Background Antibody-mediated rejection (AMR) is a recognized cause of allograft loss in kidney transplant recipients. A range of therapies targeting removal of circulating donor-specific antibodies (DSAs), blocking their effect or reducing production have been reported. Methods We conducted a systematic review to determine the efficacy of treatments for acute AMR in renal allografts. Electronic databases, reference lists, and conference proceedings were searched for controlled trials. Nonrandomized publications were reviewed for the purpose of discussion. Results We identified 10,388 citations, including five randomized and seven nonrandomized controlled trials. The randomized studies were small (median, 13 patients/arm; range, 5–23), of which, four examined plasmapheresis (one suggested benefit) and one for immunoadsorption (also suggesting benefit). Marked heterogeneity was evident, including the definition and severity of AMR and the treatment regimen. The end point of graft survival was common to all studies. Small, nonrandomized controlled studies suggested benefit from rituximab or bortezomib. The effects of dose and regimen on the clinical response to any of the current treatments were not apparent from the available data. Conclusions Data describing the efficacy of treatments for AMR in renal allografts are of low or very low quality. Larger randomized controlled trials and dose-response studies are required.
Abstract BACKGROUND: Pre-clinical tumour models lack human stromal cells and are inadequate for the assessment of novel tumour microenvironment targeted therapies. An increase in combination opportunities requires a higher throughput in vitro assay that utilised the patient relevant model. The 3D-tumour growth assay (3D-TGA) enables patient-derived tumour cells to be admixed with a basement membrane extract and bone marrow-derived mesenchymal stem cells (bmMSCs) in a 96-well format for screening. Response to standard of care (SoC) agents such as paclitaxel, targeted agents such as Erlotinib were compared to subcutaneous xenograft responses in vivo. METHODS: Tumour cells or xenograft material which is disaggregated to yield a pure epithelial population, are admixed and suspended in basement membrane extract (Cultrex®, Trevigen) with and without bmMSCs. Cells were maintained for three days before they were treated with a panel of test agents, such as paclitaxel, AZD2014, Erlotinib, carboplatin for lung PDX and final cell viability was determined on day 7 by alamar blue assay. IC50 curves were determined using GraphPad Prism 6.0. Subcutaneous tumour growth was evaluated three times a week by measuring the tumour in two dimensions using electronic callipers for the duration of the study and tumour volumes were estimated using length and width measurements. Treatment was initiated when tumour growth was established. RESULTS: A panel of PDX models which contain various mutation sites (e.g. EGFR, KRAS) were assessed with a range of SoC (e.g. carboplatin, pemetrexed and paclitaxel) or targeted agents (e.g. Erlotinib, AZ2014). A squamous NSCLC model LU6422, which harbours a heterozygous mutation in the EGF-R intracellular kinase domain (c.2573T>G (L858R)) showed exquisite sensitivity to Erlotinib in both 3D TGA and xenograft studies. Similarly, a squamous NSCLC model LU6402 was assessed with AZD2014 and Paclitaxel in 3D-TGA in the presence of bmMSCs which showed an additive effect of AZD2014 in combination of Paclitaxel on tumour cell growth. A similar efficacy was observed in subcutaneous in vivo xenograft; however, a combination finding was not evident when the stromal cells bmMSCs were absent. The data illustrates that the comparable sensitivities to various test agents between 3D-TGA and in vivo xenograft studies was observed. CONCLUSIONS: The 3D tumour growth assay fast and simple approach to restoring the interaction between the tumour and stroma in a 96-well format enabling screening to multiple dug concentrations and combinations. This assays provide unique opportunity for interrogating therapies that target the tumour microenvironment using patient relevant models. Citation Format: Simon Jiang, Jane Wrigley, Sumanjeet Malhi, Jamie Wood, Stephanie Morton, Louise Wainwright, Yinfei Yin, Rajendra Kumari. Patient-derived xenograft screening in a three-dimensional tumor growth assay incorporating stromal elements to recapitulate the human tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5033.
Abstract The heterogeneous composition of cellular transcriptomes poses a major challenge for detecting weakly expressed RNA classes, as they can be obscured by abundant RNAs. Although biochemical protocols can enrich or deplete specified RNAs, they are time-consuming, expensive and can compromise RNA integrity. Here we introduce RISER, a biochemical-free technology for the real-time enrichment or depletion of RNA classes. RISER performs selective rejection of molecules during direct RNA sequencing by identifying RNA classes directly from nanopore signals with deep learning and communicating with the sequencing hardware in real time. By targeting the dominant messenger and mitochondrial RNA classes for depletion, RISER reduces their respective read counts by more than 85%, resulting in an increase in sequencing depth of 47% on average for long non-coding RNAs. We also apply RISER for the depletion of globin mRNA in whole blood, achieving a decrease in globin reads by more than 90% as well as an increase in non-globin reads by 16% on average. Furthermore, using a GPU or a CPU, RISER is faster than GPU-accelerated basecalling and mapping. RISER’s modular and retrainable software and intuitive command-line interface allow easy adaptation to other RNA classes. RISER is available at https://github.com/comprna/riser .
Abstract Background: To determine the safety and efficacy of biological agents used in the treatment of systemic lupus erythematosus (SLE) in adults. Methods: Systematic review and meta-analysis following PRISMA guidelines Data sources: MEDLINE (through Pubmed), EMBASE, Cochrane library, Clinicaltrials.gov, Australianclinicaltrials.gov.au, ANZCTR.org.au and WHO International Clinical Trials Registry Platform for studies published from 20 May 2021 and 15 years prior. A grey literature search was performed and completed on 31 May 2021. Study criteria: Phase II, III or quasi randomised controlled trials, studies with only cerebral or cutaneous lupus were excluded. Data extraction: Two authors independently screened studies for eligibility, extracted, reviewed data for accuracy, and used the Cochrane tool to assess risk of bias. Results: 44 studies were identified, consisting of 15 groups of drugs and 25 different biological agents, totalling 16889 patients. The main outcomes assessed included Systemic Lupus Erythematosus Responder Index (SRI), BILAG-Based Composite Lupus Assessment (BICLA) and combined combined/partial renal remission (CRR/PRR). Four groups of biologics were found to improve outcomes. Anti-interferons: Anifrolumab increased BICLA response and SRI 5 to 8, decreased prednisone dosages, with increased herpes zoster infections, but fewer serious adverse events. Sifalimumab improved SRI but also increased herpes zoster infections. Anti BAFF/BLyS and/or APRIL: Belimumab consistently improved SRI 4, decreased prednisone dosages, increased combined CRR/PRR, and had no adverse safety outcomes. Tabalumab increased SRI 5 at 52 weeks with no steroid sparing effect but was associated with increased infusion related adverse events. Telitacicept improved SRI 4 at 52 weeks, with no increased adverse events, though data was rather sparse. Anti CD-20 monoclonal antibody, Obinutuzumab increased combined CRR/PRR at 1 and 2 years. Anti IL12/23 monoclonal antibody, Ustekinumab, increased SRI 4 to 6, but not BICLA at 24 weeks, with no concerning safety outcomes. Conclusion: Multiple biologic agents are shown in high quality studies to have a significant therapeutic impact on outcomes in SLE.
DNA methylation plays essential roles in regulating physiological processes, from tissue and organ development to gene expression and aging processes and has emerged as a widely used biomarker for the identification of body fluids and age prediction. Currently, methylation markers are targeted independently at specific CpG sites as part of a multiplexed assay rather than through a unified assay. Methylation detection is also dependent on divergent methodologies, ranging from enzyme digestion and affinity enrichment to bisulfite treatment, alongside various technologies for high-throughput profiling, including microarray and sequencing. In this pilot study, we test the simultaneous identification of age-associated and body fluid-specific methylation markers using a single technology, nanopore adaptive sampling. This innovative approach enables the profiling of multiple CpG marker sites across entire gene regions from a single sample without the need for specialized DNA preparation or additional biochemical treatments. Our study demonstrates that adaptive sampling achieves sufficient coverage in regions of interest to accurately determine the methylation status, shows a robust consistency with whole-genome bisulfite sequencing data, and corroborates known CpG markers of age and body fluids. Our work also resulted in the identification of new sites strongly correlated with age, suggesting new possible age methylation markers. This study lays the groundwork for the systematic development of nanopore-based methodologies in both age prediction and body fluid identification, highlighting the feasibility and potential of nanopore adaptive sampling while acknowledging the need for further validation and expansion in future research.
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