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SHMT1 / Serine hydroxymethyltransferase, cytosolic · IHC design guide
Design Immunohistochemistry for SHMT1
Plan SHMT1 paraffin IHC using the 2 μg/mL catalog antibody example from human liver cancer tissue (datasheet M02944 IHC). Interpret the cytoplasmic tissue pattern alongside possible nuclear localization, especially in proliferating cells (HPA tissue IHC; UniProt).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SHMT1 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 | Cytoplasmic tissue staining (HPA tissue IHC); nuclear pool possible (UniProt) | |
| Staining pattern | Cytoplasmic staining across several tissues (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M02944) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image M02944) | |
| Caveat | Cell cycle can shift SHMT1 toward nuclear staining (UniProt) | |
| Regulation | Nuclear SHMT1 resists degradation (UniProt) | |
| Isoform / epitope | 4 isoforms; epitope coverage is unspecified (UniProt) |
Section 1
Recommended SHMT1 IHC & IF Protocols
The catalog antibody uses EDTA pH 8.0 retrieval (datasheet M02944). The four published IHC protocols below show the conditions reported for SHMT1 staining (PMC10728000; PMC12683878; PMC11724956; PMC6373090).
| Sample | Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet M02944) |
| Fixation | Image fixative and duration unreported (datasheet M02944); 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 M02944); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M02944) |
| Primary antibody | Mouse monoclonal (clone 9C7) anti-SHMT1, 2μg/ml (datasheet M02944) |
| Primary incubation | Overnight at 4 °C (datasheet M02944) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet M02944) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SHMT1-positive staining in glandular cells of appendix (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in several tissues. No signal in the no-primary control. |
💡Decision noteStart with EDTA pH 8.0 heat retrieval for the catalog antibody (datasheet M02944). Citrate retrieval is a published alternative, with pH unspecified (PMC12683878).
Section 2
What Is the Expected SHMT1 Staining Pattern?
SHMT1 is a cytoplasmic protein that can also enter the nucleus; it has no transmembrane segment (UniProt P34896). In paraffin-section IHC, expect cytoplasmic staining in selected cells, including kidney tubule cells, hepatocytes and intestinal glandular cells (HPA: High). HPA rates the tissue IHC profile Enhanced, with medium consistency between antibody staining and RNA expression (HPA: tissue IHC).
| Clear cytoplasmic staining in kidney tubule cells or hepatocytes, with surrounding structures still distinguishable. | This fits the reported high staining in those cell types and SHMT1’s cytoplasmic location (HPA: High in kidney tubule cells and hepatocytes; UniProt P34896). Compare defined cells, since a tissue label alone does not describe every cell in the section (general IHC practice). |
| Predominantly membrane-rim or extracellular staining, without a convincing cytoplasmic component. | This is discordant with the reported cytoplasmic pattern and lack of a transmembrane segment (HPA: tissue IHC; UniProt P34896 topology). Check morphology and controls before assigning it to SHMT1; genuine nuclear signal remains possible (UniProt P34896). |
| Strong staining in adipocytes or cardiomyocytes while expected positive cells are weak. | HPA reports SHMT1 as not detected in those cell types (HPA: adipocytes and cardiomyocytes). Investigate antibody cross-reactivity or endogenous detection activity with appropriate controls (general IHC practice). An unexpected positive alone does not establish its cause. |
| Broad, hazy chromogen across cells and cell-free areas, obscuring compartment boundaries. | This limits interpretation of cytoplasmic staining (HPA: cytoplasmic expression). Review blocking, washes and detection controls for nonspecific background or endogenous activity (general IHC practice); the supplied sources do not identify an SHMT1-specific cause. |
| No convincing staining in kidney tubule cells or hepatocytes, despite intact tissue. | These are reported high-staining reference cells (HPA: High). Check the IHC-validated antibody, retrieval, detection reagents and a concurrent positive control (general IHC practice). Absence in one section cannot by itself establish absent SHMT1. |
💡Expected SHMT1 appearanceA positive IHC result shows distinct, often high cytoplasmic staining in kidney tubule cells or hepatocytes (HPA: High; HPA: cytoplasmic expression); isolated membrane-rim staining is discordant with SHMT1 topology (UniProt P34896).
| Where should cytoplasmic and nuclear signal be scored? | Score cytoplasm as the principal IHC compartment (HPA: cytoplasmic expression). Nuclear SHMT1 is biologically plausible, particularly around DNA synthesis, but nuclear staining needs control-supported interpretation (UniProt P34896: cell-cycle localization; general IHC practice). |
| How much does antibody validation establish? | HPA rates the tissue profile Enhanced and lists HPA023314 and HPA078682 as IHC Enhanced (HPA: tissue IHC; HPA: antibodies). The tissue profile has medium staining-to-RNA consistency (HPA: reliability description), so validate the observed pattern in the planned material. |
| Do isoforms or processing predict a different compartment? | UniProt lists 4 isoforms, no signal peptide or propeptide, and a chain spanning residues 2–483 (UniProt P34896). No supplied epitope position shows whether the IHC-validated antibody recognizes every isoform; do not infer isoform-specific staining from this record. |
| What should IF/ICC show? | Mainly cytosolic signal is supported; an additional nucleoplasmic location is marked uncertain (HPA: subcellular ICC-IF). HPA lists HPA023314 as ICC Supported (HPA: antibodies). Interpret IF/ICC images using the separate IF/ICC guide. |
| Situation | Likely cause | Next action |
|---|---|---|
| Kidney tubule cells and hepatocytes are both negative. | The run may have a retrieval or detection problem; these cells are reported High by HPA, but a single negative run does not identify the failure (HPA: tissue IHC; general IHC practice). | Confirm section integrity and compare a concurrent positive control; review the antibody’s validated IHC-P instructions and detection controls (general IHC practice). |
| Only nuclei stain strongly in a proposed positive tissue. | Nuclear SHMT1 is possible, but an exclusively nuclear IHC pattern differs from HPA’s predominantly cytoplasmic tissue profile (UniProt P34896; HPA: tissue IHC). | Recheck cell boundaries and the cytoplasmic channel or chromogen; assess antibody and detection controls before calling the nuclear pattern specific (general IHC practice). |
| Adipocytes or cardiomyocytes stain as strongly as the expected positive cells. | HPA lists both cell types as Not detected; cross-reactivity or endogenous detection activity warrants assessment (HPA: adipocytes and cardiomyocytes; general IHC practice). | Compare the same run’s positive cells with no-primary and detection controls; revisit antibody specificity if the unexpected cellular signal persists (general IHC practice). |
| Chromogen covers much of the section and obscures cell outlines. | Diffuse background can arise from nonspecific binding or detection activity (general IHC practice); it cannot be assigned to SHMT1 from appearance alone. | Inspect the no-primary control and review blocking, washes and detection settings, then score only staining with a resolvable cellular compartment (general IHC practice). |
| One glandular tissue is weak while another is clearly positive. | HPA reports High staining in specified glandular cells across several tissues, but its reliability description notes medium staining-to-RNA consistency (HPA: tissue IHC). | Score the named cell population and section quality separately; use a concurrent positive tissue before treating one weak sample as a failed assay (HPA: tissue IHC; general IHC practice). |
| A low-staining or HPA-negative cell population shows scattered positive cells. | HPA levels describe observed populations, not a universal prohibition on every positive cell; nonspecific signal also remains possible (HPA: tissue IHC; general IHC practice). | Check cell identity, morphology and detection controls, then report the departure from the HPA reference without assigning a mechanism from staining alone (general IHC practice). |
Experiment evidence
IHC & IF images showing SHMT1 staining
M02944 · IHCIHC analysis of SHMT1 using anti-SHMT1 antibody (M02944). SHMT1 was detected in paraffin-embedded section of human liver cancer tissue. Heat
M02944 · IFIF analysis of SHMT1 using anti-SHMT1 antibody (M02944). SHMT1 was detected in immunocytochemical section of A549 cells. Enzyme antigen retr
A02944-1 · IFIF analysis of SHMT1 using anti-SHMT1 antibody (A02944-1). SHMT1 was detected in immunocytochemical section of A431 cells. Enzyme antigen re
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000176974-SHMT1/tissue/cerebral+cortex#imid_19250253
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000176974-SHMT1/tissue/colon#imid_19238553
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000176974-SHMT1/tissue/liver#imid_19238546
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000176974-SHMT1/tissue/kidney#imid_19238555
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA023314; green = SHMT1, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA023314; green = SHMT1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SHMT1 IHC & IF
🧪Run liver first: hepatocytes should stain (HPA: High in hepatocytes). Use heart muscle as the negative tissue: cardiomyocytes should lack detectable staining (HPA: Not detected in cardiomyocytes). On the liver slide, assess morphologically distinct cells without specific signal as internal background comparators, but do not presume a cell type is negative from the hepatocyte row alone (HPA: High in hepatocytes).
Positive control tissue: Appendix (Glandular cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SHMT1 in A-431, U-251MG, U2OS, KOLF2.1J, with annotated localisation: Cytosol (supported) (HPA subcellular).
Technical controls: Include no-primary (secondary-only), a mouse IgG isotype control matched to the primary’s subclass and clonality where known, and SHMT1-knockout tissue or cells as a biological negative (caption: mouse anti-SHMT1; standard IHC practice). For liver DAB staining, quench endogenous peroxidase and control endogenous biotin when using the caption’s streptavidin–biotin detection (caption: liver cancer tissue, SABC and DAB; standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected M02944 tissue-IHC caption does not state the fixative (caption: fixative unreported). The paraffin-section example uses heat retrieval in EDTA at pH 8.0, but whether retrieval is required has not been established by the supplied evidence (caption: heat-mediated EDTA retrieval). No matched comparison establishes that frozen sections or IF are easier; with the caption’s liver SABC/DAB method, endogenous peroxidase and biotin can contribute background (caption: liver cancer tissue, SABC and DAB; standard IHC practice).
HPA tissue IHC evidence for SHMT1
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 |
|---|---|---|---|---|
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
| Epididymis | Glandular cells | High | Protein (IHC) | HPA → |
| Kidney | Cells in tubules | High | Protein (IHC) | HPA → |
| Liver | Hepatocytes | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | Not detected | Protein (IHC) | HPA → |
| Heart muscle | Cardiomyocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced SHMT1 IHC Tips
Troubleshoot SHMT1 chromogenic IHC in paraffin sections using the documented retrieval and staining workflow, with tissue and compartment controls to assess specificity.
What retrieval should I start with if SHMT1 staining is weak?
Start with heat-mediated antigen retrieval in EDTA at pH 8.0 for paraffin sections (datasheet M02944). The documented section was blocked with 10% goat serum, incubated with 2 μg/ml primary antibody overnight at 4°C, and developed with SABC/DAB (caption M02944). If staining remains weak, compare a modestly longer retrieval on adjacent sections while holding antibody concentration and detection constant (standard IHC practice). Use high-staining hepatocytes or kidney tubule cells to judge recovery, and inspect sections for tissue lifting or diffuse DAB before accepting a stronger signal (HPA: high in liver hepatocytes and kidney tubule cells; standard IHC practice).
How should I troubleshoot possible fixation effects on SHMT1 staining?
The selected paraffin-section caption does not report a fixative, so SHMT1-specific fixation sensitivity is unknown (caption M02944). Record fixative type and exposure for each specimen, then compare matched sections processed with the same pH 8.0 EDTA retrieval and detection workflow (datasheet M02944; standard IHC practice). If staining differs, examine morphology and compare internal positive cells before attributing the difference to antigen loss (standard IHC practice). Include a documented high-staining tissue as a run control, such as liver with hepatocyte staining, and keep section thickness and staining conditions consistent across the comparison (HPA: high in liver hepatocytes; standard IHC practice).
Should I score nuclear SHMT1 staining as a true positive?
Score cytoplasmic staining separately from nuclear staining because SHMT1 is annotated in both compartments, while tissue IHC shows cytoplasmic expression in several tissues (UniProt P34896: cytoplasm and nucleus; HPA: tissue IHC profile). Nuclear staining is biologically plausible: SHMT1 undergoes RAN-dependent nuclear translocation and is predominantly nuclear during S phase and G2/M when sumoylated (UniProt P34896; PubMed:30035852; PubMed:17446168). Check whether the nuclear signal is confined to intact cells and exceeds the no-primary control before scoring it (standard IHC practice). Report the percentage of positive cells and intensity for each compartment, and identify the stained cell type rather than pooling all nuclei in the section (standard IHC practice).
Can this antibody distinguish SHMT1 isoforms or modified forms in tissue?
Do not assign staining to one SHMT1 isoform without an isoform-specific epitope or independent validation, because the record lists 4 isoforms but supplies no antibody epitope map (UniProt P34896; caption M02944). SHMT1 has no transmembrane segment and carries annotated modifications, including a pyridoxal phosphate linkage at residue 257 and acetylation at residue 271 (UniProt P34896). Those annotations alone do not establish whether retrieval or fixation changes this antibody’s binding (UniProt P34896; caption M02944). If compartments or tissues disagree, compare antibody staining with an orthogonal assay and document the compartment scored before making isoform or modification claims (standard IHC practice).
How can I check the IHC localisation pattern by multiplex IF?
Use IF as a separate localisation check alongside the paraffin-section IHC result; the documented M02944 tissue workflow uses chromogenic SABC/DAB detection (caption M02944). Multiplex SHMT1 with a validated marker of the expected cell type, such as a hepatocyte marker in liver, and assess overlap cell by cell (HPA: high in liver hepatocytes; standard IF practice). Choose a fluorophore channel with low tissue autofluorescence and include single-stain and no-primary controls to identify bleed-through and intrinsic signal (standard IF practice). Because SHMT1 is intracellular and has no transmembrane segment, permeabilise cells for cytosolic or nuclear epitope access, then verify the antibody’s accessibility under the chosen conditions (UniProt P34896; standard IF practice).
What should I change when SHMT1 DAB staining looks diffuse?
First compare the tissue with a no-primary control and inspect whether DAB appears outside intact cells or preferentially along section edges (standard IHC practice). The documented workflow uses 10% goat serum, 2 μg/ml primary overnight at 4°C, and a biotinylated secondary followed by SABC/DAB (caption M02944). If background persists, check blocking, washes, secondary-only staining, and endogenous peroxidase activity before changing the primary antibody concentration (standard IHC practice). With biotin-based detection, assess endogenous biotin as another possible source of signal, especially when background follows tissue structure rather than plausible cytoplasmic SHMT1 localisation (caption M02944; UniProt P34896; standard IHC practice).
How should I quantify SHMT1 staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring; SHMT1 tissue IHC is described as cytoplasmic, with high staining in liver hepatocytes and kidney tubule cells (HPA: tissue IHC profile and positive cells). For a selected population, record the percentage of positive cells and intensity, or calculate an H-score from intensity grades 0–3 for a possible range of 0–300 (standard IHC practice). Quantify nuclear and cytoplasmic signals separately if both are present (UniProt P34896: cytoplasm and nucleus; standard IHC practice). Normalise counts or stained area to the number of eligible cells or analysed tissue area, exclude necrotic regions, and apply the same threshold across slides (standard IHC practice).
How do I distinguish true SHMT1 staining from tissue artefact?
Look for staining within intact cells in a plausible compartment: SHMT1 is cytoplasmic and can also be nuclear, while HPA tissue IHC chiefly reports cytoplasmic expression (UniProt P34896; HPA: tissue IHC profile). High staining in hepatocytes or kidney tubule cells is more consistent with the reference pattern than equally strong staining in adipocytes, where SHMT1 was not detected (HPA: positive liver and kidney cells; HPA: adipocytes not detected). Treat edge-restricted signal, necrotic areas, and deposits outside cells as suspect (standard IHC practice). Compare no-primary and secondary-only controls, and check endogenous peroxidase or biotin contributions before calling diffuse SABC/DAB signal SHMT1-positive (caption M02944; standard IHC practice).
Boster reagents
Best SHMT1 / Serine hydroxymethyltransferase, cytosolic IHC Antibodies
IHC and IF data show SHMT1 staining in human paraffin-embedded liver cancer tissue and A431 cells, respectively; the catalog lists human, monkey, mouse and rat reactivity (M02944 IHC caption; A02944-1 IF caption; catalog reactivity).
Real IHC data
Anti-SHMT1 Antibody ® (monoclonal, 9C7)
Cat # M02944
Real IF data
Anti-SHMT1 Antibody ®
Cat # A02944-1
M02944 has IHC data from human paraffin-embedded liver cancer tissue and lists IHC and IF applications (M02944 IHC caption; catalog applications). A02944-1 has IF data from A431 cells and lists IF, ICC and IHC applications (A02944-1 IF caption; catalog applications).
Which to pick: Choose mouse monoclonal M02944 for tissue IHC: its own caption documents staining of a human paraffin-embedded section at 2 μg/ml; the fixative is unreported (M02944 IHC caption; catalog clone 9C7). Choose rabbit A02944-1 for IF/ICC: its own caption documents A431 cell staining at 5 μg/ml (A02944-1 IF caption; catalog host and applications). For cross-species planning, both list human, monkey, mouse and rat reactivity, while the supplied IHC and IF figures show human samples (catalog reactivity; M02944 IHC caption; A02944-1 IF caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P34896 (GLYC_HUMAN, Serine hydroxymethyltransferase, cytosolic).
- Human Protein Atlas. SHMT1 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. SHMT1 subcellular location (ICC-IF): Mainly localized to the cytosol. In addition localized to the nucleoplasm..
- Human Protein Atlas. SHMT1 antibody validation summary (2 antibodies).
- HOXD8 suppresses renal cell carcinoma growth by upregulating SHMT1 expression. Cancer science 2023 — PMC10728000.
- SHMT1, an amino acid metabolism-related gene, is an independent prognostic biomarker in laryngeal squamous cell carcinoma. BMC cancer 2025 — PMC12683878.
- Integrative bioinformatics approach identifies novel drug targets for hyperaldosteronism, with a focus on SHMT1 as a promising therapeutic candidate. Scientific reports 2025 — PMC11724956.
- SHMT1 inhibits the metastasis of HCC by repressing NOX1-mediated ROS production. Journal of experimental & clinical cancer research : CR 2019 — PMC6373090.
- PubMed PMID:8505317 — UniProt-cited evidence.
- PubMed PMID:9056951 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SHMT1 (Serine hydroxymethyltransferase, cytosolic). Expected localisation Cytoplasmic tissue staining (HPA tissue IHC); nuclear pool possible (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet M02944). Validated IHC antibody: M02944 at 2μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Appendix (Glandular cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet M02944); 2. Fixation: Image fixative and duration unreported (datasheet M02944); 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 M02944); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet M02944); 8. Primary antibody: Mouse monoclonal (clone 9C7) anti-SHMT1, 2μg/ml (datasheet M02944); 9. Primary incubation: Overnight at 4 °C (datasheet M02944). Watch for: Fixation: Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image M02944); Caveat: Cell cycle can shift SHMT1 toward nuclear staining (UniProt); Isoform / epitope: 4 isoforms; epitope coverage is unspecified (UniProt); Regulation: Nuclear SHMT1 resists degradation (UniProt). Evidence: UniProt P34896, HPA tissue IHC · Enhanced, HPA ICC-IF · Mainly localized to the cytosol. In addition localized to the…, Datasheet M02944, PMC10728000, PMC12683878. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SHMT1/immunohistochemistry-ihc-guide.