An integrated computational pipeline for machine learning-driven diagnosis based on Raman spectra of saliva samples.

Raman Spectroscopy promises the ability to encode in spectral data the significant differences between biological samples belonging to patients affected by a disease and samples of healthy patients (controls). However, the decoding and interpretation of the Raman spectral fingerprint is still a difficult and time-consuming procedure even for domain experts. In this work, we test an end-to-end deep-learning diagnostic pipeline able to classify spectral data from saliva samples. The pipeline has been validated against the SARS-COV-2 Infection and for the screening of neurodegenerative diseases such as Parkinson's and Alzheimer's diseases. The proposed system can be used for the fast prototyping of promising non-invasive, cost and time-efficient diagnostic screening tests.

Identification of the Raman Salivary Fingerprint of Parkinson's Disease Through the Spectroscopic- Computational Combinatory Approach.

Despite the wide range of proposed biomarkers for Parkinson's disease (PD), there are no specific molecules or signals able to early and uniquely identify the pathology onset, progression and stratification. Saliva is a complex biofluid, containing a wide range of biological molecules shared with blood and cerebrospinal fluid. By means of an optimized Raman spectroscopy procedure, the salivary Raman signature of PD can be characterized and used to create a classification model. Raman analysis was applied to collect the global signal from the saliva of 23 PD patients and related pathological and healthy controls. The acquired spectra were computed using machine and deep learning approaches. The Raman database was used to create a classification model able to discriminate each spectrum to the correct belonging group, with accuracy, specificity, and sensitivity of more than 97% for the single spectra attribution. Similarly, each patient was correctly assigned with discriminatory power of more than 90%. Moreover, the extracted data were significantly correlated with clinical data used nowadays for the PD diagnosis and monitoring. The preliminary data reported highlight the potentialities of the proposed methodology that, once validated in larger cohorts and with multi-centered studies, could represent an innovative minimally invasive and accurate procedure to determine the PD onset, progression and to monitor therapies and rehabilitation efficacy.

Inhibition of neutral sphingomyelinase 2 reduces extracellular vesicle release from neurons, oligodendrocytes, and activated microglial cells following acute brain injury.

Extracellular Vesicles (EVs) are implicated in the spread of pathogenic proteinsin a growing number of neurological diseases. Given this, there is rising interest in developing inhibitors of Neutral Sphingomyelinase 2 (nSMase2), an enzyme critical in EV biogenesis. Our group recently discovered phenyl(R)-(1-(3-(3,4-dimethoxyphenyl)-2,6-dimethylimidazo[1,2-b]pyridazin-8-yl)pyrrolidin-3-yl)carbamate (PDDC), the first potent, selective, orally-available, and brain-penetrable nSMase2 inhibitor, capable of dose-dependently reducing EVs release in vitro and in vivo. Herein, using multiplexed Surface Plasmon Resonance imaging (SPRi), we evaluated which brain cell-derived EVs were affected by PDDC following acute brain injury. Mice were fed PDDC-containing chow at doses which gave steady PDDC brain exposures exceeding its nSMase2 IC50. Mice were then administered an intra-striatal IL-1ß injection and two hours later plasma and brain were collected. IL-1ß injection significantly increased striatal nSMase2 activity which was completely normalized by PDDC. Using SPRi, we found that IL-1ß-induced injury selectively increased plasma levels of CD171 + and PLP1 + EVs; this EV increase was normalized by PDDC. In contrast, GLAST1 + EVs were unchanged by IL-1ß or PDDC. IL-1ß injection selectively increased EVs released from activated versus non-activated microglia, indicated by the CD11b+/IB4 + ratio. The increase in EVs from CD11b + microglia was dramatically attenuated with PDDC. Taken together, our data demonstrate that following acute injury, brain nSMase2 activity is elevated. EVs released from neurons, oligodendrocytes, and activated microglial are increased in plasma and inhibition of nSMase2 with PDDC reduced these IL-1ß-induced changes implicating nSMase2 inhibition as a therapeutic target for acute brain injury.

Characterization of the COPD Salivary Fingerprint through Surface Enhanced Raman Spectroscopy: A Pilot Study.

Chronic Obstructive Pulmonary Disease (COPD) is a debilitating pathology characterized by reduced lung function, breathlessness and rapid and unrelenting decrease in quality of life. The severity rate and the therapy selection are strictly dependent on various parameters verifiable after years of clinical observations, missing a direct biomarker associated with COPD. In this work, we report the methodological application of Surface Enhanced Raman Spectroscopy combined with Multivariate statistics for the analysis of saliva samples collected from 15 patients affected by COPD and 15 related healthy subjects in a pilot study. The comparative Raman analysis allowed to determine a specific signature of the pathological saliva, highlighting differences in determined biological species, already studied and characterized in COPD onset, compared to the Raman signature of healthy samples. The unsupervised principal component analysis and hierarchical clustering revealed a sharp data dispersion between the two experimental groups. Using the linear discriminant analysis, we created a classification model able to discriminate the collected signals with accuracies, specificities, and sensitivities of more than 98%. The results of this preliminary study are promising for further applications of Raman spectroscopy in the COPD clinical field.

Raman Fingerprint of Extracellular Vesicles and Conditioned Media for the Reproducibility Assessment of Cell-Free Therapeutics.

Extracellular Vesicles (EVs) and Conditioned Medium (CM) are promising cell-free approaches to repair damaged and diseased tissues for regenerative rehabilitation purposes. They both entail several advantages, mostly in terms of safety and handling, compared to the cell-based treatment. Despite the growing interest in both EVs and CM preparations, in the light of a clinical translation, a number of aspects still need to be addressed mainly because of limits in the reproducibility and reliability of the proposed protocols. Raman spectroscopy (RS) is a non-destructive vibrational investigation method that provides detailed information about the biochemical composition of a sample, with reported ability in bulk characterization of clusters of EVs from different cell types. In the present brief report, we acquired and compared the Raman spectra of the two most promising cell-free therapeutics, i.e., EVs and CM, derived from two cytotypes with a history in the field of regenerative medicine, adipose-derived mesenchymal stem/stromal cells (ASCs) and dermal fibroblasts (DFs). Our results show how RS can verify the reproducibility not only of EV isolation, but also of the whole CM, thus accounting for both the soluble and the vesicular components of cell secretion. RS can provide hints for the identification of the soluble factors that synergistically cooperate with EVs in the regenerative effect of CM. Still, we believe that the application of RS in the pipeline of cell-free products preparation for therapeutic purposes could help in accelerating translation to clinics and regulatory approval.

Biophotonics for diagnostic detection of extracellular vesicles.

Extracellular Vesicles (EVs) are versatile carriers for biomarkers involved in the pathogenesis of multiple human disorders. Despite the increasing scientific and commercial interest in EV application in diagnostics, traditional biomolecular techniques usually require consistent sample amount, rely on operator-dependent and time- consuming procedures and cannot cope with the nano-size range of EVs, limiting both sensitivity and reproducibility of results. The application of biophotonics, i.e. light-based methods, for the diagnostic detection of EVs has brought to the development of innovative platforms with excellent sensitivity. In this review, we propose an overview of the most promising and emerging technologies used in the field of EV-related biomarker discovery. When tested on clinical samples, the reported biophotonic approaches in most cases have managed to discriminate between nanovesicles and contaminants, achieved much higher resolution compared to traditional procedures, and reached moderate to excellent diagnostic accuracy, thus demonstrating great potentialities for their clinical translation.

Regulation of aged skeletal muscle regeneration by circulating extracellular vesicles.

Heterochronic blood exchange (HBE) has demonstrated that circulating factors restore youthful features to aged tissues. However, the systemic mediators of those rejuvenating effects remain poorly defined. We show here that the beneficial effect of young blood on aged muscle regeneration was diminished when serum was depleted of extracellular vesicles (EVs). Whereas EVs from young animals rejuvenate aged cell bioenergetics and skeletal muscle regeneration, aging shifts EV subpopulation heterogeneity and compromises downstream benefits on recipient cells. Machine learning classifiers revealed that aging shifts the nucleic acid, but not protein, fingerprint of circulating EVs. Alterations in sub-population heterogeneity were accompanied by declines in transcript levels of the pro-longevity protein, α-Klotho, and injection of EVs improved muscle regeneration in a Klotho mRNA-dependent manner. These studies demonstrate that EVs play a key role in the rejuvenating effects of HBE and that Klotho transcripts within EVs phenocopy the effects of young serum on aged skeletal muscle.

An SPRi-based biosensor pilot study: Analysis of multiple circulating extracellular vesicles and hippocampal volume in Alzheimer's disease.

One of the main hurdles in the study of Alzheimer's Disease (AD) is the lack of easily accessible and sensitive biomarkers for the diagnosis, the prediction of the disease progression rate and the evaluation of rehabilitative and pharmacological treatments. Extracellular Vesicles (EVs) are nanoscale particles released by body cells, studied as promising biomarkers of AD as they are involved in the onset and progression of the disease. In the strive for a reliable and sensitive method to analyze EVs, we applied our recently developed biosensor based on Surface Plasmon Resonance imaging (SPRi) technology for the identification and profiling of neural EVs populations circulating in the plasma of 10 AD patients and 10 healthy subjects. The SPRi-array was designed to separate simultaneously EVs released by neurons, astrocytes, microglia and oligodendrocytes, and to evaluate the presence and the relative amount of specific surface molecules related to pathological processes including translocator protein (TSPO), ß-Amyloid and ganglioside M1. As results, significant variations in the relative amount and cargoes of specific brain-derived populations of EVs were observed comparing EVs coming from AD patients and healthy subjects, finding the main differences in the activation phenotype of microglia EVs, in the lipid moieties on generic EVs and in the ß-Amyloid expression on surfaces of neuronal EVs. Besides, the demonstrated correlation of SPRi data with Magnetic Resonance Imaging analysis, provided support for using the SPRi-based biosensor for the evaluation of neurodegeneration detecting and characterizing circulating EVs as peripheral biomarkers for the diagnosis and monitoring of progression and rehabilitation treatments in AD patients.

The Collagen-Based Medical Device MD-Tissue Acts as a Mechanical Scaffold Influencing Morpho-Functional Properties of Cultured Human Tenocytes.

Mechanotransduction is the ability of cells to translate mechanical stimuli into biochemical signals that can ultimately influence gene expression, cell morphology and cell fate. Tenocytes are responsible for tendon mechanical adaptation converting mechanical stimuli imposed during mechanical loading, thus affecting extracellular matrix homeostasis. Since we previously demonstrated that MD-Tissue, an injectable collagen-based medical compound containing swine-derived collagen as the main component, is able to affect tenocyte properties, the aim of this study was to analyze whether the effects triggered by MD-Tissue were based on mechanotransduction-related mechanisms. For this purpose, MD-Tissue was used to coat Petri dishes and cytochalasin B was used to deprive tenocytes of mechanical stimulation mediated by the actin cytoskeleton. Cell morphology, migration, collagen turnover pathways and the expression of key mechanosensors were analyzed by morphological and molecular methods. Our findings confirm that MD-Tissue affects collagen turnover pathways and favors cell migration and show that the MD-Tissue-induced effect represents a mechanical input involving the mechanotransduction machinery. Overall, MD-Tissue, acting as a mechanical scaffold, could represent an effective medical device for a novel therapeutic, regenerative and rehabilitative approach to favor tendon healing in tendinopathies.

Exosome mediated transfer of miRNA-140 promotes enhanced chondrogenic differentiation of bone marrow stem cells for enhanced cartilage repair and regeneration.

Exosomes (EXs) are nanocarrier vesicles with 20-50 nm dimensions. They are involved in cell proliferation and differentiation and in protecting the integrity of materials. They can be isolated from plasma and immunoreactive components. Recent studies demonstrated their potential role in cartilage regeneration. To enhance their regenerative effect, molecules like microRNA (miR-140) can be loaded in EX that acts as RNA delivery systems. In this study, we combined EX with miR-140 to enhance cell differentiation by inducing membrane fusion and consequent miRNA released into the cytoplasm. The carrier RNA complex was successfully synthesized through freeze and thaw method leading to the formation of EX-containing miR-140. The EX morphology was assessed through transmission electron microscopy and their miR-140 uptake efficiency through real-time polymerase chain reaction (RT-PCR). The effects on bone marrow stem cells (BMSCs) were evaluated by in vitro cell culture. Cell adhesion and morphology were studied using a bio-scanning electron microscope and confocal laser scanning microscope. Differentiation BMSCs into chondrocytes was analyzed by RT-PCR and histology. Our results confirm the bioactive role of EX loaded with miR-140 in the differentiation of BMSCs into chondrocytes. EXs were biocompatible involving in the cartilage healing process through chromogenic differentiation of BMCS exploiting the tissue engineering route.

SERS-based biosensor for Alzheimer disease evaluation through the fast analysis of human serum.

Alzheimer disease (AD) is the most common form of dementia in the elderly, progressively affecting the cognitive functions with a complex diagnostic procedure that limits the time for a prompt intervention. In this study we optimized a reliable protocol for the analysis of AD patients and healthy subjects' serum using the Surface Enhanced Raman Spectroscopy (SERS), taking into consideration the effect of different variables on the final spectra, analyzed and compared through multivariate analysis and correlated with hippocampus volume. As results, we demonstrated a statistical difference between the spectra collected from the two investigated groups, with an accuracy, precision and specificity of respectively 83%, 86%, and 86%. The correlation of these data with those obtained from MRI, demonstrated a direct correlation between Raman spectra and hippocampus degeneration showing the Raman Spectroscopy (RS) as a potential tool for the monitoring of AD progression and rehabilitation treatments.

Raman profiling of circulating extracellular vesicles for the stratification of Parkinson's patients.

Parkinson's disease (PD) is a chronic neurodegenerative disorder, characterized by considerable clinical heterogeneity. Extracellular vesicles (EVs) were proposed as new biomarkers for PD because of their role as vehicles of multiple PD related molecules, but technical limitations exist in their detection and characterization in a clinical environment. We propose herein a Raman based protocol for the label-free analysis of circulating EVs as diagnostic and predictive tool for PD. After purification from serum of PD patients and healthy subjects, EVs were analyzed by Raman spectroscopy demonstrating the feasibility and reproducibility of the proposed biophotonic approach, its moderate accuracy in distinguishing PD patients from controls by their EV profile and the correlation between Raman data and clinical scales. Once validated, the Raman spectroscopy of circulating EVs could represent a reliable, automatable and sensitive method for the stratification of PD patients and for the evaluation of the effectiveness of rehabilitation and pharmacological treatments.

Injectable taurine-loaded alginate hydrogels for retinal pigment epithelium (RPE) regeneration.

The purpose of this study is to produce injectable taurine (Tr)-loaded alginate (Agn) hydrogel for age-related macular degeneration (AMD) treatment by inducing the regeneration of RPE (retinal pigment epithelium) cells. Porosity and swelling ratio were measured to evaluate the mechanical properties of the hydrogels, and Fourier transform infrared spectroscopy (FTIR) was used to evaluate the physical and chemical properties. RPE cells extracted from the pigmented epithelium of rabbits were encapsulated in the Tr/Agn hydrogels. Cells proliferation and migration were improved in Tr/Agn hydrogels with an enhanced expression of RPE-specific genes including RPE65, CRALBP, NPR-A, MITF and collagen type I and II. In vivo tests demonstrated the excellent biocompatibility and biodegradability without inflammatory response by the host when implanted with the hydrogel. Moreover, when the Tr/Agn hydrogels were injected into the sub-retinal space, high adhesion of RPE cells and retinal regeneration were confirmed. These results demonstrated a potential role of injectable Tr/Agn hydrogels as potential therapeutic tools for the treatment of retinal diseases, including AMD.

Evaluation of silymarin/duck's feet-derived collagen/hydroxyapatite sponges for bone tissue regeneration.

Tissue engineered scaffolds, made of natural derived materials, have the potential to be used in bone regeneration fields due to the biocompatible and biodegradable features. In this study, we propose duck's feet-derived collagen (DC) sponges blended with hydroxyapatite (HAp), incorporated with different concentrations of silymarin (Smn), for improved bone regeneration. The morphological and structural properties of DC/HAp and DC/HAp loaded with 25, 50 and 100 µM of Smn sponges were analyzed using scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). In vitro evaluations were carried out on rabbit bone marrow stem cells (rBMSCs) using MTT assay for cell proliferation, ALP assay for osteogenic differentiation and reverse transcription-polymerase chain reaction (RT-PCR) for expression of mRNAs. For the evaluation of new bone formation in vivo, histological analysis and micro computed tomography (µCT) were used. Preliminary results, on Smn/DC/HAp morphology and mechanical properties, showed an interconnected porosity suitable for cells ingrowth and a higher compressive strength with the presence of Smn. Similarly, the cells proliferation and ALP activity modulation were positively influenced by the Smn content. Especially, the 100 µM Smn/DC/HAp sponge efficiently enhances the rBMSCs adhesion, growth and gene expression of osteogenic markers. The enhanced osteoinductive effects of sponges blended with Smn were confirmed using µ-CT and histological evaluations. In conclusion, results suggest that collagen sponges represent an excellent environment for cells growth and proliferation, while Smn plays an important role to improve materials osteogenic properties.

Breath Figures decorated silicon oxinitride ceramic surfaces with controlled Si ions release for enhanced osteoinduction.

Bioactive coatings are usually applied to bone and dental prostheses to enhance the integration and their stability in the bone. Recently, silicon (Si) oxynitride ceramics have been demonstrated to possess osteoconductive properties due to the release of Si ions, particularly important in the early stage of bone formation. In addition, the pattern of the bone contacting surface has been reported to affect cells' differentiation and metabolic activity. In this work, we propose the Breath Figure (BF) process combined with a pyrolysis step, starting from a photo-crosslinkable alkoxy silicone precursor, as a method to realize bioactive patterned coating on metal bone and dental prostheses. Four different surface patterned coatings were applied to Ti4Al6V disks starting from solutions with different precursor concentrations. Morphology, chemical composition, and Si ions' release were evaluated and compared. Moreover, all samples underwent to biological in vitro testing with human mesenchymal stem cells (hMSCs) in comparison with the uncoated titanium alloy. The results indicated that the Si released from the coatings determined an increase in the cellular activity with the BF pattern influencing the hMSCs' initial adhesion and proliferation. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 107B: 1284-1294, 2019.

Characterization of surface modified glycerol/silk fibroin film for application to corneal endothelial cell regeneration.

Corneal endothelial cells (CEnCs) play a fundamental role in maintaining the transparency of the cornea. CEnCs lose their full proliferating capacity when tissue damages occur. The loss in proliferation rate is associated with corneal edema and decrease in visual acuity, leading in severe cases, to blindness. In these situations, a corneal transplant is usually needed to restore the original tissue functions. Tissue engineering is an efficient alternative for the production of implantable films, which can regenerate the tissue functions regulating at the same time the immune-response. In this study, we proposed a stable and transparent film, composed of silk fibroin modified with glycerol (G/SF), as a potential substrate for corneal endothelial cells regeneration. Our results confirmed that G/SF films have a uniform structure, rougher surface and lower thickness respect to the SF film. In vitro tests show that G/SF films can induce a slight increase in CEnCs initial adhesion and proliferation rate if compared with the SF film. Morphology and gene expression evaluations demonstrated that the bioactive effects of silk fibroin were not affected by the presence of glycerol. For this reason, the G/SF films are suitable as CEnCs carrier and promising for the corneal damages treatments.

Enhanced retinal pigment epithelium (RPE) regeneration using curcumin/alginate hydrogels: In vitro evaluation.

The retinal pigment epithelium (RPE) plays a significant role in retaining structural integrity of eye. Factors such as reduction in cell regeneration due to aging and physical injury pose a major hurdle in RPE regeneration. In this study, we exploited the use of alginate (AGT) incorporated with Curcumin (CCI) forming a hydrogel based system CCI/AGT. The fabricated hydrogel could anchor RPE cell in it. In vitro cell analysis revealed that the CCI/AGT hydrogel shows good biocompatibility, enhanced cell growth ability and higher ECM formation compared to the pure AGT hydrogel. In particular, the presence of CCI in the hydrogels enhances the cells proliferation of the 23% respect to the pure alginate. Also the expression of crucial genes for retina functions and matrix production were positively affected by CCI presence, with an increment of 45% for RPE65, 32% for CRALBP and 26% for Collagen type 1. In vitro tests demonstrated the potential application of CCI/AGT hydrogels for transplantation under the sub-retinal space acting as a cell delivery vehicle and also their capability to provide an appropriate environment for RPE regeneration. These results suggest that CCI/AGT hydrogel could be translated into a potential surgical graft for biological implantation of retinal tissue engineering.