Patients with glioblastoma multiforme (GBM) are at high risk to develop a relapse despite multimodal therapy. Assumedly, glioma stem cells (GSCs) are responsible for treatment resistance of GBM. Identification of specific GSC markers may help to develop targeted therapies. Here, we performed expression analyses of stem cell (ABCG2, CD44, CD95, CD133, ELF4, Nanog, and Nestin) as well as differentiation and microglia markers (GFAP, Iba1, and Sparc) in GBM compared to nonmalignant brain. Furthermore, the role of these proteins for patient survival and their expression in LN18 stem-like neurospheres was analyzed. At mRNA level, ABCG2 and CD95 were reduced, GFAP was unchanged; all other investigated markers were increased in GBM. At protein level, CD44, ELF4, Nanog, Nestin, and Sparc were elevated in GBM, but only CD133 and Nestin were strongly associated with survival time. In addition, ABCG2 and GFAP expression was decreased in LN18 neurospheres whereas CD44, CD95, CD133, ELF4, Nanog, Nestin, and Sparc were upregulated. Altogether only CD133 and Nestin were associated with survival rates. This raises concerns regarding the suitability of the other target structures as prognostic markers, but makes both CD133 and Nestin candidates for GBM therapy. Nevertheless, a search for more specific marker proteins is urgently needed.

Background: High-fat diet (HFD) consumption is commonly linked to low-grade brain inflammation and increased risk of neurodegeneration. However, in our previous research, HFD exposure for up to 24 weeks did not increase pro-inflammatory cytokine expression or impair learning and spatial memory. To further investigate neuroimmune responses, we examined microglial activation at the transcriptional level. Methods: Male C57BL/6J mice were fed either a normal diet (ND) or HFD for 4, 12, or 24 weeks. Bulk RNA sequencing was performed across four brain regions (cerebellum, hippocampus, hypothalamus, cortex) to assess region-specific transcriptional responses. Results: HFD induced region- and time-dependent transcriptional changes. In the hypothalamus, 0/11/37 differentially expressed genes (DEGs; p-value < 0.05; fold change > 1.5) were detected at 4, 12, and 24 weeks, respectively. In the hippocampus, 2/41/42 DEGS were observed; in the cortex, 1/3/68 DEGS; and in the cerebellum, 27/0/0 DEGS at the respective time points, indicating minimal cerebellar involvement beyond the early time point. Across all conditions, three genes (Lcn2, Ch25h, Gimap9) were consistently regulated. Several DEGs were linked to microglial activation and inflammatory signaling. In the manuscript, we discuss 33 biologically relevant DEGs in detail. Transcriptomic signatures and pathway enrichment analyses suggest potential engagement of NF-κB-related pathways, although this interpretation remains indirect. Conclusions: These findings demonstrate that HFD selectively alters brain homeostasis by inducing region-specific transcriptional changes associated with microglial activation and inflammatory processes. While NF-κB-related pathways emerged as recurrent candidates, direct mechanistic validation is required.

Excessive fat consumption increases the risk of Alzheimer's disease (AD), potentially through diet‐induced neuroinflammation. Microglia, the brain's immune cells, are affected by obesity and diet. Phytosterols (PS), plant‐derived cholesterol‐like compounds, accumulate in the brain with age, and their content correlates with dietary intake. We hypothesize that the accumulation of PS modulates microglial activation and exerts anti‐inflammatory effects. We investigated the effects of a normal diet (ND), high‐fat diet (HFD), HFD with 2% PS (HFD+2% PS), and HFD with 4% PS (HFD+4% PS) on neuroinflammation in female and male C57BL/6J mice. Flow cytometry (FC) of microglia showed no significant regulation of pro‐ (IFN‐γ, IL‐1β, TNF‐α) and anti‐inflammatory (IL‐10) cytokines due to diet, but sex‐ and age‐dependent differences were observed. Immunofluorescence staining showed no TREM2 upregulation, indicating a lack of microglial activation in response to HFD. PS supplementation significantly reduced HFD‐induced weight gain, suggesting metabolic effects. Contrary to existing research, we found no evidence of HFD‐induced neuroinflammation or microglial activation. However, the reduction in weight gain with PS supplementation suggests potential metabolic benefits, which could have implications for the treatment of obesity. The potential effects on neuroinflammation remain unclear.

This study investigated the impact of tissue preservation methods on protein profiles analyzed by reversed-phase liquid chromatography-high-resolution mass spectrometry (LC-HRMS) using data-independent acquisition (DIA). Proteomic profiles from formalin-fixed, formalin-fixed and paraffin-embedded (FFPE), and fresh-frozen human brain tissues (cortex and hippocampus, n = 6) were compared, including an FFPE-specific protein extraction kit (n = 4). Formalin-fixed samples more closely resembled fresh-frozen profiles than FFPE or FFPE-Kit samples, while still showing high correlation and overlap with FFPE tissues in principal component analyses. A core set of 1753 proteins was consistently detected across all sample preparation methods. A total of 35 proteins were identified exclusively in fresh-frozen samples, but without functional enrichment. Quantitative comparisons to the proteome of fresh-frozen tissue revealed an underrepresentation of cellular processes, energy metabolism, signaling, and transport related to protein properties such as length, location, and hydrophobicity. In contrast, neuronal development and phagosome-related pathways were overrepresented in fixed tissues. In a pilot study comparing low (Braak 0-II, n = 4) and high (Braak IV-VI, n = 4) Alzheimer's disease (AD) stages using formalin-fixed samples, we identified 12 potential protein biomarkers, primarily nucleosomal proteins and carboxypeptidase M (CPM). These findings suggest that formalin-fixed brain tissue provides reliable proteomic information, making it a valuable resource for neurodegenerative disease research. SIGNIFICANCE: Proteomics offers enormous potential for investigating the molecular regulation of the human brain. Valuable tissue samples are often preserved in formalin or additionally with paraffin for later analysis. The potential value of these preserved samples for proteomic analysis has already been recognized. However, tissue preservation poses a challenge for proteome analysis. Consequently, several studies have compared different protein extraction protocols for fixed samples. In addition, studies have been published comparing protein extraction from FFPE samples with fresh-frozen samples. To our knowledge, this is the first study to compare protein extraction across all three tissue preservation methods with subsequent functional analysis using samples obtained from the same donors, thereby eliminating inter-donor variability and enabling a direct comparison of preservation effects. This study validates a protein extraction protocol from formalin-fixed samples, laying the groundwork for future research into potential biomarkers in formalin-fixed samples.