Comprehensive genotyping is necessary to identify therapy options for patients with advanced cancer; however, many cancers are not tested, partly because of tissue limitations. Next-generation ...sequencing (NGS) liquid biopsies overcome some limitations, but clinical validity is not established and adoption is limited. Herein, clinical bridging studies used pretreatment plasma samples and data from FLAURA (NCT02296125; n = 441) and AURA3 (NCT02151981; n = 450) pivotal studies to demonstrate clinical validity of Guardant360 CDx (NGS LBx) to identify patients with advanced EGFR mutant non-small-cell lung cancer who may benefit from osimertinib. The primary end point was progression-free survival (PFS). Patients with EGFR mutation as identified by NGS LBx had significant PFS benefit with first-line osimertinib over standard of care (15.2 versus 9.6 months; hazard ratio, 0.41; P < 0.0001) and with later-line osimertinib over chemotherapy (8.3 versus 4.2 months; hazard ratio, 0.34; P < 0.0001). PFS benefits were similar to the original trial cohorts selected by tissue-based EGFR testing. Analytical validation included accuracy, precision, limit of detection, and specificity. Analytical validity was established for EGFR mutation detection and pan-tumor profiling. Panel-wide limit of detection was 0.1% to 0.5%, with 98% to 100% per-sample specificity. Patients with EGFR mutant non-small-cell lung cancer by NGS LBx had improved PFS with osimertinib, confirming clinical validity. Analytical validity was established for guideline-recommended therapeutic targets across solid tumors. The resulting US Food and Drug Administration approval of NGS LBx demonstrated safety and effectiveness for its intended use and is expected to improve adherence to guideline-recommended targeted therapy use.
Parasitic infections can increase susceptibility to bacterial co-infections. This may be true for urogenital schistosomiasis and bacterial urinary tract co-infections (UTI). We previously reported ...that this co-infection is facilitated by S. haematobium eggs triggering interleukin-4 (IL-4) production and sought to dissect the underlying mechanisms. The interleukin-4-inducing principle from Schistosoma mansoni eggs (IPSE) is one of the most abundant schistosome egg-secreted proteins and binds to IgE on the surface of basophils and mast cells to trigger IL-4 release. IPSE can also translocate into host nuclei using a nuclear localization sequence (NLS) to modulate host transcription. We hypothesized that IPSE is the factor responsible for the ability of S. haematobium eggs to worsen UTI pathogenesis.
Mice were intravenously administered a single 25 μg dose of recombinant S. haematobium-derived IPSE, an NLS mutant of IPSE or PBS. Following IPSE exposure, mice were serially weighed and organs analyzed by histology to assess for toxicity. Twenty-four hours after IPSE administration, mice were challenged with the uropathogenic E. coli strain UTI89 by urethral catheterization. Bacterial CFU were measured using urine. Bladders were examined histologically for UTI-triggered pathogenesis and by PCR for antimicrobial peptide and pattern recognition receptor expression.
Unexpectedly, IPSE administration did not result in significant differences in urine bacterial CFU. However, IPSE administration did lead to a significant reduction in UTI-induced bladder pathogenesis and the expression of anti-microbial peptides in the bladder. Despite the profound effect of IPSE on UTI-triggered bladder pathogenesis and anti-microbial peptide production, mice did not demonstrate systemic ill effects from IPSE exposure.
Our data show that IPSE may play a major role in S. haematobium-associated urinary tract co-infection, albeit in an unexpected fashion. These findings also indicate that IPSE either works in concert with other IL-4-inducing factors to increase susceptibility of S. haematobium-infected hosts to bacterial co-infection or does not contribute to enhancing vulnerability to this co-infection.
With advances in precision oncology, liquid biopsies have shown promise as a minimally invasive means to diagnose cancer and guide treatment decisions. This commentary presents an assessment of the ...potential and the challenges of widespread use of liquid biopsy testing, based on the 2019 Accelerating Anticancer Agent Development Workshop.
...S. haematobium has been categorized as a Group I carcinogen ("carcinogenic to humans") by the International Agency on Research on Cancer of the World Health Organization 3. To our knowledge, ...this is the first in vivo demonstration that pharmacologic inhibition of DNA methylation can prevent preneoplastic changes in the bladder. ...manipulating DNA methylation may be a promising approach to slow or prevent bladder carcinogenesis in high-risk patient populations, namely those with extensive exposure to carcinogens such as urogenital schistosomiasis.
Although chronically implanted inferior vena cava filters may result in filter-related morbidity, there is currently no routine option for removing such filters when they become firmly embedded along ...the vena cava endothelium.
During a 3-year period, 100 consecutive patients were prospectively enrolled in a single-center study. There were 42 men and 58 women (mean age, 46 years; limits, 18-76 years). Retrieval indications included filter-related acute inferior vena cava thrombosis, chronic inferior vena cava occlusion, and pain from retroperitoneal or bowel penetration. Filter retrieval was also performed to prevent risks from prolonged implantation and to potentially eliminate the need for lifelong anticoagulation. After standard methods failed, photothermal tissue ablation was attempted with a laser sheath powered by a 308-nm xenon chloride excimer laser. Applied forces were recorded with a digital tension meter before and during laser activation. Laser-assisted retrieval was successful in 98.0% (95% confidence interval CI, 93.0%-99.8%) with mean implantation of 855 days (limits, 37-6663 days; >18 years). The following filter types were encountered in this study: Günther-Tulip (n=34), Celect (n=12), Option (n=17), Optease (n=20, 1 failure), TrapEase (n=6, 1 failure), Simon-Nitinol (n=1), 12F Stainless Steel Greenfield (n=4), and Titanium Greenfield (n=6). The average force during failed standard retrievals was 7.2 versus 4.6 pounds during laser-assisted retrievals (P<0.0001). The major complication rate was 3.0% (95% CI, 0.6%-8.5%), the minor complication rate was 7.0% (95% CI, 0.3%-13.9%), and there were 4 adverse events (2 coagulopathic hemorrhages, 1 renal infarction, and 1 cholecystitis; 4.0%; 95% CI, 1.1%-9.9%) at mean follow-up of 500 days (limits, 84-1079 days). Scar tissue ablation was histologically confirmed in 96.0% (95% CI, 89.9%-98.9%). Successful retrieval allowed cessation of anticoagulation in 30 of 30 (100%) patients and alleviated morbidity in 23 of 24 patients (96%).
Excimer laser-assisted removal is effective in removing embedded inferior vena cava filters refractory to standard retrieval and high force. This method can be safely used to prevent and alleviate filter-related morbidity.
http://www.clinicaltrials.gov. Unique identifier: NCT01158482.
Ifosfamide and other oxazaphosphorines can result in hemorrhagic cystitis, a constellation of complications caused by acrolein metabolites. We previously showed that a single dose of IPSE ...(Interleukin-4-inducing principle from Schistosoma eggs), a schistosome-derived host modulatory protein, can ameliorate ifosfamide-related cystitis; however, the mechanisms underlying this urotoxicity and its prevention are not fully understood. To provide insights into IPSE's protective mechanism, we undertook transcriptional profiling of bladders from ifosfamide-treated mice, with or without pretreatment with IPSE or IPSE-NLS (a mutant of IPSE lacking nuclear localization sequence). Ifosfamide treatment upregulated a range of proinflammatory genes. The IL-1β-TNFα-IL-6 proinflammatory cascade via NFκB and STAT3 pathways was identified as the key driver of inflammation. The NRF2-mediated oxidative stress response pathway, which regulates heme homoeostasis and expression of antioxidant enzymes, was highly activated. Anti-inflammatory cascades, namely Wnt, Hedgehog and PPAR pathways, were downregulated. IPSE drove significant downregulation of major proinflammatory pathways including the IL-1β-TNFα-IL-6 pathways, interferon signaling, and reduction in oxidative stress. IPSE-NLS reduced inflammation but not oxidative stress. Taken together, we have identified signatures of acute-phase inflammation and oxidative stress in ifosfamide-injured bladder, which are reversed by pretreatment with IPSE. This work revealed several pathways that could be therapeutically targeted to prevent ifosfamide-induced hemorrhagic cystitis.
Newborn screening for cystic fibrosis enables early detection and management of this debilitating genetic disease. Implementing comprehensive CFTR analysis using Sanger sequencing as a component of ...confirmatory testing of all screen-positive newborns has remained impractical due to relatively lengthy turnaround times and high cost. Here, we describe CFseq, a highly sensitive, specific, rapid (<3 days), and cost-effective assay for comprehensive CFTR gene analysis from dried blood spots, the common newborn screening specimen. The unique design of CFseq integrates optimized dried blood spot sample processing, a novel multiplex amplification method from as little as 1 ng of genomic DNA, and multiplex next-generation sequencing of 96 samples in a single run to detect all relevant CFTR mutation types. Sequence data analysis utilizes publicly available software supplemented by an expert-curated compendium of >2000 CFTR variants. Validation studies across 190 dried blood spots demonstrated 100% sensitivity and a positive predictive value of 100% for single-nucleotide variants and insertions and deletions and complete concordance across the polymorphic poly-TG and consecutive poly-T tracts. Additionally, we accurately detected both a known exon 2,3 deletion and a previously undetected exon 22,23 deletion. CFseq is thus able to replace all existing CFTR molecular assays with a single robust, definitive assay at significant cost and time savings and could be adapted to high-throughput screening of other inherited conditions.
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•Analyses of whole, parasite-infected organs give a broad view of the host transcriptome.•This approach has limited ability to assign gene expression to specific cells.•Computational ...deconvolution may overcome this limitation of whole organ analysis.•We show proof of principle using schistosomiasis-infected bladder microarray data.•Errors indicate further refinements are needed to study host-parasite interactions.
Analyses of whole organs from parasite-infected animals can reveal the entirety of the host tissue transcriptome, but conventional approaches make it difficult to dissect out the contributions of individual cellular subsets to observed gene expression. Computational deconvolution of gene expression data may be one solution to this problem. We tested this potential solution by deconvoluting whole bladder gene expression microarray data derived from a model of experimental urogenital schistosomiasis. A supervised technique was used to group B-cell and T-cell related genes based on their cell types, with a semi-supervised technique to calculate the proportions of urothelial cells. We demonstrate that the deconvolution technique was able to group genes into their correct cell types with good accuracy. A clustering-based methodology was also used to improve prediction. However, incorrectly predicted genes could not be discriminated using this methodology. The incorrect predictions were primarily IgH- and IgK-related genes. To our knowledge, this is the first application of computational deconvolution to complex, parasite-infected whole tissues. Other computational techniques such as neural networks may need to be used to improve prediction.
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