Spatial Multi-Omics Workflow and Analytical Guidelines for Alzheimer's Neuropathology
Xuehan Sun, Hannah R Hudson, Timothy C Orr, Srinivas Koutarapu, Alyssa Rosenbloom, Matthew Ingalls, Oliver Braubach, C Dirk Keene et al.. bioRxiv : the preprint server for biology, 2025-11-17
Topic: Genetics and APOE
Spatial biology technologies enable high-dimensional profiling within intact tissues, revealing how molecular and cellular organization drives function and disease. As these platforms gain broader adoption, standardized analytical frameworks are needed to ensure data quality and reproducibility. Here, we present an end-to-end pipeline for the GeoMx Digital Spatial Profiler that simultaneously generates whole-transcriptome and 637-protein measurements from user-defined regions within the same tissue sections. The workflow integrates morphology-guided region selection, quality control, normalization, and multi-modal data interpretation. Applied to formalin-fixed cortical tissues from Alzheimer's disease, dementia with Lewy bodies, amyotrophic lateral sclerosis, and controls, the framework resolves spatially distinct molecular domains. Transcript and protein signals diverge across amyloid plaque cores and surrounding glial-rich regions, with RNA-protein concordance varying by disease condition, while single-neuron profiling with and without pathogenic tau deposition illustrates protein assay sensitivity. This dataset provides a rigorously validated resource for spatial multi-omic analyses and establishes broadly applicable guidelines for reliable, reproducible profiling of complex tissues.
Key findings
- Here, we present an end-to-end pipeline for the GeoMx Digital Spatial Profiler that simultaneously generates whole-transcriptome and 637-protein measurements from user-defined regions within the same tissue sections.
- The workflow integrates morphology-guided region selection, quality control, normalization, and multi-modal data interpretation.
- Applied to formalin-fixed cortical tissues from Alzheimer's disease, dementia with Lewy bodies, amyotrophic lateral sclerosis, and controls, the framework resolves spatially distinct molecular domains.
- Transcript and protein signals diverge across amyloid plaque cores and surrounding glial-rich regions, with RNA-protein concordance varying by disease condition, while single-neuron profiling with and without pathogenic tau deposition illustrates protein assay sensitivity.
- This dataset provides a rigorously validated resource for spatial multi-omic analyses and establishes broadly applicable guidelines for reliable, reproducible profiling of complex tissues.
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Study details
- Evidence strengthLow
How this study scored 16/100
Preprint — not yet peer-reviewed. It scored 22 on the same rubric, but non-peer-reviewed sources are capped at 16, so it shows as 16. Scored zero for study design, sample size, effect reported, studied in people and randomised / blinded because the record does not state it. We have no data on times cited, citations per year, impact for its field and year, cited by studies here, still being cited, senior author's track record, institution's track record, multi-centre collaboration and free to read, so those were left out: it earned 13 of the 60 points we could judge it on, which is 22 out of 100.
| Component | Points | Why |
|---|---|---|
| Journal tier | 2 / 10 | Tier 4 — not a peer-reviewed journal (bioRxiv : the preprint server for biology) |
| Journal's citation record | 0 / 4 | Not a journal article, so the journal's record does not count |
| Study design | 0 / 12 | No study design recorded — scores zero, not guessed (not stated in the record — scored 0) |
| Strength of evidence | 1 / 5 | Rated “low” in our summary |
| Peer-review validation | 4 / 10 | Preprint — not yet peer-reviewed. Hosted on a preprint server. |
| How recent | 4 / 5 | 2025 — within 3 year(s) of the newest study here |
| Sample size | 0 / 4 | Participant count not stated — scores zero (not stated in the record — scored 0) |
| Effect reported | 0 / 3 | No effect size reported — scores zero (not stated in the record — scored 0) |
| Studied in people | 0 / 3 | Not stated whether this was studied in people — scores zero (not stated in the record — scored 0) |
| Randomised / blinded | 0 / 2 | No randomisation or blinding stated — scores zero (not stated in the record — scored 0) |
| Times cited | — / 7 | No citation count (not found in OpenAlex) — left out of this score |
| Citations per year | — / 5 | No citation count or no year — left out of this score |
| Impact for its field and year | — / 6 | No field-weighted citation impact (OpenAlex has none yet) — left out of this score |
| Cited by studies here | — / 6 | Not yet checked against this library's citation graph — left out of this score |
| Still being cited | — / 4 | No yearly citation counts — left out of this score |
| Senior author's track record | — / 4 | Senior author's record not available — left out of this score |
| Institution's track record | — / 3 | No institution listed in OpenAlex — left out of this score |
| Multi-centre collaboration | — / 3 | Institutions not listed — left out of this score |
| Indexed in PubMed | 2 / 2 | Indexed in PubMed (PMID 41332529) |
| Free to read | — / 2 | Access not recorded — left out of this score |
| Points | 13 / 60 | Scored on 11 of 20 parts. We have no data for the rest, so they are left out: 13 of the 60 points we could judge it on is 22 out of 100. |
| Total | 22 / 100 | Capped to 16 because this is not a peer-reviewed article. |
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APA 7th
Sun, X., Hudson, H. R., Orr, T. C., Koutarapu, S., Rosenbloom, A., Ingalls, M., et al. (2025). Spatial Multi-Omics Workflow and Analytical Guidelines for Alzheimer's Neuropathology. bioRxiv : the preprint server for biology. https://doi.org/10.1101/2025.11.16.688710
Vancouver
Sun X, Hudson HR, Orr TC, Koutarapu S, Rosenbloom A, Ingalls M, et al. Spatial Multi-Omics Workflow and Analytical Guidelines for Alzheimer's Neuropathology. bioRxiv : the preprint server for biology. 2025. doi:10.1101/2025.11.16.688710. PMID: 41332529.
BibTeX
@article{sun2025-41332529,
author = {Sun, Xuehan and Hudson, Hannah R and Orr, Timothy C and Koutarapu, Srinivas and Rosenbloom, Alyssa and Ingalls, Matthew and Braubach, Oliver and Keene, C Dirk and others},
title = {{Spatial Multi-Omics Workflow and Analytical Guidelines for Alzheimer's Neuropathology}},
journal = {bioRxiv : the preprint server for biology},
year = {2025},
doi = {10.1101/2025.11.16.688710},
pmid = {41332529},
url = {https://doi.org/10.1101/2025.11.16.688710}
}