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Ecological specialization and constrained evolution shape virulence diversity in zoonotic pathogen L. interrogans

GSE330072 Homo sapiens (human) RNA-seq (gene expression) 42 samples Submitted 2026/06/25 Platform GPL34290Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 42 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
42 samples: 20 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Summary (written by the submitters)
Host specialization is central to the emergence of zoonotic pathogens, yet mechanisms shaping bacterial adaptation across diverse hosts remain poorly understood. Leptospira interrogans circulates among an exceptionally broad range of reservoirs, but only serogroup Icterohaemorrhagiae dominates the global burden of human leptospirosis, raising fundamental questions about its ecological and pathogenic success.
Read the full summary ↓
Here, we integrate a global genomic dataset to dissect host adaptation in L. interrogans. Population genomic analyses reveal that serogroups Icterohaemorrhagiae and Pomona dominate worldwide and display signatures of ecological specialization. These serogroups have followed distinct evolutionary trajectories that are central to host specialization, characterized by extensive divergence in membrane and signaling genes, together with the acquisition of specialized functional repertoires linked to host adaptation. Transcriptomic and proteomic profiling demonstrate that these genomic differences are coupled to distinct regulatory programs, predominantly affecting virulence and stress response. Altogether, these findings demonstrate that intraspecies heterogeneity in L. interrogans emerges from the convergence of genomic constraint, membrane remodeling and regulatory divergence, shaping host specialization and zoonotic pathogenicity.
This dataset
Open GSE330072 in finder → Find more RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE330072_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1462694 and SRA study SRP697947. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
20 conditions, mostly in duplicate
Human macrophages, Uninfected, 6 hr, ×3 Murine macrophages, Uninfected, 6 hr, ×3 Human macrophages, Infected L. interrogans Ic… ×2 Human macrophages, Infected L. interrogans Ic… ×2 Human macrophages, Infected L. interrogans Ic… ×2 Human macrophages, Infected L. interrogans Ic… ×2 Human macrophages, Infected L. interrogans Ic… ×2 Human macrophages, Infected L. interrogans Po… ×2 +12 more

Supports a between-group comparison across 42 samples.

How we read this: 20 replicated groups read from 42 sample titles; they account for 42 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 2 more — browse all 42 samples with per-sample file links →

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