Brain-specific Proteins Decline in the Cerebrospinal Fluid of Humans with Huntington Disease

Abstract

We integrated five sets of proteomics data profiling the constituents of cerebrospinal fluid (CSF) derived from Huntington disease (HD)-affected and -unaffected individuals with genomics data profiling various human and mouse tissues, including the human HD brain. Based on an integrated analysis, we found that brain-specific proteins are 1.8 times more likely to be observed in CSF than in plasma, that brain-specific proteins tend to decrease in HD CSF compared with unaffected CSF, and that 81% of brainspecific proteins have quantitative changes concordant with transcriptional changes identified in different regions of HD brain. The proteins found to increase in HD CSF tend to be liver-associated. These protein changes are consistent with neurodegeneration, microgliosis, and astrocytosis known to occur in HD. We also discuss concordance between laboratories and find that ratios of individual proteins can vary greatly, but the overall trends with respect to brain or liver specificity were consistent. Concordance is highest between the two laboratories observing the largest numbers of proteins. Huntington disease (HD)1 is an inherited neurodegenerative disorder characterized by progressive cognitive decline and psychiatric and movement symptoms. The cause of the disease is the expansion of trinucleotide (CAG) repeats in the coding region of the htt gene that translates into a polyglutamine tract in the huntingtin protein (1). Currently no treatment has been shown to delay the onset of the disease or slow its progression in patients. To speed assessment of therapies in clinical trials, it is critical to identify biological markers that can accurately monitor disease progression.Several genomics and proteomics approaches to identifying biomarkers for HD have been undertaken previously. Genomics studies have determined the molecular phenotype of human HD brain (2) and different tissues of HD mouse models at the mRNA level (3-6). Proteomics approaches have been applied to brain tissues of HD mouse models and humans to identify candidate markers (7-9). Blood plasma in particular has received considerable attention recently because of its ready accessibility clinically (10, 11). The candidate protein biomarkers identified in the blood proteomics studies are largely known inflammatory markers. Because HD is regarded primarily as a neurodegenerative disease, it is not entirely clear how directly general markers of neuroinflammation relate to the pathophysiology of HD, although astrocytosis and microgliosis (12) are prominent components of HD in its mid-to late stages (13). Another concern regarding markers discovered primarily in blood is that the blood-brain barrier may restrict brain proteins from entering plasma, and so plasma candidates may not directly reflect HD progression in the brain.Cerebrospinal fluid (CSF) is a more relevant biomaterial for biomarker discovery because it is proximal to the brain; it occupies the subarachnoid space of the central nervous system and the ventricular system around and inside the b...

Ciliogenesis is regulated by a huntingtin-HAP1-PCM1 pathway and is altered in Huntington disease

“…The abnormal flow could also compromise the role of the CSF in clearing brain catabolites, raising the possibility of a defect in brain homeostasis in HD patients. In support of these observations, alterations in various factors and proteins have been detected in the CSF of HD patients (33). Such defects in brain clearance capacity could be deleterious and exacerbate the neuronal death observed in HD.…”

In-depth Exploration of Cerebrospinal Fluid by Combining Peptide Ligand Library Treatment and Label-free Protein Quantification

“…Nano-LC-MS profiling of enzymatically digested proteins using label-free quantification on high resolution mass spectrometers may provide alternative solutions. These strategies have already been used to identify new biomarkers in CSF with good results (15,27). In such approaches, very limited or no fractionation at all is usually performed on the sample because of the large number of analyses that must be performed (number of patients and technical replicates) and the intrinsic variability that may be introduced by the fractionation procedure itself.…”

Cerebrospinal Fluid Biomarkers for Huntington’s Disease

“…Inevitably they identified many proteins that were altered in HD CSF, but the majority of these disease-associated changes were in proteins which were said to be liver-specific. There was a rather sur-prising tendency for brain-derived proteins to decline in HD CSF, with the exception of neuroinflammatory markers [80]. These findings highlight the inconsistencies between proteomic techniques and the nature of such studies as hypothesis-generating engines for future targeted work in properly powered sample sets.…”

“…ApoA is a glycoprotein associated with inhibition of food intake and regulation of body weight. All three were higher in HD patients compared to matched controls [61] but these changes were not independently replicated using a more quantitative assay -though Fang and colleagues had also found robust elevations of ApoA in HD CSF in their previous proteomic work [80].…”