T cell responses at diagnosis of amyotrophic lateral sclerosis predict disease progression
SND-ID: 2022-113-1. Version: 1. DOI: https://doi.org/10.48723/xjvx-2v24
Citation
Creator/Principal investigator(s)
Fang Fang
- Karolinska Institutet, Institute of Environmental Medicine
Research principal
Karolinska Institutet
- Institute of Environmental Medicine
Description
In this project, we aimed to understand how T cell responses contribute to the disease progression of amyotrophic lateral sclerosis (ALS). The present data is on single-cell sequencing isolated from human cerebrospinal fluid (CSF) cells from both ALS patients (n=5) and controls (n=4). This analysis was conducted as part of a bigger project which is summarized in the section below.
We used flow cytometry to define T cell subsets and phenotypes in blood and CSF samples collected at the time of diagnosis on a cohort of 89 newly diagnosed ALS patients in Stockholm, Sweden. High frequency of CD4+FOXP3- effector T cells in blood and CSF was associated with a poor survival whereas high frequency of activated regulatory T (Treg) cells and high ratio between activated and resting Treg cells in blood was associated with a better survival. T cell profiles also predicted disease progression rate. On an independent cohort of cases and controls we used single cell transcriptomics data to demonstrate that ALS patients had altered T cell gene expression patterns and clonally expanded CD4+ and CD8+ T cells i
We used flow cytometry to define T cell subsets and phenotypes in blood and CSF samples collected at the time of diagnosis on a cohort of 89 newly diagnosed ALS patients in Stockholm, Sweden. High frequency of CD4+FOXP3- effector T cells in blood and CSF was associated with a poor survival whereas high frequency of activated regulatory T (Treg) cells and high ratio between activated and resting Treg cells in blood was associated with a better survival. T cell profiles also predicted disease progression rate. On an independent cohort of cases and controls we used single cell transcriptomics data to demonstrate that ALS patients had altered T cell gene expression patterns and clonally expanded CD4+ and CD8+ T cells in CSF. In summary, T cell responses contribute to disease progression of ALS, supporting modulation of adaptive immunity as a viable therapeutic option.
The data sets contain single-cell RNA sequencing data from 9 individuals (5 ALS cases and 4 controls). Immune cells were isolated from CSF. Furthermore, for each individual, we studied the T cell receptor repertoire by using V(D)J sequencing. Uploaded files are in fastq format. Show less..
Data contains personal data
Yes
Sensitive personal data
Yes
Type of personal data
human single cell RNA sequencing data
Code key exists
Yes
Language
Unit of analysis
Population
Participants were recruited from the bigger Stockholm area as part of the case-control studies ALSrisc and StopMS. For more Information on ALSrisc please visit the website: https://ki.se/en/imm/amyotrophic-lateral-sclerosis-als. For more information on StopMS please visit the website: https://ki.se/en/cns/fredrik-piehls-research-group
Study design
Observational study
Case-control study
Description of study design
Human material: Immune cells isolated from cerebral spinal fluid (CSF). CSF samples were collected from five patients with newly diagnosed ALS, and four controls (two patients with normal pressure hydrocephalus, one patient with cervical radiculopathy, and one healthy control).
Singe cell sequencing platform: 5’ scRNA-seq + V(D)J TCR repertoire sequencing using the 10x Genomics platform.
For more general inofrmation on the 10x Genomic platform please see here: https://www.10xgenomics.com/support/single-cell-immune-profiling
User guids for 5’ scRNA-seq and V(D)J TCR repertoire can be found here respectively: https://assets.ctfassets.net/an68im79xiti/1ihALQkNrgD83PmBYZ4SrW/e94dbc40c2a6c64940ebc82eca9e9334/CG000507_ChromiumSingleCell5_v2_FeatureBarcode_Automation_UG_Rev_A.pdf https://assets.ctfassets.net/an68im79xiti/2JzjFJTfslSYe6GF9eh5TL/c228c4cc6b84c4f17fc6c25c8d7a5448/CG000207_ChromiumNextGEMSingleCellV_D_J_ReagentKits_v1.1_UG_Rev_G.pdf
Sampling procedure
1. CSF sample was centrifuged at 300g, 10min, 4°C
2. Supernatant was removed expect for around 500ul of CSF (here tubes with a visible blood contammination were droped from the analysis)
3. When more than one collection tube was used, sample were combined in one collection tube.
4. CSF samples were washed with cold PBS + 0.5% BSA (w/o ETDA) by filling the collection tube up to 10 ml.
5. CSF samples was centrifuge at 300g, 10min, 4°C.
6. Supernatant was removed, cell resuspended in 500ul of cold PBS + 0.5% BSA, and transfer sample to a low binding RNA tube
7. Samples were centrifuge at 300g, 10min, 4°C.
8. supernatant was removed and cells were re-suspended cell in the remaining supernatant (~50µl)
For the remaining steps, we followed the manufacture's protocol mentioned above.
Time period(s) investigated
2020-09-23 – 2021-04-14
Number of individuals/objects
9
Response rate/participation rate
Sample were collected from 9 participants as a one time measurement.
Geographic spread
Geographic location: Stockholm County
Responsible department/unit
Institute of Environmental Medicine
Ethics Review
Swedish Ethical Review Authority - Ref. DNRs 2014/1815-31/4, 2018-1065/31 and DNRs 2009/2107-31/2 and 2021-02060
Research area
Immunology (Standard för svensk indelning av forskningsämnen 2011)
Public health, global health, social medicine and epidemiology (Standard för svensk indelning av forskningsämnen 2011)
Yazdani, S., Seitz, C., Cui, C., Lovik, A., Pan, L., Piehl, F., Pawitan, Y., Klappe, U., Press, R., Samuelsson, K., Yin, L., Vu, T., Joly, A., Westerberg, L., Evertsson, B., Ingre, C., Andersson, J., & Fang, F. (n.d.). T cell responses at diagnosis of amyotrophic lateral sclerosis predict disease progression. In Nature communications (Vol. 13, Issue 1, pp. 6733-). https://doi.org/10.1038/s41467-022-34526-9
DOI:
https://doi.org/10.1038/s41467-022-34526-9
SwePub:
oai:prod.swepub.kib.ki.se:151234387
