TMEM106B / Transmembrane protein 106B · IHC design guide

Design Immunohistochemistry for TMEM106B

Plan TMEM106B paraffin IHC using 2.5 μg/mL as the catalog antibody’s starting concentration (datasheet: IHC-P). Compare neuronal staining in cerebral cortex with adipocytes in adipose tissue, and assess the reported cytoplasmic pattern (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for TMEM106B (IHC for TMEM106B): expected localisation Cytoplasmic staining in several tissues (HPA tissue IHC), antibody A03541, validated IHC image, and IHC protocol steps
Printable TMEM106B IHC protocol sheet — expected localisation Cytoplasmic staining in several tissues (HPA tissue IHC), antibody A03541, controls and protocol steps. Open the full TMEM106B IHC guide →

TMEM106B 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 staining in several tissues (HPA tissue IHC)
Staining pattern Neuronal cytoplasmic staining in cortex and caudate (HPA tissue IHC)
Antigen retrieval Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen)
Positive control ⓘ Adrenal gland+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 A03541)
Caveat Staining and RNA expression have low consistency (HPA tissue IHC)
Regulation Low tissue RNA specificity; no regulator specified (HPA tissue RNA)
Isoform / epitope No isoforms; cytoplasmic vs lumenal epitope matters (UniProt)
Section 1

Recommended TMEM106B IHC & IF Protocols

The catalog antibody’s IHC-P protocol is accompanied by published TMEM106B staining protocols for frontal lobe sections (PMC10626444; PMC11181561).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleTissue sections; selected-image fixative not specified (standard IHC workflow)
FixationImage fixative and duration unreported (datasheet A03541); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat-induced epitope retrieval in citrate buffer, pH 6.0, 20 min at 95–98 °C (standard rule: cytoplasmic / membrane antigen)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% normal serum of the secondary host, 30 min, room temperature (standard)
Primary antibodyRabbit anti-TMEM106B, 2.5 μg/mL (datasheet A03541)
Primary incubationOvernight at 4 °C (standard)
DetectionHRP-polymer secondary, DAB chromogen 5–10 min (standard)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultTMEM106B-positive staining in glandular cells of adrenal gland (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic expression in several tissues. No signal in the no-primary control.
💡Decision noteStart with citrate pH 6.0 retrieval for the catalog antibody (page protocol); consider formic acid for the published C-terminal staining approach (PMC10626444).
Section 2

What Is the Expected TMEM106B Staining Pattern?

TMEM106B is a late endosome and lysosome membrane protein; its cytoplasmic tail spans residues 2–96, its membrane segment spans 97–117, and its lumenal region spans 118–274 (UniProt Q9NUM4 topology). In paraffin section IHC, expect cytoplasmic staining in several tissues, including neurons (HPA: tissue IHC). Treat the pattern as a guide rather than definitive proof: HPA rates the IHC antibody Approved but reports low consistency between staining and RNA expression (HPA: reliability).

What am I looking at on my slide?
Cytoplasmic granular staining in cerebral cortex or hippocampal neurons, with appreciable cell-to-cell variation (HPA: Medium in neuronal cells; HPA: cytoplasmic expression).This fits the observed IHC cell population and the late endosome/lysosome location (HPA: tissue IHC; UniProt Q9NUM4 subcellular location). At chromogenic resolution, a granular impression is compatible with intracellular organelles; individual lysosomes need not be distinguishable (standard IHC interpretation).
Predominantly nuclear staining, with little cytoplasmic staining in an HPA-positive cell population (HPA: tissue IHC).A nuclear-dominant pattern conflicts with the reported endosome/lysosome membrane location and cytoplasmic IHC profile (UniProt Q9NUM4 subcellular location; HPA: tissue IHC). Check localization and controls before assigning it to TMEM106B (standard IHC practice).
Strong, uniform staining in adipocytes or bronchial respiratory epithelial cells (HPA: Not detected in those cells).This differs from the HPA reference observations and warrants a check for antibody cross-reactivity or endogenous detection activity (HPA: tissue IHC; standard IHC troubleshooting). A 'Not detected' entry is an observation under HPA conditions, not proof of universal absence (HPA: tissue IHC).
Diffuse color across cells and surrounding tissue, obscuring cell boundaries (standard IHC interpretation).Interpret the run cautiously: nonspecific binding, endogenous enzyme activity, or excess chromogen development can obscure a localized signal (standard chromogenic IHC practice). The expected intracellular pattern offers a spatial check, but does not identify which workflow step failed (UniProt Q9NUM4 subcellular location; standard IHC practice).
No detectable staining in cerebral cortex neurons or cerebellar Purkinje cells (HPA: Medium in those cells).First investigate the run and tissue quality; a negative result in one section does not overturn the reference pattern (HPA: tissue IHC; standard IHC practice). HPA's reported low antibody-staining/RNA consistency adds reason to avoid calling a biological absence from this result alone (HPA: reliability).
💡Expected TMEM106B appearanceA convincing IHC-positive result is cytoplasmic, potentially granular staining of expected cells such as cerebral cortex neurons at a roughly medium reference level; dominant nuclear or uniform tissue-wide color is a warning pattern (HPA: tissue IHC; UniProt Q9NUM4 subcellular location; standard IHC interpretation).
How each factor affects the staining
Organelle location and topologyTMEM106B occupies late endosome and lysosome membranes, with a cytoplasmic N-terminal region and lumenal C-terminal region (UniProt Q9NUM4 topology and subcellular location). Interpret cytoplasmic IHC color in that context; the HPA tissue images establish a cytoplasmic pattern, not resolution of individual membrane faces (HPA: tissue IHC).
Cell population selected for assessmentCerebral cortex and hippocampal neuronal cells, cerebellar Purkinje cells, and caudate neuronal cells have Medium HPA IHC staining (HPA: tissue IHC). Adipocytes and bronchial respiratory epithelial cells are listed as Not detected; compare the named cells, not whole organs indiscriminately (HPA: tissue IHC).
Strength of the tissue evidenceThe tissue IHC antibody is rated Approved, with low consistency between antibody staining and RNA expression (HPA: reliability). This supports using its reported cell patterns as references while checking unexpected results with appropriate controls; it does not establish that every stained structure is specific (HPA: reliability; standard IHC interpretation).
Surface stainingA small fraction of TMEM106B resides at the cell surface, although late endosome and lysosome membranes are its principal reported locations (UniProt Q9NUM4 subcellular location). A small peripheral component is therefore possible; isolated strong, continuous surface staining without the expected cytoplasmic pattern deserves review (UniProt Q9NUM4 subcellular location; standard IHC interpretation).
IF/ICC Q&A: where should signal localize?Endosomes and lysosomes are the supported main locations in HPA ICC-IF; images are listed for A-549, U-251MG, and U2OS (HPA: subcellular). This answers localization for the separate IF/ICC guide, without supplying an IF protocol or implying that cultured-cell fluorescence predicts paraffin section intensity (HPA: subcellular; standard assay interpretation).
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
No signal in an expected-positive neuronal population (HPA: Medium in cerebral cortex neurons).The section or staining run may have failed; a single negative section cannot distinguish assay failure from sample variation (standard IHC troubleshooting; HPA: tissue IHC).Check tissue preservation, section integrity, retrieval and detection against the antibody's validated IHC-P instructions; include a known-positive section in the same run (standard IHC practice). Avoid inferring TMEM106B-specific fixation sensitivity: none is supplied here.
Nuclear color dominates while expected cytoplasmic color is absent (HPA: cytoplasmic expression).The location conflicts with the reference endosome/lysosome membrane assignment; nonspecific nuclear signal or a detection artifact is possible (UniProt Q9NUM4 subcellular location; standard IHC troubleshooting).Compare a no-primary control and an expected-positive tissue; reassess blocking, antibody concentration, and image interpretation under the same detection settings (standard IHC practice).
Uniform staining appears across HPA Not detected cells, such as adipocytes (HPA: tissue IHC).Cross-reactivity or endogenous enzyme activity could account for color outside the reference pattern (standard chromogenic IHC troubleshooting; HPA: tissue IHC).Run no-primary and detection-only controls; if background persists, address endogenous detection activity according to the detection chemistry and reassess the named cell population (standard IHC practice).
Diffuse background prevents scoring of cytoplasmic staining (HPA: cytoplasmic expression).Nonspecific binding, insufficient washing, or excessive chromogen development can reduce contrast (standard chromogenic IHC troubleshooting).Review blocking, wash steps, antibody concentration, and development time using the validated IHC-P workflow; judge the result by whether expected cells become distinguishable (standard IHC practice; HPA: tissue IHC).
A strong continuous rim is the only staining in an expected-positive cell (HPA: tissue IHC).UniProt reports a small cell-surface fraction, but surface-only dominance does not match its principal endosome/lysosome location (UniProt Q9NUM4 subcellular location).Inspect the same cell population for cytoplasmic staining and compare with a no-primary control; report peripheral-only color separately until specificity is supported (standard IHC interpretation; UniProt Q9NUM4 subcellular location).
HPA Medium cells stain weakly while another tissue stains more strongly (HPA: tissue IHC).The HPA levels describe observed reference staining, and its low staining/RNA consistency limits any claim that intensity alone measures TMEM106B abundance (HPA: tissue IHC and reliability).Score compartment and named cell type alongside intensity, compare sections stained in the same run, and document discordance with HPA rather than assigning a biological difference from color alone (standard IHC scoring; HPA: tissue IHC).

Sample controls for TMEM106B IHC & IF

🧪Run cerebral cortex first and assess neuronal cells for TMEM106B staining (HPA: Medium in cerebral cortex neuronal cells). Use adipose tissue adipocytes as the negative tissue (HPA: Not detected in adipocytes); on the cortex slide, non-neuronal cells without specific staining should show counterstain and background only, but HPA does not establish them as a validated negative population (HPA: Medium in neuronal cells).
Positive control tissue: Adrenal gland (Glandular cells, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show TMEM106B in A-549, U-251MG, U2OS, with annotated localisation: Endosomes (supported), Lysosomes (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control and a host-species- and isotype-matched control for a monoclonal primary, or host-species-matched normal IgG for a polyclonal primary; use TMEM106B knockout tissue or peptide blocking, if available, to test specificity (standard IHC practice). For chromogenic cortex IHC, block endogenous peroxidase and assess pigment that could be mistaken for chromogen; for IF, check tissue autofluorescence (standard IHC/IF practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A03541 liver IHC caption does not state a fixative (selected-SKU tissue-IHC caption). Retrieval dependency is unreported, so optimize antigen retrieval empirically for paraffin sections (standard IHC practice). IF can help assess the expected endosomal and lysosomal pattern, but the supplied evidence does not establish that IF or frozen sections are easier; cortex pigment and autofluorescence can complicate interpretation (HPA: supported endosome and lysosome localization; standard IHC/IF practice).

HPA tissue IHC evidence for TMEM106B

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low 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

TissueCell typeLevelEvidenceSource
Adrenal gland Glandular cells Medium Protein (IHC) HPA →
Caudate Neuronal cells Medium Protein (IHC) HPA →
Cerebellum Purkinje cells Medium Protein (IHC) HPA →
Cerebral cortex Neuronal cells Medium Protein (IHC) HPA →
Epididymis Glandular cells Medium 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 →
Breast Adipocytes Not detected Protein (IHC) HPA →
Bronchus Respiratory epithelial cells Not detected Protein (IHC) HPA →
Section 3

Advanced TMEM106B IHC Tips

Use compartment, cell identity and matched controls together when assessing TMEM106B staining in paraffin sections.

How should I optimize retrieval when TMEM106B staining is weak in paraffin sections?
Start with citrate buffer at pH 6.0, heated to 95–98 °C for 20 min (page retrieval setting: cytoplasmic/membrane antigen). Allow sections to cool in the retrieval buffer, then compare staining with an otherwise identically processed section to judge whether retrieval changes signal and tissue preservation (standard IHC practice). If staining remains weak, test a more stringent retrieval condition on adjacent sections as a fallback, recording its buffer, pH and heating time rather than attributing any improvement to TMEM106B biology (standard IHC practice). Evaluate discrete intracellular staining against background because TMEM106B localizes mainly to endosomes and lysosomes (HPA: supported subcellular locations).
Can fixation explain weak or variable TMEM106B IHC staining?
Target-specific sensitivity to fixation is unknown from the supplied evidence; the catalog antibody’s human liver IHC caption does not state a fixative (A03541 tissue-IHC caption). Record the specimen’s fixative and fixation duration, then compare adjacent sections processed with the same pH 6.0, 95–98 °C, 20 min retrieval setting (page retrieval setting; standard IHC practice). Review morphology and staining together, since poorly preserved or unevenly processed sections can complicate chromogenic IHC interpretation (standard IHC practice). Do not infer a TMEM106B-specific fixation effect from tissue staining patterns or its membrane topology; neither establishes fixation sensitivity (HPA: tissue IHC profile; UniProt Q9NUM4 topology).
What staining pattern is plausible for TMEM106B in tissue sections?
Expect predominantly intracellular staining consistent with endosomes and lysosomes, although chromogenic section resolution may make small compartments appear broadly cytoplasmic (HPA: supported endosomal and lysosomal localization; standard IHC practice). TMEM106B occupies late endosome and lysosome membranes and colocalizes with LAMP1; only a small fraction resides at the cell surface (UniProt Q9NUM4 subcellular location). Assess signal within the expected cell population and against an adjacent negative control, rather than treating uniform plasma membrane or nuclear staining as sufficient evidence of specificity (standard IHC practice; UniProt Q9NUM4 subcellular location). HPA reports cytoplasmic tissue expression but notes low consistency between antibody staining and RNA expression, so interpret morphology alongside controls (HPA: tissue IHC reliability).
How does epitope position affect TMEM106B IHC interpretation?
Check the catalog antibody’s stated immunogen or epitope before interpreting a negative section; the supplied evidence does not specify where A03541 binds (A03541 tissue-IHC caption). TMEM106B has a cytoplasmic region at residues 2–96, a transmembrane segment at 97–117, and a lumenal region at 118–274 (UniProt Q9NUM4 topology). Its lumenal region includes annotated glycosylation sites at 145, 151, 164, 183 and 256, while the record lists 0 isoforms (UniProt Q9NUM4 glycosylation; isoforms). If two antibodies disagree, compare their documented epitopes and staining compartments on adjacent sections before proposing a biological explanation (standard IHC practice).
How can IF help assess a TMEM106B IHC pattern?
Use IF as a complementary localization check: assess TMEM106B alongside LAMP1, with separate staining to identify the expected cell population, such as neuronal cells in cerebral cortex (UniProt Q9NUM4: LAMP1 colocalization; HPA: cerebral cortex neuronal staining; standard IF practice). Select fluorophores after inspecting unstained tissue autofluorescence, and include single-label controls to check channel bleed-through (standard IF practice). Match permeabilisation to the antibody’s documented epitope: a cytoplasmic epitope at residues 2–96 and a lumenal epitope at 118–274 require different access through membranes (UniProt Q9NUM4 topology; standard IF practice). The supplied A03541 liver caption documents IHC staining, not IF validation or an epitope position (A03541 tissue-IHC caption).
What should I check when TMEM106B DAB staining looks diffuse?
Compare the stained section with a primary-antibody omission control and inspect whether diffuse color follows tissue edges, damaged areas or the expected intracellular distribution (standard IHC practice; HPA: supported endosomal and lysosomal localization). Check the peroxidase block and DAB development using matched sections, because endogenous enzyme activity or excessive development can produce misleading chromogenic signal (standard IHC practice). Review blocking, washes and antibody concentration in the local protocol; the A03541 human liver caption reports 2.5 µg/mL but does not establish an optimum for other specimens (A03541 tissue-IHC caption; standard IHC practice). Preserve morphology while adjusting conditions, then compare candidate settings against the same control tissue and detection run (standard IHC practice).
How should I quantify TMEM106B IHC across samples? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and scoring region before reviewing outcome groups, using the same segmentation and exclusion rules across sections (standard IHC practice). Report the percentage of positive cells and, where intensity is reproducibly graded, an H-score from 0–300; for spatial comparisons, report positive-cell density per mm² (standard IHC practice). Normalize positive counts to the number of evaluable cells of the same type, and compare density only within consistently defined tissue areas (standard IHC practice). Keep retrieval, detection and counterstaining consistent, and report cell-level scores because HPA’s cytoplasmic tissue profile has low consistency with RNA expression (page retrieval setting; HPA: tissue IHC reliability).
How can I distinguish true TMEM106B staining from artefact?
Favor signal in plausible cells with an intracellular, endosomal or lysosomal pattern and reproducibility in adjacent sections (HPA: supported subcellular locations; standard IHC practice). HPA reports medium staining in cerebral cortex neuronal cells and cerebellar Purkinje cells, while its tissue IHC reliability note says antibody staining and RNA expression have low consistency (HPA: tissue IHC profile and reliability). Treat staining restricted to cut edges or necrotic regions, strong nuclear-only signal, and color persisting after primary-antibody omission as reasons to investigate artefact or endogenous enzyme activity (standard IHC practice; UniProt Q9NUM4 subcellular location). Resolve ambiguous results with cell identity, morphology, matched controls and an independently documented epitope where available (standard IHC practice).
Boster reagents

Best TMEM106B / Transmembrane protein 106B IHC Antibodies

A03541 is listed for human IHC-P and IF (catalog: applications, reactivity). Its TMEM106B IHC image shows human liver at 2.5 μg/mL (IHC image caption).

Real IHC data Immunohistochemistry of TMEM106B in human liver tissue with TMEM106B antibody at 2.5 μg/mL.
Anti-Transmembrane protein 106B TMEM106B Antibody
Cat # A03541

A03541 is listed for human IHC-P and IF (catalog: applications, reactivity). Its IHC image shows TMEM106B staining in human liver (IHC image caption); the IF caption instead names TMEM106A, so that image does not establish TMEM106B IF validation (IF image caption).

Which to pick: For tissue IHC, choose A03541 for human paraffin sections (catalog: Human, IHC-P); its own IHC image shows human liver at 2.5 μg/mL, but the fixative is unreported (IHC image caption). For IF/ICC, A03541 is IF-listed for human samples (catalog: applications, reactivity), although its IF caption names TMEM106A and clonality is unreported (IF image caption; catalog: clone). No listed SKU has reported nonhuman reactivity for cross-species work (catalog: Human).

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

References

  1. UniProt Consortium. UniProt entry Q9NUM4 (T106B_HUMAN, Transmembrane protein 106B).
  2. Human Protein Atlas. TMEM106B tissue IHC expression (reliability: Approved).
  3. Human Protein Atlas. TMEM106B subcellular location (ICC-IF): Localized to the endosomes and lysosomes..
  4. Human Protein Atlas. TMEM106B antibody validation summary (1 antibodies).
  5. Associations between TMEM106B C-terminal fragment aggregation, age, and TDP-43 or tau pathology. Brain pathology (Zurich, Switzerland) 2026 — PMC13429300.
  6. Antibody-recognizing residues 188-211 of TMEM106B exhibit immunohistochemical reactivity with the TMEM106B C-terminal fragment. Frontiers in neuroscience 2023 — PMC10626444.
  7. Cleaved TMEM106B forms amyloid aggregates in central and peripheral nervous systems. Acta neuropathologica communications 2024 — PMC11181561.
  8. C-terminal TMEM106B fragments in human brain correlate with disease-associated TMEM106B haplotypes. Brain : a journal of neurology 2023 — PMC10545506.
  9. PubMed PMID:14702039 — UniProt-cited evidence.
  10. PubMed PMID:12690205 — UniProt-cited evidence.
  11. PubMed PMID:12853948 — UniProt-cited evidence.