Details for: LINC00921

Gene ID: 283876

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: LINC00921

Ensembl ID: ENSG00000281005

Description: long intergenic non-protein coding RNA 921

Cell Significance Landscape

Significant Cells

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

  • conventional dendritic cell CL0000990
    CSI 30.57
    rCSI 25.52%
    PRS 13.06
  • suprabasal keratinocyte CL4033013
    CSI 26.54
    rCSI 43.32%
    PRS 3.07
  • CD8-positive, alpha-beta memory T cell, CD45RO-positive CL0001203
    CSI 20.98
    rCSI 25.42%
    PRS 6.11
  • chondrocyte CL0000138
    CSI 18.52
    rCSI 29.45%
    PRS 3.66
  • melanocyte of skin CL1000458
    CSI 18.16
    rCSI 24.75%
    PRS 2.65
  • cytotoxic T cell CL0000910
    CSI 9.66
    rCSI 55.35%
    PRS 6.32
  • regulatory T cell CL0000815
    CSI 9.12
    rCSI 10.57%
    PRS 14.04
  • basal cell of epidermis CL0002187
    CSI 7.32
    rCSI 12.97%
    PRS 5.49
  • pericyte CL0000669
    CSI 5.1
    rCSI 13.58%
    PRS 27
  • helper T cell CL0000912
    CSI 0.54
    rCSI 0.77%
    PRS 6.02
  • innate lymphoid cell CL0001065
    CSI -20.7
    rCSI -42.75%
    PRS 6.64

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

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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Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • 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 [LINC00921](/details-gene/283876) is a long intergenic non-protein coding RNA (lncRNA) located on chromosome 16p13.3. Expression data reveal that [LINC00921](/details-gene/283876) is a highly significant marker in a distinct and functionally diverse set of cell types. **Overall**, it shows prominent expression in both immune cells, particularly [conventional dendritic cells](/details-cell/CL0000990), and in various cells of the skin and structural tissues, including [suprabasal keratinocytes](/details-cell/CL4033013) and [chondrocytes](/details-cell/CL0000138). This dual-context expression pattern suggests that [LINC00921](/details-gene/283876) may function as a key regulatory node in processes related to both adaptive immunity and tissue homeostasis, particularly in the context of the skin. ## Cellular Roles and Expression Landscape The expression profile of [LINC00921](/details-gene/283876) points to significant roles in two primary biological systems: the immune system and cutaneous/structural tissues. **`Overall`**, its highest significance is observed in [conventional dendritic cells](/details-cell/CL0000990) (CSI: 30.57), which are critical antigen-presenting cells that initiate adaptive immune responses. The gene is also highly significant in several adaptive lymphocyte populations, including [CD8-positive, alpha-beta memory T cells](/details-cell/CL0001203) (CSI: 20.98), [cytotoxic T cells](/details-cell/CL0000910) (CSI: 9.66), and [regulatory T cells](/details-cell/CL0000815) (CSI: 9.12). This strong expression signature across key players of the adaptive immune system suggests a potential role in antigen presentation, T cell activation, and the establishment of immunological memory. Concurrently, [LINC00921](/details-gene/283876) demonstrates a nearly equal level of significance in non-immune cell types. It is a defining marker for [suprabasal keratinocytes](/details-cell/CL4033013) (CSI: 26.54), the differentiating cells of the epidermis, as well as for [chondrocytes](/details-cell/CL0000138) (CSI: 18.52) and [melanocytes of skin](/details-cell/CL1000458) (CSI: 18.16). This pattern is consistent with a role in epithelial differentiation, cartilage maintenance, or melanogenesis. The specificity of its immune role is underscored by its status as a strong anti-marker for [innate lymphoid cells](/details-cell/CL0001065) (CSI: -20.70). This suggests that the function of [LINC00921](/details-gene/283876) may be constrained to the adaptive arm of the immune system, distinguishing it from pathways active in innate lymphoid lineages. ## Pathways and Molecular Function Based on the provided data, specific pathway annotations for [LINC00921](/details-gene/283876) are not detailed. As a long non-coding RNA, it is presumed to exert its function through regulatory mechanisms, such as guiding chromatin-modifying complexes, acting as a scaffold for protein interactions, or modulating the stability and translation of target mRNAs. The observed cell-type specificity allows for inference of its potential biological functions. Its high expression in [conventional dendritic cells](/details-cell/CL0000990) and various T cell subsets is consistent with a regulatory role in pathways governing antigen processing and presentation, T cell receptor signaling, and the differentiation of effector and memory T cells. Similarly, its prominence in [suprabasal keratinocytes](/details-cell/CL4033013) suggests an involvement in signaling pathways that control epidermal stratification and skin barrier formation, such as the Notch or p63 pathways. ## Research Directions The unique co-expression of [LINC00921](/details-gene/283876) in key cells of both the skin and the adaptive immune system makes it a compelling subject for further investigation, particularly at the intersection of these two systems. ### Testable Hypotheses 1. **Role in Dendritic Cell Function:** [LINC00921](/details-gene/283876) is a critical regulator of [conventional dendritic cell](/details-cell/CL0000990) maturation and antigen presentation. Its knockdown via RNA interference would impair the ability of dendritic cells to upregulate co-stimulatory molecules (e.g., CD80/CD86) and secrete IL-12 upon stimulation, leading to a reduced capacity to activate naive T cells. 2. **Role in Epidermal Differentiation:** [LINC00921](/details-gene/283876) is required for the terminal differentiation of human keratinocytes. Its expression is induced during calcium-mediated differentiation in vitro, and its depletion would disrupt the expression of key differentiation markers like Involucrin and Filaggrin, thereby compromising epidermal barrier integrity. 3. **Role in Cutaneous Immunity:** [LINC00921](/details-gene/283876) functions as a crucial mediator in the crosstalk between keratinocytes and immune cells during inflammatory skin conditions. In a model of psoriasis, [LINC00921](/details-gene/283876) may regulate the production of pro-inflammatory cytokines by [suprabasal keratinocytes](/details-cell/CL4033013), which in turn influences the recruitment and activation of skin-resident T cells. ### Suggested Experimental Approach To test the hypothesis that **[LINC00921](/details-gene/283876) regulates dendritic cell function**, one could perform loss-of-function studies in primary human cells. Monocytes would be isolated from healthy donor blood and differentiated into immature dendritic cells (DCs). These cells would then be transfected with antisense oligonucleotides (ASOs) or siRNAs targeting [LINC00921](/details-gene/283876) or a non-targeting control. Following knockdown, DCs would be matured using a stimulus like lipopolysaccharide (LPS). The functional consequences would be assessed by: (i) quantifying the surface expression of maturation markers (CD83, CD86, HLA-DR) by flow cytometry; (ii) measuring cytokine secretion (IL-12p70, TNF-alpha) by ELISA; and (iii) evaluating their T cell-stimulatory capacity in a mixed lymphocyte reaction (MLR) with allogeneic naive CD4+ T cells. A significant reduction in these readouts in the knockdown condition would confirm its role in DC-mediated T cell activation. ### Therapeutic Potential Given its high and specific expression in cell types central to inflammatory skin diseases like psoriasis and atopic dermatitis ([conventional dendritic cells](/details-cell/CL0000990), T cells, and keratinocytes), [LINC00921](/details-gene/283876) represents an attractive therapeutic target. As a non-coding RNA, it is amenable to targeting with nucleic acid-based therapies such as ASOs or siRNAs. A strategy involving the **inhibition** of [LINC00921](/details-gene/283876) could be particularly effective. A topically delivered ASO therapy could simultaneously dampen the hyper-proliferative keratinocyte phenotype and the underlying pathological immune activation, offering a dual-pronged approach to treating inflammatory dermatoses with potentially high local efficacy and minimal systemic side effects.