Tuesday, May 09, 2017

Atlas Map for blood Dendritic cells, Monocytes, and Progenitors

I note that I have been unable to post frequently in past few weeks, since I have been very busy with work and personal travel. I have been getting a few mails enquiring if I moved to a new page. No, I havent yet. If I do, I will definetly make an announcement.

Immunology is still a very difficult subject especially when it comes to classification. The problem arises from the lack of understanding and partly cause classification system is messy. Further, the same immune cell function differently under different circumstances. Cellular subtyping and subsequent studies are based largely on the established classification rules, which has been developed decades ago. In most cases, a subtypes is based on morphology and a little understanding of function. For most of the human cells, there is no clear cut systematic cellular classification based on molecular profile. Human cell atlas in one of the ambitious project that has been announced to overcome this massive question. Sarah Teichmann states, “The cell is the key to understanding the biology of health and disease, but we are currently limited in our understanding of how cells differ across each organ, or even how many cell types there are in the body. The Human Cell Atlas initiative is the beginning of a new era of cellular understanding as we will discover new cell types, find how cells change across time, during development and disease, and gain a better understanding of biology.”

The methodology used for this is technically complex but the idea is straightforward. The cells are sorted out using a known classification system and then each cell is isolated from the pool. Then using a technique called single cell transcriptomics a cell is profiled. This gives a picture of what is the genetic expression pattern of that particular cell. By parallely doing so for a huge number of cell samples, a map can be drawn.

Dendritic cells are called so because of their structure. They are one of the most important classic APC (Antigen presenting cell). Dendritic cells (DC) were first discovered by Ralph Steinman roughly 4 decades ago for which he was awarded the Nobel prize. Though there has been some previous hints that DCs are a diverse population, the subtypes have not been recognised or typable. 


In the study by Villani et al human PBMCs were enriched from blood sample using Ficoll extraction and DCs were isolated using flow cytometry. Each cell was then isolated into a single well and transcriptome analysis was done. For the study, 742 DCs and 339 monocytes that passed quality control was profiled with an average detection of 5326 genes per cell. Based on genetic expression cluster results 6 clusters which are numbered DC1 to DC6 were identified (See Fig 1 for classification details).
  • 2 clusters mapping closely to the well-established DC subsets, with cluster DC1 mapping to CD141+ DCs and cluster DC6 to pDCs.
  • 2 clusters containing the CD1C+ cDCs, cluster DC2 and cluster DC3
  • 1 cluster corresponding to CD141–CD1C– population named DC4
  • 1 cluster DC5
Fig 1: Summary of the study and revised classification of the Dendritic cells to include 6 different subtypes based on the transcriptomic map. Source
Further analysis was able to gathered some potential markers of interest.
  • DC1 corresponds to CD141/BDCA-3+ ,which was best indentified using CLEC9A.
  • DC2 and DC3 togther corresponds with CD1C/BDCA-1+
  • DC4 corresponded with CD1C–CD141–CD11C+ which also shared some signatures with monocytes
  • DC5 was unique in itself.
  • DC6 corresponded to the interferon-producing pDC, defined by standard markers CD123, CD303/BDCA-2
The paper is very dense with lot of data. However, essentially this paper established that there are DC subtypes defined and probably there is a diversity in function. This also sits well with literature where function of DCs is called into into three categories. First, antigen presentation and activation of T cells. Second, inducing and maintaining immune tolerance. Third, maintaintainence of immune memory. However, which does what is yet to be studied and elucidated. Divya Shah comments, “In this study, scientists have used cutting-edge technologies to find that there are many more types of cell than we originally thought. The next step is to find out what each of these cell types do in our immune system, both when we’re healthy and during disease."

Reference

Villani A, Satija R, Reynolds G, Sarkizova S, Shekhar K, Fletcher J et al. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science. 2017; 356 (6335): eaah4573.

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

No comments:

Post a Comment