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Histology Across Organs: Staining Methods and the R&D Questions They Answer

  • Writer: KAMFEI WONG
    KAMFEI WONG
  • Sep 11
  • 6 min read

Updated: Sep 19

Histology is indispensable in biomedical R&D. Different staining techniques—H&E, special stains, immunohistochemistry (IHC), immunofluorescence (IF), multiplex assays, and in situ hybridization (ISH)—provide complementary insights into organ morphology and molecular biology.


This article reviews how these methods are applied across organs and highlights the specific R&D questions each stain can answer.


Brain Histology


Brain H&E staining
 Brain H&E staining. Click the image to view Whole Slide Imaging.

Techniques used:

  • H&E – neuronal loss, infarction

  • Nissl stain – neuronal cell bodies

  • IHC (GFAP, NeuN, Iba1) – astrocytes, neurons, microglia

  • IF (Tau, Amyloid) – neurodegeneration

  • ISH (RNAscope) – gene expression


R&D Questions and Stains:

  1. Do infarct models show “red neurons”? → H&E

  2. Is neuronal loss quantifiable in cortex? → Nissl / IHC (NeuN)

  3. Is gliosis evident in degeneration? → IHC (GFAP)

  4. Are Alzheimer’s markers detectable? → IF (Tau, Amyloid)

  5. Does RNAscope confirm vector delivery? → ISH


Breast Histology


Breast H&E staining
 Breast H&E staining. Click the image to view Whole Slide Imaging.

Techniques used:

  • H&E – ductal vs lobular structures

  • IHC (ER, PR, HER2, Ki-67) – receptor status

  • IF / Multiplex IF – spatial receptor co-expression


R&D Questions and Stains:

  1. Is carcinoma ductal or lobular type? → H&E

  2. Do xenograft tumors match human breast cancer? → H&E

  3. What is receptor status (ER, PR, HER2)? → IHC

  4. Is proliferation rate measurable? → IHC (Ki-67)

  5. Can multiplex IF show receptor co-expression? → IF


Colon Histology


Colon H&E staining.
Colon H&E staining. Click the image to view Whole Slide Imaging.

Techniques used:

  • H&E – crypt architecture, mucosal injury, carcinoma

  • PAS / Alcian Blue – mucin content, goblet cells

  • IHC (CD3, CD8, FOXP3) – immune infiltration

  • Multiplex IF – spatial tumor microenvironment analysis


R&D Questions and Stains:

  1. Does treatment damage mucosa or crypts? → H&E

  2. Are goblet cells depleted in IBD models? → PAS / Alcian Blue

  3. Is carcinoma progression visible in adenoma–carcinoma sequence? → H&E

  4. Are Tregs and cytotoxic T cells altered in colitis? → IHC

  5. Can multiplex IF map immune cell interactions in colon tumors? → Multiplex IF


Eye (Eyeball) Histology


Eyeball H&E staining.
Eyeball H&E staining. Click the image to view Whole Slide Imaging.

Techniques used:

  • H&E – overall structure of cornea, retina, sclera, choroid

  • Special stains (Periodic Acid–Schiff, Elastic stains) – basement membranes, vasculature

  • IHC (GFAP, Rhodopsin, Opsins, VEGF, CD31) – glial response, photoreceptors, angiogenesis

  • IF – co-localization of retinal cell markers, photoreceptor proteins

  • ISH / RNAscope – retinal gene therapy vector expression


R&D Questions and Corresponding Stains:

  1. Is retinal layering preserved in models of degeneration? → H&E

  2. Are corneal or lens basement membranes altered in injury models? → PAS

  3. Is neovascularization present in choroid or retina (e.g., AMD models)? → IHC (CD31, VEGF)

  4. Do photoreceptor populations express opsins normally? → IHC / IF (Rhodopsin, Cone Opsins)

  5. Can RNAscope confirm gene therapy vector expression in retinal cells? → ISH / RNAscope


Heart Histology


Heart H&E staining.
Heart H&E staining. Click the image to view Whole Slide Imaging.

Techniques used:

  • H&E – myocardial necrosis, myocarditis

  • Masson’s Trichrome / Sirius Red – fibrosis

  • IHC (Troponin, CD31) – myocyte injury, angiogenesis

  • IF (Connexin, calcium channels) – conduction and remodeling


R&D Questions and Stains:

  1. Is there cardiotoxicity (necrosis, hypertrophy)? → H&E

  2. Is fibrosis reduced by therapy? → Trichrome / Sirius Red

  3. Are angiogenesis markers upregulated post-infarct? → IHC (CD31)

  4. Do connexin changes predict arrhythmia risk? → IF

  5. Is inflammatory infiltration present in myocarditis? → Multiplex IF


Kidney Histology


Kidney H&E staining.
 Kidney H&E staining. Click the image to view Whole Slide Imaging.

Techniques used:

  • H&E – tubular necrosis, inflammation

  • PAS / Silver stain – basement membrane, sclerosis

  • IHC (WT1, Synaptopodin, CD68) – podocytes, immune cells

  • IF (IgA, IgG, C3) – immune complex deposition


R&D Questions and Stains:

  1. Is there tubular necrosis or glomerular damage? → H&E

  2. Are basement membranes thickened? → PAS / Silver stain

  3. Are immune complexes visible in nephritis? → IF

  4. Is there macrophage infiltration? → IHC (CD68)

  5. Are podocyte markers reduced? → IHC (WT1, Synaptopodin)


Liver Histology


 Liver H&E staining.
 Liver H&E staining. Click the image to view Whole Slide Imaging.

Techniques used:

  • H&E – necrosis, steatosis, ballooning

  • Oil Red O / PAS-D – lipid and glycogen

  • Sirius Red – fibrosis quantification

  • IHC (Ki-67, CK19, CD68) – proliferation, progenitors, macrophages

  • Multiplex IF – tumor immune environment


R&D Questions and Stains:

  1. Is there hepatocellular necrosis or ballooning? → H&E

  2. Are lipids or glycogen accumulated? → Oil Red O / PAS-D

  3. Is fibrosis advancing in chronic models? → Sirius Red

  4. Are Kupffer cells activated in NASH? → IHC (CD68)

  5. Does multiplex IF reveal immune profiles in HCC? → Multiplex IF


Lung Histology


Lung H&E staining.
Lung H&E staining. Click the image to view Whole Slide Imaging.

Techniques used:

  • H&E – alveoli, inflammation, carcinoma

  • Elastic stains – alveolar walls, fibrosis

  • IHC (Cytokeratin, PD-L1) – tumor phenotyping

  • Multiplex IF – immune-tumor interactions


R&D Questions and Stains:

  1. Are alveoli filled with exudates in pneumonia? → H&E

  2. Can adenocarcinoma vs squamous carcinoma be distinguished? → H&E / IHC

  3. Is collagen deposition visible in fibrosis models? → Elastic stains

  4. Are PD-L1 levels detectable in tumor samples? → IHC

  5. Can multiplex IF show immune checkpoint landscapes? → Multiplex IF


Pancreas Histology


Pancreas H&E staining.
 Pancreas H&E staining. Click the image to view Whole Slide Imaging.

Techniques used:

  • H&E – acini, ducts, islets

  • IHC (Insulin, Glucagon, Ki-67) – islet cell biology

  • IF – hormone co-localization


R&D Questions and Stains:

  1. Do diabetic models show islet depletion? → H&E

  2. Are exocrine tissues necrotic in pancreatitis? → H&E

  3. Is beta-cell mass quantifiable? → IHC (Insulin, Ki-67)

  4. Is alpha-to-beta cell ratio altered? → IF (Insulin vs Glucagon)

  5. Do xenografts replicate carcinoma histology? → H&E / IHC


Prostate Histology


 Prostate H&E staining.
 Prostate H&E staining. Click the image to view Whole Slide Imaging.

Techniques used:

  • H&E – gland morphology

  • IHC (PSA, AMACR, Ki-67) – tumor markers

  • IF – stromal vs epithelial interactions


R&D Questions and Stains:

  1. Is glandular hyperplasia evident? → H&E

  2. Do prostate cancers express PSA or AMACR? → IHC

  3. Is proliferation rate high? → IHC (Ki-67)

  4. Is stromal remodeling present? → H&E / IF

  5. Do xenografts replicate carcinoma histology? → H&E / IHC


Skin Histology


 Skin H&E staining.
 Skin H&E staining. Click the image to view Whole Slide Imaging.

Techniques used:

  • H&E – epidermis, dermis, tumors

  • IHC (Ki-67, Melan-A, p53) – proliferation, melanocytic markers

  • IF – tumor-immune interactions


R&D Questions and Stains:

  1. Is epidermal hyperplasia visible in psoriasis? → H&E

  2. Do skin tumors express melanocytic markers? → IHC (Melan-A)

  3. Is proliferation elevated? → IHC (Ki-67)

  4. Is UV-induced DNA damage detectable? → IHC (p53)

  5. Can IF reveal immune infiltration patterns? → IF


Spleen Histology


 Spleen H&E staining.
 Spleen H&E staining. Click the image to view Whole Slide Imaging.

Techniques used:

  • H&E – general architecture, red pulp vs white pulp

  • IHC (CD3, CD20, Ki-67) – T vs B cell zones, proliferation

  • IF – spatial mapping of immune subsets

  • Special stains (Reticulin) – stromal network evaluation


R&D Questions and Corresponding Stains:

  1. Is splenic architecture preserved under treatment? → H&E

  2. Are white pulp follicles enlarged during immune activation? → H&E

  3. Is there lymphoma infiltration disrupting splenic structure? → IHC (CD20, Ki-67)

  4. Do T cell zones expand in response to immunotherapy? → IHC (CD3)

  5. Is spatial distribution of B and T cells altered? → IF / Multiplex IF


Tongue Histology


 Tongue H&E staining.
 Tongue H&E staining. Click the image to view Whole Slide Imaging.

Techniques used:

  • H&E – stratified squamous epithelium, papillae, skeletal muscle bundles

  • Special stains (PAS, Alcian Blue) – mucins in minor salivary glands

  • IHC (Cytokeratins, Ki-67, p16, p53) – epithelial differentiation, proliferation, HPV-related lesions

  • IF – taste receptor proteins, neural markers

  • ISH / RNAscope – gene expression in taste buds or oral cancers


R&D Questions and Corresponding Stains:

  1. Are papillae and taste buds structurally preserved in normal tongue histology? → H&E

  2. Do mucin-producing minor salivary glands show functional changes? → PAS / Alcian Blue

  3. Are precancerous or HPV-related lesions identifiable? → IHC (p16, p53, Ki-67)

  4. Do taste receptor cells express expected proteins under experimental conditions? → IF

  5. Can RNAscope detect taste receptor gene expression or viral transcripts? → ISH / RNAscope


Tumor Histology


 Tumor H&E staining.
 Tumor H&E staining. Click the image to view Whole Slide Imaging.

Techniques used:

  • H&E – morphology, tumor grade, necrosis, invasion

  • Special stains (Masson’s Trichrome, PAS) – stromal fibrosis, mucin production

  • IHC (Ki-67, p53, HER2, ER/PR, PD-L1, CD3/CD8/CD68) – proliferation, mutations, receptor status, immune markers

  • IF / Multiplex IF – immune–tumor spatial interactions, checkpoint expression

  • ISH / RNAscope – oncogene expression, viral transcripts, gene therapy monitoring


R&D Questions and Corresponding Stains:

  1. What is the tumor grade and invasion pattern? → H&E

  2. Is there stromal fibrosis or mucin production associated with progression? → Masson’s Trichrome / PAS

  3. What is the proliferation index and mutation status? → IHC (Ki-67, p53)

  4. Are receptor pathways (HER2, ER/PR, PD-L1) driving tumor growth? → IHC

  5. Can multiplex IF or RNAscope define the immune landscape and oncogene expression? → Multiplex IF / ISH


Uterus Histology


 Uterus H&E staining.
 Uterus H&E staining. Click the image to view Whole Slide Imaging.

Techniques used:

  • H&E – endometrium, myometrium

  • IHC (ER, PR, Ki-67) – hormone response

  • IF – signaling pathways


R&D Questions and Stains:

  1. Is endometrial hyperplasia visible? → H&E

  2. Do leiomyomas disrupt smooth muscle? → H&E

  3. Is proliferation altered by hormones? → IHC (Ki-67)

  4. Are ER/PR receptors expressed normally? → IHC (ER, PR)

  5. Are signaling proteins localized in endometrial cells? → IF



Conclusion


Histology across organs provides a powerful toolkit for research and development. Each staining method—H&E, special stains, IHC, IF, multiplex, or ISH—answers specific scientific questions. By integrating multiple methods, researchers gain a comprehensive view of organ pathology, safety profiles, and therapeutic response.


At iHisto, we provide a full range of histology services, helping biotech, pharma, and academic partners accelerate discoveries across all organ systems.

 
 
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