Deciphering the three-dimensional biomolecular distribution in the Alzheimer's disease brain: A multiomic approach integrating immunohistochemistry with MALDI MS imaging

Kelly H Lu; Hua Zhang; Gargey B Yagnik; Mark J Lim; Kenneth J Rothschild; Wei Li; Andrew J Schneider; Luigi Puglielli; Lingjun Li

doi:10.1016/j.aca.2025.344721

Deciphering the three-dimensional biomolecular distribution in the Alzheimer's disease brain: A multiomic approach integrating immunohistochemistry with MALDI MS imaging

Anal Chim Acta. 2025 Dec 15:1379:344721. doi: 10.1016/j.aca.2025.344721. Epub 2025 Sep 28.

Authors

Kelly H Lu¹, Hua Zhang², Gargey B Yagnik³, Mark J Lim³, Kenneth J Rothschild⁴, Wei Li², Andrew J Schneider⁵, Luigi Puglielli⁵, Lingjun Li⁶

Affiliations

¹ Department of Chemistry, University of Wisconsin-Madison, WI, 53706, USA.
² School of Pharmacy, University of Wisconsin-Madison, WI, 53705, USA.
³ AmberGen Inc., Billerica, MA, 01821, USA.
⁴ AmberGen Inc., Billerica, MA, 01821, USA; Department of Physics and Photonics Center, Boston University, Boston, MA, 02215, USA.
⁵ Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA; Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.
⁶ Department of Chemistry, University of Wisconsin-Madison, WI, 53706, USA; School of Pharmacy, University of Wisconsin-Madison, WI, 53705, USA; Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA; Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA. Electronic address: lingjun.li@wisc.edu.

PMID: 41167884
DOI: 10.1016/j.aca.2025.344721

Abstract

Alzheimer's disease (AD) is characterized by complex and distinct spatial and molecular changes in the brain that contribute to its onset and progression, which includes disruptions in proteins, lipids, and neuroinflammatory pathways. In this study, we introduce a three-dimensional (3D) spatial multi-omics imaging approach that integrates lipid mass spectrometry imaging (MSI) with targeted proteomic analysis using 10-plex photo-cleavable mass tag (PC-MT) probes. Brain tissues from wild-type (WT) and AD model mice were sectioned at four coronal levels, spaced 1500 μm apart, enabling the reconstruction of a depth-resolved molecular atlas. Lipid MSI revealed region- and depth-specific alterations in phosphatidylcholine (PC), phosphatidylethanolamine (PE), and other lipid classes between AD and WT brains. In parallel, protein MSI using PC-MT probes identified spatially distinct changes in neuroinflammatory and neurodegenerative markers across the cortex, hippocampus, and thalamus at different depths. This integrative platform uncovered co-localization patterns of lipid dysregulation and protein overexpression unique to AD pathology, highlighting vulnerable brain subregions. Our findings demonstrate that combining targeted protein and untargeted lipid imaging in 3D enables the discovery of spatially coordinated molecular signatures in neurodegeneration, offering a powerful framework for biomarker discovery and therapeutic development.

Keywords: Alzheimer's disease; MALDI-IHC-MSI; Mass spectrometry imaging; Multiomic MSI; Multiplex protein MSI; Three-dimensional MALDI MSI.

MeSH terms

Alzheimer Disease* / diagnostic imaging
Alzheimer Disease* / metabolism
Alzheimer Disease* / pathology
Animals
Brain* / diagnostic imaging
Brain* / metabolism
Brain* / pathology
Imaging, Three-Dimensional*
Immunohistochemistry
Male
Mice
Mice, Inbred C57BL
Proteomics
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization*