Cancer genomics studies have identified thousands of putative cancer driver genes
. Development of high-throughput and accurate models to define the functions of these genes is a major challenge. ...Here we devised a scalable cancer-spheroid model and performed genome-wide CRISPR screens in 2D monolayers and 3D lung-cancer spheroids. CRISPR phenotypes in 3D more accurately recapitulated those of in vivo tumours, and genes with differential sensitivities between 2D and 3D conditions were highly enriched for genes that are mutated in lung cancers. These analyses also revealed drivers that are essential for cancer growth in 3D and in vivo, but not in 2D. Notably, we found that carboxypeptidase D is responsible for removal of a C-terminal RKRR motif
from the α-chain of the insulin-like growth factor 1 receptor that is critical for receptor activity. Carboxypeptidase D expression correlates with patient outcomes in patients with lung cancer, and loss of carboxypeptidase D reduced tumour growth. Our results reveal key differences between 2D and 3D cancer models, and establish a generalizable strategy for performing CRISPR screens in spheroids to reveal cancer vulnerabilities.
SummaryBackgroundImmunotherapy combination treatments can improve patient outcomes. Epacadostat, an IDO1 selective inhibitor, and pembrolizumab, a PD-1 inhibitor, showed promising antitumour activity ...in the phase 1–2 ECHO-202/KEYNOTE-037 study in advanced melanoma. In this trial, we aimed to compare progression-free survival and overall survival in patients with unresectable stage III or IV melanoma receiving epacadostat plus pembrolizumab versus placebo plus pembrolizumab. MethodsIn this international, randomised, placebo-controlled, double-blind, parallel-group, phase 3 trial, eligible participants were aged 18 years or older, with unresectable stage III or IV melanoma previously untreated with PD-1 or PD-L1 checkpoint inhibitors, an ECOG performance status of 0 or 1, and had a known BRAFV600 mutant status or consented to BRAFV600 mutation testing during screening. Patients were stratified by PD-L1 expression and BRAFV600 mutation status and randomly assigned (1:1) through a central interactive voice and integrated web response system to receive epacadostat 100 mg orally twice daily plus pembrolizumab 200 mg intravenously every 3 weeks or placebo plus pembrolizumab for up to 2 years. We used block randomisation with a block size of four in each stratum. Primary endpoints were progression-free survival and overall survival in the intention-to-treat population. The safety analysis population included randomly assigned patients who received at least one dose of study treatment. The study was stopped after the second interim analysis; follow-up for safety is ongoing. This study is registered with ClinicalTrials.gov, number NCT02752074. FindingsBetween June 21, 2016, and Aug 7, 2017, 928 patients were screened and 706 patients were randomly assigned to receive epacadostat plus pembrolizumab (n=354) or placebo plus pembrolizumab (n=352). Median follow-up was 12·4 months (IQR 10·3–14·5). No significant differences were found between the treatment groups for progression-free survival (median 4·7 months, 95% CI 2·9–6·8, for epacadostat plus pembrolizumab vs 4·9 months, 2·9–6·8, for placebo plus pembrolizumab; hazard ratio HR 1·00, 95% CI 0·83–1·21; one-sided p=0·52) or overall survival (median not reached in either group; epacadostat plus pembrolizumab vs placebo plus pembrolizumab: HR 1·13, 0·86–1·49; one-sided p=0·81). The most common grade 3 or worse treatment-related adverse event was lipase increase, which occurred in 14 (4%) of 353 patients receiving epacadostat plus pembrolizumab and 11 (3%) of 352 patients receiving placebo plus pembrolizumab. Treatment-related serious adverse events were reported in 37 (10%) of 353 patients receiving epacadostat plus pembrolizumab and 32 (9%) of 352 patients receiving placebo plus pembrolizumab. There were no treatment-related deaths in either treatment group. InterpretationEpacadostat 100 mg twice daily plus pembrolizumab did not improve progression-free survival or overall survival compared with placebo plus pembrolizumab in patients with unresectable or metastatic melanoma. The usefulness of IDO1 inhibition as a strategy to enhance anti-PD-1 therapy activity in cancer remains uncertain. FundingIncyte Corporation, in collaboration with Merck Sharp & Dohme.
Antibiotic resistance represents a growing health crisis that necessitates the immediate discovery of novel treatment strategies. One such strategy is the identification of collateral sensitivities, ...wherein evolution under a first drug induces susceptibility to a second. Here, we report that sequential drug regimens derived from in vitro evolution experiments may have overstated therapeutic benefit, predicting a collaterally sensitive response where cross-resistance ultimately occurs. We quantify the likelihood of this phenomenon by use of a mathematical model parametrised with combinatorially complete fitness landscapes for Escherichia coli. Through experimental evolution we then verify that a second drug can indeed stochastically exhibit either increased susceptibility or increased resistance when following a first. Genetic divergence is confirmed as the driver of this differential response through targeted and whole genome sequencing. Taken together, these results highlight that the success of evolutionarily-informed therapies is predicated on a rigorous probabilistic understanding of the contingencies that arise during the evolution of drug resistance.
The primary objective was to determine if vaginal cuff brachytherapy and chemotherapy (VCB/C) increases recurrence-free survival (RFS) compared with pelvic radiation therapy (RT) in high-intermediate ...and high-risk early-stage endometrial carcinoma.
A randomized phase III trial was performed in eligible patients with endometrial cancer. Eligible patients had International Federation of Gynecology and Obstetrics (2009) stage I endometrioid histology with Gynecologic Oncology Group protocol 33-based high-intermediate-risk criteria, stage II disease, or stage I to II serous or clear cell tumors. Treatment was randomly assigned between RT (45 to 50.4 Gy over 5 weeks) or VCB followed by intravenous paclitaxel 175 mg/m
(3 hours) plus carboplatin (area under the curve, 6) every 21 days for three cycles.
The median age of the 601 patients was 63 years, and 74% had stage I disease. Histologies included endometrioid (71%), serous (15%), and clear cell (5%). With a median follow-up of 53 months, the 60-month RFS was 0.76 (95% CI, 0.70 to 0.81) for RT and 0.76 (95% CI, 0.70 to 0.81) for VCB/C (hazard ratio, 0.92; 90% confidence limit, 0.69 to 1.23). The 60-month overall survival was 0.87 (95% CI, 0.83 to 0.91) for RT and 0.85 (95% CI, 0.81 to 0.90) for VCB/C (hazard ratio, 1.04; 90% confidence limit, 0.71 to 1.52). Vaginal and distant recurrence rates were similar between arms. Pelvic or para-aortic nodal recurrences were more common with VCB/C (9%
4%). There was no heterogeneity of treatment effect with respect to RFS or overall survival among clinical or pathologic variables evaluated.
Superiority of VCB/C compared with pelvic RT was not demonstrated. Acute toxicity was greater with VCB/C; late toxicity was similar. Pelvic RT alone remains an effective, well-tolerated, and appropriate adjuvant treatment in high-risk early-stage endometrial carcinomas of all histologies.
Long-term perspective on wildfires in the western USA Marlon, Jennifer R; Bartlein, Patrick J; Gavin, Daniel G ...
Proceedings of the National Academy of Sciences,
02/2012, Letnik:
109, Številka:
9
Journal Article
Recenzirano
Odprti dostop
Understanding the causes and consequences of wildfires in forests of the western United States requires integrated information about fire, climate changes, and human activity on multiple temporal ...scales. We use sedimentary charcoal accumulation rates to construct long-term variations in fire during the past 3,000 y in the American West and compare this record to independent fire-history data from historical records and fire scars. There has been a slight decline in burning over the past 3,000 y, with the lowest levels attained during the 20th century and during the Little Ice Age (LIA, ca. 1400–1700 CE Common Era). Prominent peaks in forest fires occurred during the Medieval Climate Anomaly (ca. 950–1250 CE) and during the 1800s. Analysis of climate reconstructions beginning from 500 CE and population data show that temperature and drought predict changes in biomass burning up to the late 1800s CE. Since the late 1800s , human activities and the ecological effects of recent high fire activity caused a large, abrupt decline in burning similar to the LIA fire decline. Consequently, there is now a forest "fire deficit" in the western United States attributable to the combined effects of human activities, ecological, and climate changes. Large fires in the late 20th and 21st century fires have begun to address the fire deficit, but it is continuing to grow.
An array of lake sediment proxies including paleobotanic, geochemical, and historical records has been used to determine former environments of Bugbee Pond, a small, mesotrophic pond in northeastern ...Minnesota. Much research has been produced on the history of climate and vegetation change of the region, yet we have little information on the impact of human settlement. This well-dated, high resolution, multi-proxy record is important for its length and concentration on the historic period. The lake itself became established by ~7000 years ago. Pollen evidence suggests a transition between the regional Prairie Period to the Great Lakes mixed conifer – hardwood forest was established in the region at this time. XRF data suggest dry basin accumulation early in the record after ~7000 cal yr BP, but lake levels substantially increased by ~5600 cal yr BP, during a regionwide climatic transition to more humid conditions. Birch and boreal conifers increased after about 3800 cal yr BP; further increases in boreal conifers occurred by ~2000 cal yr BP. Anthropogenic vegetation changes during the Historic period, beginning in the late 19th century, is well represented by forest clearance of white pine (Pinus strobus), followed by increases in early successional species and an increased sediment accumulation rate due to land clearance. Establishment of farming communities locally are shown by occurrence of corn (Zea mays) and oat (Avena sativa) pollen, and pasturing and grazing are documented by Rumex, Fabaceae and Poaceae pollen, as well as coprophilous fungi, such as Sordaria. The increase and subsequent decline in Pb and S concentrations in the uppermost sediments are mirrored by historically documented, nearby industrial activities.
The increasing rate of antibiotic resistance and slowing discovery of novel antibiotic treatments presents a growing threat to public health. Here, we consider a simple model of evolution in ...asexually reproducing populations which considers adaptation as a biased random walk on a fitness landscape. This model associates the global properties of the fitness landscape with the algebraic properties of a Markov chain transition matrix and allows us to derive general results on the non-commutativity and irreversibility of natural selection as well as antibiotic cycling strategies. Using this formalism, we analyze 15 empirical fitness landscapes of E. coli under selection by different β-lactam antibiotics and demonstrate that the emergence of resistance to a given antibiotic can be either hindered or promoted by different sequences of drug application. Specifically, we demonstrate that the majority, approximately 70%, of sequential drug treatments with 2-4 drugs promote resistance to the final antibiotic. Further, we derive optimal drug application sequences with which we can probabilistically 'steer' the population through genotype space to avoid the emergence of resistance. This suggests a new strategy in the war against antibiotic-resistant organisms: drug sequencing to shepherd evolution through genotype space to states from which resistance cannot emerge and by which to maximize the chance of successful therapy.
The Kenai Peninsula of south‐central Alaska is a region of high topographic diversity with a complex glacial history. The sedimentary record of two small lakes Sunken Island (SIL; 76 m a.s.l.) in the ...Kenai Lowlands; Choquette (CL; 527 m a.s.l.) in the Caribou Hills upland exemplifies the postglacial development of the conifer–hardwood forest over an elevational range there. A herb–shrub tundra was established at both sites after deglaciation. By ~10.7 ka, poplar (Populus sp.) and alder (Alnus) dominated the lowland forest, while alder with minor poplar occurred at the upland site. Lake levels lower than today occurred during the early Holocene until ~8 ka. Subsequently at SIL, the near‐modern Kenai birch (Betula kenaica) – white spruce (Picea glauca) forest maintained prominence throughout the Holocene. However, at CL, alder dominated with dwarf birch and other subshrubs; small amounts of white spruce arrived ~5.2 ka. Black spruce (Picea mariana) grew around SIL by ~4 ka, but never gained prominence at CL. Fire, a prominent agent of disturbance in the Kenai Lowlands since ~8 ka, was essentially absent at the hardwood‐dominated upland site before ~6 ka, and rare thereafter. This suggests an important link between fire and spruce in Kenai forests.
► Polycyclic aromatic hydrocarbons (PAHs) as a signature for fire in paleorecord. ► HPLC-fluorescence detection is superior to GC–MS for detecting PAHs. ► PAHs record fires within 0.5km of the lake ...in Yosemite National Park, CA. ► Low molecular weight PAHs (e.g. fluoranthene, pyrene) are the best recorders of fire. ► PAHs appear to resolve some issues inherent to other fire proxies.
Understanding the natural mechanisms that control fire occurrence in terrigenous ecosystems requires long and continuous records of past fires. Proxies, such as sedimentary charcoal and tree-ring fire scars, have temporal or spatial limitations and do not directly detect fire intensity. We show in this study that polycyclic aromatic hydrocarbons (PAHs) produced during wildfires record local fire events and fire intensity. We demonstrate that high performance liquid chromatography with fluorescence detector (HPLC-FLD) is superior to gas chromatography–mass spectrometry (GC–MS) for detecting the low concentrations of sedimentary PAHs derived from natural fires. The HPLC-FLD is at least twice as sensitive as the GC–MS in selective ion monitoring (SIM) mode for parent PAHs and five times as sensitive for retene. The annual samples extracted from varved sediments from Swamp Lake in Yosemite National Park, California are compared with the observational fire history record and show that PAH fluxes record fires within 0.5km of the lake. The low molecular weight (LMW) PAHs (e.g., fluoranthene, pyrene and benzaanthracene) are the best recorders of fire, whereas the high molecular weight (HMW) PAHs likely record fire intensity. PAHs appear to resolve some of the issues inherent to other fire proxies, such as secondary deposition of charcoal. This study advances our understanding of how PAHs can be used as markers for fire events and poses new questions regarding the distribution of these compounds in the environment.
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