Immune biomarker evaluation of sequential tyrosine kinase inhibitor and nivolumab monotherapies in renal cell carcinoma: the phase I TRIBE trial

Background

Predictive biomarkers for immune checkpoint blockade in the second-line treatment of metastatic renal cell carcinoma (mRCC) are lacking.

Materials and methods

Patients with histologically confirmed RCC who started nivolumab after at least 4 months of tyrosine kinase inhibitors (TKIs) were recruited for this study. Serial tissue and blood samples were collected for immune biomarker evaluation. The primary endpoint was to determine the association of specific T-cell subsets with clinical outcomes tested using Wilcoxon rank sum for clinical benefit rate (CBR) and log-rank test for progression-free survival (PFS).

Results

Twenty patients were included in this trial with a median age of 64 years and followed-up for a median of 12 months. The median PFS for patients who received TKI was 13.8 months, while for those subsequently treated with nivolumab following TKI therapy, the median PFS was 2.6 months. CBR of nivolumab was 20% with two partial responses. Functionally active programmed cell death protein 1+ CD4+ T cells were enriched in non-responders (q = 0.003) and associated with worse PFS on nivolumab (P = 0.04). Responders showed a significant reduction in the effector CD4+T-cell (TEF) fraction compared to non-responders at 3 months on nivolumab (0.40 versus 0.80, P = 0.0005). CD127+CD4+ T cells were enriched in patients who developed immune-related adverse effects (q = 0.003). Using in-house validated multiplex immunohistochemistry for six markers, we measured tumour-associated immune cell densities in tissue samples. Responders to nivolumab showed a significantly higher mean of immune cell densities in tissue samples compared to non-responders (346 versus 87 cells/mm2, P = 0.04).

Conclusions

In this small study, analysis of tissue-based and peripheral blood immune cell subsets predicted clinical outcomes of nivolumab. Further studies are warranted with larger populations to validate these observations.

Validation of the emergency surgery score (ESS) in a UK patient population and comparison with NELA scoring: a retrospective multicentre cohort study

INTRODUCTION

Accurate risk scoring in emergency general surgery (EGS) is vital for consent and resource allocation. The emergency surgery score (ESS) has been validated as a reliable preoperative predictor of postoperative outcomes in EGS but has been studied only in the US population. Our primary aim was to perform an external validation study of the ESS in a UK population. Our secondary aim was to compare the accuracy of ESS and National Emergency Laparotomy Audit (NELA) scores.

METHODS

We conducted an observational cohort study of adult patients undergoing emergency laparotomy over three years in two UK centres. ESS was calculated retrospectively. NELA scores and all other variables were obtained from the prospectively collected Emergency Laparotomy and Laparoscopic Scottish Audit (ELLSA) database. The primary and secondary outcomes were 30-day mortality and postoperative intensive care unit (ICU) admission, respectively.

RESULTS

A total of 609 patients were included. Median age was 65 years, 52.7% were female, the overall mortality was 9.9% and 23.8% were admitted to ICU. Both ESS and NELA were equally accurate in predicting 30-day mortality (c-statistic=0.78 (95% confidence interval (CI), 0.71-0.85) for ESS and c-statistic=0.83 (95% CI, 0.77-0.88) for NELA, p=0.196) and predicting postoperative ICU admission (c-statistic=0.76 (95% CI, 0.71-0.81) for ESS and 0.80 (95% CI, 0.76-0.85) for NELA, p=0.092).

CONCLUSIONS

In the UK population, ESS and NELA both predict 30-day mortality and ICU admission with no statistically significant difference but with higher c-statistics for NELA score. Both scores have certain advantages, with ESS being validated for a wider range of outcomes.

Microfabrication-based engineering of biomimetic dentin-like constructs to simulate dental aging

Human dentin is a highly organized dental tissue displaying a complex microarchitecture consisting of micrometer-sized tubules encased in a mineralized type-I collagen matrix. As such, it serves as an important substrate for the adhesion of microbial colonizers and oral biofilm formation in the context of dental caries disease, including root caries in the elderly. Despite this issue, there remains a current lack of effective biomimetic in vitro dentin models that facilitate the study of oral microbial adhesion by considering the surface architecture at the micro- and nanoscales. Therefore, the aim of this study was to develop a novel in vitro microfabricated biomimetic dentin surface that simulates the complex surface microarchitecture of exposed dentin. For this, a combination of soft lithography microfabrication and biomaterial science approaches were employed to construct a micropitted PDMS substrate functionalized with mineralized type-I collagen. These dentin analogs were subsequently glycated with methylglyoxal (MGO) to simulate dentin matrix aging in vitro and analyzed utilizing an interdisciplinary array of techniques including atomic force microscopy (AFM), elemental analysis, and electron microscopy. AFM force-mapping demonstrated that the nanomechanical properties of the biomimetic constructs were within the expected biological parameters, and that mineralization was mostly predominated by hydroxyapatite deposition. Finally, dual-species biofilms of Streptococcus mutans and Candida albicans were grown and characterized on the biofunctionalized PDMS microchips, demonstrating biofilm-specific morphologic characteristics and confirming the suitability of this model for the study of early biofilm formation under controlled conditions. Overall, we expect that this novel biomimetic dentin model could serve as an in vitro platform to study oral biofilm formation or dentin-biomaterial bonding in the laboratory without the need for animal or human tooth samples in the future.

Spatial biology of Ising-like synthetic genetic networks

BACKGROUND

Understanding how spatial patterns of gene expression emerge from the interaction of individual gene networks is a fundamental challenge in biology. Developing a synthetic experimental system with a common theoretical framework that captures the emergence of short- and long-range spatial correlations (and anti-correlations) from interacting gene networks could serve to uncover generic scaling properties of these ubiquitous phenomena.

RESULTS

Here, we combine synthetic biology, statistical mechanics models, and computational simulations to study the spatial behavior of synthetic gene networks (SGNs) in Escherichia coli quasi-2D colonies growing on hard agar surfaces. Guided by the combined mechanisms of the contact process lattice simulation and two-dimensional Ising model (CPIM), we describe the spatial behavior of bi-stable and chemically coupled SGNs that self-organize into patterns of long-range correlations with power-law scaling or short-range anti-correlations. These patterns, resembling ferromagnetic and anti-ferromagnetic configurations of the Ising model near critical points, maintain their scaling properties upon changes in growth rate and cell shape.

CONCLUSIONS

Our findings shed light on the spatial biology of coupled and bistable gene networks in growing cell populations. This emergent spatial behavior could provide insights into the study and engineering of self-organizing gene patterns in eukaryotic tissues and bacterial consortia.

Carrot DcALFIN4 and DcALFIN7 Transcription Factors Boost Carotenoid Levels and Participate Differentially in Salt Stress Tolerance When Expressed in Arabidopsis thaliana and Actinidia deliciosa

ALFIN-like transcription factors (ALs) are involved in several physiological processes such as seed germination, root development and abiotic stress responses in plants. In carrot (Daucus carota), the expression of DcPSY2, a gene encoding phytoene synthase required for carotenoid biosynthesis, is induced after salt and abscisic acid (ABA) treatment. Interestingly, the DcPSY2 promoter contains multiple ALFIN response elements. By in silico analysis, we identified two putative genes with the molecular characteristics of ALs, DcAL4 and DcAL7, in the carrot transcriptome. These genes encode nuclear proteins that transactivate reporter genes and bind to the carrot DcPSY2 promoter in yeast. The expression of both genes is induced in carrot under salt stress, especially DcAL4 which also responds to ABA treatment. Transgenic homozygous T3 Arabidopsis thaliana lines that stably express DcAL4 and DcAL7 show a higher survival rate with respect to control plants after chronic salt stress. Of note is that DcAL4 lines present a better performance in salt treatments, correlating with the expression level of DcAL4, AtPSY and AtDXR and an increase in carotenoid and chlorophyll contents. Likewise, DcAL4 transgenic kiwi (Actinidia deliciosa) lines show increased carotenoid and chlorophyll content and higher survival rate compared to control plants after chronic salt treatment. Therefore, DcAL4 and DcAL7 encode functional transcription factors, while ectopic expression of DcAL4 provides increased tolerance to salinity in Arabidopsis and Kiwi plants.

Ribavirin for Hepatitis E Virus Infection After Organ Transplantation: A Large European Retrospective Multicenter Study

BACKGROUND

Ribavirin is currently recommended for treating chronic hepatitis E virus (HEV) infection. This retrospective European multicenter study aimed to assess the sustained virological response (SVR) in a large cohort of solid organ transplant (SOT) recipients with chronic HEV infection treated with ribavirin monotherapy (N = 255), to identify the predictive factors for SVR, and to evaluate the impact of HEV RNA mutations on virological response.

METHODS

Data from 255 SOT recipients with chronic HEV infection from 30 European centers were analyzed. Ribavirin was given at the median dose of 600 (range, 29-1200) mg/day (mean, 8.6 ± 3.6 mg/kg/day) for a median duration of 3 (range, 0.25-18) months.

RESULTS

After a first course of ribavirin, the SVR rate was 81.2%. It increased to 89.8% when some patients were offered a second course of ribavirin. An increased lymphocyte count at the initiation of therapy was a predictive factor for SVR, while poor hematological tolerance of ribavirin requiring its dose reduction (28%) and blood transfusion (15.7%) were associated with more relapse after ribavirin cessation. Pretreatment HEV polymerase mutations and de novo mutations under ribavirin did not have a negative impact on HEV clearance. Anemia was the main adverse event.

CONCLUSIONS

This large-scale retrospective study confirms that ribavirin is highly efficient for treating chronic HEV infection in SOT recipients and shows that the predominant HEV RNA polymerase mutations found in this study do not affect the rate of HEV clearance.This large-scale retrospective study that included 255 solid organ transplant recipients confirms that ribavirin is highly efficient for treating chronic hepatitis E virus (HEV) infection and shows that HEV RNA polymerase mutations do not play a role in HEV clearance.

Investigating surface binding effects: antibacterial efficacy of bound 8-hydroxyquinoline against Staphylococcus aureus and Escherichia coli

AIMS

To investigate the binding of the antimicrobial compound 8-hydroxyquinoline (8HQ) to a material interface and to determine whether immobilization affects the antibacterial efficacy.

METHODS AND RESULTS

The 8HQ derivative 5-carboxy-8-hydroxyquinoline (5C8HQ) was attached to silica beads through amide bond coupling at the carboxyl moiety of 5C8HQ. Attachment of 5C8HQ was confirmed using a combination of mass spectrometry, thermogravimetric analysis, colorimetric testing and Soxhlet extraction. Computational modelling results indicated that this substitution did not compromise the active sites on the molecule, whereas other positions on the ring system could potentially inhibit antimicrobial activity. The antibacterial effect of 8HQ and the 5C8HQ-modified silica complex against Escherichia coli 15597 (ATCC^® 25922) and Staphylococcus aureus (ATCC 25923) was evaluated.

CONCLUSIONS

The test results show that the immobilized 8HQ continues to exhibit antibacterial activity, however, quantifying the efficacy compared to free 8HQ bears further investigation. The expected antibacterial mechanism requires that the metal chelation site of 8HQ be retained and available after attachment to a surface. The retention of antibacterial activity after surface bonding represents a novel mechanism of action not previously reported.

SIGNIFICANCE AND IMPACT OF THE STUDY

Recent changes in regulations due to environmental concerns prompted many companies and organizations to explore antimicrobial treatments that are chemically bound to the product. Chemically bonding biocidal compounds to a surface limits environmental release; however, molecular mechanisms that drive antibacterial activity when compounds are immobilized are limited. The results reported here demonstrate that the 8HQ reactive site retains antibacterial efficacy even after covalent attachment to a surface. This approach supersedes other antimicrobial treatments where the active component is gradually released from the material surface in order to elicit antimicrobial effects. This specific antibacterial activity of bound 8HQ represents a novel mechanism of action not previously reported, and a potential conduit to a new class of bound antimicrobial materials.

Re-expression of miR-200s in claudin-low mammary tumor cells alters cell shape and reduces proliferation and invasion potentially through modulating other miRNAs and SUZ12 regulated genes

Background

MicroRNAs are a class of non-coding RNAs that regulate gene expression through binding to mRNAs and preventing their translation. One family of microRNAs known as the miR-200 family is an important regulator of epithelial identity. The miR-200 family consists of five members expressed in two distinct clusters; the miR-200c/141 cluster and the miR-200b/200a/429 cluster. We have found that murine and human mammary tumor cells with claudin-low characteristics are associated with very low levels of all five miR-200s.

Methods

To determine the impact of miR-200s on claudin-low mammary tumor cells, the miR-200c/141 cluster and the miR-200b/200a/429 cluster were stably re-expressed in murine (RJ423) and human (MDA-MB-231) claudin-low mammary tumor cells. Cell proliferation and migration were assessed using BrdU incorporation and transwell migration across Matrigel coated inserts, respectively. miRNA sequencing and RNA sequencing were performed to explore miRNAs and mRNAs regulated by miR-200 re-expression while Enrichr-based pathway analysis was utilized to identify cellular functions modified by miR-200s.

Results

Re-expression of the miR-200s in murine and human claudin-low mammary tumor cells partially restored an epithelial cell morphology and significantly inhibited proliferation and cell invasion in vitro. miRNA sequencing and mRNA sequencing revealed that re-expression of miR-200s altered the expression of other microRNAs and genes regulated by SUZ12 providing insight into the complexity of miR-200 function. SUZ12 is a member of the polycomb repressor complex 2 that suppresses gene expression through methylating histone H3 at lysine 27. Flow cytometry confirmed that re-expression of miR-200s increased histone H3 methylation at lysine 27.

Conclusions

Re-expression of miR-200s in claudin-low mammary tumor cells alters cell morphology and reduces proliferation and invasion, an effect potentially mediated by SUZ12-regulated genes and other microRNAs.

A virtual ELISA to quantitate COVID-19 antibodies in patient serum

Enzyme-linked immunosorbent assays (ELISAs) are used widely in biotechnology, pharmaceutical, and clinical medicine labs. At the same time, they appear to be underrepresented in chemistry and biochemistry curricula, even though their sensitivity, selectivity, and ease of use would argue for their widespread use. We describe here an online ELISA activity suitable for stand-alone use or in conjunction with an actual wet lab ELISA. Specifically, we offer real and mock data for a hypothetical ELISA to detect plasma antibodies to COVID-19 in infected patients who have had the disease. Much of the activity focuses on chemical and mathematical models to fit ELISA or any macromolecule/ligand binding data, a skill that addresses perhaps the most relevant and difficult learning goal of an ELISA experiment.

Quantifying Soft Tissue Artefacts and Imaging Variability in Motion Capture of the Fingers

This study assessed the accuracy of marker-based kinematic analysis of the fingers, considering soft tissue artefacts (STA) and marker imaging uncertainty. We collected CT images of the hand from healthy volunteers with fingers in full extension, mid- and full-flexion, including motion capture markers. Bones and markers were segmented and meshed. The bone meshes for each volunteer's scans were aligned using the proximal phalanx to study the proximal interphalangeal joint (PIP), and using the middle phalanx to study the distal interphalangeal joint (DIP). The angle changes between positions were extracted. The HAWK protocol was used to calculate PIP and DIP joint flexion angles in each position based on the marker centroids. Finally the marker locations were 'corrected' relative to the underlying bones, and the flexion angles recalculated. Static and dynamic marker imaging uncertainty was evaluated using a wand. A strong positive correlation was observed between marker- and CT-based joint angle changes with 0.980 and 0.892 regression slopes for PIP and DIP, respectively, and Root Mean Squared Errors below 4°. Notably for the PIP joint, correlation was worsened by STA correction. The 95% imaging uncertainty interval was < ± 1° for joints, and < ± 0.25 mm for segment lengths. In summary, the HAWK marker set's accuracy was characterised for finger joint flexion angle changes in a small group of healthy individuals and static poses, and was found to benefit from skin movements during flexion.

Solid-Liquid Interdiffusion (SLID) Bonding of p-Type Skutterudite Thermoelectric Material Using Al-Ni Interlayers

Over the past few years, significant progress towards implementation of environmentally sustainable and cost-effective thermoelectric power generation has been made. However, the reliability and high-temperature stability challenges of incorporating thermoelectric materials into modules still represent a key bottleneck. Here, we demonstrate an implementation of the Solid-Liquid Interdiffusion technique used for bonding Mm_y(Fe,Co)₄Sb₁₂ p-type thermoelectric material to metallic interconnect using a novel aluminium–nickel multi-layered system. It was found that the diffusion reaction-controlled process leads to the formation of two distinct intermetallic compounds (IMCs), Al₃Ni and Al₃Ni₂, with a theoretical melting point higher than the initial bonding temperature. Different manufacturing parameters have also been investigated and their influence on electrical, mechanical and microstructural features of bonded components are reported here. The resulting electrical contact resistances and apparent shear strengths for components with residual aluminium were measured to be (2.8 ± 0.4) × 10⁻⁵ Ω∙cm² and 5.1 ± 0.5 MPa and with aluminium completely transformed into Al₃Ni and Al₃Ni₂ IMCs were (4.8 ± 0.3) × 10⁻⁵ Ω∙cm² and 4.5 ± 0.5 MPa respectively. The behaviour and microstructural changes in the joining material have been evaluated through isothermal annealing at hot-leg working temperature to investigate the stability and evolution of the contact.

Unraveling the induction of phytoene synthase 2 expression by salt stress and abscisic acid in Daucus carota

Phytoene synthase (PSY) is the first committed enzyme of the carotenoid biosynthesis pathway and the most important point of regulation. Carotenoids are precursors of abscisic acid (ABA), which mediates abiotic stress tolerance responses in plants. ABA activates the synthesis of its own precursors through induction of PSY expression. Carrot, a species that accumulates very high amounts of carotenoids in its reserve root, has two PSY paralog genes that are expressed differentially in the root. Here, we determined that DcPSY2 expression is induced by salt stress and ABA. A DcPSY2 promoter fragment was obtained and characterized. Bioinformatic analysis showed the presence of three ABA responsive elements (ABREs). Through overexpressing pPSY2:GFP in Nicotiana tabacum we determined that all three ABREs are necessary for the ABA response. In the carrot transcriptome, we identified three ABRE binding protein (DcAREB) transcription factor candidates that localized in the nucleus, but only one, DcAREB3, was induced under ABA treatment in carrot roots. We found that AREB transcription factors bind to the carrot DcPSY2 promoter and transactivate the expression of reporter genes. We conclude that DcPSY2 is involved in ABA-mediated salt stress tolerance in carrot through the binding of AREB transcription factors to its promoter.

Influence of Haemodialysis Membranes on the Release of Granulocyte Elastase

The advantages of multiparameter assessment in the evaluation of the blood compatibility of biomaterials underline the importance of investigating possible relevant parameters. In this respect, a study has been made of granulocyte elastase to establish the influence of haemodialysis membranes on the release of this serine proteinase. Plasma levels of granulocyte elastase were determined as a complex with its natural inhibiter α1-proteinase. This elastase - α1 proteinase (E- α1 Pi)inhibitor complex was measured by a highly sensitive enzyme-linked immunoassay. The membranes evaluated were Cuprophan (15-11, Travenol) and polysulphone (F40, Fresenius). Samples were taken from patients undergoing maintenance haemodialysis, before the start of dialysis, after 15 and 90 minutes and again at the end of dialysis (4 h). This investigation clearly demonstrates the different response of the dialysers, and on correcting for surface area, the end-dialysis level of E-α1 Pi remained significantly greater for the Cuprophan membrane. The results support the view that the release of granulocyte elastase is a relevant parameter for inclusion in membrane compatibility assessment.

Participation of children on the autism spectrum in home, school, and community

BACKGROUND

Children on the autism spectrum participate less frequently, and in a narrower range of activities, than their nonautistic peers, but little is known about exact participation patterns across contexts or how this is perceived by caregivers. This study aimed to document patterns of participation and caregiver views with regard to frequency and intensity of activities.

METHOD

Caregivers of children on the spectrum aged 5 (n = 90) and 9-10 years (n = 128) completed the Participation and Environment Measure for Children and Youth for home, school, and community. Caregivers reported on frequency of child's participation, level of involvement, and caregivers' desire for change in participation patterns.

RESULTS

Item-level analyses revealed similar patterns of participation across home, school, and community for both cohorts with some small age-appropriate differences. Caregivers generally desired increased diversity, frequency, and involvement in activities but a decreased use of electronics (computers, games, TV, and DVDs).

CONCLUSION

The possibility of autism-specific participation patterns could inform future interventions aimed at enhancing social inclusion. This warrants further investigation through multiinformant designs that seek the perspectives of the child and caregivers.

Straightforward Synthesis of 2- and 2,8-Substituted Tetracenes

A simple regiospecific route to otherwise problematic substituted tetracenes is described. The diverse cores (E)-1,2-Ar¹ CH₂ (HOCH₂ )C=C(CH₂ OH)I (Ar¹ =Ph, 4-MePh, 4-MeOPh, 4-FPh) and (E)-1,2-I(HOCH₂ )C=C(CH₂ OH)I, accessed from ultra-low cost HOCH₂ C≡CCH₂ OH at multi-gram scales, allow the synthesis of diol libraries (E)-1,2-Ar¹ CH₂ (HOCH₂ )C=C(CH₂ OH)CH₂ Ar² (Ar² =Ph, 4-MePh, 4-iPrPh, 4-MeOPh, 4-FPh, 4-BrPh, 4-biphenyl, 4-styryl; 14 examples) by efficient Negishi coupling. Copper-catalysed aerobic oxidation cleanly provides dialdehydes (E)-1,2-Ar¹ CH₂ (CHO)C=C(CHO)CH₂ Ar² , which in many cases undergo titanium(IV) chloride-induced double Bradsher closure, providing a convenient method for the synthesis of regiochemically and analytically pure tetracenes (12 examples). The sequence is typically chromatography-free, scalable, efficient and technically simple to carry out.