ABCA1/ABCB1 Ratio Determines Chemo- and Immune-Sensitivity in Human Osteosarcoma

The ATP Binding Cassette transporter B1 (ABCB1) induces chemoresistance in osteosarcoma, because it effluxes doxorubicin, reducing the intracellular accumulation, toxicity, and immunogenic cell death induced by the drug. The ATP Binding Cassette transporter A1 (ABCA1) effluxes isopentenyl pyrophosphate (IPP), a strong activator of anti-tumor V\u3b39V\u3b42 T-cells. Recruiting this population may represent an alternative strategy to rescue doxorubicin efficacy in ABCB1-expressing osteosarcoma. In this work, we analyzed how ABCA1 and ABCB1 are regulated in osteosarcoma, and if increasing the ABCA1-dependent activation of V\u3b39V\u3b42 T-cells could be an effective strategy against ABCB1-expressing osteosarcoma. We used 2D-cultured doxorubicin-sensitive human U-2OS and Saos-2 cells, their doxorubicin-resistant sublines (U-2OS/DX580 and Saos-2/DX580), and 3D cultures of U-2OS and Saos-2 cells. DX580-sublines and 3D cultures had higher levels of ABCB1 and higher resistance to doxorubicin than parental cells. Surprisingly, they had reduced ABCA1 levels, IPP efflux, and V\u3b39V\u3b42 T-cell-induced killing. In these chemo-immune-resistant cells, the Ras/Akt/mTOR axis inhibits the ABCA1-transcription induced by Liver X Receptor \u3b1 (LXR\u3b1); Ras/ERK1/2/HIF-1\u3b1 axis up-regulates ABCB1. Targeting the farnesylation of Ras with self-assembling nanoparticles encapsulating zoledronic acid (NZ) simultaneously inhibited both axes. In humanized mice, NZ reduced the growth of chemo-immune-resistant osteosarcomas, increased intratumor necro-apoptosis, and ABCA1/ABCB1 ratio and V\u3b39V\u3b42 T-cell infiltration. We suggest that the ABCB1 high ABCA1 low phenotype is indicative of chemo-immune-resistance. We propose aminobisphosphonates as new chemo-immune-sensitizing tools against drug-resistant osteosarcomas

Ruxolitinib – better prognostic impact in low-intermediate 1 risk score: evaluation of the ‘rete ematologica pugliese’ (REP) in primary and secondary myelofibrosis

We evaluated ruxolitinib in 65 patients with myelofibrosis according to age, sex, time of diagnosis, grade of fibrosis, prognostic score risk, Janus kinase (JAK) status, primary or secondary myelofibrosis, previous treatment, and dosage. Outcome measures were response rate, time to response, duration of response, and event-free survival and survival. Kaplan and Meier curves show a significant difference in event-free survival according to the prognostic score, in favor of patients with low int1 (p = 0.0009). The Cox stepwise model confirmed the result, the int2 high-risk score being the most powerful negative independent parameter (0.001), followed by JAK (0.008); other parameters, such as diagnosis more than 5 years earlier, grade III–IV fibrosis, and ruxolitinib dose have a negligible impact. Time to response was shorter (p = 0.001) in primary myelofibrosis. In conclusion, ruxolitinib is effective, with a better outcome in patients with a low-int1 risk score. This may suggest considering an earlier administration in the disease course

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

[Tecfidera® (delayed-release dimethylfumarate) in the treatment of relapsing-remitting multiple sclerosis]

The present health technology assessment (HTA) evaluates the clinical and economic profile of delayed-release dimethylfumarate (DMF, also known as gastro-resistant DMF) in the treatment of relapsing-remitting multiple sclerosis (RRMS) in Italy. Chapter 1 briefly introduces the condition (multiple sclerosis and, more specifically, the relapsing-remitting form) and provides an overall description of the main therapeutic options for physicians, in terms of clinical evidence, regulatory status in Europe and approval status and reimbursement (refunding) criteria in Italy. In the next sections (Chapters 2-5), key-topics regarding RRMS are analysed: epidemiology, clinical burden, quality of life/social impact and the economic implications for healthcare services, patients and society. In Chapter 6, the clinical evidence supporting the use of DMF in RRMS is summarized. Data from phase III randomized clinical trials (DEFINE, CONFIRM), plus the pooled post-hoc analysis of the two studies, were evaluated to assess the level of clinical benefit provided by DMF. Finally, in Chapter 7, a review of the health economic evidence assessing DMF is performed, with a specific focus on Italy. Overall, the methodological quality of registration studies, together with the robustness and consistency of the study results, support the conclusion that DMF is an effective and safe treatment for RRMS. The economic assessment of DMF in Italy, based on cost-effectiveness and budget impact analyses (adopting clinical input data from a mixed treatment comparison and economic input data relative to the Italian healthcare setting), confirm that DMF is a cost-effective and economically sustainable treatment for the Italian National Healthcare Service. These findings are in line with the results of most international publications and the assessments from well-recognized HTA agencies (e.g. NICE/SMC). In summary, both the clinical and economic evidence analyzed in this HTA substantiate DMF as an important therapeutic option for the treatment of RRMS

Pharmacogenomic Profiling of Cisplatin-Resistant and -Sensitive Human Osteosarcoma Cell Lines by Multimodal Targeted Next Generation Sequencing

Cisplatin (CDDP) is a drug for high-grade osteosarcoma (HGOS) treatment. Several germline pharmacogenetic studies have revealed associations between single nucleotide polymorphisms (SNPs) and CDDP-based therapy response or CDDP-related toxicity in patients with HGOS. Whether these variants could play a biological role in HGOS cells has not been studied so far. The aim of this study was to explore 28 SNPs of 14 genes in 6 CDDP-resistant and 12 drug-sensitive human HGOS cell lines. An innovative multimodal targeted next generation sequencing (mmNGS) approach with custom primers designed for the most commonly reported SNPs of genes belonging to DNA repair, CDDP transport or detoxification, or associated with CDPP-related toxicity was applied. The mmNGS approach was validated by TaqMan genotyping assays and emerged to be an innovative, reliable tool to detect genetic polymorphisms at both the DNA and RNA level. Allele changes in three SNPs (ERCC2 rs13181 and rs1799793, ERCC1 rs11615) were identified on both DNA and RNA derived libraries in association with CDDP resistance. A change of the GSTP1 rs1695 polymorphism from AA to AG genotype was observed in the RNA of all six CDDP-resistant variants. These SNPs emerged to be causally associated with CDDP resistance in HGOS cells

Unraveling unusual X-chromosome patterns during fragile-X syndrome genetic testing

BACKGROUND: Fragile X syndrome (FXS) is the most common form of inherited intellectual disability (ID). Together with fragile X-associated tremor and ataxia (FXTAS) and fragile X-associated premature ovarian failure (POF)/primary ovarian insufficiency (POI), FXS depends on dysfunctional expression of the FMR1 gene on Xq27.3. In most cases, FXS is caused by a >200 CGG repeats in FMR1 5'-untranslated region (UTR) and by promoter hypermethylation that results in gene silencing. Males and females with unmethylated premutated alleles (repeats between 55 and 200) are at risk for FXTAS and POF/POI. METHODS: FXS molecular testing relied on PCR and methylation-specific Southern blot analysis of the FMR1 5'UTR. Atypical Southern blot patterns were studied by X-chromosome microsatellite analysis, copy number dosage at DMD locus, amelogenin gender-marker analysis and array-comparative genomic hybridization (array-CGH). RESULTS: Six men affected by ID and three women affected by ID and POF/POI underwent FXS molecular testing. They had normal FMR1 CGG repeats, but atypical X chromosome patterns. Further investigations revealed that the six males had Klinefelter syndrome (XXY), one female was a Turner mosaic (X0/XX) and two women had novel rearrangements involving X chromosome. CONCLUSIONS: Diagnostic investigation of atypical patterns at FMR1 locus can address patients and/or their relatives to further verify the condition by performing karyotyping and/or array-CGH

Evaluating patient safety indicators in orthopedic surgery between Italy and the USA

Objective: To compare patient safety in major orthopedic procedures between an orthopedic hospital in Italy, and 26 US hospitals of similar size.Design: Retrospective analysis of administrative data from hospital discharge records in Italy and Florida, USA, 2011-13. Patient Safety Indicators (PSIs) developed by the Agency for Healthcare Quality and Research were used to identify inpatient adverse events (AEs). We examined the factors associated with the development of each different PSI, taking into account known confounders, using logistic regression.Setting: One Italian orthopedic hospital and 26 hospitals in Florida with 65 1000 major orthopedic procedures per year.Participants: Patients 65 18 years who underwent 1 of the 17 major orthopedic procedures, and with a length of stay (LOS) > 1 day.Intervention: Patient Safety management between Italy and the USA.Main Outcome Measure: Patient Safety Indicators.Results: A total of 14 393 patients in Italy (mean age = 59.8 years) and 131 371 in the USA (mean age = 65.4 years) were included. US patients had lower adjusted odds of developing a PSI compared to Italy for pressure ulcers (odds ratio [OR]: 0.21; 95% confidence interval [CI]: 0.10-0.45), hemorrhage or hematoma (OR: 0.42; CI 0.23-0.78), physiologic and metabolic derangement (OR: 0.08; CI 0.02-0.37). Italian patients had lower odds of pulmonary embolism/deep vein thrombosis (OR: 3.17; CI 2.16-4.67) compared to US patients.Conclusions: Important differences in patient safety events were identified across countries using US developed PSIs. Though caution about potential coding differences is wise when comparing PSIs internationally, other differences may explain AEs, and offer opportunities for cross-country learning about safe practices

An insight into the functionalisation of carbon nanotubes by diazonium chemistry: Towards a controlled decoration

The derivatisation of materials including iron, gold, and carbon by addition of diazonium salts is a reliable process to tune their interfacial interaction with the surrounding media. In this regard, the functionalisation of carbon nanostructures by diazonium chemistry is a versatile strategy to obtain soluble nanomaterials with degrees of functionalisation among the highest ever reported. Starting from these premises we have studied the functionalisation of multi-walled carbon nanotubes by addition of the aryl diazonium salts generated in situ by treatment of 4-methoxyaniline with isopentylnitrite. Following a thorough purification and characterisation protocol (UV\u2013vis, TGA, ATR-IR, cyclic voltammetry, AFM and other surface analytical techniques), we have investigated the key parameters to obtain both functionalised multi-walled carbon nanotubes, where the amount of functional groups anchored to the carbon surface is less than a monolayer, and superfunctionalised carbon nanotubes, with a carbon nanotube core and a multilayered aryl coating. The results outlined provide the basis for the design and controlled processing of novel decorated carbon nanostructures that would be useful for a number of technological applications

DataSheet1_Single-nucleotide polymorphism profiling by multimodal-targeted next-generation sequencing in methotrexate-resistant and -sensitive human osteosarcoma cell lines.PDF

Introduction: Methotrexate (MTX) is one of the most important drugs included in the first-line protocols to treat high-grade osteosarcoma (HGOS). Although several polymorphisms have been reported to be associated with drug response or MTX-related toxicity in pharmacogenetic studies, their role in the development of MTX resistance in HGOS is still unclear.Methods: Therefore, in this study, 22 single nucleotide polymorphisms (SNPs) in 4 genes of the folate metabolism, 7 MTX transporter genes, and 2 SNPs of the tumor protein p53 (TP53) gene were investigated using a custom multimodal-targeted next-generation sequencing (mmNGS) approach in 8 MTX-resistant and 12 MTX-sensitive human HGOS cell lines. The panel was validated by TaqMan genotyping assays.Results: High instability of TP53 rs1642785 was observed in all U-2OS/MTX variants. Allele changes of the solute carrier family 19 member 1/replication factor C subunit 1 (SLC19A1, previously known as RFC1) and rs1051266 were identified in all Saos-2/MTX-resistant variants in both DNA- and RNA- derived libraries compared to the parental Saos-2 cell line. Allele changes of methylenetetrahydrofolate reductase (MTHFR) rs1801133 were identified only in the RNA-derived libraries of the two U2OS variants with the highest MTX resistance level. Significantly upregulated gene expression associated with the development of MTX resistance was revealed for dihydrofolate reductase (DHFR) whereas SLC19A1 was downregulated. In addition, a fusion transcript of DHFR (ex4) and MutS Homolog 3 (MSH3) (ex9) was identified in the RNA libraries derived from the two U-2OS variants with the highest MTX resistance level.Conclusion: This innovative mmNGS approach enabled the simultaneous exploration of SNPs at DNA and RNA levels in human HGOS cell lines, providing evidence of the functional involvement of allele changes associated with the development of MTX resistance.</p