ACLY / ATP-citrate synthase · IHC design guide

Design Immunohistochemistry for ACLY

Plan ACLY staining in paraffin sections using the observed cytoplasmic and nuclear tissue pattern (HPA tissue IHC). Compare defined positive and negative cell populations while interpreting intensity cautiously because antibody staining and RNA levels show low consistency (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for ACLY (IHC for ACLY): expected localisation Cytosol expected (UniProt); cytoplasmic and nuclear tissue staining (HPA tissue IHC), antibody PB10024, validated IHC image, and IHC protocol steps
Printable ACLY IHC protocol sheet — expected localisation Cytosol expected (UniProt); cytoplasmic and nuclear tissue staining (HPA tissue IHC), antibody PB10024, controls and protocol steps. Open the full ACLY IHC guide →

ACLY 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 Cytosol expected (UniProt); cytoplasmic and nuclear tissue staining (HPA tissue IHC)
Staining pattern Cytoplasmic and nuclear staining in several tissues (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet PB10024)
Positive control ⓘ Pancreas+4 more · see all
Negative control ⓘ Esophagus+4 more · see all
Important caveats
Reasons your staining may differ from the expected pattern.
Fixation Keep fixation consistent across sections. (standard IHC practice; not target-specific)
Caveat Antibody staining and RNA levels show low consistency (HPA tissue IHC)
Regulation Staining regulation is not annotated (UniProt)
Isoform / epitope 3 isoforms; epitope coverage is unknown (UniProt)
Section 1

Recommended ACLY IHC & IF Protocols

The catalog antibody uses EDTA pH 8.0 heat retrieval (datasheet PB10024). The four published ACLY IHC protocols below provide additional staining conditions (PMC7855479; PMC4427316; PMC12806462; PMC6774899).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human colonic adenocarcinoma tissue; fixative not specified (datasheet PB10024)
FixationImage fixative and duration unreported (datasheet PB10024); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: EDTA pH 8.0 (datasheet PB10024); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet PB10024)
Primary antibodyRabbit anti-ACLY, 1-2μg/ml (datasheet PB10024)
Primary incubationOvernight at 4 °C (datasheet PB10024)
DetectionHRP-conjugated secondary, DAB chromogen (datasheet PB10024)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultACLY-positive staining in pancreatic endocrine cells of pancreas (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic and nuclear 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 PB10024). If adapting a published protocol, use its stated retrieval conditions (PMC7855479; PMC4427316; PMC12806462; PMC6774899).
Section 2

What Is the Expected ACLY Staining Pattern?

ACLY is a cytosolic enzyme with no transmembrane segment (UniProt P53396). In paraffin sections, expect mainly cytoplasmic staining, with possible nuclear staining in some tissues (HPA: tissue IHC profile). High staining is reported in pancreatic endocrine cells, prostate glandular cells, and testicular Leydig cells (HPA: tissue IHC). The HPA IHC profile is rated Enhanced, but its antibody staining has low consistency with RNA expression data (HPA: reliability description).

What am I looking at on my slide?
Strong cytoplasmic staining in pancreatic endocrine cells, prostate glandular cells, or Leyig cells.These are reported high-staining cell populations (HPA: tissue IHC). Compare staining within the identified cell population; a positive result does not require every cell in the section to stain (general IHC practice).
Cytoplasmic staining accompanied by nuclear staining in some cells.HPA describes cytoplasmic and nuclear staining across several tissues (HPA: tissue IHC profile). UniProt places ACLY in the cytosol (UniProt P53396); assess nuclear signal alongside the tissue and antibody controls rather than automatically rejecting it.
Predominantly membranous or extracellular staining, with little cytoplasmic signal.This does not match the reported cytosolic location or the absence of a transmembrane segment (UniProt P53396). Check morphology and detection controls before attributing the pattern to ACLY (general IHC practice).
Strong staining in a cell population reported as not detected by HPA.For example, HPA reports no staining in esophageal squamous epithelial cells (HPA: tissue IHC). Unexpected staining raises a specificity or endogenous detection concern; the HPA reliability caveat means it is not conclusive evidence of cross-reactivity (HPA: reliability description; general IHC practice).
Uniform color over cells and tissue spaces, without a clear cellular pattern.Diffuse color makes compartment and cell-type assessment unreliable (general IHC practice). Evaluate background with a no-primary control and compare a reported high-staining tissue in the same run (general IHC practice; HPA: tissue IHC).
💡Expected ACLY appearanceCall a section positive when identified pancreatic endocrine, prostate glandular, or Leyig cells show clear, predominantly cytoplasmic high staining; nuclear signal may occur, whereas diffuse or chiefly membranous color warrants control review (HPA: tissue IHC profile and high-staining cells; UniProt P53396; general IHC practice).
How each factor affects the staining
Tissue and cell selectionHPA reports high staining in pancreatic endocrine, prostate glandular, and Leyig cells, but no detected staining in esophageal squamous epithelial cells (HPA: tissue IHC). Use the specified cell populations when comparing controls; HPA also reports low tissue RNA specificity and low staining–RNA consistency (HPA: RNA specificity and reliability description).
Antibody evidenceFour listed rabbit polyclonal antibodies have Enhanced IHC status; the listed rabbit monoclonal has Approved IHC status (HPA: antibody validation). Enhanced indicates reproduction by independent antibodies or orthogonal data (HPA: antibody validation definition). This supports the observed pattern, subject to HPA's staining–RNA consistency caveat (HPA: reliability description).
Isoforms and epitope coverageUniProt lists three ACLY isoforms and an ATP-grasp domain at residues 4–265 (UniProt P53396). The supplied records do not map an IHC antibody epitope or establish isoform-specific staining; check the chosen antibody's documented target region before interpreting a missing cell signal as isoform absence (general IHC practice).
Intracellular target and modificationsACLY has no signal peptide, propeptide, or transmembrane segment; UniProt lists multiple modified residues, including phosphorylation sites (UniProt P53396). These facts support evaluating intracellular staining, but do not establish how processing, phosphorylation, or fixation affects this antibody's IHC signal.
IF/ICC Q&A: where should signal appear?Mainly in the cytosol (HPA: ICC-IF, supported). HPA lists nucleoplasm, primary cilium transition zone, and basal body as uncertain additional locations, and principal piece as approved (HPA: ICC-IF). Treat those location labels as ICC-IF evidence; they do not establish an IHC staining requirement.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
No staining in pancreatic endocrine cells, prostate glandular cells, or Leyig cells.These are reported high-staining populations, so a blank result may reflect a run or reagent problem (HPA: tissue IHC; general IHC practice). HPA staining–RNA inconsistency also limits certainty about any single specimen (HPA: reliability description).Confirm the expected cells are present, inspect the positive control and detection reagents, and review the antibody's validated IHC-P instructions (general IHC practice). If needed, optimize retrieval as a general IHC step; no ACLY-specific fixation effect is established here.
High background obscures the cytoplasm.Nonspecific binding or detection background can hide a cellular pattern (general IHC practice). The HPA tissue profile cannot identify which workflow step caused background in a particular section.Run a no-primary control; review blocking, wash, detection, and counterstain conditions, then compare the cellular pattern with a reported positive population (general IHC practice; HPA: tissue IHC).
Color appears chiefly on cell borders or outside cells.A border or extracellular pattern conflicts with ACLY's cytosolic annotation and lack of a transmembrane segment (UniProt P53396). Section morphology or background may complicate the apparent compartment (general IHC practice).Inspect morphology at higher magnification, compare a no-primary control, and reassess compartment assignment before scoring the section (general IHC practice).
Unexpected strong staining appears in esophageal squamous epithelium.HPA reports this cell population as not detected (HPA: tissue IHC). Cross-reactivity or endogenous detection activity is possible, but HPA's staining–RNA consistency caveat limits a categorical call (HPA: reliability description; general IHC practice).Check a no-primary control and compare staining in a reported high-staining cell population; seek independent antibody or orthogonal evidence if the unexpected result drives the conclusion (general IHC practice; HPA: tissue IHC and antibody validation).
Nuclear staining seems stronger than cytoplasmic staining.HPA reports nuclear expression in several tissues, while UniProt annotates ACLY as cytosolic (HPA: tissue IHC profile; UniProt P53396). The supplied evidence does not set a nuclear-to-cytoplasmic intensity cutoff.Score compartments separately, confirm the cell population, and compare with the no-primary control and another validated antibody where available (general IHC practice; HPA: antibody validation).
An IF/ICC image is being used to judge an IHC section.HPA supports cytosol as the main ICC-IF location, with other locations carrying distinct confidence labels (HPA: ICC-IF). ICC-IF localization alone does not define the appearance of a chromogenic tissue section.Judge the IHC section against HPA tissue IHC cell patterns and the section's controls; use the ICC-IF location labels only to inform compartment interpretation (HPA: tissue IHC and ICC-IF; general IHC practice).

Sample controls for ACLY IHC & IF

🧪Run pancreas first: pancreatic endocrine cells should stain because HPA rates them High (HPA: High in pancreatic endocrine cells). Use esophagus squamous epithelial cells as the negative tissue (HPA: Not detected in esophagus squamous epithelial cells); on the pancreas slide, assess cells without specific cytosolic staining as internal background comparators without presuming another cell type is ACLY-negative (UniProt P53396: cytosol; HPA: supported cytosol).
Positive control tissue: Pancreas (Pancreatic endocrine cells, HPA High)
Negative control tissue: Esophagus (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show ACLY in A-431, U-251MG, U2OS, ASC52telo, RPTEC/TERT1, hTERT-RPE1 (serum starved), Sperm, with annotated localisation: Cytosol (supported) (HPA subcellular).
Technical controls: Include no-primary (secondary-only) and host- and clonality-matched isotype controls, plus ACLY-knockout material if available as a biological negative (standard IHC practice; selected-SKU caption: rabbit primary antibody). For HRP/DAB staining in pancreas, quench endogenous peroxidase and check background in the same section (standard IHC practice; selected-SKU caption: HRP/DAB detection).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected PB10024 paraffin-section caption does not state the fixative (selected-SKU caption: fixative not stated). That caption uses heat retrieval in EDTA at pH 8.0, but it does not establish that retrieval is required for ACLY staining (selected-SKU caption: EDTA retrieval). Whether frozen sections or IF are easier is unreported; pancreatic background should be assessed with the control slides when interpreting chromogenic signal (standard IHC practice; HPA: High in pancreatic endocrine cells).

HPA tissue IHC evidence for ACLY

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — 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
Pancreas Pancreatic endocrine cells High Protein (IHC) HPA →
Prostate Glandular cells High Protein (IHC) HPA →
Testis Leydig cells High Protein (IHC) HPA →
Adrenal gland Glandular cells Medium Protein (IHC) HPA →
Cerebellum Cells in molecular layer Medium Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Esophagus Squamous epithelial cells Not detected Protein (IHC) HPA →
Fallopian tube Ciliated cells (cell body) Not detected Protein (IHC) HPA →
Oral mucosa Squamous epithelial cells Not detected Protein (IHC) HPA →
Ovary Ovarian stroma cells Not detected Protein (IHC) HPA →
Parathyroid gland Glandular cells Not detected Protein (IHC) HPA →
Section 3

Advanced ACLY IHC Tips

Troubleshoot ACLY staining in paraffin sections by checking retrieval, staining controls, cellular location, and how signal is scored.

What retrieval conditions should I try first for weak ACLY staining in paraffin sections?
Start with heat-mediated antigen retrieval in EDTA at pH 8.0 for the catalog antibody (datasheet PB10024). The selected paraffin-section image used that retrieval before incubation with 2 μg/ml primary antibody overnight at 4°C (caption PB10024). If staining remains weak, compare retrieval duration on adjacent sections while keeping antibody concentration, detection, and imaging conditions constant (standard IHC practice). Include a no-primary control and a section with an expected positive cell population, such as pancreatic endocrine cells, so increased DAB signal can be assessed against background (HPA: High in pancreatic endocrine cells; standard IHC practice).
How should I troubleshoot ACLY staining when fixation history is uncertain?
Target-specific fixation sensitivity is unknown from the supplied evidence; the selected paraffin-section caption does not state its fixative (caption PB10024). Record the fixative and processing history for each specimen, then compare similarly processed sections when assessing staining differences (standard IHC practice). Begin with EDTA retrieval at pH 8.0 and the documented 2 μg/ml primary incubation overnight at 4°C before adjusting one condition at a time (caption PB10024). If specimens differ in fixation history, use matched positive and no-primary controls to assess signal and background without attributing a difference to ACLY sensitivity (standard IHC practice).
Should ACLY staining appear in nuclei as well as cytoplasm?
Use cytoplasmic staining as the principal localisation check: ACLY is assigned to the cytosol, and the supported HPA subcellular location is cytosol (UniProt P53396 subcellular location; HPA subcellular: Cytosol supported). Nuclear staining warrants a separate check because HPA reports cytoplasmic and nuclear tissue staining, while its nucleoplasmic subcellular assignment is uncertain (HPA tissue IHC profile; HPA subcellular: Nucleoplasm uncertain). Compare nuclear and cytoplasmic signal in intact cells against a no-primary control, using the same retrieval and DAB development conditions (standard IHC practice). Report the compartments separately rather than treating any nuclear signal as proof of ACLY abundance or activity (standard IHC interpretation).
Can this IHC result distinguish ACLY isoforms or phosphorylation states?
Do not assign staining to a particular isoform without an antibody epitope and isoform-reactivity map: the record lists 3 ACLY isoforms, but the selected caption does not establish isoform specificity (UniProt P53396 isoforms; caption PB10024). ACLY also has documented modified residues, including phosphoserine at position 455, so total staining cannot by itself identify a phosphorylation state (UniProt P53396 modified residues; standard IHC interpretation). Check the antibody’s stated immunogen or epitope against the isoform sequences before making an isoform claim (standard IHC practice). For a modification-specific question, use a separately validated modification-specific assay and appropriate controls (standard IHC practice).
How can I adapt the localisation question to multiplex IF?
For IF, pair ACLY with a separately validated marker of the cell population being assessed, such as pancreatic endocrine cells, and acquire each channel separately to check overlap (HPA: High in pancreatic endocrine cells; standard IF practice). Choose a fluorophore whose emission can be distinguished from the specimen’s autofluorescence, and include unstained and single-label controls before interpreting faint signal (standard IF practice). Because ACLY’s supported location is cytosolic and it has no transmembrane segment, use a permeabilisation step that gives the antibody access to intracellular epitopes (HPA subcellular: Cytosol supported; UniProt P53396 topology; standard IF practice). Assess nuclear signal separately because HPA marks nucleoplasmic localisation uncertain (HPA subcellular: Nucleoplasm uncertain).
How can I separate diffuse ACLY DAB signal from background?
Run no-primary and secondary-only controls alongside the stained section to identify detection-related signal (standard IHC practice). The selected image used 10% goat serum blocking, a peroxidase-conjugated secondary, and DAB development; these document that image’s workflow rather than proving every brown deposit is ACLY (caption PB10024). Include a peroxidase-blocking step and inspect whether DAB also develops in control sections, particularly where endogenous enzyme activity may contribute (standard chromogenic IHC practice). If staining is broadly diffuse, compare controlled changes to blocking, primary concentration, wash stringency, and DAB development while retaining EDTA retrieval at pH 8.0 as the starting condition (caption PB10024; standard IHC practice).
What is a defensible way to quantify ACLY IHC across specimens? ⚠ ANSWER MARKED FOR VERIFICATION
Define the scored cell population and compartment before measuring ACLY, since HPA describes both cytoplasmic and nuclear tissue staining (HPA tissue IHC profile; standard IHC practice). Within matched tissue regions, report the percentage of positive cells and an intensity-based H-score, or positive-cell density per mm² when cell abundance differs (standard IHC practice). Normalise positive counts to the number of eligible intact cells, or density to analysed tissue area, and keep retrieval, DAB development, and scoring thresholds consistent across slides (standard IHC practice). Record cytoplasmic and nuclear scores separately, with a no-primary control informing the background threshold (standard IHC practice).
When should apparent ACLY positivity be treated cautiously?
Give greatest weight to signal in intact cell cytoplasm, consistent with the supported cytosolic location of ACLY (UniProt P53396 subcellular location; HPA subcellular: Cytosol supported). Check whether staining follows an expected cell population, such as pancreatic endocrine cells, while recognising that HPA reports low consistency between antibody staining and RNA expression (HPA: High in pancreatic endocrine cells; HPA tissue IHC reliability description). Treat isolated nuclear staining cautiously because nucleoplasmic localisation is uncertain in the subcellular record (HPA subcellular: Nucleoplasm uncertain). Compare suspicious staining at section edges, necrotic areas, or sites of endogenous peroxidase activity with controls before calling it positive (standard chromogenic IHC practice).
Boster reagents

Best ACLY / ATP-citrate synthase IHC Antibodies

The catalog includes IHC images from human, mouse, and rat paraffin sections and IF/ICC images from A594 and MCF7 cells; all four antibodies list human, mouse, and rat reactivity (catalog image captions; catalog reactivity).

Real IHC data IHC analysis of ACLY using anti-ACLY antibody (PB10024). ACLY was detected in a paraffin-embedded section of human colonic adenocarcinoma tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2 μg/ml rabbit anti-ACLY Antibody (PB10024) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-ATP citrate lyase/ACLY Antibody ®
Cat # PB10024
Real IHC data IHC analysis of ATP citrate lyase using anti-ATP citrate lyase antibody (M02372-1). ATP citrate lyase was detected in paraffin-embedded section of human pancreatic cancer tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 1μg/ml mouse anti-ATP citrate lyase Antibody (M02372-1) overnight at 4°C. Biotinylated goat anti-mouse IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using Strepavidin-Biotin-Complex (SABC) (Catalog # SA1021) with DAB as the chromogen.
Anti-ATP citrate lyase ACLY Antibody ® (monoclonal, 5I2)
Cat # M02372-1
Real IHC data Immunohistochemical analysis of paraffin-embedded human brain carcinoma, using ATP citrate lyase Antibody .
Anti-ATP citrate lyase ACLY Rabbit Monoclonal Antibody
Cat # M02372
Real IHC data Human hepatocellular carcinoma was stained with anti-ATP-Citrate Lyase rabbit antibody
Anti-ATP-Citrate Lyase Rabbit Monoclonal Antibody
Cat # M02372-3

PB10024 has human colonic adenocarcinoma paraffin IHC and A594 IF/ICC images; M02372-1 has human pancreatic cancer and mouse and rat pancreas paraffin IHC images, plus an MCF7 IF/ICC image (catalog image captions). M02372 has a human brain carcinoma paraffin IHC image, while M02372-3 has a human hepatocellular carcinoma IHC image with section processing unreported (catalog image captions).

Which to pick: For tissue IHC, PB10024 offers a documented paraffin-section example with EDTA pH 8.0 retrieval and DAB detection; the fixative is unreported (PB10024 IHC image caption). For IF/ICC, M02372-1 is a mouse monoclonal with an MCF7 IF/ICC image; it also has mouse and rat pancreas paraffin IHC images, making it the strongest pictured option for cross-species tissue work (M02372-1 catalog applications, clone, and image captions).

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

References

  1. UniProt Consortium. UniProt entry P53396 (ACLY_HUMAN, ATP-citrate synthase).
  2. Human Protein Atlas. ACLY tissue IHC expression (reliability: Enhanced).
  3. Human Protein Atlas. ACLY subcellular location (ICC-IF): Mainly localized to the cytosol. In addition localized to the nucleoplasm, primary cilium transition zone, basal body and principal piece..
  4. Human Protein Atlas. ACLY antibody validation summary (5 antibodies).
  5. A novel metabolic function of Myc in regulation of fatty acid synthesis in prostate cancer. Oncogene 2021 — PMC7855479.
  6. Prognostic Value of Malic Enzyme and ATP-Citrate Lyase in Non-Small Cell Lung Cancer of the Young and the Elderly. PloS one 2015 — PMC4427316.
  7. Role of ACLY in the development of gastric cancer under hyperglycemic conditions. Quantitative biology (Beijing, China) 2024 — PMC12806462.
  8. Leelamine Is a Novel Lipogenesis Inhibitor in Prostate Cancer Cells In Vitro and In Vivo. Molecular cancer therapeutics 2019 — PMC6774899.
  9. PubMed PMID:1371749 — UniProt-cited evidence.
  10. PubMed PMID:9116495 — UniProt-cited evidence.
  11. PubMed PMID:14702039 — UniProt-cited evidence.