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CHCHD3 / MICOS complex subunit MIC19 · IHC design guide
Design Immunohistochemistry for CHCHD3
Plan CHCHD3 staining in paraffin sections around the granular cytoplasmic tissue pattern (HPA tissue IHC). The catalog antibody’s example sections use 1:100 primary antibody with chromogenic detection (datasheet A06593-2).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
CHCHD3 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 | Granular cytoplasm in tissue (HPA tissue IHC); mitochondrial inner membrane is a molecular location (UniProt) | |
| Staining pattern | Granular cytoplasmic staining in multiple cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A06593-2) | |
| Positive control | Adipose tissue+4 more · see all | |
| Negative control | None in HPA (detected in all 45 tissues); use no-primary + isotype controls |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across paraffin sections. (standard IHC practice; not target-specific) | |
| Caveat | Staining and RNA expression show medium consistency (HPA tissue IHC) | |
| Regulation | Higher in heart and skeletal muscle (UniProt) | |
| Isoform / epitope | No isoforms listed; chain spans residues 2–227 (UniProt) |
Section 1
Recommended CHCHD3 IHC & IF Protocols
The catalog antibody’s IHC-P protocol (datasheet A06593-2) is paired with one published CHCHD3 IHC protocol (PMC8882240).
| Sample | Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet A06593-2) |
| Fixation | Image fixative and duration unreported (datasheet A06593-2); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: EDTA pH 8.0 (datasheet A06593-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A06593-2) |
| Primary antibody | Rabbit anti-CHCHD3, 1:50 recommended; image 1:100 (datasheet A06593-2) |
| Primary incubation | Overnight at 4 °C (datasheet A06593-2) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A06593-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CHCHD3-positive staining in adipocytes of adipose tissue (HPA tissue IHC: High). HPA tissue profile: General cytoplasmic expression with a granular pattern. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval (datasheet A06593-2); the published protocol does not specify retrieval (PMC8882240 Methods).
Section 2
What Is the Expected CHCHD3 Staining Pattern?
CHCHD3 is a mitochondrial inner membrane MICOS component with no transmembrane segment; UniProt also lists cytoplasm and nucleus (UniProt Q9NX63 topology and subcellular location). In paraffin section IHC, expect granular cytoplasmic staining in documented positive cells, including adipocytes, glandular cells, respiratory epithelium and neurons (HPA: tissue IHC profile; High in those cell types). HPA rates the tissue staining Enhanced, with medium consistency between antibody staining and RNA data (HPA: tissue IHC reliability).
| Discrete granular cytoplasmic staining in adipocytes, glandular cells, respiratory epithelial cells or neurons. | This matches the reported tissue IHC pattern and High staining in those cell types (HPA: tissue IHC). Compare the cell type and subcellular pattern with a control section stained in the same run (standard IHC practice). |
| Predominantly nuclear staining, with little or no granular cytoplasmic signal. | This differs from the reported general granular cytoplasmic IHC pattern (HPA: tissue IHC). UniProt also lists a nuclear location, so nuclear staining alone does not prove an artefact; check controls and whether the expected cytoplasmic pattern is present (UniProt Q9NX63 subcellular location; standard IHC practice). |
| Staining appears only in a cell population outside the documented positive cells in a reference tissue. | Check the cell identification and controls before interpreting the result: unexpected staining can reflect cross-reactivity or endogenous detection activity (standard IHC practice). The supplied HPA record lists positive cells but no negative cell populations, so it cannot establish that another cell type must be unstained (HPA: tissue IHC). |
| Diffuse brown haze obscures cell boundaries and the granular pattern. | The result cannot be scored confidently against the reported granular cytoplasmic profile (HPA: tissue IHC). Examine a no-primary control and the detection reagents for background; assess the target pattern only where cells and granules remain distinguishable (standard IHC practice). |
| No signal appears in a section containing a documented High-staining cell type. | A failed positive control is possible if a documented cell population is present yet unstained (HPA: High in adipocytes, selected glandular cells, respiratory epithelial cells and neurons). Check tissue identity, section quality, reagent performance and the assay workflow before calling the sample negative (standard IHC practice). |
💡Expected CHCHD3 appearanceCall a section positive when identifiable documented cell types show distinct granular cytoplasmic staining of interpretable intensity; treat diffuse deposits or isolated nuclear staining without the expected granules as findings to investigate, rather than confirmed CHCHD3 positivity (HPA: tissue IHC profile and High cell-type staining; UniProt Q9NX63 subcellular location; standard IHC practice).
| Cell and tissue context | HPA reports High staining in adipocytes; glandular cells of adrenal gland, appendix and breast; bronchial respiratory epithelium; and neuronal populations in the listed brain regions (HPA: tissue IHC). Use the relevant cell population as the reference, since a tissue-wide intensity claim would exceed those observations (HPA: tissue IHC). |
| Antibody evidence | The listed antibody, HPA042935, has Enhanced IHC validation; the tissue profile has Enhanced reliability with medium staining–RNA consistency (HPA: antibody validation and tissue IHC reliability). These ratings support comparison with the reported pattern but do not establish specificity for every cell or section (HPA: tissue IHC). |
| Topology and processing | CHCHD3 is assigned to the mitochondrial inner membrane and has no transmembrane segment; its annotated mature chain spans residues 2–227 (UniProt Q9NX63 topology and processing). These annotations support a mitochondrial interpretation of cytoplasmic granules; they do not identify an antibody epitope or predict retrieval performance (UniProt Q9NX63; standard IHC practice). |
| Reported expression differences | UniProt reports low detection in several organs and increased levels in heart and skeletal muscle; HPA reports tissue-enhanced RNA in skeletal muscle and tongue (UniProt Q9NX63 tissue specificity; HPA: RNA specificity). RNA and protein observations are different measurements, so neither provides an IHC intensity cutoff for an unlisted cell population (standard IHC interpretation). |
| IF/ICC Q&A: What location should IF show? | HPA reports supported mitochondrial localization by ICC-IF and lists A-431, U-251MG, U2OS and sperm among image sources (HPA: subcellular ICC-IF). Use that observation to interpret intracellular location; it is separate from the paraffin-section chromogenic IHC pattern (HPA: subcellular ICC-IF and tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| A documented positive cell type has no visible stain. | The expected control pattern has failed, or the relevant cells may be absent from the examined section (HPA: tissue IHC; standard IHC practice). | Confirm the cell population on the counterstain, then check the positive control, primary-antibody step and chromogenic detection run (standard IHC practice). Do not assign target-specific fixation sensitivity: none is supplied by HPA or UniProt. |
| The slide shows nuclear-only staining. | It is discordant with the HPA granular cytoplasmic IHC profile, although UniProt includes nucleus among reported locations (HPA: tissue IHC; UniProt Q9NX63 subcellular location). | Review staining in documented positive cells and compare no-primary and positive controls before interpreting the nuclear signal (HPA: tissue IHC; standard IHC practice). |
| Unexpected cells stain strongly. | Cross-reactivity or endogenous chromogenic activity is possible; the supplied HPA profile does not label those cells negative (HPA: tissue IHC; standard IHC practice). | Verify cell identity and inspect a no-primary control. For peroxidase detection, check whether endogenous peroxidase blocking was effective (standard IHC practice). |
| Brown signal is diffuse across cells or tissue. | Background can obscure the reported granular cytoplasmic pattern (HPA: tissue IHC; standard IHC practice). | Compare the no-primary control and review blocking, washing and detection development for general background (standard IHC practice). Score CHCHD3 only where the cellular pattern is interpretable. |
| Staining is patchy within the section. | Uneven staining or variable section quality may limit comparison with the reference cell pattern (standard IHC practice; HPA: tissue IHC profile). | Inspect section integrity and counterstain, then compare the same identifiable cell type across well-preserved areas and the run control (standard IHC practice). |
| The no-primary control develops brown signal. | The signal does not require the primary antibody; endogenous activity or detection-system background may contribute (standard IHC practice). | Check endogenous activity blocking and detection reagents, then repeat with appropriate controls before scoring the target stain (standard IHC practice). |
Experiment evidence
IHC & IF images showing CHCHD3 staining
A06593-2 · IHCIHC analysis of CHCHD3 using anti-CHCHD3 antibody (A06593-2). CHCHD3 was detected in a paraffin-embedded section of human liver cancer tissu
A06593-2 · IHCIHC analysis of CHCHD3 using anti-CHCHD3 antibody (A06593-2). CHCHD3 was detected in a paraffin-embedded section of rat heart tissue. Heat m
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000106554-CHCHD3/tissue/cerebral+cortex#imid_11838703
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000106554-CHCHD3/tissue/colon#imid_11838637
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000106554-CHCHD3/tissue/liver#imid_11838646
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000106554-CHCHD3/tissue/kidney#imid_11838639
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA042935; green = CHCHD3, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA042935; green = CHCHD3, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for CHCHD3 IHC & IF
🧪Run bronchus first and score its respiratory epithelial cells for CHCHD3 staining (HPA: High in respiratory epithelial cells). HPA detects CHCHD3 in all 45 scored tissues, so there is no supported negative tissue; use no-primary and isotype controls, and treat any cells on the positive slide that lack specific granular cytoplasmic signal as internal background references, not validated biological negatives (HPA: no negative tissue rows; HPA: detected in all 45 scored tissues; UniProt Q9NX63: mitochondrial inner-membrane location).
Positive control tissue: Adipose tissue (Adipocytes, HPA High)
Negative control tissue: None in HPA: CHCHD3 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show CHCHD3 in A-431, U-251MG, U2OS, Sperm, with annotated localisation: Mitochondria (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only slide, a host-species-matched isotype IgG control at the same concentration, and CHCHD3-knockout material where available or a peptide-block control if the immunizing peptide is known (standard IHC control practice). Quench endogenous peroxidase before HRP/DAB detection and check bronchial mucus for nonspecific chromogen retention (standard chromogenic IHC practice; selected IHC caption: HRP/DAB detection).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the selected paraffin-section caption does not state its fixative (selected IHC caption: fixative unreported). The demonstrated IHC workflow uses heat retrieval in EDTA at pH 8.0, but the evidence does not establish whether retrieval is essential for all CHCHD3 antibodies (selected IHC caption: EDTA pH 8.0). HPA supports mitochondrial localization by ICC-IF, which can help assess localization, while the supplied evidence does not establish that IF or frozen sections are easier than paraffin IHC; in bronchus, assess epithelial signal separately from mucus-associated background (HPA: mitochondria supported in ICC-IF; standard IHC practice).
HPA tissue IHC evidence for CHCHD3
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: CHCHD3 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced CHCHD3 IHC Tips
Use the catalog antibody’s paraffin-section staining conditions as the starting point, then assess CHCHD3 signal against its expected granular mitochondrial pattern.
Which retrieval condition should I start with for paraffin-section CHCHD3 IHC?
Start with heat-mediated retrieval in EDTA at pH 8.0 (datasheet A06593-2). That condition was used for the catalog antibody’s paraffin-embedded human liver cancer section, followed by 1:100 primary antibody overnight at 4°C (caption A06593-2). If staining is weak, compare a modest change in heating time on adjacent sections while keeping antibody dilution and detection constant (standard IHC practice). Assess whether the change increases granular cytoplasmic signal without increasing diffuse staining or damaged tissue edges; granular cytoplasmic staining is the reported tissue pattern (HPA tissue IHC).
How should I troubleshoot fixation-related loss of CHCHD3 staining?
The selected paraffin-section caption does not state its fixative, so CHCHD3-specific fixation sensitivity is unknown for this antibody (caption A06593-2). Record the fixative and fixation duration for each specimen, and compare sections processed with the same retrieval, 1:100 primary dilution, and detection workflow (caption A06593-2; standard IHC practice). Include a consistently processed positive control to distinguish a specimen-specific problem from a staining-run failure (standard IHC practice). If signal varies with processing, test fixation conditions using matched material; neither granular tissue staining nor mitochondrial topology establishes a target-specific fixation effect (HPA tissue IHC; UniProt Q9NX63 topology).
Where should convincing CHCHD3 staining appear in tissue sections?
Look first for granular cytoplasmic staining, the pattern reported in tissue IHC, and judge it within intact cells rather than across the section as a whole (HPA tissue IHC; standard IHC practice). CHCHD3 is a MICOS component associated with the mitochondrial inner membrane, and mitochondrial localisation is supported by subcellular imaging (UniProt Q9NX63 localisation and function; HPA subcellular). Bright staining is reported in adipocytes and several glandular or neuronal cell populations, so cell identity matters when choosing a control (HPA tissue IHC). A broad, smooth cytoplasmic haze deserves comparison with the 1:100 reference condition and a no-primary control before interpretation (caption A06593-2; standard IHC practice).
Could an isoform or modified epitope explain discordant CHCHD3 staining?
The supplied record lists 0 isoforms, so an alternative annotated isoform does not explain a different IHC pattern in this evidence set (UniProt Q9NX63 isoforms). CHCHD3 has a CHCH domain at residues 180–222, no transmembrane segment, and listed phosphorylation sites near its N terminus (UniProt Q9NX63 domains, topology and modified residues). The catalog antibody’s epitope is unspecified here; do not assign its binding to that domain or infer that phosphorylation changes staining (caption A06593-2; UniProt Q9NX63). When results disagree, compare retrieval and staining on adjacent sections, then seek independent antibody validation before attributing the difference to epitope accessibility (standard IHC practice).
How can I investigate CHCHD3 localisation with multiplex IF?
Treat IF as a separate assay: the supplied catalog-antibody evidence describes chromogenic staining in a paraffin section, while the HPA subcellular record supports mitochondrial localisation without validating this antibody for IF (caption A06593-2; HPA subcellular). Pair CHCHD3 with a marker for the expected cell population, such as an epithelial marker when examining respiratory epithelial cells, and include a mitochondrial reference marker to assess overlap (HPA tissue IHC; standard IF practice). Choose fluorophores after checking tissue autofluorescence and use separate channels with single-stain controls (standard IF practice). Because the epitope and its side of the inner membrane are unspecified, titrate permeabilisation rather than assuming one detergent condition will expose it (UniProt Q9NX63 topology; standard IF practice).
What should I change when CHCHD3 DAB staining is widespread?
First compare the section with a no-primary control and inspect whether brown signal follows tissue edges, damaged areas, or all cells indiscriminately (standard IHC practice). The reference procedure used 10% goat serum block, 1:100 primary antibody overnight at 4°C, an anti-rabbit peroxidase secondary for 30 minutes at 37°C, and DAB development (caption A06593-2). Check routine endogenous-peroxidase blocking, washing, and DAB development time before changing the primary dilution (standard IHC practice). Preserve granular cytoplasmic signal while reducing diffuse background; that pattern is more consistent with reported tissue staining than uniform brown haze (HPA tissue IHC).
How should I score CHCHD3 IHC across specimens? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and tissue region before scoring, then record the percentage of positive cells and staining intensity within viable areas (standard IHC practice). An H-score combines the percentages at intensity grades 0–3 and ranges from 0–300; apply one threshold and scoring method across the comparison (standard IHC practice). For spatial analysis, report positive-cell density per mm² of viable tissue, or normalise granular signal to the number of eligible cells in each region (standard IHC practice). Keep section processing and detection matched, and report cell type because CHCHD3 staining varies among the listed tissue populations (standard IHC practice; HPA tissue IHC).
How do I distinguish true CHCHD3 positivity from artefact?
A credible result shows granular cytoplasmic staining in intact cells, consistent with reported tissue IHC and supported mitochondrial localisation (HPA tissue IHC; HPA subcellular). Check which cells carry the signal: high staining is reported for adipocytes, respiratory epithelial cells, and several glandular and neuronal populations, but the listed examples do not establish every tissue’s expected intensity (HPA tissue IHC). Treat edge accentuation, necrotic areas, diffuse nuclear-only staining, and signal retained without primary antibody as reasons to investigate artefact or endogenous enzyme activity (standard IHC practice; UniProt Q9NX63 localisation). Interpret nuclear staining cautiously because a nuclear role is recorded, while mitochondrial localisation has direct subcellular support (UniProt Q9NX63 function and localisation; HPA subcellular).
Boster reagents
Best CHCHD3 / MICOS complex subunit MIC19 IHC Antibodies
The catalog antibody A06593-2 has paraffin-section IHC images from human liver cancer and rat and mouse heart (catalog IHC captions). IF/ICC is listed, but no IF figure is supplied (catalog applications; IF image list).
Real IHC data
Anti-CHCHD3 Antibody ®
Cat # A06593-2
Only A06593-2 will render; its IHC captions document paraffin-embedded human liver cancer, rat heart and mouse heart sections (catalog IHC captions). The same SKU lists IF/ICC and human, mouse and rat reactivity, but has no IF image (catalog applications/reactivity; IF image list).
Which to pick: For tissue IHC, choose A06593-2, a rabbit polyclonal with paraffin-section IHC images; the captions specify EDTA retrieval at pH 8.0 and a 1:100 primary dilution, but do not report the fixative (catalog host/dilution_raw; IHC captions). For IF/ICC, the same SKU lists a 1:50 dilution, although no IF image is supplied (catalog applications/IF dilution; IF image list). It is also the cross-species choice here: human, mouse and rat reactivity is listed, and its IHC captions show tissue from each species (catalog reactivity; IHC captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9NX63 (MIC19_HUMAN, MICOS complex subunit MIC19).
- Human Protein Atlas. CHCHD3 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. CHCHD3 subcellular location (ICC-IF): Localized to the mitochondria..
- Human Protein Atlas. CHCHD3 antibody validation summary (1 antibodies).
- Loss of MTX2 causes mitochondrial dysfunction, podocyte injury, nephrotic proteinuria and glomerulopathy in mice and patients. International journal of biological sciences 2024 — PMC10797693.
- Tumour cells are sensitised to ferroptosis via RB1CC1-mediated transcriptional reprogramming. Clinical and translational medicine 2022 — PMC8882240.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
- PubMed PMID:14654843 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for CHCHD3 (MICOS complex subunit MIC19). Expected localisation Granular cytoplasm in tissue (HPA tissue IHC); mitochondrial inner membrane is a molecular location (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A06593-2). Validated IHC antibody: A06593-2 at 1:50 recommended; image 1:100 (the product's own IHC validation image is shown). Controls (HPA): positive Adipose tissue (Adipocytes); negative None in HPA (detected in all 45 tissues); use no-primary + isotype controls. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet A06593-2); 2. Fixation: Image fixative and duration unreported (datasheet A06593-2); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat retrieval: EDTA pH 8.0 (datasheet A06593-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A06593-2); 8. Primary antibody: Rabbit anti-CHCHD3, 1:50 recommended; image 1:100 (datasheet A06593-2); 9. Primary incubation: Overnight at 4 °C (datasheet A06593-2). Watch for: Fixation: Keep fixation consistent across paraffin sections. (standard IHC practice; not target-specific); Caveat: Staining and RNA expression show medium consistency (HPA tissue IHC); Isoform / epitope: No isoforms listed; chain spans residues 2–227 (UniProt); Regulation: Higher in heart and skeletal muscle (UniProt). Evidence: UniProt Q9NX63, HPA tissue IHC · Enhanced, HPA ICC-IF · mitochondria., Datasheet A06593-2, PMC8882240. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/CHCHD3/immunohistochemistry-ihc-guide.