Microarray-based Gene Expression Profiling Research Articles

Ferrostatin-1 inhibits ferroptosis of vascular smooth muscle cells and alleviates abdominal aortic aneurysm formation through activating the SLC7A11/GPX4 axis.

Ferroptosis, a type of iron-catalyzed necrosis, is responsible for vascular smooth muscle cell (VSMC) death and serves as a potential therapeutic target for alleviating aortic aneurysm. Here, our study explored the underlying mechanism of ferroptosis affecting VSMC functions and the resultant formation of AAA using its inhibitor Ferrostatin-1 (Fer-1). Microarray-based gene expression profiling was employed to identify differentially expressed genes related to AAA and ferroptosis. An AAA model was established by angiotensin II (Ang II) induction in apolipoprotein E-knockout (ApoE-/- ) mice, followed by injection of Fer-1 and RSL-3 (ferroptosis inducer). Then, the role of Fer-1 and RSL-3 in the ferroptosis of VSMCs and AAA formation was analyzed in Ang II-induced mice. Primary mouse VSMCs were cultured invitro and treated with Ang II, Fer-1, sh-SLC7A11, or sh-GPX4 to assess the effect of Fer-1 via the SLC7A11/GPX axis. Bioinformatics analysis revealed that GPX4 was involved in the fibrosis formation of AAA, and there was an interaction between SLC7A11 and GPX4. Invitro assays showed that Fer-1 alleviated Ang II-induced ferroptosis of VSMCs and retard the consequent AAA formation. The mechanism was associated with activation of the SLC7A11/GPX4 pathway. Silencing of SLC7A11 or GPX4 could inhibit the ameliorating effect of Fer-1 on the ferroptosis of VSMCs. Invivo animal studies further demonstrated that Fer-1 inhibited Ang II-induced ferroptosis and vessel wall structural abnormalities in AAA mouse through activation of the SLC7A11/GPX4 pathway. Fer-1 may prevent AAA formation through activation of the SLC7A11/GPX4 pathway.

Alteration of functionality and differentiation directed by changing gene expression patterns in myeloid-derived suppressor cells (MDSCs) in tumor microenvironment and bone marrow through early to terminal phase of tumor progression.

Myeloid-derived suppressor cells are heterogenous immature myeloid lineage cells that can differentiate into neutrophils, monocytes, and dendritic cells as well. These cells have been characterized to have potent immunosuppressive capacity in neoplasia and a neoplastic chronic inflammatory microenvironment. Increased accumulation of myeloid-derived suppressor cells was reported with poor clinical outcomes in patients. They support neoplastic progression by abrogating antitumor immunity through inhibition of lymphocyte functions and directly by facilitating tumor development. Yet the shifting genetic signatures of this myeloid lineage cell toward immunosuppressive functionality in progressive tumor development remain elusive. We have attempted to identify the gene expression profile using lineage-specific markers of these unique myeloid lineage cells in a tumor microenvironment and bone marrow using a liquid transplantable mice tumor model to trace the changing influence of the tumor microenvironment on myeloid-derived suppressor cells. We analyzed the phenotype, functional shift, suppressive activity, differentiation status, and microarray-based gene expression profile of CD11b+Gr1+ lineage-specific cells isolated from the tumor microenvironment and bone marrow of 4 stages of tumor-bearing mice and compared them with control counterparts. Our analysis of differentially expressed genes of myeloid-derived suppressor cells isolated from bone marrow and the tumor microenvironment reveals unique gene expression patterns in the bone marrow and tumor microenvironment-derived myeloid-derived suppressor cells. It also suggests T-cell suppressive activity of myeloid-derived suppressor cells progressively increases toward the mid-to-late phase of the tumor and a significant differentiation bias of tumor site myeloid-derived suppressor cells toward macrophages, even in the presence of differentiating agents, indicating potential molecular characteristics of myeloid-derived suppressor cells in different stages of the tumor that can emerge as an intervention target.

Implication of biosignatures in the progression of endometriosis

Endometriosis is an estrogen-dependent chronic inflammatory disorder involving the placement and growth of endometrial tissue outside the uterine cavity. It is the most common multifactorial disease that affects the life quality of women in reproductive age. Due to its multicomponent nature, early diagnosis of the disease is challenging. Since many genetic, epigenetic alterations and non-genetic factors contribute to the pathology of endometriosis, devising a drug therapy that directly acts on the ectopic tissue is extremely difficult. Endometriosis is a hormone-driven disease with estrogen considered as a primary driver for the development of endometriotic lesions. This study aims to identify biosignatures involved in endometriosis with and without gonadotropin releasing hormone agonists (GnRHa). GnRHa is a short peptide analog of GnRH that causes inhibition of estrogen and androgen synthesis. Microarray based-gene expression profiling was performed on total RNA extracted from endometriotic tissue samples with and without GnRHa-treated patients already published in our previous paper. The untreated group were considered as the control. Genes were then selected for validation by quantitative real-time polymerase chain reaction (qRT-PCR). qRT-PCR analysis confirmed significant downregulation in(p < 0.05) expression of DARC (p = 0.0042), CDH1 (p = 0.0027), CDH5 (p = 0.0283), ATP2A3 (p < 0.001), RGS5 (p = 0.0032), and CD36 (p = 0.0162) in endometriosis patients treated with GnRHa analogs. Although, CTNNAL1 (p = 0.0136) also showed significant results but there was upregulation in their expression levels after GnRHa treatment. Thus, an altered expression of these genes makes them a possible candidate determinant of endometriosis treated with GnRHa.

Abstract 11896: Contribution of Amino Acid Transporter SLC7A5 to Pathological Ventricular Hypertrophy and Heart Failure

Introduction: Transition from compensatory to pathological ventricular hypertrophy and heart failure (HF) is associated with metabolic remodeling. It has been described that hypoxia signaling induces the expression of the amino acid (AA) transporter SLC7A5 (LAT1) and the activation of its downstream pro-hypertrophic target mTORC1. Hypothesis: Chronic pathologic stimuli induce AA metabolism reprogramming comprising increased AA transport through LAT1, which plays a key role in the development of hypertrophy and its progression to HF. Methods: C57BL/6N mice were subjected to chronic pressure overload by constriction of the aorta (TAC). The selective LAT1 inhibitor JPH203 was chronically administered (ip) after TAC surgery. Dynamics of leucine were determined in heart samples from mice treated with 13C,15N-leucine using LC-MS/MS. Microarray-based gene expression profile, echocardiographic data, and markers of cardiac remodeling were measured at different time points. Results: Microarray results showed a profound AA metabolism remodeling consisting of a general increase in the expression of AA transporters, with LAT1 as the most overexpressed and reduced expression of enzymes involved in BCAA catabolism. Overexpression of LAT1 was confirmed in isolated cardiomyocytes. These changes correlated with a marked increase in labeled leucine uptake with respect to sham mice (310%), a moderate reduction in the formation of its ketoacid (51% α-ketoisocaproate), and potent inhibition of its catabolism (21% isovalerate and 13% 3-hydroxy-3-methyl-glutarate), and enhanced activation of mTOR pathway. Administration of JPH203 reduced leucine transport and mTOR activation, partially reversed the inhibition of BCAA catabolism, and attenuated hypertrophy and cardiac dysfunction induced by TAC. Conclusions: Pressure overload induces AA metabolic reprogramming characterized by enhanced AA transport and inhibited BCAA catabolism. LAT1 overexpression occurs in cardiomyocytes and contributes to adverse cardiac remodeling via mTOR pathway activation. We propose LAT1 inhibition as a novel therapeutic strategy against HF.

Identification of key molecular players and associated pathways in cervical squamous cell carcinoma progression through network analysis.

Cervical cancer is the primary cause of mortality among women in developing countries. Preventing cervical cancer is partially possible through early vaccination against the human papillomavirus, the most common cause of the disease. Nevertheless, it is imperative to understand the genetics of the disease progression to develop new therapeutic strategies. The present study aims to identify potential genes and associated pathways associated with cervical squamous cell carcinoma progression. We used an integrative approach by combining differential expression analysis, network biology, and functional enrichment analysis with survival analysis. In the present study, differential expression analysis of the microarray-based gene expression profiles of cervical cancer resulted in identifying a total of 544 significantly differentially expressed genes (DEGs). Further, centrality and network vulnerability analysis of the protein-protein interaction network (PPIN) and not well documented in cervical cancer, resulted in seven proteins (FN1, MCM5, TRIP13, KIF11, TTK, CDC45, and BUB1B), in which four proteins were vulnerable. These genes are mostly enriched in biological processes of cell division, mitotic nuclear division, cell cycle checkpoint, and cell proliferation in gene ontology analysis. The KEGG pathway enrichment analysis of the proteins lists them as mainly associated with the cell cycle. In the survival analysis, it was found that the genes MCM5, FN1, KIF11, and CDC45 were statistically significant prognostic factors for cervical cancer. The outcome of the current study identifies and explores the key role of the candidate genes involved in the progression of cervical cancer.

The clinical and biological characterization of acute myeloid leukemia patients with S100A4 overexpression

The S100 family proteins are involved in a variety of important biological processes, most notably immune and inflammatory responses. Their dysregulation also plays a role in the pathogenesis of human cancers. S100A4, also known as metastasin, has long been regarded as a biological marker in tumor progression and metastasis in multiple solid cancers, but its clinical significance in acute myeloid leukemia (AML) has not been extensively studied. We retrospectively studied the association between S100A4 gene expression and the clinical characteristics, mutational and transcriptomic profiles of 227 AML patients treated with standard intensive chemotherapy. Genetic mutations of myeloid disease associated genes were analyzed by Sanger sequencing. Microarray-based transcriptomic gene expression profiling was performed on archived bone marrow mononuclear cells. Bioinformatic analyses, including differential gene expression and gene set enrichment analysis, were conducted to delineate the underlying pathogenic mechanisms. Higher S100A4 expression was associated with older age, monocytic differentiation of leukemic cells, and adverse clinical outcome. S100A4 high-expressors had inferior overall survival and disease-free survival; this finding could be validated in the TCGA AML cohort (both the microarray and RNA-seq platforms). Multivariate Cox regression analysis supported S100A4 as an independent prognostic factor. Bioinformatic analysis showed that AML with higher S100A4 expression was enriched for the interferon, NLRP3 inflammasome, and epithelial-mesenchymal transition pathways. This study provides evidence that S100A4 overexpression serves as a poor prognostic biomarker in AML, holds potential to guide treatment planning in the clinic, and indicates novel therapeutic directions.

Gene expression study of breast cancer using Welch Satterthwaite t-test, Kaplan-Meier estimator plot and Huber loss robust regression model

ObjectiveBreast Cancer (BC) is one of the deadliest diseases in women, causing thousands of deaths annually despite the advent of high-throughput genomic platforms in the recent past. Microarray-based gene expression profiling with different statistical methods have been extensively used to understand the disease at the molecular level. We plan to apply Welch Satterthwaite t-test, Kaplan-Meier estimator plot and Huber Loss robust regression model on microarray data to improve the analysis and find biomarkers for future diagnosis, prognosis, and treatment. MethodsWe retrieved microarray data (GSE10810 dataset) of 31 breast tumor samples and 27 normal breast samples from Gene Expression Omnibus (GEO, NCBI). Welch Satterthwaite t-test was applied to identify the most statistically significant genes, Huber loss robust regression model was applied to investigate the existing mathematical relations between tumor and control variables, and Kaplan-Meier Plotter was used to confirm their association with overall metastatic relapse-free survival of BC patients. ResultsWe identified 1837 differentially expressed genes, including 638 overexpressed (COL11A1, KIAA0101, S100P, GJB2, TOP2A, LINC01614, RRM2, INHBA, C15orf48 and CKS2) and 1199 under expressed (LEP, ADIPOQ, PLIN1, PCK1, PCOLCE2, ADH1B, LYVE1, FABP4, ABCA8, and CHRDL1) genes passing the threshold (fold change ± 2 and p value < 0.001). KM analysis revealed 12 out of 20 DEGs (log rank p value < 0.05) as potential prognostic and therapeutic biomarkers. ConclusionHuber loss robust regression model was found to be one of the best performing algorithms for the mathematical relationship between the control and breast tumor samples with co-relation coefficient of 0.4398 and mean absolute error of 1.069 ± 0.020. In conclusion, with high mathematical confidence, we detected DEGs have high potential to be BC biomarkers using Welch t-test and Kaplan-Meier plot having minimum underlying assumptions.

Molecular determinants of etoposide resistance in HL60 cells.

Chemotherapy resistance is the main reason for treatment failure in acute myeloid leukemia (AML) and the major cause of its mortality. Etoposide is a DNA topoisomerase-II inhibitor that is used either as a single agent or in combination with cytarabine, azacytidine, vinca alkaloids, and anthracyclines for the treatment of relapsed /refractory AML. In this study, we sought to determine and understand the mechanism of etoposide resistance in AML using the HL60 cell line.HL60 cells were treated with incremental doses of etoposide and resistant colonies were isolated by culturing the resistant cells in semi-solid culture media. Three clones were selected for etoposide resistance namely, HL60-EtopR H1A, HL60-EtopR H1B, and HL60-EtopR H1C which demonstrated 4.78, 2.39, and 4.42-fold higher resistance to etoposide compared with the parental cells. To determine molecular differences between the etoposide-resistant HL60-EtopR cells and the parental cells, microarray-based gene expression profiling was performed. We found up regulation of members of the src tyrosine kinase family genes in the etoposide resistant cells. Further studies are required to evaluate the role of Src inhibitors in targeting etoposide resistant cells.

Direct Reprogramming of Mouse Subchondral Bone Osteoblasts into Chondrocyte-like Cells.

Treatment of full-thickness articular cartilage defects with exposure of subchondral bone often seen in osteoarthritic conditions has long been a great challenge, especially with a focus on the feasibility of in situ cartilage regeneration through minimally invasive procedures. Osteoblasts that situate in the subchondral bone plate may be considered a potentially vital endogenous source of cells for cartilage resurfacing through direct reprogramming into chondrocytes. Microarray-based gene expression profiles were generated to compare tissue-specific transcripts between subchondral bone and cartilage of mice and to assess age-dependent differences of chondrocytes as well. On osteoblast cell lines established from mouse proximal tibial subchondral bone, sequential screening by co-transduction of transcription factor (TF) genes that distinguish chondrocytes from osteoblasts reveals a shortlist of potential reprogramming factors exhibiting combined effects in inducing chondrogenesis of subchondral bone osteoblasts. A further combinatorial approach unexpectedly identified two 3-TF combinations containing Sox9 and Sox5 that exhibit differences in reprogramming propensity with the third TF c-Myc or Plagl1, which appeared to direct the converted chondrocytes toward either a superficial or a deeper zone phenotype. Thus, our approach demonstrates the possibility of converting osteoblasts into two major chondrocyte subpopulations with two combinations of three genes (Sox9, Sox5, and c-Myc or Plagl1). The findings may have important implications for developing novel in situ regeneration strategies for the reconstruction of full-thickness cartilage defects.

23-hydroxybetulinic acid reduces tumorigenesis, metastasis and immunosuppression in a mouse model of hepatocellular carcinoma via disruption of the MAPK signaling pathway.

Hepatocellular carcinoma (HCC) shows recurrence and lung metastasis even after treatment. 23-hydroxybetulinic acid (23-HBA), a major active constituent of Pulsatilla chinensis, exhibits potent antitumor activities. We herein investigate the biological effect of 23-HBA on metastasis and immunosuppression in a mouse model of HCC. Microarray-based gene expression profiling was employed to identify the target genes of 23-HBA in the treatment of HCC. The effect of 23-HBA on the progression of HCC was evaluated by in-vitro cell function measurements along with in-vivo xenograft implantation, lung metastasis and CD11b+Gr1+ staining experiments. The potential mechanism involving target signaling pathway was investigated by western blot analysis. Bioinformatics analysis revealed that matrix metalloproteinase 2 (MMP2) was a key target gene mediated by 23-HBA in HCC, whereas Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis demonstrated that MMP2 mainly affects the development and metastasis of HCC. 23-HBA significantly reduced cell malignant functions in vitro while delaying the HCC growth and metastasis in vivo. In addition, the number of myeloid-derived suppressor cells was shown to be reduced following administration of 23-HBA in mice. Mechanistic analysis indicated that these effects of 23-HBA during HCC were involved with the mitogen-activated protein kinase (MAPK) signaling pathway inactivation and resulted in decreased phosphorylation of both mitogen-activated protein kinases 1/2 and extracellular signal-regulated kinase 1/2. Our study reveals that 23-HBA acts as a tumor suppressor agent and suppresses HCC tumorigenesis, metastasis and immunosuppression via blockade of the MAPK signaling pathway, suggesting that 23-HBA may serve as a promising drug target to treat HCC.

A Machine Learning Method to Trace Cancer Primary Lesion Using Microarray-Based Gene Expression Data.

Cancer of unknown primary site (CUP) is a heterogeneous group of cancers whose tissue of origin remains unknown after detailed investigation by conventional clinical methods. The number of CUP accounts for roughly 3%–5% of all human malignancies. CUP patients are usually treated with broad-spectrum chemotherapy, which often leads to a poor prognosis. Recent studies suggest that the treatment targeting the primary lesion of CUP will significantly improve the prognosis of the patient. Therefore, it is urgent to develop an efficient method to accurately detect tissue of origin of CUP in clinical cancer research. In this work, we developed a novel framework that uses Extreme Gradient Boosting (XGBoost) to trace the primary site of CUP based on microarray-based gene expression data. First, we downloaded the microarray-based gene expression profiles of 59,385 genes for 57,08 samples from The Cancer Genome Atlas (TCGA) and 6,364 genes for 3,101 samples from the Gene Expression Omnibus (GEO). Both data were divided into training and independent testing data with a ratio of 4:1. Then, we obtained in the training data 200 and 290 genes from TCGA and the GEO datasets, respectively, to train XGBoost models for the identification of the primary site of CUP. The overall 5-fold cross-validation accuracies of our methods were 96.9% and 95.3% on TCGA and GEO training datasets, respectively. Meanwhile, the macro-precision for the independent dataset reached 96.75% and 98.8% on, respectively, TCGA and GEO. Experimental results demonstrated that the XGBoost framework not only can reduce the cost of clinical cancer traceability but also has high efficiency, which might be useful in clinical usage.

Aberrant methylation-mediated downregulation of the LINC01554 gene accelerates the malignant progression and regulates the chemosensitivity of laryngeal squamous cell carcinoma.

Laryngeal squamous cell carcinoma (LSCC) is diagnosed as a malignant tumor with a poor prognosis, the associated mechanisms still need to be further investigated. The LINC01554 gene is confirmed to participate in the tumorigenesis of hepatocellular carcinoma, but its role in LSCC has not been investigated. The aim of this study was to investigate the function and the potential mechanism of LINC01554 in LSCC, LINC01554 further was used as a molecular target for the diagnosis and molecular targeted therapy of LSCC. The microarray-based gene expression profiling of LSCC and its adjacent non-tumor tissue were used to identify the differentially expressed long non-coding RNAs (lncRNAs). Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was applied to verify the expression levels of LINC01554 in tissue and LSCC cell lines. The DNA methylation level of the LINC01554 promoter was detected by the application of bisulfite genomic sequencing (BGS), and the bisulfite conversion-specific/methylation-specific polymerase chain reaction (BS-MSP) method. The effect of LINC01554 on the proliferation, migration, and invasion of squamous cell carcinoma was assessed by MTS, wound healing, transwell, RT-qPCR, Western blot in vitro-cultured TU177 cells, and AMC-HN-8 cells. The microarray-based gene expression profiling identified the differentially expressed lncRNAs, including LINC01554, with downregulation in the LSCC tissue vs. normal tissue. The RT-qPCR verified the downregulation of LINC01554 in the LSCC tissue (P=0.0049) and LSCC cell (P=0.0020). The BGS and BS-MSP exhibited the hypermethylation level of the LINC01554 promoter, which mediated the downregulation of LINC01554. A gain-of-function experiment showed that LINC01554 inhibited the proliferation, migration, and invasion of TU177 and AMC-HN-8. Subsequently, LINC01554 overexpression was shown to decrease cell viability in TU177 and AMC-HN-8 cells treated with cisplatin. Our findings indicated that the aberrant methylation-mediated downregulation of LINC01554 promoted malignant progression and cisplatin resistance in LSCC, and LINC01554 may serve as a potential diagnostic biomarker and a novel therapeutic target for LSCC.

Enhancer of zeste homolog 2 promotes hepatocellular cancer progression and chemoresistance by enhancing protein kinase B activation through microRNA-381-mediated SET domain bifurcated 1

ABSTRACT Metastasis and chemoresistance are the leading causes of death in patients with hepatocellular carcinoma (HCC). microRNAs (miRNAs or miRs) may be useful as diagnostic, therapeutic and prognostic markers for HCC. In this study, we set out to investigate the possible role of miR-381 in HCC development and chemoresistance along with the related mechanism. Microarray-based gene expression profiling was carried out to analyze the expression of SET domain bifurcated 1 (SETDB1) and histone methyltransferase enhancer of zeste homolog 2 (EZH2) followed by validation in clinical HCC tissues and cells. The potential binding between miR-381 and SETDB1 was found and verified. Then, the role of SETDB1 in HCC in relation to miR-381 and protein kinase B (AKT) pathway was explored through gain- and loss-of-function approaches. After expression determination of EZH2, SETDB1, miR-381, and AKT pathway-related factors, their reactions were analyzed and their functional roles in HCC progression and chemoresistance were investigated in vitro and in vivo. SETDB1 was aberrantly upregulated in clinical HCC tissues and cells. This upregulation activated AKT pathway by promoting its tri-methylation on K64. SETDB1 promoted the proliferation, migration and chemoresistance through the AKT pathway in HCC cells. In a xenograft mouse model, SETDB1 promoted HCC cell tumorigenesis in vivo by activating the AKT pathway. Furthermore, EZH2 suppressed miR-381 by catalyzing the activity of H3K27me3 on its promoter region. In conclusion, EZH2 suppressed miR-381 expression by promoting H3K27me3 activity on its promoter region to facilitate SETDB1 expression, thereby activating the AKT pathway to promote hepatocarcinogenesis and chemoresistance.

Chidamide Suppresses the Growth of Cholangiocarcinoma by Inhibiting HDAC3 and Promoting FOXO1 Acetylation.

Inhibitors for histone deacetylases (HDACs) have been identified as epigenetic drug targets to treat a variety of malignancies through several molecular mechanisms. The present study is aimed at investigating the mechanism underlying the possible antitumor effect of the HDAC inhibitor chidamide (CDM) on cholangiocarcinoma (CCA). Microarray-based gene expression profiling was conducted to predict the expression of HDACs in CCA, which was validated in clinical tissue samples from CCA patients. Next, the proliferation, migration, invasion, autophagy, and apoptosis of human CCA QBC939 and SNU308 cells were measured following treatment with CDM at different concentrations. The acetylation level of FOXO1 in the nucleus and cytoplasm of QBC939 and SNU308 cells was determined after overexpression and suppression of HDAC3. A QBC939-implanted xenograft nude mouse model was established for further exploration of CDM roles in vitro. HDAC3 was prominently expressed in CCA tissues and indicated a poor prognosis for patients with CCA. CDM significantly inhibited cell proliferation, migration, and invasion of QBC939 and SNU308 cells, while inducing their autophagy and apoptosis by reducing the expression of HDAC3. CDM promoted FOXO1 acetylation by inhibiting HDAC3, thereby inducing cell autophagy. Additionally, CDM inhibited tumor growth in vivo via HDAC3 downregulation and FOXO1 acetylation induction. Overall, this study reveals that CDM can exhibit antitumor effects against CCA by promoting HDAC3-mediated FOXO1 acetylation, thus identifying a new therapeutic avenue for the treatment of CCA.

HIF-1α aggravates pathologic myopia through the miR-150-5p/LAMA4/p38 MAPK signaling axis.

Therapeutic inhibition of hypoxia-inducible factor-1alpha (HIF-1α) action has emerged as a potential approach for managing several diseases, including myopia. Herein, we analyzed the role of HIF-1α in the progression of pathologic myopia by regulating the miR-150-5p/LAMA4/p38 MAPK axis. Microarray-based gene expression profiling of pathologic myopia was employed to identify differentially expressed genes. Human scleral fibroblasts (HSFs) were cultured under the hypoxic conditions. Interaction among HIF-1α, miR-150-5p, and LAMA4 was identified. Gain- and loss-of-function experiments were performed in hypoxia-exposed HSFs to evaluate the effect of the HIF-1α/miR-150-5p/LAMA4/p38 MAPK axis on the extracellular matrix (ECM) degradation of HSFs and the subsequent pathologic myopia progression. Increased LAMA4 but decreased miR-150-5p was found in serum sample of pathologic myopia patients. HIF-1α and LAMA4 were abundantly expressed, and p38 MAPK was activated while miR-150-5p was weakly expressed in hypoxia-exposed HSFs. HIF-1α was enriched in the promoter region of miR-150-5p and downregulated its expression, thus repressing the ECM degradation of HSFs as shown by increased COL1A1 and TIMP-2 and reduced MMP2. In addition, LAMA4 was a downstream target of miR-150-5p and under the negative regulation by miR-150-5p. Overexpression of miR-150-5p promoted the ECM degradation of HSFs by inhibiting LAMA4 expression and p38 MAPK signaling pathway. However, upregulation of LAMA4 reversed the promoting effect of miR-150-5p on ECM degradation of HSFs. Overall, our findings suggest that HIF-1α can decline miR-150-5p expression and facilitate LAMA4-mediated p38 MAPK signaling pathway activation, thus arresting ECM degradation of HSFs and eventually inducing pathologic myopia.

DNA Microarray-Based Global Gene Expression Profiling in Human Amniotic Epithelial Cells Predicts the Potential of Microalgae-Derived Squalene for the Nervous System and Metabolic Health

In recent years, perinatal stem cells, such as human amniotic epithelial cells (hAECs), have attracted increasing interest as a novel tool of stem cell-based high-throughput drug screening. In the present study, we investigated the bioactivities of squalene (SQ) derived from ethanol extract (99.5%) of a microalgae Aurantiochytrium Sp. (EEA-SQ) in hAECs using whole-genome DNA microarray analysis. Tissue enrichment analysis showed that the brain was the most significantly enriched tissue by the differentially expressed genes (DEGs) between EEA-SQ-treated and control hAECs. Further gene set enrichment analysis and tissue-specific functional analysis revealed biological functions related to nervous system development, neurogenesis, and neurotransmitter modulation. Several adipose tissue-specific genes and functions were also enriched. Gene-disease association analysis showed nervous system-, metabolic-, and immune-related diseases were enriched. Altogether, our study suggests the potential health benefits of microalgae-derived SQ and we would further encourage investigation in EEA-SQ and its derivatives as potential therapeutics for nervous system- and metabolism-related diseases.

A Review on Microarray technology in molecular diagnostics

Advances in technology opened many doors, increased opportunities in various research fields, and helped create tools and devices required for many analyses. One of them is microarray technology. It is widely used in numerous research areas including infection biology, detection of small noncoding RNAs, microarray-based gene expression profiling, and many more. Microarray implementation in molecular diagnostics and their use as diagnostic devices are considered a step closer to precision medicine. Further advances in microarray technology can potentially help with the identification of new pathogens, improvement in medicine, and better drug delivery.

Therapeutic HNF4A mRNA attenuates liver fibrosis in a preclinical model

Therapeutic targeting of injuries that require transient restoration of proteins by mRNA delivery is an attractive approach that, until recently, has remained poorly explored. In this study, we examined the therapeutic utility of mRNA delivery for liver fibrosis and cirrhosis. Specifically, we aimed to demonstrate the therapeutic efficacy of human hepatocyte nuclear factor alpha (HNF4A) mRNA in mouse models of fibrosis and cirrhosis. We investigated restoration of hepatocyte functions by HNF4A mRNA transfection invitro, and analyzed the attenuation of liver fibrosis and cirrhosis in multiple mouse models, by delivering hepatocyte-targeted biodegradable lipid nanoparticles (LNPs) encapsulating HNF4A mRNA. To identify potential mechanisms of action, we performed microarray-based gene expression profiling, single-cell RNA sequencing, and chromatin immunoprecipitation. We used primary liver cells and human liver buds for additional functional validation. Expression of HNF4A mRNA led to restoration of the metabolic activity of fibrotic primary murine and human hepatocytes invitro. Repeated invivo delivery of LNP-encapsulated HNF4A mRNA induced a robust inhibition of fibrogenesis in 4 independent mouse models of hepatotoxin- and cholestasis-induced liver fibrosis. Mechanistically, we discovered that paraoxonase 1 is a direct target of HNF4A and it contributes to HNF4A-mediated attenuation of liver fibrosis via modulation of liver macrophages and hepatic stellate cells. Collectively, our findings provide the first direct preclinical evidence of the applicability of HNF4A mRNA therapeutics for the treatment of fibrosis in the liver. Liver fibrosis and cirrhosis remain unmet medical needs and contribute to high mortality worldwide. Herein, we take advantage of a promising therapeutic approach to treat liver fibrosis and cirrhosis. We demonstrate that restoration of a key gene, HNF4A, via mRNA encapsulated in lipid nanoparticles decreased injury in multiple mouse models of fibrosis and cirrhosis. Our study provides proof-of-concept that mRNA therapy is a promising strategy for reversing liver fibrosis and cirrhosis.

A Positive Regulatory Feedback Loop between EKLF/KLF1 and TAL1/SCL Sustaining the Erythropoiesis.

The erythroid Krüppel-like factor EKLF/KLF1 is a hematopoietic transcription factor binding to the CACCC DNA motif and participating in the regulation of erythroid differentiation. With combined use of microarray-based gene expression profiling and the promoter-based ChIP-chip assay of E14.5 fetal liver cells from wild type (WT) and EKLF-knockout (Eklf−/−) mouse embryos, we identified the pathways and direct target genes activated or repressed by EKLF. This genome-wide study together with the molecular/cellular analysis of the mouse erythroleukemic cells (MEL) indicate that among the downstream direct target genes of EKLF is Tal1/Scl. Tal1/Scl encodes another DNA-binding hematopoietic transcription factor TAL1/SCL, known to be an Eklf activator and essential for definitive erythroid differentiation. Further identification of the authentic Tal gene promoter in combination with the in vivo genomic footprinting approach and DNA reporter assay demonstrate that EKLF activates the Tal gene through binding to a specific CACCC motif located in its promoter. These data establish the existence of a previously unknow positive regulatory feedback loop between two DNA-binding hematopoietic transcription factors, which sustains mammalian erythropoiesis.

Inhibition of cancer cell-derived exosomal microRNA-183 suppresses cell growth and metastasis in prostate cancer by upregulating TPM1

BackgroundEmerging evidence continues to highlight the significant role of microRNAs (miRNAs) in the regulation of cancer growth and metastasis. Herein, the current study aimed to elucidate the role of exosomal miR-183 in prostate cancer development.MethodsInitially, public microarray-based gene expression profiling of prostate cancer was employed to identify differentially expressed miRNAs. The putative target gene TPM1 of miR-183 was subsequently predicted, followed by the application of a luciferase reporter assay and examination of the expression patterns in prostate cancer patients and cell lines. The effects of miR-183 and TPM1 on processes such as cell proliferation, invasion and migration were evaluated using in vitro gain- and loss-of-function experiments. The effect of PC3 cells-derived exosomal miR-183 was validated in LNCaP cells. In vivo experiments were also performed to examine the effect of miR-183 on prostate tumor growth.ResultsHigh expression of miR-183 accompanied with low expression of TPM1 was detected in prostate cancer. Our data indicated that miR-183 could target and downregulate TPM1, with the overexpression of miR-183 and exosomal miR-183 found to promote cell proliferation, migration, and invasion in prostate cancer. Furthermore, the tumor-promoting effect of exosome-mediated delivery of miR-183 was subsequently confirmed in a tumor xenograft model.ConclusionsTaken together, the key findings of our study demonstrate that prostate cancer cell-derived exosomal miR-183 enhance prostate cancer cell proliferation, invasion and migration via the downregulation of TPM1, highlighting a promising therapeutic target against prostate cancer.