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

Associated documentation

T cell responses at diagnosis of amyotrophic lateral sclerosis predict disease progression - data documentation.pdf (100.41 KB)

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

Data contains personal data

Yes

Sensitive personal data

Yes

Type of personal data

human single cell RNA sequencing data

Code key exists

Yes

Language

English

Method and outcome

Unit of analysis

Individual/Patient

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

CSF samples were collected at the time of diagnosis from ALS patients and controls at Karolinska University Hospital. 16mL CSF sample was collected in two 10mL plastic collection tubes (Sarstedt) by lumbar puncture. Within a 3-hour time window samples were transported at 4°C for processing.
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

Response rate/participation rate

Sample were collected from 9 participants as a one time measurement.

Data format / data structure

Numeric

Text

Data collection

Geographic coverage

Geographic spread

Geographic location: Stockholm County

Administrative information

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

Topic and keywords

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)

Keywords

Immune system, Epidemiologic methods, Amyotrophic lateral sclerosis, Sequence analysis, Neurodegenerative diseases, Neurogenic inflammation

Publications

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

If you have published anything based on these data, please notify us with a reference to your publication(s). If you are responsible for the catalogue entry, you can update the metadata/data description in DORIS.