Mesenchymal Stem Cell Markers – A Complete Guide to MSC Identification

Mesenchymal stem cells (MSCs) are a type of multipotent stromal cell capable of differentiating into bone (osteogenic), cartilage (chondrogenic), and fat (adipogenic) cells. This trilineage differentiation potential makes them a powerful tool in regenerative medicine applications, especially for tissue repair, inflammation control, and immune regulation.
To confirm the identity of MSCs in culture or clinical use, scientists rely on specific surface markers—proteins found on the cell membrane that help distinguish MSCs from other cell types. These MSC markers are essential for proper classification, isolation, and ensuring therapeutic safety and efficacy.

Importance of Identifying MSCs Correctly

Accurate identification of mesenchymal stem cells (MSCs) is crucial for both scientific research and clinical applications. Proper MSC characterization ensures that the cells used truly possess the functional and phenotypic properties expected of multipotent stem cells. Misidentification can compromise the outcomes of regenerative therapies and lead to unreliable research findings.

In clinical settings, quality control is non-negotiable. For MSCs to be approved as clinical-grade stem cells, they must be validated under GMP (Good Manufacturing Practice) conditions. This includes confirming their identity through surface markers, differentiation ability, and absence of hematopoietic markers. Regulatory bodies and scientific institutions, such as the International Society for Cell and Gene Therapy (ISCT), have established strict criteria to maintain consistency and safety.

Why It Matters:

  • Ensures reproducibility in scientific experiments
  • Meets regulatory standards for MSC therapy standardization
  • Minimizes patient risk in stem cell therapy
  • Supports long-term efficacy in clinical use of MSCs
Importance of Identifying MSCs Correctly

Core Surface Markers for MSC Identification (ISCT Criteria)

The International Society for Cell & Gene Therapy (ISCT) has set standardized criteria to define and authenticate mesenchymal stem cells (MSCs), ensuring reproducibility and clinical-grade consistency. According to these guidelines, MSCs must exhibit specific surface markers that confirm their identity as mesenchymal stromal cells.

Positive MSC Markers:

MSCs must express the following core surface markers:

  • CD73 (NT5E): An ecto-5′-nucleotidase involved in purine metabolism, critical for MSC immune-modulatory function.
  • CD90 (Thy-1): A glycoprotein linked to cell-cell and cell-matrix interactions.

Negative Markers to Exclude Other Cell Types

To ensure the purity and specificity of mesenchymal stem cells (MSCs), it is equally important to confirm the absence of certain markers that are typically expressed by hematopoietic, endothelial, or immune cells. This negative selection step is crucial in MSC immunophenotyping and is required by the ISCT guidelines for identifying clinical-grade stem cells.

MSCs must not express the following markers:

  • CD34: Commonly found on hematopoietic and endothelial progenitor cells.
  • CD45: A classic marker of hematopoietic stem cells and leukocytes.
  • CD14 / CD11b: Monocyte/macrophage markers.
  • CD19: B cell marker.
  • HLA-DR: Major histocompatibility complex class II, typically absent in unstimulated MSCs.

Why Negative Markers Matter:

  • They help distinguish MSC populations from hematopoietic stem cells.
  • Ensure MSC purity in cell culture and therapeutic applications.
  • Critical for GMP compliance and clinical-grade validation of MSC-based therapies.

Methods Used to Detect MSC Markers

To confirm the identity and purity of mesenchymal stem cells (MSCs), researchers rely on advanced lab techniques to detect both positive and negative surface markers. These methods form the backbone of phenotypic profiling and are essential in both research and clinical-grade stem cell production.

Flow Cytometry

The gold standard for MSC marker detection, this technique uses fluorescently labeled antibodies to quantify surface proteins on individual cells. It allows multi-marker analysis and is highly accurate for determining the percentage of MSCs expressing CD73, CD90, and CD105.

Immunofluorescence

Used to visualize marker expression under a microscope. This method offers spatial context, helping researchers confirm MSC identity in tissue sections or cultures.

PCR (Polymerase Chain Reaction) and Western Blot

These molecular techniques detect gene expression (PCR) or protein expression (Western blot) of MSC markers, providing additional confirmation of MSC phenotype.

These tools are crucial for flow cytometry analysis, GMP-compliant stem cell validation, and ensuring accurate phenotypic profiling before any clinical or experimental use.

Variability in MSC Markers by Tissue Source

While mesenchymal stem cells (MSCs) share a core set of surface markers (like CD73, CD90, and CD105), their exact expression profiles can vary depending on the tissue source. These tissue-specific MSC characteristics influence their biological behavior, differentiation potential, and therapeutic application.

MSC Marker Differences by Tissue Type:

Bone Marrow-Derived MSCs (BM-MSCs)

Express classical markers strongly and are well-characterized. They typically show moderate proliferation and higher osteogenic potential.

Adipose-Derived MSCs (AD-MSCs)

Often display higher expression of CD36 and CD34 (in early passage), associated with their fat tissue MSC markers. Known for strong adipogenic and angiogenic potential.

Umbilical Cord-Derived MSCs (UC-MSCs)

Exhibit lower immunogenicity and high proliferation. Unique neonatal stem cell markers such as CD146 and CD271 may be present depending on isolation techniques.

Dental Pulp & Synovial MSCs

Known for neuroregenerative and chondrogenic potential, respectively. These cells may express higher levels of neural or cartilage-related surface antigens.

Functional Role of MSC Markers

Mesenchymal stem cell (MSC) markers are not only used for identification—they often have functional roles that influence how MSCs behave in the body. These markers can actively participate in processes like immunomodulation, angiogenesis, and cell migration, all of which are crucial for the success of regenerative therapies. Key Functional Contributions of MSC Markers:

Immunomodulation

Markers like CD73 contribute to anti-inflammatory effects by generating adenosine, which plays a role in MSC immunomodulatory function and immune suppression.

Angiogenesis

CD105 (Endoglin) is involved in regenerative signaling by enhancing vascular endothelial growth factor (VEGF) responses, promoting blood vessel formation in damaged tissues.

Cell Adhesion & Migration

CD90 (Thy-1) supports stem cell trafficking and cellular adhesion, allowing MSCs to home to injury sites more effectively.

These functional roles make certain markers not just identifiers, but also contributors to the therapeutic potential of MSCs.

Challenges in MSC Marker Standardization

Standardizing mesenchymal stem cell markers remains a challenge due to variations in marker expression that can occur during cell culture. As MSCs are passaged repeatedly for expansion, they may undergo phenotypic drift, where surface marker expression gradually changes, affecting identity and potency.

Additionally, culture conditions, such as the choice of basal media, serum type (e.g., FBS vs. hPL), oxygen levels, and substrate materials, can influence the MSC surface marker profile. These culture-induced variabilities complicate consistent identification, especially in clinical-grade production.

Moreover, cell passage effects can lead to reduced functionality or unintended differentiation, making quality control crucial during large-scale MSC expansion.

Emerging and Functional MSC Markers

Beyond the classical ISCT-defined markers CD73, CD90, and CD105, research is now exploring novel MSC surface antigens that offer deeper insight into functional MSC subsets. These advanced markers may correlate with enhanced immunosuppressive capacity, tissue-homing ability, or proliferation rate, making them valuable for precision therapies.

Examples of emerging markers include:

  • STRO-1 – associated with clonogenic potential in BM-MSCs
  • CD146 (MCAM) – involved in perivascular MSC identity and angiogenesis
  • CD271 (NGFR) – indicative of highly potent, anti-inflammatory subsets

This advanced MSC profiling paves the way for developing customized stem cell therapies based on tissue-specific functional markers, ensuring higher efficacy in regenerative medicine applications.

Emerging and Functional MSC Markers

FAQs

CD73, CD90, and CD105 are the key positive markers. MSCs must also be negative for CD34, CD45, CD14, CD19, and HLA-DR.

Common methods include flow cytometry, immunofluorescence, PCR, and Western blotting.

They share core markers but may differ in expression levels of additional tissue-specific markers like CD36 or CD271.

CD34 is a hematopoietic marker. MSCs must lack it to confirm non-hematopoietic identity.

Yes. Marker expression can vary with passages, media, and culture conditions.