Details for: TM4SF1 AS1

Gene ID: 100874091

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: TM4SF1 AS1

Ensembl ID: ENSG00000240541

Description: TM4SF1 antisense RNA 1

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Significant Cells

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

  • luminal epithelial cell of mammary gland CL0002326
    CSI 2.3
    rCSI 4.18%
    PRS 98.75
  • basal cell of epidermis CL0002187
    CSI 2.28
    rCSI 4.04%
    PRS 80.11
  • CD8-positive, alpha-beta memory T cell, CD45RO-positive CL0001203
    CSI 1.44
    rCSI 1.74%
    PRS 85.49
  • suprabasal keratinocyte CL4033013
    CSI 1.34
    rCSI 2.18%
    PRS 81.64

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

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  • Node Color (Target Cell CSI, relative to current network):
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    • High
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    • 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 [TM4SF1 AS1](/details-gene/100874091) is a non-coding antisense RNA located on chromosome 3. The primary role of this gene appears to be associated with epithelial cell biology. **Overall**, expression data indicates its highest significance in the [luminal epithelial cell of mammary gland](/details-cell/CL0002326) and the [basal cell of epidermis](/details-cell/CL0002187), suggesting a function in the maintenance or identity of these structural tissues. A secondary, but notable, association is observed with a subset of memory T cells, pointing towards a potential role in the adaptive immune system. ## Cellular Roles and Expression Landscape The expression pattern of [TM4SF1 AS1](/details-gene/100874091) strongly implicates it in the function of epithelial and keratinocyte lineages. Its most significant expression is found in [luminal epithelial cell of mammary gland](/details-cell/CL0002326) (CSI: 2.30) and various skin keratinocytes, including [basal cell of epidermis](/details-cell/CL0002187) (CSI: 2.28) and [suprabasal keratinocyte](/details-cell/CL4033013) (CSI: 1.34). This clustering of significance within cells of the epidermis and mammary gland suggests a specialized role in tissue homeostasis, differentiation, or barrier function within these ectoderm-derived tissues. Interestingly, [TM4SF1 AS1](/details-gene/100874091) also shows moderate significance in [CD8-positive, alpha-beta memory T cell, CD45RO-positive](/details-cell/CL0001203) (CSI: 1.44). This suggests a potential secondary function within the immune system, possibly related to the establishment or maintenance of long-term T cell memory. The significance in this lymphocyte population is less pronounced than in epithelial cells, indicating its primary role likely lies outside of the hematopoietic system. ## Pathways and Molecular Function Specific functional pathway annotations for [TM4SF1 AS1](/details-gene/100874091) are not detailed in the provided data. However, as an antisense RNA to the protein-coding gene *TM4SF1*, its primary molecular function is likely regulatory. Antisense transcripts can modulate the expression of their sense counterparts through mechanisms such as transcriptional interference, mRNA masking, or by directing epigenetic modifications. The *TM4SF1* gene encodes a tetraspanin protein involved in cell proliferation, motility, and signaling, particularly in endothelial and tumor cells. Therefore, [TM4SF1 AS1](/details-gene/100874091) may function to fine-tune these critical cellular processes in the specific epithelial and immune contexts where it is expressed. ## Research Directions The specific expression of [TM4SF1 AS1](/details-gene/100874091) in epithelial lineages and a memory T cell subset warrants further investigation to elucidate its precise biological role. ### Testable Hypotheses 1. **[TM4SF1 AS1](/details-gene/100874091) regulates keratinocyte differentiation and stratification in the epidermis.** Its high significance in both basal and suprabasal keratinocytes suggests it may control the transition between these cell states, possibly by modulating the expression of its sense partner, *TM4SF1*, a known player in cell adhesion and signaling. 2. **[TM4SF1 AS1](/details-gene/100874091) is involved in the long-term survival or recall capacity of memory CD8+ T cells.** Its expression in this specific memory subset could be crucial for maintaining cellular quiescence or enabling rapid reactivation upon secondary antigen encounter. ### Proposed Experiment To test the hypothesis that [TM4SF1 AS1](/details-gene/100874091) regulates keratinocyte differentiation, a loss-of-function study could be performed. Primary human keratinocytes could be cultured and transfected with antisense oligonucleotides (ASOs) or a CRISPRi system targeting [TM4SF1 AS1](/details-gene/100874091). The impact of its knockdown would be assessed by inducing differentiation via a calcium switch. Endpoints would include quantitative PCR and western blotting to measure markers of basal (KRT14, ITGA6) and differentiated (KRT10, Involucrin) keratinocytes, as well as the expression of the sense *TM4SF1* transcript and protein. Functional consequences could be evaluated using an in-vitro wound healing assay to assess cell migration and proliferation. ### Therapeutic Potential As a non-coding RNA, [TM4SF1 AS1](/details-gene/100874091) presents a potential therapeutic target amenable to nucleic acid-based drugs like ASOs. Given that its sense partner, *TM4SF1*, is overexpressed in various carcinomas, including breast and skin cancers, [TM4SF1 AS1](/details-gene/100874091) could be a key upstream regulator. If this lncRNA is found to promote oncogenic phenotypes in these tissues, its specific expression pattern suggests that therapeutic **inhibition** could offer a targeted strategy to reduce tumor growth or metastasis with potentially limited off-target effects on unrelated cell lineages.