CSF proteomics reveals changes in myelin and synaptic biology after Spectris treatment

To get a better understanding of the ongoing in situ environmental changes preceding the brain tumorigenesis, we assessed cerebrospinal fluid (CSF) proteome profile changes in a glioma rat model in which brain tumor invariably develop after a single in utero exposure to the neurocarcinogen ethylnitrosourea (ENU). Computationally, the CSF proteome profile dynamics during the tumorigenesis can be modeled as non-smooth or even abrupt state changes. Such brain tumor environment transition analysis, correlating the CSF composition changes with the development of early cellular hyperplasia, can reveal the pathogenesis process at network level during a time before the image detection of the tumors. In this controlled rat model study, matched ENU and salineexposed rats' CSF proteomics changes were quantified at approximately 30, 60, 90, 120, 150 days of age (P30, P60, P90, P120, P150). We applied our transition-based network entropy (TNE) method to compute the CSF proteome changes in the ENU rat model and test the hypothesis of the critical transition state prior to impending hyperplasia. Our analysis identified a dynamic driver network (DDN) of CSF proteins related with the emerging tumorigenesis progressing from the non-hyperplasia state. The DDN associated leading network CSF proteins can allow the early detection of such dynamics before the catastrophic shift to the clear clinical landmarks in gliomas. An improved understanding of the critical transition state (P60) during the brain tumor progression can provide the scientific groundwork to device novel therapeutics preventing tumor formation.

Quantitative proteomic analysis of age-related changes in human cerebrospinal fluid

Knowledge about the normal human cerebrospinal fluid (CSF) proteome serves as a baseline reference for CSF biomarker discovery and provides insight into CSF physiology. In this study, high-pH reverse-phase liquid chromatography (hp-RPLC) was first integrated with a TripleTOF 5600 mass spectrometer to comprehensively profile the normal CSF proteome. A total of 49,836 unique peptides and 3256 non-redundant proteins were identified. To obtain high-confidence results, 2513 proteins with at least 2 unique peptides were further selected as bona fide CSF proteins. Nearly 30% of the identified CSF proteins have not been previously reported in the normal CSF proteome. More than 25% of the CSF proteins were components of CNS cell microenvironments, and network analyses indicated their roles in the pathogenesis of neurological diseases. The top canonical pathway in which the CSF proteins participated was axon guidance signaling. More than one-third of the CSF proteins (788 proteins) were related to neurological diseases, and these proteins constitute potential CSF biomarker candidates. The mapping results can be freely downloaded at http://122.70.220.102:8088/csf/, which can be used to navigate the CSF proteome. For more information about the data, please refer to the related original article [1], which has been recently accepted by Journal of Proteomics.

Although cerebrospinal fluid (CSF) amyloid-β42 peptide (Aβ42) and phosphorylated tau (p-tau) and blood p-tau are valuable for differential diagnosis of Alzheimer's disease (AD) from cognitively normal (CN) there is a lack of validated biomarkers for mild cognitive impairment (MCI). This study sought to determine how plasma and CSF protein markers compared in the characterization of MCI and AD status. This cohort study included Alzheimer's Disease Neuroimaging Initiative (ADNI) participants who had baseline levels of 75 proteins measured commonly in plasma and CSF (257 total, 46 CN, 143 MCI, and 68 AD). Logistic regression, least absolute shrinkage and selection operator (LASSO) and Random Forest (RF) methods were used to identify the protein candidates for the disease classification. We observed that six plasma proteins panel (APOE, AMBP, C3, IL16, IGFBP2, APOD) outperformed the seven CSF proteins panel (VEGFA, HGF, PRL, FABP3, FGF4, CD40, RETN) as well as AD markers (CSF p-tau and Aβ42) to distinguish the MCI from AD [area under the curve (AUC) = 0.75 (plasma proteins), AUC = 0.60 (CSF proteins) and AUC = 0.56 (CSF p-tau and Aβ42)]. Also, these six plasma proteins performed better than the CSF proteins and were in line with CSF p-tau and Aβ42 in differentiating CN versus MCI subjects [AUC = 0.89 (plasma proteins), AUC = 0.85 (CSF proteins) and AUC = 0.89 (CSF p-tau and Aβ42)]. These results were adjusted for age, sex, education, and APOEϵ4 genotype. This study suggests that the combination of 6 plasma proteins can serve as an effective marker for differentiating MCI from AD and CN.

BACKGROUND The prognostic significance of cerebrospinal fluid (CSF) glucose and protein levels among patients with leptomeningeal disease (LMD) is unknown. This single-institution retrospective study aims to investigate the association of CSF glucose and protein levels with overall survival (OS) among metastatic breast cancer (MBC) patients with LMD. METHODOLOGY MBC patients diagnosed with LMD between Jan 1st, 2010, and Jan 1st, 2023, were included. Patients without known CSF glucose or protein levels at the time of LMD diagnosis were excluded. OS was evaluated using the Kaplan-Meier method and compared using the log-rank test. For multivariate analysis, a step-wise model selection was performed after the inclusion of sub-type of interest, and variables meeting entry (p<0.10) and staying criteria (p<0.05). Median glucose and protein levels were compared using the Wilcoxon rank-sum test. RESULTS 28 patients met inclusion criteria. Positive CSF cytology samples (CSF+) had significantly lower glucose levels vs CSF cytology negative samples (CSF-) [median (IQR) 40 (18-58) vs. 64 (53-92) mg/dl, p=0.006]. Prior study from this data set had shown that the CSF- group was associated with better OS vs the CSF+ group. Hence, four groups were created based on the CSF (+/-) and glucose (Low vs High/Normal). Median OS (months), 95% confidence Interval (CI) for CSF+/Glucose_Low, CSF+/Glucose_Normal/High, CSF-/Glucose_Low and CSF-/Glucose_High/Normal were 3.4(0.23-NE), 16.5(2.9-NE), 3.1(1.28-NE), 51.5(4.9-NE), p=0.03. Glucose_Low overall was associated with shorter OS in multivariate analysis [hazard ratio (HR), 95%CI 4.64 (1.71, 13.2)]. Median CSF protein was not different between CSF+/– groups. Median OS (months), 95%CI for Protein_High and Protein_Low /Normal groups were 28.5 (2.9, 51.5) vs. 6.5 (0.85, 8.0), p=0.36. In multivariate analysis, CSF protein level was not associated with OS. CONCLUSION The association between low CSF glucose level and worse survival among patients with MBC LMD was observed.

To begin to unravel the complexity of HIV-associated changes in the brain, broader, multifaceted analyses of cerebrospinal fluid (CSF) are needed that examine a wide range of proteins reflecting different functions. To provide the first broad profiles of protein changes in the CSF of HIV-infected patients, we used antibody arrays to measure 120 cytokines, chemokines, growth factors, and other proteins. CSF from HIV-infected patients with a range of cognitive deficits was compared to CSF from uninfected, cognitively normal patients to begin to identify protein changes associated with HIV infection and neurological disease progression. Uninfected patients showed relatively consistent patterns of protein expression. Highly expressed proteins in CSF included monocyte chemotactic protein-1, tissue inhibitors of metalloproteases, granulocyte colony-stimulating factor, adiponectin, soluble tumor necrosis factor receptor-1, urokinase-type plasminogen activator receptor, and insulin-like growth factor binding protein-2. Inflammatory and anti-inflammatory cytokines were expressed at low levels. HIV-infected patients showed increases in inflammatory proteins (interferon-gamma, tumor necrosis factor-alpha), anti-inflammatory proteins (IL-13), and chemokines but these correlated poorly with neurological status. The strongest correlation with increasing severity of neurological disease was a decline in growth factors, particularly, brain-derived neurotrophic factor and NT-3. These studies illustrate that HIV infection is associated with parallel changes in both inflammatory and neuroprotective proteins in the CSF. The inverse relationship between growth factors and neurological disease severity suggests that a loss of growth factor neuroprotection may contribute to the development of neural damage and may provide useful markers of disease progression.

Sex and age are major risk factors for chronic diseases. Recent studies examining age-related molecular changes in plasma provided insights into age-related disease biology. Cerebrospinal fluid (CSF) proteomics can provide additional insights into brain aging and neurodegeneration. By comprehensively examining 7,006 aptamers targeting 6,139 proteins in CSF obtained from 660 healthy individuals aged from 43 to 91 years old, we subsequently identified significant sex and aging effects on 5,097 aptamers in CSF. Many of these effects on CSF proteins had different magnitude or even opposite direction as those on plasma proteins, indicating distinctive CSF-specific signatures. Network analysis of these CSF proteins revealed not only modules associated with healthy aging but also modules showing sex differences. Through subsequent analyses, several modules were highlighted for their proteins implicated in specific diseases. Module 2 and 6 were enriched for many aging diseases including those in the circulatory systems, immune mechanisms, and neurodegeneration. Together, our findings fill a gap of current aging research and provide mechanistic understanding of proteomic changes in CSF during a healthy lifespan and insights for brain aging and diseases.

Objective To investigate the change of 14-3-3 protein in cerebrospinal fluid(CSF) in different types of meningoencephalitis in children and its value in judging brain injury. Methods CSF 14-3-3 protein bands were detected by means of Western blot in 22 patients with viral meningoencephalitis and 20 cases of purulent meningoencephalitis and with 15 cases of febrile seizures as the control group from Jul. 2009 to Jun. 2010, and in addition, the quantitative detection of 14-3-3 protein was done by way of ELISA.Correlation was analyzed between the clinical manifestations, prognosis, EEG, head CT or MRI and the changes of 14-3-3 protein. Results The positive rate of 14-3-3 protein in cases of purulent meningitis was 65.0(13/22 cases), higher than viral meningoencephalitis group(27.3%, 6/22 cases), and the difference was significant.In the quantitative detection, 14-3-3 protein was increased in both the purulent meningitis [(5.6±0.2) μg/L]and viral encephalitis groups[(3.2±0.3) μg/L]compared with the control group[(0.9±0.1) μg/L]. After treatment, 14-3-3 proteins were less than before in the purulent meningitis and viral meningoencephalitis groups.In the cases with severe clinical manifestations and severe injury brain suggested by imaging and EEG, the 14-3-3 protein in cerebrospinal fluid was elevated; and the prognosis of the cases with increased 14-3-3 protein was poor, as a result of epilepsy, death and so on. Conclusions 14-3-3 protein in the CSF increases with disease severity, so to a certain extent, it can be used to identify viral meningitis and purulent meningitis. Key words: 14-3-3 protein; Meningoencephalitis; Child

The human CSF pain proteome

Background: Alzheimer’s disease (AD) is the most common type of dementia, with progressive onset of clinical symptoms. The main pathological hallmarks are brain deposits of extracellular amyloid beta plaques and intracellular neurofibrillary tangles (NFT). Cerebrospinal fluid reflects pathological changes in the brain; amyloid beta 1-42 is a marker of amyloid plaques, while total and phosphorylated tau are markers of NFT formation. Additional biomarkers associated with disease pathogenesis are needed, for better prognosis, more specific diagnosis, prediction of disease severity and progression and for improved patient classification in clinical trials. The aim of the present study was to evaluate brain-specific proteins as potential biomarkers of progression of AD. Methods: Overall, 30 candidate proteins were quantified in cerebrospinal fluid (CSF) samples from patients with mild cognitive impairment (MCI) and mild, moderate and severe AD dementia (n=101) using mass spectrometry-based selected reaction monitoring assays. ELISA was used for neuronal pentraxin receptor-1 (NPTXR) confirmation. Results: The best discrimination between MCI and more advanced AD stages (moderate and severe dementia) was observed for protein NPTXR (area under the curve, AUC=0.799). A statistically different abundance of this protein was observed between the two groups, with severe AD patients having progressively lower levels (p<0.05). ELISA confirmed lower levels in AD, in a separate cohort that included controls, MCI and AD patients. Conclusions: We conclude that NPTXR protein in CSF is a novel potential biomarker of AD progression and could have important utility in assessing treatment success in clinical trials.

Correlations between CSF proteins and spontaneous neuronal activity in Parkinson’s disease

The cerebrospinal fluid (CSF) plays an important role in homeostasis of the brain. We previously demonstrated that major CSF proteins such as lipocalin-type prostaglandin D2 synthase (L-PGDS) and transferrin (Tf) that are biosynthesized in the brain could be biomarkers of altered CSF production. Here we report that the levels of these brain-derived CSF proteins correlated well with each other across various neurodegenerative diseases, including Alzheimer’s disease (AD). In addition, protein levels tended to be increased in the CSF samples of AD patients compared with the other diseases. Patients at memory clinics were classified into three categories, consisting of AD (n = 61), mild cognitive impairment (MCI) (n = 42), and cognitively normal (CN) (n = 23), with MMSE scores of 20.4 ± 4.2, 26.9 ± 1.7, and 29.0 ± 1.6, respectively. In each category, CSF protein levels were highly correlated with each other. In CN subjects, increased CSF protein levels correlated well with those of AD markers, including amyloid-β and tau protein, whereas in MCI and AD subjects, correlations declined with AD markers except p-tau. Future follow-up on each clinical subject may provide a clue that the CSF proteins would be AD-related biomarkers.

The insufficiency and heterogeneity of research to date primarily leads to a state of uncertainty regarding the value of CSF testing of t-tau, p-tau or p-tau/ABeta ratio for the diagnosis of Alzheimer's disease in current clinical practice. Particular attention should be paid to the risk of misdiagnosis and overdiagnosis of dementia (and therefore over-treatment) in clinical practice. These tests, like other biomarker tests which have been subject to Cochrane DTA reviews, appear to have better sensitivity than specificity and therefore might have greater utility in ruling out Alzheimer's disease as the aetiology to the individual's evident cognitive impairment, as opposed to ruling it in. The heterogeneity observed in the few studies awaiting classification suggests our initial summary will remain valid. However, these tests may have limited clinical value until uncertainties have been addressed. Future studies with more uniformed approaches to thresholds, analysis and study conduct may provide a more homogenous estimate than the one that has been available from the included studies we have identified.

Interleukin-6 (IL-6) is elevated in the cerebrospinal fluid (CSF) of humans and animals with bacterial meningitis. This study's hypothesis was that anti-IL-6 antibodies will attenuate meningeal inflammation in a rat model of bacterial meningitis. 14 male Sprague-Dawley rats were inoculated intracisternally (IC) with 0.1 mL of heat-killed pneumococci. At one hour post-inoculation, the rats received intraperitoneal doses of either 1.0 mL phosphate-buffered saline (PBS treatment group, n = 7) or 70 microg anti-IL-6 antibodies in 1.0 mL PBS (anti-IL-6 antibody treatment group, n = 7). Nine rats (normal group, n = 9) had no inoculation, and four rats (surgical sham group, n = 4) had IC inoculations of saline. At six hours post-inoculation, all the animals had CSF removed via IC tap. The CSF protein and white blood cell (WBC) count measures were compared using a t-test. Mean CSF WBC for the anti-IL-6 treatment group was 2,458/microL, versus the PBS controls' mean of 9,697/microL (p = 0.007). Mean CSF protein for the anti-IL-6 group was 180 mg/dL, versus 296 mg/dL for the controls (p = 0.032). The surgical sham and normal animals had normal CSF WBC and protein values. In this rat meningitis model, systemic treatment with anti-IL-6 antibodies after the induction of meningitis suppressed both CSF WBC count and CSF protein level, two important indices of meningeal inflammation.

We have developed a new procedure, including three affinity chromatography steps, micro-reversed phase high pressure liquid chromatography (mR-HPLC) and Western blotting/mass spectrometric analysis to study central nervous system (CNS) specific proteins in human cerebro spinal fluid (CSF) in order to find biochemical markers for neuronal and synaptic function and pathology in degenerative brain disorders. After the three affinity chromatography steps, intended to remove interfering serum proteins from CSF, mR-HPLC revealed four major peaks, which by both Western blotting and mass spectrometric analyses were found to correspond to beta 2-microglobulin, cystatin C, transthyretin (TTR) and asialotransferrin. When comparing these peaks in CSF from Alzheimer's disease (AD) patients and age-matched healthy controls, a reduction of the brain-specific TTR was found. Therefore we quantified TTR in CSF and serum samples from 8 patients with early onset AD (EAD), 18 patients with late onset AD (LAD), 8 patients with vascular dementia (VAD) and 18 healthy individuals using a nephelometric method. CSF-TTR was divided into barrier-dependent and barrier-independent TTR. The barrier-independent i.e. brain-specific TTR was significantly reduced in the EAD group compared to the controls. Transthyretin has been found to be present in the senile plaques in AD, and to specifically bind to beta/A4 protein, the major component of the amyloid deposits in AD. Therefore, the reduction of the transthyretin-isoform in CSF in AD may reflect an absorption of transthyretin to the amyloid deposits in the senile plaques.