T cell responses at diagnosis of amyotrophic lateral sclerosis predict disease progression

SND-ID: 2022-113

Creator/Principal investigator(s)

Fang Fang - Karolinska Institutet , Institute of Environmental Medicine orcid


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

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Research principal, contributors, and funding

Research principal

Karolinska Institutet

Responsible department/unit

Institute of Environmental Medicine

Protection and ethical review

Data contains personal data


Sensitive personal data


Type of personal data

human single cell RNA sequencing data

Code key exists


Ethics Review

Swedish Ethical Review Authority - Ref. DNRs 2014/1815-31/4, 2018-1065/31 and DNRs 2009/2107-31/2 and 2021-02060

Method and time period

Unit of analysis


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.
Geographic coverage

Geographic spread

Geographic location: Stockholm County

T cell responses at diagnosis of amyotrophic lateral sclerosis predict disease progression


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.

Version 1


Fang Fang. Karolinska Institutet (2022). T cell responses at diagnosis of amyotrophic lateral sclerosis predict disease progression. Swedish National Data Service. Version 1. https://doi.org/10.48723/xjvx-2v24

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Data format / data structure



Creator/Principal investigator(s)

Fang Fang - Karolinska Institutet , Institute of Environmental Medicine orcid

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.

Published: 2022-08-17