scholarly journals Transcriptomic Profiling Identifies Differentially Expressed Genes in Palbociclib-Resistant ER+ MCF7 Breast Cancer Cells

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 467 ◽  
Author(s):  
Lilibeth Lanceta ◽  
Conor O'Neill ◽  
Nadiia Lypova ◽  
Xiahong Li ◽  
Eric Rouchka ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Differentially Expressed Genes ◽  
Pathway Analysis ◽  
Metabolic Pathways ◽  
Acquired Resistance ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Kegg Database ◽  
Cyclin Dependent Kinases ◽  
Estrogen Receptor Positive

Acquired resistance to cyclin-dependent kinases 4 and 6 (CDK4/6) inhibition in estrogen receptor-positive (ER+) breast cancer remains a significant clinical challenge. Efforts to uncover the mechanisms underlying resistance are needed to establish clinically actionable targets effective against resistant tumors. In this study, we sought to identify differentially expressed genes (DEGs) associated with acquired resistance to palbociclib in ER+ breast cancer. We performed next-generation transcriptomic RNA sequencing (RNA-seq) and pathway analysis in ER+ MCF7 palbociclib-sensitive (MCF7/pS) and MCF7 palbociclib-resistant (MCF7/pR) cells. We identified 2183 up-regulated and 1548 down-regulated transcripts in MCF7/pR compared to MCF7/pS cells. Functional analysis of the DEGs using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database identified several pathways associated with breast cancer, including ‘cell cycle’, ‘DNA replication’, ‘DNA repair’ and ‘autophagy’. Additionally, Ingenuity Pathway Analysis (IPA) revealed that resistance to palbociclib is closely associated with deregulation of several key canonical and metabolic pathways. Further studies are needed to determine the utility of these DEGs and pathways as therapeutics targets against ER+ palbociclib-resistant breast cancer.

scholarly journals Differential gene expression analysis of palbociclib-resistant TNBC via RNA-seq

2021 ◽  
Author(s):  
Lilibeth Lanceta ◽  
Nadiia Lypova ◽  
Conor O’Neill ◽  
Xiaohong Li ◽  
Eric Rouchka ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Pathway Analysis ◽  
Fatty Acid Biosynthesis ◽  
Acquired Resistance ◽  
Therapy Resistance ◽  
Rna Seq ◽  
Kegg Database ◽  
Cyclin Dependent Kinases ◽  
Transcriptomic Sequencing ◽  
Differential Gene

Abstract Purpose The management of triple-negative breast cancer (TNBC) remains a significant clinical challenge due to the lack of effective targeted therapies. Inhibitors of the cyclin-dependent kinases 4 and 6 (CDK4/6) are emerging as promising therapeutic agents against TNBC; however, cells can rapidly acquire resistance through multiple mechanisms that are yet to be identified. Therefore, determining the mechanisms underlying resistance to CDK4/6 inhibition is crucial to develop combination therapies that can extend the efficacy of the CDK4/6 inhibitors or delay resistance. This study aims to identify differentially expressed genes (DEG) associated with acquired resistance to palbociclib in ER− breast cancer cells. Methods We performed next-generation transcriptomic sequencing (RNA-seq) and pathway analysis in ER− MDA-MB-231 palbociclib-sensitive (231/pS) and palbociclib-resistant (231/pR) cells. Results We identified 2247 up-regulated and 1427 down-regulated transcripts in 231/pR compared to 231/pS cells. DEGs were subjected to functional analysis using Gene Ontology (GO) and the KEGG database which identified many transduction pathways associated with breast cancer, including the PI3K/AKT, PTEN and mTOR pathways. Additionally, Ingenuity Pathway Analysis (IPA) revealed that resistance to palbociclib is closely associated with altered cholesterol and fatty acid biosynthesis suggesting that resistance to palbociclib may be dependent on lipid metabolic reprograming. Conclusion This study provides evidence that lipid metabolism is altered in TNBC with acquired resistance to palbociclib. Further studies are needed to determine if the observed lipid metabolic rewiring can be exploited to overcome therapy resistance in TNBC.

scholarly journals High p16 expression and heterozygous RB1 loss are biomarkers for CDK4/6 inhibitor resistance in ER+ breast cancer

2021 ◽  
Author(s):  
Marta Palafox ◽  
Laia Monserrat ◽  
Meritxell Bellet ◽  
Guillermo Villacampa ◽  
Abel Gonzalez-Perez ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Antitumor Activity ◽  
De Novo ◽  
Acquired Resistance ◽  
Poor Clinical Outcome ◽  
Cyclin Dependent Kinases ◽  
Estrogen Receptor Positive ◽  
Inhibitor Resistance ◽  
P16 Expression ◽  
P16 Overexpression

Abstract Cyclin-dependent kinases 4 and 6 inhibitors (CDK4/6i), combined with endocrine therapy (ET), have demonstrated higher antitumor activity than ET alone for the treatment of advanced estrogen receptor-positive (ER+) breast cancer (BC). Some ER+ BC are de novo resistant to CDK4/6i and others develop acquired resistance. Therapies for tumors after progression are needed. Here, we demonstrate that p16 overexpression is associated with reduced antitumor activity of CDK4/6i in patient-derived xenografts (PDX; n=37) and ER+ BC cell lines, and reduced response of early/advanced ER+HER2- BC patients (n=49) to CDK4/6i. We also identified heterozygous RB1 loss as biomarker of acquired resistance and poor clinical outcome in ER+, CDK4/6i-treated BC PDX and patients. Combination of CDK4/6i ribociclib with PI3K inhibitor (PI3Ki) alpelisib showed antitumor activity in ER+ non-basal-like BC PDX, independently of PIK3CA or RB1 mutation (n=25). Our results offer new insights into predicting primary and acquired resistance to CDK4/6i and post-progression therapeutic strategies.

scholarly journals Comparison of expression profiling through microarray and RNA-seq analysis for Nipah virus

2019 ◽  
Author(s):  
Akanksha Rajput ◽  
Manoj Kumar
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Drug Targets ◽  
Cholesterol Metabolism ◽  
Statistical Significance ◽  
Nipah Virus ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Pathway Gene ◽  
Upregulated Genes

AbstractThe Nipah virus is responsible various outbreaks among countries of south east Asia, most recent is in Kerala, India. It is considered to be highly contagious and having a range of vectors for transmission. The condition worsens due to the lack of effective inhibitors. This study is first study, which focused to detect the differentially expressed genes among two different NiV studies from 2012 and 2017. The transcriptomic profiling data were retrieved from the sequence archives. The multivariate gene enrichment analyses were performed on the log transformed data from them using pathway, gene ontology, disease, reactome, etc. The comparison study suggests that the down regulated differentially expressed genes are common among them as compared to up regulated ones with statistical significance. However, among the diseased category the upregulated genes are mostly from metabolic pathways and diseased category like metabolic pathways, heart failure, cholesterol metabolism while the downregulated genes linked to various cancers, and viral diseases like hepatitis, dengue, influenza, etc. We found various small molecules mapped in the pathways which are differentially expressed among the studies, which could be targeted so as to control the Nipah infection. In order to design the inhibitors, our study would be useful to extract the effective and broad-spectrum drug targets.

scholarly journals Exploration of the effects of a degS mutant on the growth of Vibrio cholerae and the global regulatory function of degS by RNA sequencing

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7959
Author(s):  
Jian Huang ◽  
Yuxi Chen ◽  
Jie Chen ◽  
Changjin Liu ◽  
Tao Zhang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Regulatory Network ◽  
Metabolic Pathways ◽  
Wild Type Strain ◽  
Mutant Phenotype ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Wild Type ◽  
Qrt Pcr ◽  
Small Colony

Background DegS is a periplasmic serine protease that is considered to be the initiator of the σE stress response pathway, and this protein plays an important role in the regulation of the stress response in E. coli. However, knowledge of the biological function and global regulatory network of DegS in Vibrio cholerae remains limited. In this study, we aimed to characterize the molecular functions and further investigate the regulatory network of degS in V. cholerae. Methods A deletion mutant of degS was constructed in the V. cholerae HN375 strain. Bacterial colony morphology was observed by a plate-based growth experiment, and bacterial growth ability was observed by a growth curve experiment. High-throughput RNA sequencing (RNA-Seq) technology was used to analyze the differential transcriptomic profiles between the wild-type and degS mutant strains. Gene ontology (GO), pathway analysis and Gene-Act-network analysis were performed to explore the main functions of the differentially expressed genes. Quantitative real-time PCR (qRT-PCR) was performed to validate the reliability and accuracy of the RNA-Seq analysis. The complementation experiments were used to test the roles of degS and ropS in the small colony degS mutant phenotype. Results When degS was deleted, the degS mutant exhibited smaller colonies on various media and slower growth than the wild-type strain. A total of 423 differentially expressed genes were identified, including 187 genes that were upregulated in the degS mutant compared to the wild-type strain and 236 genes that were relatively downregulated. GO categories and pathway analysis showed that many differentially expressed genes were associated with various cellular metabolic pathways and the cell cycle. Furthermore, Gene-Act network analysis showed that many differentially expressed genes were involved in cellular metabolic pathways and bacterial chemotaxis. The cAMP-CRP-RpoS signaling pathway and the LuxPQ signal transduction system were also affected by the degS mutant. The expression patterns of nine randomly selected differentially expressed genes were consistent between the qRT-PCR and RNA-seq results. The complementation experiments showed that the small colony degS mutant phenotype could be partially restored by complementation with the pBAD24-degS or pBAD24-rpoS plasmid. Discussion These results suggest that the degS gene is important for normal growth of V. cholerae. Some of the differentially expressed genes were involved in various cellular metabolic processes and the cell cycle, which may be associated with bacterial growth. Several new degS-related regulatory networks were identified. In addition, our results suggested that the cAMP-CRP-RpoS signaling pathway may be involved in the small colony degS mutant phenotype. Overall, we believe that these transcriptomic data will serve as useful genetic resources for research on the functions of degS in V. cholerae.

scholarly journals Transcriptomic Analysis for the Identification of Metabolic Pathway Genes Related to Toluene Response in Ardisia pusilla

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1011
Author(s):  
Junping Xu ◽  
Chang Ho Ahn ◽  
Ju Young Shin ◽  
Pil Man Park ◽  
Hye Ryun An ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Differentially Expressed Gene ◽  
Carotenoid Biosynthesis ◽  
Raw Material ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Quantitative Real Time Pcr ◽  
Phenylpropanoid Biosynthesis ◽  
Differential Gene

Toluene is an industrial raw material and solvent that can be found abundantly in our daily life products. The amount of toluene vapor is one of the most important measurements for evaluating air quality. The evaluation of toluene scavenging ability of different plants has been reported, but the mechanism of plant response to toluene is only partially understood. In this study, we performed RNA sequencing (RNA-seq) analysis to detect differential gene expression in toluene-treated and untreated leaves of Ardisiapusilla. A total of 88,444 unigenes were identified by RNA-seq analysis, of which 49,623 were successfully annotated and 4101 were differentially expressed. Gene ontology analysis revealed several subcategories of genes related to toluene response, including cell part, cellular process, organelle, and metabolic processes. We mapped the main metabolic pathways of genes related to toluene response and found that the differentially expressed genes were mainly involved in glycolysis/gluconeogenesis, starch and sucrose metabolism, glycerophospholipid metabolism, carotenoid biosynthesis, phenylpropanoid biosynthesis, and flavonoid biosynthesis. In addition, 53 transcription factors belonging to 13 transcription factor families were identified. We verified 10 differentially expressed genes related to metabolic pathways using quantitative real-time PCR and found that the results of RNA-seq were positively correlated with them, indicating that the transcriptome data were reliable. This study provides insights into the metabolic pathways involved in toluene response in plants.

Evaluation of gene expression by RNA-seq after single dose of trastuzumab (T) reveals predictors of pathologic complete response (pCR) in HER2-positive early breast cancer.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 10558-10558 ◽  
Author(s):  
Natalie Galanina ◽  
Emmet Sprecher ◽  
Veerle Bossuyt ◽  
Sudipa Sarkar ◽  
Ian E. Krop ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Single Dose ◽  
Differentially Expressed Genes ◽  
Early Breast Cancer ◽  
Single Agent ◽  
Pathologic Complete Response ◽  
Differentially Expressed ◽  
Illumina Genome Analyzer ◽  
Rna Seq

10558 Background: The use of a ‘brief exposure’ to single agent T allows the measurement of dynamic changes in the transcriptome that may predict response to T-based combinations. We have shown that most gene expression changes in HER2+ tumors treated with T occur in tumors that ultimately achieve a pCR. Our further analysis suggests several patterns of transcriptional change in pCR tumors suggesting different mechanisms of action of T. RNA-seq analysis provides more in-depth annotation of these mechanisms. Methods: Fresh tumor core biopsies were taken at a 2 week time point after a single dose of T (8mg/m2) from 80 HER2+ early breast cancer patients enrolled on a clinical trial of T>T+C. Nucleic acids were extracted using Qiagen AllPrep and were analyzed with Illumina HT12v3 Beadchip and Illumina 610 QUAD V1 SNP arrays. RNA was also processed for sequencing using the Ovation RNA-Seq System and paired-end sequenced using an Illumina Genome Analyzer IIxRNA-seq data was analyzed with Tophat/Cufflinks. Network analysis was performed with Metacore. Results: Among pCR tumors, distinct patterns of differential expression pre/post T were observed, in both microarray and RNA-seq data. ERBB2 down-regulation was characteristic of pCR in one subgroup by microarray. In this group, differentially expressed genes belonged to interaction networks involved in apoptosis and cell cycle regulation. In contrast, tumors with no change in ErbB2 showed differentially expressed genes that belonged to networks related to chromatin assembly and regulation of immune pathways. NOLC1, RPL41, ZCHHC17, and B2M had altered alternative splicing product distributions in both groups. In the ERBB2 down-regulated group, genes with changed expression were enriched for targets of STAT3 and YY1. Conclusions: RNA-seq and microarray reveal distinct responses in tumors that achieve pCR to T-containing regimens. These methods provide predictive markers for validation in subsequent clinical trials.

Deregulated Immune Pathway Associated with Palbociclib Resistance in Preclinical Breast Cancer Models: Integrative Genomics and Transcriptomics

2020 ◽  
Author(s):  
KAMAL PANDEY ◽  
Eunbyeol Lee ◽  
Nahee Park ◽  
Jin Hur ◽  
Young Bin Cho ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Differentially Expressed Genes ◽  
Immune Checkpoint ◽  
Acquired Resistance ◽  
Differentially Expressed ◽  
In Vitro Assays ◽  
Type I ◽  
Cancer Models ◽  
Immune Pathway ◽  
Resistant Cells

Abstract Background: Recently, cyclin-dependent kinase (CDK) 4/6 inhibitors have been widely used to treat advanced hormone receptor-positive breast cancer. Despite promising clinical outcomes, almost all patients eventually acquire resistance to CDK4/6 inhibitors. Hence, understanding the mechanisms of acquired resistance to CDK4/6 inhibitors is crucial for developing alternative treatment strategies. Therefore, the present study screened genes associated with palbociclib resistance through genomics and transcriptomics in preclinical breast cancer models. Methods: Palbociclib-resistant cells, MCF7-PR and T47D-PR, were generated by exposing MCF7 and T47D cells to palbociclib. After confirming acquired resistance through in vitro assays, whole-exome sequencing (WES) and mRNA microarray were performed to compare the genomic and transcriptomic landscape between palbociclib-sensitive and resistant cells. Real time-PCR was performed to confirm differentially expressed genes.Results: Microarray analysis comparing MCF7 and MCF7-PR cells revealed 651 differentially expressed genes (DEGs) (fold change >2 or <0.5), while WES comparing T47D and T47D-PR cells revealed 107 mutated genes. Furthermore, pathway analysis of both DEGs and mutated genes revealed immune pathway deregulation commonly observed in MCF7-PR and T47D-PR cells. Notably, DEG annotation revealed activation of type I interferon pathway, activation of immune checkpoint inhibitory pathway, and suppression of immune checkpoint stimulatory pathway in palbociclib-resistant cells. Moreover, mutations in NCOR1, MUC4 and MUC16 genes found in palbociclib-resistant cells were annotated to be related to the immune pathway. Conclusions: Palbociclib resistance was found to be associated with deregulated immune pathway in preclinical breast cancer models. Further studies are warranted to evaluate whether immune pathways may be a therapeutic target to overcome CDK4/6 inhibitor resistance.

scholarly journals RNA-Seq Analysis in Liver of Selenium-deficient Selenocysteine Lyase Knockout Mouse (P24-023-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Lucia Seale ◽  
Vedbar Khadka ◽  
Mark Menor ◽  
Alexandru Sasuclark ◽  
Kyrillos Guirguis ◽  
...  
Keyword(s):  
Real Time ◽  
Differentially Expressed Genes ◽  
Pathway Analysis ◽  
Differentially Expressed ◽  
Metabolic Phenotype ◽  
Rna Seq ◽  
Wild Type ◽  
Deficient Diet ◽  
Dietary Selenium ◽  
Selenocysteine Lyase

Abstract Objectives Selenium is a trace element critical for appropriate response to oxidative stress in cells. Once ingested, dietary selenium is mostly metabolized by the liver. Selenium is utilized to produce the amino acid selenocysteine, which can be incorporated into selenoproteins, most of them functioning in curbing reactive oxygen species. The enzyme selenocysteine lyase (Scly) decomposes selenocysteine into selenide, and its highest expression and activity occurs in the liver. Disrupting the Scly gene (Scly−/−) resulted in overweight mice with hyperlipidemia, hyperinsulinemia and glucose intolerance, phenotype traits that were aggravated by a selenium-deficient diet. In the liver, Scly−/−mice had lower hepatic selenium levels than their wild-type mice counterparts. Our objective was to identify differentially expressed genes and pathways in Scly−/- mice livers affected by dietary selenium levels. Methods Scly−/- and wild-type mice were fed diets containing 0.08 (mildly low) or 0.25 (adequate) ppm of sodium selenite. We extracted total RNA from livers with a commercial kit. High-quality RNA (RIN ≥ 7) as assessed by a BioAnalyzer was employed in RNA-sequencing. RNA-Seq data analysis was performed on Partek flow software followed by pathway analysis using Ingenuity Pathway Analysis software. Validation of results was pursued by real-time RT-qPCR using specific primer sets. Results Hepatic RNA-Seq analysis revealed 52 genes differentially regulated by Scly disruption and low dietary selenium levels, encompassing 41 pathways, including PXR/RXR activation, LPS/IL-1-mediated inhibition of RXR function, xenobiotic metabolism signaling, nicotine degradation, adipogenesis, and acyl-CoA hydrolysis. Ten differentially expressed genes were validated by real-time RT-qPCR, including Selenobp2, Eif4ebp3, Mt1, and Mt2. Conclusions We identified pathways and validated genes in the Scly−/- mouse liver that are implicated in the metabolic phenotype displayed by this model on a low selenium diet. Funding Sources This project was supported by the National Institutes of Health (NIH) grants U54MD007601 Ola Hawaii (subproject 5544), P30-CA071789–128, R01DK47320, and P20GM103466. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.

scholarly journals Aligning the Aligners: Comparison of RNA Sequencing Data Alignment and Gene Expression Quantification Tools for Clinical Breast Cancer Research

2019 ◽  
Vol 9 (2) ◽  
pp. 18 ◽  
Author(s):  
Isaac D. Raplee ◽  
Alexei V. Evsikov ◽  
Caralina Marín de Evsikova
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cancer Research ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Ductal Carcinoma ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Bioinformatics Tools ◽  
Ffpe Samples

The rapid expansion of transcriptomics and affordability of next-generation sequencing (NGS) technologies generate rocketing amounts of gene expression data across biology and medicine, including cancer research. Concomitantly, many bioinformatics tools were developed to streamline gene expression and quantification. We tested the concordance of NGS RNA sequencing (RNA-seq) analysis outcomes between two predominant programs for read alignment, HISAT2, and STAR, and two most popular programs for quantifying gene expression in NGS experiments, edgeR and DESeq2, using RNA-seq data from breast cancer progression series, which include histologically confirmed normal, early neoplasia, ductal carcinoma in situ and infiltrating ductal carcinoma samples microdissected from formalin fixed, paraffin embedded (FFPE) breast tissue blocks. We identified significant differences in aligners’ performance: HISAT2 was prone to misalign reads to retrogene genomic loci, STAR generated more precise alignments, especially for early neoplasia samples. edgeR and DESeq2 produced similar lists of differentially expressed genes, with edgeR producing more conservative, though shorter, lists of genes. Gene Ontology (GO) enrichment analysis revealed no skewness in significant GO terms identified among differentially expressed genes by edgeR versus DESeq2. As transcriptomics of FFPE samples becomes a vanguard of precision medicine, choice of bioinformatics tools becomes critical for clinical research. Our results indicate that STAR and edgeR are well-suited tools for differential gene expression analysis from FFPE samples.

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