Podcast
Questions and Answers
What technique was used to assess the suppressive impact of ATRA on growth in tissue slices?
What technique was used to assess the suppressive impact of ATRA on growth in tissue slices?
- Immunohistochemical techniques (correct)
- Western blotting
- Flow cytometry
- RT-PCR analysis
In the context of ATRA sensitivity, how were the findings categorized based on Ki-67 levels?
In the context of ATRA sensitivity, how were the findings categorized based on Ki-67 levels?
- High, medium, and low responses (correct)
- Positive, negative, and neutral responses
- Active, dormant, and proliferative responses
- Clinical, subclinical, and symptomatic responses
What was one of the primary results of the Gene Set Enrichment Analysis (GSEA) performed on the RNA-Seq data?
What was one of the primary results of the Gene Set Enrichment Analysis (GSEA) performed on the RNA-Seq data?
- Up-regulation of the Interferon Response & Immune Regulation (correct)
- Up-regulation of the Extracellular Matrix
- Down-regulation of the Interferon Response
- No significant pathway changes observed
Which analysis was applied to quantitatively assess the distribution of samples in the G-INT and G-DIFF groups?
Which analysis was applied to quantitatively assess the distribution of samples in the G-INT and G-DIFF groups?
What was the primary marker assessed to evaluate the effectiveness of ATRA in reducing cell proliferation?
What was the primary marker assessed to evaluate the effectiveness of ATRA in reducing cell proliferation?
How many instances indicated a reduction of Ki-67 levels as a response to ATRA?
How many instances indicated a reduction of Ki-67 levels as a response to ATRA?
What was the predominant profile observed in the 375 gastric carcinoma samples from TCGA?
What was the predominant profile observed in the 375 gastric carcinoma samples from TCGA?
What was the overall effect of ATRA on tumor growth as indicated by the results?
What was the overall effect of ATRA on tumor growth as indicated by the results?
What is indicated by the ATRA-score in assessing cell-line sensitivity to ATRA treatment?
What is indicated by the ATRA-score in assessing cell-line sensitivity to ATRA treatment?
Which gene expression characteristics are primarily affected by ATRA treatment in sensitive cell-lines?
Which gene expression characteristics are primarily affected by ATRA treatment in sensitive cell-lines?
What does a Gene Set Enrichment Analysis (GSEA) aim to identify in the context of the study?
What does a Gene Set Enrichment Analysis (GSEA) aim to identify in the context of the study?
Which of the following statements best describes the interactome associated with lipid metabolism in the study?
Which of the following statements best describes the interactome associated with lipid metabolism in the study?
What correlation does the linear-regression r-values demonstrate in this study?
What correlation does the linear-regression r-values demonstrate in this study?
Which proteins are involved in the regulation of inflammation that are part of the network centered around IRF1?
Which proteins are involved in the regulation of inflammation that are part of the network centered around IRF1?
What is the total number of genes affected by ATRA in HGC-27 and RERF-GC-1B cells combined?
What is the total number of genes affected by ATRA in HGC-27 and RERF-GC-1B cells combined?
What was the purpose of conducting RNA-seq investigations on the gastric carcinoma cell lines?
What was the purpose of conducting RNA-seq investigations on the gastric carcinoma cell lines?
How many cell lines tested are known to exhibit low sensitivity to ATRA?
How many cell lines tested are known to exhibit low sensitivity to ATRA?
Which of the following refers to the characteristic grouping observed in the transcriptomic profiles of the gastric cancer cell lines?
Which of the following refers to the characteristic grouping observed in the transcriptomic profiles of the gastric cancer cell lines?
What was conducted to ensure transcriptomic coherence with the CCLE database?
What was conducted to ensure transcriptomic coherence with the CCLE database?
Which gene, associated with epithelial polarization, is up-regulated while specific gene-products related to adhesion are down-regulated?
Which gene, associated with epithelial polarization, is up-regulated while specific gene-products related to adhesion are down-regulated?
Which component was NOT mentioned in the factors regulating pre-mRNA processing?
Which component was NOT mentioned in the factors regulating pre-mRNA processing?
What is the ATRA-score of the G-DIFF cell line that displayed poor sensitivity to ATRA?
What is the ATRA-score of the G-DIFF cell line that displayed poor sensitivity to ATRA?
What type of analysis was performed prior to measuring differential expression between treated and control cell lines?
What type of analysis was performed prior to measuring differential expression between treated and control cell lines?
Which of the following pathways is not associated with the proteins forming the largest network around IRF1?
Which of the following pathways is not associated with the proteins forming the largest network around IRF1?
Which factor from the third and fourth networks is primarily associated with metabolic regulation?
Which factor from the third and fourth networks is primarily associated with metabolic regulation?
What characterizes the interactome of down-regulated gene products identified in the study?
What characterizes the interactome of down-regulated gene products identified in the study?
Which aspect of gastric cancer did ATRA-sensitivity assessments focus on?
Which aspect of gastric cancer did ATRA-sensitivity assessments focus on?
Among G-INT cell lines, which ones are indicative of high sensitivity to ATRA?
Among G-INT cell lines, which ones are indicative of high sensitivity to ATRA?
In the context of differential expression analysis, which sample type was used as a control?
In the context of differential expression analysis, which sample type was used as a control?
What number of genes are up-regulated in response to ATRA within cell lines responsive to retinoids?
What number of genes are up-regulated in response to ATRA within cell lines responsive to retinoids?
Which gene-products are part of the second-largest interactome discussed in the context?
Which gene-products are part of the second-largest interactome discussed in the context?
What was the correlation sought between the cell lines in the laboratory and the CCLE database?
What was the correlation sought between the cell lines in the laboratory and the CCLE database?
Which gene from the networks includes a role in mediating mitochondrial homeostasis?
Which gene from the networks includes a role in mediating mitochondrial homeostasis?
What is the primary goal of developing a gene-expression model in the context of ATRA-sensitive gastric cancer patients?
What is the primary goal of developing a gene-expression model in the context of ATRA-sensitive gastric cancer patients?
Which computational method was employed to identify transcripts correlated with ATRA-sensitivity?
Which computational method was employed to identify transcripts correlated with ATRA-sensitivity?
How many protein-coding mRNAs show a positive correlation with ATRA-sensitivity?
How many protein-coding mRNAs show a positive correlation with ATRA-sensitivity?
What do the size differences of nodes in the interaction network indicate?
What do the size differences of nodes in the interaction network indicate?
What is one of the roles of proteins in the most extensive network identified?
What is one of the roles of proteins in the most extensive network identified?
What is a significant finding regarding the correlations between mRNAs and ATRA-sensitivity?
What is a significant finding regarding the correlations between mRNAs and ATRA-sensitivity?
Which of the following is not part of the network associated with ATRA-sensitivity?
Which of the following is not part of the network associated with ATRA-sensitivity?
What process does the STRING database facilitate in relation to the identified genes?
What process does the STRING database facilitate in relation to the identified genes?
Which of the following components was part of the second network identified in the research?
Which of the following components was part of the second network identified in the research?
What is a primary consideration when establishing transcriptomic coherence with the CCLE database?
What is a primary consideration when establishing transcriptomic coherence with the CCLE database?
In a differential expression analysis, what is the role of the control sample treated with DMSO?
In a differential expression analysis, what is the role of the control sample treated with DMSO?
Which outcome is typically assessed during a Gene Set Enrichment Analysis (GSEA) related to ATRA sensitivity?
Which outcome is typically assessed during a Gene Set Enrichment Analysis (GSEA) related to ATRA sensitivity?
What aspect of lipid metabolism is specifically regulated in the context of ATRA treatment?
What aspect of lipid metabolism is specifically regulated in the context of ATRA treatment?
What characterizes the assessment of ATRA sensitivity among different gastric cancer cell lines?
What characterizes the assessment of ATRA sensitivity among different gastric cancer cell lines?
What is the relationship between ATRA sensitivity and the expression of c-myc target genes?
What is the relationship between ATRA sensitivity and the expression of c-myc target genes?
Which of the following best describes the Gene Set Enrichment Analysis conducted on the RNA-Seq data?
Which of the following best describes the Gene Set Enrichment Analysis conducted on the RNA-Seq data?
What does the ATRA-score signify in the context of ATRA treatment assessment?
What does the ATRA-score signify in the context of ATRA treatment assessment?
What was the main focus of the differential expression analysis in this study?
What was the main focus of the differential expression analysis in this study?
Which outcome is primarily associated with the interaction network involved in lipid metabolism?
Which outcome is primarily associated with the interaction network involved in lipid metabolism?
How does the anti-proliferative effect of ATRA manifest at a molecular level?
How does the anti-proliferative effect of ATRA manifest at a molecular level?
Which factor is NOT included in the interactome that regulates lipid metabolism?
Which factor is NOT included in the interactome that regulates lipid metabolism?
What role does the linear-regression r-values serve in this study's analysis?
What role does the linear-regression r-values serve in this study's analysis?
Which aspect of gene regulation is primarily impacted by lifestyle and environmental factors as mentioned in the findings?
Which aspect of gene regulation is primarily impacted by lifestyle and environmental factors as mentioned in the findings?
How many genes are typically reported to experience significant up-regulation in retinoid-sensitive cell lines when treated with ATRA?
How many genes are typically reported to experience significant up-regulation in retinoid-sensitive cell lines when treated with ATRA?
Which two gene-products are specifically mentioned to interact within the second-largest network related to retinoid metabolism?
Which two gene-products are specifically mentioned to interact within the second-largest network related to retinoid metabolism?
In the context of differential expression analysis, which process is highlighted as a primary effect caused by ATRA treatment?
In the context of differential expression analysis, which process is highlighted as a primary effect caused by ATRA treatment?
What is the result of ATRA's regulation on the expression of AHNAK2 in all G-INT and G-DIFF cell lines?
What is the result of ATRA's regulation on the expression of AHNAK2 in all G-INT and G-DIFF cell lines?
Which gene is involved in the interaction with IRF1 as part of the gene networks discussed?
Which gene is involved in the interaction with IRF1 as part of the gene networks discussed?
Which of the following statements correctly describes the impact of ATRA on retinoid-resistant GSS cells?
Which of the following statements correctly describes the impact of ATRA on retinoid-resistant GSS cells?
Which cellular process do the proteins forming the second-largest interactome primarily regulate?
Which cellular process do the proteins forming the second-largest interactome primarily regulate?
Which gene-product is identified as being common to the enhanced expression in both G-DIFF and G-INT cell lines due to ATRA?
Which gene-product is identified as being common to the enhanced expression in both G-DIFF and G-INT cell lines due to ATRA?
What is the primary focus of the GSEA performed on the RNA-Seq data in relation to ATRA treatment?
What is the primary focus of the GSEA performed on the RNA-Seq data in relation to ATRA treatment?
What is a key purpose of the Gene Set Enrichment Analysis (GSEA) in the context of evaluating ATRA sensitivity?
What is a key purpose of the Gene Set Enrichment Analysis (GSEA) in the context of evaluating ATRA sensitivity?
Which aspect characterizes transcriptomic coherence with the Cancer Cell Line Encyclopedia (CCLE) database?
Which aspect characterizes transcriptomic coherence with the Cancer Cell Line Encyclopedia (CCLE) database?
What analysis is critical before differentiating expression between treated and control cell lines?
What analysis is critical before differentiating expression between treated and control cell lines?
In the context of ATRA-sensitivity assessment, which factors are primarily focused on?
In the context of ATRA-sensitivity assessment, which factors are primarily focused on?
Which of the following decisions would NOT be impacted by the results of differential expression analysis?
Which of the following decisions would NOT be impacted by the results of differential expression analysis?
What critical aspect is often overlooked when studying lipid metabolism regulation in cancer?
What critical aspect is often overlooked when studying lipid metabolism regulation in cancer?
Which feature is typically not derived from a successful application of transcriptomic analysis?
Which feature is typically not derived from a successful application of transcriptomic analysis?
Which method is least likely to contribute to the understanding of differential expression in relation to ATRA treatment?
Which method is least likely to contribute to the understanding of differential expression in relation to ATRA treatment?
What is one major limitation when interpreting results from the STRING database regarding gene interactions?
What is one major limitation when interpreting results from the STRING database regarding gene interactions?
What do alterations at the epigenetic level signify in the context of gastric cancer treatment sensitivity?
What do alterations at the epigenetic level signify in the context of gastric cancer treatment sensitivity?
What role does ATRA have in the regulation of gene expression in gastric cancer cell lines?
What role does ATRA have in the regulation of gene expression in gastric cancer cell lines?
Which cell line exhibited the highest observed sensitivity to ATRA based on the provided data?
Which cell line exhibited the highest observed sensitivity to ATRA based on the provided data?
In the context of lipid metabolism, what is a critical finding related to the down-regulated gene-products?
In the context of lipid metabolism, what is a critical finding related to the down-regulated gene-products?
What was the purpose of the Gene Set Enrichment Analysis (GSEA) conducted in this study?
What was the purpose of the Gene Set Enrichment Analysis (GSEA) conducted in this study?
Which factor contributes to the complexity of the interactome regarding lipid homeostasis in the context of ATRA treatment?
Which factor contributes to the complexity of the interactome regarding lipid homeostasis in the context of ATRA treatment?
What common trend was observed in the expression of genes across the G-INT cell lines in relation to ATRA treatment?
What common trend was observed in the expression of genes across the G-INT cell lines in relation to ATRA treatment?
In relation to epithelial polarization, which gene's up-regulation is significant during ATRA treatment?
In relation to epithelial polarization, which gene's up-regulation is significant during ATRA treatment?
What was discovered about the differential expression of genes in HGC-27 and RERF-GC-1B cells compared to LMSU and GCIY cells?
What was discovered about the differential expression of genes in HGC-27 and RERF-GC-1B cells compared to LMSU and GCIY cells?
Which gene product is particularly mentioned as part of the second-largest interactome related to ATRA effects?
Which gene product is particularly mentioned as part of the second-largest interactome related to ATRA effects?
How many genes are indicated as being significantly affected by ATRA in LMSU cells?
How many genes are indicated as being significantly affected by ATRA in LMSU cells?
Which process may be enhanced due to the decrease in expression of specific gene-products linked to lipid metabolism regulation?
Which process may be enhanced due to the decrease in expression of specific gene-products linked to lipid metabolism regulation?
Which cell-line exhibited the highest sensitivity to ATRA among those tested?
Which cell-line exhibited the highest sensitivity to ATRA among those tested?
What is a significant characteristic of the interactome that contains down-regulated gene-products?
What is a significant characteristic of the interactome that contains down-regulated gene-products?
Which gene is identified as up-regulated and previously associated with the enhancement of epithelial polarization?
Which gene is identified as up-regulated and previously associated with the enhancement of epithelial polarization?
What does the differential expression analysis indicate when comparing ATRA-treated to control cells?
What does the differential expression analysis indicate when comparing ATRA-treated to control cells?
How many genes showed up-regulation in cell lines responsive to retinoids after ATRA treatment?
How many genes showed up-regulation in cell lines responsive to retinoids after ATRA treatment?
Which statistical approach helps in establishing transcriptomic coherence with external databases?
Which statistical approach helps in establishing transcriptomic coherence with external databases?
In the STRING analysis, what do the distinct networks formed by up-regulated genes suggest?
In the STRING analysis, what do the distinct networks formed by up-regulated genes suggest?
Which gene product is part of the network involved in inflammation regulation around IRF1?
Which gene product is part of the network involved in inflammation regulation around IRF1?
What is the main purpose of the Gene Set Enrichment Analysis conducted on the collected RNA-Seq data?
What is the main purpose of the Gene Set Enrichment Analysis conducted on the collected RNA-Seq data?
Which proteins are primarily involved in lipid metabolism according to the analysis?
Which proteins are primarily involved in lipid metabolism according to the analysis?
In assessing ATRA sensitivity, which ATRA-score range indicates high sensitivity in cell-lines?
In assessing ATRA sensitivity, which ATRA-score range indicates high sensitivity in cell-lines?
What is critical for establishing transcriptomic coherence with external databases in the study?
What is critical for establishing transcriptomic coherence with external databases in the study?
Which statement regarding the differential expression analysis of ATRA-treated cell-lines is accurate?
Which statement regarding the differential expression analysis of ATRA-treated cell-lines is accurate?
What was the primary aim of conducting Gene Set Enrichment Analysis (GSEA) in the context of ATRA treatment?
What was the primary aim of conducting Gene Set Enrichment Analysis (GSEA) in the context of ATRA treatment?
Which of the following proteins is NOT known to be part of the interactome associated with lipid metabolism as discussed in the content?
Which of the following proteins is NOT known to be part of the interactome associated with lipid metabolism as discussed in the content?
What is the primary consideration for establishing transcriptomic coherence with the CCLE database?
What is the primary consideration for establishing transcriptomic coherence with the CCLE database?
Which of the following represents a significant aspect of ATRA-sensitivity assessments in gastric cancer cell lines?
Which of the following represents a significant aspect of ATRA-sensitivity assessments in gastric cancer cell lines?
Which analysis is conducted before performing differential expression analysis between treated and control samples?
Which analysis is conducted before performing differential expression analysis between treated and control samples?
In the context of Gene Set Enrichment Analysis (GSEA) regarding ATRA sensitivity, which outcome is primarily assessed?
In the context of Gene Set Enrichment Analysis (GSEA) regarding ATRA sensitivity, which outcome is primarily assessed?
What type of genes are typically up-regulated within cell lines responsive to ATRA treatment?
What type of genes are typically up-regulated within cell lines responsive to ATRA treatment?
Which factor is commonly explored when analyzing the relationship between ATRA sensitivity and lipid metabolism in gastric cancer cell lines?
Which factor is commonly explored when analyzing the relationship between ATRA sensitivity and lipid metabolism in gastric cancer cell lines?
Which approach is taken to ensure the accuracy of expression data when analyzing ATRA's effects on cell lines?
Which approach is taken to ensure the accuracy of expression data when analyzing ATRA's effects on cell lines?
In terms of transcriptomic clustering, how many gastric cancer cell lines were categorized as part of the Genomic Intestinal (G-INT) group?
In terms of transcriptomic clustering, how many gastric cancer cell lines were categorized as part of the Genomic Intestinal (G-INT) group?
What is a key characteristic of the two distinct transcriptomic profiles identified in the study?
What is a key characteristic of the two distinct transcriptomic profiles identified in the study?
Which macro-cluster is down-regulated in response to ATRA treatment according to the findings?
Which macro-cluster is down-regulated in response to ATRA treatment according to the findings?
What is a primary feature assessed in comparing ATRA-sensitivity among gastric cancer cell lines?
What is a primary feature assessed in comparing ATRA-sensitivity among gastric cancer cell lines?
In the context of establishing transcriptomic coherence, which is a crucial consideration?
In the context of establishing transcriptomic coherence, which is a crucial consideration?
What type of analysis reveals the differential gene expression results as part of ATRA validation?
What type of analysis reveals the differential gene expression results as part of ATRA validation?
Which outcome is typically measured during a Gene Set Enrichment Analysis (GSEA) related to ATRA sensitivity?
Which outcome is typically measured during a Gene Set Enrichment Analysis (GSEA) related to ATRA sensitivity?
What analysis method is used to quantitatively categorize samples into G-INT and G-DIFF groups?
What analysis method is used to quantitatively categorize samples into G-INT and G-DIFF groups?
Which component is NOT typically evaluated during differential expression analysis in ATRA studies?
Which component is NOT typically evaluated during differential expression analysis in ATRA studies?
What is a crucial aspect of lipid metabolism regulation in the context of ATRA sensitivity assessments?
What is a crucial aspect of lipid metabolism regulation in the context of ATRA sensitivity assessments?
Which protein is NOT associated with the most extensive network identified in relation to ATRA sensitivity?
Which protein is NOT associated with the most extensive network identified in relation to ATRA sensitivity?
What correlation pattern was observed among protein-coding mRNAs in relation to ATRA-sensitivity?
What correlation pattern was observed among protein-coding mRNAs in relation to ATRA-sensitivity?
Which aspect of lipid metabolism regulation is principally highlighted in the context of ATRA treatment?
Which aspect of lipid metabolism regulation is principally highlighted in the context of ATRA treatment?
Which factor is NOT considered essential when establishing transcriptomic coherence with the CCLE database?
Which factor is NOT considered essential when establishing transcriptomic coherence with the CCLE database?
In the context of differential expression analysis, what is the objective regarding ATRA treatment?
In the context of differential expression analysis, what is the objective regarding ATRA treatment?
Which outcome is a primary focus of the Gene Set Enrichment Analysis conducted related to ATRA-sensitivity?
Which outcome is a primary focus of the Gene Set Enrichment Analysis conducted related to ATRA-sensitivity?
Which specific pattern in gene expression correlates positively with ATRA-sensitivity in gastric cancer?
Which specific pattern in gene expression correlates positively with ATRA-sensitivity in gastric cancer?
Which pathway component does NOT feature in the most extensive gene interaction network identified?
Which pathway component does NOT feature in the most extensive gene interaction network identified?
In relation to gene interactions, what does the node size in the network signify?
In relation to gene interactions, what does the node size in the network signify?
What is the main aim of developing a gene-expression model for ATRA-sensitive gastric cancer patients?
What is the main aim of developing a gene-expression model for ATRA-sensitive gastric cancer patients?
Study Notes
ATRA-Sensitivity Classification
- Gene Set Variation Analysis (GSVA) used to classify gastric cancer samples based on ATRA responsiveness.
- Samples categorized into three response levels: low, medium, high.
- Combination of clustering results from G-INT and G-DIFF profiles observed after 48 hours of treatment with either vehicle (DMSO) or ATRA.
- Ki-67 proliferation marker assessment revealed ATRA reduced Ki-67 levels in nine cases: five from G-DIFF, three from G-INT, and one unspecified.
Validation through RNA-Seq Analysis
- Gene Set Enrichment Analysis (GSEA) performed to validate RNA-Seq findings in gastric cancer cell lines and xenografts.
- Major macro-cluster up-regulated: Interferon Response & Immune Regulation.
- Major macro-cluster down-regulated: Extracellular Matrix (EMC) and Cell Interaction.
TCGA Analysis of Gastric Cancer Patients
- Nearest Template Prediction Classification (NTP) indicated a dominant G-INT profile among 375 gastric carcinoma samples.
- Importance of developing gene-expression models for identifying patients likely to respond positively to ATRA.
Gene-Expression Patterns and ATRA-Sensitivity
- Correlation between specific mRNA expression levels and ATRA-sensitivity established using computational methods.
- Identification of 26 mRNAs positively correlated and 16 mRNAs negatively correlated with ATRA sensitivity.
- STRING database analysis revealed four protein interaction networks formed by these genes.
Network Analysis
- Largest network includes 28 components related to tissue development and WNT pathway (e.g., PITX2, PAX9).
- Second network focuses on myogenesis and collagen homeostasis.
- Additional networks regulate pre-mRNA processing and metabolic/mitochondrial homeostasis.
Transcriptomic Characterization of Gastric-Cancer Cell Lines
- Transcriptomic profiles of 13 gastric cancer cell lines classified into two groups: G-INT and G-DIFF consistent with Tan et al.'s classification.
- Validation of transcriptomic coherence with CCLE database enhances study reliability.
- ATRA treatment observed to inhibit growth in G-INT neoplastic cells, associated with lipid homeostasis regulation.
Differential Gene Expression Analysis
- High ATRA-sensitivity correlates with G-INT cell lines (ATRA-score > 0.55) and low sensitivity in G-DIFF cell lines (ATRA-score < 0.55).
- RNA-seq experiments conducted after 48-hour treatment with ATRA showed correlation between transcript expressions and ATRA-scores.
- GSEA conducted indicated that ATRA reduces expression of genes regulated by the G2M checkpoint and E2F transcription factor.
Pathways Affected by ATRA
- ATRA treatment decreased expression of c-myc target genes, inhibiting cell proliferation.
- Notable interactome for lipid metabolism includes numerous factors such as MOGAT3, DGAT2, and PCK1, highlighting ATRA's role in lipid metabolic pathway alterations.
Differential Expression Analysis and ATRA Treatment Effects
- ATRA sensitivity classified as high (ATRA-score > 0.55) in seven cell lines; low sensitivity (ATRA-score < 0.55) in six cell lines.
- RNA-seq experiments involved treating each cell line with either a vehicle or ATRA (1.0 µM) for 48 hours, prior to growth suppression.
- Linear regression analyses reveal a significant correlation between ATRA-scores and mRNA fluctuations in response to ATRA.
- Gene Set Enrichment Analysis (GSEA) performed to identify altered pathways with the HALLMARK dataset.
Anti-Proliferative Mechanism of ATRA
- ATRA reduces gene expression linked to the G2M-checkpoint and E2F transcription-factor, inhibiting cell proliferation.
- Specific down-regulation of c-myc target genes observed in sensitive cell lines.
- Noteworthy interactome with 28 lipid metabolism-associated components, including MOGAT3, DGAT2, and CYP family members.
- Smaller networks highlight other lipid metabolism regulators such as SPTLC3 and DEGS2.
- In retinoid-sensitive G-DIFF cell lines, four specific genes (CYP26B1, RARB, DHRS3, TINAGL1) are significantly up-regulated.
ATRA Effects on G-INT and G-DIFF Cell Lines
- ATRA increases expression of six genes (IRF1, DHRS3, CTSS, PSMB10, CYP26B1, TINAGL1) in both G-DIFF and G-INT cell lines.
- Significant decrease in expression of AHNAK2 noted across all G-INT/G-DIFF cell lines.
- Interaction established between CTSS and PSMB10 with IRF1, and between CYP26B1 and DHRS3.
Role of Epigenetic Factors
- ATRA modulates epigenetic factors by influencing DNA methylation and histone modifications.
- The interactome of down-regulated gene products related to cell adhesion and motility might enhance epithelial polarization.
- Investigated five G-INT cell lines with low ATRA-sensitivity while also studying GSS, the only G-DIFF cell line with poor sensitivity.
Gene Expression Impact of ATRA
- ATRA affects expression in various cell lines: HGC-27 (6,063 genes), RERF-GC-1B (5,557 genes), and smaller impacts on LMSU (1,886 genes) and GCIY (914 genes).
- In ATRA-responsive cell lines, 33 genes up-regulated while 10 genes down-regulated.
- STRING analysis of up-regulated genes forms three distinct networks, with the largest surrounding IRF1, comprised of inflammation and antigen presentation factors.
Transcriptomic Characterization
- Initial clustering assessment of cell line samples indicated two transcriptomic profiles: Genomic Intestinal (G-INT) and Genomic Diffuse (G-DIFF).
- Validation of transcriptomic coherence with the CCLE database was performed using control-treated (DMSO) cell lines to ensure reliability in the cell line panel.
ATRA-Sensitivity Classification
- Gene Set Variation Analysis (GSVA) used to classify gastric cancer samples based on ATRA responsiveness.
- Samples categorized into three response levels: low, medium, high.
- Combination of clustering results from G-INT and G-DIFF profiles observed after 48 hours of treatment with either vehicle (DMSO) or ATRA.
- Ki-67 proliferation marker assessment revealed ATRA reduced Ki-67 levels in nine cases: five from G-DIFF, three from G-INT, and one unspecified.
Validation through RNA-Seq Analysis
- Gene Set Enrichment Analysis (GSEA) performed to validate RNA-Seq findings in gastric cancer cell lines and xenografts.
- Major macro-cluster up-regulated: Interferon Response & Immune Regulation.
- Major macro-cluster down-regulated: Extracellular Matrix (EMC) and Cell Interaction.
TCGA Analysis of Gastric Cancer Patients
- Nearest Template Prediction Classification (NTP) indicated a dominant G-INT profile among 375 gastric carcinoma samples.
- Importance of developing gene-expression models for identifying patients likely to respond positively to ATRA.
Gene-Expression Patterns and ATRA-Sensitivity
- Correlation between specific mRNA expression levels and ATRA-sensitivity established using computational methods.
- Identification of 26 mRNAs positively correlated and 16 mRNAs negatively correlated with ATRA sensitivity.
- STRING database analysis revealed four protein interaction networks formed by these genes.
Network Analysis
- Largest network includes 28 components related to tissue development and WNT pathway (e.g., PITX2, PAX9).
- Second network focuses on myogenesis and collagen homeostasis.
- Additional networks regulate pre-mRNA processing and metabolic/mitochondrial homeostasis.
Transcriptomic Characterization of Gastric-Cancer Cell Lines
- Transcriptomic profiles of 13 gastric cancer cell lines classified into two groups: G-INT and G-DIFF consistent with Tan et al.'s classification.
- Validation of transcriptomic coherence with CCLE database enhances study reliability.
- ATRA treatment observed to inhibit growth in G-INT neoplastic cells, associated with lipid homeostasis regulation.
Differential Gene Expression Analysis
- High ATRA-sensitivity correlates with G-INT cell lines (ATRA-score > 0.55) and low sensitivity in G-DIFF cell lines (ATRA-score < 0.55).
- RNA-seq experiments conducted after 48-hour treatment with ATRA showed correlation between transcript expressions and ATRA-scores.
- GSEA conducted indicated that ATRA reduces expression of genes regulated by the G2M checkpoint and E2F transcription factor.
Pathways Affected by ATRA
- ATRA treatment decreased expression of c-myc target genes, inhibiting cell proliferation.
- Notable interactome for lipid metabolism includes numerous factors such as MOGAT3, DGAT2, and PCK1, highlighting ATRA's role in lipid metabolic pathway alterations.
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Description
Summary Overview of the Outcomes:
This chapter explores the responsiveness of gastric cancer cells to All-trans Retinoic Acid (ATRA), highlighting its capacity to limit cell proliferation. The first goal is to categorize 37 gastric-cancer cell-lines into separate subgroups using the gene expression patterns obtained from the Cancer Cell Line Encyclopedia's RNA-sequencing data. In addition, the study involves evaluating ATRA-sensitivity in a significant number of these cell lines. Furthermore, we investigate the role of RARα in the anti-proliferative effects of ATRA and the genetic networks linked to ATRA sensitivity. Moreover, our research includes the assessment of ATRA's ability to limit growth in certain cell lines and tissue samples obtained from patients.
