Clinical suspicion, diagnosis and management of cardiac amyloidosis: update document and executive summary

In recent years, the interest in cardiac amyloidosis has grown exponentially. However, there is a need to improve our understanding of amyloidosis in order to optimise early detection systems. Therefore, it is crucial to incorporate solutions to improve the suspicion, diagnosis and follow-up of cardiac amyloidosis. In this sense, we designed a tool following the different phases to reach the diagnosis of cardiac amyloidosis, as well as an optimal follow-up: a) clinical suspicion, where the importance of the "red flags" to suspect it and activate the diagnostic process is highlighted; 2) diagnosis, where the diagnostic algorithm is mainly outlined; and 3) follow-up of confirmed patients. This is a practical resource that will be of great use to all professionals caring for patients with suspected or confirmed cardiac amyloidosis, to improve its early detection, as well as to optimise its accurate diagnosis and optimal follow-up.

Sex differences in clinical characteristics and outcomes in the CLOROTIC (combining loop with thiazide diuretics for decompensated heart failure) trial

AIMS

The addition of hydrochlorothiazide (HCTZ) to furosemide improved the diuretic response in patients with acute heart failure (AHF) in the CLOROTIC trial. Our aim was to evaluate if there were differences in clinical characteristics and outcomes according to sex.

METHODS

This is a post-hoc analysis of the CLOROTIC trial, including 230 patients with AHF randomized to receive HCTZ or placebo in addition to an intravenous furosemide regimen. The primary and secondary outcomes included changes in weight and patient-reported dyspnoea 72 and 96 h after randomization, metrics of diuretic response and mortality/rehospitalizations at 30 and 90 days. The influence of sex on primary, secondary and safety outcomes was evaluated.

RESULTS

One hundred and eleven (48%) women were included in the study. Women were older and had higher values of left ventricular ejection fraction. Men had more ischemic cardiomyopathy and chronic obstructive pulmonary disease and higher values of natriuretic peptides. The addition of HCTZ to furosemide was associated to a greatest weight loss at 72/96 h, better metrics of diuretic response and higher 24-h diuresis compared to placebo without significant differences according to sex (all p-values for interaction were not significant). Worsening renal function occurred more frequently in women (OR [95%CI]: 8.68 [3.41-24.63]) than men (OR [95%CI]: 2.5 [0.99-4.87]), p = 0.027. There were no differences in mortality or rehospitalizations at 30/90 days.

CONCLUSION

Adding HCTZ to intravenous furosemide is an effective strategy to improve diuretic response in AHF with no difference according to sex, but worsening renal function was more frequent in women.

CLINICAL TRIAL REGISTRATION

Clinicaltrials.gov: NCT01647932; EudraCT Number: 2013-001852-36.

Executive summary of the 2023 update on the consensus regarding basic conduct during hospital admission for patients with acute heart failure

Acute heart failure (AHF) is associated with significant morbidity and mortality and it stands as the primary cause of hospitalization for individuals over the age of 65 in Spain. This document outlines the main recommendations as follows: (1) Upon admission, it is crucial to conduct a comprehensive assessment, taking into account the patient's standard treatment and comorbidities, as these factors determine the prognosis of the disease. (2) During the initial hours of hospital care, prioritizing decongestive treatment is essential. It is recommended to adopt an early staged diuretic therapeutic approach based on the patient's response. (3) In order to manage patients in the stable phase, it is advisable to consider initiating and/or adjusting evidence-based drug treatments such as sacubitril/valsartan or angiotensin-converting enzyme inhibitors/angiotensin II receptor blockers, beta blockers, aldosterone antagonists, and SGLT2 inhibitors. (4) Upon hospital discharge, utilizing a checklist is recommended to optimize the patient's management and identify the most efficient options for ensuring continuity of care post-discharge.

Current heart failure disease management and treatment in accredited units from Cardiology and Internal Medicine in Spain

BACKGROUND AND OBJECTIVES

Heart failure (HF) is a complex disease with high prevalence, incidence and mortality rates leading to high healthcare burden. In Spain, there are multidisciplinary HF units coordinated by Cardiology and Internal Medicine. Our objective is to describe its current organizational model and their adherence to the latest scientific recommendations.

MATERIALS AND METHODS

In late 2021, a scientific committee (with cardiology and internal medicine specialists) developed a questionnaire that was sent as an online survey to 110 H F units. 73 from cardiology (accredited by SEC-Excelente) and 37 from internal medicine, (integrated in UMIPIC program).

RESULTS

83 answers were received (75.5% total: 49 from cardiology and 34 from internal medicine). HF units are mostly integrated by specialists from cardiology, internal medicine and specialized nurse practitioners (34.9%). Patient characteristics from HF units are widely different when comparing those in cardiology to UMIPIC, being the latter older, more frequently with preserved ejection fraction and higher comorbidity burden. Most HF units (73.5%) currently use a hybrid face-to-face/virtual model to perform patient follow-up. Natriuretic peptides are the biomarkers most commonly used (90%). All four disease-modifying drug classes are mainly implemented at the same time (85%). Only 24% of HF units hold fluent communication with primary care.

CONCLUSIONS

Both models from Cardiology and Internal Medicine HF units are complementary, they include specialized nursing, they use hybrid approach for patient follow-up and they display a high adherence to the latest guideline recommendations. Coordination with primary care remains as the major improvement area.

Tumor-Derived Lysophosphatidic Acid Blunts Protective Type I Interferon Responses in Ovarian Cancer

Lysophosphatidic acid (LPA) is a bioactive lipid enriched in the tumor microenvironment of immunosuppressive malignancies such as ovarian cancer. Although LPA enhances the tumorigenic attributes of cancer cells, the immunomodulatory activity of this phospholipid messenger remains largely unexplored. Here, we report that LPA operates as a negative regulator of type I interferon (IFN) responses in ovarian cancer. Ablation of the LPA-generating enzyme autotaxin (ATX) in ovarian cancer cells reprogrammed the tumor immune microenvironment, extended host survival, and improved the effects of therapies that elicit protective responses driven by type I IFN. Mechanistically, LPA sensing by dendritic cells triggered PGE2 biosynthesis that suppressed type I IFN signaling via autocrine EP4 engagement. Moreover, we identified an LPA-controlled, immune-derived gene signature associated with poor responses to combined PARP inhibition and PD-1 blockade in patients with ovarian cancer. Controlling LPA production or sensing in tumors may therefore be useful to improve cancer immunotherapies that rely on robust induction of type I IFN.

SIGNIFICANCE

This study uncovers that ATX-LPA is a central immunosuppressive pathway in the ovarian tumor microenvironment. Ablating this axis sensitizes ovarian cancer hosts to various immunotherapies by unleashing protective type I IFN responses. Understanding the immunoregulatory programs induced by LPA could lead to new biomarkers predicting resistance to immunotherapy in patients with cancer. See related commentary by Conejo-Garcia and Curiel, p. 1841. This article is highlighted in the In This Issue feature, p. 1825.

Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation

The mechanisms regulating exhaustion of tumor-infiltrating lymphocytes (TIL) and responsiveness to PD-1 blockade remain partly unknown. In human ovarian cancer, we show that tumor-specific CD8+ TIL accumulate in tumor islets, where they engage antigen and upregulate PD-1, which restrains their functions. Intraepithelial PD-1+CD8+ TIL can be, however, polyfunctional. PD-1+ TIL indeed exhibit a continuum of exhaustion states, with variable levels of CD28 costimulation, which is provided by antigen-presenting cells (APC) in intraepithelial tumor myeloid niches. CD28 costimulation is associated with improved effector fitness of exhausted CD8+ TIL and is required for their activation upon PD-1 blockade, which also requires tumor myeloid APC. Exhausted TIL lacking proper CD28 costimulation in situ fail to respond to PD-1 blockade, and their response may be rescued by local CTLA-4 blockade and tumor APC stimulation via CD40L.

Shunt Overdrainage: Reappraisal of the Syndrome and Proposal for an Integrative Model

Although shunt overdrainage is a well-known complication in hydrocephalus management, the problem has been underestimated. Current literature suggests that the topic requires more examination. An insight into this condition is limited by a lack of universally agreed-upon diagnostic criteria, heterogeneity of published series, the multitude of different management options and misunderstanding of relationships among pathophysiological mechanisms involved. We carried out a review of the literature on clinical, radiological, intracranial pressure (ICP), pathophysiological and treatment concepts to finally propose an integrative model. Active prophylaxis and management are proposed according to this model based on determination of pathophysiological mechanisms and predisposing factors behind each individual case. As pathophysiology is progressively multifactorial, prevention of siphoning with gravitational valves or antisiphon devices is mandatory to avoid or minimize further complications. Shunt optimization or transferal and neuroendoscopy may be recommended when ventricular collapse and cerebrospinal fluid isolation appear. Cranial expansion may be useful in congenital or acquired craniocerebral disproportion and shunting the subarachnoid space in communicating venous hydrocephalus and idiopathic intracranial hypertension.

Abstract 2059: AI - optimized genomic homologous recombination deficiency test (HRDScar) to predict platinum and PARP inhibitor responses in high-grade serous ovarian cancer

High-grade serous ovarian cancer (HGSC) is the most common and most lethal subtype of ovarian cancer. More than half of the HGSCs are defective in Homologous Recombination DNA repair (HRD), and sensitive to Poly-ADP Ribose Polymerase (PARP) inhibitors. Recently, a genomic HRD test based on three types of genomic scarring events (Large scale transitions; LST, Telomeric Allelic Imbalance TAI, Loss of Heterozygosity LOH) was shown to predict which patients benefit the most from PARP inhibitors. The HRD test, however, was originally designed and optimized in breast cancer, and therefore the details of genomic scarring events occurring in ovarian cancers are unknown.

To characterize the genomic scarring events and define an optimal cut-off for HRDScar biomarker in ovarian cancer, we are using large publicly available dataset from the TCGA. We selected 103 HRD samples based on somatic and germline mutations, gene deletions or hypermethylation in the BRCA1/2 and RAD51 paralog genes, and 34 HR proficient (HRP) samples without any mutation, deletion or hypermethylation of the HR genes. To identify the detailed features of LOH, LST and TAI scarring events, we employed state-of-the-art machine-learning algorithm and statistics to optimally separate the HRD-samples from HRP in the TCGA SNP array dataset. Our new optimized genomic footprints and cut-offs showed improved accuracy to separate HRD from HRP compared to the previous algorithm (accuracy of 0.89 vs 0.79). The optimized HRDScar showed reliable performance in NGS-derived data and correlated with mutational signature 3 (p=2.2e-16, r2=0.5). Interestingly, the HRDScar levels also positively correlated with an HRD score derived from an ex-vivo RAD51-based functional assay for HRD performed in the prospective HERCULES samples (n=72). Using two independent validation cohorts (PCAWG, HERCULES), our optimized HRDScar more accurately predicted progression-free survival (PFS) and overall survival (OS) when compared to previous algorithms. Importantly, improved prediction of PFS was detected especially in patients without BRCA1/2 alterations (p= 1.9e-04, HR=0.70). We are in the process of analyzing HRDScar from a clinical trial involving PARP inhibitor Niraparib (TOPACIO/Keynote-162 (NCT02657889)) enabling direct association of the HRDScar to clinical outcomes. In conclusion, HRDScar shows promise as a fully optimized algorithm that can be used for improved selection of patients for PARP inhibitor therapies in HGSC.

Citation Format: Fernando Perez-Villatoro, Jaana Oikkonen, Manuela Tumiati, Julia Casado, Sakari Hietanen, Johanna Hynninen, Elizabeth P. Garcia, Panagiotis Konstantinopoulos, Sampsa Hautaniemi, Liisa Kauppi, Anniina Färkkilä. AI - optimized genomic homologous recombination deficiency test (HRDScar) to predict platinum and PARP inhibitor responses in high-grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2059.

Abstract 2747: Single-cell tumor-immune microenvironment of BRCA1/2 mutated high-grade serous ovarian cancer

Immune checkpoint blockade has emerged as a new therapeutic approach for multiple cancers. The majority of high-grade serous ovarian, fallopian tube or peritoneal cancers (HGSCs) are deficient in homologous recombination (HR) DNA repair, typically due to mutations or hypermethylation of BRCA1 or BRCA2 genes. A detailed understanding how tumor genotypes affect the tumor microenvironment is unknown.

We performed single-cell spatial analysis of the tumor microenvironment using a highly multiplex tissue cyclic immunofluorescence (t-CycIF) platform with a clinically annotated cohort of 31 patients with BRCA1/2 mutated (BRCAmut) tumors, and 13 patients with tumors without alterations in HR genes (HRwt) (Strickland et al, 2016). Using image analysis, we generated single-cell data for 24 markers in over 105 cells. We clustered the cells into tumor, immune, and stromal cells, and further divided the tumor cells into 7 metaclusters, immune cells into 10 subtypes and stromal cells into 9 metaclusters based on their functional states.

Overall, the BRCAmut tumors showed a higher proportion of tumor cells over stromal cells as compared to HRwt tumors (p=0.031). Moreover, we found distinct functional states of tumor cell metaclusters with opposing prognostic roles in the tumor HR-genotypes. In immune profiling, the BRCAmut tumors exhibited an increased proportion of overall macrophages as compared to HRwt tumors (p=0.024). By contrast, HRwt tumors exhibited more CD11c expressing antigen-presenting cells than BRCAmut tumors (p=0.0013). Interestingly, the tumors with high CD163 expressing, M2 macrophages exhibited a lower overall immune diversity (Simpson's diversity index) in both BRCAmut tumors (p=8.9 × 10−6) and HRwt tumors (p=0.0076). However, the BRCAmut tumors with high immune diversity also had higher proportions of CD11c expressing macrophages (p=0.029). In survival analyses, CD4+ effector T-cells associated with a prolonged platinum free interval exclusively in the BRCAmut tumors (p=0.0011, HR 0.26, 95% CI 0.10-0.66).

In correlative analyses of the tumor-immune-stromal populations, tumor metaclusters associated with distinct immune phenotypes in the BRCAmut tumors. By contrast, immune composition was shaped more by stromal metaclusters in HRwt tumors. These findings further support the differential regulation of tumor microenvironment composition in the tumor HR-genotypes. Further, our preliminary analyses on spatial arrangement of the single-cell subpopulations confirm the distinct microenvironment niches in BRCA1/2 vs HRwt HGSCs.

In conclusion, our single-cell spatial t-CycIF analyses suggest functionally and spatially distinct microenvironments in BRCAmut tumors with the potential to accelerate the development of immunotherapeutic strategies to ultimately improve the treatment and outcomes of patients with ovarian cancer.

Citation Format: Inga-Maria P. Launonen, Nuppu Lyytikäinen, Julia Casado, Ella A. Anttila, Connor A. Jacobson, Jia R. Lin, Zoltan Maliga, Sandro Santaga, Kevin M. Elias, Alan D. D'Andrea, Panagiotis A. Konstantinopoulos, Peter K. Sorger, Anniina Färkkilä. Single-cell tumor-immune microenvironment of BRCA1/2 mutated high-grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2747.

Agile workflow for interactive analysis of mass cytometry data

MOTIVATION

Single-cell proteomics technologies, such as mass cytometry, have enabled characterization of cell-to-cell variation and cell populations at a single-cell resolution. These large amounts of data, require dedicated, interactive tools for translating the data into knowledge.

RESULTS

We present a comprehensive, interactive method called Cyto to streamline analysis of large-scale cytometry data. Cyto is a workflow-based open-source solution that automates the use of state-of-the-art single-cell analysis methods with interactive visualization. We show the utility of Cyto by applying it to mass cytometry data from peripheral blood and high-grade serous ovarian cancer (HGSOC) samples. Our results show that Cyto is able to reliably capture the immune cell sub-populations from peripheral blood and cellular compositions of unique immune- and cancer cell subpopulations in HGSOC tumor and ascites samples.

AVAILABILITYAND IMPLEMENTATION

The method is available as a Docker container at https://hub.docker.com/r/anduril/cyto and the user guide and source code are available at https://bitbucket.org/anduril-dev/cyto.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Consensus on basic conduct during the hospital admission of patients with acute heart failure

Acute heart failure (AHF) is a highly prevalent clinical entity in individuals older than 45years in Spain. AHF is associated with significant morbidity and mortality and is the leading cause of hospitalisation for individuals older than 65years in Spain, a quarter of whom die within 1year of the hospitalisation. In recent years, there has been an upwards trend in hospitalisations for AHF, which increased 76.7% from 2003 to 2013. Readmissions at 30days for AHF have also increased (from 17.6% to 22.1%), at a relative mean rate of 1.36% per year, with the consequent increase in the use of resources and the economic burden for the healthcare system. The aim of this document (developed by the Heart Failure and Atrial Fibrillation Group of the Spanish Society of Internal Medicine) is to guide specialists on the most important aspects of treatment and follow-up for patients with AHF during hospitalisation and the subsequent follow-up. The main recommendations listed in this document are as follows: (1)At admission, perform a comprehensive assessment, considering the patient's standard treatment and comorbidities, given that these determine the disease prognosis to a considerable measure. (2)During the first few hours of hospital care, decongestive treatment is a priority, and a staged diuretic therapeutic approach based on the patient's response is recommended. (3)To manage patients in the stable phase, consider starting and/or adjusting evidence-based drug treatment (e.g., sacubitril/valsartan or angiotensin-converting enzyme inhibitors/angiotensinII receptor blockers, beta blockers and aldosterone antagonists). (4)At hospital discharge, use a checklist to optimise the patient's management and identify the most efficient options for maintaining continuity of care after discharge.

Consensus on basic conduct during the hospital admission of patients with acute heart failure

Acute heart failure (AHF) is a highly prevalent clinical entity in individuals older than 45 years in Spain. AHF is associated with significant morbidity and mortality and is the leading cause of hospitalisation for individuals older than 65 years in Spain, a quarter of whom die within 1 year of the hospitalisation. In recent years, there has been an upwards trend in hospitalisations for AHF, which increased 76.7% from 2003 to 2013. Readmissions at 30 days for AHF have also increased (from 17.6% to 22.1%), at a relative mean rate of 1.36% per year, with the consequent increase in the use of resources and the economic burden for the healthcare system. The aim of this document (developed by the Heart Failure and Atrial Fibrillation Group of the Spanish Society of Internal Medicine) is to guide specialists on the most important aspects of treatment and follow-up for patients with AHF during hospitalisation and the subsequent follow-up. The main recommendations listed in this document are as follows: 1) At admission, perform a comprehensive assessment, considering the patient's standard treatment and comorbidities, given that these determine the disease prognosis to a considerable measure. 2) During the first few hours of hospital care, decongestive treatment is a priority, and a staged diuretic therapeutic approach based on the patient's response is recommended. 3) To manage patients in the stable phase, consider starting and/or adjusting evidence-based drug treatment (e.g., sacubitril/valsartan or angiotensin-converting enzyme inhibitors/angiotensin II receptor blockers, beta blockers and aldosterone antagonists). 4) At hospital discharge, use a checklist to optimise the patient's management and identify the most efficient options for maintaining continuity of care after discharge.

qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets

Motivation

Non-parametric dimensionality reduction techniques, such as t-distributed stochastic neighbor embedding (t-SNE), are the most frequently used methods in the exploratory analysis of single-cell datasets. Current implementations scale poorly to massive datasets and often require downsampling or interpolative approximations, which can leave less-frequent populations undiscovered and much information unexploited.

Results

We implemented a fast t-SNE package, qSNE, which uses a quasi-Newton optimizer, allowing quadratic convergence rate and automatic perplexity (level of detail) optimizer. Our results show that these improvements make qSNE significantly faster than regular t-SNE packages and enables full analysis of large datasets, such as mass cytometry data, without downsampling.

Availability and implementation

Source code and documentation are openly available at https://bitbucket.org/anthakki/qsne/.

Supplementary information

Supplementary data are available at Bioinformatics online.

Genetically Defined Syngeneic Mouse Models of Ovarian Cancer as Tools for the Discovery of Combination Immunotherapy

Despite advances in immuno-oncology, the relationship between tumor genotypes and response to immunotherapy remains poorly understood, particularly in high-grade serous tubo-ovarian carcinomas (HGSC). We developed a series of mouse models that carry genotypes of human HGSCs and grow in syngeneic immunocompetent hosts to address this gap. We transformed murine-fallopian tube epithelial cells to phenocopy homologous recombination-deficient tumors through a combined loss of Trp53, Brca1, Pten, and Nf1 and overexpression of Myc and Trp53 ^R172H, which was contrasted with an identical model carrying wild-type Brca1. For homologous recombination-proficient tumors, we constructed genotypes combining loss of Trp53 and overexpression of Ccne1, Akt2, and Trp53 ^R172H, and driven by KRAS ^G12V or Brd4 or Smarca4 overexpression. These lines form tumors recapitulating human disease, including genotype-driven responses to treatment, and enabled us to identify follistatin as a driver of resistance to checkpoint inhibitors. These data provide proof of concept that our models can identify new immunotherapy targets in HGSC. SIGNIFICANCE: We engineered a panel of murine fallopian tube epithelial cells bearing mutations typical of HGSC and capable of forming tumors in syngeneic immunocompetent hosts. These models recapitulate tumor microenvironments and drug responses characteristic of human disease. In a Ccne1-overexpressing model, immune-checkpoint resistance was driven by follistatin.This article is highlighted in the In This Issue feature, p. 211.

Author Correction: Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer

Combined PARP and immune checkpoint inhibition has yielded encouraging results in ovarian cancer, but predictive biomarkers are lacking. We performed immunogenomic profiling and highly multiplexed single-cell imaging on tumor samples from patients enrolled in a Phase I/II trial of niraparib and pembrolizumab in ovarian cancer (NCT02657889). We identify two determinants of response; mutational signature 3 reflecting defective homologous recombination DNA repair, and positive immune score as a surrogate of interferon-primed exhausted CD8 + T-cells in the tumor microenvironment. Presence of one or both features associates with an improved outcome while concurrent absence yields no responses. Single-cell spatial analysis reveals prominent interactions of exhausted CD8 + T-cells and PD-L1 + macrophages and PD-L1 + tumor cells as mechanistic determinants of response. Furthermore, spatial analysis of two extreme responders shows differential clustering of exhausted CD8 + T-cells with PD-L1 + macrophages in the first, and exhausted CD8 + T-cells with cancer cells harboring genomic PD-L1 and PD-L2 amplification in the second.

Week 48 Resistance Analyses of the Once-Daily, Single-Tablet Regimen Darunavir/Cobicistat/Emtricitabine/Tenofovir Alafenamide (D/C/F/TAF) in Adults Living with HIV-1 from the Phase III Randomized AMBER and EMERALD Trials

Darunavir/cobicistat/emtricitabine/tenofovir alafenamide (D/C/F/TAF) 800/150/200/10 mg is being investigated in two Phase III trials, AMBER (NCT02431247; treatment-naive adults) and EMERALD (NCT02269917; treatment-experienced, virologically suppressed adults). Week 48 AMBER and EMERALD resistance analyses are presented. Postbaseline samples for genotyping/phenotyping were analyzed from protocol-defined virologic failures (PDVFs) with viral load (VL) ≥400 copies/mL at failure/later time points. Post hoc analyses were deep sequencing in AMBER, and HIV-1 proviral DNA from baseline samples (VL <50 copies/mL) in EMERALD. Through week 48 across both studies, no darunavir, primary PI, or tenofovir resistance-associated mutations (RAMs) were observed in HIV-1 viruses of 1,125 participants receiving D/C/F/TAF or 629 receiving boosted darunavir plus emtricitabine/tenofovir-disoproxil-fumarate. In AMBER, the nucleos(t)ide analog reverse transcriptase inhibitor (N(t)RTI) RAM M184I/V was identified in HIV-1 of one participant during D/C/F/TAF treatment. M184V was detected pretreatment as a minority variant (9%). In EMERALD, in participants with prior VF and genoarchive data (N = 140; 98 D/C/F/TAF and 42 control), 4% had viruses with darunavir RAMs, 38% with emtricitabine RAMs, mainly at position 184 (41% not fully susceptible to emtricitabine), 4% with tenofovir RAMs, and 21% ≥ 3 thymidine analog-associated mutations (24% not fully susceptible to tenofovir) detected at screening. All achieved VL <50 copies/mL at week 48 or prior discontinuation. D/C/F/TAF has a high genetic barrier to resistance; no darunavir, primary PI, or tenofovir RAMs were observed through 48 weeks in AMBER and EMERALD. Only one postbaseline M184I/V RAM was observed in HIV-1 of an AMBER participant. In EMERALD, baseline archived RAMs to darunavir, emtricitabine, and tenofovir in participants with prior VF did not preclude virologic response.

Drug screening approach combines epigenetic sensitization with immunochemotherapy in cancer

BACKGROUND

The epigenome plays a key role in cancer heterogeneity and drug resistance. Hence, a number of epigenetic inhibitors have been developed and tested in cancers. The major focus of most studies so far has been on the cytotoxic effect of these compounds, and only few have investigated the ability to revert the resistant phenotype in cancer cells. Hence, there is a need for a systematic methodology to unravel the mechanisms behind epigenetic sensitization.

RESULTS

We have developed a high-throughput protocol to screen non-simultaneous drug combinations, and used it to investigate the reprogramming potential of epigenetic inhibitors. We demonstrated the effectiveness of our protocol by screening 60 epigenetic compounds on diffuse large B-cell lymphoma (DLBCL) cells. We identified several histone deacetylase (HDAC) and histone methyltransferase (HMT) inhibitors that acted synergistically with doxorubicin and rituximab. These two classes of epigenetic inhibitors achieved sensitization by disrupting DNA repair, cell cycle, and apoptotic signaling. The data used to perform these analyses are easily browsable through our Results Explorer. Additionally, we showed that these inhibitors achieve sensitization at lower doses than those required to induce cytotoxicity.

CONCLUSIONS

Our drug screening approach provides a systematic framework to test non-simultaneous drug combinations. This methodology identified HDAC and HMT inhibitors as successful sensitizing compounds in treatment-resistant DLBCL. Further investigation into the mechanisms behind successful epigenetic sensitization highlighted DNA repair, cell cycle, and apoptosis as the most dysregulated pathways. Altogether, our method adds supporting evidence in the use of epigenetic inhibitors as sensitizing agents in clinical settings.

Anduril 2: upgraded large-scale data integration framework

Summary

Anduril is an analysis and integration framework that facilitates the design, use, parallelization and reproducibility of bioinformatics workflows. Anduril has been upgraded to use Scala for pipeline construction, which simplifies software maintenance, and facilitates design of complex pipelines. Additionally, Anduril’s bioinformatics repository has been expanded with multiple components, and tutorial pipelines, for next-generation sequencing data analysis.

Availabilityand implementation

Freely available at http://anduril.org.

Supplementary information

Supplementary data are available at Bioinformatics online.

The antigenic variability of HCV in viral HLA-Ag binding is related to the activation of the host immune response

Our previous data show that hepatitis C virus (HCV) genotype 1 patients expressing the HLA-DQB1 * 0301 allele have a combined response probability of 69%, while the remaining 31% do not respond, probably because the HCV immunodominant epitope (IE) against the DQB1 * 0301 allele is mutated. HCV IE (region sequenced in NS3 is a region encoding aa 1253–1272) from 37 patients (21 Sustained Virological Response, SVR; 16 non-SVR) HLA-DQB1 * 0301+, were analysed by pyrosequencing. In vitro cultures were also determined by CD4+ proliferation, using non-mutated IE (wild-type synthetic peptide) and synthetic mutated peptide. The pyrosequencing study revealed 34 different haplotypes. The SVR patients had fewer haplotypes (P = 0.07), mutations/haplotypes (P = 0.01) and polymorphic sites (P = 0.02) than non-SVR. Three polymorphic sites were associated with the non-SVR patients: haplotype 7 (L5P); haplotype 11 (L7P); and haplotype 15, (L15S) (P = 0.02). The in vitro study (n = 7) showed that in 4/7 patients (Group 1) the CD4+ proliferation obtained with wild-type synthetic peptide was higher than that obtained with the negative control and with the synthetic mutated peptide (P = 0.039). However, in the remaining 3/7 patients (Group 2) this pattern was not observed (P = 0.7). Our findings suggest that HLA-DQB1 * 0301+ patients with high antigenic variability in HCV IE (NS31253-1272) have a lower SVR rate, due to reduced CD4+ proliferation as a result of incorrect viral HLA-Ag binding.

Influence of HLA class I, HLA class II and KIRs on vertical transmission and chronicity of hepatitis C virus in children

Background & aim

There is evidence that maternal viral load of HCV during delivery influences the risk for Mother-to-child transmission (MTCT), but this does not explain all cases. We study the role of the immunogenetic profile (HLA, KIRs and KIR-ligand binding) of mothers and children in HCV-MTCT and in chronicity in the children.

Methodology

79 HCV-RNA (+) mothers and their 98 children were included. 24 children were infected, becoming chronic in 8 cases and clearing in 16. HLA-class-I and II and KIRs were determined by Luminex.

Results

MTCT study: The presence of HLA-C1-ligand in mothers and/or their children reduces the risk of transmission (mothers: Pc = 0.011, children: P = 0.033), whereas the presence of HLA-C2C2-ligand in mothers increases it (Pc = 0.011). In children KIR2DL3-HLA-C1 is a protector factor (Pc = 0.011). Chronicity in children study: Maternal DQA1*01 allele (Pc = 0.027), KIR2DS1 (Pc = 0.011) or KIR3DS1 (Pc = 0.011) favours chronicity in the child. The presence of the DQB1*03 allele (Pc = 0.027) and KIR2DS3 (P = 0.056) in the child and homozygosity for KIR3DL1/3DL1 (Pc = 0.011) and for the HLA-Bw4/Bw4 ligand (P = 0.027) is associated with viral clearance, whereas the presence of HLA-Bw6 ligand (P = 0.027), the binding of KIR3DS1-HLA-Bw4 (P = 0.037) and heterozygosity for KIR3DL1/3DS1 (Pc = 0.011) favour viral chronicity. Mother/child allele matching: In the joint HLA analysis, matching was greater between mothers and children with chronic infection vs those who had cleared the virus (67%±4.1 vs 57%±1.2, P = 0.003).

Conclusions

The HLA-C1 ligand in the mother is related to MTCT, while several genetic factors of the mother or child are involved in the chronification or clearance of infection in the child. Matching allelic data is considered to be an indicator of HCV chronicity in the child and can be used as a potential prognostic test. This implies that NK cells may play a previously undocumented role in protecting against MTCT and that both NK cell immunity and adaptive T-cell responses may influence viral clearance in infected children.

Liquid chromatography quadrupole time-of-flight mass spectrometry identification and determination of tri- and hexaaryl chloro imidazoles in sewage sludge

The identification and further quantification of 2-chloro-triarylimidazole (o-Cl-TAI) and its dimer (o-DCl-HABI) in sludge from a sewage treatment plant (STP) is reported for the first time. Liquid chromatography (LC) quadrupole time-of-flight (QTOF) mass spectrometry (MS) was used as analytical technique during screening and determination steps. Pollutants were identified following a post-run search strategy, applying the chlorine mass filter, and characterized by their accurate MS and product ion scan spectra. Finally, their identities were confirmed with authentic standards. The species (o-Cl-TAI) has been rated as potentially genotoxic and carcinogenic for mice and rats. Effects of sample preparation in the stability and the extraction efficiency of both compounds are discussed. Under final conditions, they were extracted from freeze-dried samples (0.5 g of sludge or biosolids dispersed with 2 g of C₁₈ and packed into a polypropylene syringe) with 20 ml of methanol, which also flowed through a clean-up layer of Florisil and PSA sorbents (0.5 g each). This method attained quantitative extraction yields and limits of quantification between 4 and 10 ng/g. The pollutants o-Cl-TAI and o-DCl-HABI were ubiquitous in sludge and biosolids obtained in consecutive years from the investigated STP. Their concentrations varied from 0.02 to more than 13 μg/g (freeze-dried sample). Copyright © 2016 John Wiley & Sons, Ltd.

Carbon dots obtained using hydrothermal treatment of formaldehyde. Cell imaging in vitro

Highly photoluminescent carbon dots have been prepared in a one step procedure by hydrothermal treatment of formaldehyde at 180 °C. They show green fluorescence under UV light exposure and emission spectra are centered at 440 nm. Fluorescence lifetimes comprise between 0.7 and 2.70 ns, when the synthesis process lasted for 1-7 days. TEM images of nanoparticles showed a homogeneous size/shape distribution. When the thermal treatment process was carried out for a long time (30 days) formation of aggregates occurred. Carbon dots were further analyzed using (1)H and (13)C-NMR, Raman and FTIR spectroscopy techniques and XPS. Cell imaging of nanoparticles was carried out by using mouse MC3T3-E1 pre-osteoblasts as a model. The nanoparticles were selectively localized in the cytoplasm without further functionalization and could be realized by cellular phagocytosis, so that the fluorescence of these can be used for live cell imaging in vitro.

Polyethersulfone solid-phase microextraction followed by liquid chromatography quadrupole time-of-flight mass spectrometry for benzotriazoles determination in water samples

A microextraction method for the determination of 1H-benzotriazole (BTri), and four polar derivatives (4 and 5-methyl-1H-benzotriazole, 4-TTri and 5-TTri; 5,6-dimethyl-1H-benzotriazole, XTri; and 5-chloro-1H-benzotriazole, 5-ClBTri), in surface and wastewater samples is presented. Analytes were pre-concentrated using a disposable, low cost polyethersulfone (PES) sorbent and further analysed by liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS). Parameters affecting the efficiency of sample preparation (extraction conditions and desorption solvent) and those controlling the performance of LC-MS determination were investigated. Analytes were extracted from 15mL water samples, containing a 30% (w/v) of sodium chloride (4.5g) and adjusted at pH 4.5, using a tubular PES sorbent (5cm length×0.7mm o.d., sorbent volume 42μL). After methanol desorption and solvent exchange, benzotriazoles were determined by LC-MS, with chromatograms extracted using a mass window of 20ppm, centred in their [M+H](+) ions. The identity of chromatographic peaks was confirmed with accurate ion product scan (MS/MS) spectra. The method provided limits of quantification (LOQs) between 0.005 and 0.100μgL(-1), and relative recoveries from 81% to 124% (except for XTri in sewage samples, ca. 60%) with associated standard deviations between 2% and 9%. When compared with polydimethylsiloxane covered stir-bars (coating volume 24μL), the PES polymer achieved significant higher responses (5-20-fold) for these polar pollutants. BTri and tolyltriazoles (4-TTri and 5-TTri) were found in urban sewage and river water samples, affected by wastewater discharges, with the maximum concentration (5.9μgL(-1)) corresponding to BTri in raw wastewater.

Equilibrative nucleoside transporter 2 is expressed in human umbilical vein endothelium, but is not involved in the inhibition of adenosine transport induced by hyperglycaemia

Human equilibrative, Na(+)-independent nucleoside transport is mediated by membrane proteins sensitive (system es, hENT1) or insensitive (system ei, hENT2) to nitrobenzylthioinosine (NBMPR). Gestational diabetes and elevated extracellular concentrations of D-glucose reduce adenosine transport in human umbilical vein endothelium (HUVEC). We studied hENT2 and hENT1 expression in HUVEC, and the effect of D-glucose on their activity and expression in HUVEC preincubated with 25 mM D-glucose (24 h). hENT2 and hENT1 mRNA were quantified by real-time reverse transcription polymerase chain reaction, and their proteins were detected by Western blotting. hENT2 and hENT1 proteins are co-expressed in HUVEC and are located at the plasma membrane, however, hENT2 was mainly cytoplasmatic and perinuclear in location. D-Glucose reduced hENT1 and hENT2 mRNA expression, but only hENT1 protein abundance at the plasma membrane. Adenosine transport was inhibited by D-glucose and NMBPR (1 microM) in intact cells and membrane vesicles. Hypoxanthine inhibited adenosine transport in the absence or in the presence of 1 microM NBMPR. D-Glucose reduced NBMPR maximal binding in intact cells, membrane vesicles, and plasma membrane fractions. In conclusion, the present study demonstrates that hENT2 and hENT1 are co-expressed in HUVEC, and even when adenosine transport is also mediated by hENT2, the hENT2-mediated transport activity is not involved in the d-glucose-induced down-regulation of total adenosine transport.