Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer's Disease Progression
NEURON
Authors: Bai, Bing; Wang, Xusheng; Li, Yuxin; Chen, Ping-Chung; Yu, Kaiwen; Dey, Kaushik Kumar; Yarbro, Jay M.; Han, Xian; Lutz, Brianna M.; Rao, Shuquan; Jiao, Yun; Sifford, Jeffrey M.; Han, Jonghee; Wang, Minghui; Tan, Haiyan; Shaw, Timothy, I; Cho, Ji-Hoon; Zhou, Suiping; Wang, Hong; Niu, Mingming; Mancieri, Ariana; Messler, Kaitlynn A.; Sun, Xiaojun; Wu, Zhiping; Pagala, Vishwajeeth; High, Anthony A.; Bi, Wenjian; Zhang, Hui; Chi, Hongbo; Haroutunian, Vahram; Zhang, Bin; Beach, Thomas G.; Yu, Gang; Peng, Junmin
Abstract
Alzheimer's disease (AD) displays a long asymptomatic stage before dementia. We characterize AD stage-associated molecular networks by profiling 14,513 proteins and 34,173 phosphosites in the human brain with mass spectrometry, highlighting 173 protein changes in 17 pathways. The altered proteins are validated in two independent cohorts, showing partial RNA dependency. Comparisons of brain tissue and cerebrospinal fluid proteomes reveal biomarker candidates. Combining with 5xFAD mouse analysis, we determine 15 A beta-correlated proteins (e.g., MDK, NTN1, SMOC1, SLIT2, and HTRA1). 5xFAD shows a proteomic signature similar to symptomatic AD but exhibits activation of autophagy and interferon response and lacks human-specific deleterious events, such as downregulation of neurotrophic factors and synaptic proteins. Multi-omics integration prioritizes AD-related molecules and pathways, including amyloid cascade, inflammation, complement, WNT signaling, TGF-beta and BMP signaling, lipid metabolism, iron homeostasis, and membrane transport. Some A beta-correlated proteins are colocalized with amyloid plaques. Thus, the multilayer omics approach identifies protein networks during AD progression.
Characterization of Primary Human Dermal Fibroblasts to Ensure for Instance EMF Exposure Experiments under Comparable Cell Culture Condition
HEALTH PHYSICS
Authors: Franchini, Valeria; Mueller, Thomas; Haupt, Julian M.; Ostheim, Patrick; Majewski, Matthaeus; Lista, Florigio; Port, Matthias; Abend, Michael
Abstract
HDFa (human dermal fibroblasts) are used as cellular models for EMF exposure. To ensure reproducible in vitro experiments, comparable proliferation and differentiation cell conditions must exist, and different donors, passage numbers, culture time, and growth media must be considered. In this study, the authors cultured fibroblasts in DMEM or 106 medium. Growth curves, vitality, morphology, and gene expression of genes coding for proliferation (PCNA, CDKN2A, CDKN1A, SFN), differentiation (PDGFRA, TGM2, ACTA2, PDPN, NTN1, MGP, PPP1R14), and SFN target genes (TP63, MMP1, MMP3) were examined in both media and passage numbers 3-4, 5-6 and >6. At passages 3-4, proliferating cells can be observed in both media. While cells cultured in DMEM proliferate over the passages, from passage 5, cells in 106 medium persisted around the seeded number. TGM2 down-regulation over all passages in both media and cells morphology suggest papillary-type fibroblasts. Downregulation of SFN (negative regulator of mitotic translation and cell differentiation) coincided with proliferating fibroblasts over all examined conditions. Downstream SFN target genes in proliferating cells appeared upregulated (TP63) and downregulated (MMP1/MMP3), suggestive for a status characterized by increased stemnesses (upregulated TP63) and wound healing capacity (downregulated MMP1, MMP3). Resting cells (SFN control values) were associated with control values of TP63 and MMP1/MMP3 expression, suggesting a reduced stemness and wound healing capacity. In conclusion, a set of markers related to proliferation (SFN), differentiation (TGM2), stemnesses (TP63), and wound healing (MMP1/MMP3) allow a culture characterization so that cells under two different conditions can be exposed, thus enabling reproducible EMF experiments or experiments with other exposures.