Like liver, muscle cell, kidney or other cell types? If yes, then what is relevance of BCR signaling activation in other cell types?
I am not sure if I understand your question correctly. To my knowledge, only B-cells express the BCR (B-cell receptor), so when you say BCR signaling, what do you refer to? Did you actually detect a BCR protein on these other cell types (if so, by what method?), or are you simply referring to activation of downstream signaling pathways (STAT's, ERK?). If the first (detection of BCR protein), I would be very surprised, as BCR should only be expressed by actual B-cells, and creation of a functional BCR is a multi-step and complicated/highly regulated process throughout B-cell development in the bone marrow. (However, B-cells might infiltrate other tissues in vivo, and thus "contaminate" your sample?) If the latter (detection of signaling)) that could be activation of a wide variety of signaling pathways, as many cell surface receptors use overlapping intracellular signaling mediators/pathways.
Hi Hilde,
Thanks for reply,
It was detection of signalling part rather than BCR expression. Our microarray data is populating BCR signalling pathways in cell line based experiments so the contamination issue is out of question. We see a lot many proteins including
BTK;LYN;PIK3CD;CARD11;LILRB3;IFITM1;NFKBIE;CD72;RAC2;CD22;PIK3R5;INPP5D;BLNK;PTPN6;CR2;VAV2;VAV1;CD19;FCGR2B;PLCG2;CD79B;CD79A
are highly expressed and indicating towards to BCR signalling activation. Is it possible that the these many component of BCR signalling are activated following to particular treatment?
If you have any suggestions please let me know.
That is an interesting gene-list! Definitely looks like potential B-cells. So, my suggestions are first based on questions, as I don't know your model system (what cell line) or your perturbations (one or two or more conditions?). 1st: What is your cell line? (you don't have to tell, but consider these questions in your analysis). How far away from lymphoid/B-cells is your cell line? Then, I would check basal expression of these genes in your starting cell line. Although these looks like B-cell genes, I am not sure how restricted they are (some, like CD19 is pretty B-cell specific, while some of the others might not be). I would also check how broadly vs cell-type specific the various genes are by looking at gene-expression data from various websites (google the gene-names, and a few website have microarray or other expression data for each gene from different cell types). The reason I am asking this is to find out if these genes are normally permissive for expression in your cell line, and are able to induce expression normally upon some stimuli, or, if these genes normally should be silenced in your cell line, but that you have perturbed an important gene (TF or chromatin modifier?) that has altered gene expression "program" or permissiveness. There are examples of this when over-expressing or knocking down important regulators. I have seen similar things in various expression datasets. The pathway analysis comes up with processes described in other cell types, based on where the genes are most often reported/studied. Second suggestion would be to check to what extent/level are they expressed? And checking some at protein level, etc. (some, like Cd19 and Cd79A/B are cell surface expressed, and can also be checked by FACS analysis). I hope this helps. Next steps will depend on the answer(s) to these questions (including what perturbations you have done with your cell line to get these changes in gene expression).
Good luck!
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