Details for: CLMAT3

Gene ID: 101927096

Gene Type:  ncRNA (Non-coding RNA)  - A functional RNA molecule that is transcribed from DNA but not translated into a protein. Includes classes like miRNA and lncRNA.

Symbol: CLMAT3

Ensembl ID: ENSG00000249035

Description: colorectal liver metastasis associated transcript 3

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • mural cell CL0008034
    CSI 4.84
    rCSI 16.39%
    PRS 96.63
  • adipocyte CL0000136
    CSI 2.56
    rCSI 3.28%
    PRS 94.72

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

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  • Node Color (Target Cell CSI, relative to current network):
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    • High
    • Medium
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    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

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Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [CLMAT3](/details-gene/101927096) is a long non-coding RNA (lncRNA) located on chromosome 5q33.1. Its official name, colorectal liver metastasis associated transcript 3, points towards a potential role in cancer progression. The available expression data indicates that [CLMAT3](/details-gene/101927096) is a significant transcript within the tissue microenvironment, showing prominent expression in mesenchymal cell types such as [mural cells](/details-cell/CL0008034) and [adipocytes](/details-cell/CL0000136). This suggests it may be involved in regulating the structural and metabolic components that support tissue homeostasis and pathology. ## Cellular Roles and Expression Landscape The expression profile of [CLMAT3](/details-gene/101927096) highlights its significance in specific stromal and mesenchymal cell populations. - **Primary Expression Contexts:** **Overall**, the gene shows its highest significance in [mural cells](/details-cell/CL0008034) (CSI: 4.84), which include pericytes and vascular smooth muscle cells critical for blood vessel stability and function. It is also significantly expressed in [adipocytes](/details-cell/CL0000136) (CSI: 2.56), the primary cells of adipose tissue involved in energy storage and endocrine signaling. This expression pattern suggests a specialized role for [CLMAT3](/details-gene/101927096) in the tumor microenvironment, potentially influencing processes such as angiogenesis (via [mural cells](/details-cell/CL0008034)) and metabolic reprogramming (via [adipocytes](/details-cell/CL0000136)) that are crucial for tumor growth and metastasis. ## Pathways and Molecular Function Detailed functional annotation for [CLMAT3](/details-gene/101927096) is not currently available. As a non-coding RNA, it is presumed to function by regulating the expression of other genes at the transcriptional or post-transcriptional level. Based on its name and its high expression in key cells of the tumor microenvironment, its function is likely related to the molecular pathways governing cell-cell communication, extracellular matrix remodeling, angiogenesis, and metabolic support that facilitate cancer cell invasion and colonization of distant organs like the liver. ## Research Directions The specific expression of [CLMAT3](/details-gene/101927096) in stromal cells associated with cancer progression opens up several avenues for future investigation. **Proposed Hypotheses:** 1. [CLMAT3](/details-gene/101927096) expression in [mural cells](/details-cell/CL0008034) modulates the secretion of pro-angiogenic factors, thereby promoting new blood vessel formation that is essential for tumor growth and metastasis. 2. In the context of liver metastasis, [CLMAT3](/details-gene/101927096) in peritumoral [adipocytes](/details-cell/CL0000136) drives a shift towards a cancer-associated adipocyte (CAA) phenotype, leading to the release of lipids and cytokines that fuel cancer cell proliferation. **Experimental Approach:** To test the hypothesis that [CLMAT3](/details-gene/101927096) in [mural cells](/details-cell/CL0008034) is pro-angiogenic, one could perform a knockdown of [CLMAT3](/details-gene/101927096) in primary human pericytes using antisense oligonucleotides (ASOs). Conditioned media from these knockdown pericytes could then be applied to human umbilical vein endothelial cells (HUVECs) in a Matrigel tube formation assay. A significant reduction in endothelial network formation, as measured by tube length and branch points, compared to controls would provide evidence for a non-cell-autonomous, pro-angiogenic role for [CLMAT3](/details-gene/101927096). **Therapeutic Potential:** As a lncRNA implicated in metastasis, [CLMAT3](/details-gene/101927096) represents a potential therapeutic target. Inhibition, rather than activation, would be the likely therapeutic strategy. Given its expression in stromal cells of the tumor microenvironment, targeting [CLMAT3](/details-gene/101927096) with ASOs or other RNA-targeting modalities could disrupt the supportive niche for cancer cells. This approach offers a novel strategy to interfere with tumor progression by targeting the host environment rather than the cancer cells directly, potentially overcoming resistance mechanisms.