Comparative in silico design and validation of GPS™ CoVID-19 dtec-RT-qPCR test

AIMS

Providing a ready-to-use reverse transcriptase qPCR (RT-qPCR) method fully validated to detect the SARS-CoV-2 with a higher exclusivity than this shown by early published RT-qPCR designs.

METHODS AND RESULTS

The specificity of the GPS™ CoVID-19 dtec-RT-qPCR test by analysis of sequence alignments was approached and compared with other RT-qPCR designs. The GPS™ CoVID-19 dtec-RT-qPCR test was validated following criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012. Diagnostic validation was achieved by two independent reference laboratories, the Instituto de Salud Carlos III, (Madrid, Spain), the Public Health England (Colindale, London, UK), and received the label CE-IVD. The GPS design showed the highest exclusivity and passed all parameters of validation with strict acceptance criteria. Results from reference laboratories 100% correlated with these obtained by using reference methods and showed 100% of diagnostic sensitivity and specificity.

CONCLUSIONS

The CE-IVD GPS™ CoVID-19 dtec-RT-qPCR test, available worldwide with full analytical and diagnostic validation, is the more exclusive for SARS-CoV-2 by far.

SIGNIFICANCE AND IMPACT OF THE STUDY

Considering the CoVID-19 pandemic status, the exclusivity of RT-qPCR tests is crucial to avoid false positives due to related coronaviruses. This work provides of a highly specific and validated RT-qPCR method for detection of SARS-CoV-2, which represents a case of efficient transfer of technology successfully used since the pandemic was declared.

Nature (Hole or Electron) of Charge-Transfer Ability of Substituted Cyclopyrenylene Hoop-Shaped Compounds

We theoretically investigate here by means of DFT methods how the selective substitution in cyclic organic nanorings composed of pyrene units may promote semiconducting properties, analyzing the energy needed for a hole- or electron-transfer accommodation as a function of the substitution pattern and the system size (i.e., number of pyrene units). We choose to study both [3]Cyclo-2,7-pyrenylene ([3]CPY) and [4]Cyclo-2,7-pyrenylene ([4]CPY) compounds, the latter already synthesized, with substituents other than hydrogen acting in ipso and ortho positions, as well as the effect of the per-substitution. As substituents, we selected a set of electroactive halogen atoms (F, Cl, and Br) and groups (CN) to disclose structure-property relationships allowing thus to anticipate the use of these systems as organic molecular semiconductors.

Analysis of mismatch repair (MMR) proteins expression in a series of malignant pleural mesothelioma (MPM) patients

BACKGROUND

Promising results have been reported with immune checkpoint inhibitors (ICI) in a small proportion of MPM patients. MMR deficiency (dMMR) has been well described in several malignancies and was approved as a biomarker for anti-PD-1 inhibitors. Next generation sequencing (NGS) data demonstrated that 2% of MPM harbor microsatellite instability. The aim of this study is to characterize MMR by immunohistochemistry (IHC) in a series of MPM including a subset of patients treated with immunotherapy.

METHODS

Tumors of 159 MPM p diagnosed between 2002 and 2017 were reviewed. Formalin-fixed, paraffin-embedded tissue was stained for MLH1, MSH2, MSH6 and PMS2 and tumors were classified as dMMR (MMR protein expression negative) and MMR intact (all MMR proteins positively expressed). We retrospectively collected clinical outcomes under standard chemotherapy and experimental immunotherapy in the entire cohort.

RESULTS

MMR protein expression was analyzed in 158 samples with enough tissue and was positive in all of the cases. Twenty two patients received ICI with anti-CTLA4 or anti-PD-1 blockade in clinical trials, 58% had a response or stable disease for more than 6 m, with median progression-free survival (PFS) of 5.7 m (2.1-26.1 m). The median overall survival (mOS) in all population was 15 months (m) (13.5-18.8 m). In a multivariable model factors associated to improved mOS were PS 0, neutrophil-lymphocyte ratio (NLR) < 5 and epithelioid histology (p < 0.001).

CONCLUSIONS

In our series we were unable to identify any MPM patient with dMMR by IHC. Further studies are needed to elucidate potential predictive biomarkers of ICI benefit in MPM.

Immunotherapeutic maintenance treatment with toll-like receptor 9 agonist lefitolimod in patients with extensive-stage small-cell lung cancer: results from the exploratory, controlled, randomized, international phase II IMPULSE study

Background

The immune surveillance reactivator lefitolimod (MGN1703), a DNA-based TLR9 agonist, might foster innate and adaptive immune response and thus improve immune-mediated control of residual cancer disease. The IMPULSE phase II study evaluated the efficacy and safety of lefitolimod as maintenance treatment in extensive-stage small-cell lung cancer (ES-SCLC) after objective response to first-line chemotherapy, an indication with a high unmet medical need and stagnant treatment improvement in the last decades.

Patients and methods

103 patients with ES-SCLC and objective tumor response (as per RECIST 1.1) following four cycles of platinum-based first-line induction therapy were randomized to receive either lefitolimod maintenance therapy or local standard of care at a ratio of 3 : 2 until progression or unacceptable toxicity.

Results

From 103 patients enrolled, 62 were randomized to lefitolimod, 41 to the control arm. Patient demographics and response patterns to first-line therapy were balanced. Lefitolimod exhibited a favorable safety profile and pharmacodynamic assessment confirmed the mode-of-action showing a clear activation of monocytes and production of interferon-gamma-induced protein 10 (IP-10). While in the intent-to-treat (ITT) population no relevant effect of lefitolimod on progression-free and overall survival (OS) could be observed, two predefined patient subgroups indicated promising results, favoring lefitolimod with respect to OS: in patients with a low frequency of activated CD86⁺ B cells (hazard ratio, HR 0.53, 95% CI: 0.26–1.08; n = 38 of 88 analyzed) and in patients with reported chronic obstructive pulmonary disease (COPD) (HR 0.48, 95% CI: 0.20–1.17, n = 25 of 103).

Conclusions

The IMPULSE study showed no relevant effect of lefitolimod on the main efficacy end point OS in the ITT, but (1) the expected pharmacodynamic response to lefitolimod, (2) positive OS efficacy signals in two predefined subgroups and (3) a favorable safety profile. These data support further exploration of lefitolimod in SCLC.

Short communication: Molecular characterization and antimicrobial resistance of pathogenic Escherichia coli isolated from raw milk and Minas Frescal cheeses in Brazil

The aim of this study was to quantify, identify, evaluate antimicrobial resistance, and characterize the virulence factors of enteropathogenic (EPEC), Shiga-toxigenic (STEC), and enterohemorrhagic (EHEC) Escherichia coli in raw milk (RM) and legal (LMFC) and illegal (IMFC) Minas Frescal cheeses in southern and northeast Brazil. Illegal cheeses are those made without official inspection service or sanitary surveillance. We evaluated samples of RM produced in Paraná (southern) and Maranhão (northeast) States, LMFC produced using pasteurized milk in inspected industries, and IMFC potentially produced with raw milk. Mean total coliform counts were 8.4 × 10⁴ cfu/mL for RM, 1.4 × 10⁷ cfu/mL for LMFC, and 2.9 × 10⁷ cfu/mL for IMFC. Mean E. coli counts were 2.4 × 10³ cfu/mL for RM, 1.9 × 10² cfu/mL for LMFC, and 1.1 × 10⁵ cfu/mL for IMFC. Among the 205 E. coli isolates from RM, 9.75% were identified as EPEC, mainly (90%) in samples from Paraná. Of the total isolates from the cheese samples, 97.4% (n = 111) came from IMFC, of which 1.8 and 2.7% were identified as EPEC and STEC, respectively; no EHEC was detected. The phylogenetic group A (60%) and typical EPEC (68%) predominated, which confirms the possible human origin of pathogenic isolates in RM and IMFC. Of these, 50% were resistant to at least one antibiotic, and streptomycin was the antimicrobial with the highest number (8) of EPEC and STEC resistant isolates. This study reports the first isolation of serogroup O28ac in Brazilian milk. We found no predominance of a specific serogroup of EPEC or STEC in milk or cheese or clonal isolates in the same sample, indicating different origins of the contamination in these products, presumably mostly related to poor hygienic handling.

Effect of the pulsation type (alternate or simultaneous) on milk yield and health status of the mammary gland of Murciano-Granadina goats

Recent research into how the pulsation type affects goat milking concluded that alternate pulsation (AP) and simultaneous pulsation (SP) similarly affect the milking efficiency (milking duration and milking fractioning) and teat end condition after milking when both pulsations are employed in short-term experiments. However, the use of SP in high pipeline milking machines led to higher vacuum fluctuations, which, in the long term, may entail a potential risk factor for the mammary gland health status. The aim of this work was to study how AP and SP affect the milk yield, mammary gland health status, and milk composition of goats in the long term, during a complete lactation period, in a high pipeline milking machine. With this objective, 100 Murciano-Granadina goats with similar parturition dates (4 ± 1 postpartum weeks) were divided into 2 similar groups (50 goats per group) according their parity, milk yield, mammary gland health status, and milking duration (after a 15-d pre-experimental period). Throughout the experimental period (7 mo), one group was milked using SP and the other group using AP. Every month, samplings were carried out of the variables related to sanitary status of the mammary gland, milk fractioning, milking duration, average and maximum milk flows, milk composition, teat end status, vacuum fluctuations at the short milk tube during milking, and pulsation tests. Results showed that the use of SP in a high pipeline milking machine showed higher vacuum fluctuations without involving any difference in the other variables studied. We concluded that the use of AP in the milking of Murciano-Granadina goats offers little improvement of the milking performance and increases the investment required for installation and maintenance of the milking machines.

Study of arterial stiffness in patients with an acute coronary event and chronic obstructive pulmonary disease confirmed by spirometry

BACKGROUND AND OBJECTIVES

Chronic obstructive pulmonary disease (COPD) worsens the prognosis for patients with an acute coronary event (ACE) treated with percutaneous coronary intervention. Objective To assess the effect of COPD on arterial stiffness in patients with an ACE.

METHODS

The study included patients with an ACE treated with percutaneous coronary intervention. At 1 month, postbronchodilation spirometry was performed, and arterial stiffness and markers of myocardial damage (troponin T and ProBNP) were measured.

RESULTS

We included 68 patients, 33% of whom had COPD (59% undiagnosed). The patients with COPD presented higher arterial stiffness values after adjusting for age and blood pressure readings. The troponin T and ProBNP levels were higher in the patients with COPD.

CONCLUSIONS

Arterial stiffness is greater in patients with an ACE if they have concomitant COPD. These findings can help explain the poorer prognosis of patients with both conditions.

128 Next-generation RNA sequencing of horse adipose and endometrial mesenchymal stem cells from the same donors unveils striking differences in their transcriptomic pattern

Earlier we successfully isolated and characterised endometrial (eMSC) and adipose (aMSC) mesenchymal stem cells from the same donors. Mesenchymal stem cells share biological traits but display different surface marker phenotype and migration ability. Here we extended our research to their mRNA signature using next-generation sequencing. The RNA from cells (3 biological replicates from each cell type and 3 technical replicates) at 90% confluence was extracted using a total RNA extraction kit and sent for mRNA-Seq (Norgen, Ontario, Canada; Illumina Sequencing Platform NextSEqn 500). Raw 76-bp single-end reads were aligned against the EquCab3 genome using RNA-STAR aligner. Counts were filtrated at a minimum of 5. Pairwise comparisons between the cell types were the input for gene ontology enrichment analysis. Only genes differentially expressed (DE) with 5 folds change (FC; P&lt;0.05) were analysed. For DE analysis, eMSC were set as control and compared with aMSC. Unsupervised hierarchical clustering of the global gene expression signatures was done to compare the samples from each line using principal component analysis (PCA) and EdgeR: v3.20.9. Gene expression was normalized using FPKM. The heat map was built using R studio with G-plot package. A total of 14,896 transcripts with at least 5 reads were found; of these, 1598 were DE: 627 up-regulated (FC range: 2 to 236×) and 971 down-regulated (FC range: 2 to 464×) in eMSC. There was a marked dispersion in the FC of up- and down-regulated genes (&gt;50×: 8 and 13; &gt;20×, &lt;50×: 9 and 17; &gt;10×, &lt;20×: 29 and 63; &gt;5×, &lt;10×: 91 and 130 and &gt;2×, &lt;5×: 490 and 748, respectively). Only genes DE with FC at least 5× were used for gene ontology and PCA analysis. Though 14,058 genes were common to both cell types, specific set of genes were found only in eMSC (n=162) or aMSC (n=676). Among the top 50 genes overexpressed in eMSC, several genes key for stem cell growth, immune response, migration and angiogenesis were found: TRIL, CXCL8, PDGF-D, SEMA5A, PTGS2, FGD, LAMA2, IL36G. In the top 50 down-regulated genes, some pivotal for osteoblast, adipogenic and neural differentiation were dramatically down-regulated (GPM6B, SCARA5 and NOTCH3 or NEFM, respectively), but no genes involved in immune rejection or stem cell proliferation were found. In gene ontology, the categories represented the most were cellular, developmental, metabolic, and immune system processes, as well as biological regulation, response to stimuli, organellar biogenesis, locomotion, localization and biological adhesion. Heat map and PCA analysis showed that one individual cell line from each type diverged markedly from the shared pattern. Individual variability of the donors may impinge upon the results; nevertheless, striking differences in the mRNA portfolio of eMSC and aMSC were detected. The importance and potential biological role of several of the genes and processes named above will be discussed in detail elsewhere. This work was supported by grant FONDECYT REGULAR 1150757 and the Government of Chile.