Details for: LEF1

Gene ID: 51176

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: LEF1

Ensembl ID: ENSG00000138795

Description: lymphoid enhancer binding factor 1

Cell Significance Landscape

Associated with

Significant Cells

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

  • central memory CD8-positive, alpha-beta T cell CL0000907
    CSI 39.58
    rCSI 26.66%
    PRS 93.16
  • double-positive, alpha-beta thymocyte CL0000809
    CSI 35.79
    rCSI 36.48%
    PRS 90.63
  • naive thymus-derived CD8-positive, alpha-beta T cell CL0000900
    CSI 29.7
    rCSI 20.86%
    PRS 93.32
  • cerebral cortex endothelial cell CL1001602
    CSI 27.95
    rCSI 48.34%
    PRS 73.95
  • naive thymus-derived CD4-positive, alpha-beta T cell CL0000895
    CSI 24.2
    rCSI 30.41%
    PRS 94.24
  • neural crest cell CL0011012
    CSI 19.14
    rCSI 15.13%
    PRS 71.36
  • central memory CD4-positive, alpha-beta T cell CL0000904
    CSI 18.18
    rCSI 10.73%
    PRS 94.93
  • pro-B cell CL0000826
    CSI 16.52
    rCSI 13.68%
    PRS 84.07
  • mature NK T cell CL0000814
    CSI 14.43
    rCSI 18.45%
    PRS 90.28
  • erythrocyte CL0000232
    CSI 12.03
    rCSI 27.3%
    PRS 82.19
  • CD4-positive, CD25-positive, alpha-beta regulatory T cell CL0000792
    CSI 11.57
    rCSI 11.37%
    PRS 93.46
  • melanocyte CL0000148
    CSI 11.48
    rCSI 8.5%
    PRS 75.75
  • double negative thymocyte CL0002489
    CSI 10.94
    rCSI 7.61%
    PRS 92.23
  • neuroblast (sensu Vertebrata) CL0000031
    CSI 7.53
    rCSI 9.67%
    PRS 78.08
  • thymocyte CL0000893
    CSI 7.43
    rCSI 26.4%
    PRS 96.68
  • vascular leptomeningeal cell CL4023051
    CSI 7.39
    rCSI 12.95%
    PRS 76.22
  • naive T cell CL0000898
    CSI 7.24
    rCSI 5.04%
    PRS 93.84
  • mature alpha-beta T cell CL0000791
    CSI 7.06
    rCSI 25.55%
    PRS 94.96
  • precursor B cell CL0000817
    CSI 7.05
    rCSI 6.18%
    PRS 88.49
  • neuroblast (sensu Nematoda and Protostomia) CL0000338
    CSI 6.91
    rCSI 7.98%
    PRS 74.2
  • CD4-positive helper T cell CL0000492
    CSI 6.45
    rCSI 4.88%
    PRS 92.73
  • CD4-positive, alpha-beta thymocyte CL0000810
    CSI 6.31
    rCSI 5.05%
    PRS 93.1
  • mononuclear phagocyte CL0000113
    CSI 6.04
    rCSI 13.3%
    PRS 85.46
  • effector CD8-positive, alpha-beta T cell CL0001050
    CSI 5.85
    rCSI 4.45%
    PRS 93.14
  • fraction A pre-pro B cell CL0002045
    CSI 5.7
    rCSI 6.53%
    PRS 91.06
  • activated CD4-positive, alpha-beta T cell CL0000896
    CSI 5.56
    rCSI 5.14%
    PRS 94.41
  • radial glial cell CL0000681
    CSI 5.28
    rCSI 7.34%
    PRS 80.38
  • fallopian tube secretory epithelial cell CL4030006
    CSI 5.07
    rCSI 4.88%
    PRS 81.34
  • mesenchymal cell CL0008019
    CSI 4.85
    rCSI 12.32%
    PRS 75.64
  • renal alpha-intercalated cell CL0005011
    CSI 4.85
    rCSI 6.48%
    PRS 87.4
  • CD4-positive, alpha-beta memory T cell CL0000897
    CSI 4.8
    rCSI 3.44%
    PRS 93.12
  • mature T cell CL0002419
    CSI 4.58
    rCSI 3.56%
    PRS 93.68
  • lymphoid lineage restricted progenitor cell CL0000838
    CSI 4.55
    rCSI 17.69%
    PRS 94.62
  • T follicular helper cell CL0002038
    CSI 4.36
    rCSI 3.26%
    PRS 93.07
  • CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell CL0000915
    CSI 4.21
    rCSI 19.12%
    PRS 95.12
  • kidney collecting duct intercalated cell CL1001432
    CSI 4.09
    rCSI 29.19%
    PRS 79.55
  • suprabasal keratinocyte CL4033013
    CSI 4.04
    rCSI 6.6%
    PRS 49.09
  • chondrocyte CL0000138
    CSI 3.85
    rCSI 6.13%
    PRS 75.29
  • ciliated epithelial cell CL0000067
    CSI 3.79
    rCSI 3.33%
    PRS 71.44
  • blood vessel endothelial cell CL0000071
    CSI 3.68
    rCSI 7.63%
    PRS 78.83
  • alpha-beta T cell CL0000789
    CSI 3.67
    rCSI 4.3%
    PRS 93.56
  • regulatory T cell CL0000815
    CSI 3.52
    rCSI 4.08%
    PRS 81.35
  • basal cell of epidermis CL0002187
    CSI 3.47
    rCSI 6.15%
    PRS 51.02
  • effector memory CD8-positive, alpha-beta T cell CL0000913
    CSI 3.29
    rCSI 2.99%
    PRS 92.31
  • early lymphoid progenitor CL0000936
    CSI 3.12
    rCSI 2.74%
    PRS 86.7
  • T-helper 17 cell CL0000899
    CSI 3.11
    rCSI 2.47%
    PRS 95.93
  • choroid plexus epithelial cell CL0000706
    CSI 2.89
    rCSI 4.73%
    PRS 71.77
  • effector memory CD4-positive, alpha-beta T cell CL0000905
    CSI 2.86
    rCSI 3.89%
    PRS 95.55
  • retinal blood vessel endothelial cell CL0002585
    CSI 2.83
    rCSI 4.52%
    PRS 85.45
  • lung pericyte CL0009089
    CSI 2.71
    rCSI 7.15%
    PRS 88.04
  • parietal epithelial cell CL1000452
    CSI 2.58
    rCSI 6.89%
    PRS 74.1
  • endothelial cell of vascular tree CL0002139
    CSI 2.45
    rCSI 13.37%
    PRS 78.38
  • megakaryocyte-erythroid progenitor cell CL0000050
    CSI 2.32
    rCSI 2.09%
    PRS 80.12
  • small pre-B-II cell CL0000954
    CSI 2.28
    rCSI 2.2%
    PRS 93.33
  • memory T cell CL0000813
    CSI 2.25
    rCSI 4.34%
    PRS 96
  • group 3 innate lymphoid cell CL0001071
    CSI 2.06
    rCSI 1.55%
    PRS 87.38
  • effector CD4-positive, alpha-beta T cell CL0001044
    CSI 2
    rCSI 5.75%
    PRS 95.77
  • large pre-B-II cell CL0000957
    CSI 1.96
    rCSI 5.6%
    PRS 86.43
  • granulocyte CL0000094
    CSI 1.88
    rCSI 2.88%
    PRS 88.45
  • CD8-positive, CD28-negative, alpha-beta regulatory T cell CL0000920
    CSI 1.78
    rCSI 3.56%
    PRS 92.16
  • brain vascular cell CL4023072
    CSI 1.69
    rCSI 17.45%
    PRS 75.63
  • mesothelial cell CL0000077
    CSI 1.59
    rCSI 6.23%
    PRS 60.73
  • activated CD4-positive, alpha-beta T cell, human CL0001043
    CSI 1.58
    rCSI 3.81%
    PRS 96.37
  • late pro-B cell CL0002048
    CSI 1.57
    rCSI 3.93%
    PRS 93.48
  • CD8-positive, alpha-beta cytotoxic T cell CL0000794
    CSI 1.43
    rCSI 1.71%
    PRS 94.69
  • innate lymphoid cell CL0001065
    CSI 1.37
    rCSI 2.82%
    PRS 78.43
  • chandelier pvalb GABAergic cortical interneuron CL4023036
    CSI 1.28
    rCSI 4.02%
    PRS 68.48
  • T-helper 1 cell CL0000545
    CSI 1.18
    rCSI 2.13%
    PRS 94.6
  • CD8-positive, alpha-beta memory T cell, CD45RO-positive CL0001203
    CSI 1.06
    rCSI 1.28%
    PRS 62.59
  • double negative T regulatory cell CL0011024
    CSI 0.98
    rCSI 18.67%
    PRS 94.9
  • endothelial cell of uterus CL0009095
    CSI 0.98
    rCSI 7.16%
    PRS 89.28
  • helper T cell CL0000912
    CSI 0.9
    rCSI 1.27%
    PRS 80.39
  • blood vessel smooth muscle cell CL0019018
    CSI 0.66
    rCSI 5.33%
    PRS 76.61
  • melanocyte of skin CL1000458
    CSI 0.6
    rCSI 0.82%
    PRS 49.07
  • group 2 innate lymphoid cell CL0001069
    CSI 0.4
    rCSI 2.17%
    PRS 95.66

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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Comma-separated if multiple.

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 [LEF1](/details-gene/51176) (Lymphoid Enhancer Binding Factor 1) is a protein-coding gene located on chromosome 4q25 that encodes a crucial transcription factor belonging to the T-cell factor (TCF)/LEF family. As a key nuclear effector of the [Canonical wnt signaling pathway](/details-ontology/GO:0060070) ([GO:0060070](https://www.ebi.ac.uk/QuickGO/term/GO:0060070)), [LEF1](/details-gene/51176) plays a central role in embryonic development, hematopoiesis, and tissue homeostasis. Its expression is particularly significant throughout T-cell development, with high levels observed in [double-positive, alpha-beta thymocyte](/details-cell/CL0000809)s and various naive and memory T-cell subsets. Functionally, [LEF1](/details-gene/51176) binds to DNA through its high-mobility group (HMG) box domain and, upon interaction with beta-catenin, activates the transcription of Wnt target genes. Its dysregulation is associated with various developmental abnormalities and cancers, and it is linked to OMIM entry [153245](https://omim.org/entry/153245). ## Cellular Roles and Expression Landscape The expression profile of [LEF1](/details-gene/51176) underscores its fundamental role in the adaptive immune system, particularly within the T-lymphocyte lineage. **Overall**, the gene shows the highest significance in T-cell progenitors and mature T-cell subtypes. It is a defining marker for [central memory CD8-positive, alpha-beta T cell](/details-cell/CL0000907), [double-positive, alpha-beta thymocyte](/details-cell/CL0000809), and [naive thymus-derived CD8-positive, alpha-beta T cell](/details-cell/CL0000900), indicating its continuous involvement from thymic selection to the establishment of memory populations. Its high significance extends to CD4-positive lineages, including [naive thymus-derived CD4-positive, alpha-beta T cell](/details-cell/CL0000895) and [central memory CD4-positive, alpha-beta T cell](/details-cell/CL0000904). Early lymphocyte development is also heavily influenced by [LEF1](/details-gene/51176), as evidenced by its expression in [pro-B cell](/details-cell/CL0000826)s and [double negative thymocyte](/details-cell/CL0002489)s. Beyond the hematopoietic system, [LEF1](/details-gene/51176) exhibits significant expression in several non-immune cell types, consistent with its established role in embryonic development. Its high CSI in [cerebral cortex endothelial cell](/details-cell/CL1001602), [neural crest cell](/details-cell/CL0011012), [melanocyte](/details-cell/CL0000148), and [neuroblast (sensu Vertebrata)](/details-cell/CL0000031) suggests its participation in vasculogenesis, neural development, and pigmentation, processes known to be regulated by Wnt signaling. This broad but specific expression pattern highlights [LEF1](/details-gene/51176) as a master regulator in cell fate decisions across multiple tissues. ## Pathways and Molecular Function [LEF1](/details-gene/51176) functions primarily as a DNA-binding transcription factor ([GO:0003700](https://www.ebi.ac.uk/QuickGO/term/GO:0003700)) that acts as the terminal effector of the Wnt/beta-catenin signaling cascade ([R-HSA-195721](https://reactome.org/content/detail/R-HSA-195721)). Its molecular function involves binding to specific DNA sequences and, through interaction with co-activators like beta-catenin ([GO:0008013](https://www.ebi.ac.uk/QuickGO/term/GO:0008013)) or co-repressors of the Groucho/TLE family, modulating gene expression ([Link](https://doi.org/10.1073/pnas.95.20.11590)). This dual capacity allows it to either activate or repress transcription, depending on the cellular context and the presence of signaling molecules. Reactome pathway analysis confirms its central role in the [Formation of the beta-catenin:tcf transactivating complex](/details-pathway/R-HSA-201722) ([R-HSA-201722](https://reactome.org/content/detail/R-HSA-201722)) and the subsequent [Binding of tcf/lef:ctnnb1 to target gene promoters](/details-pathway/R-HSA-4411364) ([R-HSA-4411364](https://reactome.org/content/detail/R-HSA-4411364)). The biological processes regulated by [LEF1](/details-gene/51176) are extensive, reflecting the pleiotropic nature of Wnt signaling. Its high expression in lymphocytes is consistent with its involvement in [T cell receptor V(D)J recombination](/details-ontology/GO:0033153) ([GO:0033153](https://www.ebi.ac.uk/QuickGO/term/GO:0033153)) and [B cell proliferation](/details-ontology/GO:0042100) ([GO:0042100](https://www.ebi.ac.uk/QuickGO/term/GO:0042100)). Early studies identified it as a critical regulator of the T-cell receptor alpha enhancer ([Link](https://doi.org/10.1101/gad.5.4.656)). Furthermore, its function is integral to numerous developmental events, including [somitogenesis](/details-ontology/GO:0001756) ([GO:0001756](https://www.ebi.ac.uk/QuickGO/term/GO:0001756)), [odontogenesis of dentin-containing tooth](/details-ontology/GO:0042475) ([GO:0042475](https://www.ebi.ac.uk/QuickGO/term/GO:0042475)), and [epithelial to mesenchymal transition](/details-ontology/GO:0001837) ([GO:0001837](https://www.ebi.ac.uk/QuickGO/term/GO:0001837)). The existence of multiple [LEF1](/details-gene/51176) isoforms derived from alternative splicing further diversifies its regulatory capacity, allowing for the control of different sets of target genes ([Link](https://doi.org/10.1002/ijc.24802)). ## Research Directions The central role of [LEF1](/details-gene/51176) in both lymphocyte development and oncogenic signaling presents several avenues for future investigation. Its high and specific expression pattern in T-cell subsets makes it a key candidate for understanding immune cell fate and function. **Proposed Hypotheses:** 1. Given that distinct [LEF1](/details-gene/51176) isoforms can regulate different target genes ([Link](https://doi.org/10.1002/ijc.24802)), the expression ratio of these isoforms may be a critical determinant in the lineage commitment of [double-positive, alpha-beta thymocyte](/details-cell/CL0000809)s, with certain isoforms preferentially driving differentiation towards either the CD4+ or CD8+ lineage. 2. In the context of cancer, particularly hematological malignancies like T-cell acute lymphoblastic leukemia (T-ALL), aberrant overexpression or mutational activation of [LEF1](/details-gene/51176) may drive oncogenesis by constitutively activating Wnt target genes involved in cell proliferation ([GO:0090068](https://www.ebi.ac.uk/QuickGO/term/GO:0090068)) and survival ([GO:0043066](https://www.ebi.ac.uk/QuickGO/term/GO:0043066)), thus locking cells in a proliferative, undifferentiated state. **Experimental Approach for Hypothesis 1:** To dissect the role of [LEF1](/details-gene/51176) isoforms in thymocyte fate decisions, isoform-specific knockout mouse models could be generated using CRISPR-Cas9 base editing to disrupt specific splice sites. Fetal liver-derived hematopoietic stem cells from these models could be transplanted into irradiated hosts. Thymic development could then be profiled using a combination of flow cytometry to quantify CD4+ and CD8+ populations and single-cell RNA sequencing (scRNA-seq) on thymocyte subsets to map the developmental trajectories and identify the downstream transcriptional programs uniquely regulated by each [LEF1](/details-gene/51176) isoform. **Therapeutic Potential:** As a transcription factor, [LEF1](/details-gene/51176) is a challenging direct drug target. However, its critical function as a downstream node in the Wnt pathway, which is frequently hyperactivated in cancers like colorectal carcinoma and certain leukemias ([Link](https://doi.org/10.1038/ng0501-53)), makes it highly relevant therapeutically. Strategies would likely focus on **inhibition**. This could involve developing small molecules that disrupt the protein-protein interaction between [LEF1](/details-gene/51176) and its co-activator beta-catenin, thereby preventing the formation of the active transcriptional complex. Such an approach would selectively block Wnt-dependent gene expression in cancer cells while potentially sparing other cellular functions, offering a targeted therapeutic strategy for Wnt-addicted tumors.

Genular Protein ID: 91882950

Symbol: LEF1_HUMAN

Name: T cell-specific transcription factor 1-alpha

UniProtKB Accession Codes:

Database IDs:

Citations:

PubMed ID: 2010090

Title: A thymus-specific member of the HMG protein family regulates the human T cell receptor C alpha enhancer.

PubMed ID: 2010090

DOI: 10.1101/gad.5.4.656

PubMed ID: 10756202

Title: The human LEF-1 gene contains a promoter preferentially active in lymphocytes and encodes multiple isoforms derived from alternative splicing.

PubMed ID: 10756202

DOI: 10.1093/nar/28.9.1994

PubMed ID: 19653274

Title: Lef-1 isoforms regulate different target genes and reduce cellular adhesion.

PubMed ID: 19653274

DOI: 10.1002/ijc.24802

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 15815621

Title: Generation and annotation of the DNA sequences of human chromosomes 2 and 4.

PubMed ID: 15815621

DOI: 10.1038/nature03466

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 9119228

Title: ALY, a context-dependent coactivator of LEF-1 and AML-1, is required for TCRalpha enhancer function.

PubMed ID: 9119228

DOI: 10.1101/gad.11.5.640

PubMed ID: 9488439

Title: Two members of the Tcf family implicated in Wnt/b-catenin signaling during embryogenesis in the mouse.

PubMed ID: 9488439

DOI: 10.1128/mcb.18.3.1248

PubMed ID: 9751710

Title: Transcriptional repression by AML1 and LEF-1 is mediated by the TLE/Groucho corepressors.

PubMed ID: 9751710

DOI: 10.1073/pnas.95.20.11590

PubMed ID: 11326276

Title: Beta-catenin-sensitive isoforms of lymphoid enhancer factor-1 are selectively expressed in colon cancer.

PubMed ID: 11326276

DOI: 10.1038/ng0501-53

PubMed ID: 11266540

Title: All Tcf HMG box transcription factors interact with Groucho-related co-repressors.

PubMed ID: 11266540

DOI: 10.1093/nar/29.7.1410

PubMed ID: 12192039

Title: I-mfa domain proteins interact with Axin and affect its regulation of the Wnt and c-Jun N-terminal kinase signaling pathways.

PubMed ID: 12192039

DOI: 10.1128/mcb.22.18.6393-6405.2002

PubMed ID: 12556497

Title: Regulation of lymphoid enhancer factor 1/T-cell factor by mitogen-activated protein kinase-related Nemo-like kinase-dependent phosphorylation in Wnt/beta-catenin signaling.

PubMed ID: 12556497

DOI: 10.1128/mcb.23.4.1379-1389.2003

PubMed ID: 14759258

Title: An unappreciated role for RNA surveillance.

PubMed ID: 14759258

DOI: 10.1186/gb-2004-5-2-r8

PubMed ID: 19304756

Title: Dazap2 modulates transcription driven by the Wnt effector TCF-4.

PubMed ID: 19304756

DOI: 10.1093/nar/gkp179

PubMed ID: 19690332

Title: Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.

PubMed ID: 19690332

DOI: 10.1126/scisignal.2000007

PubMed ID: 16959974

Title: The consensus coding sequences of human breast and colorectal cancers.

PubMed ID: 16959974

DOI: 10.1126/science.1133427

Sequence Information:

  • Length: 399
  • Mass: 44201
  • Checksum: D480D440698EEFE3
  • Sequence:
  • MPQLSGGGGG GGGDPELCAT DEMIPFKDEG DPQKEKIFAE ISHPEEEGDL ADIKSSLVNE 
    SEIIPASNGH EVARQAQTSQ EPYHDKAREH PDDGKHPDGG LYNKGPSYSS YSGYIMMPNM 
    NNDPYMSNGS LSPPIPRTSN KVPVVQPSHA VHPLTPLITY SDEHFSPGSH PSHIPSDVNS 
    KQGMSRHPPA PDIPTFYPLS PGGVGQITPP LGWQGQPVYP ITGGFRQPYP SSLSVDTSMS 
    RFSHHMIPGP PGPHTTGIPH PAIVTPQVKQ EHPHTDSDLM HVKPQHEQRK EQEPKRPHIK 
    KPLNAFMLYM KEMRANVVAE CTLKESAAIN QILGRRWHAL SREEQAKYYE LARKERQLHM 
    QLYPGWSARD NYGKKKKRKR EKLQESASGT GPRMTAAYI

Genular Protein ID: 257884789

Symbol: Q659G9_HUMAN

Name: N/A

UniProtKB Accession Codes:

Database IDs:

Sequence Information:

  • Length: 69
  • Mass: 8251
  • Checksum: CBF29BD0C3287867
  • Sequence:
  • QILGRRWHAL SREEQAKYYE LARKERQLHM QLYPGWSARD NYGKKKKRKR EKLQESASGT 
    GPRMTAAYI