Dynamic clonal progression in xenografts of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21

Intrachromosomal amplification of chromosome 21 is a heterogeneous chromosomal rearrangement occurring in 2% of childhood precursor B-cell acute lymphoblastic leukemia. There are no cell lines with iAMP21 and these abnormalities are too complex to faithfully engineer in animal models. As a resource for future functional and pre-clinical studies, we have created xenografts from intrachromosomal amplification of chromosome 21 leukemia patient blasts and characterised them by in-vivo and ex-vivo luminescent imaging, FLOW immunophenotyping, and histological and ultrastructural analysis of bone marrow and the central nervous system. Investigation of up to three generations of xenografts revealed phenotypic evolution, branching genomic architecture and, compared with other B-cell acute lymphoblastic leukemia genetic subtypes, greater clonal diversity of leukemia initiating cells. In support of intrachromosomal amplification of chromosome 21 as a primary genetic abnormality, it was always retained through generations of xenografts, although we also observed the first example of structural evolution of this rearrangement. Clonal segregation in xenografts revealed convergent evolution of different secondary genomic abnormalities implicating several known tumour suppressor genes and a region, containing the B-cell adaptor, PIK3AP1, and nuclear receptor co-repressor, LCOR, in the progression of B-ALL. Tracking of mutations in patients and derived xenografts provided evidence for co-operation between abnormalities activating the RAS pathway in B-ALL and for their aggressive clonal expansion in the xeno-environment. Bi-allelic loss of the CDKN2A/B locus was recurrently maintained or emergent in xenografts and also strongly selected as RNA sequencing demonstrated a complete absence of reads for genes associated with the deletions

A Phase II Basket Trial of Dual Anti-CTLA-4 and Anti-PD-1 Blockade in Rare Tumors (DART SWOG 1609) in Patients with Nonpancreatic Neuroendocrine Tumors.

PurposeImmune checkpoint blockade has improved outcomes across tumor types; little is known about the efficacy of these agents in rare tumors. We report the results of the (nonpancreatic) neuroendocrine neoplasm cohort of SWOG S1609 dual anti-CTLA-4 and anti-PD-1 blockade in rare tumors (DART).Patients and methodsWe performed a prospective, open-label, multicenter phase II clinical trial of ipilimumab plus nivolumab across multiple rare tumor cohorts, with the (nonpancreatic) neuroendocrine cohort reported here. Response assessment by grade was not prespecified. The primary endpoint was overall response rate [ORR; RECIST v1.1; complete response (CR) and partial response (PR)]; secondary endpoints included progression-free survival (PFS), overall survival (OS), stable disease >6 months, and toxicity.ResultsThirty-two eligible patients received therapy; 18 (56%) had high-grade disease. Most common primary sites were gastrointestinal (47%; N = 15) and lung (19%; N = 6). The overall ORR was 25% [95% confidence interval (CI) 13-64%; CR, 3%, N = 1; PR, 22%, N = 7]. Patients with high-grade neuroendocrine carcinoma had an ORR of 44% (8/18 patients) versus 0% in low/intermediate grade tumors (0/14 patients; P = 0.004). The 6-month PFS was 31% (95% CI, 19%-52%); median OS was 11 months (95% CI, 6-∞). The most common toxicities were hypothyroidism (31%), fatigue (28%), and nausea (28%), with alanine aminotransferase elevation (9%) as the most common grade 3/4 immune-related adverse event, and no grade 5 events.ConclusionsIpilimumab plus nivolumab demonstrated a 44% ORR in patients with nonpancreatic high-grade neuroendocrine carcinoma, with 0% ORR in low/intermediate grade disease

The UK Crop Microbiome Cryobank: a utility and model for supporting Phytobiomes research

Plant microbiomes are the microbial communities essential to the functioning of the phytobiome—the system that consist of plants, their environment, and their associated communities of organisms. A healthy, functional phytobiome is critical to crop health, improved yields and quality food. However, crop microbiomes are relatively under-researched, and this is associated with a fundamental need to underpin phytobiome research through the provision of a supporting infrastructure. The UK Crop Microbiome Cryobank (UKCMC) project is developing a unique, integrated and open-access resource to enable the development of solutions to improve soil and crop health. Six economically important crops (Barley, Fava Bean, Oats, Oil Seed Rape, Sugar Beet and Wheat) are targeted, and the methods as well as data outputs will underpin research activity both in the UK and internationally. This manuscript describes the approaches being taken, from characterisation, cryopreservation and analysis of the crop microbiome through to potential applications. We believe that the model research framework proposed is transferable to different crop and soil systems, acting not only as a mechanism to conserve biodiversity, but as a potential facilitator of sustainable agriculture systems

Cross-Species Array Comparative Genomic Hybridization Identifies Novel Oncogenic Events in Zebrafish and Human Embryonal Rhabdomyosarcoma

Human cancer genomes are highly complex, making it challenging to identify specific drivers of cancer growth, progression, and tumor maintenance. To bypass this obstacle, we have applied array comparative genomic hybridization (array CGH) to zebrafish embryonal rhabdomyosaroma (ERMS) and utilized cross-species comparison to rapidly identify genomic copy number aberrations and novel candidate oncogenes in human disease. Zebrafish ERMS contain small, focal regions of low-copy amplification. These same regions were commonly amplified in human disease. For example, 16 of 19 chromosomal gains identified in zebrafish ERMS also exhibited focal, low-copy gains in human disease. Genes found in amplified genomic regions were assessed for functional roles in promoting continued tumor growth in human and zebrafish ERMS – identifying critical genes associated with tumor maintenance. Knockdown studies identified important roles for Cyclin D2 (CCND2), Homeobox Protein C6 (HOXC6) and PlexinA1 (PLXNA1) in human ERMS cell proliferation. PLXNA1 knockdown also enhanced differentiation, reduced migration, and altered anchorage-independent growth. By contrast, chemical inhibition of vascular endothelial growth factor (VEGF) signaling reduced angiogenesis and tumor size in ERMS-bearing zebrafish. Importantly, VEGFA expression correlated with poor clinical outcome in patients with ERMS, implicating inhibitors of the VEGF pathway as a promising therapy for improving patient survival. Our results demonstrate the utility of array CGH and cross-species comparisons to identify candidate oncogenes essential for the pathogenesis of human cancer

Connecting the progenitors, pre-explosion variability and giant outbursts of luminous blue variables with Gaia16cfr

We present multi-epoch, multicolour pre-outburst photometry and post-outburst light curves and spectra of the luminous blue variable (LBV) outburst Gaia16cfr discovered by the Gaia satellite on 2016 December 1 UT. We detect Gaia16cfr in 13 epochs of Hubble Space Telescope imaging spanning phases of 10 yr to 8 months before the outburst and in Spitzer Space Telescope imaging 13 yr before outburst. Pre-outburst optical photometry is consistent with an 18 M⊙ F8 I star, although the star was likely reddened and closer to 30 M⊙. The pre-outburst source exhibited a significant near-infrared excess consistent with a 120 au shell with 4 × 10−6 M⊙ of dust. We infer that the source was enshrouded by an optically thick and compact shell of circumstellar material from an LBV wind, which formed a pseudo-photosphere consistent with S Dor-like variables in their ‘maximum’ phase. Within a year of outburst, the source was highly variable on 10–30  d time-scales. The outburst light curve closely matches that of the 2012 outburst of SN 2009ip, although the observed velocities are significantly slower than in that event. In H α, the outburst had an excess of blueshifted emission at late times centred around −1500 km s−1, similar to that of double-peaked Type IIn supernovae and the LBV outburst SN 2015bh. From the pre-outburst and post-outburst photometry, we infer that the outburst ejecta are evolving into a dense, highly structured circumstellar environment from precursor outbursts within years of the 2016 December event.The work of AVF was conducted in part at the Aspen Center for Physics, which is supported by NSF grant PHY-1607611; the author thanks the Center for its hospitality during the neutron stars workshop in 2017 June and July. AVF is grateful for financial assistance from the TABASGO Foundation, the Christopher R. Redlich Fund, the Miller Institute for Basic Research in Science (U.C. Berkeley) and HST grants GO-13646 and AR-14295 from the Space Telescope Science Institute (STScI), which is operated by AURA under NASA contract NAS 5-26555

LIF-dependent survival of embryonic stem cells is regulated by a novel palmitoylated Gab1 signalling protein.

The cytokine leukaemia inhibitory factor (LIF) promotes self-renewal of mouse embryonic stem cells (ESCs) through activation of the transcription factor Stat3. However, the contribution of other ancillary pathways stimulated by LIF in ESCs, such as the MAPK and PI3K pathways, is less well understood. We show here that naive-type mouse ESCs express high levels of a novel effector of the MAPK and PI3K pathways. This effector is an isoform of the Gab1 (Grb2-associated binder protein 1) adaptor protein that lacks the N-terminal pleckstrin homology (PH) membrane-binding domain. Although not essential for rapid unrestricted growth of ESCs under optimal conditions, the novel Gab1 variant (Gab1β) is required for LIF-mediated cell survival under conditions of limited nutrient availability. This enhanced survival is absolutely dependent upon a latent palmitoylation site that targets Gab1β directly to ESC membranes. These results show that constitutive association of Gab1 with membranes through a novel mechanism promotes LIF-dependent survival of murine ESCs in nutrient-poor conditions

Lee Silverman Voice Treatment versus NHS Speech and Language Therapy versus control for dysarthria in Parkinson’s disease (PD COMM):a UK, multicentre, pragmatic, randomised controlled trial

Objectives: We aimed to assess the clinical effectiveness of two speech and language therapy (SLT) approaches versus no speech and language therapy for dysarthria in people with Parkinson’s disease. Design: This was a pragmatic, UK-wide, multicentre, three-arm, parallel group, unblinded, randomised controlled trial. Participants were randomly assigned using minimisation in a 1:1:1 ratio to Lee Silverman Voice Treatment (LSVT LOUD®), NHS SLT, or no SLT. Analyses were based on the intention to treat principle.Setting: The speech and language therapy interventions were delivered in outpatient or home settings.Participants: Between September 2016 and March 2020, 388 people with Parkinson’s disease and dysarthria were randomised into the trial: 130 to LSVT LOUD®, 129 to NHS SLT, and 129 to no SLT.Interventions: Lee Silverman Voice Treatment (LSVT LOUD®) consisted of four, face-to-face or remote, 50-minute sessions each week delivered over 4 weeks. Home-based practice activities were set for up to 5 to 10 minutes daily on treatment days and 15 minutes twice daily on non-treatment days. NHS Speech and language therapy (NHS SLT) dosage was determined by the local therapist in response to individual participants’ needs. Prior research suggested that NHS SLT participants would receive an average of one session per week over 6 to 8 weeks. Local practices for NHS SLT were accepted, except for those within the LSVT LOUD® protocol. Main outcome measures: The primary outcome was the self-reported Voice Handicap Index (VHI) total score at 3 months.Results: People randomised to LSVT LOUD® reported lower VHI scores at 3 months post-randomisation than those who were randomised to no SLT (-8·0 points (99%CI: -13·3 to -2·6); p = 0·0001). There was no evidence of a difference in VHI scores between NHS SLT and no SLT (1·7 points; (99%Cl: -3·8 to 7·1); p = 0·43). Patients randomised to LSVT LOUD® also reported lower VHI scores than those randomised to NHS SLT (-9·6 points; (99%CI: -14·9 to -4·4); p &lt; 0.0001). There were 93 adverse events (predominately vocal strain) in the LSVT LOUD® group, 46 in the NHS SLT group, and none in the no SLT group. There were no serious adverse events. Conclusions: LSVT LOUD® was more effective at reducing the participant reported impact of voice problems than no SLT and NHS SLT. NHS SLT showed no evidence of benefit compared to no SLT. Trial registration: The completed trial registration is ISRCTN12421382. Funding: NIHR HTA Programme, project number HTA 10/135/02. <br/