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Low-intensity pulsed ultrasound promotes peripheral nerve regeneration by alleviating Schwann cells pyroptosis.

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Paper

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The authors' code

R · 141 lines · 3.6 KB · no license

  1. library(DESeq2)
  2. library(dplyr)
  3. library(ggplot2)
  4. library(ggrepel)
  5. library(pheatmap)
  6. library(clusterProfiler)
  7. library(org.Rn.eg.db)
  8. library(enrichplot)
  9. library(tibble)
  11. data[is.na(data)] <- 0
  13. group <- factor(c(rep("C", 3), rep("T", ncol(data) - 3)), levels = c("C", "T"))
  14. counts <- data
  16. conditions <- data.frame(
  17. sample = colnames(counts),
  18. group = group
  19. ) %>%
  20. column_to_rownames("sample")
  22. dds <- DESeqDataSetFromMatrix(
  23. countData = counts,
  24. colData = conditions,
  25. design = ~ group
  26. )
  28. dds <- DESeq(dds, betaPrior = TRUE)
  29. res <- results(dds, contrast = c("group", "T", "C"))
  30. res$padj <- p.adjust(res$pvalue, method = "BH")
  31. res_df <- as.data.frame(res)
  33. sig_res <- res_df %>%
  34. filter(pvalue < 0.05, abs(log2FoldChange) > 0.5)
  36. up_genes <- rownames(res_df)[res_df$pvalue < 0.05 & res_df$log2FoldChange > 0.5]
  37. down_genes <- rownames(res_df)[res_df$pvalue < 0.05 & res_df$log2FoldChange < -0.5]
  39. write.csv(res_df[res_df$pvalue < 0.05, ], "diffgene_sig.csv", row.names = TRUE)
  40. write.csv(res_df, "gene_all.csv", row.names = TRUE)
  41. write.csv(sig_res, "gene.csv", row.names = TRUE)
  43. res_df <- res_df %>%
  44. mutate(
  45. gene = rownames(.),
  46. neg_log10_p = -log10(pvalue),
  47. category = case_when(
  48. pvalue < 0.05 & log2FoldChange > 0.5 ~ "Upregulated",
  49. pvalue < 0.05 & log2FoldChange < -0.5 ~ "Downregulated",
  50. TRUE ~ "Not significant"
  51. )
  52. )
  54. genes_to_label <- res_df %>%
  55. filter(pvalue < 0.05, abs(log2FoldChange) > 0.5) %>%
  56. arrange(desc(neg_log10_p)) %>%
  57. head(15)
  59. ggplot(res_df, aes(log2FoldChange, neg_log10_p, color = category)) +
  60. geom_point(alpha = 0.8, size = 2) +
  61. geom_hline(yintercept = -log10(0.05), linetype = "dashed", color = "black") +
  62. geom_vline(xintercept = c(-0.5, 0.5), linetype = "dashed", color = "black") +
  63. geom_text_repel(
  64. data = genes_to_label,
  65. aes(label = gene),
  66. size = 3,
  67. box.padding = 0.3,
  68. point.padding = 0.5,
  69. max.overlaps = 10
  70. ) +
  71. scale_color_manual(values = c(
  72. "Upregulated" = "#d1979e",
  73. "Downregulated" = "#a5c3d4",
  74. "Not significant" = "gray"
  75. )) +
  76. theme_minimal() +
  77. labs(
  78. title = "Volcano Plot",
  79. x = "log2(Fold Change)",
  80. y = "-log10(p-value)"
  81. ) +
  82. theme(
  83. legend.title = element_blank(),
  84. legend.position = "top"
  85. )
  87. sig_gene_names <- rownames(sig_res)
  88. heatmap_data <- data[sig_gene_names, ]
  90. heatmap_data_scaled <- t(scale(t(heatmap_data)))
  92. annotation_col <- data.frame(Group = group)
  93. rownames(annotation_col) <- colnames(heatmap_data_scaled)
  95. heatmap_colors <- colorRampPalette(c("#a5c3d4", "white", "#d1979e"))(50)
  97. pheatmap(
  98. heatmap_data_scaled,
  99. cluster_rows = TRUE,
  100. cluster_cols = TRUE,
  101. annotation_col = annotation_col,
  102. show_rownames = FALSE,
  103. show_colnames = TRUE,
  104. fontsize_row = 8,
  105. fontsize_col = 10,
  106. color = heatmap_colors,
  107. main = "Heatmap of Differentially Expressed Genes"
  108. )
  110. gene_list <- down_genes
  112. gene_entrez_ids <- bitr(
  113. gene_list,
  114. fromType = "SYMBOL",
  115. toType = "ENTREZID",
  116. OrgDb = org.Rn.eg.db
  117. )
  119. go_results <- enrichGO(
  120. gene = gene_entrez_ids$ENTREZID,
  121. OrgDb = org.Rn.eg.db,
  122. keyType = "ENTREZID",
  123. ont = "BP",
  124. pvalueCutoff = 0.05,
  125. pAdjustMethod = "BH",
  126. qvalueCutoff = 0.2,
  127. minGSSize = 10,
  128. maxGSSize = 500,
  129. readable = TRUE
  130. )
  132. write.csv(as.data.frame(go_results), "GO.csv", row.names = TRUE)
  134. dotplot(go_results, showCategory = 10) + ggtitle("GO Enrichment: Biological Process")
  135. barplot(go_results, showCategory = 10, title = "Top 10 GO Terms")
  136. emapplot(pairwise_termsim(go_results), showCategory = 15)
  138. pdf("ctrl_vs_hurt_downgene_GO.pdf", width = 10, height = 8)
  139. print(dotplot(go_results, showCategory = 10) + ggtitle("GO Enrichment: Biological Process"))
  140. print(barplot(go_results, showCategory = 10, title = "Top 10 GO Terms"))
  141. dev.off()

Fig4b-e.R at commit 1a234c5, no license · at the source

Overview

Authors: Junfeng Chen1,2, Lu Yu1,2, Yansong Lu1,2, Yufei Zhang1,2, Cheng-kung Cheng1,2, Yifei Yao1,2
ORCID iDs: Lu Yu, Yifei Yao
  1. School of Biomedical Engineering, Shanghai Jiao Tong University,Shanghai, China
  2. Engineering Research Center of Digital Medicine of the Ministry of Education, Shanghai Jiao Tong University,Shanghai, China
Institutions: Shanghai Jiao Tong University (China)
Journal: Communications biology, volume 9, issue 1, article 914
Dates: received 25 October 2025; accepted 21 April 2026; published online 2 May 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s42003-026-10160-9 · PMID 42069902 · PMCID PMC13342520 · OpenAlex W7159965595
Open access: gold, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: other (modality), rat (organism), other condition (population), cellular / molecular (subfield)
Methods: Preprocessing, Statistics
Keywords: Regeneration and repair in the nervous system, Cell death, Peripheral neuropathies
MeSH: Nerve Regeneration*, Peripheral Nerve Injuries*, Pyroptosis*, Schwann Cells*, Ultrasonic Therapy*, Ultrasonic Waves*, Animals, Axons, Male, Rats, Rats, Sprague-Dawley, Recovery of Function, Sciatic Nerve (* major topic)
Topic: Nerve injury and regeneration (Cellular and Molecular Neuroscience, Neuroscience), according to OpenAlex
Funding: National Natural Science Foundation of China (NO. 32201067)
Citations: not cited yet (Europe PMC); 67 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

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

chen-jf-96/nerve

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: 1a234c55781034368fdae6d5d0dd584490b9b73e, 12 April 2026
Languages: R (1)
Size: 1 file, 1 script
Software Heritage: not archived
Found in: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: clusterProfiler (1 file), DESeq2 (1 file), ggplot2 (1 file), pheatmap (1 file), tidyverse (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
1 file
At the source: github.com/chen-jf-96/nerve

Code availability statement

The paper has a code availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1038/s42003-026-10160-9.

Tracing map

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Data

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Data availability statement

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  • it says that the data are available on request

Read it in the paper: doi.org/10.1038/s42003-026-10160-9.

Versions

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Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 3 keywords, 13 MeSH terms, 1 funder, 67 references.

Cite

This paper

Chen, J., Yu, L., Lu, Y., Zhang, Y., Cheng, C.-k., & Yao, Y. (2026). Low-intensity pulsed ultrasound promotes peripheral nerve regeneration by alleviating Schwann cells pyroptosis. Communications biology, 9(1), 914. https://doi.org/10.1038/s42003-026-10160-9

BibTeX

@article{chen2026low,
author = {Chen, Junfeng and Yu, Lu and Lu, Yansong and Zhang, Yufei and Cheng, Cheng-kung and Yao, Yifei},
title = {{Low-intensity pulsed ultrasound promotes peripheral nerve regeneration by alleviating Schwann cells pyroptosis}},
journal = {Communications biology},
year = {2026},
month = may,
volume = {9},
number = {1},
pages = {914},
publisher = {Nature Publishing Group},
issn = {2399-3642},
doi = {10.1038/s42003-026-10160-9},
url = {https://doi.org/10.1038/s42003-026-10160-9},
pmid = {42069902},
pmcid = {PMC13342520}
}

RIS

TY - JOUR
AU - Chen, Junfeng
AU - Yu, Lu
AU - Lu, Yansong
AU - Zhang, Yufei
AU - Cheng, Cheng-kung
AU - Yao, Yifei
TI - Low-intensity pulsed ultrasound promotes peripheral nerve regeneration by alleviating Schwann cells pyroptosis
T2 - Communications biology
J2 - Commun Biol
PY - 2026
DA - 2026/05/02
VL - 9
IS - 1
SP - 914
SN - 2399-3642
PB - Nature Publishing Group
DO - 10.1038/s42003-026-10160-9
UR - https://doi.org/10.1038/s42003-026-10160-9
LA - en
ER -

CSL-JSON

{
"id": "10.1038/s42003-026-10160-9",
"type": "article-journal",
"title": "Low-intensity pulsed ultrasound promotes peripheral nerve regeneration by alleviating Schwann cells pyroptosis",
"container-title": "Communications biology",
"author": [
{
"family": "Chen",
"given": "Junfeng"
},
{
"family": "Yu",
"given": "Lu"
},
{
"family": "Lu",
"given": "Yansong"
},
{
"family": "Zhang",
"given": "Yufei"
},
{
"family": "Cheng",
"given": "Cheng-kung"
},
{
"family": "Yao",
"given": "Yifei"
}
],
"container-title-short": "Commun Biol",
"volume": "9",
"issue": "1",
"page": "914",
"DOI": "10.1038/s42003-026-10160-9",
"PMID": "42069902",
"PMCID": "PMC13342520",
"ISSN": "2399-3642",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s42003-026-10160-9",
"language": "en",
"issued": {
"date-parts": [
[
2026,
5,
2
]
]
}
}

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