Genome-Wide Multiple Sclerosis Association Data and Coagulation

The emerging concept of a crosstalk between hemostasis, inflammation, and immune system prompt recent works on coagulation cascade in multiple sclerosis (MS). Studies on MS pathology identified several coagulation factors since the beginning of the disease pathophysiology: fibrin deposition with breakdown of blood brain barrier, and coagulation factors within active plaques may exert pathogenic role, especially through the innate immune system. Studies on circulating coagulation factors showed complex imbalance involving several components of hemostasis cascade (thrombin, factor X, factor XII). To analyze the role of the coagulation process in connection with other pathogenic pathways, we implemented a systematic matching of genome-wide association studies (GWAS) data with an informative and unbiased network of coagulation pathways. Using MetaCore (version 6.35 build 69300, 2018) we analyzed the connectivity (i.e., direct and indirect interactions among two networks) between the network of the coagulation process and the network resulting from feeding into MetaCore the MS GWAS data. The two networks presented a remarkable over-connectivity: 958 connections vs. 561 expected by chance; z-score = 17.39; p-value < 0.00001. Moreover, genes coding for cluster of differentiation 40 (CD40) and plasminogen activator, urokinase (PLAU) shared both networks, pointed to an integral interplay between coagulation cascade and main pathogenic immune effectors. In fact, CD40 pathways is especially operative in B cells, that are currently a major therapeutic target in MS field. The potential interaction of PLAU with a signal of paramount importance for B cell pathogenicity, such as CD40, suggest new lines of research and pave the way to implement new therapeutic targets

Noise in multiple sclerosis: unwanted and necessary

As our knowledge about the etiology of multiple sclerosis (MS) increases, deterministic paradigms appear insufficient to describe the pathogenesis of the disease, and the impression is that stochastic phenomena (i.e. random events not necessarily resulting in disease in all individuals) may contribute to the development of MS. However, sources and mechanisms of stochastic behavior have not been investigated and there is no proposed framework to incorporate nondeterministic processes into disease biology. In this report, we will first describe analogies between physics of nonlinear systems and cell biology, showing how small-scale random perturbations can impact on large-scale phenomena, including cell function. We will then review growing and solid evidence showing that stochastic gene expression (or gene expression “noise”) can be a driver of phenotypic variation. Moreover, we will describe new methods that open unprecedented opportunities for the study of such phenomena in patients and the impact of this information on our understanding of MS course and therapy

OREMP: Ontology Reasoning Engine for Molecular Pathways

The information about molecular processes is shared continuously in the form of runnable pathway collections, and biomedical ontologies provide a semantic context to the majority of those pathways. Recent advances in both fields pave the way for a scalable information integration based on aggregate knowledge repositories, but the lack of overall standard formats impedes this progress. Here we propose a strategy that integrates these resources by means of extended ontologies built on top of a common meta-format. Information sharing, integration and discovery are the primary features provided by the system; additionally, two current field applications of the system are reported

Methylation-dependent PAD2 upregulation in multiple sclerosis peripheral blood

Background: Peptidylarginine deiminase 2 (PAD2) and peptidylarginine deiminase 4 (PAD4) are two members of PAD family which are over-expressed in the multiple sclerosis (MS) brain. Through its enzymatic activity PAD2 converts myelin basic protein (MBP) arginines into citrullines - an event that may favour autoimmunity - while peptidylarginine deiminase 4 (PAD4) is involved in chromatin remodelling. Objectives: Our aim was to verify whether an altered epigenetic control of PAD2, as already shown in the MS brain, can be observed in peripheral blood mononuclear cells (PBMCs) of patients with MS since some of these cells also synthesize MBP. Methods: The expression of most suitable reference genes and of PAD2 and PAD4 was assessed by qPCR. Analysis of DNA methylation was performed by bisulfite method. Results: The comparison of PAD2 expression level in PBMCs from patients with MS vs. healthy donors showed that, as well as in the white matter of MS patients, the enzyme is significantly upregulated in affected subjects. Methylation pattern analysis of a CpG island located in the PAD2 promoter showed that over-expression is associated with promoter demethylation. Conclusion: Defective regulation of PAD2 in the periphery, without the immunological shelter of the blood-brain barrier, may contribute to the development of the autoimmune responses in MS

A staged screening of registered drugs highlights remyelinating drug candidates for clinical trials

There is no treatment for the myelin loss in multiple sclerosis, ultimately resulting in the axonal degeneration that leads to the progressive phase of the disease. We established a multi-tiered platform for the sequential screening of drugs that could be repurposed as remyelinating agents. We screened a library of 2,000 compounds (mainly Food and Drug Administration (FDA)-approved compounds and natural products) for cellular metabolic activity on mouse oligodendrocyte precursors (OPC), identifying 42 molecules with significant stimulating effects. We then characterized the effects of these compounds on OPC proliferation and differentiation in mouse glial cultures, and on myelination and remyelination in organotypic cultures. Three molecules, edaravone, 5-methyl-7-methoxyisoflavone and lovastatin, gave positive results in all screening tiers. We validated the results by retesting independent stocks of the compounds, analyzing their purity, and performing dose-response curves. To identify the chemical features that may be modified to enhance the compounds' activity, we tested chemical analogs and identified, for edaravone, the functional groups that may be essential for its activity. Among the selected remyelinating candidates, edaravone appears to be of strong interest, also considering that this drug has been approved as a neuroprotective agent for acute ischemic stroke and amyotrophic lateral sclerosis in Japan

Periodic and aperiodic liquid crystal-polymer composite structures realized via spatial light modulator direct holography

In this work we present the first realization and characterization of two-dimensional periodic and aperiodic POLICRYPS (Polymer Liquid Crystal Polymer Slices) structures, obtained by means of a single-beam holographic technique exploiting a high resolution spatial light modulator (SLM). A first investigation shows that the gratings, operating in the Raman Nath regime, exhibit a morphology and a electro-optical behavior that are typical of the POLICRYPS gratings realized by two-beam interference holography

GWAS-associated Variants, Non-genetic Factors, and Transient Transcriptome in Multiple Sclerosis Etiopathogenesis: a Colocalization Analysis [preprint]

A clinically actionable understanding of multiple sclerosis (MS) etiology goes through GWAS interpretation, prompting research on new gene regulatory models. Our previous works on these topics suggested a stochastic etiologic model where small-scale random perturbations could eventually reach a threshold for MS onset and progression. A new sequencing technology has mapped the transient transcriptome (TT), including intergenic RNAs, and antisense intronic RNAs. Through a rigorous colocalization analysis, here we show that genomic regions coding for the TT were significantly enriched for both MS-associated GWAS variants, and DNA binding sites for molecular transducers mediating putative, non-genetic, etiopathogenetic factors for MS (e.g., vitamin D deficiency, Epstein Barr virus latent infection, B cell dysfunction). These results suggest a model whereby TT-coding regions are hotspots of convergence between genetic ad non-genetic factors of risk/protection for MS (and plausibly for other complex disorders). Our colocalization analysis also provides a freely available data resource at www.mscoloc.com for future research on transcriptional regulation in MS

Thermoplasmonics with Gold Nanoparticles: A New Weapon in Modern Optics and Biomedicine

Thermoplasmonics deals with the generation and manipulation of nanoscale heating associated with noble metallic nanoparticles. To this end, gold nanoparticles (AuNPs) are unique nanomaterials with the intrinsic capability to generate a nanoscale confined light‐triggered thermal effect. This phenomenon is produced under the excitation of a suitable light of a wavelength that matches the localized surface plasmonic resonance frequency of AuNPs. Liquid crystals (LCs) and hydrogels are temperature‐sensitive materials that can detect the host AuNPs and their photo‐induced temperature variations. In this perspective, new insight into thermoplasmonics, by describing a series of methodologies for monitoring, detecting, and exploiting the photothermal properties of AuNPs, is offered. From conventional infrared thermography to highly sophisticated temperature‐sensitive materials such as LCs and hydrogels, a new scenario in thermoplasmonic‐based, next generation, photonic components is presented and discussed. Moreover, a new road in thermoplasmonic‐driven biomedical applications, by describing compelling and innovative health technologies such as on‐demand drug‐release and smart face masks with smart nano‐assisted destruction of pathogens, is proposed. The latter represents a new weapon in the fight against COVID‐19

Antimicrobial effects of chemically functionalized and/or photo-heated nanoparticles

Antibiotic resistance refers to when microorganisms survive and grow in the presence of specific antibiotics, a phenomenon mainly related to the indiscriminate widespread use and abuse of antibiotics. In this framework, thanks to the design and fabrication of original functional nanomaterials, nanotechnology offers a powerful weapon against several diseases such as cancer and pathogenic illness. Smart nanomaterials, such as metallic nanoparticles and semiconductor nanocrystals, enable the realization of novel drug-free medical therapies for fighting against antibiotic-resistant bacteria. In the light of the latest developments, we highlight the outstanding capabilities of several nanotechnology-inspired approaches to kill antibiotic-resistant bacteria. Chemically functionalized silver and titanium dioxide nanoparticles have been employed for their intrinsic toxicity, which enables them to exhibit an antimicrobial activity while, in a different approach, photo-thermal properties of metallic nanoparticles have been theoretically studied and experimentally tested against several temperature sensitive (mesophilic) bacteria. We also show that it is possible to combine a highly localized targeting with a plasmonic-based heating therapy by properly functionalizing nanoparticle surfaces with covalently linked antibodies. As a perspective, the utilization of properly engineered and chemically functionalized nanomaterials opens a new roads for realizing antibiotic free treatments against pathogens and related diseases