Network based analysis to identify master regulators in prostate carcinogenesis

Prostate cancer (PCa) is the second most common tumor diagnosed in man, for which robust prognostic markers and novel targets for therapy are lacking. Major challenges in PCa therapeutical management arise from the marked intra and inter-tumors heterogeneity, hampering the discernment of molecular subtypes that can be used to guide treatment decisions. For this reason, virtually all patients undergoing standard of care androgen deprivation therapy for locally advanced or metastatic cancer, will eventually progress into the more aggressive and currently incurable form of PCa, referred to as castration resistant prostate cancer (CRPC). By exploiting the richness of information stored in gene-gene interactions, I tested the hypothesis that a gene regulatory network derived from transcriptomic profiles of PCa orthografts can reveal transcriptional regulators to be subsequently adopted as robust biomarkers or as target for novel therapies. Among the 1308 regulons identified from the preclinical models, Cox regression analysis coherently associated JMJD6 regulon activity with disease-free survival in three clinical cohorts, outperforming three published prognostic gene signatures (TMCC11, BROMO-10 and HYPOXIA-28). Given its potential role in a number of cancers, in-depth investigations of JMJD6 mediated function in PCa is warranted to test if it has a driver role in tumor progression. Encouraged by the predictive abilities of the gene regulatory network inferred from transcriptomics data, I explored the possibility of integrating the regulons structure with data from the proteomes of the same preclinical orthografts studied by RNA sequencing. This approach leverages the complementarity between gene and protein expression, to increase the robustness of the statistical analysis. Similar to gene-gene co-expression profiles, protein-protein co-expression data can provide a distinct representation of the molecular alterations underlying a biological phenotype. By implementing a pipeline to integrate modules derived from transcriptomic based regulons and proteinprotein interactions respectively from matched RNA-seq and quantitative proteomic data, I obtained 516 joint modules entailing a median of four protein complexes (range 1-41) per individual transcription factor regulon, providing new insight into its regulatory mechanisms. In the final step of the analysis, a permutation-based enrichment of the genes/proteins integrative modules implicated MID1 (an E3 ubiquitin ligase belonging to the family of tripartite motif containing protein) to be a driver transcriptional regulator in CRPC. In fact, MID1 module was the only candidate for which gene-gene and proteinprotein interactions were supported (p-value < 0.05) by both differentially expressed genes and proteins obtained from the CRPC vs PC contrast. Finally, I wished to test the usefulness of a network based investigation as a tool to identify predictors of treatment response. To this end, I obtained transcriptomics data from an in vivo subcutaneous xenograft treatment experiment (namely mychophenolic acid or abiraterone/ARN-509 as stand alone treatment or in combination) and determined which regulons were inferred to be active in the tumours following treatment. The androgen receptor positive human LNCaP C4-2b prostate cancer cells were injected into mice. The effects of treatment were assessed by collecting serial tumor sizes and by performing RNAseq at the designed endpoint of the study. Noteworthy, the gene graph enrichment analysis provided novel hypothesisbehind the anti- proliferative effect of mychophenolic acid (MPA), suggesting the SET proto-oncogene to be a target for MPA mediated suppression of proliferation. Of note, standard gene-set enrichment analysis, without input on specific gene-gene interactions, was not effective in prioritising the SET protooncogene, demonstrating the usefulness of the network based investigation. Collectively, data presented in this thesis provides an alternative perspective for the analysis of multi-omics profiles from PCa and highlights the importance of gene-gene and protein protein interactions in prostate cancer growth and progression

A Cross-Sectional Study on Cognitive Vulnerability Patterns in Dental Anxiety: The Italian Validation of the Dental Fear Maintenance Questionnaire (DFMQ)

Dental anxiety is a crucial problem for dentistry because it may represent a significant risk to oral health. Within the framework of the Cognitive Vulnerability Model (CVM), which sheds light on the cognitive vulnerability patterns that may cause dental anxiety, this study aimed to assess the psychometric characteristics of the Italian version of the Dental Fear Maintenance Questionnaire (DFMQ). The DFMQ is a 32-item questionnaire that assesses four cognitive vulnerability patterns, i.e., dangerousness, disgust, unpredictability, and uncontrollability. In a sample of 200 dental patients who had accessed public-university-hospital dental surgery, this study assessed the model fit of the DFMQ and different types of validity (i.e., predictive, convergent, construct, and discriminant validity). In addition, potential differences between DFMQ dimensions were assessed based on gender (men vs. women) and age ranges. All indicators of cognitive vulnerability were significantly associated with high dental anxiety when each variable was included independently. In contrast, when the DFMQ subscales were considered together, only unpredictability and uncontrollability were found to be associated with high dental anxiety. Women had higher scores for unpredictability, uncontrollability, and general dangerousness than men. In addition, older patients had higher scores for some vulnerability cognitive patterns than younger patients. This study provides Italian dentists and researchers with a valid questionnaire to assess cognitive factors associated with dental anxiety

Increased Expression and Altered Cellular Localization of Fibroblast Growth Factor Receptor-Like 1 (FGFRL1) Are Associated with Prostate Cancer Progression

Fibroblast growth factor receptors (FGFRs) 1–4 are involved in prostate cancer (PCa) regulation, but the role of FGFR-like 1 (FGFRL1) in PCa is unclear. FGFRL1 expression was studied by qRT-PCR and immunohistochemistry of patient tissue microarrays (TMAs) and correlated with clinical patient data. The effects of FGFRL1 knockdown (KD) in PC3M were studied in in vitro culture models and in mouse xenograft tumors. Our results showed that FGFRL1 was significantly upregulated in PCa. The level of membranous FGFRL1 was negatively associated with high Gleason scores (GSs) and Ki67, while increased cytoplasmic and nuclear FGFRL1 showed a positive correlation. Cox regression analysis indicated that nuclear FGFRL1 was an independent prognostic marker for biochemical recurrence after radical prostatectomy. Functional studies indicated that FGFRL1-KD in PC3M cells increases FGFR signaling, whereas FGFRL1 overexpression attenuates it, supporting decoy receptor actions of membrane-localized FGFRL1. In accordance with clinical data, FGFRL1-KD markedly suppressed PC3M xenograft growth. Transcriptomics of FGFRL1-KD cells and xenografts revealed major changes in genes regulating differentiation, ECM turnover, and tumor–stromal interactions associated with decreased growth in FGFRL1-KD xenografts. Our results suggest that FGFRL1 upregulation and altered cellular compartmentalization contribute to PCa progression. The nuclear FGFRL1 could serve as a prognostic marker for PCa patients

Increased Expression and Altered Cellular Localization of Fibroblast Growth Factor Receptor-Like 1 (FGFRL1) Are Associated with Prostate Cancer Progression

Fibroblast growth factor receptors (FGFRs) 1–4 are involved in prostate cancer (PCa) regulation, but the role of FGFR-like 1 (FGFRL1) in PCa is unclear. FGFRL1 expression was studied by qRT-PCR and immunohistochemistry of patient tissue microarrays (TMAs) and correlated with clinical patient data. The effects of FGFRL1 knockdown (KD) in PC3M were studied in in vitro culture models and in mouse xenograft tumors. Our results showed that FGFRL1 was significantly upregulated in PCa. The level of membranous FGFRL1 was negatively associated with high Gleason scores (GSs) and Ki67, while increased cytoplasmic and nuclear FGFRL1 showed a positive correlation. Cox regression analysis indicated that nuclear FGFRL1 was an independent prognostic marker for biochemical recurrence after radical prostatectomy. Functional studies indicated that FGFRL1-KD in PC3M cells increases FGFR signaling, whereas FGFRL1 overexpression attenuates it, supporting decoy receptor actions of membrane-localized FGFRL1. In accordance with clinical data, FGFRL1-KD markedly suppressed PC3M xenograft growth. Transcriptomics of FGFRL1-KD cells and xenografts revealed major changes in genes regulating differentiation, ECM turnover, and tumor–stromal interactions associated with decreased growth in FGFRL1-KD xenografts. Our results suggest that FGFRL1 upregulation and altered cellular compartmentalization contribute to PCa progression. The nuclear FGFRL1 could serve as a prognostic marker for PCa patients

Formalin-Fixed, Paraffin-Embedded–Targeted Locus Capture:A Next-Generation Sequencing Technology for Accurate DNA-Based Gene Fusion Detection in Bone and Soft Tissue Tumors

Chromosomal rearrangements are important drivers in cancer, and their robust detection is essential for diagnosis, prognosis, and treatment selection, particularly for bone and soft tissue tumors. Current diagnostic methods are hindered by limitations, including difficulties with multiplexing targets and poor quality of RNA. A novel targeted DNA-based next-generation sequencing method, formalin-fixed, paraffin-embedded–targeted locus capture (FFPE-TLC), has shown advantages over current diagnostic methods when applied on FFPE lymphomas, including the ability to detect novel rearrangements. We evaluated the utility of FFPE-TLC in bone and soft tissue tumor diagnostics. FFPE-TLC sequencing was successfully applied on noncalcified and decalcified FFPE samples (n = 44) and control samples (n = 19). In total, 58 rearrangements were identified in 40 FFPE tumor samples, including three previously negative samples, and none was identified in the FFPE control samples. In all five discordant cases, FFPE-TLC could identify gene fusions where other methods had failed due to either detection limits or poor sample quality. FFPE-TLC achieved a high specificity and sensitivity (no false positives and negatives). These results indicate that FFPE-TLC is applicable in cancer diagnostics to simultaneously analyze many genes for their involvement in gene fusions. Similar to the observation in lymphomas, FFPE-TLC is a good DNA-based alternative to the conventional methods for detection of rearrangements in bone and soft tissue tumors.</p

Gene regulation network analysis on human prostate orthografts highlights a potential role for the JMJD6 regulon in clinical prostate cancer

Background: Prostate cancer (PCa) is the second most common tumour diagnosed in men. Tumoral heterogeneity in PCa creates a significant challenge to develop robust prognostic markers and novel targets for therapy. An analysis of gene regulatory networks (GRNs) in PCa may provide insight into progressive PCa. Herein, we exploited a graph-based enrichment score to integrate data from GRNs identified in preclinical prostate orthografts and differentially expressed genes in clinical resected PCa. We identified active regulons (transcriptional regulators and their targeted genes) associated with PCa recurrence following radical prostatectomy. Methods: The expression of known transcription factors and co-factors was analysed in a panel of prostate orthografts (n = 18). We searched for genes (as part of individual GRNs) predicted to be regulated by the highest number of transcriptional factors. Using differentially expressed gene analysis (on a per sample basis) coupled with gene graph enrichment analysis, we identified candidate genes and associated GRNs in PCa within the UTA cohort, with the most enriched regulon being JMJD6, which was further validated in two additional cohorts, namely EMC and ICGC cohorts. Cox regression analysis was performed to evaluate the association of the JMJD6 regulon activity with disease-free survival time in the three clinical cohorts as well as compared to three published prognostic gene signatures (TMCC11, BROMO-10 and HYPOXIA-28). Results: 1308 regulons were correlated to transcriptomic data from the three clinical prostatectomy cohorts. The JMJD6 regulon was identified as the top enriched regulon in the UTA cohort and again validated in the EMC cohort as the top-ranking regulon. In both UTA and EMC cohorts, the JMJD6 regulon was significantly associated with cancer recurrence. Active JMJD6 regulon also correlated with disease recurrence in the ICGC cohort. Furthermore, Kaplan–Meier analysis confirmed shorter time to recurrence in patients with active JMJD6 regulon for all three clinical cohorts (UTA, EMC and ICGC), which was not the case for three published prognostic gene signatures (TMCC11, BROMO-10 and HYPOXIA-28). In multivariate analysis, the JMJD6 regulon status significantly predicted disease recurrence in the UTA and EMC, but not ICGC datasets, while none of the three published signatures significantly prognosticate for cancer recurrence. Conclusions: We have characterised gene regulatory networks from preclinical prostate orthografts and applied transcriptomic data from three clinical cohorts to evaluate the prognostic potential of the JMJD6 regulon

Prevention of Recurrent Benign Paroxysmal Positional Vertigo: The Role of Combined Supplementation with Vitamin D and Antioxidants

Benign paroxysmal positional vertigo (BPPV) usually has a favorable course, although it is possible to observe BPPV with a high recurrence rate. Previous studies suggested that vitamin D deficiency might affect BPPV recurrences, and oxidative stress might play a complementary role in BPPV pathogenesis. This multicentric trial aimed to evaluate the effectiveness of oral nutritional supplementation with a compound of alpha-lipoic acid, Carnosine, and Zinc (LICA (R) (Difass International, Coriano (RN), Italy)), vitamins of group B and vitamin D in preventing BPPV recurrences. A total of 128 patients with high recurrence-BPPV were randomized in three arms: Arm 1 consisted of subjects with "insufficient" or "deficient" vitamin D blood levels, treated with daily oral supplementation of LICA (R), vitamins of group B and vitamin D3 (800 UI), Arm 2 included BPPV subjects with "sufficient" vitamin D who did not receive any nutritional support, and Arm 3 included subjects with a "sufficient" serum concentration of vitamin D who received supplementation with a compound of LICA (R) and Curcumin. After six months of follow-up, a significant reduction of BPPV relapses compared to the baseline was found only in Arm 1 (-2.32, 95% CI: 3.41-1.62, p-value &lt; 0.0001). Study results suggested that oral nutritional supplementation with vitamin D3 plus antioxidants can prevent relapses in patients suffering from high recurrence-BPPV

Increased Expression and Altered Cellular Localization of Fibroblast Growth Factor Receptor-Like 1 (FGFRL1) Are Associated with Prostate Cancer Progression

Fibroblast growth factor receptors (FGFRs) 1-4 are involved in prostate cancer (PCa) regulation, but the role of FGFR-like 1 (FGFRL1) in PCa is unclear. FGFRL1 expression was studied by qRT-PCR and immunohistochemistry of patient tissue microarrays (TMAs) and correlated with clinical patient data. The effects of FGFRL1 knockdown (KD) in PC3M were studied in in vitro culture models and in mouse xenograft tumors. Our results showed that FGFRL1 was significantly upregulated in PCa. The level of membranous FGFRL1 was negatively associated with high Gleason scores (GSs) and Ki67, while increased cytoplasmic and nuclear FGFRL1 showed a positive correlation. Cox regression analysis indicated that nuclear FGFRL1 was an independent prognostic marker for biochemical recurrence after radical prostatectomy. Functional studies indicated that FGFRL1-KD in PC3M cells increases FGFR signaling, whereas FGFRL1 overexpression attenuates it, supporting decoy receptor actions of membrane-localized FGFRL1. In accordance with clinical data, FGFRL1-KD markedly suppressed PC3M xenograft growth. Transcriptomics of FGFRL1-KD cells and xenografts revealed major changes in genes regulating differentiation, ECM turnover, and tumor-stromal interactions associated with decreased growth in FGFRL1-KD xenografts. Our results suggest that FGFRL1 upregulation and altered cellular compartmentalization contribute to PCa progression. The nuclear FGFRL1 could serve as a prognostic marker for PCa patients

A cross-sectional study evaluating hospitalization rates for chronic limb-threatening ischemia during the COVID-19 outbreak in Campania, Italy

The expansion of coronavirus disease 2019 (COVID-19) prompted measures of disease containment by the Italian government with a national lockdown on March 9, 2020. The purpose of this study is to evaluate the rate of hospitalization and mode of in-hospital treatment of patients with chronic limb-threatening ischemia (CLTI) before and during lockdown in the Campania region of Italy. The study population includes all patients with CLTI hospitalized in Campania over a 10-week period: 5 weeks before and 5 weeks during lockdown (n = 453). Patients were treated medically and/or underwent urgent revascularization and/or major amputation of the lower extremities. Mean age was 69.2 +/- 10.6 years and 27.6% of the patients were women. During hospitalization, 21.9% of patients were treated medically, 78.1% underwent revascularization, and 17.4% required amputations. In the weeks during the lockdown, a reduced rate of hospitalization for CLTI was observed compared with the weeks before lockdown (25 vs 74/100,000 inhabitants/year; incidence rate ratio: 0.34, 95% CI 0.32-0.37). This effect persisted to the end of the study period. An increased amputation rate in the weeks during lockdown was observed (29.3% vs 13.4%; p &lt; 0.001). This study reports a reduced rate of CLTI-related hospitalization and an increased in-hospital amputation rate during lockdown in Campania. Ensuring appropriate treatment for patients with CLTI should be prioritized, even during disease containment measures due to the COVID-19 pandemic or other similar conditions