Contribution of Rare and Low-Frequency Variants to Multiple Sclerosis Susceptibility in the Italian Continental Population

Genome-wide association studies identified over 200 risk loci for multiple sclerosis (MS) focusing on common variants, which account for about 50% of disease heritability. The goal of this study was to investigate whether low-frequency and rare functional variants, located in MS-established associated loci, may contribute to disease risk in a relatively homogeneous population, testing their cumulative effect (burden) with gene-wise tests. We sequenced 98 genes in 588 Italian patients with MS and 408 matched healthy controls (HCs). Variants were selected using different filtering criteria based on allelic frequency and in silico functional impacts. Genes showing a significant burden (n = 17) were sequenced in an independent cohort of 504 MS and 504 HC. The highest signal in both cohorts was observed for the disruptive variants (stop-gain, stop-loss, or splicing variants) located in EFCAB13, a gene coding for a protein of an unknown function (p < 10^-4). Among these variants, the minor allele of a stop-gain variant showed a significantly higher frequency in MS versus HC in both sequenced cohorts (p = 0.0093 and p = 0.025), confirmed by a meta-analysis on a third independent cohort of 1298 MS and 1430 HC (p = 0.001) assayed with an SNP array. Real-time PCR on 14 heterozygous individuals for this variant did not evidence the presence of the stop-gain allele, suggesting a transcript degradation by non-sense mediated decay, supported by the evidence that the carriers of the stop-gain variant had a lower expression of this gene (p = 0.0184). In conclusion, we identified a novel low-frequency functional variant associated with MS susceptibility, suggesting the possible role of rare/low-frequency variants in MS as reported for other complex diseases.

Burden of rare coding variants in an Italian cohort of familial multiple sclerosis

BACKGROUND

Multiple Sclerosis (MS) is a chronic inflammatory and neurodegenerative demyelinating disease of the central nervous system. It is a complex and heterogeneous disease caused by a combination of genetic and environmental factors, and it can cluster in families.

OBJECTIVE

to evaluate at gene-level the aggregate contribution of predicted damaging low-frequency and rare variants to MS risk in multiplex families.

METHODS

We performed whole exome sequencing (WES) in 28 multiplex MS families with at least 3 MS cases (81 affected and 42 unaffected relatives) and 38 unrelated healthy controls. A gene-based burden test was then performed, focusing on two sets of candidate genes: i) literature-driven selection and ii) data-driven selection.

RESULTS

We identified 11 genes enriched with predicted damaging low-frequency and rare variants in MS compared to healthy individuals. Among them, UBR2 and DST were the two genes with the strongest enrichment (p = 5 × 10^-4 and 3 × 10^-4, respectively); interestingly enough the association signal in UBR2 is driven by rs62414610, which was present in 25% of analysed families.

CONCLUSION

Despite limitations, this is one of the first studies evaluating the aggregate contribution of predicted damaging low-frequency and rare variants in MS families using WES data. A replication effort in independent cohorts is warranted to validate our findings and to evaluate the role of identified genes in MS pathogenesis.

An Investigation of the Role of Common and Rare Variants in a Large Italian Multiplex Family of Multiple Sclerosis Patients

Known multiple sclerosis (MS) susceptibility variants can only explain half of the disease's estimated heritability, whereas low-frequency and rare variants may partly account for the missing heritability. Thus, here we sought to determine the occurrence of rare functional variants in a large Italian MS multiplex family with five affected members. For this purpose, we combined linkage analysis and next-generation sequencing (NGS)-based whole exome and whole genome sequencing (WES and WGS, respectively). The genetic burden attributable to known common MS variants was also assessed by weighted genetic risk score (wGRS). We found a significantly higher burden of common variants in the affected family members compared to that observed among sporadic MS patients and healthy controls (HCs). We also identified 34 genes containing at least one low-frequency functional variant shared among all affected family members, showing a significant enrichment in genes involved in specific biological processes-particularly mRNA transport-or neurodegenerative diseases. Altogether, our findings point to a possible pathogenic role of different low-frequency functional MS variants belonging to shared pathways. We propose that these rare variants, together with other known common MS variants, may account for the high number of affected family members within this MS multiplex family.

Targeted Next-Generation Sequencing for the Identification of Genetic Predictors of Radiation-Induced Late Skin Toxicity in Breast Cancer Patients: A Preliminary Study

Normal tissue radiosensitivity is thought to be influenced by an individual’s genetic background. However, the specific genetic variants underlying the risk of late skin reactions following radiotherapy for breast cancer remain elusive. To unravel the genetic basis for radiation-induced late skin toxicity, we carried out targeted next-generation sequencing of germline DNA samples from 48 breast cancer patients with extreme late skin toxicity phenotypes, consisting of 24 cases with grade 2–3 subcutaneous fibrosis and/or grade 2–3 telangiectasia (LENT-SOMA scales) and 24 controls with grade 0 fibrosis and grade 0 telangiectasia. In this exploratory study, a total of five single-nucleotide variants (SNVs) located in three genes (TP53, ERCC2, and LIG1) reached nominal levels of statistical significance (p < 0.05). In the replication study, which consisted of an additional 45 cases and 192 controls, none of the SNVs identified by targeted NGS achieved nominal replication. Nevertheless, TP53 rs1042522 (G > C, Pro72Arg) in the replication cohort had an effect (OR per C allele: 1.52, 95%CI: 0.82–2.83, p = 0.186) in the same direction as in the exploratory cohort (OR per C allele: 4.70, 95%CI: 1.51–14.6, p = 0.007) and was found be nominally associated to the risk of radiation-induced late skin toxicity in the overall combined cohort (OR per C allele: 1.79, 95%CI: 1.06–3.02, p = 0.028). These results raise the possibility of an association between TP53 rs1042522 and risk of radiation-induced late skin toxicity in breast cancer patients; however, large replication studies are warranted for conclusive evidence.

Vitamin D Supplementation Modulates ICOS+ and ICOS- Regulatory T Cell in Siblings of Children With Type 1 Diabetes

OBJECTIVES

Vitamin D plays an immunoregulatory activity. The aim of this study was to assess the correlation between blood serum 25(OH)D levels and Th17 and Treg circulating subsets, mainly Treg/inducible costimulatory-positive (ICOS+), which seems to have a protective role in autoimmunity, in children with type 1 diabetes mellitus (T1D) and their healthy siblings (S). The secondary aim was to evaluate the impact of vitamin D supplementation on these subsets.

PATIENTS AND METHODS

22 T1D and 33 S were enrolled. Glucose, hemoglobin A1c, 25 OH vitamin D (25[OH]D), T helper type 17 (Th17; CD4+CCR6+), regulatory T cells (Treg; CD4+CD25+Foxp3+), and Treg/ICOS+ cells were evaluated. According to human leukocyte antigen (HLA) haplotypes, subjects were classified as "at risk" (HLA+), "protective haplotypes" (HLA-; "nested controls"), and "undetermined" (HLAUND). T1D and S subjects were supplemented with cholecalciferol 1000 IU/die and evaluated after 6 months.

RESULTS

Vitamin D insufficiency (74.4%) and deficiency (43%) were frequent. S subjects with 25(OH)D levels <25 nmol/L had Th17, Treg (p < 0.01), and Treg/ICOS+ (P < 0.05) percentages higher than subjects with 25(OH)D >75 nmol/L. Treg/ICOS+ percentages (P < 0.05) were higher in HLA- S subjects compared to percentages observed in S with T1D. At baseline, in S subjects, a decreasing trend in Th17 and Treg/ICOS+ values (P < 0.05) from vitamin D deficiency to sufficiency was observed; 25(OH)D levels were negative predictors of Treg/ICOS+ (R2 = 0.301) and Th17 percentages (R2 = 0.138). After 6 months, supplemented S subjects showed higher 25(OH)D levels (P < 0.0001), and lower Th17 (P < 0.0001) and Treg/ICOS+ (P < 0.05) percentages than at baseline; supplemented T1D patients only had a decrease in Th17 levels (P < 0.05).

CONCLUSION

Serum 25(OH)D levels seem to affect Th17 and Treg cell subsets in S subjects, consistent with its immunomodulating role. HLA role should be investigated in a larger population.

Carbapenem-resistant enterobacteriaceae: don’t trust your neighbour

Background

The spread of carbapenem-resistant enterobacteriaceae (CRE) outbreaks consists not only of germs producing KPC and OXA-48, endemic already, but also metallo-beta-lactamase such as NDM or VIM. In Tuscany, Italy, a multidisciplinary regional task force has extended, since NDM alert spread out, from 1st Oct 2019 the CRE screening programme, via molecular testing, to newly admitted patients in high risk settings (medical, intensive care, oncology, transplant, infectious diseases, cardiac surgery units) to fight cross-contamination. The aim of the study is to assess levels and types of CRE in an italian teaching hospital (615 beds) after the programme became effective.

Methods

The surveillance team began recording daily all the CRE positive cases, defined as laboratory confirmed colonizations/infections with CRE. Our retrospective, descriptive study covers the time span between 30th Sep - 16th Dec 2019. Cases were classified by infected apparatus and by resistance phenotype, and we calculated descriptive statistics.

Results

In total we identified 97 cases (male 60.82%, mean (+/-SD) age 71.58+/-17.34 years, 74.23% in medical wards); 5 patients had two body districts infected and 9 carried two different phenotypes. Out of 102 positive samples, 92.16% were bowel colonization, 1.96% BSI, 3.92% urinary and 1.96% respiratory. Among these, 21 were NDM (19.81%), 29 KPC (27.36%), 4 OXA-48 (3.77%), 52 VIM (49.06%). The most detected germ was Klebsiella pneumoniae (30.19%), followed by Escherichia coli (2.83%), Enterobacter cloacae (2.83%), Citrobacter freundii and braakii (2.83%), Klebsiella oxytoca (1.89%). 61 agents were unspecified (57.55%). Among the 21 NDM, 76.19% were K. pneumoniae, only one was a BSI.

Conclusions

CREs continue to be present despite constant surveillance. Although high levels of KPC-producing agents persist, the new spread of VIM phenotype is significant, highlighting, however, that the pathogen wasn't detected in over 50% of the samples.

Key messages

Despite increased surveillance, there is still a consistent portion of patients colonized with unidentified CRE. A surveillance mainly focused on NDM-producing CREs had incidentally highlighted an unexpected spread of VIM phenotype.

Know your enemy, fight the outbreak: an Italian experience

Issue

The New Delhi-Enterobateriaceae producing metallo-beta-lactamase NDM, resistant to carbapenems, are responsible of hospital outbreaks. The European Centre for disease prevention and control has published a report about the NDM outbreaks in Italy. Knowledge and application of all types of precautions is necessary to obtain adequate control.

Description

Between June and August 2019 an outbreak of Klebsiella pneumoniae producing NDM-1 occurred in an acute cardiac surgery setting from medium to high intensity, in a third level-hospital in Italy. Every patient with at least one positive typing test for NDM in clinical specimens was defined as a case. The infection control team sought patient 0, reviewed patients' daily records and created a timeline to control movements, verifying risk factors and time to positivity. The correct application of isolation and standard precautions was assessed. Auditing and training sessions were carried out. Our aim is to verify if these actions sufficed to control and halt the outbreak.

Results

Fourteen cases were identified, mean age=66.28 (SD = 13.55), 71.43% of them had a previous negative test. Positivity was found in samples from 13 rectal swabs (prevalence 12.38%), 7 lung aspirates, 3 urine cultures, 2 blood cultures and 2 wound swabs. Eight patients were positive in multiple body districts, 5 have been admitted to the same hospital within the year before, 3 came from other hospitals. The patient 0 has been moved in from a medical ward. After auditing, a training class was given to healthcare staff. The class concerned NDM phenotype, hand hygiene, isolation and personal protective equipment, with further observation in wards. In the following three months no new cases were registered.

Lessons

A continuous high-level adherence to standard precautions and hand hygiene by healthcare staff should be supported by adequate training. This is confirmed to be a strong action to prevent or stop cross-contamination.

Key messages

Colonization of multiresistant germs in healthcare due to cross-contamination has to be tackled promptly. Auditing and training actions should be taken into serious account in order to ensure an effective reaction from healthcare staff.

Antibiotic consumption and healthcare associated infection in a third level Italian hospital

Background

The extended length of stay (LoS) is one of the main causes of hospital infections (HAI), followed by an increase in antibiotics consumption. The final step is the development of multiresistant microorganisms, with a consequent increase in costs for the national healthcare system. Aim of this study is to evaluate the prevalence of HAI and to analyze ATB consumption in a teaching hospital

Methods

Between 17-21 June 2019 the infection control team collected the clinical records of 425 patients to perform a point of prevalence analysis (PPA). Eligible patients were hospitalized in surgical and medical wards of the teaching Hospital (615 beds) in Siena, Italy. For each patients according to guidelines of European Centers for Disease Control and Prevention (ECDC 4.2) we searched for evidence of HAI and for all indication of ATB consumption. Data were processed using Stata12

Results

Overall 425 patients have been analyzed (48.24% female), mean age was 60.88 (SD 26.11) years, mean LoS 8.37 (min 1 max 86) days. Patients were admitted mostly in General Medicine wards (48.94%); 34% underwent surgery. 63.8% of patients had Peripheral Venous Catheter, 20% Central Venous Catheter and 31.06% Urinary Catheter. Twenty-nine HAI were discovered (PPA 6.82%); the higher prevalence (19.23%) was in Intensive Care Unit. LoS (OR:1.07;IC95%1.04-1.1) and devices (OR:2.17;IC95%1.39-3.37) were the two variables that significantly influenced the infection risk. Forty-six percent of all patients received ATB, the most used were third generation Cephalosporines (26,18%), followed by Penicillines (24,73%). The main use was to treat community infections (62.12%), followed by medical prophylaxis (30.81%)

Conclusions

PPA of HAI was 6.82%, comparable to 2017 national PPA (6.5%); prolonged LoS is probably the main cause of this result. Our analysis showed that ATB consumption was quite high, in agreement with the Italian prevalence (44.9%), but the percentage of medical prophylaxis was still high.

Key messages

The way to achieve the health care infection control is still long, the length of the hospitalization could be a field to be improved. High consumption of antibiotics for prophylaxis is still the main point to fight in the battle against the multiresistant microorganisms.

A new radioguided procedure for localization and surgical treatment of neck node metastasis of papillary thyroid cancer

AIM OF THE STUDY

We intended to use a radioguided technique for pre-operative localization of neck node recurrences in patients with papillary thyroid cancer (PTC) already submitted to thyroidectomy and radioiodine treatment.

PATIENTS AND METHODS

We selected 20 patients affected by PTC with evidence of neck nodes recurrences at ultrasound examination. Our method has been derived from the Radioguided Occult Lesion Localization technique used for pre-operative localization of occult breast lesions. The technique involves the inoculation of human albumin macroaggregates labeled with radioactive technetium (0.4 mCi in a volume of 0.05 ml) directly in the suspicious lesion, under ultrasound guidance. The persistence of the radioactive tracer in the nodes is confirmed by a scintigraphy performed 2 h after injection. During surgery, a gamma detecting probe is used to locate the suspicious lesions as "hot spots".

RESULTS

Fifty lymph-nodes were injected with the tracer. All radiolabeled lymph-nodes were located and removed during surgery. At histology, metastasis of PTC was confirmed in 38/50 (76%) lymph-nodes. At least one metastatic lymph-node per patient was removed. In 8/20 (40%) patients, reactive lymphoid hyperplasia was found in 12/50 (24%) lymph-nodes.

CONCLUSIONS

This radioguided technique has been highly effective for localization and surgical treatment of suspicious lymph-node detected at neck ultrasound and may play a valuable role in case of node metastases of thyroid cancer that show no radioiodine uptake.

Prevention and cure of rhinogenous deafness at the Thermal Baths "Bagni delle Galleraie"

INTRODUCTION

Hearing is foundamental for human social life. Secretory Otitis Media (SOM) is the most important cause of trasmissive hypoacusis in early childhood.

METHODS

The Department of Physiopathology, Experimental Medicine and Public Health of Siena University in collaboration with the Thermal Baths "Bagni delle Galleraie" proposed a prevention and cure campaign of rhinogenous deafness in June 2002 in some primary schools in the Colle val D'Elsa district. A sample of 87 children was involved in the study (average age of 5,64 +/- 1,41 years). On entering the thermal baths a questionnaire was administered to the parents, to point out possible risk factors.

RESULTS

Among the 87 children, 28 cases of SOM and 21 cases of severe tubal disorder were found. Only 19 cases out of 49 were already known to the parents and only 28 joined the study and were examined for three years consecutively.

DISCUSSION

Out of the 35 children examined in 2002, 28 returned to "The Galleraie" for the two following years. They repeated the thermal cure for two years as a preventive measure. At present they are not affected by SOM and during the winters suffered a lower number of infections in the primary airways and took less antibiotics.

CONCLUSIONS

Our study focuses on infant school children because of their critical age for linguistic and social development. Early diagnosis and therapy prevent any negative social development.