Efficient quantitative hyperspectral image unmixing method for large-scale Raman micro-spectroscopy data analysis

Vibrational micro-spectroscopy is a powerful optical tool, providing a non-invasive label-free chemically specific imaging for many chemical and biomedical applications. However, hyperspectral image produced by Raman micro-spectroscopy typically consists of thousands discrete pixel points, each having individual Raman spectrum at thousand wavenumbers, and therefore requires appropriate image unmixing computational methods to retrieve non-negative spatial concentration and corresponding non-negative spectra of the image biochemical constituents. Here, we present a new efficient Quantitative Hyperspectral Image Unmixing (Q-HIU) method for large-scale Raman micro-spectroscopy data analysis. This method enables to simultaneously analyse multi-set Raman hyperspectral images in three steps: (i) Singular Value Decomposition with innovative Automatic Divisive Correlation which autonomously filters spatially and spectrally uncorrelated noise from data; (ii) a robust subtraction of fluorescent background from the data using a newly developed algorithm called Bottom Gaussian Fitting; (iii) an efficient Quantitative Unsupervised/Partially Supervised Non-negative Matrix Factorization method, which rigorously retrieves non-negative spatial concentration maps and spectral profiles of the samples' biochemical constituents with no a priori information or when one or several samples’ constituents are known. As compared with state-of-the-art methods, our approach allows to achieve significantly more accurate results and efficient quantification with several orders of magnitude shorter computational time as verified on both artificial and real experimental data. We apply Q-HIU to the analysis of large-scale Raman hyperspectral images of human atherosclerotic aortic tissues and our results show a proof-of-principle for the proposed method to retrieve and quantify the biochemical composition of the tissues, consisting of both high and low concentrated compounds. Along with the established hallmarks of atherosclerosis including cholesterol/cholesterol ester, triglyceride and calcium hydroxyapatite crystals, our Q-HIU allowed to identify the significant accumulations of oxidatively modified lipids co-localizing with the atherosclerotic plaque lesions in the aortic tissues, possibly reflecting the persistent presence of inflammation and oxidative damage in these regions, which are in turn able to promote the disease pathology. For minor chemical components in the diseased tissues, our Q-HIU was able to detect the signatures of calcium hydroxyapatite and β-carotene with relative mean Raman concentrations as low as 0.09% and 0.04% from the original Raman intensity matrix with noise and fluorescent background contributions of 3% and 94%, respectively

Imaging protein aggregates in Parkinson’s Disease serum using aptamer-assisted single-molecule pull-down

The formation of soluble α-synuclein (α-syn) and amyloid-β (Aβ) aggregates is associated with the development of Parkinson’s disease (PD). Current methods mainly focus on the measurement of the aggregate concentration and are unable to determine their heterogeneous size and shape, which potentially also change during the development of PD due to increased protein aggregation. In this work, we introduce aptamer-assisted single-molecule pull-down (APSiMPull) combined with super-resolution fluorescence imaging of α-syn and Aβ aggregates in human serum from early PD patients and age-matched controls. Our diffraction-limited imaging results indicate that the proportion of α-syn aggregates (α-syn/(α-syn+Aβ)) can be used to distinguish PD and control groups with an area under the curve (AUC) of 0.85. Further, super resolution fluorescence imaging reveals that PD serums have a higher portion of larger and rounder α-syn aggregates than controls. Little difference was observed for Aβ aggregates. Combining these two metrics, we constructed a new biomarker and achieved an AUC of 0.90. The combination of the aggregate number and morphology provides a new approach to early PD diagnosis

Soluble amyloid beta-containing aggregates are present throughout the brain at early stages of Alzheimer's disease.

Protein aggregation likely plays a key role in the initiation and spreading of Alzheimer's disease pathology through the brain. Soluble aggregates of amyloid beta are believed to play a key role in this process. However, the aggregates present in humans are still poorly characterized due to a lack of suitable methods required for characterizing the low concentration of heterogeneous aggregates present. We have used a variety of biophysical methods to characterize the aggregates present in human Alzheimer's disease brains at Braak stage III. We find soluble amyloid beta-containing aggregates in all regions of the brain up to 200 nm in length, capable of causing an inflammatory response. Rather than aggregates spreading through the brain as disease progresses, it appears that aggregation occurs all over the brain and that different brain regions are at earlier or later stages of the same process, with the later stages causing increased inflammation

Linking amyloid, inflammation and lipids to Alzheimer’s Disease using state-of-the-art imaging techniques

Alzheimer's disease (AD) is a neurodegenerative disorder and the most common cause of dementia in the elderly. The extracellular accumulation of amyloid-β (Aβ) in senile plaques is a principal event in the pathogenesis and there is growing evidence that the dysregulation of lipid pathways and neuroinflammation are implicated in the disease, however the link between these three is still under study. My multidisciplinary PhD study utilizes label-free Raman micro-spectroscopy combined with quantitative image analysis and high-resolution fluorescent microscopy to investigate the spatio-chemical composition and correlation of Aβ plaques with both neuroinflammatory biomarkers and lipids in post-mortem AD human brains. The results have proved the capability of Raman micro-spectroscopy to identify novel chemical imaging biomarkers of oxidative damage and neuroinflammation, colocalized to Aβ-affected regions of AD human brains, thereby delivering a useful imaging tool for detecting molecular signs of AD tissue neuropathology without the use of dyes or labels. Along with a pathogenic Aβ protein, two types of lipid aggregates co-depositing with the Aβ plaques of AD brains and in spectral characteristics resembling oxidized forms of free polyunsaturated fatty acids (FAs) and saturated cholesteryl esters (CEs) were found in this study. Correlation of the label-free Raman images of unmixed lipids with confocal fluorescence microscopy of the immunolabelled pro-inflammatory markers of AD brains revealed the CE lipidomic halo around the Aβ plaque co-localizing with significant ASC speck and pore-forming gasdermin D accumulations in the membrane of the NLRP3 inflammasome-activated microglia. Also, Raman micro-spectroscopy combined with fluorescence microscopy of Aβ pathology lesions in diseased tissues allowed to find colocalization of a pore-forming protein component 9 of a membrane attack complex (MAC) with the ASC specks and calcium crystals in the Aβ plaque cores, possibly reflecting the MAC as a driver of neuroinflammation and oxidative damage in AD. Thus, my thesis proposes Raman micro-spectroscopy profiles of the oxidized lipids and calcium crystals as novel biomarkers for label-free chemically specific and non-destructive imaging of Aβ-associated neuropathology and neuroinflammation in AD human brains

Imaging Protein Aggregates in Parkinson’s Disease Serum Using Aptamer-Assisted Single-Molecule Pull-Down

Publication status: PublishedThe formation of soluble α-synuclein (α-syn) and amyloid-β (Aβ) aggregates is associated with the development of Parkinson’s disease (PD). Current methods mainly focus on the measurement of the aggregate concentration and are unable to determine their heterogeneous size and shape, which potentially also change during the development of PD due to increased protein aggregation. In this work, we introduce aptamer-assisted single-molecule pull-down (APSiMPull) combined with super-resolution fluorescence imaging of α-syn and Aβ aggregates in human serum from early PD patients and age-matched controls. Our diffraction-limited imaging results indicate that the proportion of α-syn aggregates (α-syn/(α-syn+Aβ)) can be used to distinguish PD and control groups with an area under the curve (AUC) of 0.85. Further, super resolution fluorescence imaging reveals that PD serums have a higher portion of larger and rounder α-syn aggregates than controls. Little difference was observed for Aβ aggregates. Combining these two metrics, we constructed a new biomarker and achieved an AUC of 0.90. The combination of the aggregate number and morphology provides a new approach to early PD diagnosis

Novel Dimethylacetamide-Containing Formulation Improves Infraorbital Anaesthesia Efficacy in Rats with Periodontitis

Background. To evaluate acute toxicity and local anaesthetic activity of a formulation containing a novel dimethylacetamide derivative, antioxidant, and vasoconstrictor in rats with chronic periodontitis. Methods. Novel anaesthetic dimethylacetamide-containing formulation LHT-15-32 was studied as 2% water solution. Its acute intravenous and subcutaneous toxicity was determined in mice. Pain sensitivity threshold of the upper second molar was determined in rats with experimental periodontitis. Oxidative stress activity and total antioxidant capacity were determined in rats’ gingival mucosa by induced chemiluminescence. Local changes were evaluated in periodontal tissue by morphological examination. Tissue IL-1β, IL-10, and TNF-α concentration was quantitatively assessed by an enzyme-linked immunosorbent assay. LHT-15-31 Na-blocking activity was studied on isolated neurons of Limnaea stagnalis’ parapharyngeal ganglion. Isolated sciatic nerve of Rana radibunda was perfused with different concentrations of LHT-15-32 to assess its conductivity. Statistical analysis was used, and continuous variables were presented as mean ± square deviation. The normality of distribution was determined using ANOVA. Newman–Keuls parametric criterion was used for intergroup comparison. LD50 indexes were calculated by probit analysis. Results. LHT-15-32 acute intravenous and subcutaneous toxicity was lower than that of its active substance. The formulation by infraorbital administration induced deep dental anaesthesia which lasted over 70 min and activated the local antioxidant defense system and decreased IL-1β level in gingival tissue. LHT-15-32 triggered tissue reparation around the impacted upper molar in rats assessed five days after administration. At 10−6 to 10−3 M concentration, LHT-15-32 inhibited sciatic nerve conductivity and blocked Na+ channels of isolated neurons in a dose-dependent manner. Conclusions. The formulation may be considered as an effective and safe approach to anaesthetize upper molars with periodontitis

Imaging protein aggregates in the serum and cerebrospinal fluid in Parkinson's disease.

Aggregation of α-synuclein plays a key role in the development of Parkinson's disease. Soluble aggregates are present not only within human brain but also the CSF and blood. Characterizing the aggregates present in these biofluids may provide insights into disease mechanisms and also have potential for aiding diagnosis. We used two optical single-molecule imaging methods called aptamer DNA-PAINT and single-aggregate confocal fluorescence, together with high-resolution atomic force microscopy for specific detection and characterization of individual aggregates with intermolecular β-sheet structure, present in the CSF and serum of 15 early stage Parkinson's disease patients compared to 10 healthy age-matched controls. We found aggregates ranging in size from 20 nm to 200 nm, in both CSF and serum. There was a difference in aggregate size distribution between Parkinson's disease and control groups with a significantly increased number of larger aggregates (longer than 150 nm) in the serum of patients with Parkinson's disease. To determine the chemical composition of the aggregates, we performed aptamer DNA-PAINT on serum following α-synuclein and amyloid-β immunodepletion in an independent cohort of 11 patients with early stage Parkinson's disease and 10 control subjects. β-Sheet aggregates in the serum of Parkinson's disease patients were found to consist of, on average, 50% α-synuclein and 50% amyloid-β in contrast to 30% α-synuclein and 70% amyloid-β in control serum [the differences in the proportion of these aggregates were statistically significant between diseased and control groups (P = 1.7 × 10-5 for each species)]. The ratio of the number of β-sheet α-synuclein aggregates to β-sheet amyloid-β aggregates in serum extracted using our super-resolution method discriminated Parkinson's disease cases from controls with an accuracy of 98.2% (AUC = 98.2%, P = 4.3 × 10-5). Our data suggest that studying the protein aggregates present in serum can provide information about the disruption of protein homeostasis occurring in Parkinson's disease and warrants further investigation as a potential biomarker of disease

An antibody scanning method for the detection of α-synuclein oligomers in the serum of Parkinson's disease patients.

Misfolded α-synuclein oligomers are closely implicated in the pathology of Parkinson's disease and related synucleinopathies. The elusive nature of these aberrant assemblies makes it challenging to develop quantitative methods to detect them and modify their behavior. Existing detection methods use antibodies to bind α-synuclein aggregates in biofluids, although it remains challenging to raise antibodies against α-synuclein oligomers. To address this problem, we used an antibody scanning approach in which we designed a panel of 9 single-domain epitope-specific antibodies against α-synuclein. We screened these antibodies for their ability to inhibit the aggregation process of α-synuclein, finding that they affected the generation of α-synuclein oligomers to different extents. We then used these antibodies to investigate the size distribution and morphology of soluble α-synuclein aggregates in serum and cerebrospinal fluid samples from Parkinson's disease patients. Our results indicate that the approach that we present offers a promising route for the development of antibodies to characterize soluble α-synuclein aggregates in biofluids