight into the functional characteristics of MDD through integrative analysis of GEO data, and suggest potential biomarkers and therapeutic targets for MDD.

Prognostic value and oncogene function of heterogeneous nuclear ribonucleoprotein A1 overexpression in HBV-related hepatocellular carcinoma.

Previous study has shown heterogeneous nuclear ribonucleoprotein A1(HNRNPA1) is highly expressed in various human cancers. In order to study the clinical value and potential function of HNRNPA1 in HBV-related hepatocellular carcinoma (HCC), three datasets from the GEPIA, GEO and TCGA were analyzed. HNRNPA1 expression was found to be significantly higher in HBV-positive HCC samples, which was supported with IHC validation. Both GO and KEGG analyses demonstrated that HNRNPA1 co-expressed genes were involved in translation, ribonucleoprotein complex biogenesis and assembly, ribosome biogenesis, RNA processing, RNA splicing, etc. Survival analysis showed a significant reduction in overall survival of patients with high HNRNPA1 expression from both the GSE14520 cohort and 151 patients with HBV-related HCC cohort. Furthermore, Gene set enrichment analysis (GSEA) revealed that HNRNPA1 may regulate HCC progression by influencing the cell cycle and WNT signaling pathway, etc. HNRNPA1 overexpression has diagnostic value in distinguishing between HCC and non-HCC liver tissue (AUC = 0.730). Finally, HNRNPA1 was a directly target gene of miR-22 manifested by the reduced luciferase activity and decreased HNRNPA1 expression in the cells with overexpression of miR-22. HNRNPA1 might function as an oncogene through the EGFR signaling pathway in HBV-related HCC, which has not been reported in previous studies.

RNA-Binding Proteomics Reveals MATR3 Interacting with lncRNA SNHG1 To Enhance Neuroblastoma Progression.

The interaction of long noncoding RNAs (lncRNAs) with one or more RNA-binding proteins (RBPs) is important to a plethora of cellular and physiological processes. The lncRNA SNHG1 was reported to be aberrantly expressed and associated with poor patient prognosis in several cancers including neuroblastoma. However, the interacting RBPs and biological functions associated with SNHG1 in neuroblastoma remain unknown. In this study, we identified 283, 31, and 164 SNHG1-interacting proteins in SK-N-BE(2)C, SK-N-DZ, and SK-N-AS neuroblastoma cells, respectively, using a RNA-protein pull-down assay coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Twenty-four SNHG1-interacting RBPs were identified in common from these three neuroblastoma cell lines. RBPs MATR3, YBX1, and HNRNPL have the binding sites for SNHG1 predicted by DeepBind motif analysis. Furthermore, the direct binding of MATR3 with SNHG1 was validated by Western blot and confirmed by RNA immunoprecipitation assay (RIP). Coexpression analysis revealed that the expression of SNHG1 is positively correlated with MATR3 ( P = 3.402 × 10-13). The high expression of MATR3 is associated with poor event-free survival ( P = 0.00711) and overall survival ( P = 0.00064). Biological functions such as ribonucleoprotein complex biogenesis, RNA processing, and RNA splicing are significantly enriched and in common between SNHG1 and MATR3. In conclusion, we identified MATR3 as binding to SNHG1 and the interaction might be involved in splicing events that enhance neuroblastoma progression.