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CTSF / Cathepsin F · IHC design guide
Design Immunohistochemistry for CTSF
Plan chromogenic CTSF IHC in paraffin sections using cortical neurons and hepatocytes as high-staining references (HPA tissue IHC). Assess granular cytoplasmic staining alongside CTSF’s lysosomal annotation, while allowing for medium consistency between tissue staining and RNA expression (HPA tissue IHC; UniProt).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
CTSF Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Granular cytoplasm (HPA tissue IHC); lysosome (UniProt) | |
| Staining pattern | Granular cytoplasm; high in cortical neurons and hepatocytes (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A06600-1) | |
| Positive control | Cerebellum+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Staining has medium consistency with RNA expression (HPA tissue IHC) | |
| Regulation | No specific regulator annotated (UniProt) | |
| Isoform / epitope | 0 isoforms annotated; map epitopes to propeptide or mature chain (UniProt) |
Section 1
Recommended CTSF IHC & IF Protocols
The catalog antibody protocol uses EDTA pH 8.0 heat retrieval (datasheet A06600-1). The published protocols below report CTSF IHC in brain metastasis tissue (PMC9174239) and human skin (PMC9886782).
| Sample | Paraffin-embedded human stomach cancer tissue; fixative not specified (datasheet A06600-1) |
| Fixation | Image fixative and duration unreported (datasheet A06600-1); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: EDTA pH 8.0 (datasheet A06600-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A06600-1) |
| Primary antibody | Rabbit anti-CTSF, 2-5 μg/ml (datasheet A06600-1) |
| Primary incubation | Overnight at 4 °C (datasheet A06600-1) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A06600-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CTSF-positive staining in cells in molecular layer of cerebellum (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression with a granular pattern in most tissues. No signal in the no-primary control. |
💡Decision noteStart with EDTA pH 8.0 heat retrieval (datasheet A06600-1). One published protocol also used EDTA (PMC9174239); the skin protocol specifies heat retrieval without naming a buffer (PMC9886782).
Section 2
What Is the Expected CTSF Staining Pattern?
CTSF is a lysosomal protein with no transmembrane segment (UniProt Q9UBX1: location, topology). In paraffin section IHC, expect granular cytoplasmic staining, especially in hepatocytes, cortical and hippocampal neurons, cerebellar molecular layer cells, Leydig cells, and seminal vesicle glandular cells (HPA tissue IHC: High). HPA rates the tissue profile Enhanced, while describing medium consistency between antibody staining and RNA expression (HPA tissue IHC: reliability).
| Distinct cytoplasmic granules in hepatocytes or neuronal cells. | This fits the reported pattern in most tissues and the high staining of these cells (HPA tissue IHC: profile, Liver, Cerebral cortex, Hippocampus). Score the named cell population and its granular pattern together; staining anywhere in a positive tissue does not establish the expected result. |
| Predominantly nuclear staining, or a smooth outline around cells with little granular cytoplasm. | That differs from the tissue IHC profile (HPA tissue IHC: granular cytoplasmic pattern). Treat it as a possible artefact and check controls and morphology. Plasma membrane localisation is uncertain in ICC-IF and does not establish a membrane-only paraffin section pattern (HPA subcellular: additional location). |
| Strong staining of colon glandular cells or bone marrow hematopoietic cells. | Both populations are reported as not detected (HPA tissue IHC: Colon, Bone marrow). Unexpected signal raises possible cross-reactivity or endogenous detection activity; inspect the negative control and the detection system before assigning it to CTSF. A tissue label alone cannot resolve which cells stained. |
| Diffuse colour across cells, stroma, and otherwise unstained areas. | Diffuse background obscures the expected granular cytoplasmic pattern (HPA tissue IHC: profile). In chromogenic IHC, consider nonspecific binding, excess detection reagent, or endogenous enzyme activity as general workflow possibilities; a diffuse deposit alone cannot identify its cause or establish CTSF expression. |
| No discernible granules in a liver section's hepatocytes. | Hepatocytes are reported High (HPA tissue IHC: Liver). Check section morphology and a matched positive control, then review antibody and detection performance. An absent signal in one run does not overturn the tissue reference; HPA also reports only medium antibody and RNA consistency (HPA tissue IHC: reliability description). |
💡Expected CTSF appearanceCall positive a distinct, granular cytoplasmic signal in an HPA High cell population, such as hepatocytes or cortical neurons (HPA tissue IHC: profile, Liver, Cerebral cortex); diffuse colour, nuclear-only staining, or signal confined to a reported not-detected cell population warrants investigation (HPA tissue IHC: profile, Colon).
| Tissue and cell population | Use the reported cell type when choosing and scoring controls: hepatocytes are High, while colon glandular cells are Not detected (HPA tissue IHC: Liver, Colon). UniProt reports moderate expression in colon at the tissue level (UniProt Q9UBX1: tissue specificity); these statements answer different questions. |
| Subcellular context | Lysosomal localisation (UniProt Q9UBX1: subcellular location) is consistent with granular cytoplasm in tissue IHC (HPA tissue IHC: profile). ICC-IF mainly places CTSF in vesicles; its additional endoplasmic reticulum and plasma membrane calls are uncertain (HPA subcellular: main and additional locations). |
| Antibody validation | The listed mouse monoclonal CAB002141 has Enhanced IHC validation, while HPA031431 has Supported ICC validation and no listed IHC status (HPA antibodies: CAB002141, HPA031431). These statuses apply to different applications; use the IHC evidence when assessing a paraffin section result. |
| Protein processing and epitope | UniProt places the signal sequence at residues 1–19, propeptide at 20–270, and Cathepsin F chain at 271–484 (UniProt Q9UBX1: processing). Epitope location is not supplied, so the record cannot predict whether an antibody recognises precursor, mature chain, or both. |
| Glycosylation | Five glycosylation sites are listed (UniProt Q9UBX1: glycosylation). No supplied evidence links them to this antibody's staining, antigen retrieval, or fixation sensitivity; do not infer a retrieval setting or explain a negative section from the sites alone. |
| Situation | Likely cause | Next action |
|---|---|---|
| A putative positive section has no hepatocyte signal. | Hepatocytes are High in the tissue reference (HPA tissue IHC: Liver); the failed run could reflect a general IHC workflow issue. | Check morphology, a matched positive control, antibody identity, and detection reagents; review retrieval against the chosen antibody's validated IHC instructions. |
| A reported negative cell population stains strongly. | Colon glandular cells are Not detected (HPA tissue IHC: Colon); nonspecific binding or endogenous chromogenic activity are possible general IHC causes. | Confirm cell identity, inspect the no-primary control, and review blocking and detection controls before scoring the signal as CTSF. |
| Signal is mainly nuclear or outlines cell surfaces. | That distribution conflicts with granular cytoplasmic tissue staining (HPA tissue IHC: profile); membrane staining is uncertain in ICC-IF (HPA subcellular: additional location). | Recheck the compartment under higher magnification and compare with an HPA High cell population and control section. |
| Chromogen forms a diffuse haze. | The haze prevents assessment of granules (HPA tissue IHC: profile); excess reagent or incomplete blocking can cause background in general IHC practice. | Inspect the no-primary control and review blocking, washing, antibody concentration, and chromogen development for the detection system used. |
| Two antibodies give different paraffin section patterns. | Only CAB002141 has listed Enhanced IHC validation; HPA031431's listed support is for ICC (HPA antibodies: CAB002141, HPA031431). Epitope locations are not supplied. | Assess each antibody's IHC validation separately and compare cell type, compartment, and controls without assuming the ICC result predicts IHC. |
| Q: Should vesicular ICC-IF images determine the paraffin IHC result? | A: Vesicles are the supported main ICC-IF location (HPA subcellular: main location), while tissue IHC reports granular cytoplasm (HPA tissue IHC: profile). | Use the tissue IHC pattern for this guide's slide interpretation; assess IF/ICC staining on its separate guide page. |
Experiment evidence
IHC & IF images showing CTSF staining
A06600-1 · IHCIHC analysis of Cathepsin F/CTSF using anti-Cathepsin F/CTSF antibody (A06600-1). Cathepsin F/CTSF was detected in a paraffin-embedded secti
A06600-1 · IHCIHC analysis of Cathepsin F/CTSF using anti-Cathepsin F/CTSF antibody (A06600-1). Cathepsin F/CTSF was detected in a paraffin-embedded secti
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000174080-CTSF/tissue/cerebral+cortex#imid_720632
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000174080-CTSF/tissue/colon#imid_720550
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000174080-CTSF/tissue/liver#imid_720567
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000174080-CTSF/tissue/kidney#imid_720552
HPA · ICC-IF A-549Human Protein Atlas immunofluorescence, A-549, antibody HPA031431; green = CTSF, blue = nucleus, red = microtubules.
HPA · ICC-IF A-549Human Protein Atlas immunofluorescence, A-549, antibody HPA031431; green = CTSF, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for CTSF IHC & IF
🧪Run cerebral cortex first: neuronal cells show High CTSF staining (HPA: cerebral cortex, neuronal cells, High). Use adipose tissue as the negative tissue: adipocytes are Not detected (HPA: adipose tissue, adipocytes, Not detected); cells without specific staining on the cortex slide should show counterstain alone, without discrete chromogenic deposits (standard IHC practice).
Positive control tissue: Cerebellum (Cells in molecular layer, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show CTSF in A-549, SK-MEL-30, U2OS, with annotated localisation: Vesicles (supported) (HPA subcellular).
Technical controls: Include no-primary (secondary-only) and host-species- and clonality-matched isotype controls, plus CTSF-knockout tissue if available or an immunizing-peptide block when the peptide is available (standard IHC practice). Quench endogenous peroxidase for chromogenic detection; for any IF comparison in cortex, assess tissue autofluorescence with an unstained section (standard IHC/IF practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the exact A06600-1 paraffin-section caption does not state a fixative (selected-SKU tissue-IHC caption). That caption uses heat retrieval in EDTA at pH 8.0 for stomach cancer tissue, so retrieval conditions need optimization for cortex rather than assuming the same response (selected-SKU tissue-IHC caption). Frozen sections or IF cannot be judged easier from the supplied evidence; cortical autofluorescence can complicate IF assessment (HPA: ICC-IF images; standard IF practice).
HPA tissue IHC evidence for CTSF
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Cerebellum | Cells in molecular layer | High | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
| Hippocampus | Neuronal cells | High | Protein (IHC) | HPA → |
| Liver | Hepatocytes | High | Protein (IHC) | HPA → |
| Seminal vesicle | Glandular cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Colon | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Kidney | Cells in glomeruli | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced CTSF IHC Tips
Troubleshoot CTSF staining in paraffin sections by checking retrieval, compartment, controls and scoring before interpreting chromogenic signal.
How should I adjust retrieval when CTSF staining is weak or uneven?
Start with heat-mediated retrieval in EDTA at pH 8.0 for paraffin sections (datasheet A06600-1). The selected tissue image used this retrieval before 2 μg/ml primary antibody overnight at 4°C, so reproduce those conditions when comparing sections (datasheet A06600-1). If staining remains weak, vary heating duration or cooling consistently across a small test series while keeping the EDTA buffer and antibody concentration fixed (standard IHC practice). Include a neuronal region with reported high staining and a no-primary control to distinguish inadequate retrieval from nonspecific chromogen deposition (HPA tissue IHC: cerebral cortex neuronal cells, High; standard IHC practice).
Could fixation explain weak CTSF staining in my paraffin sections?
Target-specific CTSF sensitivity to fixation is unknown from the supplied evidence; the selected paraffin-section caption does not state a fixative (datasheet A06600-1). Record the actual fixative, fixation time and tissue-processing history before comparing signal across specimens, because these variables can change epitope accessibility in IHC (standard IHC practice). Process a control section alongside each comparison and apply the stated EDTA retrieval at pH 8.0 under matched conditions (datasheet A06600-1; standard IHC practice). If signal varies, test processing variables systematically and assess tissue preservation; neither the reported tissue staining nor CTSF sequence annotations establish a fixation-specific effect (HPA tissue IHC; UniProt Q9UBX1).
Where should convincing CTSF signal appear in a tissue section?
Look first for granular cytoplasmic staining, the pattern reported across most tissues, consistent with lysosomal CTSF (HPA tissue IHC; UniProt Q9UBX1: lysosome). HPA also places CTSF mainly in vesicles by subcellular imaging; its endoplasmic-reticulum and plasma-membrane assignments are uncertain (HPA subcellular: supported vesicles, uncertain additional locations). In tissue, compare the granules with cell borders and nuclei at the same magnification, and check whether the pattern repeats in intact cells rather than only along section edges (standard IHC practice). Strong uniform nuclear staining or a crisp membrane-only outline warrants scrutiny against no-primary controls and reported positive cells before assigning it to CTSF (HPA tissue IHC; standard IHC practice).
How might CTSF processing affect which cells or compartments stain?
CTSF is annotated with a signal peptide at residues 1–19, a propeptide at 20–270 and a Cathepsin F chain at 271–484 (UniProt Q9UBX1). Five glycosylation sites are annotated at residues 160, 195, 367, 378 and 440, while no isoforms are listed in the supplied record (UniProt Q9UBX1). Check the antibody's documented epitope, if available, before treating differences in staining as differences in total CTSF: an epitope confined to one processed region could change what the assay detects (UniProt Q9UBX1: processing; standard IHC interpretation). Without an epitope assignment, compare staining under matched retrieval and detection conditions and describe the result as antibody-detected CTSF rather than a particular molecular form (standard IHC practice).
How can IF help verify a granular CTSF pattern?
For a separate IF experiment, multiplex CTSF with a marker identifying the expected cell population, such as neuronal cells in cerebral cortex, and assess whether puncta occur within those cells (HPA tissue IHC: cerebral cortex neuronal cells, High; HPA subcellular: vesicles supported). Choose fluorophores after checking the specimen's autofluorescence in each channel, and include single-label controls to assess bleed-through (standard IF practice). CTSF has no annotated transmembrane segment and is lysosomal, so use permeabilisation sufficient to access intracellular epitopes while preserving vesicular structure (UniProt Q9UBX1: topology and lysosome; standard IF practice). Match fixation and permeabilisation across samples, and use a no-primary control before comparing puncta counts or intensity (standard IF practice).
What should I check when CTSF DAB staining looks diffuse?
Compare the diffuse signal with a no-primary section and inspect whether it follows cells, damaged areas or tissue edges (standard IHC practice). The selected image used 10% goat serum block, 2 μg/ml primary antibody overnight at 4°C, and peroxidase-based DAB detection (datasheet A06600-1). If your signal persists without primary antibody, check peroxidase blocking, secondary-antibody binding and chromogen development as general IHC sources of background (standard IHC practice). If background depends on primary antibody, titrate its concentration and shorten development in matched sections, then judge whether granular cytoplasmic staining remains distinguishable (HPA tissue IHC: granular cytoplasmic pattern; standard IHC practice).
How should I score CTSF staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, using granular cytoplasmic staining as the primary readout (HPA tissue IHC: granular cytoplasmic pattern). Record percentage of positive cells and intensity by category to calculate an H-score, or measure positive-cell density per mm² of viable tissue when cell counts better fit the question (standard IHC practice). Normalize within the same defined tissue compartment and viable area, and keep retrieval, exposure to DAB and threshold settings consistent between sections (standard IHC practice). Report cell type separately where appropriate: HPA rates hepatocytes and cerebral cortex neuronal cells High, but colon glandular cells Not detected (HPA tissue IHC).
When is apparent CTSF positivity more likely to be artefact?
Give greater weight to reproducible granular cytoplasmic staining in intact cells, which fits the reported tissue pattern and lysosomal annotation (HPA tissue IHC; UniProt Q9UBX1: lysosome). Scrutinize nuclear-only signal, sharp edge staining and deposits concentrated in necrotic regions against adjacent preserved tissue and a no-primary section (standard IHC practice). Cell identity also matters: HPA reports High staining in cerebral cortex neuronal cells and Not detected in colon glandular cells, so apply the relevant cell-specific reference cautiously (HPA tissue IHC). If DAB appears without primary antibody, investigate endogenous peroxidase activity and detection reagents before interpreting it as CTSF; HPA reports only medium consistency between antibody staining and RNA expression (standard IHC practice; HPA tissue IHC: Enhanced reliability description).
Boster reagents
Best CTSF / Cathepsin F IHC Antibodies
One human-reactive anti-CTSF antibody has real IHC data from paraffin-embedded human stomach and thyroid cancer sections (catalog A06600-1 image captions); no IF data are provided (catalog A06600-1).
Real IHC data
Anti-Cathepsin F/CTSF Antibody ®
Cat # A06600-1
A06600-1 is listed for human IHC, and its images show staining of paraffin-embedded human stomach and thyroid cancer sections (catalog A06600-1 applications, reactivity and image captions). A06600-1 has no IF image or listed IF/ICC application (catalog A06600-1 applications and image data).
Which to pick: Choose A06600-1 for human paraffin-section IHC; its caption uses EDTA retrieval at pH 8.0 and 2 μg/ml primary antibody, while the fixative is unreported (catalog A06600-1 image captions). There is no IF/ICC-validated or cross-species option in this payload: A06600-1 lists IHC but not IF/ICC, and human is its only listed reactivity (catalog A06600-1 applications and reactivity).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9UBX1 (CATF_HUMAN, Cathepsin F).
- Human Protein Atlas. CTSF tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. CTSF subcellular location (ICC-IF): Mainly localized to vesicles. In addition localized to the plasma membrane and endoplasmic reticulum..
- Human Protein Atlas. CTSF antibody validation summary (2 antibodies).
- Adipose-derived stem cells alleviate radiation-induced dermatitis by suppressing apoptosis and downregulating cathepsin F expression. Stem cell research & therapy 2021 — PMC8351374.
- Overexpression of cathepsin F, matrix metalloproteinases 11 and 12 in cervical cancer. BMC cancer 2005 — PMC1175083.
- Cathepsin F and Fibulin-1 as novel diagnostic biomarkers for brain metastasis of non-small cell lung cancer. British journal of cancer 2022 — PMC9174239.
- Cathepsin F is a potential marker for senescent human skin fibroblasts and keratinocytes associated with skin aging. GeroScience 2023 — PMC9886782.
- PubMed PMID:10318784 — UniProt-cited evidence.
- PubMed PMID:10198209 — UniProt-cited evidence.
- PubMed PMID:10661872 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for CTSF (Cathepsin F). Expected localisation Granular cytoplasm (HPA tissue IHC); lysosome (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A06600-1). Validated IHC antibody: A06600-1 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Cerebellum (Cells in molecular layer); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human stomach cancer tissue; fixative not specified (datasheet A06600-1); 2. Fixation: Image fixative and duration unreported (datasheet A06600-1); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat retrieval: EDTA pH 8.0 (datasheet A06600-1); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A06600-1); 8. Primary antibody: Rabbit anti-CTSF, 2-5 μg/ml (datasheet A06600-1); 9. Primary incubation: Overnight at 4 °C (datasheet A06600-1). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Staining has medium consistency with RNA expression (HPA tissue IHC); Isoform / epitope: 0 isoforms annotated; map epitopes to propeptide or mature chain (UniProt); Regulation: No specific regulator annotated (UniProt). Evidence: UniProt Q9UBX1, HPA tissue IHC · Enhanced, HPA ICC-IF · Mainly localized to vesicles. In addition localized to the plasma…, Datasheet A06600-1, PMC9174239, PMC9886782. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/CTSF/immunohistochemistry-ihc-guide.