"Paradoxical" p16 overexpression in cutaneous melanoma: Molecular and immunohistochemical analysis of a rare phenomenon with a focus on cell cycle regulatory molecules

Background: One of the most relevant genetic alterations in cutaneous melanoma (CM) is the biallelic inactivation/loss-of-heterozygosis (LOH) of cyclin-dependent kinase inhibitor 2 A (CDKN2A), which results in the immunohistochemical loss of p16 frequently found in CM. However, we recently described a rare case of dermal/deep-seated melanoma arising in giant congenital nevus (DDM-GCN) with p16 overexpression combined with p53 loss and tumor protein 53 (TP53) mutation. Herein, we reported a case series of CM with p16 overexpression and analyzed their clinicopathologic features, immunohistochemical expression of the cell cycle regulatory molecules (CCRM: p53, p21, Cyclin D1, Rb), and mutational landscape. Methods: We retrospectively tested for p16 all cases of CM diagnosed at our institution between January 1st 2019-April 1st 2022. In CM with p16 overexpression, we reported clinicopathologic features, immunohistochemical results for melanocytic markers and CCRM, and mutational landscape investigated with a next-generation sequencing (NGS) panel. In cases with zonal p16 overexpression, the immunohistochemical assessment for melanocytic markers and CCRM, as well as the NGS analysis have been performed in both components {with and without p16 overexpression [p16(+)c and p16(-)]}. Results: Overexpression of p16 was found in 10/2879 (0.35%) CM [5/10 (50%) diffuse and 5/10 (50%) zonal]. We combined the immunohistochemical results for CCRM and molecular data to classify the cases as follows: a) Group 1 with altered expression of at least one CCRM but no TP53 mutations [3/10 (30%), all with Rb altered/lost]; b) Group 2 with altered expression of at least one CCRM and TP53 mutations [4/10 (40%), all with p53 altered]; c) Group 3 with normal expression of CCRM and no TP53 mutations [3/10 (30%), all with mutations in MAPK pathway genes (NRAS and BRAF)]. In CM with zonal p16 overexpression, the histologic appearance of p16(+)c was heterogeneous, whereas combining CCRM profiles and molecular data the cases could be categorized as follows: a) cases with the same CCRM and molecular profiles in both p16(+)c and p16(-)c; b) cases with p16(+)c showing additional genetic mutations and/or modifications of CCRM expression. Conclusions: p16 overexpression is a rare event, occurring in advanced-stage, clinically- and histologically-heterogeneous CM. These lesions may be classified into three different groups based on CCRM expression and mutational profiles (including TP53 mutation). The analysis of CM with zonal p16 overexpression suggests that, at least in a subset of cases, this phenomenon could represent a sign of "molecular progression" due to the acquisition of additional genetic mutations and/or modifications of the CCRM profile

Rare Variants in Autophagy and Non-Autophagy Genes in Late-Onset Pompe Disease: Suggestions of Their Disease-Modifying Role in Two Italian Families

Pompe disease is an autosomal recessive disorder caused by a deficiency in the enzyme acid alpha-glucosidase. The late-onset form of Pompe disease (LOPD) is characterized by a slowly progressing proximal muscle weakness, often involving respiratory muscles. In LOPD, the levels of GAA enzyme activity and the severity of the clinical pictures may be highly variable among individuals, even in those who harbour the same combination of GAA mutations. The result is an unpredictable genotype–phenotype correlation. The purpose of this study was to identify the genetic factors responsible for the progression, severity and drug response in LOPD. We report here on a detailed clinical, morphological and genetic study, including a whole exome sequencing (WES) analysis of 11 adult LOPD siblings belonging to two Italian families carrying compound heterozygous GAA mutations. We disclosed a heterogeneous pattern of myopathic impairment, associated, among others, with cardiac defects, intracranial vessels abnormality, osteoporosis, vitamin D deficiency, obesity and adverse response to enzyme replacement therapy (ERT). We identified deleterious variants in the genes involved in autophagy, immunity and bone metabolism, which contributed to the severity of the clinical symptoms observed in the LOPD patients. This study emphasizes the multisystem nature of LOPD and highlights the polygenic nature of the complex phenotype disclosed in these patients

Shifts of Faecal Microbiota during Sporadic Colorectal Carcinogenesis

Gut microbiota has been implicated in the etiopathogenesis of colorectal cancer. The development of colorectal cancer is a multistep process by which healthy epithelium slowly develops into preneoplastic lesions, which in turn progress into malignant carcinomas over time. In particular, sporadic colorectal cancers can arise from adenomas (about 85% of cases) or serrated polyps through the "adenoma-carcinoma" or the "serrated polyp-carcinoma" sequences, respectively. In this study, we performed 16 S rRNA gene sequencing of bacterial DNA extracted from faecal samples to compare the microbiota of healthy subjects and patients with different preneoplastic and neoplastic lesions. We identified putative microbial biomarkers associated with stage-specific progression of colorectal cancer. In particular, bacteria belonging to the Firmicutes and Actinobacteria phyla, as well as members of the Lachnospiraceae family, proved to be specific of the faecal microbiota of patients with preneoplastic lesions, including adenomas and hyperplastic polyps. On the other hand, two families of the Proteobacteria phylum, Alcaligeneaceae and Enterobacteriaceae, with Sutterella and Escherichia/Shigella being the most representative genera, appeared to be associated with malignancy. These findings, once confirmed on larger cohorts of patients, can represent an important step towards the development of more effective diagnostic strategies

Penile metastasis from primary cholangiocarcinoma: the first case report

BACKGROUND: Metastatic penile carcinoma derived from cholangiocarcinoma (CCA) has not been previously reported in the literature. Common metastatic sites for CCA include the regional lymph nodes and adjacent organs. CCAs are not highly vascularised tumours, making hematogenous metastases uncommon. Hematogenous CCA metastases commonly occur at distant organs such as the lungs, adrenal glands, and bones. Median survival for patients with metastatic disease is generally less than 1 year. CASE PRESENTATION: A 74-year-old Caucasian man consulted us after having undergone penile ultrasonography for pain and increased thickness at the base of the penis after self-examination. The patient presented with a history of hepatitis C-related cirrhosis and intrahepatic CCA, diagnosed 3 years previously. A biopsy of the corpora cavernosa on both sides revealed a carcinoma harbouring the same histological and immunophenotypical features as the primary hepatic lesion. CONCLUSIONS: To date, there is no case of penile or urogenital system metastasis from CCA described in the literature. Therefore, this article represents the first case report of penile metastasis from CCA

Routes of dispersion of antibiotic resistance genes from the poultry farm system

Poultry farms are hotspots for the development and spread of antibiotic resistance genes (ARGs), due to high stocking densities and extensive use of antibiotics, posing a threat of spread and contagion to workers and the external environment. Here, we applied shotgun metagenome sequencing to characterize the gut microbiome and resistome of poultry, workers and their households - also including microbiomes from the internal and external farm environment – in three different farms in Italy during a complete rearing cycle. Our results highlighted a relevant overlap among the microbiomes of poultry, workers, and their families (gut and skin), with clinically relevant ARGs and associated mobile elements shared in both poultry and human samples. On a finer scale, the reconstruction of species-level genome bins (SGBs) allowed us to delineate the dynamics of microorganism and ARGs dispersion from farm systems. We found the associations with worker microbiomes representing the main route of ARGs dispersion from poultry to human populations. Collectively, our findings clearly demonstrate the urgent need to implement more effective procedures to counteract ARGs dispersion from poultry food systems and the relevance of metagenomics-based metacommunity approaches to monitor the ARGs dispersion process for the safety of the working environment on farms

Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits

Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences of COR and LUC using datasets of 65.8M and 56.4M of 30–150bp paired-end reads, respectively. New contigs including reads that could not be mapped to the tomato reference genome were assembled, and a total of 43, 054 and 44, 579 gene loci were annotated in COR and LUC. Both genomes showed novel regions with similarity to Solanum pimpinellifolium and Solanum pennellii. In addition to small deletions and insertions, 2, 000 and 1, 700 single nucleotide polymorphisms (SNPs) could exert potentially disruptive effects on 1, 371 and 1, 201 genes in COR and LUC, respectively. A detailed survey of the SNPs occurring in fruit quality, shelf life and stress tolerance related-genes identified several candidates of potential relevance. Variations in ethylene response components may concur in determining peculiar phenotypes of COR and LUC

Hematopoietic Cell Transplantation Cures Adenosine Deaminase 2 Deficiency: Report on 30 Patients

PURPOSE: Deficiency of adenosine deaminase 2 (DADA2) is an inherited inborn error of immunity, characterized by autoinflammation (recurrent fever), vasculopathy (livedo racemosa, polyarteritis nodosa, lacunar ischemic strokes, and intracranial hemorrhages), immunodeficiency, lymphoproliferation, immune cytopenias, and bone marrow failure (BMF). Tumor necrosis factor (TNF-α) blockade is the treatment of choice for the vasculopathy, but often fails to reverse refractory cytopenia. We aimed to study the outcome of hematopoietic cell transplantation (HCT) in patients with DADA2. METHODS: We conducted a retrospective study on the outcome of HCT in patients with DADA2. The primary outcome was overall survival (OS). RESULTS: Thirty DADA2 patients from 12 countries received a total of 38 HCTs. The indications for HCT were BMF, immune cytopenia, malignancy, or immunodeficiency. Median age at HCT was 9 years (range: 2-28 years). The conditioning regimens for the final transplants were myeloablative (n = 20), reduced intensity (n = 8), or non-myeloablative (n = 2). Donors were HLA-matched related (n = 4), HLA-matched unrelated (n = 16), HLA-haploidentical (n = 2), or HLA-mismatched unrelated (n = 8). After a median follow-up of 2 years (range: 0.5-16 years), 2-year OS was 97%, and 2-year GvHD-free relapse-free survival was 73%. The hematological and immunological phenotypes resolved, and there were no new vascular events. Plasma ADA2 enzyme activity normalized in 16/17 patients tested. Six patients required more than one HCT. CONCLUSION: HCT was an effective treatment for DADA2, successfully reversing the refractory cytopenia, as well as the vasculopathy and immunodeficiency. CLINICAL IMPLICATIONS: HCT is a definitive cure for DADA2 with > 95% survival

Inquinamento atmosferico e ricoveri ospedalieri urgenti in 25 citt? italiane: risultati del progetto EpiAir2 Air pollution and urgent hospital admissions in 25 Italian cities: results from the EpiAir2 project

OBJECTIVE: to evaluate the relationship between air pollution and hospital admissions in 25 Italian cities that took part in the EpiAir (Epidemiological surveillance of air pollution effects among Italian cities) project. DESIGN: study of time series with case-crossover methodology, with adjustment for meteorological and time-dependent variables. The association air pollution hospitalisation was analyzed in each of the 25 cities involved in the study; the overall estimates of effect were obtained subsequently by means of a meta-analysis. The pollutants considered were PM10, PM2.5 (in 13 cities only), NO2 and ozone (O3); this last pollutant restricted to the summer season (April-September). SETTING AND PARTICIPANTS: the study has analyzed 2,246,448 urgent hospital admissions for non-accidental diseases in 25 Italian cities during the period 2006- 2010; 10 out of 25 cities took part also in the first phase of the project (2001-2005). MAIN OUTCOME MEASURES: urgent hospital admissions for cardiac, cerebrovascular and respiratory diseases, for all age groups, were considered. The respiratory hospital admissions were analysed also for the 0-14-year subgroup. Percentage increases risk of hospitalization associated with increments of 10 μg/m3 and interquartile range (IQR) of the concentration of each pollutant were calculated. RESULTS: reported results were related to an increment of 10 μg/m3 of air pollutant. The percent increase for PM10 for cardiac causes was 0.34% at lag 0 (95%CI 0.04-0.63), for respiratory causes 0.75%at lag 0-5 (95%CI 0.25-1.25). For PM2.5, the percent increase for respiratory causes was 1.23% at lag 0- 5 (95%CI 0.58-1.88). For NO2, the percent increase for cardiac causes was 0.57%at lag 0 (95%CI 0.13-1.02); 1.29% at lag 0-5 (95%CI 0.52-2.06) for respiratory causes. Ozone (O3) did not turned out to be positively associated neither with cardiac nor with respiratory causes as noted in the previous period (2001-2005). CONCLUSION: the results of the study confirm an association between PM10, PM2.5, and NO2 on hospital admissions among 25 Italian cities. No positive associations for ozone was noted in this period.OBIETTIVO: valutare la relazione tra inquinamento atmosferico e ricoveri ospedalieri nelle citt? italiane partecipanti alla seconda fase del progetto EpiAir (Sorveglianza epidemiologica dell\u27inquinamento atmosferico: valutazione dei rischi e degli impatti nelle citt? italiane). DISEGNO: studio di serie temporali con metodologia case-crossover, con aggiustamento per i fattori temporali e meteorologici rilevanti. L\u27associazione inquinamento atmosferico- ospedalizzazioni ? stata analizzata in ciascuna delle 25 citt? in studio, le stime complessive di effetto sono state ottenute successivamente mediante una metanalisi. Gli inquinanti considerati sono stati il particolato (PM10), il biossido di azoto (NO2) e l\u27ozono (O3), quest\u27ultimo limitatamente al semestre estivo (da aprile a settembre). In 13 citt? in cui i dati erano disponibili ? stata analizzata anche la frazione fine del particolato (PM2.5). SETTING E PARTECIPANTI: lo studio ha esaminato 2.246.448 ricoveri ospedalieri urgenti per cause naturali di pazienti residenti e ricoverati, nel periodo 2006-2010, in 25 citt? italiane, di cui 10 gi? partecipanti alla prima fase del progetto EpiAir (2001-2005). PRINCIPALIMISURE DI OUTCOME: sono stati considerati i ricoveri ospedalieri urgenti per malattie cardiache, cerebrovascolari e respiratorie per tutte le fasce di et?. I ricoveri per cause respiratorie sono stati analizzati separatamente anche per la fascia di et? 0-14 anni. L\u27esposizione ? stata valutata per incremento sia di 10 μg/m3 sia pari all\u27intervallo interquartile (IQR) della concentrazione di ciascun inquinante. RISULTATI: considerando un incremento di 10 μg/m3 per inquinante, per il PM10 ? stato osservato un incremento percentuale di rischio per patologie cardiache dello 0,34%a lag 0 (IC95% 0,04-0,63), e per patologie respiratorie dello 0,75% a lag 0-5 (IC95% 0,25-1,25). Per il PM2.5 l\u27incremento percentuale di rischio per patologie respiratorie ? risultato dell\u271,23%a lag 0-5 (IC95%0,58-1,88). Per l\u27NO2 la stima di effetto per patologie cardiache ? risultata dello 0,57% a lag 0 (IC95% 0,13-1,02), e per patologie respiratorie dell\u271,29% a lag 0-5 (IC95% 0,52-2,06). L\u27ozono non ? risultato positivamente associato n? alle patologie cardiache n? a quelle respiratorie (a differenza del periodo 2001-2005). CONCLUSIONE: i risultati dello studio confermano l\u27effetto a breve termine dell\u27inquinamento atmosferico da PM10, PM2.5 e NO2 sulla morbosit?, in particolare respiratoria, nelle citt? italiane. Non sono state rilevate associazioni positive per l\u27O3

Influence of FTO rs9939609 and Mediterranean diet on body composition and weight loss: a randomized clinical trial

Background The Mediterranean diet (MeD) plays a key role in the prevention of obesity. Among the genes involved in obesity, the Fat mass and obesity-associated gene (FTO) is one of the most known, but its interaction with MeD remained uncertain so far. Methods We carried out a study on a sample of 188 Italian subjects, analyzing their FTO rs9939609 alleles, and the difference in body composition between the baseline and a 4-weeks nutritional intervention. The sample was divided into two groups: the control group of 49 subjects, and the MeD group of 139 subjects. Results We found significant relations between MeD and both variation of total body fat (ΔTBFat) (p = 0.00) and gynoid body fat (p = 0.04). ∆TBFat (kg) demonstrated to have a significant relation with the interaction diet-gene (p = 0.04), whereas FTO was associated with the variation of total body water (p = 0.02). Conclusions MeD demonstrated to be a good nutritional treatment to reduce the body fat mass, whereas data about FTO remain uncertain. Confirming or rejecting the hypothesis of FTO and its influence on body tissues during nutritional treatments is fundamental to decide whether its effect has to be taken into consideration during both development of dietetic plans and patients monitoring. Trial Registration ClinicalTrials.gov Id: NCT01890070. Registered 01 July 2013, https://clinicaltrials.gov/ct2/show/NCT0189007