Inflammatory bowel disease (IBD) includes patients affected by Crohn’s disease or ulcerative colitis. IBD is thought to be a chronic immune-mediated disease, but its origin remains elusive, and this limits new therapeutic approaches. Human endogenous retroviruses (HERVs) originate from ancestral infections and represent 8% of the human genome. HERVs are no longer infectious, but some retroviral sequences can be activated, and their aberrant expressions have been implicated in inflammatory and autoimmune disorders. HERV transcription is regulated by TRIM28 and SETDB1, which are also directly involved in epigenetic processes and modulation of the immune response. Using a PCR real-time Taqman amplification assay, we assessed, for the first time, the transcription levels of pol genes of HERV-H, -K, and -W families of env genes of syncytin 1 (SYN1), SYN2, and HERV-W, as well as of TRIM28 and SETDB1 in the whole blood of 48 patients with Crohn’s disease (CD), 20 with ulcerative colitis (UC), and in healthy controls (HC) of comparable age. The transcriptional levels of HERV-H-pol (p = 0.0003) and HERV-K-pol (p = 0.001) were significantly higher in IBD patients compared with HC, with no differences between patients with CD and UC. No significant differences were found for the remaining HERVs between IBD patients and HC. The transcript levels of TRIM28 were significantly downregulated in IBD patients (p < 0.001), without differences between CD and UC, while the SETDB1 levels were preserved. The enhanced transcription of HERV-H-pol and HERV-K-pol, as well as the impaired activation of TRIM28, were not influenced by clinical disease activity and type of treatment. The overexpression of HERVs and impaired transcription of TRIM28 in patients affected by CD or UC suggest that they might be the main actors in the pathophysiology of IBD, opening the way to innovative targeted interventions.

Peripheral blood is the most practical tissue for human immune system gene expression profiling because it is easily accessible, whereas the site of primary infection in certain diseases may not be easily accessible. Due to the ex vivo instability of RNA transcripts, a key challenge in the gene expression analysis of blood samples is the rapid sample handling and stabilization of the mRNA by adding an RNA preservative (PAXgene^TM Blood RNA Tubes, Tempus^TM Blood RNA tubes, RNAlater Stabilization Reagent, RNAgard^® Blood Tubes). BioMole (Turin, Italy) has developed a novel blood stabilizer, called RNApro, in which RNA is stabilized during phlebotomy and sample storage. In this study, RNApro performance intended as RNA yield, integrity, and stability was evaluated. Our results show that blood samples stored at −80 °C and re-extracted after 7 years show no differences in terms of quantity, quality, and amplificability. The samples in the RNAlater stabilization solution can be stored at room temperature for up to one week or at 4 °C for up to one month. Similar results can also be observed for PAXgene tubes, Tempus tubes, and RNAgard tubes. In agreement with these data, the RNApro stabilization solution preserves the RNA from degradation for up to 1 month at 4 °C and 1 week at room temperature. RNApro can be stored indifferently at −80, −20, 4 °C, or room temperature for up to 2 months after, and then could be stored at −80 °C for up to seven years. In summary, our study is the first to analyze the performance of an RNA stabilizer called RNApro. We can conclude that several studies have shown significant differences in gene expression analysis when the sample was preserved in different RNA stabilizers. Therefore, it is desirable to standardize the method of nucleic acid conservation when comparing data from transcriptomic analyses.

Background: Over the past decade, TNF inhibitors such as Infliximab and Adalimumab have become central to Inflammatory Bowel Diseases treatment, greatly enhancing patient outcomes. However, immunogenicity—where anti-drug antibodies diminish effectiveness—remains an issue, often requiring dose changes or combination therapies. Pharmacogenomics is increasingly applied in IBD to personalise treatment, especially since genetic factors like the HLA-DQA1*05 variant heighten the immunogenicity risk with IFX. This study aims to examine the relationship between the HLA-DQA1*05 variant and response loss or antibody development in patients regularly monitored on IFX or ADA. Methods: Sixty-five paediatric IBD patients were enrolled, with therapeutic drug monitoring (TDM) of IFX and ADA, conducted using immunoenzymatic assays. The presence of the HLA-DQA1*05 T>C allele variant was also tested using a Biomole HLA-DQA1 Real-time PCR kit. Results: The HLA-DQA1*05 rs2097432 T>C allele was present in 54% of patients on IFX and 69% of those on ADA. No statistically significant differences were found between HLA carriers and non-carriers across any of the three analysed groups: IFX, ADA and the overall anti-TNFα. Conclusions: Our study suggests that the HLA-DQA1*05 allele does not increase the risk of secondary loss of response to anti-TNF therapy, likely because most patients were on a combination of anti-TNF agents and immunomodulators, which can lower anti-drug antibody production. Testing for HLA-DQA105 can aid in personalising treatment and optimising therapy to minimise immunogenicity risks.

Bronchiolitis is an acute lower respiratory tract infection mainly affecting children under 24 months, primarily caused by Respiratory Syncytial Virus (RSV). Interferons (IFNs), cytokines central to innate and adaptive immunity, are secreted in response to viral infections. In RSV bronchiolitis, Type I and III IFN Signatures modulate antiviral responses and impact disease severity. This study aimed to evaluate the correlation between Type I and III IFNs transcriptional signatures in blood and nasal swabs with clinical presentation. We analyzed transcription levels of Type I and III IFN Signatures using a PCR real-time TaqMan assay in blood and nasal swabs from children hospitalized for RSV bronchiolitis and from healthy controls (HC). Interferon score I was significantly higher in bronchiolitis patients at admission than at discharge and compared to HC, in both blood and nasal swabs (p < 0.0001). A strong positive correlation for IFN score I between the two sample types was found (p < 0.0001). Patients with severe disease (requiring intensive care) had lower IFN score I than those with milder disease, in both blood (p = 0.0005) and nasal swabs (p = 0.0078). IFN score III was down-regulated in bronchiolitis patients compared to HC in blood samples (p < 0.0001), while in nasal swabs, this down-regulation was evident only at discharge (p < 0.0001 vs admission; p = 0.0546 vs HC). This study enhances understanding of IFN signature dynamics in RSV bronchiolitis, emphasizing the importance of sample type and signature specificity, and suggests their potential use as prognostic tools to improve patient management.

Background: Respiratory syncytial virus (RSV) bronchiolitis is a leading cause of lower respiratory tract infections in children under two years of age. NF-κB is a key transcription factor in antiviral and inflammatory responses. This study investigates the expression of NF-κB mRNA in both blood and buccal swab samples of pediatric patients hospitalized for RSV bronchiolitis, comparing levels at admission and discharge. Methods: Paired peripheral blood and buccal swab samples were collected from pediatric patients (n = 85) at hospital admission and discharge. Quantitative real-time PCR was used to assess NF-κB mRNA levels. Results: NF-κB mRNA levels significantly decreased in blood between admission and discharge (p < 0.05), while no significant change was observed in buccal swabs. Conclusions: These results suggest a compartment-specific regulation of NF-κB, with systemic inflammatory resolution at discharge and persistent or distinct mucosal immune activity. Understanding these dynamics may improve our approach to monitoring and treating RSV bronchiolitis.

Background and Objectives: In this study, we applied one-step real time rt-PCR technology type II INF signature to blood and nasopharyngeal (NPS) swabs of acute early recovery children < 1 years hospitalized for bronchiolitis with laboratory-confirmed RSV infection. Materials and Methods: A prospective observational case–control study was conducted in 2021–2022. The study took place in Children Hospital “Regina Margherita”, Torino Italy. The study included 66 infants, of which 30 patients were hospitalized for bronchiolitis due to RSV infection and 36 age-matched controls. Inclusion criteria included a positive RSV test for infants with bronchiolitis. We collected peripheral blood and nasopharyngeal swabs for relative quantification of type II Interferon signature by One-Step Multiplex PCR real time. Results: IFN levels were downregulated in the peripheral blood of bronchiolitis patients; these data were not confirmed in the nasopharyngeal swab. There was no correlation between NPS and the type II IFN score in peripheral blood. Conclusions: our study shows for the first time that type II IFN score was significant reduced in peripheral blood of infants with bronchiolitis by RSV compared to age-matched healthy controls; in the NPS swab this resulted downregulation was not statistically significant and the type II IFN score in the NPS swab can be used as marker of resolution of infection or improvement of clinical conditions.