Smart Approach for the Design of Highly Selective Aptamer-Based Biosensors

Aptamers are chemically synthesized single-stranded DNA or RNA oligonucleotides widely used nowadays in sensors and nanoscale devices as highly sensitive biorecognition elements. With proper design, aptamers are able to bind to a specific target molecule with high selectivity. To date, the systematic evolution of ligands by exponential enrichment (SELEX) process is employed to isolate aptamers. Nevertheless, this method requires complex and time-consuming procedures. In silico methods comprising machine learning models have been recently proposed to reduce the time and cost of aptamer design. In this work, we present a new in silico approach allowing the generation of highly sensitive and selective RNA aptamers towards a specific target, here represented by ammonium dissolved in water. By using machine learning and bioinformatics tools, a rational design of aptamers is demonstrated. This "smart" SELEX method is experimentally proved by choosing the best five aptamer candidates obtained from the design process and applying them as functional elements in an electrochemical sensor to detect, as the target molecule, ammonium at different concentrations. We observed that the use of five different aptamers leads to a significant difference in the sensor's response. This can be explained by considering the aptamers' conformational change due to their interaction with the target molecule. We studied these conformational changes using a molecular dynamics simulation and suggested a possible explanation of the experimental observations. Finally, electrochemical measurements exposing the same sensors to different molecules were used to confirm the high selectivity of the designed aptamers. The proposed in silico SELEX approach can potentially reduce the cost and the time needed to identify the aptamers and potentially be applied to any target molecule

Pseudoprogressione in pazienti trattati con radio-chemioterapia per gliomi di alto grado: valutazioni cliniche, dosimetriche e biomolecolari.

Circa il 50% dei pazienti con gliomi di alto grado trattati con radio-chemioterapia postoperatoria presenta a distanza di circa 12 settimane dal termine del trattamento immagini radiologiche che mimano progressione di malattia, condizione nota come pseudoprogressione. Dall’analisi dei dati presenti in letteratura emerge la mancanza di una tipizzazione dei fenomeni legati all’insorgenza della pseudoprogressione: obiettivo del presente lavoro è un’analisi retrospettiva di un campione di pazienti affetti da glioma di alto grado trattati con radio-chemioterapia con temozolomide fino a un massimo di 12 cicli presso l’Unità Operativa di Radioterapia Universitaria dell’Azienda Ospedaliero Universitaria Pisana con lo scopo di individuare la presenza di fattori clinici, biologici e dosimetrici predittivi di pseudoprogressione e la rilevanza di tale evento in termini di sopravvivenza mediana

Ruolo della radioterapia nel trattamento multidisciplinare delle metastasi scheletriche

Nella seguente tesi vengono descritte le principali opzioni terapeutiche per il trattamento delle metastasi ossee. In particolare , vengono analizzati i meccanismi fisiopatologici e le manifestazioni cliniche riferite dal paziente affetto da localizzazioni ossee metastatiche. Vengono esaminate le principali opzioni terapeutiche con particolare riferimento alla terapia radiante descrivendone meccanismo d’azione, modalità d’esecuzione, frazionamento ed effetti terapeutici

Stereotactic radiotherapy for oligometastases in the lymph nodes

Even though systemic therapy is standard treatment for lymph node metastases, metastasis-directed stereotactic radiotherapy (SRT) seems to be a valid option in oligometastatic patients with a low disease burden. Positron emission tomography/computed tomography (PET-CT) is the gold standard for assessing metastases to the lymph nodes; co-registration of PET-CT images and planning CT images are the basis for gross tumor volume (GTV) delineation. Appropriate techniques are needed to overcome target motion. SRT schedules depend on the irradiation site, target volume and dose constraints to the organs at risk (OARs) of toxicity. Although several fractionation schemes were reported, total doses of 48–60 Gy in 4–8 fractions were proposed for mediastinal lymph node SRT, with the spinal cord, esophagus, heart and proximal bronchial tree being the dose limiting OARs. Total doses ranged from 30 to 45 Gy, with daily fractions of 7–12 Gy for abdominal lymph nodes, with dose limiting OARs being the liver, kidneys, bowel and bladder. SRT on lymph node metastases is safe; late side effects, particularly severe, are rare

Salvage Hypofractionated Radiotherapy in Combination with Bevacizumab in Patients with Recurrent High Grade Glioma: A Mono-institutional Experience

Background: After the detection of recurrent high-grade glioma, there are no standard approaches; salvage surgery, chemotherapy and radiotherapy are often used despite the fact that no real clinical benefit has been confirmed and the combination of these approaches has not yet been fully investigated. Objective: In the present retrospective study, we reported the results of a mono-institutional experience studying the association of salvage hypofractionated stereotactic radiotherapy in combination with bevacizumab in patients with recurrent glioblastoma after standard up-front therapy with the Stupp protocol. Method: From May 2010 to December 2016, eight patients with recurrent glioblastoma were treated with hypofractionated radiotherapy 25 Gy in 5 fractions in combination with bevacizumab at the University Hospital of Pisa. Results: All patients showed appreciable improvements in Karnofsky Performance Status and median survival following the beginning of radiotherapy treatment to 7 months (range 3–15 months). Severe toxicity has not been recorded. Conclusion: Hypofractionated radiotherapy associated with bevacizumab may represent a valid therapeutic option in selected patients with recurrent high-grade gliom

Clinical Outcomes of Stereotactic Body Radiotherapy in Oligometastatic Gynecological Cancer

Abstract OBJECTIVE: The objective of this study was to assess the role of stereotactic body radiotherapy (SBRT) in the treatment of distantly recurrent, oligometastatic gynecological cancer. METHODS: The hospital records of 45 patients with F-fluorodeoxyglucose (F-FDG) positron emission tomography positive, distantly recurrent, oligometastatic gynecological cancer were reviewed. All these patients had a number of target lesions less than 5, with largest diameter less than 6 cm. The treatment was delivered with a TrueBeam LINAC and RapidArc technique, using 10 or 6 MV FFF beams. A total of 70 lesions were treated, and lymph nodes represented the most common site of metastases, followed by lung, liver, and soft tissues. Twenty lesions were treated with one single fraction of 24 Gy and 5 lesions received 27 Gy delivered in 3 fractions, depending on the ability to fulfill adequate target coverage and safe dose/volume constraints for the organ at risk with either regimen. RESULTS: Positron emission tomography scan 3 months after SBRT showed a complete response (CR) in 45 lesions (64.3%), a partial response in 14 (20.0%), a stable disease in 5 (7.1%), and a progressive disease in 6 (8.6%). No lesions in CR after SBRT subsequently progressed. Overall acute toxicity occurred in 13 (28.9%) patients. The most common grade 1 to 2 adverse event was pain (n = 9, 20.0%), followed by nausea and vomiting (n = 5, 11.1%). No grade 3 to 4 acute toxicities occurred, and no late toxicities were observed. Patients who failed to achieve a CR had a 2.37-fold higher risk of progression and a 3.60-fold higher risk of death compared with complete responders (P = 0.04 and P = 0.03, respectively). CONCLUSIONS: Stereotactic body radiotherapy offers an effective and safe approach for selected cases of oligometastatic gynecological cancer

LINE-1 hypermethylation in white blood cell DNA is associated with high-grade cervical intraepithelial neoplasia

Abstract Background Long Interspersed Nuclear Elements-1 (LINEs-1) methylation from white blood cells (WBCs) DNA has been proposed as biomarker associated with different types of cancer. The aim of the present study was to investigate the degree of WBCs LINE-1 methylation, according to high-risk Human Papilloma Virus (hrHPV) status in a healthy population, and the association with high-grade Cervical Intraepithelial Neoplasia (CIN2+) in hrHPV positive women. Methods Women with abnormal cervical cells were enrolled and classified by histological diagnosis and hrHPV infection. A structured questionnaire was used to obtain information on socio-demographic variables and lifestyle factors. LINE-1 methylation level in WBCs was measured by pyrosequencing-based methylation analysis after bisulfite conversion. Results Among 252 women diagnosed with normal cervical epithelium, with regard to LINE-1 methylation level no significant difference was observed between hrHPV positive and hrHPV negative women, also adjusting for known risk factors of infection. The association between WBCs LINE-1 methylation and CIN2+ status was analyzed in hrHPV positive women. The median value of LINE-1 methylation levels was higher in cases (CIN2+) than in controls (75.00% versus 73.17%; p = 0.002). For a one-unit increase in LINE-1 methylation level, the odds of being diagnosed with CIN2+ increased by 10%, adjusting for known factors related to LINE-1 methylation (adjOR: 1.10; 95% CI:1.01–1.20; p = 0.032). The Receiver-Operating Characteristic (ROC) curve analysis identified the cut-off value of 73.8% as the best threshold to separate cases from controls (sensitivity: 63.4% and specificity: 61.8%). Conclusions LINE-1 methylation status in WBCs DNA may represent a cost-effective and tissue-accessible biomarker for high-grade CIN in hrHPV positive women. However, LINE-1 hypermethylation cannot be considered specific for cervical cancer (CC) and a model based solely on LINE-1 methylation levels has limited performance. Further investigations are necessary to propose and validate a novel methylation biomarker panel, based on LINE-1 methylation and other differentially methylated regions, for the screening of women at risk of CC

Hybrid nickel-free graphene/porphyrin rings for photodegradation of emerging pollutants in water

A novel hybrid photoactive material based on graphene foam (G) coupled with porphyrin-based polymers (Porph rings) was formulated by using a time-saving procedure to remove nickel from the final device

Stereotactic body radiotherapy of bone metastases in oligometastatic disease: prognostic factors of oncologic outcomes

Background: To evaluate the safety of stereotactic body radiotherapy (SBRT) of bone metastases in oligometastatic disease and to investigate prognostic factors of local control (LC), progression/disease-free survival (PDFS), and overall survival (OS). Methods: Eligibility criteria were number of metastates ≤5, controlled primary tumor without evidence of progression under systemic therapy, exclusion of surgery, and no previous radiotherapy of the lesion of interest. Oligometastatic status was classified into only bone (BOD) and outside bone disease (OBOD), whereas SBRT was delivered to bone lesions using 2 different schedules: 24 Gy/1 fraction or 27 Gy/3 fractions. A positron emission tomography study of the lesion of interest was performed at baseline and at 3 months after SBRT to evaluate metabolic response according to European Organization for Research and Treatment of Cancer (EORTC) criteria. A Cox regression model was used for univariate and multivariate analysis. Results: Between January 2010 and December 2013, 40 patients were enrolled. Only 1 patient experienced severe late toxicity (radiation-related fracture). Local control was longer among responders’ than nonresponders’ lesions (94.2% and 91.2% versus 63% and 35% at 1 and 2 years, respectively) (p = 0.004; hazard ratio = 9.958). The multivariate analysis of PDFS showed a significant correlation with planning target volume (PTV) size (p = 0.003) and oligometastatic status (p = 0.002). The multivariate analysis of OS confirmed a statistically significant value of the oligometastatic status (p = 0.002) and a significant trend for PTV size (p = 0.065). Conclusions: Stereotactic body radiotherapy is safe with a low incidence of severe toxicity. Positron emission tomography response was a strong prognostic factor of LC whereas BOD status and small PTV size could identify a subset of oligometastatic patients at better prognosis