4 Outline of Research Objectives:

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Questions and Answers

What is a primary goal of the PhD thesis related to ATRA?

To develop traditional chemotherapy methods for Gastric Cancer.

To provide pre-clinical data for ATRA's potential in treating Gastric Cancer. (correct)

To analyze the dietary impacts on Gastric Cancer progression.

To study the history of Gastric Cancer treatment.

What methodologies will be used to define the genomic profiles in the research?

Microarray analysis followed by Western blotting.

Whole exome sequencing combined with CRISPR technology.

SNP genotyping associated with classical genetic mapping.

RNA-sequencing based on non-oriented gene-expression approaches. (correct)

How does the project aim to classify Gastric Cancer cell lines?

Based on their geographical location.

Relating them to patient demographics and symptoms.

Using molecular profiles to identify different sub-groups. (correct)

According to their response to various drug treatments.

Which RNA-Sequencing tool is mentioned for analyzing Gastric Cancer cell lines?

NextSeq-500 Illumina. Signup and view all the answers

What is one of the short-term goals related to ATRA in the project?

To develop a diagnostic tool for selecting patients for ATRA therapy. Signup and view all the answers

What aspect of Gastric Cancer does the research identify as heterogeneous?

The underlying genomic profiles among cell lines. Signup and view all the answers

What is a long-term objective related to ATRA therapies proposed in the research?

To develop therapeutic combinations with gene-network targeting. Signup and view all the answers

What is one method used in the experimental design of Aim 1?

Applying NextSeq-500 for RNA-Sequencing. Signup and view all the answers

What does the differential analysis in Aim 1 seek to evaluate?

Gene transcription effects activated by ATRA treatment. Signup and view all the answers

What aspect of Gastric Cancer treatment is being explored in relation to ATRA?

Sensitivity of Gastric Cancer cells to ATRA Signup and view all the answers

What is a major limitation noted regarding ATRA's application in Gastric Cancer?

Lack of systematic data on its anti-tumor action Signup and view all the answers

Which innovative strategy may be considered if ATRA is found to promote Gastric Cancer cell proliferation?

Investigation of inverse-agonists of retinoid receptors Signup and view all the answers

What is the purpose of developing diagnostic tools in the context of ATRA therapies?

To predict patient sensitivity to ATRA Signup and view all the answers

What type of studies does the proposed research not foresee any technical problems with?

High-throughput genomic studies Signup and view all the answers

What emerging theme in medicine is highlighted as relevant to the ongoing research?

Personalized medicine Signup and view all the answers

What characteristic distinguishes ATRA from conventional chemotherapeutics?

Its mechanism of action Signup and view all the answers

Why is the exploration of ATRA's therapeutic potential in Gastric Cancer considered limited?

Very few studies conducted on ATRA in this context Signup and view all the answers

What is a potential outcome of completing the project exploring ATRA in Gastric Cancer?

Foundation for phase I/II trials based on ATRA in gastric cancer Signup and view all the answers

What type of data is being collected through high-throughput genomic studies?

Genomic profiles of various cancers Signup and view all the answers

What is the primary focus of the tissue-slice culture model developed in the study?

To evaluate the activity of pharmacological agents on primary-tumor specimens. Signup and view all the answers

Which technique is used to validate the gene-networks modulated by ATRA in Gastric Cancer tissue slices?

RNA-sequencing experiments. Signup and view all the answers

What is the required time frame for processing surgical samples after collection?

Within 24 hours from collection. Signup and view all the answers

What measurement technique is employed to assess cell growth inhibition and apoptosis in the study?

Gene expression profiling. Signup and view all the answers

In the context of ATRA sensitivity, what main outcome does the study aim to correlate with in vitro responses?

The genomic profiles associated with ATRA sensitivity. Signup and view all the answers

What is the primary focus of the study regarding ATRA in Gastric Cancer?

To assess the therapeutic potential of ATRA in specific groups. Signup and view all the answers

Which biomarker is used to assess apoptosis in the study?

Active caspase-3 Signup and view all the answers

What technique is employed to measure gene expression changes in the treated tissue slices?

RNA-sequencing Signup and view all the answers

What is the significance of evaluating Ki67 levels in this study?

To define growth inhibition. Signup and view all the answers

What is the role of the computational model mentioned in the study?

To establish correlations with in vitro sensitivity to ATRA. Signup and view all the answers

What type of culture medium is used for incubating tissue slices with ATRA?

Optimized culture medium with ATRA. Signup and view all the answers

Which gene expression technology is utilized in the evaluation of proliferation associated genes?

PCR technologies. Signup and view all the answers

What is the consequence of ATRA treatment that the study aims to explore?

Alteration in gene expression profiles. Signup and view all the answers

What kind of samples are prioritized for confirming the predictive model?

Primary Gastric Cancer samples. Signup and view all the answers

What is the expected outcome regarding ATRA's effect on Ki67 levels?

A significant reduction in Ki67 levels is expected. Signup and view all the answers

What is the primary purpose of developing a new gene-expression model in the context of Gastric Cancer?

To predict ATRA sensitivity in stomach tumors Signup and view all the answers

Which methodology is emphasized for clustering and subgroup identification according to molecular profiles?

Unsupervised and unbiased clustering techniques Signup and view all the answers

What does the AUC/ATRA-score reflect in the context of the study?

In vitro sensitivity to the anti-proliferative action of ATRA Signup and view all the answers

How many Gastric Cancer cell lines are utilized in the experimental design for predicting ATRA sensitivity?

27 Signup and view all the answers

What is the main goal of using bioinformatics methodologies in the study?

To create a model predicting ATRA sensitivity independent of tumor type Signup and view all the answers

What is the significance of optimizing and validating the new gene-expression model?

To maximize specificity and achieve optimal results in Gastric Cancer Signup and view all the answers

Which approach enables the retrieval of transcriptomic expression data for the Gastric Cancer cell lines?

CCLE (Cancer Cell Line Encyclopaedia) Signup and view all the answers

Why is there a focus on selecting Gastric Cancer patients who may benefit from ATRA-based treatments?

To provide personalized treatment options for better outcomes Signup and view all the answers

Study Notes

Study Objectives and Aims

Primary goal: Provide pre-clinical data on all-trans retinoic acid (ATRA) for personalized treatment of Gastric Cancer.
Define molecular mechanisms and gene-networks linked to ATRA's anti-tumor activity in specific subgroups of Gastric Cancer.
Develop a diagnostic tool for selecting Gastric Cancer patients suitable for ATRA-based therapies.
Long-term aim: Create rationale for therapeutic combinations of ATRA with agents targeting specific gene-networks.

Specific Aim 1: ATRA-Sensitivity and Genomic Profiles

Objective: Assess ATRA-sensitivity of Gastric Cancer cell lines and classify molecular profiles to identify sub-groups.
Perform RNA-Sequencing on a panel of 15 Gastric Cancer cell lines (NextSeq-500 Illumina) to investigate transcriptomic profiles.
Characterize gene transcription effects induced by ATRA treatment.

Specific Aim 2: Gene-Expression Model Development

Utilize a larger panel of 27 Gastric Cancer cell lines to establish a predictive gene-expression model for ATRA sensitivity.
Evaluate response to ATRA using an in vitro sensitivity scoring system (AUC/ATRA-score).
Profile gene-expression data retrieved from the Cancer Cell Line Encyclopedia (CCLE) for model validation and optimization.

Specific Aim 3: Validation Using Primary Tumor Samples

Transition from cell line studies to short-term tissue-slice cultures of primary Gastric Cancer specimens.
Test ATRA's anti-tumor activity on fresh surgical samples from patients while monitoring cell growth inhibition and apoptosis.
Establish correlation between in vitro ATRA responses and genomic profiles to refine predictive capacity of the gene-expression model.

Materials & Methods Overview

Apply comprehensive bioinformatics and computational techniques for data analysis and gene expression profiling.
Assess growth inhibition through quantitative Ki67 expression and apoptosis using activated caspase-3 markers.
Implement RNA extraction from treated tissue slices for subsequent RNA-sequencing.

Risk Analysis

Anticipated technical feasibility for genomic studies, with no major challenges expected.
Lack of systematic literature on ATRA’s anti-tumor effects in Gastric Cancer may influence the study direction.
If ATRA promotes rather than inhibits Gastric Cancer cell proliferation, future research may shift towards retinoid receptor inverse-agonists.

Significance and Innovation

ATRA presents a non-traditional cancer treatment contrasting typical chemotherapeutics, with limited studies on its efficacy in Gastric Cancer.
Project aims to elucidate the therapeutic potential of ATRA, promoting insights into novel anti-cancer agents, particularly in personalized medicine.
Development of precise diagnostic tools to predict patient sensitivity to ATRA-based therapies is essential for tailoring treatment plans.
Completion of the project could establish justification for Phase I/II clinical trials involving ATRA and related retinoids in Gastric Cancer patients.

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Description

The primary purpose of the PhD thesis is to provide pre-clinical data on the potential use of ATRA in the personalized treatment of Gastric Cancer. In addition, the project aims to define the molecular mechanisms and gene-networks underlying the expected anti-tumor activity exerted by ATRA in specific subgroups of Gastric Cancer using non-oriented gene-expression approaches based on RNA-sequencing. A further goal is to develop a novel diagnostic tool to be used for the selection of Gastric Cancer patients who may benefit from ATRA-based therapies. A final and long-term goal of the project is to develop rationale therapeutic combinations between ATRA and compounds targeting specific components of the gene-networks identified in the previous points.The primary purpose of the PhD thesis is to provide pre-clinical data on the potential use of ATRA in the personalized treatment of Gastric Cancer. In addition, the project aims to define the molecular mechanisms and gene-networks underlying the expected anti-tumor activity exerted by ATRA in specific subgroups of Gastric Cancer using non-oriented gene-expression approaches based on RNA-sequencing. A further goal is to develop a novel diagnostic tool to be used for the selection of Gastric Cancer patients who may benefit from ATRA-based therapies. A final and long-term goal of the project is to develop rationale therapeutic combinations between ATRA and compounds targeting specific components of the gene-networks identified in the previous points.