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Šibanc N, Clark DR, Helgason T, Dumbrell AJ, Maček I. Extreme environments simplify reassembly of communities of arbuscular mycorrhizal fungi. mSystems 2024; 9:e0133123. [PMID: 38376262 PMCID: PMC10949450 DOI: 10.1128/msystems.01331-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/18/2024] [Indexed: 02/21/2024] Open
Abstract
The ecological impacts of long-term (press) disturbance on mechanisms regulating the relative abundance (i.e., commonness or rarity) and temporal dynamics of species within a community remain largely unknown. This is particularly true for the functionally important arbuscular mycorrhizal (AM) fungi; obligate plant-root endosymbionts that colonize more than two-thirds of terrestrial plant species. Here, we use high-resolution amplicon sequencing to examine how AM fungal communities in a specific extreme ecosystem-mofettes or natural CO2 springs caused by geological CO2 exhalations-are affected by long-term stress. We found that in mofettes, specific and temporally stable communities form as a subset of the local metacommunity. These communities are less diverse and dominated by adapted, "stress tolerant" taxa. Those taxa are rare in control locations and more benign environments worldwide, but show a stable temporal pattern in the extreme sites, consistently dominating the communities in grassland mofettes. This pattern of lower diversity and high dominance of specific taxa has been confirmed as relatively stable over several sampling years and is independently observed across multiple geographic locations (mofettes in different countries). This study implies that the response of soil microbial community composition to long-term stress is relatively predictable, which can also reflect the community response to other anthropogenic stressors (e.g., heavy metal pollution or land use change). Moreover, as AM fungi are functionally differentiated, with different taxa providing different benefits to host plants, changes in community structure in response to long-term environmental change have the potential to impact terrestrial plant communities and their productivity.IMPORTANCEArbuscular mycorrhizal (AM) fungi form symbiotic relationships with more than two-thirds of plant species. In return for using plant carbon as their sole energy source, AM fungi improve plant mineral supply, water balance, and protection against pathogens. This work demonstrates the importance of long-term experiments to understand the effects of long-term environmental change and long-term disturbance on terrestrial ecosystems. We demonstrated a consistent response of the AM fungal community to a long-term stress, with lower diversity and a less variable AM fungal community over time under stress conditions compared to the surrounding controls. We have also identified, for the first time, a suite of AM fungal taxa that are consistently observed across broad geographic scales in stressed and anthropogenically heavily influenced ecosystems. This is critical because global environmental change in terrestrial ecosystems requires an integrative approach that considers both above- and below-ground changes and examines patterns over a longer geographic and temporal scale, rather than just single sampling events.
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Affiliation(s)
- Nataša Šibanc
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Department of forest physiology and genetics, Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Dave R. Clark
- School of Life Sciences, University of Essex, Colchester, United Kingdom
- Institute for Analytics and Data Science, University of Essex, Colchester, United Kingdom
| | - Thorunn Helgason
- Department of Biology, University of York, York, United Kingdom
- Institute for Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Alex J. Dumbrell
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Irena Maček
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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2
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Guest EJ, Palfreeman LJ, Holden J, Chapman PJ, Firbank LG, Lappage MG, Helgason T, Leake JR. Soil macroaggregation drives sequestration of organic carbon and nitrogen with three-year grass-clover leys in arable rotations. Sci Total Environ 2022; 852:158358. [PMID: 36049686 DOI: 10.1016/j.scitotenv.2022.158358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 08/04/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Conventional arable cropping with annual crops established by ploughing and harrowing degrades larger soil aggregates that contribute to storing soil organic carbon (SOC). The urgent need to increase SOC content of arable soils to improve their functioning and sequester atmospheric CO2 has motivated studies into the effects of reintroducing leys into long-term conventional arable fields. However, effects of short-term leys on total SOC accumulation have been equivocal. As soil aggregation may be important for carbon storage, we investigated the effects of arable-to-ley conversion on cambisol soil after three years of ley, on concentrations and stocks of SOC, nitrogen and their distributions in different sized water-stable aggregates. These values were benchmarked against soil from beneath hedgerow margins. SOC stocks (0-7 cm depth) rose from 20.3 to 22.6 Mg ha-1 in the arable-to-ley conversion, compared to 30 Mg ha-1 in hedgerows, but this 2.3 Mg ha-1 difference (or 0.77 Mg C ha-1 yr-1) was not significant). However, the proportion of large macroaggregates (> 2000 μm) increased 5.4-fold in the arable-to-ley conversion, recovering to similar abundance as hedgerow soils, driving near parallel increases in SOC and nitrogen within large macroaggregates (5.1 and 5.7-fold respectively). The total SOC (0-7 cm depth) stored in large macroaggregates increased from 2.0 to 9.6 Mg ha-1 in the arable-to-ley conversion, which no longer differed significantly from the 12.1 Mg ha-1 under hedgerows. The carbon therefore accumulated three times faster, at 2.53 Mg C ha-1 yr-1, in the large macroaggregates compared to the bulk soil. These findings highlight the value of monitoring large macroaggregate-bound SOC as a key early indicator of shifts in soil quality in response to change in field management, and the benefits of leys in soil aggregation, carbon accumulation, and soil functioning, providing justification for fiscal incentives that encourage wider use of leys in arable rotations.
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Affiliation(s)
- Emily J Guest
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK; ADAS Boxworth, Battle Gate Road, Cambridge CB23 4NN, UK.
| | - Lucy J Palfreeman
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK.
| | - Joseph Holden
- School of Geography, The University of Leeds, Leeds LS2 9JT, UK.
| | - Pippa J Chapman
- School of Geography, The University of Leeds, Leeds LS2 9JT, UK.
| | - Les G Firbank
- School of Biology, The University of Leeds, Leeds LS2 9JT, UK.
| | | | - Thorunn Helgason
- Department of Biology, The University of York, York, YO10 5DD, UK; School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3JR, UK.
| | - Jonathan R Leake
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK.
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3
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Castro-Gutierrez V, Fuller E, Garcillán-Barcia MP, Helgason T, Hassard F, Moir J. Dissemination of metaldehyde catabolic pathways is driven by mobile genetic elements in Proteobacteria. Microb Genom 2022; 8. [DOI: 10.1099/mgen.0.000881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bioremediation of metaldehyde from drinking water using metaldehyde-degrading strains has recently emerged as a promising alternative. Whole-genome sequencing was used to obtain full genomes for metaldehyde degraders
Acinetobacter calcoaceticus
E1 and
Sphingobium
CMET-H. For the former, the genetic context of the metaldehyde-degrading genes had not been explored, while for the latter, none of the degrading genes themselves had been identified. In
A. calcoaceticus
E1, IS91 and IS6-family insertion sequences (ISs) were found surrounding the metaldehyde-degrading gene cluster located in plasmid pAME76. This cluster was located in closely-related plasmids and associated to identical ISs in most metaldehyde-degrading β- and γ-Proteobacteria, indicating horizontal gene transfer (HGT). For
Sphingobium
CMET-H, sequence analysis suggested a phytanoyl-CoA family oxygenase as a metaldehyde-degrading gene candidate due to its close homology to a previously identified metaldehyde-degrading gene known as mahX. Heterologous gene expression in
Escherichia coli
alongside degradation tests verified its functional significance and the degrading gene homolog was henceforth called mahS. It was found that mahS is hosted within the conjugative plasmid pSM1 and its genetic context suggested a crossover between the metaldehyde and acetoin degradation pathways. Here, specific replicons and ISs responsible for maintaining and dispersing metaldehyde-degrading genes in α, β and γ-Proteobacteria through HGT were identified and described. In addition, a homologous gene implicated in the first step of metaldehyde utilisation in an α-Proteobacteria was uncovered. Insights into specific steps of this possible degradation pathway are provided.
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Affiliation(s)
- Víctor Castro-Gutierrez
- Environmental Pollution Research Center (CICA), University of Costa Rica, Montes de Oca, 11501, Costa Rica
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
- Department of Biology, University of York, Heslington, York, UK
| | - Edward Fuller
- Department of Biology, University of York, Heslington, York, UK
| | - María Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, Santander, Cantabria, Spain
| | | | - Francis Hassard
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
| | - James Moir
- Department of Biology, University of York, Heslington, York, UK
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4
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Austen N, Tille S, Berdeni D, Firbank LG, Lappage M, Nelson M, Helgason T, Marshall-Harries E, Hughes HB, Summers R, Cameron DD, Leake JR. Experimental evaluation of biological regeneration of arable soil: The effects of grass-clover leys and arbuscular mycorrhizal inoculants on wheat growth, yield, and shoot pathology. Front Plant Sci 2022; 13:955985. [PMID: 36092419 PMCID: PMC9450525 DOI: 10.3389/fpls.2022.955985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Wheat yields have plateaued in the UK over the last 25 years, during which time most arable land has been annually cropped continuously with short rotations dominated by cereals. Arable intensification has depleted soil organic matter and biology, including mycorrhizas, which are affected by tillage, herbicides, and crop genotype. Here, we test whether winter wheat yields, mycorrhization, and shoot health can be improved simply by adopting less intensive tillage and adding commercial mycorrhizal inoculum to long-term arable fields, or if 3-year grass-clover leys followed direct drilling is more effective for biological regeneration of soil with reduced N fertiliser. We report a trial of mycorrhization, ear pathology, and yield performance of the parents and four double haploid lines from the Avalon x Cadenza winter wheat population in a long-term arable field that is divided into replicated treatment plots. These plots comprised wheat lines grown using ploughing or disc cultivation for 3 years, half of which received annual additions of commercial arbuscular mycorrhizal (AM) inoculum, compared to 3-year mown grass-clover ley plots treated with glyphosate and direct-drilled. All plots annually received 35 kg of N ha-1 fertiliser without fungicides. The wheat lines did not differ in mycorrhization, which averaged only 34% and 40% of root length colonised (RLC) in the ploughed and disc-cultivated plots, respectively, and decreased with inoculation. In the ley, RLC increased to 52%. Two wheat lines were very susceptible to a sooty ear mould, which was lowest in the ley, and highest with disc cultivation. AM inoculation reduced ear infections by >50% in the susceptible lines. In the ley, yields ranged from 7.2 to 8.3 t ha-1, achieving 92 to 106% of UK average wheat yield in 2018 (7.8 t ha-1) but using only 25% of average N fertiliser. Yields with ploughing and disc cultivation averaged only 3.9 and 3.4 t ha-1, respectively, with AM inoculum reducing yields from 4.3 to 3.5 t ha-1 in ploughed plots, with no effect of disc cultivation. The findings reveal multiple benefits of reintegrating legume-rich leys into arable rotations as part of a strategy to regenerate soil quality and wheat crop health, reduce dependence on nitrogen fertilisers, enhance mycorrhization, and achieve good yields.
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Affiliation(s)
- Nichola Austen
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Stefanie Tille
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Despina Berdeni
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | | | - Martin Lappage
- School of Biology, University of Leeds, Leeds, United Kingdom
| | - Michaela Nelson
- Department of Biology, University of York, York, United Kingdom
| | | | - Ewan Marshall-Harries
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - H. Bleddyn Hughes
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | | | - Duncan D. Cameron
- The Institute for Sustainable Food at the University of Sheffield, Sheffield, United Kingdom
| | - Jonathan R. Leake
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
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5
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Chaudhary VB, Holland EP, Charman-Anderson S, Guzman A, Bell-Dereske L, Cheeke TE, Corrales A, Duchicela J, Egan C, Gupta MM, Hannula SE, Hestrin R, Hoosein S, Kumar A, Mhretu G, Neuenkamp L, Soti P, Xie Y, Helgason T. What are mycorrhizal traits? Trends Ecol Evol 2022; 37:573-581. [PMID: 35504748 DOI: 10.1016/j.tree.2022.04.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/02/2022] [Accepted: 04/06/2022] [Indexed: 12/29/2022]
Abstract
Traits are inherent properties of organisms, but how are they defined for organismal networks such as mycorrhizal symbioses? Mycorrhizal symbioses are complex and diverse belowground symbioses between plants and fungi that have proved challenging to fit into a unified and coherent trait framework. We propose an inclusive mycorrhizal trait framework that classifies traits as morphological, physiological, and phenological features that have functional implications for the symbiosis. We further classify mycorrhizal traits by location - plant, fungus, or the symbiosis - which highlights new questions in trait-based mycorrhizal ecology designed to charge and challenge the scientific community. This new framework is an opportunity for researchers to interrogate their data to identify novel insights and gaps in our understanding of mycorrhizal symbioses.
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Affiliation(s)
- V Bala Chaudhary
- Department of Environmental Studies, Dartmouth College, Hanover, NH 03755, USA.
| | | | | | - Aidee Guzman
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lukas Bell-Dereske
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Tanya E Cheeke
- School of Biological Sciences, Washington State University, Richland, WA 99354, USA
| | - Adriana Corrales
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 110151, Colombia
| | - Jessica Duchicela
- Departamento de Ciencias de la Vida, Universidad de las Fuerzas Armadas ESPE, Sangolquí 171103, Ecuador
| | - Cameron Egan
- Department of Biology, Okanagan College, 1000 KLO Rd, Kelowna, BC, Canada V1Y 4X8
| | - Manju M Gupta
- Department of Biology, University of Delhi, Sri Aurobindo College, Delhi 110017, India
| | - S Emilia Hannula
- Institute of Environmental Sciences, Leiden University, Leiden 2333, The Netherlands
| | - Rachel Hestrin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Shabana Hoosein
- Department of Forest and Rangeland Stewardship, Colorado State University, Fort Collins, CO 80523, USA
| | - Amit Kumar
- Institute of Ecology, Faculty of Sustainability, Leuphana University of Lüneburg, 21335 Lüneburg, Germany
| | - Genet Mhretu
- Department of Biology, Mekelle University, Mekelle 231, Ethiopia
| | - Lena Neuenkamp
- University of Bern, Institute of Plant Sciences, Berne 3013, Switzerland; Department of Ecology and Multidisciplinary Institute for Environment Studies 'Ramon Margalef', University of Alicante, Alicante 03009, Spain
| | - Pushpa Soti
- Biology Department, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Yichun Xie
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR 999077
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6
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Castro-Gutierrez VM, Pickering L, Cambronero-Heinrichs JC, Holden B, Haley J, Jarvis P, Jefferson B, Helgason T, Moir JW, Hassard F. Bioaugmentation of pilot-scale slow sand filters can achieve compliant levels for the micropollutant metaldehyde in a real water matrix. Water Res 2022; 211:118071. [PMID: 35063927 DOI: 10.1016/j.watres.2022.118071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/23/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Metaldehyde is a polar, mobile, low molecular weight pesticide that is challenging to remove from drinking water with current adsorption-based micropollutant treatment technologies. Alternative strategies to remove this and compounds with similar properties are necessary to ensure an adequate supply of safe and regulation-compliant drinking water. Biological removal of metaldehyde below the 0.1 µg•L-1 regulatory concentration was attained in pilot-scale slow sand filters (SSFs) subject to bioaugmentation with metaldehyde-degrading bacteria. To achieve this, a library of degraders was first screened in bench-scale assays for removal at micropollutant concentrations in progressively more challenging conditions, including a mixed microbial community with multiple carbon sources. The best performing strains, A. calcoaceticus E1 and Sphingobium CMET-H, showed removal rates of 0.0012 µg•h-1•107 cells-1 and 0.019 µg•h-1•107 cells-1 at this scale. These candidates were then used as inocula for bioaugmentation of pilot-scale SSFs. Here, removal of metaldehyde by A. calcoaceticus E1, was insufficient to achieve compliant water regardless testing increasing cell concentrations. Quantification of metaldehyde-degrading genes indicated that aggregation and inadequate distribution of the inoculum in the filters were the likely causes of this outcome. Conversely, bioaugmentation with Sphingobium CMET-H enabled sufficient metaldehyde removal to achieve compliance, with undetectable levels in treated water for at least 14 d (volumetric removal: 0.57 µg•L-1•h-1). Bioaugmentation did not affect the background SSF microbial community, and filter function was maintained throughout the trial. Here it has been shown for the first time that bioaugmentation is an efficient strategy to remove the adsorption-resistant pesticide metaldehyde from a real water matrix in upscaled systems. Swift contaminant removal after inoculum addition and persistent activity are two remarkable attributes of this approach that would allow it to effectively manage peaks in metaldehyde concentrations (due to precipitation or increased application) in incoming raw water by matching them with high enough degrading populations. This study provides an example of how stepwise screening of a diverse collection of degraders can lead to successful bioaugmentation and can be used as a template for other problematic adsorption-resistant compounds in drinking water purification.
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Affiliation(s)
- V M Castro-Gutierrez
- Department of Biology, University of York, Heslington, York, UK; Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK; Environmental Pollution Research Center (CICA), University of Costa Rica, Montes de Oca, 11501, Costa Rica
| | - L Pickering
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK
| | - J C Cambronero-Heinrichs
- Environmental Pollution Research Center (CICA), University of Costa Rica, Montes de Oca, 11501, Costa Rica
| | - B Holden
- UK Water Industry Research Limited, London, UK
| | - J Haley
- UK Water Industry Research Limited, London, UK
| | - P Jarvis
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK
| | - B Jefferson
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK
| | - T Helgason
- Department of Biology, University of York, Heslington, York, UK
| | - J W Moir
- Department of Biology, University of York, Heslington, York, UK
| | - F Hassard
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK.
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Moulton-Brown CE, Feng T, Kumar SS, Xu L, Dytham C, Helgason T, Cooper JM, Moir JWB. Long-term fertilization and tillage regimes have limited effects on structuring bacterial and denitrifier communities in a sandy loam UK soil. Environ Microbiol 2021; 24:298-308. [PMID: 34913554 DOI: 10.1111/1462-2920.15873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 11/30/2021] [Accepted: 12/08/2021] [Indexed: 11/30/2022]
Abstract
Denitrification causes loss of available nitrogen from soil systems, thereby reducing crop productivity and increasing reliance on agrochemicals. The dynamics of denitrification and denitrifying communities are thought to be altered by land management practices, which affect the physicochemical properties of the soil. In this study, we look at the effects of long-term tillage and fertilization regimes on arable soils following 16 years of treatment in a factorial field trial. By studying the bacterial community composition based on 16S rRNA amplicons, absolute bacterial abundance and diversity of denitrification functional genes (nirK, nirS and nosZ), under conditions of minimum/conventional tillage and organic/synthetic mineral fertilizer, we tested how specific land management histories affect the diversity and distribution of both bacteria and denitrification genes. Bacterial and denitrifier communities were largely unaffected by land management history and clustered predominantly by spatial location, indicating that the variability in bacterial community composition in these arable soils is governed by innate environmental differences and Euclidean distance rather than agricultural management intervention.
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Affiliation(s)
| | - Tianer Feng
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Shreiya Shivagni Kumar
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Luxi Xu
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Calvin Dytham
- Department of Biology, University of York, Heslington, York, UK
| | | | - Julia M Cooper
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - James W B Moir
- Department of Biology, University of York, Heslington, York, UK
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Prendergast-Miller MT, Jones DT, Berdeni D, Bird S, Chapman PJ, Firbank L, Grayson R, Helgason T, Holden J, Lappage M, Leake J, Hodson ME. Arable fields as potential reservoirs of biodiversity: Earthworm populations increase in new leys. Sci Total Environ 2021; 789:147880. [PMID: 34058593 DOI: 10.1016/j.scitotenv.2021.147880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
Managing soil to support biodiversity is important to sustain the ecosystem services provided by soils upon which society depends. There is increasing evidence that functional diversity of soil biota is important for ecosystem services, and has been degraded by intensive agriculture. Importantly, the spatial distribution of reservoirs of soil biota in and surrounding arable fields is poorly understood. In a field experiment, grass-clover ley strips were introduced into four arable fields which had been under continuous intensive/conventional arable rotation for more than 10 years. Earthworm communities in arable fields and newly established grass-clover leys, as well as field boundary land uses (hedgerows and grassy field margins), were monitored over 2 years after arable-to-ley conversions. Within 2 years, earthworm abundance in new leys was 732 ± 244 earthworms m-2, similar to that in field margin soils (619 ± 355 earthworms m-2 yr-1) and four times higher than in adjacent arable soil (185 ± 132 earthworms m-2). Relative to the arable soils, earthworm abundance under the new leys showed changes in community composition, structure and functional group, which were particularly associated with an increase in anecic earthworms; thus new leys became more similar to grassy field margins. Earthworm abundance was similar in new leys that were either connected to biodiversity reservoirs i.e. field margins and hedgerows, or not (installed earthworm barriers). This suggests that, for earthworm communities in typical arable fields, biodiversity reservoirs in adjacent field margins and hedgerows may not be critical for earthworm populations to increase. We conclude that the increase in earthworm abundance in the new leys observed over 2 years was driven by recruitment from the existing residual population in arable soils. Therefore, arable soils are also potential reservoirs of biodiversity.
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Affiliation(s)
- Miranda T Prendergast-Miller
- Department of Environment and Geography, University of York, Wentworth Way, York YO10 5NG, UK; Department of Geography and Environmental Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK.
| | - David T Jones
- Life Sciences Department, Natural History Museum, London SW7 5BD, UK
| | - Despina Berdeni
- The University of Sheffield, Department of Animal and Plant Sciences, Sheffield S10 2TN, UK; Crop Physiology, ADAS Gleadthorpe, Meden Vale, Mansfield, Nottinghamshire NG20 9PD, UK
| | - Susannah Bird
- Department of Biology, University of York, Wentworth Way, YO10 5DD, UK
| | - Pippa J Chapman
- water@leeds, School of Geography, University of Leeds, Leeds LS2 9JT, UK
| | - Leslie Firbank
- water@leeds, School of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Richard Grayson
- water@leeds, School of Geography, University of Leeds, Leeds LS2 9JT, UK
| | - Thorunn Helgason
- Department of Biology, University of York, Wentworth Way, YO10 5DD, UK
| | - Joseph Holden
- water@leeds, School of Geography, University of Leeds, Leeds LS2 9JT, UK
| | - Martin Lappage
- water@leeds, School of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Jonathan Leake
- The University of Sheffield, Department of Animal and Plant Sciences, Sheffield S10 2TN, UK
| | - Mark E Hodson
- Department of Environment and Geography, University of York, Wentworth Way, York YO10 5NG, UK
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9
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Leadbeater DR, Oates NC, Bennett JP, Li Y, Dowle AA, Taylor JD, Alponti JS, Setchfield AT, Alessi AM, Helgason T, McQueen-Mason SJ, Bruce NC. Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh. Microbiome 2021; 9:48. [PMID: 33597033 PMCID: PMC7890819 DOI: 10.1186/s40168-020-00964-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/06/2020] [Indexed: 05/29/2023]
Abstract
BACKGROUND Salt marshes are major natural repositories of sequestered organic carbon with high burial rates of organic matter, produced by highly productive native flora. Accumulated carbon predominantly exists as lignocellulose which is metabolised by communities of functionally diverse microbes. However, the organisms that orchestrate this process and the enzymatic mechanisms employed that regulate the accumulation, composition and permanence of this carbon stock are not yet known. We applied meta-exo-proteome proteomics and 16S rRNA gene profiling to study lignocellulose decomposition in situ within the surface level sediments of a natural established UK salt marsh. RESULTS Our studies revealed a community dominated by Gammaproteobacteria, Bacteroidetes and Deltaproteobacteria that drive lignocellulose degradation in the salt marsh. We identify 42 families of lignocellulolytic bacteria of which the most active secretors of carbohydrate-active enzymes were observed to be Prolixibacteracea, Flavobacteriaceae, Cellvibrionaceae, Saccharospirillaceae, Alteromonadaceae, Vibrionaceae and Cytophagaceae. These families secreted lignocellulose-active glycoside hydrolase (GH) family enzymes GH3, GH5, GH6, GH9, GH10, GH11, GH13 and GH43 that were associated with degrading Spartina biomass. While fungi were present, we did not detect a lignocellulolytic contribution from fungi which are major contributors to terrestrial lignocellulose deconstruction. Oxidative enzymes such as laccases, peroxidases and lytic polysaccharide monooxygenases that are important for lignocellulose degradation in the terrestrial environment were present but not abundant, while a notable abundance of putative esterases (such as carbohydrate esterase family 1) associated with decoupling lignin from polysaccharides in lignocellulose was observed. CONCLUSIONS Here, we identify a diverse cohort of previously undefined bacteria that drive lignocellulose degradation in the surface sediments of the salt marsh environment and describe the enzymatic mechanisms they employ to facilitate this process. Our results increase the understanding of the microbial and molecular mechanisms that underpin carbon sequestration from lignocellulose within salt marsh surface sediments in situ and provide insights into the potential enzymatic mechanisms regulating the enrichment of polyphenolics in salt marsh sediments. Video Abstract.
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Affiliation(s)
- Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
| | - Nicola C Oates
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Joseph P Bennett
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Adam A Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York, YO10 5DD, UK
| | - Joe D Taylor
- School of Chemistry and Biosciences, University of Bradford, Bradford, West Yorkshire, BD7 1DP, UK
| | - Juliana Sanchez Alponti
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Alexander T Setchfield
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Anna M Alessi
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | | | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
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10
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Janku F, Zhang HH, Pezeshki A, Goel S, Murthy R, Wang-Gillam A, Shepard DR, Helgason T, Masters T, Hong DS, Piha-Paul SA, Karp DD, Klang M, Huang SY, Sakamuri D, Raina A, Torrisi J, Solomon SB, Weissfeld A, Trevino E, DeCrescenzo G, Collins A, Miller M, Salstrom JL, Korn RL, Zhang L, Saha S, Leontovich AA, Tung D, Kreider B, Varterasian M, Khazaie K, Gounder MM. Intratumoral Injection of Clostridium novyi-NT Spores in Patients with Treatment-refractory Advanced Solid Tumors. Clin Cancer Res 2020; 27:96-106. [PMID: 33046513 DOI: 10.1158/1078-0432.ccr-20-2065] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/24/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Intratumorally injected Clostridium novyi-NT (nontoxic; lacking the alpha toxin), an attenuated strain of C. novyi, replicates within hypoxic tumor regions resulting in tumor-confined cell lysis and inflammatory response in animals, which warrants clinical investigation. PATIENTS AND METHODS This first-in-human study (NCT01924689) enrolled patients with injectable, treatment-refractory solid tumors to receive a single intratumoral injection of C. novyi-NT across 6 dose cohorts (1 × 104 to 3 × 106 spores, 3+3 dose-escalation design) to determine dose-limiting toxicities (DLT), and the maximum tolerated dose. RESULTS Among 24 patients, a single intratumoral injection of C. novyi-NT led to bacterial spores germination and the resultant lysis of injected tumor masses in 10 patients (42%) across all doses. The cohort 5 dose (1 × 106 spores) was defined as the maximum tolerated dose; DLTs were grade 4 sepsis (n = 2) and grade 4 gas gangrene (n = 1), all occurring in three patients with injected tumors >8 cm. Other treatment-related grade ≥3 toxicities included pathologic fracture (n = 1), limb abscess (n = 1), soft-tissue infection (n = 1), respiratory insufficiency (n = 1), and rash (n = 1), which occurred across four patients. Of 22 evaluable patients, nine (41%) had a decrease in size of the injected tumor and 19 (86%) had stable disease as the best overall response in injected and noninjected lesions combined. C. novyi-NT injection elicited a transient systemic cytokine response and enhanced systemic tumor-specific T-cell responses. CONCLUSIONS Single intratumoral injection of C. novyi-NT is feasible. Toxicities can be significant but manageable. Signals of antitumor activity and the host immune response support additional studies of C. novyi-NT in humans.
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Affiliation(s)
- Filip Janku
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | | | | | - Sanjay Goel
- Montefiore/Albert Einstein Cancer Center, Bronx, New York
| | - Ravi Murthy
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Radiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Thorunn Helgason
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tyler Masters
- Early Drug Development Service, Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - David S Hong
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarina A Piha-Paul
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel D Karp
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark Klang
- Early Drug Development Service, Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Steven Y Huang
- Department of Radiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Divya Sakamuri
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anjali Raina
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jean Torrisi
- Early Drug Development Service, Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Stephen B Solomon
- Early Drug Development Service, Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | | | | | | | | | - Maria Miller
- BioMed Valley Discoveries Inc., Kansas City, Missouri
| | | | | | - Linping Zhang
- BioMed Valley Discoveries Inc., Kansas City, Missouri
| | - Saurabh Saha
- BioMed Valley Discoveries Inc., Kansas City, Missouri.,Atlas Venture, Boston, Massachusetts
| | | | - David Tung
- BioMed Valley Discoveries Inc., Kansas City, Missouri
| | - Brent Kreider
- BioMed Valley Discoveries Inc., Kansas City, Missouri
| | | | | | - Mrinal M Gounder
- Early Drug Development Service, Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College, New York, New York.
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11
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Liang M, Johnson D, Burslem DFRP, Yu S, Fang M, Taylor JD, Taylor AFS, Helgason T, Liu X. Soil fungal networks maintain local dominance of ectomycorrhizal trees. Nat Commun 2020; 11:2636. [PMID: 32457288 PMCID: PMC7250933 DOI: 10.1038/s41467-020-16507-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/05/2020] [Indexed: 11/08/2022] Open
Abstract
The mechanisms regulating community composition and local dominance of trees in species-rich forests are poorly resolved, but the importance of interactions with soil microbes is increasingly acknowledged. Here, we show that tree seedlings that interact via root-associated fungal hyphae with soils beneath neighbouring adult trees grow faster and have greater survival than seedlings that are isolated from external fungal mycelia, but these effects are observed for species possessing ectomycorrhizas (ECM) and not arbuscular mycorrhizal (AM) fungi. Moreover, survival of naturally-regenerating AM seedlings over ten years is negatively related to the density of surrounding conspecific plants, while survival of ECM tree seedlings displays positive density dependence over this interval, and AM seedling roots contain greater abundance of pathogenic fungi than roots of ECM seedlings. Our findings show that neighbourhood interactions mediated by beneficial and pathogenic soil fungi regulate plant demography and community structure in hyperdiverse forests.
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Affiliation(s)
- Minxia Liang
- Department of Ecology, School of Life Sciences and State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, China
| | - David Johnson
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - David F R P Burslem
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Shixiao Yu
- Department of Ecology, School of Life Sciences and State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, China
| | - Miao Fang
- Department of Ecology, School of Life Sciences and State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, China
| | - Joe D Taylor
- School of Environment and Life Sciences, University of Salford, Salford, M5 4WT, UK
| | - Andy F S Taylor
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
- The James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, UK
| | - Thorunn Helgason
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Xubing Liu
- Department of Ecology, School of Life Sciences and State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, China.
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12
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Bueno CG, Aldrich-Wolfe L, Chaudhary VB, Gerz M, Helgason T, Hoeksema JD, Klironomos J, Lekberg Y, Leon D, Maherali H, Öpik M, Zobel M, Moora M. Misdiagnosis and uncritical use of plant mycorrhizal data are not the only elephants in the room. New Phytol 2019; 224:1415-1418. [PMID: 31246312 DOI: 10.1111/nph.15976] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/08/2019] [Indexed: 06/09/2023]
Affiliation(s)
- C Guillermo Bueno
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005, Tartu, Estonia
| | - Laura Aldrich-Wolfe
- Department of Biological Sciences, North Dakota State University, PO Box 6050, Fargo, ND, 58108, USA
| | - V Bala Chaudhary
- Department of Environmental Science and Studies, DePaul University, 1110 West Belden Ave, Chicago, IL, 60614-2245, USA
| | - Maret Gerz
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005, Tartu, Estonia
| | - Thorunn Helgason
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Jason D Hoeksema
- Department of Biology, University of Mississippi, PO Box 1848, University, MS, 38677, USA
| | - John Klironomos
- Department of Biology, University of British Columbia-Okanagan, Kelowna, BC, V1V 1V7, Canada
| | - Ylva Lekberg
- MPG Ranch, 1001 S. Higgins Ave, Missoula, MT, 59801, USA
- Department of Ecosystem Conservation Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Daniela Leon
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005, Tartu, Estonia
| | - Hafiz Maherali
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005, Tartu, Estonia
| | - Martin Zobel
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005, Tartu, Estonia
| | - Mari Moora
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005, Tartu, Estonia
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13
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Veresoglou SD, Chen B, Fischer MM, Helgason T, Mamolos AP, Rillig MC, Roldán A, Johnson D. Latitudinal constraints in responsiveness of plants to arbuscular mycorrhiza: the 'sun-worshipper' hypothesis. New Phytol 2019; 224:552-556. [PMID: 31087653 DOI: 10.1111/nph.15918] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/03/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Stavros D Veresoglou
- Plant Ecology, Institut für Biologie, Freie Universität Berlin, D-14195, Berlin, Germany
- Laboratory of Ecology and Environmental Protection, Faculty of Agriculture, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100091, China
- University of Chinese Academy of Sciences, PO Box 2871, Beijing, China
| | - Matthias M Fischer
- Plant Ecology, Institut für Biologie, Freie Universität Berlin, D-14195, Berlin, Germany
| | | | - Andreas P Mamolos
- Laboratory of Ecology and Environmental Protection, Faculty of Agriculture, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece
| | - Matthias C Rillig
- Plant Ecology, Institut für Biologie, Freie Universität Berlin, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195,, Berlin, Germany
| | - Antonio Roldán
- Department of Soil and Water Conservation, CSIC-Centro de Edafología y Biología Aplicada del Segura, PO Box 164, Campus de Espinardo, 30100, Murcia, Spain
| | - David Johnson
- School of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PT, UK
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14
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Litton JK, Scoggins ME, Hess KR, Adrada BE, Murthy RK, Damodaran S, DeSnyder SM, Brewster AM, Barcenas CH, Valero V, Whitman GJ, Schwartz-Gomez J, Mittendorf EA, Thompson AM, Helgason T, Ibrahim N, Piwnica-Worms H, Moulder SL, Arun BK. Neoadjuvant Talazoparib for Patients With Operable Breast Cancer With a Germline BRCA Pathogenic Variant. J Clin Oncol 2019; 38:388-394. [PMID: 31461380 DOI: 10.1200/jco.19.01304] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Talazoparib has demonstrated efficacy in patients with BRCA-positive metastatic breast cancer. This study evaluated the pathologic response of talazoparib alone for 6 months in patients with a known germline BRCA pathogenic variant (gBRCA-positive) and operable breast cancer. METHODS Eligibility included 1 cm or larger invasive tumor and gBRCA-positive disease. Human epidermal growth factor receptor 2-positive tumors were excluded. Twenty patients underwent a pretreatment biopsy, 6 months of once per day oral talazoparib (1 mg), followed by definitive surgery. Patients received adjuvant therapy at physician's discretion. The primary end point was residual cancer burden (RCB). With 20 patients, the RCB-0 plus RCB-I response rate can be estimated with a 95% CI with half width less than 20%. RESULTS Twenty patients were enrolled from August 2016 to September 2017. Median age was 38 years (range, 23 to 58 years); 16 patients were gBRCA1 positive and 4 patients were gBRCA2 positive. Fifteen patients had triple-negative breast cancer (estrogen receptor/progesterone receptor < 10%), and five had hormone receptor-positive disease. Five patients had clinical stage I disease, 12 had stage II, and three had stage III, including one patient with inflammatory breast carcinoma and one with metaplastic chondrosarcomatous carcinoma. One patient chose to receive chemotherapy before surgery and was not included in RCB analyses. RCB-0 (pathologic complete response) rate was 53% and RCB-0/I was 63%. Eight patients (40%) had grade 3 anemia and required a transfusion, three patients had grade 3 neutropenia, and 1 patient had grade 4 thrombocytopenia. Common grade 1 or 2 toxicities were nausea, fatigue, neutropenia, alopecia, dizziness, and dyspnea. Toxicities were managed by dose reduction and transfusions. Nine patients required dose reduction. CONCLUSION Neoadjuvant single-agent oral talazoparib once per day for 6 months without chemotherapy produced substantial RCB-0 rate with manageable toxicity. The substantive pathologic response to single-agent talazoparib supports the larger, ongoing neoadjuvant trial (ClinicalTrials.gov identifier: NCT03499353).
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Affiliation(s)
| | | | - Kenneth R Hess
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Rashmi K Murthy
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Vicente Valero
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gary J Whitman
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Nuhad Ibrahim
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Stacy L Moulder
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Banu K Arun
- The University of Texas MD Anderson Cancer Center, Houston, TX
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15
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Helgason T, Damodaran S, Hess KR, Symmans WF, Moulder SL. CLO19-036: Folate Receptor alpha Expression in Metastatic Triple-Negative Breast Cancer (TNBC). J Natl Compr Canc Netw 2019. [DOI: 10.6004/jnccn.2018.7115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background: Folate receptor alpha (FRα) is a glycosyl phosphatidylinositol (GPI)-anchored cell surface protein that binds and internalizes folate, which is a cofactor required for DNA/RNA synthesis and cell growth and proliferation. There is a marked up-regulation of FRα in many solid tumors; in contrast, FRα has a minimal expression in adult normal tissue. Mirvetuximab soravtansine is an antibody drug conjugate (ADC) consisting of a maytansinoid, N2'-Deacetyl-N2'-(4-mercapto-4-methyl-1-oxopentyl)-maytansine (DM4), conjugated to an anti-FRα antibody, M9346A. Once bound to the FRα and internalized, the anti-mitotic agents are released and inhibit tubulin polymerization and microtubule assembly, leading to cell death. Here we report the expression of FRα+ on residual tumor samples in metastatic TNBC. Methods: 68 patients (Pts) with stage IV TNBC underwent prescreening to determine if residual tumor tissue expressed FRα. Formalin fixed paraffin embedded (FFPE) samples were sent to Ventana Translational Diagnostics CAP/CLIA Laboratory for analysis using an in-house developed assay, Ventana OptiView DAB Detection kit, and the Ventana BenchMark Ultra automated slide stainer. FRα expression was evaluated by board certified pathologists using a scoring scale 1+ (low), 2+ (medium), and 3+ (high). For the purposes of study entry, FRα expression on cell surface was required to be low, defined as >25% of cells having 1+ expression. Results: 12% (8/68) of evaluated TNBCs had moderate to high rates of FRα expression. The median age of pts screened for FRα was 53 years. Moderate to high FRα expression rates were more common in Black and Asian patients (Table 1). Conclusion: Our prospective study has demonstrated that moderate to high expression of FRα in metastatic TNBC is 12%, which is lower than previously reported. An ongoing phase II study will determine efficacy for mirvetuximab soravtansine in advanced TNBC. Acknowledgement: This study was approved and funded in part by the NCCN Oncology Research Program from general research support provided by ImmunoGen, Inc.
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Affiliation(s)
| | | | - Kenneth R. Hess
- The University of Texas MD Anderson Cancer Center; Houston, TX
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16
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Brown C, Helgason T, Dytham C, Moir J. Distance-decay patterns overshadow effects of long-term fertilization and tillage on microbial community structure in agricultural soils. Access Microbiol 2019. [DOI: 10.1099/acmi.ac2019.po0276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | | | | | - James Moir
- University of York, York, United Kingdom
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17
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Adrada BE, Candelaria R, Moulder S, Lane D, Santiago L, Arribas E, Hess KR, Valero V, Thompson A, Helgason T, Ravenberg E, Yang W, Rauch GM. Abstract P6-02-10: Early ultrasound evaluation for prediction of treatment response to neoadjuvant chemotherapy in triple negative breast cancer patients. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p6-02-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Triple negative breast cancer (TNBC) is molecularly heterogeneous disease. Genomic profiling to identify the distinct TNBC subtypes is costly with long turnaround time. Early ultrasound after two cycles of neoadjuvant chemotherapy (NAC) has the potential to identify patients who are likely to have pathological complete response. Suspected non-responder patients can undergo comprehensive genetic testing and triaged for specific targeted therapeutic trials.
Aim: To determine the value of ultrasound evaluation after two cycles of NAC to predict complete pathologic response in TNBC breast cancer patients.
Methods: 98 patients enrolled in “A randomized triple Negative Breast Cancer Enrolling Trial to Confirm Molecular Profiling Improves Survival” (Artemis) at the University of Texas MD Anderson Cancer Center had ultrasound evaluation before treatment and after two cycles of NAC (Adriamycin and Cyclophosphamide). Three-dimensional measurements of the tumor were obtained at baseline and after 2 cycles of the NAC. Change in the tumor volume after 2 cycles of NAC was calculated. Residual cancer Volume (RCB) was calculated based on the final histopathology at surgery. Linear regression analysis evaluated associations between residual cancer burden (RCB) and change in volume of the index tumor.
Results: Median tumor size at diagnosis was 3 cm, range 0.6-11.9cm. Median size after two cycles was 2 cm, range 0.6-12.8 cm. RCB 0-I was seen in 55% of patients (54/98). Linear regression analysis demonstrated that of 22 patients with volume reduction >75%, 18 patients (82%) had RCB0-I (95%CI, 61%-93%).
Conclusion: Our data suggest that ultrasound exam after 2 cycles of NAC can identify TNBC patients who are unlikely to respond to standard NAC. These non-responder TNBC patients can be triaged for additional genetic testing and subsequent targeted clinical trials. Study on the larger number of patients is currently on the way.
Citation Format: Adrada BE, Candelaria R, Moulder S, Lane D, Santiago L, Arribas E, Hess KR, Valero V, Thompson A, Helgason T, Ravenberg E, Yang W, Rauch GM. Early ultrasound evaluation for prediction of treatment response to neoadjuvant chemotherapy in triple negative breast cancer patients [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-02-10.
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Affiliation(s)
- BE Adrada
- MD Anderson Cancer Center, Houston, TX
| | | | - S Moulder
- MD Anderson Cancer Center, Houston, TX
| | - D Lane
- MD Anderson Cancer Center, Houston, TX
| | | | - E Arribas
- MD Anderson Cancer Center, Houston, TX
| | - KR Hess
- MD Anderson Cancer Center, Houston, TX
| | - V Valero
- MD Anderson Cancer Center, Houston, TX
| | | | | | | | - W Yang
- MD Anderson Cancer Center, Houston, TX
| | - GM Rauch
- MD Anderson Cancer Center, Houston, TX
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18
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Abstract
We know a lot about the potential functions of mycorrhizas, but whether or not these are realized in the field where plants simultaneously experience a range of biotic interactions and fluctuating abiotic conditions is more or less unknown. In this Viewpoint, we present findings from a literature survey of papers on mycorrhizal function published in New Phytologist during the past 30 years. This survey showed that most functional studies are still conducted under controlled conditions, target mostly arbuscular and ectomycorrhizas, and focus on nutrient and carbon dynamics of the symbiosis. We also share discussions from a workshop, 'In situ mycorrhizal function: how do we get relevant data from a messy world?', held at the 9th International Conference on Mycorrhiza (ICOM9) in August 2017. In this workshop, we examined possibilities and limitations of old and new techniques for field research, and participants expressed the need to learn more about fungal traits and how they may relate to function. We argue that moving mycorrhizal experiments into the field will allow us not only to quantify realized functions, but also to revisit old paradigms and possibly discover new functions.
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Affiliation(s)
- Ylva Lekberg
- MPG Ranch, Missoula, MT, 59803, USA
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Thorunn Helgason
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
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19
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Litton J, Moulder S, Hess K, Damodaran S, Rauch G, Candelaria R, Adrada B, Symmans F, Murthy R, Helgason T, Clayborn A, Prabhakaran S, Valero V, Thompson A, Mittendorf E. Neoadjuvant trial of nab-paclitaxel and atezolizumab (Atezo), a PD-L1 inhibitor, in patients (pts) with chemo-insensitive triple negative breast cancer (TNBC). Ann Oncol 2018. [DOI: 10.1093/annonc/mdy270.219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Yam C, Seth S, Hess K, Mittendorf E, Murthy R, Damodaran S, Helgason T, Huo L, Thompson A, Barton M, Huang M, Arribas E, Lane D, Rauch G, Adrada B, Gilcrease M, Chang J, Moulder S. Impact of clinical, morphologic and molecular characteristics on response to neoadjuvant systemic therapy (NAST) in metaplastic breast cancer (MpBC). Ann Oncol 2018. [DOI: 10.1093/annonc/mdy270.223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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21
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Basho RK, Yam C, Gilcrease M, Murthy RK, Helgason T, Karp DD, Meric-Bernstam F, Hess KR, Valero V, Albarracin C, Litton JK, Chavez-MacGregor M, Hong D, Kurzrock R, Hortobagyi GN, Janku F, Moulder SL. Comparative Effectiveness of an mTOR-Based Systemic Therapy Regimen in Advanced, Metaplastic and Nonmetaplastic Triple-Negative Breast Cancer. Oncologist 2018; 23:1300-1309. [PMID: 30139837 DOI: 10.1634/theoncologist.2017-0498] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 06/25/2018] [Accepted: 07/10/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is a heterogeneous disease with subtypes having different "targetable" molecular aberrations. Metaplastic breast cancers (MpBCs) are typically TNBCs and commonly have alterations in the PI3K/Akt/mTOR pathway. We previously reported efficacy for an mTOR-based chemotherapy regimen in MpBC. To determine if tumor subtype influences prognosis, we compared treatment outcomes of patients with MpBC with those of patients with nonmetaplastic TNBC receiving an mTOR-based systemic therapy regimen. PATIENTS AND METHODS Patients with advanced MpBC and nonmetaplastic TNBC were treated at our institution from April 16, 2009, through November 4, 2014, using mTOR inhibition (temsirolimus or everolimus) with liposomal doxorubicin and bevacizumab (DAT/DAE). Median progression-free survival (PFS) and overall survival (OS) were estimated by the Kaplan-Meier method. Cox regression analyses were used to evaluate associations between tumor histology and outcomes. Multivariable models were adjusted for all covariates. RESULTS Fourteen patients with nonmetaplastic TNBC and 59 patients with advanced MpBC were treated with DAT/DAE. MpBC patients were older (p = .002) and less likely to have a history of bevacizumab use (p = .023). Median PFS for the nonmetaplastic TNBC and MpBC patients was 2.5 months and 4.8 months, respectively. This difference in PFS was statistically significant on univariable (p = .006) but not multivariable analysis (p = .087). Median OS for the nonmetaplastic TNBC and MpBC patients was 3.7 months and 10.0 months, respectively (p = .0003). MpBC remained significantly associated with improved OS on multivariable analysis (p < .0001). CONCLUSION In our study, DAT/DAE appeared to be more effective in MpBC compared with nonmetaplastic TNBC. These data support patient selection for targeted therapy in TNBC. IMPLICATIONS FOR PRACTICE Metaplastic breast cancers (MpBCs) represent <1% of all breast cancers, demonstrate mesenchymal differentiation, and are typically resistant to chemotherapy. Patients with advanced MpBC treated with an mTOR-based systemic therapy regimen had better long-term outcomes compared with patients with nonmetaplastic triple-negative breast cancer treated with the same regimen, suggesting that metaplastic histology may predict benefit from agents targeting the PI3K/Akt/mTOR pathway.
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Affiliation(s)
- Reva K Basho
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Clinton Yam
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael Gilcrease
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rashmi K Murthy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Thorunn Helgason
- Department of Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Daniel D Karp
- Department of Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kenneth R Hess
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Vicente Valero
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Constance Albarracin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jennifer K Litton
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mariana Chavez-MacGregor
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Health Services Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - David Hong
- Department of Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Razelle Kurzrock
- Department of Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Division of Hematology and Oncology, The University of California San Diego Moores Cancer Center, San Diego, California, USA
| | - Gabriel N Hortobagyi
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Filip Janku
- Department of Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Stacy L Moulder
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Yam C, Hess KR, Litton JK, Yang WT, Santiago L, Candelaria RP, Mittendorf EA, Murthy RK, Damodaran S, Helgason T, Huo L, Thompson AM, Barton M, Huang ML, Arribas EM, Lane DL, Rauch GM, Adrada BE, Gilcrease MZ, Moulder SL. Impact of metaplastic histology (MpBC) in triple-negative breast cancer (TNBC) patients (pts) receiving neoadjuvant systemic therapy (NAST). J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Clinton Yam
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kenneth R. Hess
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Wei Tse Yang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Senthil Damodaran
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Lei Huo
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Michelle Barton
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Monica L Huang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Elsa M Arribas
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Deanna L Lane
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gaiane M Rauch
- The University of Texas MD Anderson Cancer Center, Houston, TX
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Liu X, Burslem DFRP, Taylor JD, Taylor AFS, Khoo E, Majalap-Lee N, Helgason T, Johnson D. Partitioning of soil phosphorus among arbuscular and ectomycorrhizal trees in tropical and subtropical forests. Ecol Lett 2018. [DOI: 10.1111/ele.12939] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Xubing Liu
- School of Biological Sciences; University of Aberdeen; Cruickshank Building, St Machar Drive Aberdeen AB24 3UU UK
- Department of Ecology; School of Life Sciences; Sun Yat-sen University; Guangzhou 510275 China
| | - David F. R. P. Burslem
- School of Biological Sciences; University of Aberdeen; Cruickshank Building, St Machar Drive Aberdeen AB24 3UU UK
| | - Joe D. Taylor
- Department of Biology; University of York; Heslington York YO10 5DD UK
- School of Environment and Life Sciences; University of Salford; The Crescent Salford M5 4WT UK
| | - Andy F. S. Taylor
- School of Biological Sciences; University of Aberdeen; Cruickshank Building, St Machar Drive Aberdeen AB24 3UU UK
- The James Hutton Institute; Craigiebuckler, Aberdeen AB15 8QH UK
| | - Eyen Khoo
- Forest Research Centre; Sabah Forestry Department; Sandakan 90715 Malaysia
| | - Noreen Majalap-Lee
- Forest Research Centre; Sabah Forestry Department; Sandakan 90715 Malaysia
| | - Thorunn Helgason
- Department of Biology; University of York; Heslington York YO10 5DD UK
| | - David Johnson
- School of Earth and Environmental Sciences; The University of Manchester; Manchester M13 9PT UK
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Yam C, Santiago L, Candelaria RP, Adrada BE, Rauch GM, Hess KR, Litton JK, Piwnica-Worms H, Mittendorf EA, Ueno NT, Lim B, Murthy RK, Damodaran S, Helgason T, Huo L, Thompson AM, Gilcrease MZ, Symmans WF, Moulder SL, Yang W. Abstract P6-03-05: Risk of needle-track seeding with serial ultrasound guided biopsies in triple negative breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p6-03-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Image-guided percutaneous needle biopsy of the breast is a common procedure. In breast cancer patients (pts) undergoing core biopsies and surgical resection on the same day, the rate of tumor cell displacement along the needle track has been reported to be up to 50%. However, the clinical significance of this finding in triple negative breast cancer (TNBC) patients (pts) undergoing serial biopsies while receiving neoadjuvant chemotherapy (NACT) is unknown. Here we report the incidence of needle-track seeding (NTS) in a cohort of TNBC pts enrolled on a molecular triaging protocol involving serial biopsies of the index breast lesion.
Methods: We reviewed the clinical records of 144 consecutive TNBC pts enrolled on a molecular triaging protocol at MD Anderson Cancer Center. Per protocol, all pts underwent a pre-treatment research biopsy and were initiated on anthracycline based NACT (AC). Pts with inadequate response to front-line NACT were encouraged to undergo additional biopsies of the index breast lesion prior to switching therapies. Serial breast ultrasound (US) was performed to monitor therapeutic response and incidental evidence of needle-track seeding noted on US was documented.
Results: Clinicopathological characteristics of the pts are summarized in Table 1. 89% (128/144) of pts had a diagnostic breast biopsy done at another center prior to presenting at MDACC. To date, we have performed 209 US guided biopsies of index breast lesions in 144 pts. 92% (193/209) of these biopsies were done mainly for research purposes. 1.4% (2/144) of pts were found to have evidence of NTS on follow up US. The first pt had a T1N0 (1.9cm), grade 3, invasive ductal carcinoma (IDC) at diagnosis. She underwent a diagnostic biopsy followed by a research biopsy before initiating AC. She was found to have NTS as well as progression of disease (PD) on follow up US after 2 cycles of AC. The second pt had a T2N0 (3cm), grade 3 IDC at diagnosis. She underwent a diagnostic biopsy at another center, followed by a research biopsy before initiating AC. Like the first pt, she was found to have NTS and PD on follow up US after 2 cycles of AC. Both pts are currently on neoadjuvant clinical trials of novel agents.
Conclusion: The rate of NTS detected on US in TNBC pts undergoing serial biopsies of index breast lesions while receiving NACT is low and further studies are needed to determine the impact of serial biopsies on long term outcomes in TNBC.
Table 1: Patient CharacteristicsCharacteristicN=144Age - Median (years, interquartile range)55 (46-62)Tumor Size Mean (cm, standard deviation)3.4 (2.2)T1 – n(%)35 (24)T2 – n(%)89 (62)T3 – n(%)19 (13)T4 – n(%)1 (1)Clinical Nodal Status Negative – n(%)74 (51)Positive – n(%)70 (49)Grade 1 – n(%)1 (1)2 – n(%)17 (12)3 – n(%)124 (86)Unknown – n(%)2 (1)Histologic Subtype Invasive ductal carcinoma – n(%)121 (84)Invasive lobular carcinoma – n(%)2 (1)Mixed ductal and lobular carcinoma – n(%)3 (2)Metaplastic carcinoma – n(%)13 (9)Not specified – n(%)5 (3)Laterality Right – n(%)72 (50)Left – n(%)72 (50)
Citation Format: Yam C, Santiago L, Candelaria RP, Adrada BE, Rauch GM, Hess KR, Litton JK, Piwnica-Worms H, Mittendorf EA, Ueno NT, Lim B, Murthy RK, Damodaran S, Helgason T, Huo L, Thompson AM, Gilcrease MZ, Symmans WF, Moulder SL, Yang W. Risk of needle-track seeding with serial ultrasound guided biopsies in triple negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P6-03-05.
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Affiliation(s)
- C Yam
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - L Santiago
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - RP Candelaria
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - BE Adrada
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - GM Rauch
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - KR Hess
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - JK Litton
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - H Piwnica-Worms
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - EA Mittendorf
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - NT Ueno
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - B Lim
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - RK Murthy
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - S Damodaran
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - T Helgason
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - L Huo
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - AM Thompson
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - MZ Gilcrease
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - WF Symmans
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - SL Moulder
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - W Yang
- The University of Texas MD Anderson Cancer Center, Houston, TX
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Yam C, Huo L, Hess KR, Litton JK, Yang W, Piwnica-Worms H, Mittendorf EA, Ueno NT, Lim B, Murthy RK, Damodaran S, Helgason T, Thompson AM, Santiago L, Candelaria RP, Rauch GM, Adrada BE, Symmans WF, Gilcrease MZ, Moulder SL. Abstract P1-07-22: Androgen receptor positivity is associated with nodal disease in triple negative breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p1-07-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Gene expression profiling (GEP) has identified several molecularly distinct subtypes of triple negative breast cancer (TNBC). Currently, GEP-based molecular diagnostics are not routinely used in clinical decision making due to the lack of proven benefit, costs involved and long turnaround time. However, two molecularly distinct subtypes of TNBC, the luminal androgen receptor (AR) and mesenchymal subtypes, have surrogate CLIA-certified immunohistochemical (IHC) markers, AR and vimentin (VM), respectively, which have the potential for application in the clinic. Here we report the rates of AR and VM positivity and their association with clinicopathological characteristics in a cohort of TNBC pts receiving NACT.
Methods: As part of an ongoing molecular triaging protocol, 144 pts with stage I-III TNBC underwent a pretreatment biopsy for molecular characterization (MC) prior to initiating neoadjuvant chemotherapy (NACT). IHC for AR and VM were performed using commercially available antibodies. AR+ and VM+ were defined as ≥10% and ≥50% staining, respectively. Pts were randomized 2:1 to know (intervention arm, n=93) and not know (control arm, n=51) the MC results. The charts of pts randomized to the intervention arm were reviewed. Categorical variables were analyzed using Fisher's exact test. Ordinal and continuous variables were analyzed using the Wilcoxon rank-sum test and Student's t test as appropriate.
Results: 31% (29/93) and 16% (15/93) of pts were AR+ and VM+, respectively. Only 4% (4/93) of pts were both AR+ and VM+. Clinicopathological characteristics are summarized in Table 1. AR+ pts were more likely to have clinically node positive disease as compared to AR- pts (66% vs 34%, p=0.007). There were no significant differences in clinical tumor size or grade between AR+ and AR- pts. VM+ and VM- pts had similar clinicopathological characteristics.
Conclusion: Pts with AR+ TNBC were more likely to have node positive disease. The impact of AR+ on long term outcomes should be investigated in prospective studies.
Table 1: Association between patient characteristics and AR/VM status AR VM AR+ (n=29)AR- (n=64)p-valueVM+ (n=15)VM- (n=78)p-valueAge - Median (years, interquartile range)58 (48-65)52 (46-61)0.05855 (48-64)56 (47-62)0.88Clinical Tumor Size Mean (cm, standard deviation)3.5 (1.8)3.0 (1.8)0.2872.7 (1.7)3.3 (1.9)0.31T1 – n(%)5 (17)21 (33)0.2307 (47)19 (24)0.098T2 – n(%)21 (72)36 (56) 7 (47)50 (64) T3 – n(%)3 (10)7 (11) 1 (7)9 (12) Clinical Nodal Status Negative – n(%)10 (34)42 (66)0.0078 (53)44 (56)1.00Positive – n(%)19 (66)22 (34) 7 (47)34 (44) Grade 2 – n(%)6 (21)5 (8)0.0763 (20)8 (10)0.293 – n(%)23 (79)59 (92) 12 (80)70 (90)
Citation Format: Yam C, Huo L, Hess KR, Litton JK, Yang W, Piwnica-Worms H, Mittendorf EA, Ueno NT, Lim B, Murthy RK, Damodaran S, Helgason T, Thompson AM, Santiago L, Candelaria RP, Rauch GM, Adrada BE, Symmans WF, Gilcrease MZ, Moulder SL. Androgen receptor positivity is associated with nodal disease in triple negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-07-22.
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Affiliation(s)
- C Yam
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - L Huo
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - KR Hess
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - JK Litton
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - W Yang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - H Piwnica-Worms
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - EA Mittendorf
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - NT Ueno
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - B Lim
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - RK Murthy
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - S Damodaran
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - T Helgason
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - AM Thompson
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - L Santiago
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - RP Candelaria
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - GM Rauch
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - BE Adrada
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - WF Symmans
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - MZ Gilcrease
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - SL Moulder
- The University of Texas MD Anderson Cancer Center, Houston, TX
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Hibbett D, Abarenkov K, Kõljalg U, Öpik M, Chai B, Cole J, Wang Q, Crous P, Robert V, Helgason T, Herr JR, Kirk P, Lueschow S, O'Donnell K, Nilsson RH, Oono R, Schoch C, Smyth C, Walker DM, Porras-Alfaro A, Taylor JW, Geiser DM. Sequence-based classification and identification of Fungi. Mycologia 2018; 108:1049-1068. [PMID: 27760854 DOI: 10.3852/16-130] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable validPUBLICation of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.
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Affiliation(s)
- David Hibbett
- a Biology Department, Clark University, Worcester, Massachusetts 01610
| | | | | | - Maarja Öpik
- b Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu 51005, Estonia
| | | | | | - Qiong Wang
- c Department of Plant, Soil, and Microbial Sciences, Michigan State University, Plant and Soil Sciences Building, 1066 Bogue St. Room 540, East Lansing, Michigan 48824
| | | | - Vincent Robert
- d Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre (CBS-KNAW), 3508 AD, Utrecht, the Netherlands
| | - Thorunn Helgason
- e Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Joshua R Herr
- f Department of Plant Pathology and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68503
| | - Paul Kirk
- g Biodiversity Informatics and Spatial Analysis, Royal Botanic Gardens, Kew, Surrey TW9 3AF, United Kingdom
| | | | - Kerry O'Donnell
- h NCAUR ARS USDA, 1815 N. University St., Peoria, Illinois 61604
| | - R Henrik Nilsson
- i University of Gothenburg, Department of Biological and Environmental Sciences, Box 461, 405 30 Göteborg, Sweden
| | - Ryoko Oono
- j Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, California 93106
| | - Conrad Schoch
- k National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892
| | - Christopher Smyth
- l Department of Plant Pathology and Environmental Microbiology, 121 Buckhout Laboratory, Penn State University, University Park, Pennsylvania 16802
| | - Donald M Walker
- m Department of Biology, Tennessee Technological University, 1100 N. Dixie Ave., Cookeville, Tennessee 38505
| | - Andrea Porras-Alfaro
- n Department of Biological Sciences, Western Illinois University, Waggoner Hall 372, 1 University Circle Macomb, Illinois 61455
| | - John W Taylor
- o University of California, Department of Plant and Microbial Biology, 111 Koshland Hall, Berkeley, California 94720
| | - David M Geiser
- l Department of Plant Pathology and Environmental Microbiology, 121 Buckhout Laboratory, Penn State University, University Park, Pennsylvania 16802
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Redeker KR, Cai LL, Dumbrell AJ, Bardill A, Chong JP, Helgason T. Noninvasive Analysis of the Soil Microbiome: Biomonitoring Strategies Using the Volatilome, Community Analysis, and Environmental Data. ADV ECOL RES 2018. [DOI: 10.1016/bs.aecr.2018.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Litton JK, Scoggins M, Ramirez DL, Murthy RK, Whitman GJ, Hess KR, Adrada BE, Moulder SL, Barcenas CH, Valero V, Gomez JS, Mittendorf EA, Thompson A, Helgason T, Mills GB, Piwnica-Worms H, Arun BK. A feasibility study of neoadjuvant talazoparib for operable breast cancer patients with a germline BRCA mutation demonstrates marked activity. NPJ Breast Cancer 2017; 3:49. [PMID: 29238749 PMCID: PMC5719044 DOI: 10.1038/s41523-017-0052-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 11/03/2017] [Accepted: 11/20/2017] [Indexed: 02/07/2023] Open
Abstract
This study was undertaken to determine the feasibility of enrolling breast cancer patients on a single-agent-targeted therapy trial before neoadjuvant chemotherapy. Specifically, we evaluated talazoparib in patients harboring a deleterious BRCA mutation (BRCA+). Patients with a germline BRCA mutation and ≥1 cm, HER2-negative primary tumors were eligible. Study participants underwent a pretreatment biopsy, 2 months of talazoparib, off-study core biopsy, anthracycline, and taxane-based chemotherapy ± carboplatin, followed by surgery. Volumetric changes in tumor size were determined by ultrasound at 1 and 2 months of therapy. Success was defined as 20 patients accrued within 2 years and <33% experienced a grade 4 toxicity. The study was stopped early after 13 patients (BRCA1 + n = 10; BRCA2 + n = 3) were accrued within 8 months with no grade 4 toxicities and only one patient requiring dose reduction due to grade 3 neutropenia. The median age was 40 years (range 25–55) and clinical stage included I (n = 2), II (n = 9), and III (n = 2). Most tumors (n = 9) were hormone receptor-negative, and one of these was metaplastic. Decreases in tumor volume occurred in all patients following 2 months of talazoparib; the median was 88% (range 30–98%). Common toxicities were neutropenia, anemia, thrombocytopenia, nausea, dizziness, and fatigue. Single-agent-targeted therapy trials are feasible in BRCA+ patients. Given the rapid rate of accrual, profound response and favorable toxicity profile, the feasibility study was modified into a phase II study to determine pathologic complete response rates after 4–6 months of single-agent talazoparib. An investigational PARP inhibitor seems safe and possibly effective when given ahead of surgery to women with BRCA-mutated breast cancer. Jennifer Litton and colleagues from the University of Texas MD Anderson Cancer Center in Houston, USA, conducted a small feasibility study to see if patients with stage I-III breast cancer and inherited mutations in BRCA1 or BRCA2 would put off their standard course of chemotherapy ahead of surgery to first receive two months of talazoparib, an experimental inhibitor of poly ADP ribose polymerase (PARP), an enzyme involved in DNA damage repair. The trial was a resounding success. In fact, owing to rapid patient enrollment, decreases in tumor volume among all 13 participants and few signs of serious side effects, the researchers amended the study protocol to give talazoparib for longer and test for therapeutic efficacy.
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Affiliation(s)
- J K Litton
- Department of Breast Medical Oncology, Clinical Cancer Genetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - M Scoggins
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - D L Ramirez
- Department of Breast Medical Oncology, Clinical Cancer Genetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - R K Murthy
- Department of Breast Medical Oncology, Clinical Cancer Genetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - G J Whitman
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - K R Hess
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - B E Adrada
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - S L Moulder
- Department of Breast Medical Oncology, Clinical Cancer Genetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - C H Barcenas
- Department of Breast Medical Oncology, Clinical Cancer Genetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - V Valero
- Department of Breast Medical Oncology, Clinical Cancer Genetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - J Schwartz Gomez
- Department of Breast Medical Oncology, Clinical Cancer Genetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - E A Mittendorf
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - A Thompson
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - T Helgason
- Department of Breast Medical Oncology, Clinical Cancer Genetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - G B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - H Piwnica-Worms
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - B K Arun
- Department of Breast Medical Oncology, Clinical Cancer Genetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
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Randle-Boggis RJ, Ashton PD, Helgason T. Increasing flooding frequency alters soil microbial communities and functions under laboratory conditions. Microbiologyopen 2017; 7. [PMID: 29115058 PMCID: PMC5822339 DOI: 10.1002/mbo3.548] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/28/2017] [Accepted: 09/04/2017] [Indexed: 12/11/2022] Open
Abstract
The impacts of increased flooding frequency on soil microbial communities and potential functions, in line with predicted environmental changes, were investigated in a laboratory‐controlled environment. More frequent flooding events altered microbial community composition and significantly increased the resolved species alpha‐diversity (Shannon index). The Bacteria:Archaea ratio was greater at the end of the experiment than at the start, more‐so after only one flood. Significant changes in taxa and functional gene abundances were identified and quantified. These include genes related to the reduction and oxidation of substances associated with anoxia, for example, those involved in nitrogen and sulfur cycling. No significant changes were observed in the methanogenesis pathway, another function associated with anoxia and which contributes to the emission of greenhouse gases.
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Thomas JC, Helgason T, Sinclair CJ, Moir JWB. Isolation and characterization of metaldehyde-degrading bacteria from domestic soils. Microb Biotechnol 2017; 10:1824-1829. [PMID: 28707368 PMCID: PMC5658602 DOI: 10.1111/1751-7915.12719] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 11/29/2022] Open
Abstract
Metaldehyde is a common molluscicide, used to control slugs in agriculture and horticulture. It is resistant to breakdown by current water treatment processes, and its accumulation in drinking water sources leads to regular regulatory failures in drinking water quality. To address this problem, we isolated metaldehyde-degrading microbes from domestic soils. Two distinct bacterial isolates were cultured, that were able to grow prototrophically using metaldehyde as sole carbon and energy source. One isolate belonged to the genus Acinetobacter (strain designation E1) and the other isolate belonged to the genus Variovorax (strain designation E3). Acinetobacter E1 was able to degrade metaldehyde to a residual concentration < 1 nM, whereas closely related Acinetobacter strains were completely unable to degrade metaldehyde. Variovorax E3 grew and degraded metaldehyde more slowly than Acinetobacter E1, and residual metaldehyde remained at the end of growth of the Variovorax E3 strain. Biological degradation of metaldehyde using these bacterial strains or approaches that allow in situ amplification of metaldehyde-degrading bacteria may represent a way forward for dealing with metaldehyde contamination in soils and water.
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Affiliation(s)
- John C. Thomas
- Department of BiologyUniversity of YorkHeslingtonYorkYO10 5DDUK
- FERA Science Ltd (Fera)National Agri‐Food Innovation CampusSand HuttonYorkUK
| | | | - Chris J. Sinclair
- FERA Science Ltd (Fera)National Agri‐Food Innovation CampusSand HuttonYorkUK
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Pärtel M, Öpik M, Moora M, Tedersoo L, Szava-Kovats R, Rosendahl S, Rillig MC, Lekberg Y, Kreft H, Helgason T, Eriksson O, Davison J, de Bello F, Caruso T, Zobel M. Historical biome distribution and recent human disturbance shape the diversity of arbuscular mycorrhizal fungi. New Phytol 2017; 216:227-238. [PMID: 28722181 DOI: 10.1111/nph.14695] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/06/2017] [Indexed: 05/24/2023]
Abstract
The availability of global microbial diversity data, collected using standardized metabarcoding techniques, makes microorganisms promising models for investigating the role of regional and local factors in driving biodiversity. Here we modelled the global diversity of symbiotic arbuscular mycorrhizal (AM) fungi using currently available data on AM fungal molecular diversity (small subunit (SSU) ribosomal RNA (rRNA) gene sequences) in field samples. To differentiate between regional and local effects, we estimated species pools (sets of potentially suitable taxa) for each site, which are expected to reflect regional processes. We then calculated community completeness, an index showing the fraction of the species pool present, which is expected to reflect local processes. We found significant spatial variation, globally in species pool size, as well as in local and dark diversity (absent members of the species pool). Species pool size was larger close to areas containing tropical grasslands during the last glacial maximum, which are possible centres of diversification. Community completeness was greater in regions of high wilderness (remoteness from human disturbance). Local diversity was correlated with wilderness and current connectivity to mountain grasslands. Applying the species pool concept to symbiotic fungi facilitated a better understanding of how biodiversity can be jointly shaped by large-scale historical processes and recent human disturbance.
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Affiliation(s)
- Meelis Pärtel
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Mari Moora
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Leho Tedersoo
- Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - Robert Szava-Kovats
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Søren Rosendahl
- Department of Biology, Sect. Ecology & Evolution, University of Copenhagen, Universitetsparken 15, Building 3, DK-2100, Copenhagen, Denmark
| | - Matthias C Rillig
- Freie Universität Berlin, Institute of Biology, Altensteinstr. 6, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Ylva Lekberg
- MPG Ranch, 1001 S. Higgins Ave, Missoula, MT, 59801, USA
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Holger Kreft
- Department of Biodiversity, Macroecology and Biogeography, Georg-August-University Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Thorunn Helgason
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Ove Eriksson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691, Stockholm, Sweden
| | - John Davison
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Francesco de Bello
- Department of Botany, Faculty of Sciences, University of South Bohemia, Na Zlate Stoce 1, CZ-370 05, České Budějovice, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Dukelská 135, CZ-379 82, Třeboň, Czech Republic
| | - Tancredi Caruso
- School of Biological Sciences, Queen's University of Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland
| | - Martin Zobel
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
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Damodaran S, Symmans F, Helgason T, Mittendorf E, Tripathy D, Hess K, Litton J, Moulder S. A phase II trial of mirvetuximab soravtansine in patients with localized triple-negative breast cancer (TNBC) with tumors predicted insensitive to standard neoadjuvant chemotherapy (NACT) including a lead-in cohort to establish activity in patients with metastatic TNBC. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx365.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Hugosdottir R, Mørch C, Andersen O, Helgason T, Arendt-Nielsen L. Evaluating the ability of non-rectangular electrical pulse forms to preferentially activate nociceptive fibers by comparing perception thresholds. Scand J Pain 2017. [DOI: 10.1016/j.sjpain.2017.04.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Aims
Selective activation of nociceptive fibers is difficult using electrical stimulation as the activation threshold is higher than for non-nociceptive fibers. It remains unclear to what extent accommodation of non-nociceptive fibers during slowly rising electrical pulses can be utilized to reverse this activation order. The aim of this study was to evaluate the ability of different pulse forms to activate nociceptive fibers with minimal co-activation of non-nociceptive fibers by comparing subjective perception thresholds (PT).
Methods
Electrical pulses were applied on the volar forearm of 25 subjects with (1) small diameter pin electrodes providing high current density in the skin epidermis, where primarily nociceptive fibers terminate and (2) standard patch electrodes (2.63 cm2). PTs were obtained for exponential current increase, linear current increase, increasing form of exponential current decay (ED), and standard rectangular current pulses. All pulse forms were tested at two relatively long durations (5 and 50 ms). The PT ratio between patch- and pin electrode was calculated as an estimate of the ability of a pulse form to preferentially activate nociceptive fibers. The short form McGill pain questionnaire (SF-MPQ) was used to assess perceived quality of pain for all pulse forms.
Results
For the pin electrode, PT tended to decrease with increasing pulse area. Patch electrode PT tended to increase for increasing pulse area for non-rectangular 50 ms pulses, in contrast to 5 ms pulses, indicating accommodation of non-nociceptive fibers. Largest PT ratio was obtained for the 50 ms ED. SF-MPQ scores were higher for the pin- compared to the patch electrode. Pin electrode pain qualities were mainly described as stabbing and sharp. SF-MPQ scores did not differ between pulse forms.
Conclusions
Long duration ED pulses seem to activate nociceptive fibers better than regular, short duration pulses; most likely reflecting accommodation of non-nociceptive fibers.
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Affiliation(s)
- R. Hugosdottir
- Department of Health Science and Technology, SMI , Center of Neuroplasticity and Pain , Aalborg University , Aalborg , Denmark
- School of Engineering and Science , Reykjavik University , Reykjavik , Iceland
| | - C.D. Mørch
- Department of Health Science and Technology, SMI , Center of Neuroplasticity and Pain , Aalborg University , Aalborg , Denmark
- School of Engineering and Science , Reykjavik University , Reykjavik , Iceland
| | - O.K. Andersen
- Department of Health Science and Technology, SMI , Center of Neuroplasticity and Pain , Aalborg University , Aalborg , Denmark
- School of Engineering and Science , Reykjavik University , Reykjavik , Iceland
| | - T. Helgason
- Department of Health Science and Technology, SMI , Center of Neuroplasticity and Pain , Aalborg University , Aalborg , Denmark
- School of Engineering and Science , Reykjavik University , Reykjavik , Iceland
| | - L. Arendt-Nielsen
- Department of Health Science and Technology, SMI , Center of Neuroplasticity and Pain , Aalborg University , Aalborg , Denmark
- School of Engineering and Science , Reykjavik University , Reykjavik , Iceland
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Yam C, Hess KR, Litton JK, Yang WT, Piwnica-Worms H, Mittendorf EA, Ueno NT, Lim B, Murthy RK, Damodaran SK, Helgason T, Huo L, Thompson AM, Gilcrease M, Santiago L, Candelaria RP, Rauch G, Adrada B, Symmans WF, Moulder SL. A randomized, triple negative breast cancer enrolling trial to confirm molecular profiling improves survival (ARTEMIS). J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.tps590] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
TPS590 Background: Following neoadjuvant chemotherapy (NACT), patients (pts) with triple negative breast cancer (TNBC) achieving pathologic complete response/residual cancer burden-0 (pCR/RCB-0) or minimal residual disease (RCB-I) have an improved relapse free survival when compared to pts with more extensive residual disease (RCB-II/III) (Symmans et al, JCO 2017). Pts with chemo-resistant TNBC have a poor prognosis as there are currently no FDA-approved targeted agents available for TNBC. We previously reported the ability of a novel gene expression signature (GES) to predict sensitivity to NACT (Hatzis et al, JAMA 2011). Here we seek to prospectively validate the use of this GES in combination with imaging to predict response to NACT and establish the clinical impact of selecting pts predicted to have non-responsive disease (NRD) for enrollment in clinical trials of targeted therapy. Methods: All pts will undergo a biopsy of the primary tumor for molecular characterization (MC) and will be randomized 2:1 to know their MC results (intervention arm) or not (control arm). A maximum of 360 pts will be enrolled and randomized using a group sequential design with one-sided O’Brien-Fleming boundaries, with two equally spaced binding interim tests for futility and superiority and one final test, having an overall Type I error of 0.05 and power of 0.80 to detect an improvement in pCR/RCB-I from 50% to 64%. Secondary endpoints include rates of clinical trial enrollment, disease free survival and integrated biomarker analyses. All pts will receive 4 cycles of anthracycline-based NACT with imaging done every 2 cycles to assess response. After completion or progression on anthracycline-based NACT, pts predicted to have NRD based on MC/imaging (intervention arm) or imaging alone (control arm) will be offered enrollment on a clinical trial. Pts are eligible if they have stage I-III TNBC with a primary tumor that is ≥1.5cm. Pts with contraindications to anthracyclines and/or taxanes are excluded. Enrollment began in November 2015. 105 pts have been enrolled to date with 71 and 34 pts randomized to the intervention and control arms, respectively. Clinical trial information: NCT02276443.
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Affiliation(s)
- Clinton Yam
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kenneth R. Hess
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Wei Tse Yang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Naoto T. Ueno
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bora Lim
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Lei Huo
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Gaiane Rauch
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Beatriz Adrada
- The University of Texas MD Anderson Cancer Center, Houston, TX
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Litton JK, Scoggins M, Whitman GJ, Barcenas CH, Moulder SL, Murthy RK, Abouharb S, Adrada B, Helgason T, Schwartz-Gomez J, Mittendorf EA, Thompson AM, Arun B. A feasibility study of neoadjuvant talazoparib for early-stage breast cancer patients with a germline BRCA pathogenic variant: NCT02282345. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.tps595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
TPS595 Background: Poly-(adenosine diphosphate [ADP]-ribose) polymerase (PARP) is a family of enzymes responsible for DNA repair via base excision repair as well as maintenance of genetic stability. BRCA mutation carriers appear to have significant sensitivity to PARP inhibitors, not only from synthetic lethality but also potentially PARP trapping in the metastatic setting. A 2-month window study of talazoparib was reported at ESMO in 2016. In 13 patients treated, the median % tumor shrinkage by ultrasound was 88% (range 30-98%) and the study was halted early to allow for this expansion of neoadjuvant talzoparib as the only treatment prior to surgery to evaluate pathologic response. Primary Objective: Evaluate the rate of pathologic complete response (pCR)/RCB-0 + residual cancer burden (RCB)-I responses in patients with early stage breast cancer and a known BRCA pathogenic variant. Methods: 20 patients with stage I-III breast cancer and a known BRCA mutation will be accrued on this IRB-approved study. Patients will receive 4-6 months of neoadjuvant talazoparib and then proceed to surgery. Radiation, chemotherapy and endocrine therapy will be given when appropriate in teh adjuvant setting. Brief Eligibility Criteria: Patients with an identified BRCA pathogenic variant and diagnosed with a stage I-III breast cancer at least 1 cm in size are eligible. Tumors can have any ER or PR status but HER2 over-expressed cancers were excluded. Prior systemic or radiation therapy for previous breast cancer is excluded, but prior surgical treatment for contralateral DCIS is allowed. Correlative Science: Blood and biopsies prior to initiation of therapy will be collected to evaluate biomarkers of therapy efficacy as well as to initiate patient derived xenograft (PDX) models. Other studies will include: immunohistochemistry, targeted or whole exome sequencing for BRCA pathway mutations and other somatic and germline alterations; RNA sequencing; immune response; transcriptional profiles to assess TNBC subtype, reverse phase protein array (RPPA); generation of PDX models and mammosphere cultures. Clinical trial information: NCT02282345.
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Affiliation(s)
| | - Marion Scoggins
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gary J Whitman
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Carlos Hernando Barcenas
- Department of Breast Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Beatriz Adrada
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Banu Arun
- MD Anderson Cancer Center, Houston, TX
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Basho RK, Gilcrease M, Murthy RK, Helgason T, Karp DD, Meric-Bernstam F, Hess KR, Herbrich SM, Valero V, Albarracin C, Litton JK, Chavez-MacGregor M, Ibrahim NK, Murray JL, Koenig KB, Hong D, Subbiah V, Kurzrock R, Janku F, Moulder SL. Targeting the PI3K/AKT/mTOR Pathway for the Treatment of Mesenchymal Triple-Negative Breast Cancer: Evidence From a Phase 1 Trial of mTOR Inhibition in Combination With Liposomal Doxorubicin and Bevacizumab. JAMA Oncol 2017; 3:509-515. [PMID: 27893038 DOI: 10.1001/jamaoncol.2016.5281] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Triple-negative breast cancer (TNBC) classified by transcriptional profiling as the mesenchymal subtype frequently harbors aberrations in the phosphoinositide 3-kinase (PI3K) pathway, raising the possibility of targeting this pathway to enhance chemotherapy response. Up to 30% of mesenchymal TNBC can be classified histologically as metaplastic breast cancer, a chemorefractory group of tumors with a mixture of epithelial and mesenchymal components identifiable by light microscopy. While assays to identify mesenchymal TNBC are under development, metaplastic breast cancer serves as a clinically identifiable surrogate to evaluate potential regimens for mesenchymal TNBC. Objective To assess safety and efficacy of mammalian target of rapamycin (mTOR) inhibition in combination with liposomal doxorubicin and bevacizumab in patients with advanced metaplastic TNBC. Design, Setting, and Participants Phase 1 study with dose escalation and dose expansion at the University of Texas MD Anderson Cancer Center of patients with advanced metaplastic TNBC. Patients were enrolled from April 16, 2009, to November 4, 2014, and followed for outcomes with a cutoff date of November 1, 2015, for data analysis. Interventions Liposomal doxorubicin, bevacizumab, and the mTOR inhibitors temsirolimus or everolimus using 21-day cycles. Main Outcomes and Measures Safety and response. When available, archived tissue was evaluated for aberrations in the PI3K pathway. Results Fifty-two women with metaplastic TNBC (median age, 58 years; range, 37-79 years) were treated with liposomal doxorubicin, bevacizumab, and temsirolimus (DAT) (N = 39) or liposomal doxorubicin, bevacizumab, and everolimus (DAE) (N = 13). The objective response rate was 21% (complete response = 4 [8%]; partial response = 7 [13%]) and 10 (19%) patients had stable disease for at least 6 months, for a clinical benefit rate of 40%. Tissue was available for testing in 43 patients, and 32 (74%) had a PI3K pathway aberration. Presence of PI3K pathway aberration was associated with a significant improvement in objective response rate (31% vs 0%; P = .04) but not clinical benefit rate (44% vs 45%; P > .99). Conclusions and Relevance Using metaplastic TNBC as a surrogate for mesenchymal TNBC, DAT and DAE had notable activity in mesenchymal TNBC. Objective response was limited to patients with PI3K pathway aberration. A randomized trial should be performed to test DAT and DAE for metaplastic TNBC, as well as nonmetaplastic, mesenchymal TNBC, especially when PI3K pathway aberrations are identified.
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Affiliation(s)
- Reva K Basho
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Michael Gilcrease
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston
| | - Rashmi K Murthy
- Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Thorunn Helgason
- Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - Daniel D Karp
- Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - Funda Meric-Bernstam
- Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston5Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston6Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Kenneth R Hess
- Biostatistics, The University of Texas MD Anderson Cancer Center, Houston
| | | | - Vicente Valero
- Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Constance Albarracin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston
| | - Jennifer K Litton
- Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Mariana Chavez-MacGregor
- Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston9Health Services Research, The University of Texas MD Anderson Cancer Center, Houston
| | - Nuhad K Ibrahim
- Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - James L Murray
- Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Kimberly B Koenig
- Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - David Hong
- Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - Vivek Subbiah
- Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - Razelle Kurzrock
- Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston10Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, La Jolla
| | - Filip Janku
- Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - Stacy L Moulder
- Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston4Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston
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Litton JK, Moulder S, Helgason T, Clayborn AR, Rauch GM, Gilcrease M, Adrada BE, Huo L, Hess KR, Symmans WF, Thompson A, Tripathy D, Mittendorf EA. Abstract OT2-01-14: Triple-negative first-line study: Neoadjuvant trial of nab-paclitaxel and atezolizumab, a PD-L1 inhibitor, in patients with triple negative breast cancer (TNBC) (NCT02530489). Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-ot2-01-14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
BACKGROUND: TNBC has an especially poor prognosis in patients (pts) whose tumor does not respond to anthracycline and taxane-based chemotherapy. Approximately 50% will have chemo-insensitive disease (CID) resulting in extensive residual disease at the time of surgery. 40-80% of these pts will recur < 3 years. Recently developed molecular profiling techniques to identify TNBC subsets detect distinct molecular hallmarks. We designed a clinical trial to identify and characterize CID (ARTEMIS: A Randomized, TNBC Enrolling trial to confirm Molecular profiling Improves Survival). Treatment naïve pts with localized TNBC undergo a pretreatment biopsy followed by anthracycline-based chemotherapy (AC). During AC the molecular profile is determined; these results along with the response assessment (clinical exam/diagnostic imaging) will identify CID and guide the second phase of neoadjuvant chemotherapy. Tumor-infiltrating lymphocytes (TIL) have been identified as having prognostic and predictive significance in TNBC pts leading to higher pCR rates post NACT. However, the tumor microenvironment also contains regulatory T cells and myeloid-derived suppressor cells that are immunosuppressive. Programmed death ligand 1 (PD-L1) is expressed in 20% TNBC. Targeting this may lead to a more durable response as compared to chemotherapy alone.
PRIMARY OBJECTIVE: Evaluate the rate of pathologic complete response (pCR)/RCB-0 + residual cancer burden (RCB)-I responses in TNBC pts, determined to have CID after anthracycline-based chemotherapy, then treat with atezolizumab + nab-paclitaxel preoperatively.
TRIAL DESIGN AND STATISITCAL METHODS: Pts deemed to have CID on the ARTEMIS trial can enter this non-randomized phase II study. Pts without response to their initial chemotherapy cycles have a low likelihood (5%) of achieving pCR with additional cycles of chemotherapy. It would be clinically meaningful for pCR to improve to 20%. Counting pCR (RCB-0) or RCB-I as response given similar survival outcomes, a two-stage Gehan-type design will be employed with 14 pts in the first stage. If at least one pt responds, 23 more will be added. This design has a 49% chance of terminating after the first stage if the true response rate is 0.05, 23% chance if the true rate is 0.10, 10% if the true rate is 0.15 and 4% if the true rate is 0.20. If accrual continues to the second stage, the 95% confidence interval for a 0.20 response rate will extend from 0.10 to 0.35.
BRIEF ELIGIBILITY CRITERIA: Inclusion: localized TNBC enrolled onto ARTEMIS and determined to have CID at the time of response assessment after anthracycline chemotherapy, adequate organ, bone marrow and cardiac parameters. Exclusion: prior immunotherapy, IBC, history of autoimmune disease, HIV, Hep-B, Hep-C, active tuberculosis, pregnant.
CORRELATIVE SCIENCE: Evaluate the presence and phenotype of TIL and other immune cell populations in tumor tissue pre/post treatment; determine changes in expression of co-stimulatory and co-inhibitory molecules on tumor cells and immune cells in the microenvironment; evaluate the immune repertoire and cytokine responses in serially collected peripheral blood mononuclear cells and serum respectively.
Citation Format: Litton JK, Moulder S, Helgason T, Clayborn AR, Rauch GM, Gilcrease M, Adrada BE, Huo L, Hess KR, Symmans WF, Thompson A, Tripathy D, Mittendorf EA. Triple-negative first-line study: Neoadjuvant trial of nab-paclitaxel and atezolizumab, a PD-L1 inhibitor, in patients with triple negative breast cancer (TNBC) (NCT02530489) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT2-01-14.
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Affiliation(s)
- JK Litton
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - S Moulder
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - T Helgason
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - AR Clayborn
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - GM Rauch
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - M Gilcrease
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - BE Adrada
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - L Huo
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - KR Hess
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - WF Symmans
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - A Thompson
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - D Tripathy
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - EA Mittendorf
- The University of Texas MD Anderson Cancer Center, Houston, TX
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Fujii T, Lim B, Helgason T, Hess KR, Gilcrease MZ, Willey JS, Tripathy D, Litton JK, Moulder S, Krishnamurthy S, Yang W, Reuben JM, Symmans WF, Ueno NT. Abstract OT3-02-05: NCI-2016-00367: A phase IIB study of neoadjuvant ZT regimen (enzalutamide therapy in combination with weekly paclitaxel) for androgen receptor (AR)-positive triple-negative breast cancer (TNBC). Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-ot3-02-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
BACKGROUND: Approximately 50% of TNBC expresses AR by immunohistochemical (IHC) staining. Luminal androgen receptor (LAR) subtype is heavily enriched in hormonally regulated genes, yet negative for ER by IHC. LAR is associated with low pCR rates and long survival. Preclinical data have shown that taxanes inhibit translocation of AR from the cytoplasm to the nucleus where AR is activated. Combining paclitaxel with enzalutamide may inhibit the AR pathway synergistically thereby increasing pCR rates. We hypothesized that patients with AR-positive TNBC who have chemo-insensitive disease (CID) after initial anthracycline-based chemotherapy treated with ZT would have higher RCB-0 and RCB-I rates than those who receive conventional taxane-based chemotherapy. Our team developed a clinical trial to identify patients with CID (ARTEMIS: A Randomized, TNBC Enrolling trial to confirm Molecular profiling Improves Survival). In the ARTEMIS trial, treatment-naïve patients with localized TNBC undergo a pretreatment biopsy and then begin anthracycline-based chemotherapy. Molecular testing results and radiographic response assessment are used to identify CID and will guide the second phase of neoadjuvant chemotherapy (NACT) to overcome CID.
PRIMARY OBJECTIVE: To determine RCB-0 and RCB-I rates of patients with TNBC who have CID to initial anthracycline-based chemotherapy and who received ZT.
TRIAL DESIGN AND STATISTICAL METHODS: Patients with CID from the ARTEMIS trial can enroll in the 12-week ZT (paclitaxel, 80 mg/m2 intravenously per week; enzalutamide, 160 mg orally per day). We will define pCR (RCB-0) or RCB-I as a response, using a Simon optimal 2-stage design with alpha=beta=10% and then setting the threshold for an acceptable pCR or RCB-I rate at 20%. We will enroll 12 patients into the first stage. If no patients experience pCR or RCB-I, we will stop the study after the first stage. If at least 1 patient experiences pCR or RCB-I, we will enroll 25 more patients for a total of 37 patients. We would declare the treatment worthy of further study if at least 4 of the 37 patients experience pCR or RCB-I. This design has a 54% probability of early termination after the first stage if the true pCR or RCB-I probability is 5%. Because patients with CID have a very low chance (5%) of achieving pCR with additional chemotherapy, improving pCR rates to 20% in this patient population would be clinically meaningful.
BRIEF ELIGIBILITY CRITERIA: Inclusion criteria: Primary invasive TNBC patients who have CID under the ARTEMIS trial; AR+ ≥1% nuclear staining by IHC; and adequate physical, organ, bone marrow, and cardiac functions. Exclusion criteria: Pregnant or lactating patients, history of colitis or absorption abnormality, known or suspected brain metastasis or leptomeningeal disease, or history of seizure.
CORRELATIVE SCIENCE: Enumeration of circulating tumor cells (CTCs) and expression of CTC-related gene transcripts will be measured to correlate CTC characteristics and/or gene profiles related to the AR pathway and treatment response to ZT.
Citation Format: Fujii T, Lim B, Helgason T, Hess KR, Gilcrease MZ, Willey JS, Tripathy D, Litton JK, Moulder S, Krishnamurthy S, Yang W, Reuben JM, Symmans WF, Ueno NT. NCI-2016-00367: A phase IIB study of neoadjuvant ZT regimen (enzalutamide therapy in combination with weekly paclitaxel) for androgen receptor (AR)-positive triple-negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT3-02-05.
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Affiliation(s)
- T Fujii
- The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center
| | - B Lim
- The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center
| | - T Helgason
- The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center
| | - KR Hess
- The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center
| | - MZ Gilcrease
- The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center
| | - JS Willey
- The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center
| | - D Tripathy
- The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center
| | - JK Litton
- The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center
| | - S Moulder
- The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center
| | - S Krishnamurthy
- The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center
| | - W Yang
- The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center
| | - JM Reuben
- The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center
| | - WF Symmans
- The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center
| | - NT Ueno
- The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center
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Lim B, Helgason T, Hess KR, Piwnica-Worms H, Yang W, Adrada BE, Rauch GM, Gilcrease M, Symmans FW, Huo L, Mittendorf EA, Thompson A, Stacy MTL, Debu T, Ueno NT. Abstract OT2-01-20: Phase IIB study of neoadjuvant panitumumab combined with carboplatin and paclitaxel (PaCT) for anthracycline-resistant triple-negative breast cancer (TNBC). Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-ot2-01-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
BACKGROUND: Approximately 50% of patients with TNBC treatedwithstandardtaxane/anthracycline-based neoadjuvant chemotherapy (NACT)have chemo-insensitive disease (CID), i.e., residual disease burden (RCB)-II/III at the time of surgery, and 40-80% of patients develop recurrence within 3 years. Recent developments in molecular profiling have identified subsets of TNBC with distinct, targetable molecular features. We developed a clinical trial to identify and characterize CID (ARTEMIS: A Randomized, TNBC-Enrolling trial to confirm Molecular profiling Improves Survival). In ARTEMIS, patients with localized TNBC will undergo a pretreatment biopsy, then begin anthracycline-based NACT. During NACT, we use molecular profiling and response assessment to identify CID and allocate patients to alternative therapies to overcome CID. Epidermal growth factor receptor (EGFR) is overexpressed in 25-30% of TNBC. In preclinical studies, suppression of EGFR signaling has shown efficacy in controlling cancers through suppression of the stem cell population, enhanced apoptosis via MAPK/PI3K signaling, and modulation of epithelial-mesenchymal transition (EMT). Moreover, in a phase II trial of triple negative inflammatory breast cancer, neoadjuvant PaCT yielded significantly higher pathologic complete response (pCR) rates than historic control. Taken together, we hypothesize that using PaCT to suppress EGFR in TNBC will enhance the pCR rate.
OBJECTIVES: Primary objective: determine pCR and RCB-0/I rates in TNBC patients with CID given PaCT. Secondary objective: determine the benefit of using baseline genomic signatures to develop an alternative second phase of NACT.
TRIAL DESIGN AND STATISTICAL METHODS: Patients with >10% volume reduction for non-CID or <80% for CID will enroll in a biomarker-guided, experimental, nonrandomized phase II study and be given PaCT (panitumumab 2.5 mg/kg, carboplatin AUC 5, paclitaxel 80 mg/m2). Because pCR rates in pts with CID with additional cycles of taxane-based therapy are low (∼5%), a 20% response rate (RCB-0 or RCB-I) will be considered clinically meaningful. A two-stage Gehan-type design will be employed. If at least 1 of 14 patients responds, 23 more patients will be added, for a total of 37 patients. This design has a 49% chance of terminating after the first stage if the true response rate is 0.05, 23% if the rate is 0.10, 10% if the rate is 0.15, and 4% if the rate is 0.20. If accrual continues to the second stage and 37 patients are enrolled, the 95% confidence interval for a 0.20 response rate will be 0.10 to 0.35.
BRIEF ELIGIBILITY CRITERIA: Inclusion: localized TNBC; enrolled in ARTEMIS trial; adequate organ, bone marrow, and cardiac parameters; Exclusion: pregnant or lactating, known or suspected metastasis.
CORRELATIVE SCIENCE: Circulating tumor cells (CTCs) and cell free (cf) DNA in baseline and subsequent blood samples, EGFR expression (immunohistochemistry), stem cell/EMT/apoptosis marker changes in tissue and CTCs, PD-L1 glycosylation for EGFR sensitivity.
Citation Format: Lim B, Helgason T, Hess KR, Piwnica-Worms H, Yang W, Adrada BE, Rauch GM, Gilcrease M, Symmans FW, Huo L, Mittendorf EA, Thompson A, Stacy M-TL, Debu T, Ueno NT. Phase IIB study of neoadjuvant panitumumab combined with carboplatin and paclitaxel (PaCT) for anthracycline-resistant triple-negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT2-01-20.
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Affiliation(s)
- B Lim
- The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - T Helgason
- The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - KR Hess
- The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - H Piwnica-Worms
- The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - W Yang
- The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - BE Adrada
- The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - GM Rauch
- The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - M Gilcrease
- The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - FW Symmans
- The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - L Huo
- The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - EA Mittendorf
- The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - A Thompson
- The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - M-TL Stacy
- The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - T Debu
- The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - NT Ueno
- The University of Texas, MD Anderson Cancer Center, Houston, TX
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Toet S, Oliver V, Ineson P, McLoughlin S, Helgason T, Peacock S, Stott AW, Barnes J, Ashmore M. How does elevated ozone reduce methane emissions from peatlands? Sci Total Environ 2017; 579:60-71. [PMID: 27866746 DOI: 10.1016/j.scitotenv.2016.10.188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 10/23/2016] [Accepted: 10/25/2016] [Indexed: 06/06/2023]
Abstract
The effects of increased tropospheric ozone (O3) pollution levels on methane (CH4) emissions from peatlands, and their underlying mechanisms, remain unclear. In this study, we exposed peatland mesocosms from a temperate wet heath dominated by the sedge Schoenus nigricans and Sphagnum papillosum to four O3 treatments in open-top chambers for 2.5years, to investigate the O3 impacts on CH4 emissions and the processes that underpin these responses. Summer CH4 emissions, were significantly reduced, by 27% over the experiment, due to summer daytime (8hday-1) O3 exposure to non-filtered air (NFA) plus 35ppb O3, but were not significantly affected by year-round, 24hday-1, exposure to NFA plus 10ppb or NFA plus 25ppb O3. There was no evidence that the reduced CH4 emissions in response to elevated summer O3 exposure were caused by reduced plant-derived carbon availability below-ground, because we found no significant effect of high summer O3 exposure on root biomass, pore water dissolved organic carbon concentrations or the contribution of recent photosynthate to CH4 emissions. Our CH4 production potential and CH4 oxidation potential measurements in the different O3 treatments could also not explain the observed CH4 emission responses to O3. However, pore water ammonium concentrations at 20cm depth were consistently reduced during the experiment by elevated summer O3 exposure, and strong positive correlations were observed between CH4 emission and pore water ammonium concentration at three peat depths over the 2.5-year study. Our results therefore imply that elevated regional O3 exposures in summer, but not the small increases in northern hemisphere annual mean background O3 concentrations predicted over this century, may lead to reduced CH4 emissions from temperate peatlands as a consequence of reductions in soil inorganic nitrogen affecting methanogenic and/or methanotrophic activity.
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Affiliation(s)
- Sylvia Toet
- Environment Department, University of York, York YO10 5NG, UK.
| | - Viktoria Oliver
- Environment Department, University of York, York YO10 5NG, UK
| | - Phil Ineson
- Department of Biology, University of York, York YO10 5DD, UK
| | | | | | - Simon Peacock
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Andrew W Stott
- Natural Environment Research Council Life Sciences Mass Spectrometry Facility, Centre for Ecology and Hydrology, Lancaster LA1 4AP, UK
| | - Jeremy Barnes
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Mike Ashmore
- Stockholm Environment Institute, University of York, York YO10 5NG, UK
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Janku F, Murthy R, Wang-Gillam A, Shepard D, Helgason T, Henry T, Rudin C, Huang S, Sakamuri D, Solomon S, Collins A, Kreider B, Miller M, Saha S, Tung D, Varterasian M, Zhang L, Zhang H, Gounder M. Phase I clinical study of intratumoral injection of oncolytic Clostridium novyi-NT spores in patients with advanced cancers. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)32878-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Jain RK, Hong DS, Naing A, Wheler J, Helgason T, Shi NY, Gad Y, Kurzrock R. Novel phase I study combining G1 phase, S phase, and G2/M phase cell cycle inhibitors in patients with advanced malignancies. Cell Cycle 2016; 14:3434-40. [PMID: 26467427 DOI: 10.1080/15384101.2015.1090065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
PURPOSE Cancer is a manifestation of aberrant cellular proliferation, and the cell cycle is one of the most successfully drugged targets in oncology. No prior study has been reported that simultaneously targets the 3 principal cell cycle phases populated by proliferating cells--G1, S, and G2/M. METHODS Temsirolimus (G1 inhibitor), topotecan (S inhibitor), and bortezomib (G2/M inhibitor) were administered in combination to patients with advanced malignancies using a 3+3 dose escalation schedule to assess the safety and establish the maximum tolerated dose (primary endpoints) of this cell cycle targeting approach. An in silico pharmacodynamic model using established effects of each of these agents on the cell cycle was used to validate the regimen and to guide the dosing regimen. RESULTS Sixty-two subjects were enrolled. The most common adverse events and dose-limiting toxicities were cytopenias, consistent with the cell cycle targeting approach employed. All cytopenias resolved to baseline values upon holding study drug administration. The maximum tolerated dose was temsirolimus 15 mg/kg IV D1, 8, 15; topotecan 2.8 mg/m(2) IV D1, 8; and bortezomib 0.6 mg/m2 IV D1, 4, 8, 11 [DOSAGE ERROR CORRECTED] of a 21-day cycle. In silico modeling suggests the regimen induces cell population shifts from G2/M and S phases to G1 phase and the quiescent G0 phase. Eighteen percent of subjects (11/62) achieved partial response (n = 2, serous ovarian and papillary thyroid) or stable disease for > 6 months (n = 9). CONCLUSION Combining drugs with inhibitory activity of G1 phase, S phase, and G2/M phase is safe and warrants further evaluation.
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Affiliation(s)
- Rajul K Jain
- a Department of Investigational Cancer Therapeutics (Phase I Program) ; MD Anderson Cancer Center ; Houston , TX USA
| | - David S Hong
- a Department of Investigational Cancer Therapeutics (Phase I Program) ; MD Anderson Cancer Center ; Houston , TX USA
| | - Aung Naing
- a Department of Investigational Cancer Therapeutics (Phase I Program) ; MD Anderson Cancer Center ; Houston , TX USA
| | - Jennifer Wheler
- a Department of Investigational Cancer Therapeutics (Phase I Program) ; MD Anderson Cancer Center ; Houston , TX USA
| | - Thorunn Helgason
- a Department of Investigational Cancer Therapeutics (Phase I Program) ; MD Anderson Cancer Center ; Houston , TX USA
| | - Nai-Yi Shi
- a Department of Investigational Cancer Therapeutics (Phase I Program) ; MD Anderson Cancer Center ; Houston , TX USA
| | | | - Razelle Kurzrock
- c Moores Cancer Center; University of California San Diego ; La Jolla , CA USA
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Basho RK, Gilcrease M, Murthy RK, Helgason T, Booser DJ, Karp DD, Meric-Bernstam F, Hess KR, Herbrich SM, Valero V, Albarracin C, Litton J, Chavez-MacGregor M, Ibrahim NK, Murray JL, Koenig KB, Hong D, Subbiah V, Kurzrock R, Janku F, Moulder S. Abstract 2273: Targeting the PI3K/AKT/mTOR pathway for the treatment of metaplastic breast cancer: Does location of PIK3CA mutation or histology affect response. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Metaplastic breast cancers (MpBCs) are a chemo-refractory group of tumors that contain a component of squamous and/or mesenchymal differentiation identifiable by light microscopy. MpBCs contain a high frequency of aberrations in the PI3K/AKT/mTOR pathway, making this pathway a potential target for therapy.
Methods: Patients with advanced MpBC (N = 52) were treated with liposomal doxorubicin (D), bevacizumab (A) and the mTOR inhibitors temsirolimus (T) or everolimus (E). D and A were administered IV on day 1 with T (IV on days 1, 8 and 15) or E (continuous daily oral administration) using 21 day cycles. All tumors were evaluated to assess histology of metaplasia (spindle, mixed spindle vs non-spindle cell). Response was assessed every 6 weeks using RECIST. When available, archived tissue was evaluated for aberrations in the PI3K pathway using standard assays.
Results: Fifty-two MpBC patients were treated with DAT (N = 39) or DAE (N = 13). Median age was 58 (range 37-79); median number of prior regimens for metastatic disease was 1 (range 0-5). The objective response rate (ORR) was 21% [complete response (CR) = 4 (8%); partial response (PR) = 7 (13%)] and 10 (19%) pts had stable disease (SD)≥6 months for a clinical benefit rate (CBR) of 40%. Tissue was available in 43 pts and 32 (74%) had a PI3K pathway activating aberrations. PI3K pathway aberration was associated with a significant improvement in ORR (31 vs 0%; P = 0.04) but not CBR (44 vs 45%; P = 1.00) or progression-free survival (median 5 vs 3 months; P = 0.35). The most frequent PI3K pathway aberration was mutation in PIK3CA, occurring in 19 patients. Outcomes were similar if mutations of PIK3CA were located in the helical or kinase domain (ORR 25% vs 27%; P = 1.00 and CBR 38% vs 47%; P = 1.00, respectively). Spindle cell was the most frequent metaplastic histology seen, occurring in 18 tumors and mixed with other metaplastic histologies including squamous, chondroid and osseous in 14 additional tumors, while 20 tumors had non-spindle cell morphologies. The incidence of PI3K pathway aberration was similar across histologies (61% in spindle vs 67% in mixed spindle vs 60% in non-spindle cell). Tumors with mixed histology had lower ORR, CBR and PFS, but this was not statistically significant, likely due to small numbers in each cohort: ORR 22% in spindle vs 7% in mixed spindle vs 30% in non-spindle cell, P = 0.27; CBR 50% in spindle vs 21% in mixed spindle vs 40% in non-spindle cell, P = 0.25; and PFS median 4 months in spindle vs 2 months in mixed spindle vs 5 months in non-spindle cell, P = 0.68.
Conclusions: Response to mTOR inhibition is enhanced in MpBCs with PI3K pathway aberrations. However, specific aberrations in PIK3CA do not lead to differential response to mTOR inhibition. PI3K pathway aberrations and response to mTOR inhibition are seen across all histologies of MpBC, and the response is not enhanced in particular histologies.
Citation Format: Reva K. Basho, Michael Gilcrease, Rashmi K. Murthy, Thorunn Helgason, Daniel J. Booser, Daniel D. Karp, Funda Meric-Bernstam, Kenneth R. Hess, Shelley M. Herbrich, Vicente Valero, Constance Albarracin, Jennifer Litton, Mariana Chavez-MacGregor, Nuhad K. Ibrahim, James L. Murray, Kimberly B. Koenig, David Hong, Vivek Subbiah, Razelle Kurzrock, Filip Janku, Stacy Moulder. Targeting the PI3K/AKT/mTOR pathway for the treatment of metaplastic breast cancer: Does location of PIK3CA mutation or histology affect response. [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 2273.
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Affiliation(s)
- Reva K. Basho
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Daniel D. Karp
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Kenneth R. Hess
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Vicente Valero
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Jennifer Litton
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - James L. Murray
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - David Hong
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vivek Subbiah
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Razelle Kurzrock
- 2University of California San Diego Moores Cancer Center, San Diego, CA
| | - Filip Janku
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Stacy Moulder
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
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Randle-Boggis RJ, Helgason T, Sapp M, Ashton PD. Evaluating techniques for metagenome annotation using simulated sequence data. FEMS Microbiol Ecol 2016; 92:fiw095. [PMID: 27162180 PMCID: PMC4892715 DOI: 10.1093/femsec/fiw095] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2016] [Indexed: 11/29/2022] Open
Abstract
The advent of next-generation sequencing has allowed huge amounts of DNA sequence data to be produced, advancing the capabilities of microbial ecosystem studies. The current challenge is to identify from which microorganisms and genes the DNA originated. Several tools and databases are available for annotating DNA sequences. The tools, databases and parameters used can have a significant impact on the results: naïve choice of these factors can result in a false representation of community composition and function. We use a simulated metagenome to show how different parameters affect annotation accuracy by evaluating the sequence annotation performances of MEGAN, MG-RAST, One Codex and Megablast. This simulated metagenome allowed the recovery of known organism and function abundances to be quantitatively evaluated, which is not possible for environmental metagenomes. The performance of each program and database varied, e.g. One Codex correctly annotated many sequences at the genus level, whereas MG-RAST RefSeq produced many false positive annotations. This effect decreased as the taxonomic level investigated increased. Selecting more stringent parameters decreases the annotation sensitivity, but increases precision. Ultimately, there is a trade-off between taxonomic resolution and annotation accuracy. These results should be considered when annotating metagenomes and interpreting results from previous studies. The sequence annotation accuracies of metagenomic analysis tools were evaluated using a simulated metagenome.
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Affiliation(s)
| | | | - Melanie Sapp
- Fera Science Ltd, Sand Hutton, York YO41 1LZ, UK
| | - Peter D Ashton
- Department of Biology, University of York, York YO10 5DD, UK
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Basho RK, Gilcrease M, Murthy RK, Helgason T, Booser DJ, Karp DD, Meric-Bernstam F, Wheler JJ, Valero V, Albarracin C, Litton J, Chavez-MacGregor M, Ibrahim NK, Murray JL, Koenig KB, Hong D, Subbiah V, Kurzrock R, Janku F, Moulder S. Abstract P3-14-02: Targeting the PI3K/AKT/mTOR pathway for the treatment of mesenchymal triple-negative breast cancer (TNBC): Evidence of efficacy and proof of concept from a phase I trial with dose expansion of mTOR inhibition in combination with liposomal doxorubicin and bevacizumab. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p3-14-02] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Approximately 30% of TNBCs are characterized by microarray as claudin-low, mesenchymal or mesenchymal stem cell-like and, unlike basal TNBCs, these tumors frequently harbor aberrations in the PI3K/AKT/mTOR axis, raising the possibility of targeting this axis to enhance chemotherapy response. Assays to clinically identify mesenchymal TNBCs are under development, but published results confirm that up to 30% are metaplastic breast cancers (MpBCs), a chemo-refractory group of tumors that contain a mixture of epithelial and mesenchymal components, making them identifiable by microscopy. As such, MpBCs serve as surrogates of response for potential regimens to treat mesenchymal TNBC.
Methods: Patients (pts) with advanced TNBC (N=64) were treated with liposomal doxorubicin (D), bevacizumab (A) and the mTOR inhibitors temsirolimus (T) or everolimus (E). D and A were administered IV on day 1 with T (IV on days 1, 8 and 15) or E (continuous daily oral administration) using 21 day cycles. Response was assessed every 6 weeks using RECIST. When available, archived tissue was evaluated for aberrations in the PI3K pathway using standard assays.
Results: Fifty-two MpBC pts were treated with DAT (N=39) or DAE (N=13). Median age was 58 (range 37-79); median # of prior regimens for metastatic disease was 1 (range 0-5). The objective response rate (ORR) was 21% [complete response (CR)=4 (8%); partial response (PR)=7 (13%)] and 10 (19%) pts had stable disease (SD)≥6 months for a clinical benefit rate (CBR) of 40%. Tissue was available for testing in 43 pts and 32 (74%) had a PI3K pathway activating aberration (Table 1).
Response According to PI3K Pathway AberrationPI3K Pathway AberrationN (%)CRPRSD≥6monthsCBRORRAny PI3K Pathway Aberration*32 (74)46444%31%PIK3CA Mutation19 (59)23447%26%p.H1047R12 (38)21350%25%p.E545K6 (19)02150%33%p.G1007R1 (3)010100%100%p.E545A1 (3)0000%0%p.H1047Y1 (3)0000%0%p.K111E1 (3)0000%0%p.E542K1 (3)0000%0%PIK3CA Amplification1 (3)010100%100%PTEN Mutation5 (16)0000%0%PTEN Loss5 (16)02040%40%AKT1 p.E17K Mutation2 (6)0000%0%AKT2 Amplification1 (3)100100%100%PIK3R1 Mutation2 (6)01050%50%NF2 Mutation1 (3)100100%100%No PI3K Pathway Aberration11 (26)00545%0%*Some tumors had >1 aberration detected
PI3K pathway activation was associated with a significant improvement in ORR (31 vs 0%; P=0.043) but not CBR (44 vs 45%; P=1.000) or progression-free survival (median 5.1 vs 2.9 months; P=0.352). A pt with 5 year+ durable CR (on maintenance everolimus) had a mutation in NF2. To emphasize the importance of pt selection, it is notable that 12 pts with non-metaplastic TNBC were also treated with DAT, and only 1 pt had a response (CR/PR=1; SD≥6 months=0), for a CBR that was significantly worse than pts with MpBC (8 vs 40%; P=0.045).
Conclusions: Using MpBC as a surrogate of response, DAT/DAE has significantly better activity in mesenchymal compared to non-selected TNBC. Response is enhanced in pts with PI3K pathway activation. DAT/DAE should be tested in non-metaplastic, mesenchymal TNBC once a diagnostic assay is available.
Citation Format: Basho RK, Gilcrease M, Murthy RK, Helgason T, Booser DJ, Karp DD, Meric-Bernstam F, Wheler JJ, Valero V, Albarracin C, Litton J, Chavez-MacGregor M, Ibrahim NK, Murray JL, Koenig KB, Hong D, Subbiah V, Kurzrock R, Janku F, Moulder S. Targeting the PI3K/AKT/mTOR pathway for the treatment of mesenchymal triple-negative breast cancer (TNBC): Evidence of efficacy and proof of concept from a phase I trial with dose expansion of mTOR inhibition in combination with liposomal doxorubicin and bevacizumab. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-14-02.
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Affiliation(s)
- RK Basho
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - M Gilcrease
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - RK Murthy
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - T Helgason
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - DJ Booser
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - DD Karp
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - F Meric-Bernstam
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - JJ Wheler
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - V Valero
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - C Albarracin
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - J Litton
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - M Chavez-MacGregor
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - NK Ibrahim
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - JL Murray
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - KB Koenig
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - D Hong
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - V Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - R Kurzrock
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - F Janku
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
| | - S Moulder
- The University of Texas MD Anderson Cancer Center, Houston, TX; UC San Diego Moores Cancer Center, La Jolla, CA
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Gudfinnsdottir H, Helgason T. Evaluation of CT capability for the detection of thin bone structures. Current Directions in Biomedical Engineering 2015. [DOI: 10.1515/cdbme-2015-0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Evaluation of CT capability for the detection of thin bone structures by means of modeling small bone structures and comparing with quantitative measurements. Knowledge of how thin bone structures can be or of what low density to be detectable in clinical CT images can increase the diagnostic competence to diagnose various diseases. Correlation between size and density of detectable bone structures is the key for many diagnosis purposes. This paper describes the use of clinical 64 detector scanner to image the skeletons of codfish and salmon species. Fish skeletons, such as codfish and salmon, have petite structures and lower bone density than humans. Bone structures were segmented out of the image data and 3D models of their skeletons developed. Evaluation was done by means of comparing quantitative measurements of selected bones to parameters observed from the model. Results show the limits where thin bones and of low density disappear from the clinical CT. It shows ability to reconstruct closely the diameter of the codfish bones but to a less extent the small bones of the salmon.
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Affiliation(s)
| | - T. Helgason
- Reykjavik University, Menntavegur 1, 101 Reykjavik, Iceland and Landspitali-University Hospital, Menntavegur 1, 101 Reykjavik, Iceland
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48
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Basho R, Janku F, Helgason T, Gilcrease M, Booser D, Karp D, Meric-Bernstam F, Wheler J, Valero V, Albarracin C, Litton J, Chavez-MacGregor M, Ibrahim N, Murray J, Koenig K, Hong D, Subbiah V, Kurzrock R, Moulder S. 1871 Inhibition of mTOR in combination with chemotherapy and angiogenic blockade shows activity in metaplastic breast cancer, an aggressive, chemo-refractory subtype of triple-negative breast cancer (TNBC). Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)30821-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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49
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Hart MM, Aleklett K, Chagnon PL, Egan C, Ghignone S, Helgason T, Lekberg Y, Öpik M, Pickles BJ, Waller L. Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi. New Phytol 2015; 207:235-247. [PMID: 25737096 DOI: 10.1111/nph.13340] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 01/18/2015] [Indexed: 05/02/2023]
Abstract
Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities.
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Affiliation(s)
- Miranda M Hart
- Biology University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Kristin Aleklett
- Biology University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Pierre-Luc Chagnon
- Département de Biologie, Université de Sherbrooke, 2500 Boulevard de l'université, Sherbrooke, QC, Canada
| | - Cameron Egan
- Biology University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Stefano Ghignone
- Istituto per la Protezione Sostenibile delle Piante (UOS Torino), C.N.R., Torino, Italy
| | - Thorunn Helgason
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Ylva Lekberg
- MPG Ranch and Department for Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, USA
| | - Maarja Öpik
- Department of Botany, University of Tartu, 40 Lai St, 51005, Tartu, Estonia
| | - Brian J Pickles
- Biology University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Lauren Waller
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
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50
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Moulder S, Helgason T, Janku F, Wheler J, Moroney J, Booser D, Albarracin C, Morrow PK, Atkins J, Koenig K, Gilcrease M, Kurzrock R. Inhibition of the phosphoinositide 3-kinase pathway for the treatment of patients with metastatic metaplastic breast cancer. Ann Oncol 2015; 26:1346-52. [PMID: 25878190 DOI: 10.1093/annonc/mdv163] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 03/16/2015] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Mesenchymal/metaplastic breast cancers (MpBCs) are often triple-negative (TNBC), and chemo-refractory, and can harbor phosphoinositide 3-kinase (PI3kinase) alterations; thus, therapy with mTor inhibitors may demonstrate activity. PATIENTS AND METHODS Patients with mesenchymal/MpBC treated with temsirolimus-based regimens were evaluated. Mutational analyses [polymerase chain reaction (PCR)-based DNA sequencing method, mass spectrometric detection (Sequenom MassARRAY), or next-generation sequencing] as well as loss of phosphatase and tensin homolog (PTEN) (immunohistochemistry) were performed (archived tissue when available). RESULTS Twenty-three patients (one of whom was on two separate trials) were treated using temsirolimus-containing regimens: temsirolimus alone (n = 1 patient) or combined with the following: liposomal doxorubicin and bevacizumab (DAT, n = 18); liposomal doxorubicin (DT, n = 1); paclitaxel and bevacizumab (TAT, n = 2); paclitaxel (TT, n = 1); carboplatin and bevacizumab (CAT, n = 1). Response rate [complete response (CR) + partial response (PR)] was 25% across all regimens; 32% in the anthracycline-based regimens [DAT and DT (CR = 2, PR = 4; N = 19)]. An additional two patients achieved stable disease (SD) ≥6 months [total SD ≥6 months/CR/PR = 8 (33%)]. Molecular aberrations in the PI3K pathway were common: PIK3CA mutation = 6/15 (40%), PTEN mutation = 3/11 (27%), and PTEN loss = 2/11 (18%). A point mutation in the NF2 gene (K159fs*16; NF2 alterations can activate mTor) was found in one patient who attained CR (3+ years). Of the eight patients who achieved SD ≥6 months/CR/PR, all 4 patients with available tissue had a molecular aberration that activate the PIK3CA/Akt/mTOR axis: PIK3CA mutation = 2; PTEN loss = 1; NF2 aberration = 1. CONCLUSIONS DAT has activity in MpBCs including complete CRs. Molecular aberrations that can activate the PI3 K/Akt/mTOR axis are common in MpBC.
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Affiliation(s)
- S Moulder
- Department of Investigational Cancer Therapeutics (Phase I), The University of Texas, M.D. Anderson Cancer Center, Houston Department of Breast Medical Oncology, The University of Texas, M.D. Anderson Cancer Center, Houston
| | - T Helgason
- Department of Investigational Cancer Therapeutics (Phase I), The University of Texas, M.D. Anderson Cancer Center, Houston
| | - F Janku
- Department of Investigational Cancer Therapeutics (Phase I), The University of Texas, M.D. Anderson Cancer Center, Houston
| | - J Wheler
- Department of Investigational Cancer Therapeutics (Phase I), The University of Texas, M.D. Anderson Cancer Center, Houston
| | - J Moroney
- Department of Investigational Cancer Therapeutics (Phase I), The University of Texas, M.D. Anderson Cancer Center, Houston
| | - D Booser
- Department of Breast Medical Oncology, The University of Texas, M.D. Anderson Cancer Center, Houston
| | - C Albarracin
- Department of Pathology, The University of Texas, M.D. Anderson Cancer Center, Houston
| | - P K Morrow
- Department of Breast Medical Oncology, The University of Texas, M.D. Anderson Cancer Center, Houston
| | - J Atkins
- Department of Investigational Cancer Therapeutics (Phase I), The University of Texas, M.D. Anderson Cancer Center, Houston
| | - K Koenig
- Department of Breast Medical Oncology, The University of Texas, M.D. Anderson Cancer Center, Houston
| | - M Gilcrease
- Department of Pathology, The University of Texas, M.D. Anderson Cancer Center, Houston
| | - R Kurzrock
- Department of Hematology and Oncology, UCSD Moores Cancer Center, San Diego, USA
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