Mitochondrial toxins cause widespread downregulation of pathways in X-linked dystonia-parkinsonism patient-derived neurons.

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Paper

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The authors' code

Rust · 38 lines · 1.5 KB · BSD-3-Clause

//! Replicate a BAM N times into a larger BAM for align-mode timing benchmarks.
//! Each copy's records stay contiguous, so per-fragment name grouping (by
//! adjacency) is preserved — copies are simply counted as additional fragments.
//!
//! Usage: replicate_bam <in.bam> <out.bam> <n>
use noodles_bam as bam;
use noodles_sam::alignment::io::Write as _;
fn main() -> anyhow::Result<()> {
let mut args = std::env::args().skip(1);
let input = args.next().expect("in.bam");
let output = args.next().expect("out.bam");
let n: usize = args.next().expect("n").parse()?;
// Read the whole input into memory: this is a benchmarking aid run on small
// BAMs, so simplicity beats streaming.
let mut reader = bam::io::Reader::new(std::fs::File::open(&input)?);
let header = reader.read_header()?;
let recs: Vec<_> = reader
.record_bufs(&header)
.collect::<std::io::Result<Vec<_>>>()?;
eprintln!("read {} records; writing {} copies", recs.len(), n);
let mut writer = bam::io::Writer::new(std::io::BufWriter::new(std::fs::File::create(&output)?));
writer.write_header(&header)?;
// Emit the records N times *in blocks*, not interleaved. Alignment mode
// groups a fragment's records by adjacency, so each block's copies read as
// additional fragments rather than corrupting the grouping.
for _ in 0..n {
for r in &recs {
writer.write_alignment_record(&header, r)?;
}
}
writer.finish(&header)?;
eprintln!("wrote {} records total", recs.len() * n);
Ok(())
}

replicate_bam.rs at commit ed926b8, under BSD-3-Clause · at the source

Overview

Authors: Karen Grütz¹, Axel Künstner², Christin Krause³, Letizia Santinelli¹, Sören Franzenburg⁴, Jenny Ghelfi⁵, Anne Grünewald⁵, Raymond L Rosales⁶, Norbert Brüggemann^1,7, Hauke Busch², Christine Klein¹, Philip Seibler¹

ORCID iDs: Philip Seibler

Institutions: University Hospital Schleswig-Holstein (Germany); University of Lübeck (Germany); Christian-Albrechts-Universität zu Kiel (Germany); University of Luxembourg (Luxembourg); Luxembourg Centre for Systems Biomedicine (Luxembourg); University of Santo Tomas (Philippines)

Journal: Stem cell reports, volume 21, issue 6, article 102920

Dates: received 4 July 2025; accepted 9 April 2026; published online 7 May 2026; in print June 2026

Type: Brief report · Language: English

License: CC BY

Identifiers: DOI 10.1016/j.stemcr.2026.102920 · PMID 42102821 · PMCID PMC13261877 · OpenAlex W7160514374

Open access: gold, a free copy (OpenAlex)

Status: code verified

Categories: genetics / omics (modality), human (organism), other condition (population), Parkinson's (population), cellular / molecular (subfield)

Methods: Statistics

Keywords: X-linked dystonia-parkinsonism, iPSC, cortical neurons, transcriptome analysis, DNA damage

MeSH: Down-Regulation*, Dystonic Disorders*, Genetic Diseases, X-Linked*, Mitochondria*, Neurons*, DNA Damage, Histone Acetyltransferases, Humans, Mutation, TATA-Binding Protein Associated Factors, Transcription Factor TFIID, Transcriptome (* major topic)

Topic: Neurological disorders and treatments (Neurology, Medicine), according to OpenAlex

Funding: German Research Foundation (FOR2488); Universität zu Lübeck; Federal Ministry of Education and Research Bonn Office (FKZ 01KD2103A)

Citations: not cited yet (Europe PMC); 30 references in the paper

Research resources: Rat monoclonal anti-CTIP2 RRID:AB_2064130, Rabbit polyclonal anti-Tbr1 RRID:AB_2200219, Mouse monoclonal anti-TUJ1 RRID:AB_2313773, Rabbit polyclonal anti-vGlut1 RRID:AB_887875, Mouse monoclonal anti-MAP2 RRID:AB_94856

Abstract

The genetic mechanism underlying the neurodegenerative movement disorder X-linked dystonia-parkinsonism (XDP) involves a retrotransposon insertion within the TAF1 gene. TAF1 encodes the TATA-box binding protein-associated factor 1, the largest subunit of the basal transcription factor TFIID, which connects transcription activation to the assembly of the RNA polymerase II preinitiation complex at the core promoter of genes. This study investigated how the TAF1 mutation affects the transcriptomes of XDP patient-derived neurons under basal conditions and in response to mitochondrial toxins. Gene set enrichment analysis revealed that, under basal conditions, patient-derived neurons exhibited predominantly upregulated pathways compared to controls. However, exposure to mitochondrial toxins induced a global shift toward downregulation of pathways in XDP neurons, affecting genome maintenance, epigenetic regulation, adaptive neuronal function, and transcription. Our findings suggest that neurons from XDP patients are more susceptible to mitochondrial stress than controls, leading to widespread transcriptomic downregulation and increased DNA damage.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above.

COMBINE-lab/Salmon

License: BSD-3-Clause

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: ed926b8f6120c592ba13e696fe24732004ee0132, 25 September 2026

Languages: Rust (88), Shell (4), TypeScript (1)

Size: 176 files, 93 scripts

Software Heritage: not archived

Found in: the resources table

Holds: README, license file, environment (Dockerfile), tests, continuous integration, documentation

Not found: CITATION.cff

Availability: 1 check, the latest on 27 September 2026: the link answers

27 September 2026: the link answers

95 files

crates/salmon-align/examples/replicate_bam.rs, Rust, 38 lines
crates/salmon-align/src/bam_rad.rs, Rust, 900 lines
crates/salmon-align/src/error_model.rs, Rust, 654 lines
crates/salmon-align/src/genome_project.rs, Rust, 751 lines
crates/salmon-align/src/lib.rs, Rust, 3,526 lines
crates/salmon-align/src/rad.rs, Rust, 2,660 lines
crates/salmon-align/tests/alignment_bias.rs, Rust, 80 lines
crates/salmon-align/tests/bootstrap_output.rs, Rust, 133 lines
crates/salmon-align/tests/deterministic_bam.rs, Rust, 577 lines
crates/salmon-align/tests/output_contract.rs, Rust, 199 lines
crates/salmon-align/tests/rad_input.rs, Rust, 1,278 lines
crates/salmon-align/tests/rad_lib_format_counts.rs, Rust, 293 lines
crates/salmon-align/tests/stranded_num_mapped.rs, Rust, 297 lines
crates/salmon-cli/examples/cache_bench.rs, Rust, 51 lines
crates/salmon-cli/src/global_alloc.rs, Rust, 31 lines
crates/salmon-cli/src/main.rs, Rust, 3,757 lines
crates/salmon-cli/tests/decoy_bias.rs, Rust, 144 lines
crates/salmon-cli/tests/deterministic_default.rs, Rust, 152 lines
crates/salmon-cli/tests/deterministic_skip_quant.rs, Rust, 196 lines
crates/salmon-cli/tests/dump_eq_deterministic.rs, Rust, 224 lines
crates/salmon-cli/tests/flag_matrix.rs, Rust, 241 lines
crates/salmon-cli/tests/input_validation.rs, Rust, 683 lines
crates/salmon-cli/tests/metadata_truth.rs, Rust, 408 lines
crates/salmon-cli/tests/mode_applicability.rs, Rust, 332 lines
crates/salmon-cli/tests/output_contract.rs, Rust, 166 lines
crates/salmon-cli/tests/readiness_blockers.rs, Rust, 226 lines
crates/salmon-core/src/atomic.rs, Rust, 89 lines
crates/salmon-core/src/compress.rs, Rust, 200 lines
crates/salmon-core/src/diagnostics.rs, Rust, 260 lines
crates/salmon-core/src/error.rs, Rust, 42 lines
crates/salmon-core/src/genemap.rs, Rust, 762 lines
crates/salmon-core/src/lib.rs, Rust, 224 lines
crates/salmon-core/src/libtype.rs, Rust, 833 lines
crates/salmon-core/src/mate.rs, Rust, 47 lines
crates/salmon-core/src/math.rs, Rust, 151 lines
crates/salmon-core/src/progress.rs, Rust, 25 lines
crates/salmon-core/src/quantmerge.rs, Rust, 207 lines
crates/salmon-core/src/refprovider.rs, Rust, 36 lines
crates/salmon-core/src/timing.rs, Rust, 57 lines
crates/salmon-eqclass/src/lib.rs, Rust, 894 lines
crates/salmon-index/src/lib.rs, Rust, 1,661 lines
crates/salmon-infer/benches/em_step.rs, Rust, 207 lines
crates/salmon-infer/src/daarem.rs, Rust, 874 lines
crates/salmon-infer/src/lib.rs, Rust, 1,329 lines
crates/salmon-infer/src/online.rs, Rust, 242 lines
crates/salmon-infer/src/packed.rs, Rust, 1,262 lines
crates/salmon-infer/src/uncertainty.rs, Rust, 583 lines
crates/salmon-map/benches/align.rs, Rust, 110 lines
crates/salmon-map/examples/dump_txome.rs, Rust, 33 lines
crates/salmon-map/examples/trace_pair.rs, Rust, 83 lines
crates/salmon-map/examples/trace_reads.rs, Rust, 190 lines
crates/salmon-map/src/align.rs, Rust, 1,144 lines
crates/salmon-map/src/chain.rs, Rust, 567 lines
crates/salmon-map/src/collect.rs, Rust, 397 lines
crates/salmon-map/src/extend.rs, Rust, 628 lines
crates/salmon-map/src/lib.rs, Rust, 82 lines
crates/salmon-map/src/mapper.rs, Rust, 782 lines
crates/salmon-map/src/mem.rs, Rust, 138 lines
crates/salmon-map/src/pair.rs, Rust, 772 lines
crates/salmon-map/src/score.rs, Rust, 720 lines
crates/salmon-map/src/sketch.rs, Rust, 379 lines
crates/salmon-map/tests/collect_on_index.rs, Rust, 441 lines
crates/salmon-model/examples/conv_bench.rs, Rust, 123 lines
crates/salmon-model/src/bias.rs, Rust, 509 lines
crates/salmon-model/src/dumps.rs, Rust, 209 lines
crates/salmon-model/src/fld.rs, Rust, 830 lines
crates/salmon-model/src/gcbias.rs, Rust, 849 lines
crates/salmon-model/src/lib.rs, Rust, 78 lines
crates/salmon-model/src/libdetect.rs, Rust, 408 lines
crates/salmon-model/src/posbias.rs, Rust, 340 lines
crates/salmon-model/src/seqbias.rs, Rust, 1,168 lines
crates/salmon-model/src/spline.rs, Rust, 342 lines
crates/salmon-quant/src/bam.rs, Rust, 558 lines
crates/salmon-quant/src/decode.rs, Rust, 405 lines
crates/salmon-quant/src/lib.rs, Rust, 1,488 lines
crates/salmon-quant/src/mapping_record.rs, Rust, 451 lines
crates/salmon-quant/src/output.rs, Rust, 608 lines
crates/salmon-quant/src/processor.rs, Rust, 1,723 lines
crates/salmon-quant/src/sam.rs, Rust, 139 lines
crates/salmon-quant/tests/bgzf_worker_count.rs, Rust, 64 lines
crates/salmon-quant/tests/decoder_per_file.rs, Rust, 163 lines
crates/salmon-quant/tests/pool_resize_flush_safety.rs, Rust, 263 lines
crates/salmon-quant/tests/quant_end_to_end.rs, Rust, 1,320 lines
crates/salmon-rad/src/lib.rs, Rust, 665 lines
crates/salmon-rad/src/record.rs, Rust, 198 lines
crates/salmon-rad/src/schema.rs, Rust, 201 lines
crates/salmon-rad/src/writer.rs, Rust, 414 lines
crates/salmon-rad/tests/roundtrip.rs, Rust, 527 lines
scripts/bench_em_rad.sh, Shell, 131 lines
scripts/bump_and_publish.sh, Shell, 212 lines
scripts/decode_crossover.sh, Shell, 159 lines
scripts/profile.sh, Shell, 106 lines
website/src/content.config.ts, TypeScript, 7 lines
LICENSE, License, 28 lines
README.md, Text, 99 lines

At the source: github.com/COMBINE-lab/Salmon

pachterlab/sleuth

License: GPL-3.0

State: the link answers, verified on 28 September 2026

Evidence: files inventoried

Commit: 15457c45697bf9c4e0b593c2a9e187c3bb6a5cb3, 28 May 2025

Languages: R (22), Shell (1), Python (1)

Size: 105 files, 24 scripts

Software Heritage: archived

Found in: the resources table

Holds: README, license file, environment (DESCRIPTION), tests, documentation, 1 notebook

Not found: CITATION.cff, continuous integration

Tools: tidyverse (15 files), data.table (10 files), reshape2 (2 files), ggplot2 (1 file), pheatmap (1 file)

Availability: 1 check, the latest on 28 September 2026: the link answers

28 September 2026: the link answers

26 files

R/bootstrap.R, R, 525 lines
R/gene_analysis.R, R, 29 lines
R/hexamers.R, R, 4,097 lines
R/import.R, R, 24 lines
R/kallisto.R, R, 178 lines
R/likelihood.R, R, 114 lines
R/matrix.R, R, 61 lines
R/measurement_error.R, R, 583 lines
R/misc.R, R, 206 lines
R/model.R, R, 550 lines
R/plots.R, R, 1,095 lines
R/read_write.R, R, 455 lines
R/shiny.R, R, 2,106 lines
R/sleuth.R, R, 1,306 lines
R/units.R, R, 52 lines
inst/scripts/gen_hexamers.sh, Shell, 5 lines
inst/scripts/hexamers.py, Python, 3 lines
tests/testthat.R, R, 4 lines
tests/testthat/helper-setup.R, R, 31 lines
tests/testthat/test-analysis.R, R, 33 lines
tests/testthat/test-lintr.R, R, 6 lines
tests/testthat/test-prep.R, R, 65 lines
tests/testthat/test-read.R, R, 71 lines
vignettes/intro.Rmd, R, 230 lines
LICENSE, License, 621 lines
README.md, Text, 74 lines

At the source: github.com/pachterlab/sleuth

datapplab/gage

License: none: the authors keep all their rights

State: the link answers, verified on 28 September 2026

Evidence: files inventoried

Commit: d99df9a469281bb763888db97df56b0d0b41bbc5, 27 August 2022

Languages: R (32)

Size: 70 files, 32 scripts

Software Heritage: archived

Found in: the resources table

Holds: README, environment (DESCRIPTION), documentation

Not found: license file, CITATION.cff, tests, continuous integration

Availability: 1 check, the latest on 28 September 2026: the link answers

28 September 2026: the link answers

33 files

R/colorpanel.R, R, 35 lines
R/deComp.R, R, 80 lines
R/eg2sym.R, R, 3 lines
R/essGene.R, R, 34 lines
R/esset.grp.R, R, 160 lines
R/gage-internal.R, R, 126 lines
R/gage.R, R, 23 lines
R/gageComp.R, R, 49 lines
R/gagePipe.R, R, 176 lines
R/gagePrep.R, R, 94 lines
R/gageSum.R, R, 88 lines
R/geneData.R, R, 109 lines
R/go.gsets.R, R, 58 lines
R/greenred.R, R, 3 lines
R/gs.KSTest.R, R, 66 lines
R/gs.heatmap.R, R, 33 lines
R/gs.tTest.R, R, 63 lines
R/gs.zTest.R, R, 59 lines
R/heatmap2.R, R, 344 lines
R/heter.gage.R, R, 9 lines
R/invalid.R, R, 10 lines
R/kegg.gsets.R, R, 56 lines
R/kegg.species.code.R, R, 34 lines
R/odd.R, R, 2 lines
R/pairData.R, R, 50 lines
R/readExpData.R, R, 3 lines
R/readList.R, R, 8 lines
R/rownorm.R, R, 7 lines
R/sigGeneSet.R, R, 94 lines
R/sym2eg.R, R, 3 lines
R/vennCounts.R, R, 22 lines
R/vennDiagram2.R, R, 92 lines
README.md, Text, 65 lines

At the source: github.com/datapplab/gage

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

3 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
149 scripts, each with its path and the digest of its content;
no match between paragraphs and code yet;
neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

geo:GSE300875, at NCBI GEO; found in “Data and code availability”

Data and code availability

RNA-seq data have been deposited at GEO: GSE300875 (https://ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE300875) and are publicly available as of the date of publication. All other data will be shared with the research community upon reasonable request.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 2, 28 September 2026

Authors: added Philip Seibler (0000-0002-3496-7194); removed Philip Seibler

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 12 authors, 5 keywords, 12 MeSH terms, 3 funders, 29 references, 5 RRIDs.

Cite

This paper

Grütz, K., Künstner, A., Krause, C., Santinelli, L., Franzenburg, S., Ghelfi, J., Grünewald, A., Rosales, R. L., Brüggemann, N., Busch, H., Klein, C., & Seibler, P. (2026). Mitochondrial toxins cause widespread downregulation of pathways in X-linked dystonia-parkinsonism patient-derived neurons. Stem cell reports, 21(6), 102920. https://doi.org/10.1016/j.stemcr.2026.102920

BibTeX

@article{grutz2026mitochondrial, author = {Grütz, Karen and Künstner, Axel and Krause, Christin and Santinelli, Letizia and Franzenburg, Sören and Ghelfi, Jenny and Grünewald, Anne and Rosales, Raymond L and Brüggemann, Norbert and Busch, Hauke and Klein, Christine and Seibler, Philip}, title = {{Mitochondrial toxins cause widespread downregulation of pathways in X-linked dystonia-parkinsonism patient-derived neurons}}, journal = {Stem cell reports}, year = {2026}, month = may, volume = {21}, number = {6}, pages = {102920}, publisher = {Elsevier}, issn = {2213-6711}, doi = {10.1016/j.stemcr.2026.102920}, url = {https://doi.org/10.1016/j.stemcr.2026.102920}, pmid = {42102821}, pmcid = {PMC13261877} }

RIS

TY - JOUR AU - Grütz, Karen AU - Künstner, Axel AU - Krause, Christin AU - Santinelli, Letizia AU - Franzenburg, Sören AU - Ghelfi, Jenny AU - Grünewald, Anne AU - Rosales, Raymond L AU - Brüggemann, Norbert AU - Busch, Hauke AU - Klein, Christine AU - Seibler, Philip TI - Mitochondrial toxins cause widespread downregulation of pathways in X-linked dystonia-parkinsonism patient-derived neurons T2 - Stem cell reports J2 - Stem Cell Reports PY - 2026 DA - 2026/05/07 VL - 21 IS - 6 SP - 102920 SN - 2213-6711 PB - Elsevier DO - 10.1016/j.stemcr.2026.102920 UR - https://doi.org/10.1016/j.stemcr.2026.102920 LA - en ER -

CSL-JSON

{ "id": "10.1016/j.stemcr.2026.102920", "type": "article-journal", "title": "Mitochondrial toxins cause widespread downregulation of pathways in X-linked dystonia-parkinsonism patient-derived neurons", "container-title": "Stem cell reports", "author": [ { "family": "Grütz", "given": "Karen" }, { "family": "Künstner", "given": "Axel" }, { "family": "Krause", "given": "Christin" }, { "family": "Santinelli", "given": "Letizia" }, { "family": "Franzenburg", "given": "Sören" }, { "family": "Ghelfi", "given": "Jenny" }, { "family": "Grünewald", "given": "Anne" }, { "family": "Rosales", "given": "Raymond L" }, { "family": "Brüggemann", "given": "Norbert" }, { "family": "Busch", "given": "Hauke" }, { "family": "Klein", "given": "Christine" }, { "family": "Seibler", "given": "Philip" } ], "container-title-short": "Stem Cell Reports", "volume": "21", "issue": "6", "page": "102920", "DOI": "10.1016/j.stemcr.2026.102920", "PMID": "42102821", "PMCID": "PMC13261877", "ISSN": "2213-6711", "publisher": "Elsevier", "URL": "https://doi.org/10.1016/j.stemcr.2026.102920", "language": "en", "issued": { "date-parts": [ [ 2026, 5, 7 ] ] } }

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Mitochondrial toxins cause widespread downregulation of pathways in X-linked dystonia-parkinsonism patient-derived neurons.

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