KDM1A / Lysine-specific histone demethylase 1A · IHC design guide

Design Immunohistochemistry for KDM1A

Plan chromogenic KDM1A IHC in paraffin sections around the expected nuclear staining (HPA tissue IHC). Use high staining bone marrow hematopoietic cells as a positive reference and interpret prostate glandular-cell staining cautiously (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use

Immunohistochemistry protocol sheet for KDM1A (IHC for KDM1A): expected localisation Nuclear tissue staining (HPA tissue IHC), antibody M00532-3, validated IHC image, and IHC protocol steps — Printable **KDM1A** IHC protocol sheet — expected localisation Nuclear tissue staining (HPA tissue IHC), antibody M00532-3, controls and protocol steps. Open the full KDM1A IHC guide →

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KDM1A 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	Nuclear tissue staining (HPA tissue IHC)
	Staining pattern	Widespread nuclear staining across tissue cell types (HPA tissue IHC)
	Antigen retrieval	Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen)
	Positive control ⓘ	Adrenal gland+4 more · see all
	Negative control ⓘ	Prostate

Important caveats

Reasons your staining may differ from the expected pattern.

	Fixation	Keep fixation consistent across sections (standard IHC practice; not target-specific)
	Caveat	Prostate glandular cells were not detected (HPA tissue IHC)
	Regulation	Ubiquitously expressed (UniProt)
	Isoform / epitope	Four isoforms; check antibody epitope coverage (UniProt)

Section 1

Recommended KDM1A IHC & IF Protocols

The catalog antibody protocol is followed by published KDM1A IHC protocols for papillary thyroid cancer and medulloblastoma tissue (PMC6653290; PMC3893444).

Recommended immunohistochemistry (IHC-P) protocol parameters
Sample	Tissue sections; selected-image fixative not specified (standard IHC workflow)
Fixation	Image fixative and duration unreported (datasheet M00532-3); verify before use.
Sectioning	4–5 µm sections on charged slides (standard)
Deparaffinisation	Xylene, graded ethanol series to water (standard)
Antigen retrieval	Heat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear antigen)
Peroxidase block	3% H2O2, 10 min, room temperature (standard)
Blocking	10% normal serum of the secondary host, 30 min, room temperature (standard)
Primary antibody	Rabbit anti-KDM1A, 1:200-1:1000 (datasheet M00532-3)
Primary incubation	Overnight at 4 °C (standard)
Detection	HRP-polymer secondary, DAB chromogen 5–10 min (standard)
Counterstain	Hematoxylin, blue, dehydrate and mount (standard)
Expected result	KDM1A-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control.

💡Decision noteStart with Tris-EDTA pH 9.0 retrieval at 95–98 °C for 20 min for nuclear KDM1A (UniProt: nucleus; page retrieval guidance).

Section 2

What Is the Expected KDM1A Staining Pattern?

KDM1A should appear predominantly in nuclei, consistent with its chromatin association and lack of a transmembrane segment (UniProt O60341: subcellular location and topology). HPA describes ubiquitous nuclear expression, with high staining in several specified cell populations (HPA: tissue IHC). Treat tissue comparisons as guides rather than absolute controls because the tissue IHC assessment is Supported with medium consistency between staining and RNA data (HPA: reliability).

What am I looking at on my slide?
Distinct nuclear chromogen in hematopoietic cells of bone marrow or cells in the cerebellar granular layer (HPA: High in both).	This fits the expected compartment and two reported high-staining populations (UniProt O60341: nucleus; HPA: tissue IHC). Judge intensity against nearby background and tissue morphology; a dark nucleus alone cannot establish antibody specificity (general IHC practice).
Predominantly cytoplasmic or membranous staining, with little nuclear signal (UniProt O60341: nucleus; HPA: ubiquitous nuclear expression).	This conflicts with the principal IHC pattern and warrants an artefact check (UniProt O60341: chromatin association; HPA: tissue IHC). Review morphology, counterstain and detection controls before assigning the signal to KDM1A (general IHC practice).
Strong staining of prostate glandular cells, reported as Not detected by HPA (HPA: prostate glandular cells).	An unexpected positive population can reflect cross-reactivity or endogenous chromogenic activity; it is not proof of either (general IHC practice). Compare nuclear localization, background and controls, allowing for HPA's medium consistency rating (HPA: reliability).
Diffuse color across nuclei, cytoplasm and extracellular areas, without clear cellular boundaries (general IHC practice).	Broad background makes nuclear scoring unreliable (general IHC practice). Assess the no-primary control, blocking and detection conditions before interpreting intensity; HPA's nuclear profile does not validate diffuse extracellular signal (HPA: tissue IHC).
No nuclear signal in a high-staining reference population, such as adrenal glandular cells (HPA: High in adrenal glandular cells).	Check tissue preservation, retrieval, antibody and detection performance before calling the specimen negative (general IHC practice). A failed reference weakens interpretation, while an HPA High designation does not guarantee every section will stain (HPA: tissue IHC).

💡Expected KDM1A appearanceCall a positive result when cellular nuclei show clear chromogen, potentially strong in HPA High populations such as bone-marrow hematopoietic cells; diffuse extracellular, membranous or predominantly cytoplasmic color is suspect (UniProt O60341: nucleus and chromatin; HPA: tissue IHC; general IHC practice).

How each factor affects the staining
Compartment and topology (UniProt O60341: nucleus, chromosome, chromatin association; no transmembrane segment).	Prioritize nuclear staining when scoring IHC. The record gives no basis to expect a membrane pattern from KDM1A itself (UniProt O60341: subcellular location and topology).
Tissue distribution and contrast (UniProt O60341: ubiquitous expression; HPA: low tissue specificity).	HPA reports High staining in selected cells of eight listed tissues, Low in several others, and Not detected in prostate glandular cells (HPA: tissue IHC). Interpret the specified cell population rather than an entire organ as uniformly positive.
Strength of tissue evidence (HPA: Supported; medium staining–RNA consistency).	Use HPA patterns as comparison points, with room for discordance between staining and RNA measurements (HPA: reliability description). Neither the rating nor a single slide independently proves that an unexpected signal is specific.
Antibody validation (HPA: CAB005884 IHC Supported; HPA053660 IHC status unreported).	The listed IHC support applies to CAB005884; the supplied record does not assign an IHC status to HPA053660 (HPA: antibody validation). Do not transfer validation between antibodies or infer that an unreported status means failure.
Isoforms and epitope (UniProt O60341: four isoforms; SWIRM domain at residues 174–273).	The supplied sources give no epitope coordinates for the catalog antibody, so isoform coverage and domain-specific staining cannot be predicted (UniProt O60341: isoforms and domain; supplied HPA antibody record).
Processing and modifications (UniProt O60341: no signal peptide or propeptide; 13 listed modified residues).	The annotated chain spans residues 1–852, with no annotated shedding step in this record (UniProt O60341: processing). Listed modifications do not establish an IHC intensity change or target-specific fixation sensitivity (UniProt O60341: modified residues).
IF/ICC Q&A: Where should signal appear? (HPA: subcellular ICC-IF).	Mainly in the nucleoplasm; HPA lists additional cytosolic localization as uncertain (HPA: supported nucleoplasm; uncertain cytosol). This IF/ICC observation does not turn cytoplasmic chromogen into an expected dominant IHC pattern (HPA: tissue IHC).

Why is my staining missing, weak or wrong?
Situation	Likely cause	Next action
High-staining reference tissue lacks nuclear chromogen (HPA: High in adrenal glandular cells, among others).	The reference may have failed during staining or detection; HPA's High designation is an observed tissue pattern, not a guarantee for every section (general IHC practice; HPA: tissue IHC).	Check tissue morphology, the run's positive control, retrieval conditions and detection reagents before interpreting sample negatives (general IHC practice). Do not attribute the failure to KDM1A-specific fixation sensitivity; none is supplied.
Predominantly cytoplasmic color in an IHC section (HPA: ubiquitous nuclear tissue expression).	Background or nonspecific detection is possible (general IHC practice). HPA's additional cytosolic IF/ICC location is uncertain and comes from a different application (HPA: subcellular ICC-IF).	Compare the nuclear-to-cytoplasmic pattern with controls and morphology, then review antibody and detection conditions (general IHC practice). Score a dominant cytoplasmic IHC pattern cautiously (HPA: tissue IHC).
Prostate glandular cells stain strongly (HPA: Not detected in prostate glandular cells).	Possible causes include cross-reactivity or endogenous chromogenic activity; the unexpected pattern alone cannot identify its cause (general IHC practice; HPA: prostate tissue IHC).	Inspect nuclear localization and compare a no-primary control with a known high-staining cell population in the run (general IHC practice; HPA: tissue IHC). Interpret disagreement in light of HPA's medium consistency rating (HPA: reliability).
Diffuse chromogen obscures nuclei throughout the section (general IHC practice).	Nonspecific binding, inadequate washing or endogenous detection activity may elevate background in chromogenic IHC (general IHC practice). The supplied sources do not identify a KDM1A-specific background mechanism.	Review the no-primary control, blocking, washes and detection controls; restore readable nuclear boundaries before scoring (general IHC practice). Compare the resolved pattern with HPA's ubiquitous nuclear profile (HPA: tissue IHC).
One cell population stains weakly while another is strong (HPA: variable tissue IHC levels).	Expression varies by annotated population: HPA reports High in kidney glomerular cells and Low in small-intestine glandular cells, for example (HPA: tissue IHC).	Identify the cells on the counterstained section and compare each with its own HPA entry (general IHC practice; HPA: tissue IHC). Avoid treating a Low population as a failed positive control.
Two antibodies yield different nuclear patterns or intensities (HPA: antibody validation entries).	Their IHC evidence differs: CAB005884 is Supported, while HPA053660 has no reported IHC status in the supplied record (HPA: antibody validation). Epitope coordinates are not supplied, so the discrepancy cannot be assigned to isoform recognition.	Check each antibody's documented IHC validation and matched run controls, then compare compartment and cell population rather than intensity alone (HPA: antibody validation and tissue IHC; general IHC practice).

Source: UniProt O60341 Human Protein Atlas tissue Human Protein Atlas subcellular

Experiment evidence

IHC & IF images showing KDM1A staining

M00532-3 · IHCMouse colon was stained with anti-KDM1A rabbit antibody

M00532-3 · IHCRat colon was stained with anti-KDM1A rabbit antibody

M00532-1 · IHCImmunohistochemical analysis of paraffin-embedded human colon, using KDM1/LSD1 Antibody.

HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000004487-KDM1A/tissue/cerebral+cortex#imid_1789444

HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000004487-KDM1A/tissue/colon#imid_1789354

HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000004487-KDM1A/tissue/liver#imid_1789355

HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000004487-KDM1A/tissue/kidney#imid_1789364

HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA053660; green = KDM1A, blue = nucleus, red = microtubules.

← swipe / scroll for more images →

Real IHC / IF data behind the staining-pattern expectations in this section.

Sample controls for KDM1A IHC & IF

🧪Run bone marrow first: hematopoietic cells should show nuclear staining (HPA: High in bone marrow hematopoietic cells; UniProt O60341: nucleus). Run prostate as the negative tissue, focusing on glandular cells (HPA: Not detected in prostate glandular cells); on the positive slide, use cells without nuclear signal to assess local background, without assuming a particular cell type is KDM1A-negative (standard IHC practice).

Positive control tissue: Adrenal gland (Glandular cells, HPA High)

Negative control tissue: Prostate (HPA Not detected)

ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show KDM1A in A-431, U-251MG, U2OS, KOLF2.1J, NIH 3T3, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).

Technical controls: Include no-primary (secondary-only), a rabbit isotype control matched to the primary antibody’s clonality, and a matched KDM1A-knockout section as a biological negative (caption: rabbit anti-KDM1A antibody; standard IHC practice). Block endogenous peroxidase in bone marrow before chromogenic detection, since hematopoietic cells can contribute peroxidase background (standard IHC practice).

⚠️Feasibility: No supplied target or application evidence reports a KDM1A-specific fixation window, an antigen-retrieval dependency, or whether frozen sections or IF are easier; assess retrieval empirically for paraffin IHC (supplied evidence; standard IHC practice). The selected M00532-3 mouse-colon staining caption does not report a fixative (caption: fixative unreported). In bone marrow, endogenous peroxidase can complicate interpretation of chromogenic signal (standard IHC practice).

HPA tissue IHC evidence for KDM1A

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — 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
Adrenal gland	Glandular cells	High	Protein (IHC)	HPA →
Bone marrow	Hematopoietic cells	High	Protein (IHC)	HPA →
Cerebellum	Cells in granular layer	High	Protein (IHC)	HPA →
Endometrium	Cells in endometrial stroma	High	Protein (IHC)	HPA →
Gallbladder	Glandular cells	High	Protein (IHC)	HPA →

Undetected expression · recommended negative controls

Tissue	Cell type	Level	Evidence	Source
Prostate	Glandular cells	Not detected	Protein (IHC)	HPA →

Section 3

Advanced KDM1A IHC Tips

Troubleshoot KDM1A staining by checking nuclear localization, section processing, and cell-specific controls before interpreting chromogenic signal.

How should I adjust retrieval when nuclear KDM1A staining is weak?

Start with Tris-EDTA at pH 9.0, heated to 95–98 °C for 20 minutes (page retrieval rule: nuclear antigen). Let sections cool in retrieval buffer, then compare staining with a matched section processed in the same run (standard IHC practice). If nuclear staining remains weak, test a shorter or longer heating time while holding buffer and detection conditions constant (standard IHC practice). Judge improvement by sharper nuclear signal and preserved tissue structure, because KDM1A associates with chromatin (UniProt O60341 localization). Record the retrieval time for every slide so differences in staining can be traced to processing (standard IHC practice).

Can fixation explain variable KDM1A staining between paraffin sections?

Target-specific fixation sensitivity is unknown from the supplied evidence; the selected mouse colon IHC caption does not state its fixative (caption: M00532-3). Record the actual fixative and fixation duration for each specimen before comparing staining intensity (standard IHC practice). If processing histories differ, optimize retrieval on matched sections and include a reference section in every staining run (standard IHC practice). Avoid attributing weak staining to a specific KDM1A epitope or modification without direct evidence, although modified residues are annotated for this protein (UniProt O60341 modified residues). Evaluate nuclear signal alongside tissue preservation and the negative control under identical chromogenic conditions (standard IHC practice).

What staining compartment should I expect in a KDM1A IHC section?

Expect predominantly nuclear staining, since KDM1A localizes to the nucleus and associates with chromatin (UniProt O60341 localization). The tissue atlas describes ubiquitous nuclear expression, with supported tissue IHC reliability and medium agreement between staining and RNA data (HPA tissue IHC). Score nuclei within identified cell populations instead of treating diffuse cytoplasmic color as equivalent KDM1A signal (standard IHC practice; UniProt O60341 localization). A secondary cytosolic location is reported with uncertain support in cell imaging, so investigate convincing cytoplasmic staining with an independent control (HPA subcellular). Check the counterstain and section morphology before assigning faint nuclear boundaries (standard IHC practice).

Could an antibody epitope affect which KDM1A isoforms I detect?

KDM1A has 4 annotated isoforms and a SWIRM domain spanning residues 174–273 (UniProt O60341 isoforms and domains). Determine the catalog antibody's immunogen or mapped epitope before claiming that its IHC signal represents every isoform (standard IHC practice). If the epitope location is unavailable, report staining as antibody-detected KDM1A without assigning an isoform (standard IHC practice; UniProt O60341 isoforms). The record also lists modified residues, including Thr59 and Ser126, but gives no evidence that these change this antibody's binding (UniProt O60341 modified residues). Compare antibody staining with an independently validated reagent or orthogonal expression evidence when isoform specificity matters (standard IHC practice).

How can I cross-check KDM1A localization by IF without confusing tissue background?

Use IF as a complementary localization check, while keeping the chromogenic paraffin workflow as the basis for this IHC guide (standard IHC practice). Multiplex KDM1A with a marker for the expected cell population, such as a hematopoietic marker in bone marrow, where hematopoietic cells show high staining (HPA tissue IHC). Choose fluorophores after examining unstained tissue autofluorescence, and include single-label controls when signals overlap (standard IF practice). Permeabilize sufficiently to expose a nuclear epitope; KDM1A has no transmembrane segment and is mainly nuclear (UniProt O60341 topology and localization). Expect nucleoplasmic signal, while treating cytosolic signal cautiously because its additional localization is uncertain (HPA subcellular).

How do I reduce diffuse brown background without losing nuclear KDM1A signal?

First compare the stained section with a primary-antibody omission control to separate detection background from antibody-associated signal (standard IHC practice). Block endogenous peroxidase before chromogenic detection, particularly when evaluating hematopoietic cells, which have high KDM1A staining in bone marrow (standard IHC practice; HPA tissue IHC). Titrate the catalog antibody and detection reagent on adjacent sections, keeping retrieval at Tris-EDTA pH 9.0, 95–98 °C for 20 minutes during that comparison (standard IHC practice; page retrieval rule). Shorten DAB development if the control darkens or nuclear boundaries become obscured (standard IHC practice). Retain a condition that resolves nuclear staining from surrounding tissue (UniProt O60341 localization; standard IHC practice).

What should I measure when comparing KDM1A staining across specimens? ⚠ ANSWER MARKED FOR VERIFICATION

Define the cell population and tissue area before scoring, because tissue IHC reports KDM1A across many cell types (HPA tissue IHC). For chromogenic sections, report the percentage of positive nuclei and an H-score from nuclear intensity categories, using identical thresholds across the comparison (standard IHC practice). Normalize positive counts to the number of evaluable nuclei in the same population; use positive nuclei per mm² when cell density is itself relevant (standard IHC practice). Exclude folds, damaged edges, and necrotic regions by a prespecified morphology rule (standard IHC practice). Include a reference section across staining runs, and report cell composition alongside scores (standard IHC practice).

When is apparent KDM1A positivity more likely to be an artefact?

A convincing result is nuclear staining in intact cells, consistent with KDM1A's chromatin association and the tissue atlas pattern (UniProt O60341 localization; HPA tissue IHC). Treat staining limited to section edges, folds, or necrotic areas as suspect, and inspect the same regions on a counterstained section (standard IHC practice). Compare unexpectedly diffuse cytoplasmic color with controls: cytosolic localization has uncertain support in cell imaging (HPA subcellular). Check a primary-antibody omission control for endogenous enzyme or detection signal before counting brown deposits as positive nuclei (standard IHC practice). Interpret cell identity explicitly, since atlas staining differs among annotated cell populations (HPA tissue IHC).

Boster reagents

Best KDM1A / Lysine-specific histone demethylase 1A IHC Antibodies

Both anti-KDM1A antibodies have IHC tissue images (catalog IHC captions) and list IF as an application (catalog applications); the catalog provides no IF images (catalog image inventory).

Real IHC data Mouse colon was stained with anti-KDM1A rabbit antibody

Anti-KDM1A Rabbit Monoclonal Antibody

Cat # M00532-3

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Real IHC data Immunohistochemical analysis of paraffin-embedded human colon, using KDM1/LSD1 Antibody.

Anti-KDM1/LSD1 KDM1A Rabbit Monoclonal Antibody

Cat # M00532-1

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M00532-3 has IHC images of mouse and rat colon and human prostate and prostate carcinoma (catalog IHC captions); its listed reactivity is Human, Mouse, and Rat (catalog reactivity). M00532-1 has an IHC image of paraffin-embedded human colon (catalog IHC caption), lists IHC, IF, and ICC applications (catalog applications), and lists Human, Mouse, and Rat reactivity (catalog reactivity).

Which to pick: For tissue IHC across the pictured species, choose M00532-3: its own captions show mouse and rat colon and human prostate tissue, but do not report section processing or fixative (catalog IHC captions). For paraffin-section IHC in human colon or for ICC/IF, choose M00532-1: its own caption specifies paraffin-embedded human colon without reporting the fixative, and ICC/IF is listed as an application (catalog IHC caption; catalog applications). Both are rabbit monoclonals (catalog titles), list Human, Mouse, and Rat reactivity (catalog reactivity), and list IF as an application without an IF image in the payload (catalog applications; catalog image inventory).

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

References

UniProt Consortium. UniProt entry O60341 (KDM1A_HUMAN, Lysine-specific histone demethylase 1A).
Human Protein Atlas. KDM1A tissue IHC expression (reliability: Supported).
Human Protein Atlas. KDM1A subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the cytosol..
Human Protein Atlas. KDM1A antibody validation summary (2 antibodies).
Knockdown of KDM1A suppresses tumour migration and invasion by epigenetically regulating the TIMP1/MMP9 pathway in papillary thyroid cancer. Journal of cellular and molecular medicine 2019 — PMC6653290.
Nuclear GSK3β promotes tumorigenesis by phosphorylating KDM1A and inducing its deubiquitylation by USP22. Nature cell biology 2016 — PMC5026327.
KDM1A promotes thyroid cancer progression and maintains stemness through the Wnt/β-catenin signaling pathway. Theranostics 2022 — PMC8825597.
The KDM1A histone demethylase is a promising new target for the epigenetic therapy of medulloblastoma. Acta neuropathologica communications 2013 — PMC3893444.
PubMed PMID:9628581 — UniProt-cited evidence.
PubMed PMID:16710414 — UniProt-cited evidence.
PubMed PMID:15489334 — UniProt-cited evidence.