Details for: CTSF

Gene ID: 8722

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: CTSF

Ensembl ID: ENSG00000174080

Description: cathepsin F

Cell Significance Landscape

Associated with

Significant Cells

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

  • retina horizontal cell CL0000745
    CSI 12.53
    rCSI 19.1%
    PRS 57.73
  • skin fibroblast CL0002620
    CSI 11.46
    rCSI 9.88%
    PRS 66.99
  • melanocyte CL0000148
    CSI 10.29
    rCSI 7.62%
    PRS 54.07
  • hepatocyte CL0000182
    CSI 6.3
    rCSI 11.27%
    PRS 60.57
  • amacrine cell CL0000561
    CSI 6.09
    rCSI 17.66%
    PRS 51.14
  • cardiac muscle cell CL0000746
    CSI 5.77
    rCSI 8.29%
    PRS 51.19
  • GABAergic amacrine cell CL4030027
    CSI 5.68
    rCSI 19.45%
    PRS 50.31
  • OFF-bipolar cell CL0000750
    CSI 4.77
    rCSI 6.52%
    PRS 68.38
  • retinal ganglion cell CL0000740
    CSI 4.77
    rCSI 10.53%
    PRS 47.66
  • stromal cell of ovary CL0002132
    CSI 4.43
    rCSI 12.17%
    PRS 74.14
  • pulmonary artery endothelial cell CL1001568
    CSI 4.14
    rCSI 5.64%
    PRS 73.23
  • myoepithelial cell CL0000185
    CSI 4.06
    rCSI 10.27%
    PRS 69.42
  • Mueller cell CL0000636
    CSI 4.04
    rCSI 9.21%
    PRS 53.27
  • vascular associated smooth muscle cell CL0000359
    CSI 3.85
    rCSI 12.47%
    PRS 61.89
  • cerebellar granule cell CL0001031
    CSI 3.76
    rCSI 5.53%
    PRS 55.09
  • mucus secreting cell CL0000319
    CSI 3.72
    rCSI 5.91%
    PRS 72.55
  • alveolar type 1 fibroblast cell CL4028004
    CSI 3.49
    rCSI 3.82%
    PRS 65.23
  • myofibroblast cell CL0000186
    CSI 3.44
    rCSI 4.77%
    PRS 62.57
  • enteroendocrine cell CL0000164
    CSI 3.35
    rCSI 4.58%
    PRS 63.14
  • tracheobronchial smooth muscle cell CL0019019
    CSI 3.29
    rCSI 5.8%
    PRS 69.66
  • kidney loop of Henle thin descending limb epithelial cell CL1001111
    CSI 3.28
    rCSI 4.64%
    PRS 57.78
  • keratocyte CL0002363
    CSI 3.06
    rCSI 7.36%
    PRS 69.24
  • alveolar adventitial fibroblast CL4028006
    CSI 3.01
    rCSI 4.76%
    PRS 63.77
  • bronchus fibroblast of lung CL2000093
    CSI 2.95
    rCSI 2.4%
    PRS 61.99
  • fibroblast of lung CL0002553
    CSI 2.9
    rCSI 2.7%
    PRS 62.13
  • perivascular cell CL4033054
    CSI 2.88
    rCSI 3.93%
    PRS 67.46
  • epithelial cell of lower respiratory tract CL0002632
    CSI 2.86
    rCSI 2.21%
    PRS 63.31
  • smooth muscle cell CL0000192
    CSI 2.82
    rCSI 6.73%
    PRS 65.84
  • luminal cell of prostate epithelium CL0002340
    CSI 2.72
    rCSI 14.64%
    PRS 73.84
  • glial cell CL0000125
    CSI 2.71
    rCSI 10.33%
    PRS 52.39
  • ON-bipolar cell CL0000749
    CSI 2.69
    rCSI 4%
    PRS 63.01
  • fallopian tube secretory epithelial cell CL4030006
    CSI 2.67
    rCSI 2.57%
    PRS 61.53
  • epithelial cell CL0000066
    CSI 2.64
    rCSI 4.06%
    PRS 57.44
  • tracheobronchial serous cell CL0019001
    CSI 2.63
    rCSI 11.35%
    PRS 74.07
  • epithelial cell of lung CL0000082
    CSI 2.61
    rCSI 2.16%
    PRS 60.65
  • hematopoietic stem cell CL0000037
    CSI 2.59
    rCSI 1.72%
    PRS 64.5
  • glioblast CL0000030
    CSI 2.54
    rCSI 4.05%
    PRS 54.1
  • adventitial cell CL0002503
    CSI 2.51
    rCSI 6%
    PRS 70.09
  • pancreatic A cell CL0000171
    CSI 2.48
    rCSI 2.6%
    PRS 65.05
  • group 3 innate lymphoid cell CL0001071
    CSI 2.41
    rCSI 1.81%
    PRS 66.93
  • duct epithelial cell CL0000068
    CSI 2.32
    rCSI 3.39%
    PRS 66.06
  • inhibitory interneuron CL0000498
    CSI 2.27
    rCSI 5.24%
    PRS 50.57
  • type B pancreatic cell CL0000169
    CSI 2.25
    rCSI 4.99%
    PRS 59.4
  • pancreatic D cell CL0000173
    CSI 2.23
    rCSI 2.19%
    PRS 64.01
  • mucous neck cell CL0000651
    CSI 2.2
    rCSI 3.17%
    PRS 72.23
  • myeloid leukocyte CL0000766
    CSI 2.18
    rCSI 2.02%
    PRS 62.88
  • vascular leptomeningeal cell CL4023051
    CSI 2.16
    rCSI 3.79%
    PRS 53.44
  • corticothalamic-projecting glutamatergic cortical neuron CL4023013
    CSI 2.06
    rCSI 12.1%
    PRS 44.54
  • cerebral cortex endothelial cell CL1001602
    CSI 1.98
    rCSI 3.43%
    PRS 51.66
  • microcirculation associated smooth muscle cell CL0008035
    CSI 1.93
    rCSI 5.58%
    PRS 62.87
  • sst GABAergic cortical interneuron CL4023017
    CSI 1.84
    rCSI 2.37%
    PRS 44.5
  • blood vessel smooth muscle cell CL0019018
    CSI 1.84
    rCSI 14.93%
    PRS 54.77
  • Bergmann glial cell CL0000644
    CSI 1.8
    rCSI 2.47%
    PRS 55.05
  • choroid plexus epithelial cell CL0000706
    CSI 1.79
    rCSI 2.93%
    PRS 50.73
  • peripheral nervous system neuron CL2000032
    CSI 1.78
    rCSI 2.42%
    PRS 53.22
  • stromal cell CL0000499
    CSI 1.74
    rCSI 4.9%
    PRS 58.13
  • lung neuroendocrine cell CL1000223
    CSI 1.7
    rCSI 2.52%
    PRS 66.72
  • enteric smooth muscle cell CL0002504
    CSI 1.7
    rCSI 2.43%
    PRS 63.76
  • rod bipolar cell CL0000751
    CSI 1.66
    rCSI 2.98%
    PRS 54.51
  • podocyte CL0000653
    CSI 1.65
    rCSI 7.34%
    PRS 60.97
  • chondrocyte CL0000138
    CSI 1.62
    rCSI 2.58%
    PRS 53.83
  • megakaryocyte-erythroid progenitor cell CL0000050
    CSI 1.6
    rCSI 1.45%
    PRS 58.3
  • retinal bipolar neuron CL0000748
    CSI 1.6
    rCSI 2.99%
    PRS 49.83
  • basal cell of prostate epithelium CL0002341
    CSI 1.59
    rCSI 4.61%
    PRS 73.91
  • VIP GABAergic cortical interneuron CL4023016
    CSI 1.57
    rCSI 1.88%
    PRS 43.01
  • basal cell CL0000646
    CSI 1.52
    rCSI 2.03%
    PRS 61.75
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 1.51
    rCSI 2.67%
    PRS 42.29
  • respiratory basal cell CL0002633
    CSI 1.5
    rCSI 1.56%
    PRS 67.08
  • mononuclear phagocyte CL0000113
    CSI 1.48
    rCSI 3.25%
    PRS 65.72
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 1.47
    rCSI 1.83%
    PRS 41.31
  • sncg GABAergic cortical interneuron CL4023015
    CSI 1.46
    rCSI 2.35%
    PRS 45.28
  • lung pericyte CL0009089
    CSI 1.46
    rCSI 3.85%
    PRS 70.31
  • mesenchymal cell CL0008019
    CSI 1.45
    rCSI 3.68%
    PRS 55.7
  • astrocyte of the cerebral cortex CL0002605
    CSI 1.41
    rCSI 3.16%
    PRS 43.98
  • neural progenitor cell CL0011020
    CSI 1.33
    rCSI 5.87%
    PRS 51.88
  • basal cell of epidermis CL0002187
    CSI 1.33
    rCSI 2.36%
    PRS 35.98
  • kidney loop of Henle thin ascending limb epithelial cell CL1001107
    CSI 1.31
    rCSI 3.39%
    PRS 56.46
  • retinal pigment epithelial cell CL0002586
    CSI 1.27
    rCSI 2.52%
    PRS 59.2
  • mammary gland epithelial cell CL0002327
    CSI 1.25
    rCSI 4.38%
    PRS 73.86
  • chandelier pvalb GABAergic cortical interneuron CL4023036
    CSI 1.23
    rCSI 3.86%
    PRS 47.38
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 1.15
    rCSI 1.93%
    PRS 43.24
  • forebrain radial glial cell CL0013000
    CSI 1.01
    rCSI 3.24%
    PRS 66.52
  • dopaminergic neuron CL0000700
    CSI 0.91
    rCSI 5.14%
    PRS 46.57
  • L2/3-6 intratelencephalic projecting glutamatergic neuron CL4023040
    CSI 0.77
    rCSI 1.87%
    PRS 41.85
  • P/D1 enteroendocrine cell CL0002268
    CSI 0.62
    rCSI 3.37%
    PRS 77.11
  • L6b glutamatergic cortical neuron CL4023038
    CSI 0.57
    rCSI 1.78%
    PRS 44.86
  • basal cell of epithelium of trachea CL1000348
    CSI 0.56
    rCSI 3.95%
    PRS 75.7
  • bronchiolar smooth muscle cell CL4033017
    CSI 0.55
    rCSI 8.21%
    PRS 78.05
  • near-projecting glutamatergic cortical neuron CL4023012
    CSI 0.52
    rCSI 1.96%
    PRS 44.02
  • pancreatic stellate cell CL0002410
    CSI 0.45
    rCSI 2.64%
    PRS 70.46
  • L5 extratelencephalic projecting glutamatergic cortical neuron CL4023041
    CSI 0.38
    rCSI 1.38%
    PRS 41.65
  • odontoblast CL0000060
    CSI 0.35
    rCSI 7.85%
    PRS 82.14
  • acinar cell of salivary gland CL0002623
    CSI 0.24
    rCSI 5.69%
    PRS 80.47
  • peptic cell CL0000155
    CSI 0.21
    rCSI 2.1%
    PRS 79.84
  • mesenchymal stem cell CL0000134
    CSI 0.09
    rCSI 0.96%
    PRS 73.95

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 [CTSF](/details-gene/8722), or Cathepsin F, is a protein-coding gene located on chromosome 11q13.2 that encodes a lysosomal cysteine protease of the papain family. It is characterized by a unique long propeptide domain which includes a cystatin-like motif ([Link](https://doi.org/10.1006/bbrc.1999.0461)). Functionally, [CTSF](/details-gene/8722) is involved in proteolysis and plays a role in the adaptive immune system, specifically in the processing and presentation of exogenous antigens via the MHC class II pathway ([Link](https://reactome.org/content/detail/R-HSA-2132295)). Expression data reveals its high significance in a diverse array of cell types, most notably in neuronal cells of the retina such as [retina horizontal cells](/details-cell/CL0000745), as well as in structural cells like [skin fibroblasts](/details-cell/CL0002620) and [melanocytes](/details-cell/CL0000148). Clinically, loss-of-function mutations in [CTSF](/details-gene/8722) are known to cause Type B Kufs disease, an adult-onset neuronal ceroid lipofuscinosis, highlighting its critical role in neuronal homeostasis ([Link](https://doi.org/10.1093/hmg/dds558)). ## Cellular Roles and Expression Landscape The expression profile of [CTSF](/details-gene/8722) suggests a broad but highly specific set of cellular functions. **Overall**, the gene shows the highest significance in several distinct cellular compartments. A striking feature is its prominent role within the retina, where it is a top marker for multiple neuronal and glial cell types, including [retina horizontal cell](/details-cell/CL0000745), [amacrine cell](/details-cell/CL0000561), [GABAergic amacrine cell](/details-cell/CL4030027), [retinal ganglion cell](/details-cell/CL0000740), and [Mueller cell](/details-cell/CL0000636). This concentrated expression pattern strongly suggests a specialized and critical function in retinal protein turnover, synaptic maintenance, and the clearance of cellular debris in these long-lived, metabolically active cells. Beyond the nervous system, [CTSF](/details-gene/8722) is highly significant in various structural and mesenchymal cells. It is a key marker in [skin fibroblast](/details-cell/CL0002620), [melanocyte](/details-cell/CL0000148), [cardiac muscle cell](/details-cell/CL0000746), and [vascular associated smooth muscle cell](/details-cell/CL0000359). This pattern is consistent with its annotated presence in the [extracellular matrix](/details-cell/GO:0062023) and suggests a role in tissue remodeling and maintenance. Interestingly, while functional annotations link [CTSF](/details-gene/8722) to the [adaptive immune system](/details-cell/R-HSA-1280218), canonical immune cell populations are not among its top expressed cell types in a general context. This may indicate that its role in antigen presentation is either highly context-dependent (e.g., upregulated during inflammation in professional antigen-presenting cells) or that its basal proteolytic function is co-opted for this purpose without requiring exceptionally high expression levels compared to its roles in other tissues. ## Pathways and Molecular Function [CTSF](/details-gene/8722) encodes an enzyme with [cysteine-type endopeptidase activity](/details-cell/GO:0004197), primarily functioning within the acidic environment of the [lysosome](/details-cell/GO:0005764). Its principal biological process is [proteolysis](/details-cell/GO:0006508), contributing to the catabolism of proteins for cellular recycling and homeostasis. This proteolytic activity is integral to its role in the immune system, specifically in the [MHC class II antigen presentation](/details-cell/R-HSA-2132295) pathway. Within antigen-presenting cells, [CTSF](/details-gene/8722) likely participates in the degradation of endocytosed pathogens into peptide fragments that can be loaded onto MHC class II molecules for presentation to T-helper cells. The crystal structure of the protein has been resolved, providing insights that could aid in the development of immunomodulators ([Link](https://doi.org/10.1016/s0022-2836(02)00780-5)). Furthermore, its annotated localization to the [extracellular space](/details-cell/GO:0005615) and [extracellular exosomes](/details-cell/GO:0070062) suggests it may have functions beyond intracellular degradation. Secreted [CTSF](/details-gene/8722) could be involved in remodeling the [collagen-containing extracellular matrix](/details-cell/GO:0062023), a role consistent with its high expression in [skin fibroblasts](/details-cell/CL0002620). ## Research Directions The available data highlights [CTSF](/details-gene/8722) as a protease with critical roles in neuronal health and potential context-specific immune functions. This provides a foundation for several testable hypotheses. 1. **Hypothesis on Neurodegeneration:** The exceptionally high significance of [CTSF](/details-gene/8722) in multiple retinal cell types, combined with its causal link to a neuronal ceroid lipofuscinosis, suggests a specific role in neural waste clearance. We hypothesize that [CTSF](/details-gene/8722) is essential for the lysosomal degradation of specific, potentially lipidated, protein aggregates unique to neuronal and glial cells, and its absence leads directly to the cytotoxic accumulation of lipofuscin characteristic of Type B Kufs disease. 2. **Hypothesis on Functional Dichotomy:** The discrepancy between strong immune-related functional annotations and the lack of high significance in immune cells in the general context suggests a dual or regulated role. We hypothesize that the constitutive expression of [CTSF](/details-gene/8722) in structural cells like [skin fibroblasts](/details-cell/CL0002620) is primarily for extracellular matrix maintenance, while its role in antigen presentation is inducibly upregulated in immune cells upon specific inflammatory stimuli. **Experimental Approach to Test Hypothesis 1:** To investigate the specific role of [CTSF](/details-gene/8722) in retinal pathology, a human iPSC-based model could be employed. iPSCs derived from patients with [CTSF](/details-gene/8722) mutations and healthy controls would be differentiated into retinal organoids. Using CRISPR-Cas9, the pathogenic mutation could be corrected in patient cells to create an isogenic control. The resulting organoids would be subjected to comparative analysis, including advanced microscopy to quantify lipofuscin accumulation (autofluorescence), and multi-omics profiling (proteomics and lipidomics) to identify the specific substrates that fail to be cleared in the CTSF-deficient retinal cells. **Therapeutic Potential:** As Type B Kufs disease is a loss-of-function disorder, the therapeutic goal would be to restore or augment CTSF activity rather than inhibit it. This makes [CTSF](/details-gene/8722) a candidate for enzyme replacement therapy (ERT) or gene therapy. Given the neurological nature of the disease, a gene therapy approach using an AAV vector to deliver a functional copy of the [CTSF](/details-gene/8722) gene to the central nervous system and retina presents a promising, albeit challenging, long-term therapeutic strategy.

Genular Protein ID: 2123590231

Symbol: CATF_HUMAN

Name: Cathepsin F

UniProtKB Accession Codes:

Database IDs:

Citations:

PubMed ID: 10318784

Title: Molecular cloning and structural and functional characterization of human cathepsin F, a new cysteine proteinase of the papain family with a long propeptide domain.

PubMed ID: 10318784

DOI: 10.1074/jbc.274.20.13800

PubMed ID: 10198209

Title: Full-length cDNA of human cathepsin F predicts the presence of a cystatin domain at the N-terminus of the cysteine protease zymogen.

PubMed ID: 10198209

DOI: 10.1006/bbrc.1999.0461

PubMed ID: 10661872

Title: The human cathepsin F gene -- a fusion product between an ancestral cathepsin and cystatin gene.

PubMed ID: 10661872

DOI: 10.1515/bc.1999.185

PubMed ID: 10362521

Title: Human cathepsins F and W: a new subgroup of cathepsins.

PubMed ID: 10362521

DOI: 10.1006/bbrc.1999.0700

PubMed ID: 14702039

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

PubMed ID: 14702039

DOI: 10.1038/ng1285

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: 9822672

Title: Human cathepsin F. Molecular cloning, functional expression, tissue localization, and enzymatic characterization.

PubMed ID: 9822672

DOI: 10.1074/jbc.273.48.32000

PubMed ID: 17974005

Title: The full-ORF clone resource of the German cDNA consortium.

PubMed ID: 17974005

DOI: 10.1186/1471-2164-8-399

PubMed ID: 19159218

Title: Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.

PubMed ID: 19159218

DOI: 10.1021/pr8008012

PubMed ID: 12225749

Title: The crystal structure of human cathepsin F and its implications for the development of novel immunomodulators.

PubMed ID: 12225749

DOI: 10.1016/s0022-2836(02)00780-5

PubMed ID: 23297359

Title: Cathepsin F mutations cause Type B Kufs disease, an adult-onset neuronal ceroid lipofuscinosis.

PubMed ID: 23297359

DOI: 10.1093/hmg/dds558

Sequence Information:

  • Length: 484
  • Mass: 53366
  • Checksum: 1D5D551B489D822B
  • Sequence:
  • MAPWLQLLSL LGLLPGAVAA PAQPRAASFQ AWGPPSPELL APTRFALEMF NRGRAAGTRA 
    VLGLVRGRVR RAGQGSLYSL EATLEEPPCN DPMVCRLPVS KKTLLCSFQV LDELGRHVLL 
    RKDCGPVDTK VPGAGEPKSA FTQGSAMISS LSQNHPDNRN ETFSSVISLL NEDPLSQDLP 
    VKMASIFKNF VITYNRTYES KEEARWRLSV FVNNMVRAQK IQALDRGTAQ YGVTKFSDLT 
    EEEFRTIYLN TLLRKEPGNK MKQAKSVGDL APPEWDWRSK GAVTKVKDQG MCGSCWAFSV 
    TGNVEGQWFL NQGTLLSLSE QELLDCDKMD KACMGGLPSN AYSAIKNLGG LETEDDYSYQ 
    GHMQSCNFSA EKAKVYINDS VELSQNEQKL AAWLAKRGPI SVAINAFGMQ FYRHGISRPL 
    RPLCSPWLID HAVLLVGYGN RSDVPFWAIK NSWGTDWGEK GYYYLHRGSG ACGVNTMASS 
    AVVD