Cellular Mass Response to Therapy Correlates With Clinical Response for a Range of Malignancies.

PURPOSE: Cancer patients with advanced-stage disease have poor prognosis, typically having limited options for efficacious treatment, and genomics-based therapy guidance continues to benefit only a fraction of patients. Next-generation ex vivo approaches, such as cell mass-based response testing (MRT), offer an alternative precision medicine approach for a broader population of patients with cancer, but validation of clinical feasibility and potential impact remain necessary. MATERIALS AND METHODS: We evaluated the clinical feasibility and accuracy of using live-cell MRT to predict patient drug sensitivity. Using a unified measurement workflow with a 48-hour result turnaround time, samples were subjected to MRT after treatment with a panel of drugs in vitro. After completion of therapeutic course, clinical response data were correlated with MRT-based predictions of outcome. Specimens were collected from 104 patients with solid (n = 69) and hematologic (n = 35) malignancies, using tissue formats including needle biopsies, malignant fluids, bone marrow aspirates, and blood samples. Of the 81 (78%) specimens qualified for MRT, 41 (51%) patients receiving physician-selected therapies had treatments matched to MRT. RESULTS: MRT demonstrated high concordance with clinical responses with an odds ratio (OR) of 14.80 (P = .0003 [95% CI, 2.83 to 102.9]). This performance held for both solid and hematologic malignances with ORs of 20.67 (P = .0128 [95% CI, 1.45 to 1,375.57]) and 8.20 (P = .045 [95% CI, 0.77 to 133.56]), respectively. Overall, these results had a predictive accuracy of 80% (P = .0026 [95% CI, 65 to 91]). CONCLUSION: MRT showed highly significant correlation with clinical response to therapy. Routine clinical use is technically feasible and broadly applicable to a wide range of samples and malignancy types, supporting the need for future validation studies.

Biosecurity and Management Strategies for Economically Important Exotic Tephritid Fruit Fly Species in Australia.

Exotic tephritid incursions are of high concern to Australia's biosecurity and its horticultural industries. It is vital that Australia remains ready to respond to incursions as they arise, as an incursion of tephritid fruit fly species will result in significant economic losses. In this review, we compared Australian incursion management strategies for fruit flies with global management strategies and identified possible areas where improvements could be made in an Australian context. Overall, Australia has a good understanding of the main tephritid threats, of which Bactrocera species from across the Torres Strait (northern Australia) are of most concern. Effective tools for tephritid detection and early warning surveillance at points of entry are in place at ports and in horticultural areas Australia-wide and provide the basis for initiating biosecurity responses in the event of an incursion. Area-wide control measures used in successful eradication attempts globally are available for use in Australia. However, a specific tephritid emergency response plan identifying suitable response measures and control options for species of concern is not yet available. We have identified that Australia has the policies and management tools available to respond to an exotic tephritid incursion, but the speed at which this could be accomplished would be greatly improved by the development of species-specific emergency response plans.

A pipeline for malignancy and therapy agnostic assessment of cancer drug response using cell mass measurements.

Functional precision medicine offers a promising complement to genomics-based cancer therapy guidance by testing drug efficacy directly on a patient's tumor cells. Here, we describe a workflow that utilizes single-cell mass measurements with inline brightfield imaging and machine-learning based image classification to broaden the clinical utility of such functional testing for cancer. Using these image-curated mass measurements, we characterize mass response signals for 60 different drugs with various mechanisms of action across twelve different cell types, demonstrating an improved ability to detect response for several slow acting drugs as compared with standard cell viability assays. Furthermore, we use this workflow to assess drug responses for various primary tumor specimen formats including blood, bone marrow, fine needle aspirates (FNA), and malignant fluids, all with reports generated within two days and with results consistent with patient clinical responses. The combination of high-resolution measurement, broad drug and malignancy applicability, and rapid return of results offered by this workflow suggests that it is well-suited to performing clinically relevant functional assessment of cancer drug response.

Triple MAPK inhibition salvaged a relapsed post-BCMA CAR-T cell therapy multiple myeloma patient with a BRAF V600E subclonal mutation.

BACKGROUND: Multiple Myeloma (MM) is a progressive plasma cell neoplasm characterized by heterogeneous clonal expansion. Despite promising response rates achieved with anti-BCMA CAR-T cell therapy, patients may still relapse and there are currently no clear therapeutic options in post-CAR-T settings. In this report, we present a case of a post-BCMA CAR-T relapsed/refractory (RR) MM patient with skin extramedullary disease (EMD) in which a novel MAPK inhibition combinatorial strategy was implemented based on next-generation sequencing and in vitro experiments. CASE PRESENTATION: A 61-year-old male with penta-refractory MM penta- (IgA lambda), ISS stage 3 with hyperdiploidy, gain of 1q21 and del13 was treated with anti-BCMA CAR-T cell therapy, achieving a best response of VGPR. He progressed after 6 months and was salvaged for a short period with autologous stem cell transplantation. Eventually, he progressed with extramedullary disease manifested as subcutaneous nodules. Based on whole-exome sequencing, we identified a BRAF (V600E) dominant subclone in both bone marrow and cutaneous plasmacytoma. Following in vitro experiments, and according to our previous studies, we implemented a triple MAPK inhibition strategy under which the patient achieved a very good partial response for 110 days, which allowed to bridge him to subsequent clinical trials and eventually achieve a stringent complete response (sCR). CONCLUSION: Here, we show the applicability, effectiveness, and tolerability the triple MAPK inhibition strategy in the context of post-BCMA CAR-T failure in specific subset of patients. The triple therapy could bridge our hospice bound RRMM patient with BRAF (V600E) to further therapeutic options where sCR was achieved. We will further evaluate triple MAPK inhibition in patients with BRAF V600E in a precision medicine clinical trial launching soon.

Topical and dietary toxicity of emamectin benzoate, chlorantraniliprole, cyantraniliprole and indoxacarb to larvae of the common armyworm Mythimna convecta (Lepidoptera: Noctuidae).

BACKGROUND: The common armyworm Mythimna convecta is an important pest of pastures and graminaceous crops in Australia, but materials currently registered for its control are limited to broad-spectrum compounds incompatible with integrated pest management (IPM) systems. In this study we assessed the response of M. convecta larvae to four alternative compounds using topical and dietary bioassays. RESULTS: Emamectin benzoate [LC50 (lethal concentration for 50% of insects tested) values 2.69 µg mL-1 topical, 0.017 µg active ingredient (AI) g-1 dietary] and chlorantraniliprole (LC50 values 4.87 µg mL-1  topical, 0.080 µg AI g-1 dietary) were significantly more active than either indoxacarb or cyantraniliprole. Our results showed strong parallels with data on the more extensively studied Australian strains of Helicoverpa armigera, with the most notable differences being the higher contact toxicity of emamectin benzoate to M. convecta and the lower acute dietary activity of formulated cyantraniliprole to this species, which was linked to feeding deterrence. Cyantraniliprole at dietary concentrations of ≥0.02 µg AI g-1 significantly reduced the weight of surviving larvae and frass production (an indirect measure of food consumption) over the seven-day exposure period. There was also some evidence of chlorantraniliprole deterring larval feeding, although to a much more limited extent. CONCLUSIONS: Both emamectin benzoate and chlorantraniliprole are suitable for use against M. convecta. The decision as to which of these compounds should be prioritized for further development should be based on their potential effects on beneficial species once their optimal field rates have been determined.

Transmission of Metarhizium anisopliae and Beauveria bassiana to adults of Kuschelorhynchus macadamiae (Coleoptera: Curculionidae) from infected adults and conidiated cadavers.

Kuschelorhynchus macadamiae is a major pest of macadamias in Australia, causing yield losses of up to 15%. Our previous studies have shown the weevil is susceptible to Beauveria bassiana and Metarhizium anisopliae. The aim of this study was to investigate horizontal transmission of both fungal species to healthy weevils from both infected adults and weevil cadavers. In a confined environment the mortality of healthy adults caused by the transmission of conidia from live fungus-infected adults was < 50%. Under similar experimental conditions, the mortality of healthy adults reached 100% when exposed to conidiated cadavers. However, when conidiated cadavers were used in more spacious environments (insect cages), the mortality of adults was < 80%. Using scanning electron microscopy, it was observed that all healthy adults had conidia attached to all external parts of the body. This suggests that although the conidia were readily transferred to the adults, the lower mortality in the larger insect cages could be the result of an unfavourable environmental factor such as low humidity. The presence of conidia attached to all the adults indicated that they did not show any discriminatory behaviour such as avoidance of conidiated cadavers infected by these two fungal species. The results from this study show that there is potential for enhanced control of adult K. macadamiae via transmission from either fungus-infected adults or conidiated cadavers and this could strengthen sustainable pest management in macadamias.

Compatibility of Metarhizium anisopliae and Beauveria bassiana with insecticides and fungicides used in macadamia production in Australia.

BACKGROUND: Integrating fungal biocontrol agents into crop protection programs dominated by synthetic pesticides is an important first step towards developing an integrated pest management (IPM) program; however, their successful integration relies on an understanding of how their performance may be impacted by the remaining agrochemicals deployed for managing other pests and diseases. In this study we tested 10 formulated pesticides used in macadamia production at different concentrations to determine their effects on the germination, mycelial growth and sporulation of Metarhizium anisopliae and Beauveria bassiana in vitro. Further tests with laboratory-grade actives of the noncompatible pesticides were conducted to determine whether any antagonistic effects were caused by the active constituent or by formulation additives. RESULTS: At their registered concentrations, formulated trichlorfon, acephate and indoxacarb were compatible with M. anisopliae, whereas B. bassiana showed compatibility with formulated trichlorfon, acephate, indoxacarb, sulfoxaflor and spinetoram. Bioassays using laboratory-grade active constituents indicated that the adverse impact of formulated beta-cyfluthrin on both fungal species and that of formulated methidathion on B. bassiana is probably due to components of the emulsifiable concentrate formulations rather than their active constituents. Diazinon was the only insecticidal active that showed high toxicity to both fungal species. The two fungicides, carbendazim and pyraclostrobin, were toxic to both fungal species at all tested concentrations. CONCLUSION: Our results identify which pesticides used on macadamias in Australia are compatible and incompatible with entomopathogenic fungi. Future studies on pesticide degradation rates will help define the spray intervals required to eliminate these adverse effects.

Integration of Entomopathogenic Fungi into IPM Programs: Studies Involving Weevils (Coleoptera: Curculionoidea) Affecting Horticultural Crops.

Weevils are significant pests of horticultural crops and are largely managed with insecticides. In response to concerns about negative impacts of synthetic insecticides on humans and the environment, entomopathogenic fungi (EPF) have been developed as an alternative method of control, and as such appear to be "ready-made" components of integrated pest management (IPM) programs. As the success of pest control requires a thorough knowledge of the biology of the pests, this review summarises our current knowledge of weevil biology on nut trees, fruit crops, plant storage roots, and palm trees. In addition, three groups of life cycles are defined based on weevil developmental habitats, and together with information from studies of EPF activity on these groups, we discuss the tactics for integrating EPF into IPM programs. Finally, we highlight the gaps in the research required to optimise the performance of EPF and provide recommendations for the improvement of EPF efficacy for the management of key weevils of horticultural crops.

Author Correction: Cooperative nutrient accumulation sustains growth of mammalian cells.

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

Response of the macadamia seed weevil Kuschelorhynchus macadamiae (Coleoptera: Curculionidae) to Metarhizium anisopliae and Beauveria bassiana in laboratory bioassays.

Macadamia seed weevil, Kuschelorhynchus macadamiae Jennings and Oberprieler, is a major pest of macadamia in eastern Australia, causing yield losses of up to 15%. Current control methods involve two applications of acephate per season but more recently have moved to a single application of indoxacarb, combined with the collection and destruction of fallen nuts that contain developing larvae. As a first step towards reducing the dependence of the industry on synthetic insecticides, we tested six isolates of M. anisopliae, six isolates of B. bassiana and one commercial B. bassiana product (Velifer® biological insecticide) against adult macadamia seed weevil under laboratory conditions. All isolates were pathogenic against adult weevils with M. anisopliae accession ECS1/BRIP 70272 and B. bassiana accession B27/BRIP 70267 causing 97.5% and 92.5% mortality 12 days after being treated at 1 × 107 conidia/mL. Isolates ECS1/BRIP 70272 and B27/BRIP 70267 had the shortest LT50 values of 5.13 days and 5.37 days respectively. The median lethal concentrations (LC50) for ECS1/BRIP 70272 and B27/BRIP 70267 were 1.48 × 105 and 1.65 × 105 conidia/mL respectively. Results of this study indicate that M. anisopliae accession ECS1/BRIP 70272 and B. bassiana accession B27/BRIP 70267 have considerable potential for K. macadamiae control, and should be developed into biological insecticides for integration into macadamia pest management programs.

Linking single-cell measurements of mass, growth rate, and gene expression.

Mass and growth rate are highly integrative measures of cell physiology not discernable via genomic measurements. Here, we introduce a microfluidic platform enabling direct measurement of single-cell mass and growth rate upstream of highly multiplexed single-cell profiling such as single-cell RNA sequencing. We resolve transcriptional signatures associated with single-cell mass and growth rate in L1210 and FL5.12 cell lines and activated CD8+ T cells. Further, we demonstrate a framework using these linked measurements to characterize biophysical heterogeneity in a patient-derived glioblastoma cell line with and without drug treatment. Our results highlight the value of coupled phenotypic metrics in guiding single-cell genomics.

Microfluidic active loading of single cells enables analysis of complex clinical specimens.

A fundamental trade-off between flow rate and measurement precision limits performance of many single-cell detection strategies, especially for applications that require biophysical measurements from living cells within complex and low-input samples. To address this, we introduce 'active loading', an automated, optically-triggered fluidic system that improves measurement throughput and robustness by controlling entry of individual cells into a measurement channel. We apply active loading to samples over a range of concentrations (1-1000 particles µL-1), demonstrate that measurement time can be decreased by up to 20-fold, and show theoretically that performance of some types of existing single-cell microfluidic devices can be improved by implementing active loading. Finally, we demonstrate how active loading improves clinical feasibility for acute, single-cell drug sensitivity measurements by deploying it to a preclinical setting where we assess patient samples from normal brain, primary and metastatic brain cancers containing a complex, difficult-to-measure mixture of confounding biological debris.

Determining therapeutic susceptibility in multiple myeloma by single-cell mass accumulation.

Multiple myeloma (MM) has benefited from significant advancements in treatment that have improved outcomes and reduced morbidity. However, the disease remains incurable and is characterized by high rates of drug resistance and relapse. Consequently, methods to select the most efficacious therapy are of great interest. Here we utilize a functional assay to assess the ex vivo drug sensitivity of single multiple myeloma cells based on measuring their mass accumulation rate (MAR). We show that MAR accurately and rapidly defines therapeutic susceptibility across human multiple myeloma cell lines to a gamut of standard-of-care therapies. Finally, we demonstrate that our MAR assay, without the need for extended culture ex vivo, correctly defines the response of nine patients to standard-of-care drugs according to their clinical diagnoses. This data highlights the MAR assay in both research and clinical applications as a promising tool for predicting therapeutic response using clinical samples.

Sweetpotato weevil, Cylas formicarius (Fab.) (Coleoptera: Brentidae) avoids its host plant when a virulent Metarhizium anisopliae isolate is present.

Metarhizium anisopliae has a wide range of coleopteran hosts, including weevils. Some susceptible insects are known to modify their behavior to prevent infection, typically detecting virulent strains by olfaction, and avoiding physical contact with sources of infection. Laboratory olfactometer assays were conducted on the sweetpotato weevil Cylas formicarius to test the hypothesis that insects would avoid a more virulent strain of M. anisopliae when presented with a strain of low virulence or an untreated control. When adult weevils were allowed to choose between paired test arenas containing sweetpotato roots and M. anisopliae isolates on agar cores, weevils avoided arenas with the highly virulent isolate QS155, showing a preference for either roots with uninoculated agar cores or cores with the low virulence isolate QS002-3. When roots or whole sweetpotato plants were inoculated with M. anisopliae, the preferences of weevils remained broadly similar; weevils were repelled by the highly virulent isolate QS155 when tested against either QS002-3 or uninoculated roots and plants, however weevils were not repelled by the low virulence isolate QS002-3 tested against uninoculated controls. When single-sex groups of weevils were tested separately in the olfactometer using uninoculated whole plants and plants treated with isolate QS155, males and females responded similarly and statistically identical preferences were found for the untreated plants. When weevils were released singly at different times of the day the response time for males was significantly shorter in the afternoon compared to the morning. Males were always significantly faster to respond to olfactory stimuli than females. Understanding factors that may lead to avoidance of virulent M. anisopliae strains by C. formicarius will be an essential part of developing an 'attract-and-infect' strategy for the management of C. formicarius.

The response of Isidorella newcombi to copper exposure: Using an integrated biological framework to interpret transcriptomic responses from RNA-seq analysis.

This study describes the transcriptomic response of the Australian endemic freshwater gastropod Isidorella newcombi exposed to 80±1µg/L of copper for 3days. Analysis of copper tissue concentration, lysosomal membrane destabilisation and RNA-seq were conducted. Copper tissue concentrations confirmed that copper was bioaccumulated by the snails. Increased lysosomal membrane destabilisation in the copper-exposed snails indicated that the snails were stressed as a result of the exposure. Both copper tissue concentrations and lysosomal destabilisation were significantly greater in snails exposed to copper. In order to interpret the RNA-seq data from an ecotoxicological perspective an integrated biological response model was developed that grouped transcriptomic responses into those associated with copper transport and storage, survival mechanisms and cell death. A conceptual model of expected transcriptomic changes resulting from the copper exposure was developed as a basis to assess transcriptomic responses. Transcriptomic changes were evident at all the three levels of the integrated biological response model. Despite lacking statistical significance, increased expression of the gene encoding copper transporting ATPase provided an indication of increased internal transport of copper. Increased expression of genes associated with endocytosis are associated with increased transport of copper to the lysosome for storage in a detoxified form. Survival mechanisms included metabolic depression and processes associated with cellular repair and recycling. There was transcriptomic evidence of increased cell death by apoptosis in the copper-exposed organisms. Increased apoptosis is supported by the increase in lysosomal membrane destabilisation in the copper-exposed snails. Transcriptomic changes relating to apoptosis, phagocytosis, protein degradation and the lysosome were evident and these processes can be linked to the degradation of post-apoptotic debris. The study identified contaminant specific transcriptomic markers as well as markers of general stress. From an ecotoxicological perspective, the use of a framework to group transcriptomic responses into those associated with copper transport, survival and cell death assisted with the complex process of interpretation of RNA-seq data. The broad adoption of such a framework in ecotoxicology studies would assist in comparison between studies and the identification of reliable transcriptomic markers of contaminant exposure and response.

Drug sensitivity of single cancer cells is predicted by changes in mass accumulation rate.

Assays that can determine the response of tumor cells to cancer therapeutics could greatly aid the selection of drug regimens for individual patients. However, the utility of current functional assays is limited, and predictive genetic biomarkers are available for only a small fraction of cancer therapies. We found that the single-cell mass accumulation rate (MAR), profiled over many hours with a suspended microchannel resonator, accurately defined the drug sensitivity or resistance of glioblastoma and B-cell acute lymphocytic leukemia cells. MAR revealed heterogeneity in drug sensitivity not only between different tumors, but also within individual tumors and tumor-derived cell lines. MAR measurement predicted drug response using samples as small as 25 µl of peripheral blood while maintaining cell viability and compatibility with downstream characterization. MAR measurement is a promising approach for directly assaying single-cell therapeutic responses and for identifying cellular subpopulations with phenotypic resistance in heterogeneous tumors.

High-throughput measurement of single-cell growth rates using serial microfluidic mass sensor arrays.

Methods to rapidly assess cell growth would be useful for many applications, including drug susceptibility testing, but current technologies have limited sensitivity or throughput. Here we present an approach to precisely and rapidly measure growth rates of many individual cells simultaneously. We flow cells in suspension through a microfluidic channel with 10-12 resonant mass sensors distributed along its length, weighing each cell repeatedly over the 4-20 min it spends in the channel. Because multiple cells traverse the channel at the same time, we obtain growth rates for >60 cells/h with a resolution of 0.2 pg/h for mammalian cells and 0.02 pg/h for bacteria. We measure the growth of single lymphocytic cells, mouse and human T cells, primary human leukemia cells, yeast, Escherichia coli and Enterococcus faecalis. Our system reveals subpopulations of cells with divergent growth kinetics and enables assessment of cellular responses to antibiotics and antimicrobial peptides within minutes.

Biophysical changes reduce energetic demand in growth factor-deprived lymphocytes.

Cytokine regulation of lymphocyte growth and proliferation is essential for matching nutrient consumption with cell state. Here, we examine how cellular biophysical changes that occur immediately after growth factor depletion promote adaptation to reduced nutrient uptake. After growth factor withdrawal, nutrient uptake decreases, leading to apoptosis. Bcl-xL expression prevents cell death, with autophagy facilitating long-term cell survival. However, autophagy induction is slow relative to the reduction of nutrient uptake, suggesting that cells must engage additional adaptive mechanisms to respond initially to growth factor depletion. We describe an acute biophysical response to growth factor withdrawal, characterized by a simultaneous decrease in cell volume and increase in cell density, which occurs before autophagy initiation and is observed in both FL5.12 Bcl-xL cells depleted of IL-3 and primary CD8(+) T cells depleted of IL-2 that are differentiating toward memory cells. The response reduces cell surface area to minimize energy expenditure while conserving biomass, suggesting that the biophysical properties of cells can be regulated to promote survival under conditions of nutrient stress.