Predicting response to immune checkpoint blockade in NSCLC with tumour-only RNA-seq.

BACKGROUND: Targeted RNA sequencing (RNA-seq) from FFPE specimens is used clinically in cancer for its ability to estimate gene expression and to detect fusions. Using a cohort of NSCLC patients, we sought to determine whether targeted RNA-seq could be used to measure tumour mutational burden (TMB) and the expression of immune-cell-restricted genes from FFPE specimens and whether these could predict response to immune checkpoint blockade. METHODS: Using The Cancer Genome Atlas LUAD dataset, we developed a method for determining TMB from tumour-only RNA-seq and showed a correlation with DNA sequencing derived TMB calculated from tumour/normal sample pairs (Spearman correlation = 0.79, 95% CI [0.73, 0.83]. We applied this method to targeted sequencing data from our patient cohort and validated these results against TMB estimates obtained using an orthogonal assay (Spearman correlation = 0.49, 95% CI [0.24, 0.68]). RESULTS: We observed that the RNA measure of TMB was significantly higher in responders to immune blockade treatment (P = 0.028) and that it was predictive of response (AUC = 0.640 with 95% CI [0.493, 0.786]). By contrast, the expression of immune-cell-restricted genes was uncorrelated with patient outcome. CONCLUSION: TMB calculated from targeted RNA sequencing has a similar diagnostic ability to TMB generated from targeted DNA sequencing.

The Effect of Frankia and Hebeloma crustiliniforme on Alnus alnobetula subsp. Crispa Growing in Saline Soil.

The mining of the oil sands region of Canada's boreal forest creates disturbed land with elevated levels of salts. Understanding how native plants respond to salt stress is critical in reclaiming these lands. The native species, Alnus alnobetula subsp. crispa forms nitrogen-fixing nodules with Frankia, and ectomycorrhizae with a number of fungal species. These relationships may make the plant particularly well suited for restoring disturbed land. We inoculated A. alnobetula subsp. crispa with Frankia and Hebeloma crustiliniforme and exposed the plants to 0, 50, or 100 mM NaCl for seven weeks. Frankia-inoculated plants had increased biomass regardless of salt exposure, even though salt exposure reduced nitrogen fixation and reduced the efficiency of nitrogen-fixing nodules. The nitrogen-fixing symbiosis also decreased leaf stress and increased root phosphatase levels. This suggests that N-fixing plants not only have increased nitrogen nutrition but also have increased access to soil phosphorus. Mycorrhizae did not affect plant growth but did reduce nodule numbers and nodule efficiency. These results suggest that the nitrogen-fixing trait is more critical than mycorrhizae. While salt stress inhibits nitrogen-fixing symbiosis, plants still benefit from nitrogen fixation when exposed to salt.

Forest soil biotic communities show few responses to wood ash applications at multiple sites across Canada.

There is interest in utilizing wood ash as an amendment in forestry operations as a mechanism to return nutrients to soils that are removed during harvesting, with the added benefit of diverting this bioenergy waste material from landfill sites. Existing studies have not arrived at a consensus on what the effects of wood ash amendments are on soil biota. We collected forest soil samples from studies in managed forests across Canada that were amended with wood ash to evaluate the effects on arthropod, bacterial and fungal communities using metabarcoding of F230, 16S, 18S and ITS2 sequences as well as enzyme analyses to assess its effects on soil biotic function. Ash amendment did not result in consistent effects across sites, and those effects that were detected were small. Overall, this study suggests that ash amendment applied to managed forest systems in amounts (up to 20 Mg ha-1) applied across the 8 study sties had little to no detectable effects on soil biotic community structure or function. When effects were detected, they were small, and site-specific. These non-results support the application of wood ash to harvested forest sites to replace macronutrients (e.g., calcium) removed by logging operations, thereby diverting it from landfill sites, and potentially increasing stand productivity.

Single-cell sequencing demonstrates complex resistance landscape in CLL and MCL treated with BTK and BCL2 inhibitors.

The genomic landscape of resistance to targeted agents (TAs) used as monotherapy in chronic lymphocytic leukemia (CLL) is complex and often heterogeneous at the patient level. To gain insight into the clonal architecture of acquired genomic resistance to Bruton tyrosine kinase (BTK) inhibitors and B-cell lymphoma 2 (BCL2) inhibitors in CLL, particularly in patients carrying multiple resistance mutations, we performed targeted single-cell DNA sequencing of 8 patients who developed progressive disease (PD) on TAs (either class). In all cases, analysis of single-cell architecture revealed mutual exclusivity between multiple resistance mutations to the same TA class, variable clonal co-occurrence of multiple mutations affecting different TAs in patients exposed to both classes, and a phenomenon of multiple independent emergences of identical nucleotide changes leading to canonical resistance mutations. We also report the first observation of established BCL2 resistance mutations in a patient with mantle cell lymphoma (MCL) following PD on sequential monotherapy, implicating BCL2 as a venetoclax resistance mechanism in MCL. Taken together, these data reveal the significant clonal complexity of CLL and MCL progression on TAs at the nucleotide level and confirm the presence of multiple, clonally independent, mechanisms of TA resistance within each individual disease context.

Characterisation of immune checkpoints in Richter syndrome identifies LAG3 as a potential therapeutic target.

Richter syndrome (RS), an aggressive lymphoma occurring in the context of chronic lymphocytic leukaemia/small lymphocytic lymphoma, is associated with poor prognosis when treated with conventional immunochemotherapy, therefore, improved treatments are required. Immune checkpoint blockade has shown efficacy in some B-cell malignancies and modest responses in early clinical trials for RS. We investigated the immune checkpoint profile of RS as a basis to inform rational therapeutic investigations in RS. Formalin-fixed, paraffin-embedded biopsies of RS (n = 19), de novo diffuse large B-cell lymphoma (DLBCL; n = 58), transformed indolent lymphomas (follicular [tFL], n = 16; marginal zone [tMZL], n = 24) and non-transformed small lymphocytic lymphoma (SLL; n = 15) underwent gene expression profiling using the NanoString Human Immunology panel. Copy number assessment was performed using next-generation sequencing. Immunohistochemistry (IHC) for LAG3 and PD-1 was performed. LAG3 gene expression was higher in RS compared to DLBCL (P = 0·0002, log2FC 1·96), tFL (P < 0·0001, log2FC 2·61), tMZL (P = 0·0004, log2FC 1·79) and SLL (P = 0·0057, log2FC 1·45). LAG3 gene expression correlated with the gene expression of human leukocyte antigen Class I and II, and related immune genes and immune checkpoints. IHC revealed LAG3 protein expression on both malignant RS cells and tumour-infiltrating lymphocytes. Our findings support the investigation of LAG3 inhibition to enhance anti-tumour responses in RS.

The Interactive Effect of Elevated CO2 and Herbivores on the Nitrogen-Fixing Plant Alnus incana ssp. rugosa.

Many studies have found that future predicted CO2 levels can increase plant mass but dilute N content in leaves, impacting antiherbivore compounds. Nitrogen-fixing plants may balance their leaf C:N ratio under elevated CO2, counteracting this dilution effect. However, we know little of how plants respond to herbivores at the higher CO2 levels that occurred when nitrogen-fixing plants first evolved. We grew Alnus incana ssp. rugosa was grown at 400, 800, or 1600 ppm CO2 in soil collected from the field, inoculated with Frankia and exposed to herbivores (Orgyia leucostigma). Elevated CO2 increased nodulated plant biomass and stimulated the nitrogen fixation rate in the early growth stage. However, nitrogen-fixing plants were not able to balance their C:N ratio under elevated CO2 after growing for 19 weeks. When plants were grown at 400 and 1600 ppm CO2, herbivores preferred to feed on leaves of nodulated plants. At 800 ppm CO2, nodulated plants accumulated more total phenolic compounds in response to herbivore damage than plants in the non-Frankia and non-herbivore treatments. Our results suggest that plant leaf defence, not leaf nutritional content, is the dominant driver of herbivory and nitrogen-fixing plants have limited ability to balance C:N ratios at elevated CO2 in natural soil.

Foxes fertilize the subarctic forest and modify vegetation through denning.

Ecosystem engineers modify habitats through processes other than trophic interactions, such as by regulating soil nutrients, and can influence resource availability and quality for other organisms. Predator-mediated elemental cycling may be especially important in determining plant diversity and growth in ecosystems where soil fertility and primary productivity are low. Red foxes (Vulpes vulpes L.), top predators in the Subarctic, could engineer local ecosystems through denning, which could create biogeochemical hotspots of nutrients due to continual input of feces, urine and prey remains. We examined soil and vegetation characteristics on red fox dens and paired control sites in woodland habitats near the Arctic treeline in Manitoba, Canada. The organic soil layer on den sites had 81% more inorganic nitrogen and 250% more extractable phosphorus than in control areas. Denning also increased soil respiration and pH in the organic layer, suggesting improved soil quality and nutrient availability for plants. By enriching nutrients and disturbing soils through digging, den sites had a higher plant species ß-diversity and a greater cover of erect woody shrubs (Salix spp.), grasses (Leymus mollis (Trinius) Pilger) and weedy ephemerals compared to control sites, resulting in a regional increase in plant species richness. Our research highlights the importance of considering impacts of predators other than through their consumption of prey, and provides insight into the role of red foxes in modifying plant diversity and productivity in the Subarctic.

Ancient CO2 levels favor nitrogen fixing plants over a broader range of soil N compared to present.

Small inreases in CO2 stimulate nitrogen fixation and plant growth. Increasing soil N can inhibit nitrogen fixation. However, no studies to date have tested how nitrogen fixing plants perform under ancient CO2 levels (100 MYA), when nitrogen fixing plants evolved, with different levels of N additions. The aim of this study was to assess if ancient CO2, compared to present, favors nitrogen fixers over a range of soil nitrogen concentrations. Nitrogen fixers (Alnus incana ssp. rugosa, Alnus viridis ssp. crispa, and Alnus rubra) and their close non-nitrogen fixing relatives (Betula pumila, Betula papyrifera, Betula glandulosa) were grown at ancient (1600 ppm) or present (400 ppm) CO2 over a range of soil N levels, equivalent to 0, 10, 50, and 200 kg N ha-1 year-1. The growth of non-N fixing plants increased more than N fixing plants in response to the increasing N levels. When grown at an ancient CO2 level, the N level at which non-nitrogen fixing plant biomass exceeded nitrogen fixing plant biomass was twice as high (61 kg N ha-1 year-1) as the N level when plants were grown at the ambient CO2 level. Specific nodule activity was also reduced with an increasing level of soil N. Our results show there was a greater advantage in being a nitrogen fixer under ancient levels of CO2 compared with the present CO2 level.

Bryophyte and lichen biomass and nitrogen fixation in a high elevation cloud forest in Cerro de La Muerte, Costa Rica.

Cloud forests have been found to lose more nitrogen in stream discharge than they gain from atmospheric deposition. They also support a large diversity and biomass of tree epiphytes, predominately composed of cryptogams. Since cryptogam epiphytes harbor nitrogen fixing cyanobacteria, they may help make up for the nitrogen loss from ecosystems. We assessed cryptogam biomass on the ground, boles and branches in Quercus costaricensis dominated stands near the tree line in the Cordillera de Talamanca, Costa Rica. Nitrogen fixation was assayed using 15N2 uptake. Total cryptogam biomass was 2 977 kg ha-1, with 67% being found on the lower branches. Bryophytes and chlorolichens made up 53% and 44%, respectively, of the biomass. Half of the bryophyte mass was composed of the liverwort Plagiochila heterophylla, and 66% of the chlorolichen of Lobariella pallida. There were no significant differences in nitrogen fixation rates between the cryptogam species, with a mean rate of 5.04 µg N g-1 day-1 during the predominantly wet condition in the forest. The overall nitrogen input from fixation was 6.1 kg N ha-1 year-1, of which 78% came from bryophytes, 18% from chlorolichens, and 4% from cyanolichens. Only 2.0% of the fixation occurred in cryptogams on the ground, whereas 67%, 24%, and 7% occurred on the lower branches, boles, and upper branches, respectively. These results show that tree epiphytes constitute a significant source of nitrogen for these forests, due to the trees' large surface area, and can make up for the nitrogen lost from these ecosystems.

Using microcontrollers and sensors to build an inexpensive CO2 control system for growth chambers.

PREMISE: A CO2 control system is important for investigating how elevated CO2 affects plant growth. Our automatic CO2 monitoring and control system offers an inexpensive and flexible way to make CO2-enriched environments. METHOD AND RESULTS: Using microcontrollers paired with non-dispersive infrared CO2 sensors, relays, and valves, we developed a low-cost system for monitoring and controlling CO2 levels in growth chambers. CONCLUSIONS: Compared with existing commercially available CO2 control systems, Arduino-based microcontrollers offer affordable access to the data logging of CO2 levels in growth chambers, thereby reducing budget limitations for creating growth conditions with highly controlled CO2 concentrations.

Lower Nitrogen Availability Enhances Resistance to Whiteflies in Tomato.

Soil nitrogen (N) supplementation via fertilizers may increase crop yields substantially. However, by increasing tissue N content, added N can make plants more attractive to herbivores, effectively reducing their resistance to herbivores (ability to avoid herbivore damage). In turn, greater pest infestation may cause more severe reductions in fruit production than a moderate N scarcity. In this study, we tested whether lower N supplementation results in greater resistance to whiteflies and lower fruit production in four tomato varieties. We assessed the effects of N availability on tolerance to herbivores (degree to which fitness is affected by damage) and tested for the long-hypothesized trade-off between resistance and tolerance. Plants grown at half of an agronomically recommended amount of N had greater resistance without a significant drop in fruit production. Tomato varieties differed in resistance and tolerance to whiteflies, and showed a clear trade-off between these modes of defense. Root:shoot ratios were greater at lower N, but had no clear relation to tolerance. We estimated that the economic benefit of decreasing N addition almost fully compensates for losses due to lower tomato production. Additionally, lower fertilization rates would contribute to reduce environmental costs of large-scale use of agrochemicals.

Publisher Correction: CNspector: a web-based tool for visualisation and clinical diagnosis of copy number variation from next generation sequencing.

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

Comparative genomic analyses of Mycoplasma synoviae vaccine strain MS-H and its wild-type parent strain 86079/7NS: implications for the identification of virulence factors and applications in diagnosis of M. synoviae.

Mycoplasma synoviae is an economically important avian pathogen worldwide, causing respiratory disease, infectious synovitis, airsacculitis and eggshell apex abnormalities in commercial chickens. Despite the widespread use of MS-H as a live attenuated vaccine over the past two decades, the precise molecular basis for loss of virulence in this vaccine is not yet fully understood. To address this, the whole genome sequence of the vaccine parent strain, 86079/7NS, was obtained and compared to that of the MS-H vaccine. Except for the vlhA expressed region, both genomes were nearly identical. Thirty-two single nucleotide polymorphisms (SNPs) were identified in MS-H, including 11 non-synonymous mutations that were predicted, by bioinformatics analysis, to have changed the secondary structure of the deduced proteins. One of these mutations caused truncation of the oppF-1 gene, which encodes the ATP-binding protein of an oligopeptide permease transporter. Overall, the attenuation of MS-H strain may be caused by the cumulative and complex effects of several mutations. The SNPs identified in MS-H were further analyzed by comparing the MS-H and 86079/7NS sequences with the strains WVU-1853 and MS53. In the genomic regions conserved between all strains, 30 SNPs were found to be unique to MS-H lineage. These results have provided a foundation for developing novel biomarkers for the detection of virulence in M. synoviae and also for designing new genotyping assays for discrimination of MS-H from field strains.

CNspector: a web-based tool for visualisation and clinical diagnosis of copy number variation from next generation sequencing.

Next Generation Sequencing is now routinely used in the practice of diagnostic pathology to detect clinically relevant somatic and germline sequence variations in patient samples. However, clinical assessment of copy number variations (CNVs) and large-scale structural variations (SVs) is still challenging. While tools exist to estimate both, their results are typically presented separately in tables or static plots which can be difficult to read and are unable to show the context needed for clinical interpretation and reporting. We have addressed this problem with CNspector, a multi-scale interactive browser that shows CNVs in the context of other relevant genomic features to enable fast and effective clinical reporting. We illustrate the utility of CNspector at different genomic scales across a variety of sample types in a range of case studies. We show how CNspector can be used for diagnosis and reporting of exon-level deletions, focal gene-level amplifications, chromosome and chromosome arm level amplifications/deletions and in complex genomic rearrangements. CNspector is a web-based clinical variant browser tailored to the clinical application of next generation sequencing for CNV assessment. We have demonstrated the utility of this interactive software in typical applications across a range of tissue types and disease contexts encountered in the context of diagnostic pathology. CNspector is written in R and the source code is available for download under the GPL3 Licence from https://github.com/PapenfussLab/CNspector . A server running CNspector loaded with the figures from this paper can be accessed at https://shiny.wehi.edu.au/jmarkham/CNspector/index.html .

Stochastically Timed Competition Between Division and Differentiation Fates Regulates the Transition From B Lymphoblast to Plasma Cell.

In response to external stimuli, naïve B cells proliferate and take on a range of fates important for immunity. How their fate is determined is a topic of much recent research, with candidates including asymmetric cell division, lineage priming, stochastic assignment, and microenvironment instruction. Here we manipulate the generation of plasmablasts from B lymphocytes in vitro by varying CD40 stimulation strength to determine its influence on potential sources of fate control. Using long-term live cell imaging, we directly measure times to differentiate, divide, and die of hundreds of pairs of sibling cells. These data reveal that while the allocation of fates is significantly altered by signal strength, the proportion of siblings identified with asymmetric fates is unchanged. In contrast, we find that plasmablast generation is enhanced by slowing times to divide, which is consistent with a hypothesis of competing timed stochastic fate outcomes. We conclude that this mechanistically simple source of alternative fate regulation is important, and that useful quantitative models of signal integration can be developed based on its principles.

Novel genomic findings in multiple myeloma identified through routine diagnostic sequencing.

AIMS: Multiple myeloma is a genomically complex haematological malignancy with many genomic alterations recognised as important in diagnosis, prognosis and therapeutic decision making. Here, we provide a summary of genomic findings identified through routine diagnostic next-generation sequencing at our centre. METHODS: A cohort of 86 patients with multiple myeloma underwent diagnostic sequencing using a custom hybridisation-based panel targeting 104 genes. Sequence variants, genome-wide copy number changes and structural rearrangements were detected using an inhouse-developed bioinformatics pipeline. RESULTS: At least one mutation was found in 69 (80%) patients. Frequently mutated genes included TP53 (36%), KRAS (22.1%), NRAS (15.1%), FAM46C/DIS3 (8.1%) and TET2/FGFR3 (5.8%), including multiple mutations not previously described in myeloma. Importantly we observed TP53 mutations in the absence of a 17 p deletion in 8% of the cohort, highlighting the need for sequencing-based assessment in addition to cytogenetics to identify these high-risk patients. Multiple novel copy number changes and immunoglobulin heavy chain translocations are also discussed. CONCLUSIONS: Our results demonstrate that many clinically relevant genomic findings remain in multiple myeloma which have not yet been identified through large-scale sequencing efforts, and provide important mechanistic insights into plasma cell pathobiology.

Genome analysis of Mycoplasma synoviae strain MS-H, the most common M. synoviae strain with a worldwide distribution.

BACKGROUND: The bacterial pathogen Mycoplasma synoviae can cause subclinical respiratory disease, synovitis, airsacculitis and reproductive tract disease in poultry and is a major cause of economic loss worldwide. The M. synoviae strain MS-H was developed by chemical mutagenesis of an Australian isolate and has been used as a live attenuated vaccine in many countries over the past two decades. As a result it may now be the most prevalent strain of M. synoviae globally. Differentiation of the MS-H vaccine from local field strains is important for epidemiological investigations and is often required for registration of the vaccine. RESULTS: The complete genomic sequence of the MS-H strain was determined using a combination of Illumina and Nanopore methods and compared to WVU-1853, the M. synoviae type strain isolated in the USA 30 years before the parent strain of MS-H, and MS53, a more recent isolate from Brazil. The vaccine strain genome had a slightly larger number of pseudogenes than the two other strains and contained a unique 55 kb chromosomal inversion partially affecting a putative genomic island. Variations in gene content were also noted, including a deoxyribose-phosphate aldolase (deoC) fragment and an ATP-dependent DNA helicase gene found only in MS-H. Some of these sequences may have been acquired horizontally from other avian mycoplasma species. CONCLUSIONS: MS-H was somewhat more similar to WVU-1853 than to MS53. The genome sequence of MS-H will enable identification of vaccine-specific genetic markers for use as diagnostic and epidemiological tools to better control M. synoviae.

Increased resistance to a generalist herbivore in a salinity-stressed non-halophytic plant.

Plants often grow under the combined stress of several factors. Salinity and herbivory, separately, can severely hinder plant growth and reproduction, but the combined effects of both factors are still not clearly understood. Salinity is known to reduce plant tissue nitrogen content and growth rates. Since herbivores prefer tissues with high N content, and biochemical pathways leading to resistance are commonly elicited by salt-stress, we hypothesized that plants growing in saline conditions would have enhanced resistance against herbivores. The non-halophyte, Brassica juncea, and the generalist herbivore Trichoplusia ni were used to test the prediction that plants subjected to salinity stress would be both more resistant and more tolerant to herbivory than those growing without salt stress. Plants were grown under different NaCl levels, and either exposed to herbivores and followed by removal of half of their leaves, or left intact. Plants were left to grow and reproduce until senescence. Tissue quality was assessed, seeds were counted and biomass of different organs measured. Plants exposed to salinity grew less, had reduced tissue nitrogen, protein and chlorophyll content, although proline levels increased. Specific leaf area, leaf water content, transpiration and root:shoot ratio remained unaffected. Plants growing under saline condition had greater constitutive resistance than unstressed plants. However, induced resistance and tolerance were not affected by salinity. These results support the hypothesis that plants growing under salt-stress are better defended against herbivores, although in B. juncea this may be mostly through resistance, and less through tolerance.