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Related Concept Videos

Tumor Progression02:07

Tumor Progression

Tumor progression is a phenomenon where the pre-formed tumor acquires successive mutations to become clinically more aggressive and malignant. In the 1950s, Foulds first described the stepwise progression of cancer cells through successive stages.
Colon cancer is one of the best-documented examples of tumor progression. Early mutation in the APC gene in colon cells causes a small growth on the colon wall called a polyp. With time, this polyp grows into a benign, pre-cancerous tumor. Further...
Targeted Cancer Therapies02:57

Targeted Cancer Therapies

The targeted cancer therapies, also known as “molecular targeted therapies,” take advantage of the molecular and genetic differences between the cancer cells and the normal cells. It needs a thorough understanding of the cancer cells to develop drugs that can target specific molecular aspects that drive the growth, progression, and spread of cancer cells without affecting the growth and survival of other normal cells in the body.
There are several types of targeted therapies against specific...
Tumor Progression02:07

Tumor Progression

Tumor progression is a phenomenon where the pre-formed tumor acquires successive mutations to become clinically more aggressive and malignant. In the 1950s, Foulds first described the stepwise progression of cancer cells through successive stages.
Colon cancer is one of the best-documented examples of tumor progression. Early mutation in the APC gene in colon cells causes a small growth on the colon wall called a polyp. With time, this polyp grows into a benign, pre-cancerous tumor. Further...
The Tumor Microenvironment02:17

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Every normal cell or tissue is embedded in a complex local environment called stroma, consisting of different cell types, a basal membrane, and blood vessels. As normal cells mutate and develop into cancer cells, their local environment also changes to allow cancer progression. The tumor microenvironment (TME) consists of a complex cellular matrix of stromal cells and the developing tumor. The cross-talk between cancer cells and surrounding stromal cells is critical to disrupt normal tissue...
Targeted Cancer Therapies02:57

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The targeted cancer therapies, also known as “molecular targeted therapies,” take advantage of the molecular and genetic differences between the cancer cells and the normal cells. It needs a thorough understanding of the cancer cells to develop drugs that can target specific molecular aspects that drive the growth, progression, and spread of cancer cells without affecting the growth and survival of other normal cells in the body.
There are several types of targeted therapies against specific...
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Tumor Immunotherapy

Immunotherapy is a treatment that boosts or manipulates the immune system to fight diseases, including cancer. For instance, by stimulating an immune response through vaccinations against viruses that cause cancers, like hepatitis B virus and human papillomavirus, these diseases can be prevented. Nonetheless, some cancer cells can avoid the immune system due to their rapid mutation and division. The immune response to many cancers involves three phases: elimination, equilibrium, and escape.

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ShinyTHOR app: Shiny-built tumor high-throughput omics-based roadmap.

Eduardo Navarrete-Bencomo1,2, Anthony Vladimir Campos Segura3,4,5, Orlando R Sevillano6

  • 1Unidad Profesional Interdisciplinaria de Biotecnología del Instituto Politécnico Nacional, Av. Luis Enrique Erro S/N, Zacatenco, Alcaldía Gustavo A. Madero, Ciudad de México, CP 07738, México.

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|May 19, 2025
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Summary

ShinyTHOR offers a user-friendly web app for exploring multi-omic and drug response data from cancer cell lines. This tool enhances accessibility for researchers, facilitating deeper insights into cancer biology and drug sensitivity.

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Area of Science:

  • Cancer research
  • Bioinformatics
  • Genomics

Background:

  • The Cancer Cell Line Encyclopedia (CCLE) provides extensive multi-omic and drug response data for over 1000 cancer cell lines.
  • Current tools like DepMap lack integrated analysis capabilities for diverse molecular data types and drug responses.
  • Accessing and comparing this complex data often requires specialized bioinformatics expertise, limiting its use for many researchers.

Purpose of the Study:

  • To develop ShinyTHOR, an intuitive web application for accessing and analyzing multi-omic and drug-related data from cancer cell lines.
  • To integrate data from CCLE, miRTarBase, circInteractome, and the Genomics of Drug Sensitivity in Cancer (GDSC) within a single platform.
  • To provide researchers with tools for comparative analysis of gene expression, drug sensitivity, and molecular interactions.

Main Methods:

  • Development of a web application utilizing the Shiny framework.
  • Integration of diverse datasets including transcriptomic, metabolomic, methylomic, proteomic, and miRNomic data.
  • Implementation of six distinct analytical modules for exploring cell line data, gene sets, molecular interactions, and drug responses.

Main Results:

  • ShinyTHOR provides intuitive access to multi-omic and drug sensitivity data.
  • The application enables comparative analysis of molecular markers, drug IC50 values, and gene set enrichment.
  • Modules facilitate exploration of miRNA-target interactions, miRNA effects on translation, and circRNA/miRNA modulation.
  • Validation using a gastric cancer prognosis study (GES7) demonstrated the tool's utility.

Conclusions:

  • ShinyTHOR democratizes access to complex cancer cell line data for a broader research community.
  • The web app facilitates hypothesis generation and discovery in cancer biology and precision medicine.
  • ShinyTHOR serves as a valuable resource for researchers investigating cancer cell line dependencies and drug responses.