SYNPO2 / Synaptopodin-2 · IHC design guide

Design Immunohistochemistry for SYNPO2

Plan SYNPO2 chromogenic IHC-P around cytoplasmic myocyte staining (HPA tissue IHC). Start the catalog antibody at 5 μg/mL (datasheet: IHC-P), and use skeletal or heart muscle as positive tissue (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for SYNPO2 (IHC for SYNPO2): expected localisation Cytoplasm in myocytes (HPA tissue IHC), antibody A07616, validated IHC image, and IHC protocol steps
Printable SYNPO2 IHC protocol sheet — expected localisation Cytoplasm in myocytes (HPA tissue IHC), antibody A07616, controls and protocol steps. Open the full SYNPO2 IHC guide →

SYNPO2 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 Cytoplasm in myocytes (HPA tissue IHC)
Staining pattern Mainly cytoplasmic staining in myocytes (HPA tissue IHC)
Antigen retrieval Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen)
Positive control ⓘ Endometrium+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); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A07616)
Caveat Stress can shift cytoplasmic signal to nuclei (UniProt)
Regulation Isoform 5 is skeletal muscle-specific (UniProt)
Isoform / epitope 5 isoforms; epitope coverage is unspecified (UniProt)
Section 1

Recommended SYNPO2 IHC & IF Protocols

The catalog antibody protocol is followed by published SYNPO2 IHC methods for gastric cancer, nasopharyngeal carcinoma, and bladder cancer samples (PMC10660625; PMC10378812; PMC10758676).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleTissue sections; selected-image fixative not specified (standard IHC workflow)
FixationImage fixative and duration unreported (datasheet A07616); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear antigen)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% normal serum of the secondary host, 30 min, room temperature (standard)
Primary antibodyRabbit anti-SYNPO2, 5 μg/mL (datasheet A07616)
Primary incubationOvernight at 4 °C (standard)
DetectionHRP-polymer secondary, DAB chromogen 5–10 min (standard)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultSYNPO2-positive staining in smooth muscle cells of endometrium (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression mainly in myocytes. No signal in the no-primary control.
💡Decision noteStart with pH 9.0 Tris-EDTA retrieval at 95–98 °C for 20 min (page retrieval); the cited tissue protocols report different citrate conditions (PMC10378812; PMC10758676).
Section 2

What Is the Expected SYNPO2 Staining Pattern?

SYNPO2 is mainly cytoplasmic in myocytes, with high IHC staining in skeletal and smooth muscle myocytes and cardiomyocytes (HPA: tissue IHC). Nuclear, actin-associated and Z-line localization can occur according to cell state (UniProt Q9UMS6: subcellular location). SYNPO2 has no transmembrane segment, so a membrane-only pattern is unexpected (UniProt Q9UMS6: topology). HPA rates the tissue pattern Enhanced but notes that external verification is pending (HPA: tissue IHC reliability).

What am I looking at on my slide?
Strong cytoplasmic staining in myocytes, especially in skeletal muscle, smooth muscle or heart (HPA: High in these cells).This matches the principal tissue pattern. Score the relevant myocytes separately from adjacent cells; a positive area alone does not establish which cell type stained (HPA: cytoplasmic expression mainly in myocytes).
Actin-associated or Z-line staining, with some nuclear signal in muscle cells (UniProt Q9UMS6: subcellular location).These compartments are plausible: SYNPO2 associates with actin and can move between cytoplasm and nucleus with differentiation or stress (UniProt Q9UMS6: localization and function). Interpret nuclear staining alongside cell identity and morphology.
Only sharp plasma-membrane outlines appear, without a myocyte cytoplasmic pattern (HPA: tissue IHC; UniProt Q9UMS6: topology).Treat this as an unexpected compartment pattern requiring review. SYNPO2 has no transmembrane segment; a membrane-only result does not match the reported predominant cytoplasmic IHC pattern (UniProt Q9UMS6: topology; HPA: tissue IHC).
Adipocytes or appendix glandular cells stain strongly, while nearby expected-positive muscle cells do not (HPA: Not detected in those cell types; High in myocytes).Investigate antibody cross-reactivity or endogenous detection activity before calling those cells SYNPO2-positive (standard IHC practice). HPA's negative entries describe particular cells, not every cell in the tissue (HPA: tissue IHC).
A uniform haze covers many cell types, or a known-positive myocyte region has no signal (HPA: cytoplasmic expression mainly in myocytes).Haze obscures compartment and cell-type scoring; absent signal in a positive control makes a negative study result inconclusive. Check background and detection controls, then repeat the affected staining run (standard IHC practice).
💡Expected SYNPO2 appearanceCall positive when myocytes show clear, predominantly cytoplasmic staining, expected to be high in the HPA-listed muscle cells; an isolated membrane rim or broad staining of HPA-negative cell types needs investigation (HPA: tissue IHC; UniProt Q9UMS6: topology).
How each factor affects the staining
Cell type and tissue used as controls (HPA: tissue IHC).Skeletal muscle myocytes, cardiomyocytes and smooth muscle cells are High; breast myoepithelial cells are Medium. Choose a documented positive cell population and score it by cell type (HPA: tissue IHC).
Differentiation and stress state (UniProt Q9UMS6: subcellular location).SYNPO2 can shift between nucleus and cytoplasm; differentiated myotubes can show Z-line localization. A nuclear component is therefore context dependent, not automatically an artefact (UniProt Q9UMS6: subcellular location).
Isoform coverage (UniProt Q9UMS6: isoforms and tissue specificity).UniProt lists 5 isoforms and reports isoform 5 specifically in skeletal muscle. Without a supplied antibody epitope, isoform recognition cannot be inferred from tissue staining alone (UniProt Q9UMS6: isoforms; HPA: tissue IHC).
Antibody evidence (HPA: antibody validation).HPA030665 and HPA068563 have Enhanced IHC evidence; CAB037231 is Supported for IHC. These ratings guide confidence in the observed pattern but do not validate every new specimen or staining run (HPA: antibody validation).
IF/ICC Q: What localization is reported? (HPA: subcellular ICC-IF).A: HPA reports mainly vesicles and actin filaments, both Enhanced, in ICC-IF; UniProt also describes nuclear shuttling. Interpret IF/ICC with its own guide, since these observations do not supply an IHC-P protocol (HPA: subcellular ICC-IF; UniProt Q9UMS6: localization).
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
No staining in a skeletal muscle myocyte positive control (HPA: High in skeletal muscle myocytes).A failed IHC run or a missed positive cell population is possible (standard IHC practice).Verify muscle-cell morphology and control performance; review the antibody's supplied IHC-P instructions, retrieval and detection steps, then repeat the run (standard IHC practice).
Myocytes are faint, but background is also low (HPA: High in listed muscle myocytes).Signal may be below the assay's useful range; this result alone cannot establish a SYNPO2-specific fixation effect (standard IHC practice).Check positive-control staining and the supplied IHC-P antibody dilution and detection instructions before adjusting the assay (standard IHC practice).
Diffuse chromogen masks cell borders or cytoplasmic detail (HPA: cytoplasmic expression mainly in myocytes).Nonspecific binding, inadequate blocking or excessive chromogen development can obscure localization (standard IHC practice).Inspect the negative detection control; review blocking, washes and development time, then score only a run with interpretable cell detail (standard IHC practice).
Staining appears only as a plasma-membrane rim (UniProt Q9UMS6: no transmembrane segment).The compartment disagrees with the predominant cytoplasmic IHC profile (HPA: tissue IHC).Recheck tissue morphology and detection controls; compare with a documented myocyte positive control before assigning SYNPO2 localization (standard IHC practice; HPA: tissue IHC).
Strong signal appears in adipocytes or appendix glandular cells (HPA: Not detected in those cells).Cross-reactivity or endogenous chromogenic detection activity is possible (standard IHC practice).Run an appropriate negative detection control, assess background and confirm the stained cell identity; interpret other cells in that tissue separately (standard IHC practice; HPA: tissue IHC).
Nuclear staining accompanies myocyte cytoplasmic staining (UniProt Q9UMS6: nuclear shuttling).Differentiation or stress can change SYNPO2 distribution, although the slide alone does not identify the cause (UniProt Q9UMS6: subcellular location).Record nuclear and cytoplasmic staining separately and compare the pattern across the same cell type and controls (standard IHC practice).

Sample controls for SYNPO2 IHC & IF

🧪Run skeletal muscle first: myocytes should stain (HPA: High in skeletal-muscle myocytes; catalog antibody A07616 tissue-IHC caption: mouse skeletal muscle staining). Use adipose tissue as the negative comparator, focusing on adipocytes (HPA: Not detected in adipocytes); on the positive slide, independently verified negative nonmyocyte cells should show counterstain without specific chromogen, but their negative status cannot be assumed from the myocyte result alone (standard IHC control practice).
Positive control tissue: Endometrium (Smooth muscle cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SYNPO2 in BJ [Human fibroblast], SH-SY5Y, with annotated localisation: Vesicles (enhanced), Actin filaments (enhanced) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only slide, a host-species-matched control antibody with matching isotype for a monoclonal primary, and SYNPO2-knockout tissue or cells as a biological negative (standard IHC control practice). For chromogenic detection in skeletal muscle, quench endogenous peroxidase when using HRP and block endogenous biotin if using a biotin-based system (standard IHC practice).
⚠️Feasibility: A target-specific fixation window, fixation effect, and antigen-retrieval dependency are unreported in the supplied evidence; the selected tissue-IHC caption reports 5 μg/mL antibody in mouse skeletal muscle but does not state the fixative (catalog antibody A07616 tissue-IHC caption). The evidence does not establish that frozen sections or IF are easier; IF/ICC images are available for BJ and SH-SY5Y cells, with mainly vesicle and actin-filament localization (HPA: subcellular). In skeletal muscle, evaluate fiber-associated staining against the tissue architecture and avoid treating nuclear signal alone as artefact, because SYNPO2 can localize to Z lines and shuttle to the nucleus under stress (UniProt Q9UMS6: subcellular location).

HPA tissue IHC evidence for SYNPO2

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Antibody staining in cells/structures not annotated, view images. Pending external verification.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.

Positive expression · recommended positive controls

TissueCell typeLevelEvidenceSource
Endometrium Smooth muscle cells High Protein (IHC) HPA →
Heart muscle Cardiomyocytes High Protein (IHC) HPA →
Placenta Decidual cells High Protein (IHC) HPA →
Skeletal muscle Myocytes High Protein (IHC) HPA →
Smooth muscle Smooth muscle cells High Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
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 →
Bronchus Respiratory epithelial cells Not detected Protein (IHC) HPA →
Caudate Glial cells Not detected Protein (IHC) HPA →
Section 3

Advanced SYNPO2 IHC Tips

Troubleshoot SYNPO2 staining in paraffin sections by checking retrieval, tissue context, subcellular pattern, and matched controls before scoring chromogenic signal.

How should I retrieve SYNPO2 when staining is weak in paraffin sections?
Start with Tris-EDTA pH 9.0 heat-induced epitope retrieval at 95–98 °C for 20 min (page setting: nuclear-antigen retrieval). Let sections cool in the retrieval buffer before washing, and keep heating and cooling conditions identical across cases (standard IHC practice). Check a skeletal-muscle section alongside the test tissue because myocytes show high staining in the tissue reference (HPA: high in skeletal-muscle myocytes). If staining remains weak, compare a pH 6.0 citrate retrieval arm while retaining the prescribed condition as the reference (standard IHC troubleshooting). Judge improvement by cellular pattern and background together, rather than intensity alone (standard IHC practice).
Could fixation explain weak or uneven SYNPO2 staining?
Target-specific fixation sensitivity is unknown: the selected antibody’s mouse skeletal-muscle IHC caption does not state a fixative (A07616 tissue-IHC caption: fixative not stated). For newly collected material, compare documented 6 h and 24 h intervals in 10% neutral buffered formalin, holding processing and staining constant (standard IHC practice). Record specimen thickness and time before fixation because those variables can create uneven antigen preservation within a section (standard IHC practice). Compare staining in viable myocytes at similar depths, with the same retrieval and detection run, before attributing differences to fixation (HPA: high in skeletal-muscle myocytes; standard IHC practice).
Which SYNPO2 staining patterns should I expect in myocytes?
Assess cytoplasmic staining in morphologically identified myocytes first, since the tissue reference describes mainly cytoplasmic expression in myocytes (HPA: tissue-IHC profile). In organized muscle, a striated pattern may align with sarcomeric Z lines; nuclear staining can also be biologically plausible because SYNPO2 shuttles with differentiation and stress (UniProt Q9UMS6: subcellular location). Compare staining on 2 adjacent sections, one stained and one primary-antibody omission control, to distinguish repeatable structure from deposits (standard IHC practice). Do not require every positive cell to show the same nuclear-to-cytoplasmic balance, but verify that any proposed pattern follows cell anatomy (UniProt Q9UMS6: shuttling; standard IHC practice).
Could the antibody epitope miss a SYNPO2 isoform or modification?
SYNPO2 has 5 listed isoforms, and isoform 5 is specifically expressed in skeletal muscle (UniProt Q9UMS6: isoforms and tissue specificity). Before comparing tissues, obtain the antibody’s immunogen coordinates and map them against each isoform; recognition of all isoforms cannot be assumed without that information (UniProt Q9UMS6: isoforms; standard antibody validation practice). The protein contains a PDZ domain at residues 6–88 and multiple reported phosphorylation sites, so epitope position matters when interpreting differential staining (UniProt Q9UMS6: domain and modified residues). If staining differs, compare positive tissue, retrieval, and antibody conditions before assigning the difference to an isoform or phosphorylation state (standard IHC practice).
How can IF help assess SYNPO2 localisation alongside chromogenic IHC?
In a separate IF/ICC experiment, pair SYNPO2 with a myocyte marker such as ACTN2 to identify the expected cell type and examine possible Z-line alignment (UniProt Q9UMS6: ACTN2 interaction and Z-line localisation). Choose a far-red fluorophore when tissue autofluorescence compromises shorter wavelengths, and include single-stain and unstained controls for channel assessment (standard IF practice). SYNPO2 lacks a transmembrane segment and has cytoplasmic and nuclear locations, so test mild permeabilisation, such as 0.1% Triton X-100 for 5 min, for intracellular access (UniProt Q9UMS6: topology and localisation; standard IF practice). Evaluate actin-associated and vesicular signal cautiously because those patterns come from ICC/IF observations, not this antibody’s tissue caption (HPA: subcellular ICC/IF; A07616 tissue-IHC caption).
How do I separate SYNPO2 signal from chromogenic background?
Run a primary-antibody omission section and block endogenous peroxidase, for example with 3% hydrogen peroxide for 10 min, before peroxidase-based detection (standard IHC practice). Compare diffuse staining with the mainly cytoplasmic myocyte pattern reported in tissue sections; deposits unrelated to cell boundaries warrant closer inspection (HPA: tissue-IHC profile; standard IHC practice). Titrate the catalog antibody around the concentration shown in its mouse skeletal-muscle image, 5 µg/mL, while keeping DAB development time fixed (A07616 tissue-IHC caption; standard IHC practice). Check wash quality, blocking, section folds, and edges on the control section before treating widespread brown signal as SYNPO2 expression (standard IHC practice).
What should I score when comparing SYNPO2 across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the analyzable compartment as viable, morphologically identified myocytes when comparing muscle specimens, because the tissue reference reports high staining in myocytes (HPA: skeletal-muscle myocytes). Record the percentage of positive myocytes and an intensity score of 0–3, then calculate an H-score from 0–300 using intensity-weighted percentages (standard IHC scoring practice). Normalize counts to the total number of evaluable myocytes, or staining density to the measured viable tissue area in mm², and state which denominator was used (standard IHC quantification practice). Hold retrieval, detection, counterstain, imaging, and positivity thresholds constant, and score nuclear and cytoplasmic compartments separately when both are present (UniProt Q9UMS6: shuttling; standard IHC practice).
When is an unexpected SYNPO2-positive area likely to be artefact?
A true result should reproduce a cell-associated pattern in an appropriate tissue context, such as cytoplasmic myocytes in skeletal or heart muscle (HPA: tissue-IHC profile and positive cells). Nuclear signal is not automatically artefactual because SYNPO2 can move into nuclei with differentiation or stress, but isolated staining in cells outside the proposed compartment needs validation (UniProt Q9UMS6: shuttling; standard IHC interpretation). Inspect 2 adjacent sections for edge-only staining, necrotic areas, pigment, and precipitate, and compare them with a primary-antibody omission control (standard IHC practice). If brown signal persists without primary antibody, investigate endogenous enzyme activity and detection background before reporting SYNPO2 positivity (standard IHC practice).
Boster reagents

Best SYNPO2 / Synaptopodin-2 IHC Antibodies

A07616 has IHC and IF images of mouse skeletal muscle (catalog image captions) and lists Human and Mouse reactivity (catalog reactivity).

Real IHC data Immunohistochemistry of SYNPO2 in mouse skeletal muscle tissue with SYNPO2 antibody at 5 μg/mL.
Anti-Synaptopodin-2 SYNPO2 Antibody
Cat # A07616

A07616 lists IHC-P and has a mouse skeletal muscle IHC image at 5 μg/mL (catalog applications; A07616 IHC image caption). A07616 also lists IF and has a mouse skeletal muscle IF image at 20 μg/mL (catalog applications; A07616 IF image caption).

Which to pick: Choose A07616 for paraffin-section tissue IHC (catalog: IHC-P); its own IHC image shows mouse skeletal muscle, while the fixative is unreported (A07616 IHC image caption). For IF, choose A07616 based on its mouse skeletal muscle image; ICC validation is unreported (A07616 IF image caption; catalog applications). For Human or Mouse samples, A07616 lists reactivity in both species, but its IHC and IF images show Mouse samples only; clonality is unreported (catalog reactivity; A07616 image captions; catalog clone field).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

  1. UniProt Consortium. UniProt entry Q9UMS6 (SYNP2_HUMAN, Synaptopodin-2).
  2. Human Protein Atlas. SYNPO2 tissue IHC expression (reliability: Enhanced).
  3. Human Protein Atlas. SYNPO2 subcellular location (ICC-IF): Mainly localized to vesicles and actin filaments..
  4. Human Protein Atlas. SYNPO2 antibody validation summary (4 antibodies).
  5. Gastric cancer peritoneal metastasis related signature predicts prognosis and sensitivity to immunotherapy in gastric cancer. Journal of cellular and molecular medicine 2023 — PMC10660625.
  6. SYNPO2 upregulation is an unfavorable prognostic factor for nasopharyngeal carcinoma patients. Medicine 2023 — PMC10378812.
  7. SYNPO2 promotes the development of BLCA by upregulating the infiltration of resting mast cells and increasing the resistance to immunotherapy. Oncology reports 2024 — PMC10758676.
  8. Bone marrow mesenchymal stem cells alleviate neurological dysfunction by reducing autophagy damage via downregulation of SYNPO2 in neonatal hypoxic-ischemic encephalopathy rats. Cell death & disease 2025 — PMC11862179.
  9. PubMed PMID:18371299 — UniProt-cited evidence.
  10. PubMed PMID:24005909 — UniProt-cited evidence.
  11. PubMed PMID:20554076 — UniProt-cited evidence.