A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups.

Shared research resource facilities, also known as core laboratories (Cores), are responsible for generating a significant and growing portion of the research data in academic biomedical research institutions. Cores represent a central repository for institutional knowledge management, with deep expertise in the strengths and limitations of technology and its applications. They inherently support transparency and scientific reproducibility by protecting against cognitive bias in research design and data analysis, and thedy have institutional responsibility for the conduct of research (research ethics, regulatory compliance, and financial accountability) performed in their Cores. The Association of Biomolecular Resource Facilities (ABRF) is a FASEB-member scientific society whose members are scientists and administrators that manage or support Cores. The ABRF Research Groups (RGs), representing expertise for an array of cutting-edge and established technology platforms, perform multicenter research studies to determine and communicate best practices and community-based standards. This review provides a summary of the contributions of the ABRF RGs to promote scientific rigor and reproducibility in Cores from the published literature, ABRF meetings, and ABRF RGs communications

Complex structural rearrangements are present in high-grade dysplastic Barrett\u27s oesophagus samples

Background: Oesophageal adenocarcinoma (EAC) incidence is increasing and has a poor survival rate. Barrett’s oesophagus (BE) is a precursor condition that is associated with EAC and often occurs in conjunction with chronic gastro-oesophageal reflux, however many individuals diagnosed with BE never progress to cancer. An understanding of the genomic features of BE and EAC may help with the early identification of at-risk individuals. Methods: In this study, we assessed the genomic features of 16 BE samples using whole-genome sequencing. These included non-dysplastic samples collected at two time-points from two BE patients who had not progressed to EAC over several years. Seven other non-dysplastic samples and five dysplastic BE samples with high-grade dysplasia were also examined. We compared the genome profiles of these 16 BE samples with 22 EAC samples. Results: We observed that samples from the two non-progressor individuals had low numbers of somatic single nucleotide variants, indels and structural variation events compared to dysplastic and the remaining non-dysplastic BE. EAC had the highest level of somatic genomic variations. Mutational signature 17, which is common in EAC, was also present in non-dysplastic and dysplastic BE, but was not present in the non-progressors. Many dysplastic samples had mutations in genes previously reported in EAC, whereas only mutations in CDKN2A or in the fragile site genes appeared common in non-dysplastic samples. Rearrangement signatures were used to identify a signature associated with localised complex events such as chromothripsis and breakage fusion-bridge that are characteristic of EACs. Two dysplastic BE samples had a high contribution of this signature and contained evidence of localised rearrangements. Two other dysplastic samples also had regions of localised structural rearrangements. There was no evidence for complex events in non-dysplastic samples. Conclusions: The presence of complex localised rearrangements in dysplastic samples indicates a need for further investigations into the role such events play in the progression from BE to EAC

Incorporating organic matter alters soil greenhouse gas emissions and increases grain yield in a semi-arid climate

© 2016 The Authors Increasing soil organic matter (OM) is promoted as a strategy for improving the resilience of coarse-textured cropping soils in semi-arid climates. While increasing soil OM can benefit crop productivity, it can also enhance nitrous oxide (N2O) emissions in temperate climates. Our objective was to investigate if increasing soil OM affected soil greenhouse gas (GHG) fluxes and grain production in a semi-arid region in south-western Australia. We firstly measured N2O and methane (CH4) fluxes from a free-draining sandy soil with contrasting soil OM content for 2.5 years using automated soil chambers. The randomized block design included two OM additions (no OM, plus OM) by two nitrogen (N) fertilizer rates (0, 0N; 100 kg N ha-1 yr-1, +N) by three replicate plots. Organic matter (chaff) had been applied to the plus OM treatments every three years since 2003, with 80 t OM ha-1applied in total. Secondly, we investigated the interaction between soil OM content and N fertilizer addition on grain yield for two growing seasons. The randomized split-plot design included two OM treatments by five N fertilizer rates (0, 25, 50, 75 and 100 kg N ha-1), by three replicates. Increasing soil OM increased grain yields and soil mineral N, but also enhanced soil N2O emissions. Nitrous oxide emissions were low by international standards (<0.12% of the N fertilizer applied), with total N2O emissions after two years ranked: plus OM (+N; 427 g N2O-N ha-1) > plus OM (0N; 194 g N2O-N ha-1) > no OM (+N; 41 g N2O-N ha-1) = no OM (0N; 14 g N2O-N ha-1). Increasing soil OM also decreased CH4uptake by 30%. Management practices that increase soil OM in sandy-textured rainfed, cropping soils in semi-arid regions should be encouraged as they can improve grain yield without substantial increases in soil N2O or CH4emissions

Crop Updates - 2003 Lupins

This session covers twenty one papers from different authors LUPIN ISSUES AND R & D DIRECTIONS Mark Sweetingham, Department of Agriculture ACKNOWLEDGEMENTS VARIETIES AND BREEDING New lupin line for release – WALAN2141, Bevan J, Buirchell, Mark Sweetingham, Geoff Thomas, Amelia McLarty, Harmohinder Dhammu and CVT and Lupin Breeding teams, Department of Agriculture Lupin variety trial, Martin Harries and Wayne Parker, Department of Agriculture Herbicide tolerance of new lupins, Harmohinder S. Dhammu, Terry Piper and David Nicholson, Department of Agriculture YELLOW AND ALBUS LUPINS Selection for high lupin yield under terminal drought, Jairo A. Palta1&2, Neil C. Turner1&2 Bob French2&3 and Bevan Buirchell2&3 , 1CSIRO Plant Industry, Floreat, WA, 2CLIMA, University of Western Australia, Crawley, WA, 3Department of Agriculture Outcrossing and isolation distance in yellow lupins, Kedar Adhikari, Bevan Buirchell and Katia Stefanova, Department of Agriculture Development of aphid tolerant yellow lupins in Western Australia, Kedar Adhikari, Bevan Buirchell, Mark Sweetingham and Françoise Berlandier, Department of Agriculture ESTABLISHMENT Development of anthracnose resistant albus lupins for Western Australia, Kedar Adhikari, Bevan Buirchell, Mark Sweetingham and Geoff Thomas, Department of Agriculture Lupin sowing methods for improved yields, Glen Riethmuller, Department of Agriculture Moisture delving = more reliable lupin establishment, Paul Blackwell and Wayne Parker, Department of Agriculture Effect of time of sewing, plant density and row orientation on lupins at various row spacings, Geoff Fosbery, Farm Focus Consultants, Bill Crabtree, Crabtree Consulting and Tracy Gilham, WANTFA Influence of row spacing on water stress and water use of lupins, Bob French and Laurie Wahlsten, Department of Agriculture AGRONOMY Effect on lupin protein and yield from variety, planting time and seed rate, Pierre Fievez, Pierre Fievez and Associates Lupin row cropping: herbicides to band, shield design and economics, Mike Collins, WANTFA and John Holmes, 4 Farmers Harvest options for narrow leaf lupins, Martin Harries and Dirranie Kirby, Department of Agriculture NUTRITION Additional nutrients on lupin yield and protein, Pierre Fievez, Pierre Fievez and Associates Demonstrating the effect of phosphorous placement on yields of narrow leaf lupin and yellow lupin on high phosphorus retention soils, Martin Harries and Wayne Parker, Department of Agriculture PESTS AND DISEASES How far are anthracnose spores spread by rain splash? Geoff Thomas, Mark Sweetingham and Ken Adcock, Department of Agriculture Height of cereal stubble affects spread of lupin anthracnose, Geoff Thomas, Bill MacLeod and Ken Adcock, Department of Agriculture Controlling non-necrotic strains of bean yellow mosaic virus in lupins by cultural methods, Roger Jones and Rohan Prince, Department of Agriculture, and Centre for Legumes in Mediterranean Agriculture MARKET DEVELOPMENT Australian sweet lupin – is it the next human health food? Stuart Johnson, Deakin University; Ramon Hall, ARC SPIRT PhD Scholar; Madeleine Ball, University of Tasmania; Sofia Sipsas and David Petterson; Department of Agriculture CONTACT DETAILS FOR PRINCIPAL AUTHOR

Sustained proliferation in cancer: mechanisms and novel therapeutic targets

Proliferation is an important part of cancer development and progression. This is manifest by altered expression and/or activity of cell cycle related proteins. Constitutive activation of many signal transduction pathways also stimulates cell growth. Early steps in tumor development are associated with a fibrogenic response and the development of a hypoxic environment which favors the survival and proliferation of cancer stem cells. Part of the survival strategy of cancer stem cells may manifested by alterations in cell metabolism. Once tumors appear, growth and metastasis may be supported by overproduction of appropriate hormones (in hormonally dependent cancers), by promoting angiogenesis, by undergoing epithelial to mesenchymal transition, by triggering autophagy, and by taking cues from surrounding stromal cells. A number of natural compounds (e.g., curcumin, resveratrol, indole-3-carbinol, brassinin, sulforaphane, epigallocatechin-3-gallate, genistein, ellagitannins, lycopene and quercetin) have been found to inhibit one or more pathways that contribute to proliferation (e.g., hypoxia inducible factor 1, nuclear factor kappa B, phosphoinositide 3 kinase/Akt, insulin-like growth factor receptor 1, Wnt, cell cycle associated proteins, as well as androgen and estrogen receptor signaling). These data, in combination with bioinformatics analyses, will be very important for identifying signaling pathways and molecular targets that may provide early diagnostic markers and/or critical targets for the development of new drugs or drug combinations that block tumor formation and progression

ROR1 and ROR2 expression in pancreatic cancer

Background: The Wnt receptors ROR1 and ROR2 are generating increased interest as cancer therapeutic targets but remain understudied in pancreatic ductal adenocarcinoma (PDAC). Compared to canonical Wnt/ β-catenin signalling, the role of noncanonical Wnt signalling in PDAC remains largely unknown. Only one study has investigated the prognostic significance of the noncanonical Wnt signalling receptor, ROR2 in PDAC. No studies have investigated the prognostic role of ROR1 in PDAC. Methods: Here, we performed analysis of ROR1 and ROR2 mRNA expression in three publicly available datasets ICGC-PACA-AU (n = 81), TCGA-PAAD (n = 150) and CPTAC-PDAC (n = 137). ROR1 and ROR2 protein expression from the CPTAC-PDAC discovery cohort were also analysed. Immunohistochemistry (IHC) using the validated anti ROR1 monoclonal antibody (4A5) was performed on the Australian Pancreatic Cancer Genome Initiative (APGI) cohort of PDAC samples (n = 152). Association between ROR1 cytoplasmic staining intensity and clinicopathological parameters including stage, grade and overall survival (OS) was investigated. Results: High ROR1 mRNA expression levels correlated with a favourable OS outcome in all of the ICGC-PACA-AU, TCGA-PAAD and CPTAC-PDAC cohorts. ROR1 protein expression was not associated with stage, grade or OS in the APGI cohort. Conclusion: ROR1 and ROR2 have potential as prognostic markers when measured at the mRNA level in PDAC. Our IHC cohort did not support ROR1 protein expression in predicting OS, and highlighted the discrepancy of prognostic biomarkers when measured by MS, IHC and RNAseq

Complex structural rearrangements are present in high-grade dysplastic Barrett’s oesophagus samples

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.Abstract Background Oesophageal adenocarcinoma (EAC) incidence is increasing and has a poor survival rate. Barrett’s oesophagus (BE) is a precursor condition that is associated with EAC and often occurs in conjunction with chronic gastro-oesophageal reflux, however many individuals diagnosed with BE never progress to cancer. An understanding of the genomic features of BE and EAC may help with the early identification of at-risk individuals. Methods In this study, we assessed the genomic features of 16 BE samples using whole-genome sequencing. These included non-dysplastic samples collected at two time-points from two BE patients who had not progressed to EAC over several years. Seven other non-dysplastic samples and five dysplastic BE samples with high-grade dysplasia were also examined. We compared the genome profiles of these 16 BE samples with 22 EAC samples. Results We observed that samples from the two non-progressor individuals had low numbers of somatic single nucleotide variants, indels and structural variation events compared to dysplastic and the remaining non-dysplastic BE. EAC had the highest level of somatic genomic variations. Mutational signature 17, which is common in EAC, was also present in non-dysplastic and dysplastic BE, but was not present in the non-progressors. Many dysplastic samples had mutations in genes previously reported in EAC, whereas only mutations in CDKN2A or in the fragile site genes appeared common in non-dysplastic samples. Rearrangement signatures were used to identify a signature associated with localised complex events such as chromothripsis and breakage fusion-bridge that are characteristic of EACs. Two dysplastic BE samples had a high contribution of this signature and contained evidence of localised rearrangements. Two other dysplastic samples also had regions of localised structural rearrangements. There was no evidence for complex events in non-dysplastic samples. Conclusions The presence of complex localised rearrangements in dysplastic samples indicates a need for further investigations into the role such events play in the progression from BE to EAC

Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer

Pancreatic ductal adenocarcinoma is a lethal cancer with fewer than 7% of patients surviving past 5 years. T-cell immunity has been linked to the exceptional outcome of the few long-term survivors1,2, yet the relevant antigens remain unknown. Here we use genetic, immunohistochemical and transcriptional immunoprofiling, computational biophysics, and functional assays to identify T-cell antigens in long-term survivors of pancreatic cancer. Using whole-exome sequencing and in silico neoantigen prediction, we found that tumours with both the highest neoantigen number and the most abundant CD8+ T-cell infiltrates, but neither alone, stratified patients with the longest survival. Investigating the specific neoantigen qualities promoting T-cell activation in long-term survivors, we discovered that these individuals were enriched in neoantigen qualities defined by a fitness model, and neoantigens in the tumour antigen MUC16 (also known as CA125). A neoantigen quality fitness model conferring greater immunogenicity to neoantigens with differential presentation and homology to infectious disease-derived peptides identified long-term survivors in two independent datasets, whereas a neoantigen quantity model ascribing greater immunogenicity to increasing neoantigen number alone did not. We detected intratumoural and lasting circulating T-cell reactivity to both high-quality and MUC16 neoantigens in long-term survivors of pancreatic cancer, including clones with specificity to both high-quality neoantigens and predicted cross-reactive microbial epitopes, consistent with neoantigen molecular mimicry. Notably, we observed selective loss of high-quality and MUC16 neoantigenic clones on metastatic progression, suggesting neoantigen immunoediting. Our results identify neoantigens with unique qualities as T-cell targets in pancreatic ductal adenocarcinoma. More broadly, we identify neoantigen quality as a biomarker for immunogenic tumours that may guide the application of immunotherapies

Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer

Background and aims: Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress and novel therapeutic response in PC to develop a biomarker driven therapeutic strategy targeting DDR and replication stress in PC. Methods: We interrogated the transcriptome, genome, proteome and functional characteristics of 61 novel PC patient-derived cell lines to define novel therapeutic strategies targeting DDR and replication stress. Validation was done in patient derived xenografts and human PC organoids. Results: Patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, co-segregates with response to platinum (P < 0.001) and PARP inhibitor therapy (P < 0.001) in vitro and in vivo. We generated a novel signature of replication stress with which predicts response to ATR (P < 0.018) and WEE1 inhibitor (P < 0.029) treatment in both cell lines and human PC organoids. Replication stress was enriched in the squamous subtype of PC (P < 0.001) but not associated with DDR deficiency. Conclusions: Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR proficient PC, and post-platinum therapy