Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. perenne European ecotype collection identifies genomic contexts associated with agriculturally important traits

BACKGROUND AND AIMS

Lolium perenne (perennial ryegrass) is the most widely cultivated forage and amenity grass species in temperate areas worldwide and there is a need to understand the genetic architectures of key agricultural traits and crop characteristics that deliver wider environmental services. Our aim was to identify genomic regions associated with agriculturally important traits by integrating a bacterial artificial chromosome (BAC)-based physical map with a genome-wide association study (GWAS).

METHODS

BAC-based physical maps for L. perenne were constructed from ~212 000 high-information-content fingerprints using Fingerprint Contig and Linear Topology Contig software. BAC clones were associated with both BAC-end sequences and a partial minimum tiling path sequence. A panel of 716 L. perenne diploid genotypes from 90 European accessions was assessed in the field over 2 years, and genotyped using a Lolium Infinium SNP array. The GWAS was carried out using a linear mixed model implemented in TASSEL, and extended genomic regions associated with significant markers were identified through integration with the physical map.

KEY RESULTS

Between ~3600 and 7500 physical map contigs were derived, depending on the software and probability thresholds used, and integrated with ~35 k sequenced BAC clones to develop a resource predicted to span the majority of the L. perenne genome. From the GWAS, eight different loci were significantly associated with heading date, plant width, plant biomass and water-soluble carbohydrate accumulation, seven of which could be associated with physical map contigs. This allowed the identification of a number of candidate genes.

CONCLUSIONS

Combining the physical mapping resource with the GWAS has allowed us to extend the search for candidate genes across larger regions of the L. perenne genome and identified a number of interesting gene model annotations. These physical maps will aid in validating future sequence-based assemblies of the L. perenne genome.

Differential expression of secreted factors SOSTDC1 and ADAMTS8 cause profibrotic changes in linear morphoea fibroblasts

BACKGROUND

Linear morphoea (LM) is a rare connective tissue disorder characterized by a line of thickened skin and subcutaneous tissue and can also affect the underlying muscle and bone. Little is known about the disease aetiology, with treatment currently limited to immune suppression, and disease recurrence post-treatment is common.

OBJECTIVES

In order to uncover new therapeutic avenues, the cell-intrinsic changes in LM fibroblasts compared with site-matched controls were characterized.

METHODS

We grew fibroblasts from site-matched affected and unaffected regions from five patients with LM, we subjected them to gene expression analysis and investigation of SMAD signalling.

RESULTS

Fibroblasts from LM lesions showed increased migration, proliferation, altered collagen processing, and abnormally high basal levels of phosphorylated SMAD2, thereby rendering them less responsive to transforming growth factor (TGF)-β1 and reducing the degree of myofibroblast differentiation, which is a key component of the wound-healing and scarring process in normal skin. Conditioned media from normal fibroblasts could reverse LM-affected fibroblast migration and proliferation, suggesting that the LM phenotype is driven by an altered secretome. Gene array analysis and RNA-Seq indicated upregulation of ADAMTS8 and downregulation of FRAS1 and SOSTDC1. SOSTDC1 knock-down recapitulated the reduced TGF-β1 responsiveness and LM fibroblast migration, while overexpression of ADAMTS8 induced myofibroblast markers.

CONCLUSIONS

We demonstrate that cell-intrinsic changes in the LM fibroblast secretome lead to changes observed in the disease, and that secretome modulation could be a viable therapeutic approach in the treatment of LM.

Use of an alternative method to evaluate erythema severity in a clinical trial: difference in vehicle response with evaluation of baseline and postdose photographs for effect of oxymetazoline cream 1·0% for persistent erythema of rosacea in a phase IV study

Background

Once‐daily topical oxymetazoline cream 1·0% significantly reduced persistent facial erythema of rosacea in trials requiring live, static patient assessments.

Objectives

To evaluate critically the methodology of clinical trials that require live, static patient assessments by determining whether assessment of erythema is different when reference to the baseline photograph is allowed.

Methods

In two identically designed, randomized, phase III trials, adults with persistent facial erythema of rosacea applied oxymetazoline or vehicle once daily. This phase IV study evaluated standardized digital facial photographs from the phase III trials to record ≥ 1‐grade Clinician Erythema Assessment (CEA) improvement at 1, 3, 6, 9 and 12 h postdose.

Results

Among 835 patients (oxymetazoline n = 415, vehicle n = 420), significantly greater proportions of patients treated with oxymetazoline vs. vehicle achieved ≥ 1‐grade CEA improvement. For the comparison between phase IV study results and the original phase III analysis, when reference to baseline photographs was allowed while evaluating post‐treatment photographs, the results for oxymetazoline were similar to results of the phase III trials (up to 85.7%), but a significantly lower proportion of vehicle recipients achieved ≥ 1‐grade CEA improvement (up to 29.7% [phase 4] vs. 52.3% [phase 3]; P<0.001). In the phase IV study, up to 80·2% of patients treated with oxymetazoline achieved at least moderate erythema improvement vs. up to 22·9% of patients treated with vehicle. The association between patients’ satisfaction with facial skin redness and percentage of erythema improvement was statistically significant.

Conclusions

Assessment of study photographs, with comparison to baseline, confirmed significant erythema reduction with oxymetazoline on the first day of application. Compared with the phase III trial results, significantly fewer vehicle recipients attained ≥ 1‐grade CEA improvement, suggesting a mitigated vehicle effect. This methodology may improve the accuracy of clinical trials evaluating erythema severity.

What's already known about this topic?

Phase III studies that evaluate the effects of medications on persistent facial erythema associated with rosacea require investigator assessments without allowing comparison with baseline images.

What does this study add?

Grading of facial erythema of rosacea that utilized baseline photographs compared with post‐treatment photographs enhanced the accuracy of persistent facial erythema assessments.

Furthermore, this method more accurately differentiated active treatment with oxymetazoline cream 1·0% from vehicle compared with live, static assessments.

Methodology that allows for comparison to baseline photographs may improve the accuracy of clinical trials that evaluate erythema severity.

Linked Comment: https://doi.org/10.1111/bjd.17725.

https://www.bjdonline.com/article/

Abstract A214: An in vitro preclinical package to assess the safety and efficacy of ImmTAC™ molecules

Immune Mobilising Monoclonal TCRs Against Cancer (ImmTAC) molecules are a new class of bi-specific biologic specifically designed to recognize and eradicate cancer cells. ImmTAC molecules are composed of an affinity-enhanced T-cell receptor (TCR) fused to an anti-CD3 effector function engineered to recognize peptides presented by human leukocyte antigen (HLA) and induce T-cell activation and T-cell mediated killing of tumor cells. TCR-based immunotherapeutic strategies offer distinct advantages over traditional antibody-based therapies, most notably providing access to up to nine-fold more cancer targets by targeting intracellularly processed peptides presented by HLA as opposed to cell surface proteins. Preclinical testing of ImmTAC molecules can prove particularly challenging as these molecules are exquisitely human-specific, requiring a human peptidome and intact human immune system; thus the use of conventional animal models is inappropriate. Given that these molecules harness the full force of the immune system, robust preclinical testing is essential to predict safety and efficacy and inform on clinical dosing for first-in-human studies. Here we present, to our knowledge, the first entirely in vitro preclinical package that comprises a range of cellular and molecular assays to assess the efficacy, safety and specificity of ImmTAC molecules. To exemplify our approach, we draw upon the preclinical testing of multiple ImmTAC molecules, including IMCgp100, the first ImmTAC molecule to reach the clinic. We propose that this preclinical package can be applied to the testing of other TCR-based therapies to deliver a more physiologically relevant model.

Citation Format: Ana Ribeiro, Tomasz Dobrzycki, Jane Harper, Giovanna Bossi, Debbie Wright, Andrea Stacey, Nicole Bedke, Ruth Martinez-Hague, Dan Blat, Laure Humbert, Zoe Donellan, Samantha Paston, Luise Weigand, Martina Canestraro, Sophie Botta Gordon-Smith, Bent K. Jakobsen, Joseph Dukes. An in vitro preclinical package to assess the safety and efficacy of ImmTAC™ molecules [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A214.

Survey and genetic characterization of Vibrio cholerae in Apalachicola Bay, Florida (2012-2014)

AIMS

A small outbreak of gastroenteritis in 2011 in Apalachicola Bay, FL was attributed to consumption of raw oysters carrying Vibrio cholerae serotype O75. To better understand possible health risks, V. cholerae was surveyed in oysters, fish and seawater, and results were compared to data for Vibrio vulnificus and Vibrio parahaemolyticus.

METHODS AND RESULTS

Enrichment protocols were used to compare prevalence of V. cholerae (0, 48, 50%), V. vulnificus (89, 97, 100%) and V. parahaemolyticus (83, 83, 100%) in fish, seawater and oysters respectively. Compared to other species, Most probable number results indicated significantly (P < 0·001) lower abundance of V. cholerae, which was also detected more frequently at lower salinity, near-shore sites; other species were more widely distributed throughout the bay. Genes for expression (ctxA, ctxB) and acquisition (tcpA) of cholera toxin were absent in all strains by PCR, which was confirmed by whole genome sequencing; however, other putative virulence genes (toxR, rtxA, hlyA, opmU) were common. Multi-locus sequence typing revealed 78% of isolates were genetically closer to V. cholerae O75 lineage or other non-O1 serogroups than to O1 or O139 serogroups. Resistance to amoxicillin, kanamycin, streptomycin, amikacin, tetracycline and cephalothin, as well as multidrug resistance, was noted.

CONCLUSIONS

Results indicated minimal human health risk posed by V. cholerae, as all isolates recovered from Apalachicola Bay did not have the genetic capacity to produce cholera toxin. Vibrio cholerae was less prevalent and abundant relative to other pathogenic Vibrio species.

SIGNIFICANCE AND IMPACT OF THE STUDY

These studies provide important baseline observations for V. cholerae virulence potential regarding: (i) genetic relatedness to V. cholerae O75, (ii) antibiotic resistance and (iii) prevalence of multiple virulence genes. These data will serve as a biomonitoring tool to better understand ecosystem status and management if bacterial densities and virulence potential are altered by environmental and climatic changes over time.

An approved in vitro approach to preclinical safety and efficacy evaluation of engineered T cell receptor anti-CD3 bispecific (ImmTAC) molecules

Robust preclinical testing is essential to predict clinical safety and efficacy and provide data to determine safe dose for first-in-man studies. There are a growing number of examples where the preclinical development of drugs failed to adequately predict clinical adverse events in part due to their assessment with inappropriate preclinical models. Preclinical investigations of T cell receptor (TCR)-based immunotherapies prove particularly challenging as these biologics are human-specific and thus the conventional testing in animal models is inadequate. As these molecules harness the full force of the immune system, and demonstrate tremendous potency, we set out to design a preclinical package that would ensure adequate evaluation of these therapeutics. Immune Mobilising Monoclonal TCR Against Cancer (ImmTAC) molecules are bi-specific biologics formed of an affinity-enhanced TCR fused to an anti-CD3 effector function. ImmTAC molecules are designed to activate human T lymphocytes and target peptides within the context of a human leukocyte antigen (HLA), thus require an intact human immune system and peptidome for suitable preclinical screening. Here we draw upon the preclinical testing of four ImmTAC molecules, including IMCgp100, the first ImmTAC molecule to reach the clinic, to present our comprehensive, informative and robust approach to in vitro preclinical efficacy and safety screening. This package comprises a broad range of cellular and molecular assays using human tissues and cultured cells to test efficacy, safety and specificity, and hence predict human responses in clinical trials. We propose that this entirely in vitro package offers a potential model to be applied to screening other TCR-based biologics.

A Case of Lassa Fever Diagnosed at a Community Hospital-Minnesota 2014

Background

In April 2014, a 46-year-old returning traveler from Liberia was transported by emergency medical services to a community hospital in Minnesota with fever and altered mental status. Twenty-four hours later, he developed gingival bleeding. Blood samples tested positive for Lassa fever RNA by reverse transcriptase polymerase chain reaction.

Methods

Blood and urine samples were obtained from the patient and tested for evidence of Lassa fever virus infection. Hospital infection control personnel and health department personnel reviewed infection control practices with health care personnel. In addition to standard precautions, infection control measures were upgraded to include contact, droplet, and airborne precautions. State and federal public health officials conducted contract tracing activities among family contacts, health care personnel, and fellow airline travelers.

Results

The patient was discharged from the hospital after 14 days. However, his recovery was complicated by the development of near complete bilateral sensorineural hearing loss. Lassa virus RNA continued to be detected in his urine for several weeks after hospital discharge. State and federal public health authorities identified and monitored individuals who had contact with the patient while he was ill. No secondary cases of Lassa fever were identified among 75 contacts.

Conclusions

Given the nonspecific presentation of viral hemorrhagic fevers, isolation of ill travelers and consistent implementation of basic infection control measures are key to preventing secondary transmission. When consistently applied, these measures can prevent secondary transmission even if travel history information is not obtained, not immediately available, or the diagnosis of a viral hemorrhagic fever is delayed.

Improving the magnetoelectric performance of Metglas/PZT laminates by annealing in a magnetic field

A comprehensive investigation of magnetostriction optimization in Metglas 2605SA1 ribbons is performed to enhance magnetoelectric performance. We explore a range of annealing conditions to relieve remnant stress and align the magnetic domains in the Metglas, while minimizing unwanted crystallization. The magnetostriction coefficient, magnetoelectric coefficient, and magnetic domain alignment are correlated to optimize magnetoelectric performance. We report on direct magnetostriction observed by in-plane Doppler vibrometer and domain imagining using scanning electron microscopy with polarization analysis for a range of annealing conditions. We find that annealing in an oxygen-free environment at 400 °C for 30 min yields an optimal magnetoelectric coefficient, magnetostriction and magnetostriction coefficient. The optimized ribbons had a magnetostriction of 50.6 ± 0.2 μm m-1 and magnetoelectric coefficient of 79.3 ± 1.5 μm m-1 mT-1. The optimized Metglas 2605SA1 ribbons and PZT-5A (d31 mode) sensor achieves a magnetic noise floor of approximately 600 pT Hz-1/2 at 100 Hz and a magnetoelectric coefficient of 6.1 ± 0.03 MV m-1 T-1.

Highly Pathogenic Avian Influenza (H5N1) Virus in Feathers

H5N1 highly pathogenic avian influenza (HPAI) virus causes high mortality of infected birds, with infection in multiple organs, including in feathers. Feathers have been proposed as samples for diagnosis of HPAI infection in birds, and this study is part of a broader investigation validating the use of feathers for diagnostic purposes. To understand and characterize the morphological basis for feather infection, sections from 7 different skin tracts of ducks and chickens infected with 3 different clades of H5N1 HPAI virus from Indonesia and Vietnam were examined histologically. Results showed that in ducks, lesions and viral antigen were mainly detected in the epidermis of feathers and follicles, whereas in chickens, they were mostly found in the dermis of these structures. Abundant viral antigen was found in nearly all the feathers examined from chickens, and there was no apparent difference between virus isolates or skin tracts in the proportion of feathers that were antigen positive. By immunohistochemistry, the majority of feathers from most skin tracts from ducks infected with a Vietnamese H5N1 HPAI virus contained abundant levels of viral antigen, while few feathers were antigen positive from ducks infected with 2 Indonesian viruses. These results support and inform the use of feathers for diagnostic detection of H5N1 HPAI virus in birds.

Abstract 4873: ImmTACs re-direct the immune system efficiently to eradicate cancer

Immunotherapy strategies that are able to induce T cell infiltration into tumors and activate a cytotoxic T cell response have the potential to destroy the tumor. Although T cells can mediate clearance of a tumor, thymic selection and the suppressive microenvironment limit their effectiveness. To overcome poor tumor immunogenicity, we have developed a unique platform that enables the generation of ImmTACs (Immune-mobilising monoclonal TCRs Against Cancer); these are comprised of an affinity enhanced TCR specific for a cancer antigen fused to an anti-CD3 scFv. The TCR end targets and binds MHC class I/peptide complex displayed on cancerous cells while the anti-CD3 scFv end engages polyclonal T cells to mediate a potent anti-tumor response.

The most advanced ImmTAC, IMCgp100, targets the HLA-A2/gp100280-288 epitope presented by melanoma cells. IMCgp100 is currently in a Phase I/IIa clinical trial for advance malignant melanoma and is showing promising clinical efficacy in some patients. Here we report a series of in vitro experiments evaluating IMCgp100 mechanism of action. IMCgp100 is able to redirect T cells from healthy donors or from melanoma patients to destroy cancer cells and secrete a range of inflammatory cytokines and chemokines associated with T cell trafficking into tumors; some of these cytokines also induce upregulation of inhibitory pathway molecules. We show that effector memory cells in the CD8+ and CD4+ T cell compartments are very efficient in eliminating melanoma cells and in expanding upon IMCgp100 engagement. The effects of combining IMCgp100 with agents that relieve the suppression imposed by immune check-point molecules have also been investigated.

Citation Format: Giovanna Bossi, Rupert Kenefeck, Caroline Caroline Boudousquie, Jane Harper, Joseph Dukes, Nathaniel Liddy, Samantha Paston, Tara Mahon, Peter Molloy, Malkit Sami, Emma Baston, Brian Cameron, Annelise Vuidepot, Namir Hassan, Bent K. Jakobsen. ImmTACs re-direct the immune system efficiently to eradicate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4873.

Abstract 4872: Developing high affinity, soluble T cell receptors for the treatment of cancer

Immunotherapeutic strategies that drive activation of cytotoxic T cells possess significant potential to eradicate tumours. Whereas monoclonal antibodies are restricted to targeting secreted or cell surface proteins, T cell receptors (TCRs) are able to recognise a wider range of targets. This is achieved through binding to short peptide fragments derived from proteins that are degraded intracellularly and presented at the cell surface by human leukocyte antigens (HLAs). Natural cancer specific TCRs however, have weak affinities and cancer cells often develop escape mechanisms to avoid destruction by T cells.

To overcome this, we have developed Immune mobilising monoclonal TCRs Against Cancer (ImmTACs); a new class of soluble bi-specific molecules comprising affinity-enhanced, monoclonal T cell receptors (mTCRs) fused to an anti-CD3 scFv. ImmTACs target peptides presented by HLA, and through the anti-CD3 effector, re-direct cytotoxic T cells to achieve highly specific and potent tumour cell killing.

At Immunocore, we have developed an integrated in-house process for the generation of ImmTACs and here describe the critical engineering steps involved. T-cell clones that specifically recognise validated cancer antigens are isolated from peripheral blood lymphocytes and the TCR-encoding sequences are identified by RACE. To confirm antigen binding, TCR á and â chains are expressed as inclusion bodies in bacteria, co-refolded in vitro, and their binding to the target peptide:HLA tested by Surface Plasmon Resonance (SPR). The affinity of the TCR is then enhanced up to a million-fold through directed evolution, utilising phage display. Individual mutants are screened by SPR and combined to generate ImmTACs with pM affinities (KD) and binding half-lives of many hours. A range of biochemical and cellular assays are then performed to assess the potency and specificity of each ImmTAC generated.

This process has been successfully applied to produce ImmTACs for a wide range of targets, demonstrating the robustness of the platform. Our lead candidate, IMCgp100, is undergoing Phase IIa clinical trials in patients with advanced malignant melanoma. This reagent, which specifically targets the gp100 (280-288) peptide presented by HLA-A2 on melanoma cells, is well tolerated and shows very promising therapeutic potential.

Citation Format: Andrew Knox, Fiona Chester, Frayne Bianchi, Sarah Bailey, Lucie Bouard, Nathaniel Liddy, Giovanna Bossi, Jane Harper, Joseph Dukes, Samantha Paston, Tara Mahon, Jessie Gavarret, Peter Molloy, Malkit Sami, Emma Baston, Brian Cameron, Alex Powlesland, Penio Todorov, Andrew Johnson, Martin Ebner, Yvonne McGrath, Namir Hassan, Annelise Vuidepot, Bent Jakobsen. Developing high affinity, soluble T cell receptors for the treatment of cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4872.