SINEUPs, a new class of antisense long non-coding RNAs that enhance synthesis of target proteins in cells: molecular mechanisms and applications

Thanks to continuous advances in sequencing technologies, we know that a huge number of non-coding RNAs are transcribed from mammalian genomes. Of these, long non-coding RNAs (lncRNAs) represent the widest and most heterogeneous class. An increasing number of studies are unveiling lncRNA functions, supporting their active role in regulating gene expression. Regardless of lncRNAs specific functional features, their organization into discrete domains seems to represent a common denominator. Through such domains lncRNAs can recruit and coordinate the activity of multiple effectors, thus working as \u201cflexible modular scaffolds\u201d. This model has globally driven towards the quest for regulatory elements within lncRNAs, with a special attention on functional cues deriving from RNA folding. Since transposable elements (TEs) represent 40% of nucleotides of lncRNA sequences, they have been proposed as candidate functional modules. Carrieri and colleagues recently reported that an embedded inverted SINEB2 element acts as a functional domain in antisense (AS) Uchl1, an AS lncRNA able to increase translation of partially-overlapping protein-coding sense Uchl1 mRNA. AS Uchl1 regulatory properties depend on two RNA domains. A 5' overlapping sequence to the sense transcript is the Binding Domain (BD) and drives specificity of action. An embedded inverted SINEB2 element functions as Effector Domain (ED) conferring translational activation power. AS Uchl1 is the representative member of a new class of lncRNAs, named SINEUPs, as they rely on a SINEB2 element to UP-regulate translation. AS Uchl1 activity can be transferred to a synthetic construct by manipulating the AS sequence in the BD, suggesting the potential use of AS Uchl1- derived synthetic SINEUPs as tools to increase translation of selected targets. This work was the first example of a specific biological function assigned to an embedded TE leading to the hypothesis that embedded TEs provide functional modules to lncRNAs. A major limit to the application of SINEUPs is represented by the poor knowledge of the basic mechanisms underlying the biological activity of the ED. A crucial challenge becomes the identification of secondary structures that may confer characteristic protein binding properties. Protein partners would modulate SINEUPs action and contribute to achieve specific functional outputs. In this thesis, I focus on understanding the molecular basis of SINEUPs activity in cells and I discuss the potential applications of synthetic SINEUPs as translation enhancers. First, I investigated the structural basis for translation activation mediated by the ED of SINEUPs. I pointed out that specific structural regions, containing a short terminal hairpin, are involved in the ability of natural and synthetic SINEUPs to increase translation of target mRNAs. Next, I identified protein partners modulating the activity of SINEUPs in cells. I found that AS Uchl1 interacts with the interleukin enhancer-binding factor 3 (ILF3) and that the presence of the inverted SINEB2 favors binding in vivo. In particular, I demonstrated that the AS Uchl1-embedded TEs, inverted SINEB2 and Alu, direct AS Uchl1 localization to ILF3-containing complexes, thus contributing to AS Uchl1 bias towards nuclear localization. I thus suggest that nuclear retention could represent a possible mechanism regulating SINEUP activity. I also validated the scalability of synthetic SINEUPs as tools to increase protein synthesis of targets of choice. I showed that SINEUP technology can be adapted to a broader number of targets, with interesting potential applications in different fields, from biotechnology to therapy. SINEUPs function in an array of cell lines and can be efficiently directed toward N-terminally tagged proteins. Their biological activity is retained in a miniaturized version within the range of small RNAs length. Their modular structure can be exploited to successfully design synthetic SINEUPs against selected endogenous targets, supporting their efficacy as tools to modulate gene expression in vitro and in vivo. Hence, I propose SINEUPs as versatile tools to enhance translation of mRNAs of choice

Semaphorin 4D regulates gonadotropin hormone–releasing hormone-1 neuronal migration through PlexinB1–Met complex

In mammals, reproduction is dependent on specific neurons secreting the neuropeptide gonadotropin hormone–releasing hormone-1 (GnRH-1). These cells originate during embryonic development in the olfactory placode and migrate into the forebrain, where they become integral members of the hypothalamic–pituitary–gonadal axis. This migratory process is regulated by a wide range of guidance cues, which allow GnRH-1 cells to travel over long distances to reach their appropriate destinations. The Semaphorin4D (Sema4D) receptor, PlexinB1, is highly expressed in the developing olfactory placode, but its function in this context is still unknown. Here, we demonstrate that PlexinB1-deficient mice exhibit a migratory defect of GnRH-1 neurons, resulting in reduction of this cell population in the adult brain. Moreover, Sema4D promotes directional migration in GnRH-1 cells by coupling PlexinB1 with activation of the Met tyrosine kinase (hepatocyte growth factor receptor). This work identifies a function for PlexinB1 during brain development and provides evidence that Sema4D controls migration of GnRH-1 neurons

The role of topical povidone-iodine in the management of infectious keratitis: a pilot study

The aim of this prospective explorative study was to evaluate the safety and the effectiveness of topical polyvinylpyrrolidone-iodine (PVP-I) administered during the time-to-results period for pathogen identification and susceptibility testing in patients with infectious keratitis (IK). A corneal swab (CS) for antimicrobial evaluation was performed at enrollment (T0) and topical 0.66%-PVP-I was administered until the laboratory results were available (T1). Ulcer and infiltrate areas and infiltrate depths were compared between T0 and T1 (i.e., time-to-result period). Patients were then shifted to a specific antimicrobial therapy and followed up until resolution of their infiltrates (Tlast-TL). Twenty-five eyes were enrolled, and none showed clinical worsening leading to protocol withdrawal. At T1, ulcer and infiltrate areas showed significant improvement in Gram-positive IK (n = 13-52%; p = 0.027 and p = 0.019, respectively), remained stable in fungal IK (n = 5-20%; both p = 0.98) and increased in those with Gram-negative bacteria (n = 4-16%; p = 0.58 and p = 0.27). Eyes with negative cultures (n = 3-12%) showed complete resolution at T1 and did not initiate any additional antimicrobial therapy. The administration of 0.66% PVP-I during the time-to-result period seems to be a safe strategy in patients with IK while often sparing broad-spectrum antimicrobial agents. In addition, it showed to be effective in eyes with a Gram-positive bacterial infection

Microscopic corneal epithelial changes and clinical outcomes in simple limbal epithelial transplantation surgery after treatment with amniotic membrane eye drops (AMED): A case report

Purpose: To describe the microscopic epithelial changes and the clinical outcomes of a patient treated with amniotic membrane eye drops (AMED) because of a persistent epithelial defect (PED) and a partial limbal stem cell deficiency (LSCD) after simple limbal epithelial transplantation (SLET) and deep anterior lamellar keratoplasty (DALK). Observations: A 72-year-old patient, who had previously undergone SLET and DALK due to a total LSCD, presented with a PED related to a partial LSCD, and was treated with AMED for one month. We evaluated the patient's visual acuity, the Oxford grading scale, the Wong-Baker Pain Rating Scale, and in vivo confocal microscopy, both at baseline and 3 months after the end of treatment. Visual acuity improved from 0.5 to 0.4 LogMAR, the Oxford grading scale changed from grade III to grade I and the Wong-Baker Pain Rating Scale from grade 4 to grade 1. The corneal surface, which initially showed conjunctival characteristics over approximately 50% of the whole area, consisted mainly (75%) of mature corneal epithelium 3 months after the end of treatment. Conclusions and importance: While improving symptoms and clinical characteristics, AMED was also able to restore the normal corneal epithelium's morphology in a case of partial LSCD after SLET and DALK

Autism Spectrum Disorder and screen time during lockdown: an Italian study.

Background: Lockdown due to Covid-19 pandemic brought deep changes to the daily lives of children with Autism Spectrum Disorder (ASD), greatly increasing their amount of time spent at home. Methods: A cohort of 243 parents of children with ASD (2-15 years old) completed an original online survey regarding the child's screen time and the modification of the ASD symptomatology during lockdown to investigate the relationship between them. Results: The data show that high solitary screen time is related with the worsening of ASD core symptoms. Conclusions: This study may help to increase awareness in the excessive use of screen in children with ASD during the lockdown, both during the pandemic as well as after it ends

SINEUPs are modular antisense long non-coding RNAs that increase synthesis of target proteins in cells

Despite recent efforts in discovering novel long non-coding RNAs (lncRNAs) and unveiling their functions in a wide range of biological processes their applications as biotechnological or therapeutic tools are still at their infancy. We have recently shown that AS Uchl1, a natural lncRNA antisense to the Parkinson's disease-associated gene Ubiquitin carboxyl-terminal esterase L1 (Uchl1), is able to increase UchL1 protein synthesis at post-transcriptional level. Its activity requires two RNA elements: an embedded inverted SINEB2 sequence to increase translation and the overlapping region to target its sense mRNA. This functional organization is shared with several mouse lncRNAs antisense to protein coding genes. The potential use of AS Uchl1-derived lncRNAs as enhancers of target mRNA translation remains unexplored. Here we define AS Uchl1 as the representative member of a new functional class of natural and synthetic antisense lncRNAs that activate translation. We named this class of RNAs SINEUPs for their requirement of the inverted SINEB2 sequence to UP-regulate translation in a gene-specific manner. The overlapping region is indicated as the Binding Doman (BD) while the embedded inverted SINEB2 element is the Effector Domain (ED). By swapping BD, synthetic SINEUPs are designed targeting mRNAs of interest. SINEUPs function in an array of cell lines and can be efficiently directed toward N-terminally tagged proteins. Their biological activity is retained in a miniaturized version within the range of small RNAs length. Its modular structure was exploited to successfully design synthetic SINEUPs targeting endogenous Parkinson's disease-associated DJ-1 and proved to be active in different neuronal cell lines. In summary, SINEUPs represent the first scalable tool to increase synthesis of proteins of interest. We propose SINEUPs as reagents for molecular biology experiments, in protein manufacturing as well as in therapy of haploinsufficiencies

Prevalence and risk factors of eye diseases in adult patients with obstructive sleep apnoea: results from the SLE.E.P.Y cohort study

OBJECTIVES: To assess the occurrence of glaucoma, eyelid, corneal and macular disorders in a cohort of patients with obstructive sleep apnoea (OSA) diagnosed by overnight polysomnography and to investigate into the risk factors for the above eye diseases (EDs). DESIGN: Cross-sectional cohort study between 2014 and 2015. SETTING: Unit of Respiratory Medicine and Eye Clinic of the University of Verona. PARTICIPANTS: 431 consecutive patients were considered eligible. Of these, 87 declined to participate, 35 were untraceable and 13 were deceased. INTERVENTIONS: A complete ophthalmic evaluation of both eyes for each patient. PRIMARY AND SECONDARY OUTCOME MEASURES: Best-corrected distance visual acuity, intraocular pressure, corneal, macular and optic nerve optical coherence tomography, ocular aberrometry, optic nerve laser polarimetry, visual field test, and eyelid examination. RESULTS: 296 patients aged 64.5±12.8 years, 23% female and 77% male, underwent ophthalmic examination. There was 56% (n=166) prevalence of eyelid disorders, 27% (n=80) of corneal disorders, 13% (n=39) of macular disorders and 11% (n=33) of glaucoma. Advancing age was not associated with the severity of OSA, while significant differences were found for gender, body mass index, Oxygen Desaturation Index, smoking habit, hypertension and diabetes. Severe OSA was significantly associated with glaucoma (OR, 95% CI 1.05 to 5.93, p=0.037). CONCLUSIONS: EDs were more prevalent in our patinets with OSA than in the general population. Severe Apnoea/Hypopnoea Index level seemed to play a role as risk factor only for glaucoma

Association of Mild Anemia with Cognitive, Functional, Mood and Quality of Life Outcomes in the Elderly: The “Health and Anemia” Study

BACKGROUND: In the elderly persons, hemoglobin concentrations slightly below the lower limit of normal are common, but scant evidence is available on their relationship with significant health indicators. The objective of the present study was to cross-sectionally investigate the association of mild grade anemia with cognitive, functional, mood, and quality of life (QoL) variables in community-dwelling elderly persons. METHODS: Among the 4,068 eligible individuals aged 65-84 years, all persons with mild anemia (n = 170) and a randomly selected sample of non-anemic controls (n = 547) were included in the study. Anemia was defined according to World Health Organization (WHO) criteria and mild grade anemia was defined as a hemoglobin concentration between 10.0 and 11.9 g/dL in women and between 10.0 and 12.9 g/dL in men. Cognition and functional status were assessed using measures of selective attention, episodic memory, cognitive flexibility and instrumental and basic activities of daily living. Mood and QoL were evaluated by means of the Geriatric Depression Scale-10, the Short-Form health survey (SF-12), and the Functional Assessment of Cancer Therapy-Anemia. RESULTS: In univariate analyses, mild anemic elderly persons had significantly worse results on almost all cognitive, functional, mood, and QoL measures. In multivariable logistic regressions, after adjustment for a large number of demographic and clinical confounders, mild anemia remained significantly associated with measures of selective attention and disease-specific QoL (all fully adjusted p<.046). When the lower limit of normal hemoglobin concentration according to WHO criteria was raised to define anemia (+0.2 g/dL), differences between mild anemic and non anemic elderly persons tended to increase on almost every variable. CONCLUSIONS: Cross-sectionally, mild grade anemia was independently associated with worse selective attention performance and disease-specific QoL ratings