Identification of Differentially Expressed Genes in the Rituximab- Resistant Clone (Ramos RR1) Compared to Wildtype Sensitive Ramos: Therapeutic Implications in Rituximab-Resistance

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 3770-3770
Author(s):  
Stavroula Baritaki ◽  
Jose Rodriguez ◽  
Gustavo Helguera ◽  
Melisa Martinez-Paniagua ◽  
Mario Vega ◽  
...  
Keyword(s):  
Cell Signaling ◽  
Differentially Expressed Genes ◽  
Tyrosine Phosphatase ◽  
Critical Role ◽  
Differentially Expressed ◽  
Gene Products ◽  
Therapeutic Implications ◽  
Growth Promoting ◽  
Survival Signaling ◽  
Tyrosyl Phosphorylation

Abstract Treatment of patients with relapsed or refractory B-NHL with rituximab alone or in combination with CHOP has resulted in significant clinical response. However, a subset of patients does not initially respond or develops resistance to such therapies. The mechanism underlying rituximab resistance is not fully understood. We have explored a possible mechanism by generating in the laboratory rituximab resistant clones (Ramos RR, Daudi RR, and 2F7 RR) and reported that the clones, unlike the parental wild type (wt), no longer respond to rituximab-induced cell signaling and chemo- immuno-sensitization. For instance, we have demonstrated that the resistant clones exhibit hyperactivation of cell survival signaling pathways, such as the NF-kB and Raf-1/MEK/ERK pathways, and overexpress several anti-apoptotic gene products that regulate apoptosis (Jazirehi et al., Cancer Research 67:1270–1281, 2007). To further characterize the molecular basis of rituximab-resistance, we analyzed the gene expression profile of Ramos and Ramos RR1 using oligonucleotide microarrays. There were only a few genes that were significantly modified and we have focused on such genes for analysis. First, we analyzed genes that were present in Ramos RR1 and silenced in wtRamos, namely, KIAA0738, DHTKDU1, PTPRO, REG3A, and ATXN10. Analysis of some of these gene products revealed their possible role in the regulation of resistance. For instance, REG3A, regenerating islet-derived 3α, a growth promoting lectin, has been reported to be involved in various biological functions including proliferation and resistance to apoptosis and silenced by hypermethylation. This suggests that REG3A expression in Ramos RR1 may be due to inhibition of hypermethylation. Another gene product silenced in wtRamos but expressed in Ramos RR1 is the protein tyrosine phosphatase receptor type O (PTPRO), which is known to be hypermethylated in response to rituximab therapy. Overexpression of PTPRO inhibits BCR-triggered syk tyrosyl phosphorylation and cell signaling. Hence, rituximab has been reported to trigger cells through the association of BCR with CD20 on the membrane. Second, we analyzed differentially expressed genes between Ramos RR1 and wtRamos. Two gene products, MAP3K14, and ACN9 were most overexpressed, whereas PAM, SDCCAG33, and NPAS4 were most downregulated in Ramos RR1. Overexpression of MAP3K14 (NIK) is in agreement with the hyperactivated state of Ramos RR1, and in addition to our findings of hyperactivation of the canonical NF-κB pathway, would suggest that the non-canonical pathway is also activated. Hyperactivation of NIK in Ramos RR1 may be due to its stabilization by NF-κB-dependent degradation of TRAF-3 and our findings are consistent with NIK overexpression in other blood malignancies. PAM (phosphatydyl-glycine α amidating monooxygenase) is an enzyme that has been reported to play a critical role in an autocrine pathway promoting proliferation. Its downregulation in Ramos RR1 suggests PAM-independence. Findings will be presented on the validation and roles of the above gene products in the regulation of rituximab resistance and approaches to target such gene products to reverse resistance.

scholarly journals Can We Assume the Gene Expression Profile as a Proxy for Signaling Network Activity?

Biomolecules ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 850 ◽  
Author(s):  
Mehran Piran ◽  
Reza Karbalaei ◽  
Mehrdad Piran ◽  
Jehad Aldahdooh ◽  
Mehdi Mirzaie ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signaling Pathways ◽  
Differentially Expressed Genes ◽  
Expression Profile ◽  
Signaling Network ◽  
Differentially Expressed ◽  
Network Activity ◽  
Gene Products ◽  
Expression Data ◽  
Gene Pairs

Studying relationships among gene products by expression profile analysis is a common approach in systems biology. Many studies have generalized the outcomes to the different levels of central dogma information flow and assumed a correlation of transcript and protein expression levels. However, the relation between the various types of interaction (i.e., activation and inhibition) of gene products to their expression profiles has not been widely studied. In fact, looking for any perturbation according to differentially expressed genes is the common approach, while analyzing the effects of altered expression on the activity of signaling pathways is often ignored. In this study, we examine whether significant changes in gene expression necessarily lead to dysregulated signaling pathways. Using four commonly used and comprehensive databases, we extracted all relevant gene expression data and all relationships among directly linked gene pairs. We aimed to evaluate the ratio of coherency or sign consistency between the expression level as well as the causal relationships among the gene pairs. Through a comparison with random unconnected gene pairs, we illustrate that the signaling network is incoherent, and inconsistent with the recorded expression profile. Finally, we demonstrate that, to infer perturbed signaling pathways, we need to consider the type of relationships in addition to gene-product expression data, especially at the transcript level. We assert that identifying enriched biological processes via differentially expressed genes is limited when attempting to infer dysregulated pathways.

scholarly journals Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain

2019 ◽  
Author(s):  
Ailing Liu ◽  
Zhibo Zhou ◽  
Yake Yi ◽  
Guanghui Chen
Keyword(s):  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Critical Role ◽  
Differentially Expressed ◽  
Rice Grain ◽  
Rna Seq ◽  
Cd Stress ◽  
Cd Accumulation ◽  
Cadmium Transport ◽  
Central Organ

Abstract Background: Node is the central organ of xylem to phloem transfer of nutrients and ions in plants. Cadmium (Cd)-induced crop pollution threatens food safety. Breeding cultivar with low Cd accumulation is a chance to resolve this universal problem. This study was performed to identify tissue specific genes involved in Cd accumulation in different rice stem nodes. Panicle node and the first node under panicle (node I) were sampled in two rice cultivars: Xiangwanxian No. 12 with low Cd accumulation and Yuzhenxiang with high Cd accumulation in the grains. RNA-seq analysis was performed to identify differentially expressed genes (DEGs) and microRNAs. Results: Xiangwanxian No. 12 had lower Cd concentration in panicle node, node I and grain compared with Yuzhenxiang , and node Ⅰ had the highest Cd concentration in the two cultivars. RNA seq analysis identified 4,535 differentially expressed genes and 70 miRNAs between the two cultivars. Most genes ( OsIRT1 , OsNramp5, OsVIT2 , OsNRT1.5A, and OsABCC1 ) related to the “transporter activity” blocked the transport of Cd up to panicle and accumulation in grains of low Cd-accumulative cultivar. Among the genes related to “response to stimulus”, we identified OsHSP70 and OsHSFA2d/B2c in “X”, but not in “y”, were all down-regulated by Cd stimulus. The up-regulation of miRNAs ( osa-miR528 and osa-miR408 ) played a potent role in lowering Cd accumulation via down regulation of genes, such as bZIP , ERF , MYB , SnRK1 and HSPs in Xiangwanxian No. 12 cultivar. Conclusions: Both panicle node and node I of Xiangwanxian No. 12 played a key role in blocking the upward transportation of Cd, while node I played a critical role in Yuzhenxiang . Distinct expression patterns of various transporter genes such as OsNRT1.5A, OsNramp5, OsIRT1, OsVIT2 and OsABCC1 resulted in differential Cd accumulation in different nodes. Likewise, distinct expression patterns of these transporter genes are likely responsible for the low Cd accumulation in Xiangwanxian No. 12 cultivar . MiRNAs drove multiple transcription factors, such as OsbZIPs, OsERFs, OsMYBs , to play a role in stress response, which contribute to the response to Cd stress in rice.

Transcript profiling of neuroendocrine tumors (NETs) to identify new targets and mechanism of progression.

2019 ◽  
Vol 37 (4_suppl) ◽  
pp. 292-292
Author(s):  
Emily Walzer ◽  
Suraj Peri ◽  
Karthik Devarajan ◽  
Jianming Pei ◽  
Kathy Q. Cai ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Count Data ◽  
Transcriptional Repression ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Future Research ◽  
Linear Modeling ◽  
M Cell ◽  
Therapeutic Implications

292 Background: Few studies have characterized the molecular drivers of NET growth and mechanisms differentiating poorly differentiated (PD) and well differentiated (WD) NETs. We explored the role of dysregulated transcriptome as the principal molecular mechanism of NETs with the goal to identify novel targets and biomarkers of differentiation. Methods: With IRB approval, de-identified, formalin fixed NET samples were used to extract total RNA for transcriptome analysis. All pathology specimens were centrally reviewed. Gene expression profiles of 774 genes were obtained using nCounter platform (PanCancer pathway panel, Nanostring TechnologiesTM). The resulting count data was voom normalized and differentially expressed genes between PD and WD NETs were identified using linear modeling methods available in R-Bioconductor LIMMA package. Candidate genes with potential therapeutic implications were validated in tissue microarrays by immunohistochemistry (IHC). Results: Analysis of gene count data between 16 PD and 23 WD NETs resulted in 154 differentially expressed genes on the 774 gene panel (FDR < 10% and 2 fold change (FC) up- or down-regulated), some of which may be potential drug targets (Figure 1). E.g. Enhancer of zeste homolog 2 (EZH2), a histone methyltransferase responsible for transcriptional repression, and CHK1, a G2/M cell cycle regulator, were upregulated in PD compared to WD NETs (2.7 and 3.1 FC, respectively) and serine/threonine-protein kinase PAK 3, involved in cytoskeleton reorganization, was upregulated in WD NETs (3.4 FC). IHC staining also suggested overexpression of EZH2 and its enzymatic substrate H3K27me in PD NETs (p < 0.001). PAK 3, another novel therapeutic candidate overexpressed in WD NETs (p < 0.001) was confirmed using IHC, validating the transcriptome analysis at protein level. Conclusions: These findings, combined with previously reported pathway analysis (Vijayvergia et.al 2017)], highlight biological differences between PD and WD NETs and serve as a platform for future research. They also support investigation of novel drugs that inhibit activity of EZH2 (e.g. EPZ6438) in PD NETs and PAK3 (e.g FRAX597) in WD NETs.

scholarly journals Regulation of Early Events in Integrin Signaling by Protein Tyrosine Phosphatase SHP-2

1999 ◽  
Vol 19 (4) ◽  
pp. 3205-3215 ◽  
Author(s):  
Eok-Soo Oh ◽  
Haihua Gu ◽  
Tracy M. Saxton ◽  
John F. Timms ◽  
Sharon Hausdorff ◽  
...  
Keyword(s):  
Protein Tyrosine Phosphatase ◽  
Tyrosine Phosphatase ◽  
Critical Role ◽  
Mitogen Activated Protein Kinase ◽  
In Vivo Studies ◽  
Integrin Signaling ◽  
Cytokine Signaling ◽  
Mapk Activation ◽  
Protein Tyrosine ◽  
Tyrosyl Phosphorylation

ABSTRACT The nontransmembrane protein tyrosine phosphatase SHP-2 plays a critical role in growth factor and cytokine signaling pathways. Previous studies revealed that a fraction of SHP-2 moves to focal contacts upon integrin engagement and that SHP-2 binds to SHP substrate 1 (SHPS-1)/SIRP-1α, a transmembrane glycoprotein with adhesion molecule characteristics (Y. Fujioka et al., Mol. Cell. Biol. 16:6887–6899, 1996; M. Tsuda et al., J. Biol. Chem. 273:13223–13229). Therefore, we asked whether SHP2–SHPS-1 complexes participate in integrin signaling. SHPS-1 tyrosyl phosphorylation increased upon plating of murine fibroblasts onto specific extracellular matrices. Both in vitro and in vivo studies indicate that SHPS-1 tyrosyl phosphorylation is catalyzed by Src family protein tyrosine kinases (PTKs). Overexpression of SHPS-1 in 293 cells potentiated integrin-induced mitogen-activated protein kinase (MAPK) activation, and potentiation required functional SHP-2. To further explore the role of SHP-2 in integrin signaling, we analyzed the responses of SHP-2 exon 3−/− and wild-type cell lines to being plated on fibronectin. Integrin-induced activation of Src family PTKs, tyrosyl phosphorylation of several focal adhesion proteins, MAPK activation, and the ability to spread on fibronectin were defective in SHP-2 mutant fibroblasts but were restored upon SHP-2 expression. Our data suggest a positive-feedback model in which, upon integrin engagement, basal levels of c-Src activity catalyze the tyrosyl phosphorylation of SHPS-1, thereby recruiting SHP-2 to the plasma membrane, where, perhaps by further activating Src PTKs, SHP-2 transduces positive signals for downstream events such as MAPK activation and cell shape changes.

scholarly journals A hybrid systems biology and systems pharmacology investigation of Zingerone’s effects on reconstructed human epidermal tissues

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Elham Amjad ◽  
Babak Sokouti ◽  
Solmaz Asnaashari
Keyword(s):  
Systems Biology ◽  
Differentially Expressed Genes ◽  
Critical Role ◽  
Microarray Dataset ◽  
Skin Aging ◽  
Differentially Expressed ◽  
Systems Pharmacology ◽  
Skin Disorders ◽  
Beneficial Effects ◽  
Similar Chemical

Abstract Background As individuals live longer, elderly populations can be expected to face issues. This pattern urges researchers to investigate the aging concept further to produce successful anti-aging agents. In the current study, the effects of Zingerone (a natural compound) on epidermal tissues were analyzed using a bioinformatics approach. Methods For this purpose, we chose the GEO dataset GSE133338 to carry out the systems biology and systems pharmacology approaches, ranging from identifying the differentially expressed genes to analyzing the gene ontology, determining similar structures of Zingerone and their features (i.e., anti-oxidant, anti-inflammatory, and skin disorders), constructing the gene–chemicals network, analyzing gene–disease relationships, and validating significant genes through the evidence presented in the literature. Results The post-processing of the microarray dataset identified thirteen essential genes among control and Zingerone-treated samples. The procedure revealed various structurally similar chemical and herbal compounds with possible skin-related effects. Additionally, we studied the relationships of differentially expressed genes with skin-related diseases and validated their direct connections with skin disorders the evidence available in the literature. Also, the analysis of the microarray profiling dataset revealed the critical role of interleukins as a part of the cytokines family on skin aging progress. Conclusions Zingerone, and potentially any constituents of Zingerone (e.g., their similar compound scan functionality), can be used as therapeutic agents in managing skin disorders such as skin aging. However, the beneficial effects of Zingerone should be assessed in other models (i.e., human or animal) in future studies.

scholarly journals Gene expression of endangered coral (Orbicella spp.) in the Flower Garden Banks National Marine Sanctuary after Hurricane Harvey

2019 ◽  
Author(s):  
Rachel M. Wright ◽  
Adrienne M.S. Correa ◽  
Lucinda A. Quigley ◽  
Sarah W. Davies
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Stress Responses ◽  
Expression Patterns ◽  
Critical Role ◽  
Sampling Time ◽  
Differentially Expressed ◽  
Tissue Loss ◽  
Time Points ◽  
East And West

AbstractAbout 160 km south of the Texas–Louisiana border, the East and West Flower Garden Banks (FGB) have maintained >50% coral cover with infrequent and minor incidents of disease or bleaching since monitoring began in the 1970s. However, a storm that generated coastal flooding, which ultimately interacted with the reef system, triggered a mortality event in 2016 that killed 2.6% of the East FGB. To capture the immediate effects of storm-driven freshwater runoff on coral and symbiont physiology, we leveraged the heavy rainfall associated with Hurricane Harvey in late August 2017 by sampling FGB corals at two times: September 2017, when salinity was reduced; and one month later when salinity had returned to typical levels (~36 ppt in October 2017). Tissue samples (N = 47) collected midday were immediately preserved for gene expression profiling from two congeneric coral species (Orbicella faveolata and Orbicella franksi) from the East and West FGB to determine the physiological consequences of storm-derived runoff. In the coral, differences between host species and sampling time points accounted for the majority of differentially expressed genes. Gene ontology enrichment for genes differentially expressed immediately after Hurricane Harvey indicated increases in cellular oxidative stress responses. Although tissue loss was not observed on FGB reefs following Hurricane Harvey, our results suggest that poor water quality following this storm caused FGB corals to experience sub-lethal stress. We also found dramatic expression differences across sampling time points in the coral’s algal symbiont, Breviolum minutum. Some of these differentially expressed genes may be involved in the symbionts’ response to changing environments, whereas a group of differentially expressed post-transcriptional RNA modification genes also suggest a critical role of post-transcriptional processing in symbiont acclimatization. In this study, we cannot disentangle the effects of reduced salinity from the collection time point, so these expression patterns may also be related to seasonality. These findings highlight the urgent need for continued monitoring of these reef systems to establish a baseline for gene expression of healthy corals in the FGB system across seasons, as well as the need for integrated solutions to manage stormwater runoff in the Gulf of Mexico.

scholarly journals Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain

2019 ◽  
Author(s):  
Ailing Liu ◽  
Zhibo Zhou ◽  
Yake Yi ◽  
Guanghui Chen
Keyword(s):  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Critical Role ◽  
Differentially Expressed ◽  
Rice Grain ◽  
Rna Seq ◽  
Cd Accumulation ◽  
Cadmium Transport ◽  
Upward Transport ◽  
Central Organ

Abstract Background: Node is the central organ of xylem to phloem transfer of nutrients and ions in plants. Cadmium (Cd)-induced crop pollution threatens food safety. Breeding cultivar with low Cd accumulation is a chance to resolve this universal problem. This study was performed to identify tissue specific genes involved in Cd accumulation in different rice stem nodes. Panicle node and the first node under panicle (node I) were sampled in two rice cultivars: Xiangwanxian No. 12 with low Cd accumulation and Yuzhenxiang with high Cd accumulation in the grains. RNA-seq analysis was performed to identify differentially expressed genes (DEGs) and microRNAs. Results: Xiangwanxian No. 12 had lower Cd concentration in panicle node, node I and grain compared with Yuzhenxiang, and node Ⅰ had the highest Cd concentration in the two cultivars. RNA seq analysis identified 4,535 differentially expressed genes and 70 miRNAs between the two cultivars. Most genes (OsIRT1, OsNramp5, OsVIT2, OsNRT1.5A, and OsABCC1) related to the “transporter activity” play roles in blocking the upward transport of Cd in the low Cd-accumulative cultivar. Among the genes related to “response to stimulus”, we identified OsHSP70 and OsHSFA2d/B2c in Xiangwanxian No. 12, but not in Yuzhenxiang, were all down-regulated by Cd stimulus. The up-regulation of miRNAs (osa-miR528 and osa-miR408) played a potent role in lowering Cd accumulation via down regulation of genes, such as bZIP, ERF, MYB, SnRK1 and HSPs in Xiangwanxian No. 12 cultivar. Conclusions: Both panicle node and node I of Xiangwanxian No. 12 played a key role in blocking the upward transportation of Cd, while node I played a critical role in Yuzhenxiang. Distinct expression patterns of various transporter genes such as OsNRT1.5A, OsNramp5, OsIRT1, OsVIT2 and OsABCC1 resulted in differential Cd accumulation in different nodes. Likewise, distinct expression patterns of these transporter genes are likely responsible for the low Cd accumulation in Xiangwanxian No. 12 cultivar. MiRNAs drove multiple transcription factors, such as OsbZIPs, OsERFs, OsMYBs, to play a role in stress response, which contribute to the response to Cd stress in rice.

Gene Expression in CLL Cells Associated with Lymphadenopathy and Chromosome 11q23 Deletion.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 971-971
Author(s):  
John D. Dickinson ◽  
Avadhut Joshi ◽  
Jamie Gilmore ◽  
Philip J. Bierman ◽  
Sanger Warren ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Cell Signaling ◽  
Differentially Expressed Genes ◽  
Peripheral Blood ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Mediastinal Lymphadenopathy ◽  
Fibroblast Growth Factor 21 ◽  
Mutational Status

Abstract Previously we have demonstrated that peripheral blood samples with B-cell Chronic Lymphocytic Leukemia (CLL) have different gene expression profiles associated with chromosome aberrations detected by fluorescence in situ hybridization (FISH). In particular, the vast majority of differentially expressed genes were related to the presence of the 11q23 deletion. The 11q23 deletion has previously been shown to be correlated with shortened over-all survival and extensive/bulky lymphadenopathy. In this study we sought to identify genes whose expression may play role in the progression of CLL in patients that carry the 11q23 deletion. Gene expression from 10,700 human gene specific 50-mer oligos (MWG Biotech, Ebersberg, Germany) was compared between two groups of peripheral blood CLL samples. The first group consisted of CLL patients with the 11q23 deletion detected by FISH as well as with the presence of abdominal/mediastinal lymphadenopathy. The second group consisted of CLL patients without the 11q23 deletion and without the presence of known abdominal/mediastinal lymphadenopathy. The non-11q deletion group included CLL patients with the 13q14 deletion, trisomy 12, 17p13 deletion, as well as several without any detectable abnormality. Immunoglobulin heavy chain variable region (IgVH) mutational status was compared in CLL samples in both groups to ensure that resulting expression differences were not the result of this known prognostic marker. Median of ratios was compared between the two groups. Eighty-eight (87) genes had a p-value < 0.01. Gene function was classified at the European Molecular Biology Laboratory (EMBL) Bioinformatic Harvester website. Twenty of these differentially expressed genes were cell cycle/cell signaling related genes that were over-expressed in the 11q23 deletion group. Examples include: activating transcription factor 4, rho-associated coiled-coil containing protein kinase 2, fibroblast growth factor 21 precursor, signal transducing adaptor molecule 1, mad2-like 1, interferon receptor 1, pim-2 oncogene, and zw10 interactor. In comparison, using the same peripheral blood CLL samples, 78 genes were differentially expressed (p < 0.01) between those samples that had a mutated IgVH versus those that had an unmutated IgVH. Therefore, the presence of both the 11q23 deletion and bulky abdominal/mediastinal lymphadenopathy significantly alters the gene expression profile of peripheral blood CLL cells, particularly genes related to the cell cycle and cell signaling related processes. Biological roles of some of these genes may help further elucidate the basis of the clinical behavior of CLL patients

scholarly journals miR-146b-5p Plays a Critical Role in the Regulation of Autophagy in ∆per Brucella melitensis-Infected RAW264.7 Cells

2020 ◽  
Vol 2020 ◽  
pp. 1-16 ◽  
Author(s):  
Jiao Hanwei ◽  
Xin Nie ◽  
Huapei Zhu ◽  
Baobao Li ◽  
Feng Pang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
High Throughput ◽  
Brucella Melitensis ◽  
Critical Role ◽  
Differentially Expressed ◽  
Raw264.7 Cells ◽  
Luciferase Reporter ◽  
Qrt Pcr ◽  
Protective Antibodies ◽  
Molecular Patterns

Brucella-caused brucellosis is one of the most widespread worldwide zoonoses. Lipopolysaccharide (LPS) of Brucella, which functions as pathogen-associated molecular patterns (PAMPs), is an important virulence factor that elicits protective antibodies. Per of B. melitensis is involved in the biosynthesis of the O-side chain of LPS. Autophagy is a crucial element of the innate immune response against intracellular pathogens including Brucella. In this study, we observed that autophagy was inhibited in RAW264.7 cells infected with Brucella melitensis ∆per. And, a high-throughput array-based screen and qRT-PCR validation were performed to identify the differentially expressed miRNAs in RAW264.7 cells infected with B. melitensis M5-90 ∆per. The results suggested that mmu-miR-146a-5p, mmu-miR-155-5p, mmu-miR-146b-5p, and mmu-miR-3473a were upregulated and mmu-miR-30c-5p was downregulated. During B. melitensis M5-90 ∆per infection, the increased expression of miR-146b-5p inhibited the autophagy activation in RAW264.7 cells. Using a bioinformatics approach, Tbc1d14 was predicted to be a potential target of miR-146b-5p. The results of a luciferase reporter assay indicated that miR-146b-5p directly targeted the 3′-UTR of Tbc1d14, and the interaction between miR-146b-5p and the 3′-UTR of Tbc1d14 was sequence-specific. High-throughput RNA-Seq-based screening was performed to identify differentially expressed genes in Tbc1d14-expressing RAW264.7 cells, and these were validated by qRT-PCR. Among the differentially expressed genes, four autophagy associated genes, IFNγ-inducible p47 GTPase 1 (IIGP1), nuclear receptor binding protein 2 (Nrbp2), transformation related protein 53 inducible nuclear protein 1 (Trp53inp1), and immunity-related GTPase family M member 1 (Irgm1), were obtained. Our findings provide important insights into the functional mechanism of LPS of B. melitensis.

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