71 research outputs found

    A pilot study evaluating concordance between blood-based and patient-matched tumor molecular testing within pancreatic cancer patients participating in the Know Your Tumor (KYT) initiative

    Get PDF
    Recent improvements in next-generation sequencing (NGS) technology have enabled detection of biomarkers in cell-free DNA in blood and may ultimately replace invasive tissue biopsies. However, a better understanding of the performance of blood-based NGS assays is needed prior to routine clinical use. As part of an IRBapproved molecular profiling registry trial of pancreatic ductal adenocarcinoma (PDA) patients, we facilitated blood-based NGS testing of 34 patients from multiple community-based and high-volume academic oncology practices. 23 of these patients also underwent traditional tumor tissue-based NGS testing. cfDNA was not detected in 9/34 (26%) patients. Overall concordance between blood and tumor tissue NGS assays was low, with only 25% sensitivity of blood-based NGS for tumor tissue NGS. Mutations in KRAS, the major PDA oncogene, were only detected in 10/34 (29%) blood samples, compared to 20/23 (87%) tumor tissue biopsies. The presence of mutations in circulating DNA was associated with reduced overall survival (54% in mutation-positive versus 90% in mutation-negative). Our results suggest that in the setting of previously treated, advanced PDA, liquid biopsies are not yet an adequate substitute for tissue biopsies. Further refinement in defining the optimal patient population and timing of blood sampling may improve the value of a blood-based test. © Pishvaian et al

    Whole-genome sequencing of trypanosoma brucei reveals introgression between subspecies that is associated with virulence

    Get PDF
    Human African trypanosomiasis is caused by two subspecies of Trypanosoma brucei. Trypanosoma brucei rhodesiense is found in East Africa and frequently causes acute disease, while Trypanosoma brucei gambiense is found in West Africa and is associated with chronic disease. Samples taken from a single focus of a Ugandan outbreak of T. b. rhodesiense in the 1980s were associated with either chronic or acute disease. We sequenced the whole genomes of two of these isolates, which showed that they are genetically distinct from each other. Analysis of single nucleotide polymorphism markers in a panel of 31 Ugandan isolates plus 32 controls revealed a mixture of East African and West African haplotypes, and some of these haplotypes were associated with the different virulence phenotypes. It has been shown recently that T. b. brucei and T. b. rhodesiense populations undergo genetic exchange in natural populations. Our analysis showed that these strains from the Ugandan epidemic were intermediate between the reference genome sequences of T. b. gambiense and T. b. brucei and contained haplotypes that were present in both subspecies. This suggests that the human-infective subspecies of T. brucei are not genetically isolated, and our data are consistent with genomic introgression between East African and West African T. b. brucei subspecies. This has implications for the control of the parasite, the spread of drug resistance, and understanding the variation in virulence and the emergence of human infectivity.<p></p> IMPORTANCE We present a genetic study of the acute form of “sleeping sickness” caused by the protozoan parasite Trypanosoma brucei rhodesiense from a single outbreak in Uganda. This represents an advance in our understanding of the relationship between the T. b. rhodesiense and Trypanosoma brucei gambiense subspecies that have previously been considered geographically distinct. Our data suggest that introgression of West African-derived T. brucei haplotypes may be associated with differences in disease presentation in the East African disease. These findings are not only of scientific interest but also important for parasite control, as they suggest that the human-infective T. brucei subspecies are not genetically isolated.<p></p&gt

    A randomized phase II study of SM-88 plus methoxsalen, phenytoin, and sirolimus in patients with metastatic pancreatic cancer treated in the second line and beyond

    Get PDF
    BACKGROUND: This trial explores SM-88 used with methoxsalen, phenytoin, and sirolimus (MPS) in pretreated metastatic pancreatic ductal adenocarcinoma (mPDAC) METHODS: Forty-nine patients were randomized to daily 460 or 920 mg oral SM-88 with MPS (SM-88 Regimen). The primary endpoint was objective response rate (RECIST 1.1). RESULTS: Thirty-seven patients completed ≥ one cycle of SM-88 Regimen (response evaluable population). Disease control rate (DCR), overall survival (OS), and progression-free survival (PFS) did not differ significantly between dose levels. Stable disease was achieved in 9/37 patients (DCR, 24.3%); there were no complete or partial responses. Quality-of-life (QOL) was maintained and trended in favor of 920 mg. SM-88 Regimen was well tolerated; a single patient (1/49) had related grade 3 and 4 adverse events, which later resolved. In the intention-to-treat population of 49 patients, the median overall survival (mOS) was 3.4 months (95% CI: 2.7-4.9 months). Those treated in the second line had an mOS of 8.1 months and a median PFS of 3.8 months. Survival was higher for patients with stable versus progressive disease (any line; mOS: 10.6 months vs. 3.9 months; p = 0.01). CONCLUSIONS: SM-88 Regimen has a favorable safety profile with encouraging QOL effects, disease control, and survival trends. This regimen should be explored in the second-line treatment of patients with mPDAC. CLINICALTRIALS: gov Identifier: NCT03512756

    Influence of orbital character on the ground state electronic properties in the van Der Waals transition metal iodides VI3 and CrI3

    Get PDF
    This work was performed in the framework of the Nanoscience Foundry and Fine Analysis (NFFA-MUR Italy) facility and was supported by JST-CREST (No. JPMJCR18T1). A part of the computation in this work, using the VASP code (43) in the GGA approximation (44), was performed by using the facilities of the Supercomputer Center, the Institute for Solid State Physics, the University of Tokyo and MASAMUNE-IMR, Center for Computational Materials Science, Institute for Materials Research, Tohoku University (Project No. 20K0045).Two-dimensional van der Waals magnetic semiconductors display emergent chemical and physical properties and hold promise for novel optical, electronic and magnetic “few-layers” functionalities. Transition-metal iodides such as CrI3 and VI3 are relevant for future electronic and spintronic applications; however, detailed experimental information on their ground state electronic properties is lacking often due to their challenging chemical environment. By combining X-ray electron spectroscopies and first-principles calculations, we report a complete determination of CrI3 and VI3 electronic ground states. We show that the transition metal-induced orbital filling drives the stabilization of distinct electronic phases: a wide bandgap in CrI3 and a Mott insulating state in VI3. Comparison of surface-sensitive (angular-resolved photoemission spectroscopy) and bulk-sensitive (X-ray absorption spectroscopy) measurements in VI3 reveals a surface-only V2+ oxidation state, suggesting that ground state electronic properties are strongly influenced by dimensionality effects. Our results have direct implications in band engineering and layer-dependent properties of two-dimensional systems.Publisher PDFPeer reviewe

    A Phase IIb, randomized, multicenter study of the efficacy of GVAX pancreas vaccine and CRS-207 compared to chemotherapy or to CRS-207 alone in adults with previously-treated metastatic pancreatic adenocarcinoma (eclipse study)

    Get PDF
    A heterologous prime-boost vaccination strategy using GVAX pancreas vaccine and CRS-207 is showing promise in patients with metastatic pancreatic adenocarcinoma (PDA). GVAX is composed of lethally-irradiated, allogeneic pancreatic cancer cells modified to express GM-CSF and induces a broad response against multiple tumor antigens. GVAX is given with low-dose cyclophosphamide (CY) to inhibit regulatory T cells. CRS-207 is live-attenuated Listeria monocytogenes engineered to express the tumor-associated antigen mesothelin. CRS-207 boosts responses against mesothelin and is unique in its capacity to stimulate both innate and adaptive immunity by activating T cells and NK cells. In a recently completed Phase II study, the CY/GVAX plus CRS-207 combination resulted in statistically-significant improvement of overall survival (OS) compared to CY/GVAX alone (Le, GI ASCO 2014)

    90Y-clivatuzumab tetraxetan with or without low-dose gemcitabine: A phase Ib study in patients with metastatic pancreatic cancer after two or more prior therapies

    Get PDF
    AbstractBackgroundFor patients with metastatic pancreatic adenocarcinoma, there are no approved or established treatments beyond the 2nd line. A Phase Ib study of fractionated radioimmunotherapy was undertaken in this setting, administering 90Y-clivatuzumab tetraxetan (yttrium-90-radiolabelled humanised antibody targeting pancreatic adenocarcinoma mucin) with or without low radiosensitising doses of gemcitabine.MethodsFifty-eight patients with three (2–7) median prior treatments were treated on Arm A (N=29, 90Y-clivatuzumab tetraxetan, weekly 6.5mCi/m2doses×3, plus gemcitabine, weekly 200mg/m2 doses×4 starting 1week earlier) or Arm B (N=29, 90Y-clivatuzumab tetraxetan alone, weekly 6.5mCi/m2doses×3), repeating cycles after 4-week delays. Safety was the primary endpoint; efficacy was also evaluated.ResultsCytopaenias (predominantly transient thrombocytopenia) were the only significant toxicities. Fifty-three patients (27 Arm A, 26 Arm B, 91% overall) completed ⩾1 full treatment cycles, with 23 (12 Arm A, 11 Arm B; 40%) receiving multiple cycles, including seven (6 Arm A, 1 Arm B; 12%) given 3–9 cycles. Two patients in Arm A had partial responses by RECIST criteria. Kaplan–Meier overall survival (OS) appeared improved in Arm A versus B (hazard ratio [HR] 0.55, 95% CI: 0.29–0.86; P=0.017, log-rank) and the median OS for Arm A versus Arm B increased to 7.9 versus 3.4months with multiple cycles (HR 0.32, P=0.004), including three patients in Arm A surviving >1year.ConclusionsClinical studies of 90Y-clivatuzumab tetraxetan combined with low-dose gemcitabine appear feasible in metastatic pancreatic cancer patients beyond 2nd line and a Phase III trial of this combination is now underway in this setting

    Covalency, correlations, and interlayer interactions governing the magnetic and electronic structure of Mn3Si2Te6

    Get PDF
    Mn3Si2Te6 is a rare example of a layered ferrimagnet. It has recently been shown to host a colossal angular magnetoresistance as the spin orientation is rotated from the in- to out-of-plane direction, proposed to be underpinned by a topological nodal-line degeneracy in its electronic structure. Nonetheless, the origins of its ferrimagnetic structure remain controversial, while its experimental electronic structure, and the role of correlations in shaping this, are little explored to date. Here, we combine x-ray and photoemission-based spectroscopies with first-principles calculations to probe the elemental-selective electronic structure and magnetic order in Mn3Si2Te6. Through these, we identify a marked Mn-Te hybridization, which weakens the electronic correlations and enhances the magnetic anisotropy.We demonstrate how this strengthens the magnetic frustration in Mn3Si2Te6, which is key to stabilizing its ferrimagnetic order, and find a crucial role of both exchange interactions extending beyond nearest-neighbors and antisymmetric exchange in dictating its ordering temperature. Together, our results demonstrate a powerful methodology of using experimental electronic structure probes to constrain the parameter space for first-principles calculations of magnetic materials, and through this approach, reveal a pivotal role played by covalency in stabilizing the ferrimagnetic order in Mn3Si2Te6

    No evidence for association with APOL1 kidney disease risk alleles and Human African Trypanosomiasis in two Ugandan populations:

    Get PDF
    Human African trypanosomiasis (HAT) manifests as an acute form caused by Trypanosoma brucei rhodesiense (Tbr) and a chronic form caused by Trypanosoma brucei gambiense (Tbg). Previous studies have suggested a host genetic role in infection outcomes, particularly for APOL1. We have undertaken a candidate gene association studies (CGAS) in a Ugandan Tbr and a Tbg HAT endemic area, to determine whether polymorphisms in IL10, IL8, IL4, HLAG, TNFA, TNX4LB, IL6, IFNG, MIF, APOL1, HLAA, IL1B, IL4R, IL12B, IL12R, HP, HPR, and CFH have a role in HAT
    • …
    corecore