Proteomic interrogation of human hippocampal CA1 pyramidal neuron sublayers in Alzheimer’s disease

Abstract

AbstractBackgroundHippocampal CA1 pyramidal neurons (PNs) are highly vulnerable to Alzheimer’s disease (AD). There is increasing evidence that superficial and deep CA1 PNs are molecularly and functionally distinct. Yet, it is unknown if these sublayers show differential molecular profiles in human AD.MethodLaser capture microdissection was used to extract superficial and deep CA1 PN sublayers from hippocampal slices derived from formalin‐fixed, paraffin‐embedded (FFPE) Braak VI human AD brains (n = 8). Proteomics was performed using label‐free, quantitative liquid chromatography‐mass spectrometry (LC‐MS). Paired t‐test was used to identify protein hits whose abundance was significantly different (permutation‐based FDR correction, FDR cutoff at 5%) between neuron types.ResultLC‐MS on these samples was high yield, with detection of 3159 unique proteins spanning ∼6 orders of magnitude in abundance, with ∼15% of identifications related to synaptic and ion channel function. Differences between superficial and deep CA1 PN sublayers included those related to AMPAR regulation (SIRT2), synapse function (ARHGAP23, SEPTIN4), neurodegeneration markers (NEFH), and markers of late versus early vulnerability in AD (INA). Differences that were nearly significant included CNTN2, associated with hippocampal PN Kv1 channels, components of the postsynaptic density dysregulated in AD (DLG4 and variants), and KCTD16, which impacts GABAB currents.ConclusionProteomics combining LCM and LC‐MS from FFPE samples can be readily applied to address differences between PN sublayers. As such, these data support novel molecular differences between these layers in advanced AD, as related to physiologic dysfunction and disease‐related changes.