Analysis of iNKT phenotype and TCR repertoire by single cell analysis with CD1d dCODE Dextramer®

Study iNKT TCR repertoire with CD1d dCODE Dextramer® 

T-cell receptors of iNKT cells are semi-invariant. The majority of iNKT cells feature an invariant α-chain, but a variable β-chain with a highly diverse CDR3 region. Although the β-chain doesn’t interact directly with lipid antigens it determines the affinity of TCR CD1d-lipid interaction through contacts with the α​-chain and CD1d. It therefore likely plays an important role in regulating the immune response of iNKT cells to commensals, pathogens, tumor cells and autoantigens.

Our knowledge of iNKT TCR repertoire derives from bulk sequencing of expanded cells. And little is known about the relationship between TCR repertoire and tissue type in humans and how the repertoire is shaped in response to environmental changes, such as invasion of pathogens and emergence of tumors. Such questions can now be addressed by single cell multi-omics with DNA barcoded CD1d dCODE Dextramer® enabling in-depth analysis of iNKT surface markers, gene expression and TCR sequences.

A distinguishing feature of iNKT cells is their reactivity with the lipid α-Galactosylceramide (α-GalCer) when presented by CD1d. 

Immudex provides dCODE Dextramer® with CD1d:

  • Loaded with α-GalCer – for selective staining of iNKT cells
  • Unloaded – to be used as a negative control

iNKT TCR Discovery

DNA barcodes of CD1d dCODE Dextramer® are compatible with 10x Chromium and BD Rhapsody single cell analysis platforms which makes it possible to link TCR sequence, surface marker expression and whole transcriptome analysis in individual CD1d/α-GalCer stained cells. 

In a proof-of-concept study we used CD1d/α-GalCer dCODE Dextramer® to sequence the TCR of CD3+ iNKT cells directly from a PBMC sample without prior expansion. The experiment also involved multiplex dCODE Dextramer staining for additional four more cell types (results not reported here).  

In accordance with previously published results, we found that five out of six paired sequences had an invariable α-VJ region encoded by TRAV10-TRAJ18 segments, with identical CDR3α sequence: VVSDRGSTLGRLY.

All six identified variable β-VDJ regions were encoded by TRBV25-1 and various TRBJ segments and all CDR3β sequences were different.

The α-chain of the last TCR in the list is different. iNKT cells in blood with diverse glycolipid antigen recognition and atypical TCRs have been reported before.

Learn more about compatibility with the BD Rhapsody™ or 10x Chromium platforms.

The CD1d Product Portfolio

Immudex provides flexibility to your iNKT cell research by offering biotinylated CD1d Monomers and CD1d Dextramer® and CD1d dCODE Dextramer® reagents for your assay of choice.

Order CD1d dCODE Dextramer®

To order CD1d products, please send an e-mail to [email protected] specifying information on:

  • Your preferred reagent format: CD1d dCODE Dextramer®
  • Species – human or mouse
  • Your preferred ligand; α-GalCer or unloaded (negative control)
  • Test size
  • Your preferred single cell platform (10X Chromium or BD Rhapsody)

Please note: CD1d dCODE Dextramer® is available as a standard product with the PE fluorochrome, or with FITC or APC fluorochromes (or no fluorochrome) via Custom Solutions and Services.

 

Cat No

Product

CD1d

Antigen

Label

Amount

XD08001XG

XD08001RG

CD1d dCODE Dextramer® (10x)

CD1d dCODE Dextramer® (RiO)

Human CD1d

Unloaded

PE

25 / 50 /150 tests*

XD08002XG

XD08002RG

CD1d dCODE Dextramer® (10x)

CD1d dCODE Dextramer® (RiO)

Human CD1d

α-GalCer

PE

25 / 50 /150 tests*

YD08001XG

YD08001RG

CD1d dCODE Dextramer® (10x)

CD1d dCODE Dextramer® (RiO)

Mouse CD1d

Unloaded

PE

25 / 50 /150 tests*

YD08002XG

YD08002RG

CD1d dCODE Dextramer® (10x)

CD1d dCODE Dextramer® (RiO)

Mouse CD1d

α-GalCer

PE

25 / 50 /150 tests*

*Higher amounts or test sizes are available upon request.

Questions?

Do you have questions about the CD1d dCODE Dextramer® technology, implementing our technology into your experimental workflow, protocol optimization, or data analysis and interpretation?

Our technical support team consists of highly skilled scientists that are here to empower you to improve your results, provide you with the tools for success, and share our expertise.