Magnetic hydrogel particles improve nanopore sequencing of SARS-CoV-2 and other respiratory viruses

Presented here is a magnetic hydrogel particle enabled workflow for capturing and concentrating SARS-CoV-2 from diagnostic remnant swab samples that significantly improves sequencing results using the Oxford Nanopore Technologies MinION sequencing platform. Our approach utilizes a novel affinity-based magnetic hydrogel particle, circumventing low input sample volumes and allowing for both rapid manual and automated high throughput workflows that are compatible with Nanopore sequencing. This approach enhances standard RNA extraction protocols, providing up to 40 × improvements in viral mapped reads, and improves sequencing coverage by 20-80% from lower titer diagnostic remnant samples. Furthermore, we demonstrate that this approach works for contrived influenza virus and respiratory syncytial virus samples, suggesting that it can be used to identify and improve sequencing results of multiple viruses in VTM samples. These methods can be performed manually or on a KingFisher automation platform.

Tumefactive Demyelinating Lesions in Children: A Rare Case of Conus Medullaris Involvement and Systematic Review of the Literature

Tumefactive demyelinating lesions are an uncommon manifestation of demyelinating disease that mimic primary central nervous system neoplasms and can pose a diagnostic challenge in patients without a pre-existing diagnosis of multiple sclerosis. Although a biopsy may be required to distinguish TDL from neoplasms or infection, certain ancillary and radiographic findings may preclude the need for invasive diagnostic procedures. We describe the case of a 15-year-old boy with a tumefactive demyelinating lesion involving the conus medullaris. An exhaustive systematic literature search of pediatric cases of TDL yielded an additional 78 cases. This review summarizes the current knowledge and recommendations for the diagnosis and management of this condition, highlighting the clinical, demographic, and radiologic features of 79 reported cases, including our own. Furthermore, it underscores areas of the literature where evidence is still lacking. Further research is needed to optimize clinical detection and medical management of this condition.

Regional variations in medical trainee diet and nutrition counseling competencies: Machine learning-augmented propensity score analysis of a prospective multi-site cohort study

BACKGROUND

Medical professionals and students are inadequately trained to respond to rising global obesity and nutrition-related chronic disease epidemics, primarily focusing on cardiovascular disease. Yet, there are no multi-site studies testing evidence-based nutrition education for medical students in preventive cardiology, let alone establishing student dietary and competency patterns.

METHODS

Cooking for Health Optimization with Patients (CHOP; NIH NCT03443635) was the first multi-national cohort study using hands-on cooking and nutrition education as preventive cardiology, monitoring and improving student diets and competencies in patient nutrition education. Propensity-score adjusted multivariable regression was augmented by 43 supervised machine learning algorithms to assess students outcomes from UT Health versus the remaining study sites.

RESULTS

3,248 medical trainees from 20 medical centers and colleges met study criteria from 1 August 2012 to 31 December 2017 with 60 (1.49%) being from UTHealth. Compared to the other study sites, trainees from UTHealth were more likely to consume vegetables daily (OR 1.82, 95%CI 1.04-3.17, p=0.035), strongly agree that nutrition assessment should be routine clinical practice (OR 2.43, 95%CI 1.45-4.05, p=0.001), and that providers can improve patients' health with nutrition education (OR 1.73, 95%CI 1.03-2.91, p=0.038). UTHealth trainees were more likely to have mastered 12 of the 25 competency topics, with the top three being moderate alcohol intake (OR 1.74, 95%CI 0.97-3.11, p=0.062), dietary fats (OR 1.26, 95%CI 0.57-2.80, p=0.568), and calories (OR 1.26, 95%CI 0.70-2.28, p=0.446).

CONCLUSION

This machine learning-augmented causal inference analysis provides the first results that compare medical students nationally in their diets and competencies in nutrition education, highlighting the results from UTHealth. Additional studies are required to determine which factors in the hands-on cooking and nutrition curriculum for UTHealth and other sites produce optimal student - and, eventually, preventive cardiology - outcomes when they educate patients in those classes.

A phase I dose-escalation and dose-expansion study of brontictuzumab in subjects with selected solid tumors

Background

Brontictuzumab is a monoclonal antibody that targets Notch1 and inhibits pathway activation. The purpose of this first-in-human study was to determine the maximum tolerated dose (MTD), safety, pharmacokinetics, immunogenicity and preliminary efficacy of brontictuzumab in patients with solid tumors.

Patients and methods

Subjects with selected refractory solid tumors were eligible. Brontictuzumab was administered intravenously at various dose levels and schedule during dose escalation, and at 1.5 mg/kg every 3 weeks (Q3W) during expansion. Evidence of Notch1 pathway activation as determined by an immunohistochemistry assay was required for entry in the expansion cohort. Adverse events were graded according to the NCI-CTCAE v 4.03. Efficacy was assessed by RECIST 1.1.

Results

Forty-eight subjects enrolled (33 in dose escalation and 15 in the expansion phase). The MTD was 1.5 mg/kg Q3W. Dose-limiting toxicities were grade 3 diarrhea in two subjects and grade 3 fatigue in one subject. The most common drug-related adverse events of any grade were diarrhea (71%), fatigue (44%), nausea (40%), vomiting (21%), and AST increase (21%). Brontictuzumab exhibited nonlinear pharmacokinetics with dose-dependent terminal half-life ranging 1-4 days. Clinical benefit was seen in 6 of 36 (17%) assessable subjects: 2 had unconfirmed partial response (PR) and 4 subjects had prolonged (≥ 6 months) disease stabilization (SD). Both PRs and three prolonged SD occurred in adenoid cystic carcinoma (ACC) subjects with evidence of Notch1 pathway activation. Pharmacodynamic effects of brontictuzumab were seen in patients' blood and tumor.

Conclusion

Brontictuzumab was well tolerated at the MTD. The main toxicity was diarrhea, an on-target effect of Notch1 inhibition. An efficacy signal was noted in subjects with ACC and Notch1 pathway activation.

ClinicalTrials.gov identifier

NCT01778439.

Five-year survival outcomes for patients with advanced melanoma treated with pembrolizumab in KEYNOTE-001

BACKGROUND

Pembrolizumab demonstrated robust antitumor activity and safety in the phase Ib KEYNOTE-001 study (NCT01295827) of advanced melanoma. Five-year outcomes in all patients and treatment-naive patients are reported herein. Patients whose disease progressed following initial response and who received a second course of pembrolizumab were also analyzed.

PATIENTS AND METHODS

Patients aged ≥18 years with previously treated or treatment-naive advanced/metastatic melanoma received pembrolizumab 2 mg/kg every 3 weeks, 10 mg/kg every 3 weeks, or 10 mg/kg every 2 weeks until disease progression, intolerable toxicity, or patient/investigator decision to withdraw. Kaplan-Meier estimates of overall survival (OS) and progression-free survival (PFS) were calculated. Objective response rate and PFS were based on immune-related response criteria by investigator assessment (data cut-off, September 1, 2017).

RESULTS

KEYNOTE-001 enrolled 655 patients with melanoma; median follow-up was 55 months. Estimated 5-year OS was 34% in all patients and 41% in treatment-naive patients; median OS was 23.8 months (95% CI, 20.2-30.4) and 38.6 months (95% CI, 27.2-not reached), respectively. Estimated 5-year PFS rates were 21% in all patients and 29% in treatment-naive patients; median PFS was 8.3 months (95% CI, 5.8-11.1) and 16.9 months (95% CI, 9.3-35.5), respectively. Median response duration was not reached; 73% of all responses and 82% of treatment-naive responses were ongoing at data cut-off; the longest response was ongoing at 66 months. Four patients [all with prior response of complete response (CR)] whose disease progressed during observation subsequently received second-course pembrolizumab. One patient each achieved CR and partial response (after data cut-off). Treatment-related AEs (TRAEs) occurred in 86% of patients and resulted in study discontinuation in 7.8%; 17% experienced grade 3/4 TRAE.

CONCLUSIONS

This 5-year analysis of KEYNOTE-001 represents the longest follow-up for pembrolizumab to date and confirms the durable antitumor activity and tolerability of pembrolizumab in advanced melanoma.

CLINICAL TRIAL REGISTRY

ClinicalTrials.gov, NCT01295827.

Abstract P5-20-06: Phase 1 dose escalation with ZW25, a HER2-targeted bispecific antibody, in patients (pts) with HER2-high breast cancer (BC)

Background: ZW25, a novel IgG1-like bispecific antibody, targets the same domains of HER2 as trastuzumab (T) and pertuzumab (P). In preclinical studies, ZW25 demonstrated increased tumor cell binding density and internalization relative to T and activity in T-resistant cell lines as well as models of HER2-low to high cancers. Initial dose escalation data demonstrated that once-weekly ZW25 was well tolerated at all doses evaluated and associated with single-agent anti-tumor activity in pts with heavily pre-treated (tx) HER2-expressing cancers.

Methods: 3+3 dose escalation of ZW25 given weekly (QW; 5, 10 or 15 mg/kg) or biweekly (Q2W; 20 mg/kg) in 4-week cycles. Eligibility included HER2 IHC 1, 2 or 3+ or FISH+ BC, progression after T, P and T-DM1, and measurable or non-measureable disease per RECIST 1.1. Active brain metastases were excluded. Baseline brain MRI was performed in QW cohorts only if pts had prior history (hx) of CNS mets, and in all Q2W pts regardless of hx. Assessments included AEs, LVEF, immunogenicity, PK and tumor response every 2 cycles.

Results: 8 pts with HER2-high BC were tx with ZW25 QW at 5 (n=2), 10 (n=2) or 15 mg/kg (n=4); 20 mg/kg Q2W is enrolling. 5/8 pts were HR+; 7 had measurable disease, 6 visceral disease, and 3 stable CNS disease. Median years since initial dx was 6 (range 5-16). Prior tx included T and T-DM1 (n=8); P (n= 6), and lapatinib (n=5). Median number of prior HER2-targeted regimens for metastatic disease was 6 (range 3-7) and non-hormonal HER2 regimens was 5 (range 3-7).

ZW25 was well tolerated with no DLTs or decreases in cardiac function. Most common related AEs (all Gr 1 or 2) were diarrhea (n=4), infusion reaction (IR) (n=4) and vomiting (n=3). All IRs occurred only with 1st dose. There were no treatment-related SAEs. Related Gr 3 AEs (hypophosphatemia, fatigue and arthralgia) were reported in 1 pt (10 mg/kg).

At data cut-off, pts had received 2-10 cycles of treatment, with 3 pts active. Best overall response was 2 PR (10 mg/kg), 3 SD (1 at 5 mg/kg, 2 at 15 mg/kg), and 3 PD (1 at 5 mg/kg, 2 at 15 mg/kg) for a disease control rate of 63%. Decreases in target lesions were seen in 6/7 patients with at least one tumor re-staging. One pt with SD (5 mg/kg; active on study) had an 8% decrease after C2, and 29% decrease after C8. One PR pt with prior hx of brain mets had a 33% decrease after C2 and 44% decrease after C4, although was found to have new leptomeningeal disease (LMD) at that time. Two additional pts with systemic SD (15 mg/kg; no prior hx of CNS mets) were also considered to have PD due to symptomatic brain mets. One of these pts remains on study after receiving stereotactic radiotherapy.

Conclusions: ZW25 was associated with single-agent anti-tumor activity and systemic disease control in HER2-high BC pts after a median of 6 prior HER2-targeted regimens for metastatic disease. Systemic disease control was maintained despite PD due to brain mets or LMD. The presence of CNS disease in an unscreened population is consistent with the biology of late-stage HER2-high BC. The activity and tolerability of ZW25 support further evaluation as a single agent and in combination including with CNS-directed therapies in early and late lines of treatment for HER2-expressing BC.

Citation Format: Hamilton E, Meric-Bernstam F, Infante J, Murthy R, Patnaik A, Piha-Paul SA, Tolcher A, Hausman D, Royer N, Beeram M. Phase 1 dose escalation with ZW25, a HER2-targeted bispecific antibody, in patients (pts) with HER2-high breast cancer (BC) [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 P5-20-06.

First-in-human phase I study of copanlisib (BAY 80-6946), an intravenous pan-class I phosphatidylinositol 3-kinase inhibitor, in patients with advanced solid tumors and non-Hodgkin's lymphomas

BACKGROUND

To evaluate the safety, tolerability, pharmacokinetics, and maximum tolerated dose (MTD) of copanlisib, a phosphatidylinositol 3-kinase inhibitor, in patients with advanced solid tumors or non-Hodgkin's lymphoma (NHL).

PATIENTS AND METHODS

Phase I dose-escalation study including patients with advanced solid tumors or NHL, and a cohort of patients with type 2 diabetes mellitus. Patients received three weekly intravenous infusions of copanlisib per 28-day cycle over the dose range 0.1-1.2 mg/kg. Plasma copanlisib levels were analyzed for pharmacokinetics. Biomarker analysis included PIK3CA, KRAS, BRAF, and PTEN mutational status and PTEN immunohistochemistry. Whole-body [(18)F]-fluorodeoxyglucose positron emission tomography ((18)FDG-PET) was carried out at baseline and following the first dose to assess early pharmacodynamic effects. Plasma glucose and insulin levels were evaluated serially.

RESULTS

Fifty-seven patients received treatment. The MTD was 0.8 mg/kg copanlisib. The most frequent treatment-related adverse events were nausea and transient hyperglycemia. Copanlisib exposure was dose-proportional with no accumulation; peak exposure positively correlated with transient hyperglycemia post-infusion. Sixteen of 20 patients treated at the MTD had reduced (18)FDG-PET uptake; 7 (33%) had a reduction >25%. One patient achieved a complete response (CR; endometrial carcinoma exhibiting both PIK3CA and PTEN mutations and complete PTEN loss) and two had a partial response (PR; both metastatic breast cancer). Among the nine NHL patients, all six with follicular lymphoma (FL) responded (one CR and five PRs) and one patient with diffuse large B-cell lymphoma had a PR by investigator assessment; two patients with FL who achieved CR (per post hoc independent radiologic review) were on treatment >3 years.

CONCLUSION

Copanlisib, dosed intermittently on days 1, 8, and 15 of a 28-day cycle, was well tolerated and the MTD was determined to be 0.8 mg/kg. Copanlisib exhibited dose-proportional pharmacokinetics and promising anti-tumor activity, particularly in patients with NHL.

CLINICALTRIALSGOV

NCT00962611; https://clinicaltrials.gov/ct2/show/NCT00962611.

A Phase 1 study of ARQ 087, an oral pan-FGFR inhibitor in patients with advanced solid tumours

Background:

ARQ 087 is an orally administered pan-FGFR inhibitor with multi-kinase activity. This Phase 1 study evaluated safety, pharmacokinetics, and pharmacodynamics of ARQ 087 and defined the recommended Phase 2 dose (RP2D).

Methods:

Patients with advanced solid tumours received ARQ 087 administered initially at 25 mg every other day and dose-escalated from 25 to 425 mg daily (QD) continuous dosing. FGF19, 21, 23, and serum phosphate were assessed as potential biomarkers of target engagement.

Results:

80 patients were enrolled, 61 in dose-escalation/food-effect cohorts and 19 with pre-defined tumour types in the expansion cohort. The most common ARQ 087-related adverse events were fatigue (49%), nausea (46%), aspartate aminotransferase (AST) increase (30%), and diarrhoea (23%). Four patients (5%) experienced grade 1 treatment-related hyperphosphataemia. Dose-limiting toxicity was reversible grade 3 AST increase. The RP2D was 300 mg QD. Pharmacokinetics were linear and dose-proportional from 25 to 325 mg QD, and were unaffected by food. Statistically significant changes (P-value<0.05) suggest phosphate and FGF19 levels as markers of target engagement. In 18 evaluable patients with FGFR genetic alterations, 3 confirmed partial responses (two intrahepatic cholangiocarcinomas (iCCA) with FGFR2 fusions and one urothelial cancer with FGFR2 and FGF19 amplification) and two durable stable disease at ⩾16 weeks with tumour reduction (FGFR2 fusion-positive iCCA and adrenocortical carcinoma with FGFR1 amplification) were observed.

Conclusions:

ARQ 087 had manageable toxicity at the RP2D of 300 mg QD, showed pharmacodynamics effects, and achieved objective responses, notably in patients with FGFR2 genetic alterations.

Pembrolizumab as first-line therapy for patients with PD-L1-positive advanced non-small cell lung cancer: a phase 1 trial

Background

Pembrolizumab improved survival as first- and second-line therapy compared with chemotherapy in patients with highly programmed death ligand 1 (PD-L1) expressing advanced non-small cell lung cancer (NSCLC). We report the long-term safety and clinical activity of pembrolizumab as first-line therapy for patients with advanced NSCLC and the correlation between PD-L1 expression and efficacy.

Patients and methods

In the open-label phase 1b KEYNOTE-001 trial, treatment-naive patients with advanced NSCLC whose tumors expressed PD-L1 (≥1% staining, assessed using a prototype assay) were randomly assigned to intravenous pembrolizumab 2 or 10 mg/kg every 3 (Q3W) or 2 (Q2W) weeks. Response was assessed per central RECIST v1.1 every 9 weeks in all patients who received ≥1 pembrolizumab dose. Using pre-treatment tumor tissue, a clinical assay quantified the percentage of tumor cells expressing PD-L1 as tumor proportion score (TPS).

Results

Between 1 March 2013 and 18 September 2015, 101 patients received pembrolizumab 2 mg/kg Q3W (n = 6), 10 mg/kg Q3W (n = 49), or 10 mg/kg Q2W (n = 46). Of these, 27 (26.7%) had TPS ≥50%, 52 (51.5%) had TPS 1%-49%, and 12 (11.9%) had TPS <1%. The objective response rate (ORR) was 27% (27/101, 95% CI 18-37) and median overall survival was 22.1 months (95% CI 17.1-27.2). In patients with PD-L1 TPS ≥50%, ORR, 12-month PFS, and 12-month OS were higher [14/27 (51.9%; 95% CI 32%-71%), 54%, and 85%, respectively] than the overall population [27/101 (26.7%; 95% CI 18.4%-36.5%), 35%, 71%]. Pembrolizumab was well tolerated, with only 12 (11.9%) patients experiencing grade 3/4 treatment-related adverse events and no treatment-related deaths.

Conclusions

Pembrolizumab provides promising long-term OS benefit with a manageable safety profile for PD-L1-expressing treatment-naive advanced NSCLC, with greatest efficacy observed in patients with TPS ≥50%.

Clinical trial name and number

KEYNOTE-001 (ClinicalTrials.gov, NCT01295827).

Abstract P3-04-26: Establishment and characterization of ST941/C; an ESR1-mutant ER+ breast cancer cell line and xenograft from a patient with acquired resistance to endocrine therapy

Background: The estrogen receptor (ERα) plays an integral role in the progression of luminal type breast cancers and while targeted endocrine therapies provide effective initial treatment many patients develop acquired resistance to treatment even with continued ER receptor expression. Recently studies identified ER mutations as a possible mechanism for acquired resistance and several activating point mutations have been identified including Y537S (ESR1Y537S) resulting in hormone independent proliferation in preclinical studies. However, lack of validated ESR1-mutant cell lines has limited detailed mechanistic studies of these mutations in endocrine-resistant ER+ breast cancer. Previously we established and evaluated a patient derived xenograft (PDX) designated ST941 representing ESR1Y537S-mutated ER+ breast cancer (Wick et al, SABCS 2015). To better understand the role of ESR1-mutations in endocrine resistant breast cancer we established an immortalized cell line from ST941 designated ST941/C to use for in vitro mechanistic assays and correlative in vivo studies.

Methods: The ST941/C cell line was generated from harvested low-passage ST941 PDX tissue using published methods. Once established the line was characterized by immunohistochemistry and NGS and its tumorigenicity assessed. Drug sensitivity studies were carried out evaluating relevant endocrine and chemotherapy agents and results compared with in vivo drug studies. Timepoints for cell proliferation assays were Days 4, 7 and 10 following cell plating using standard MTS assay. Endpoints for in vivo studies were a mean group tumor volume of ~1 cm3 or sixty days following treatment initiation.

Results: Subcutaneous cell injection into athymic nude mice produced xenografts which grew in the absence of exogenous hormone. The ST941/C cell line and resulting xenograft retained immunohistologic and NGS characteristics of the parent model including receptor expression and ER mutation. Both the cell line and xenograft were insensitive to most endocrine therapies including tamoxifen, fulvestrant and aromatase inhibitors and reported correlative activity towards docetaxel and other chemotherapies.

Conclusion: We have established and evaluated an ESR1-mutant cell line designated ST941/C which is tumorigenic in nude mice and potentially useful for mechanistic and correlative in vivo studies to better understand acquired resistance in endocrine-treated ER+ breast cancer.

Citation Format: Wick MJ, Diaz A, Thomas M, Moriarty A, Quinn M, Guerra M, Zhu P, Smith P, Tolcher AW, Puyang X, Patnaik A, Korpal M, Rasco D, Papadopoulos KP. Establishment and characterization of ST941/C; an ESR1-mutant ER+ breast cancer cell line and xenograft from a patient with acquired resistance to endocrine therapy [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 P3-04-26.

Numerical Simulation and Experimental Validation of Granite Powder Filled Jute Epoxy Composite for Slurry Jet Erosive Wear

In the polymer composite the benefits of utilizing the excellent wear resisting properties in terms of light weight structural design are immediately apparent. Hence, the focus of this study is to propose new sets of unfilled and particulate filled treated jute epoxy composites. Therefore, initially five different weight percentages of alkali treated jute epoxy composites are fabricated (10, 20, 30 40 and 50 wt.%) and studied their slurry erosive wear in experimentally at different operating conditions such as by varying impact velocity and impingement angle by keeping all other factors constant. The steady state erosion results for jute epoxy composites shows better wear resistant behavior for 40 wt.% jute fiber loading. Hence, for further fabrication of series of hybrid composite 40 wt.% jute fiber is kept constant and granite powder is varied in three different (8, 16 and 24 wt.%) weight percentages. The granite filler content in the jute epoxy composite played a major contribution for slurry erosion resistance. Finally, the obtained experimental results are compared with simulated model results by using a computational fluid dynamics tool. The eroded samples are observed through scanning electron microscope to study the wear mechanism.

Abstract P3-03-05: Establishment and evaluation of ER+ breast cancer models using an optimized methodology for exogenous hormone delivery

Preclinical in vivo models of estrogen receptor positive (ER+) breast cancer rely on exogenous supplementation of hormones for growth. This requirement leads to animal toxicity and mortality over time, limiting development and drug testing in these types of models. Efficacy of test agents, particularly endocrine therapies, may also be altered in these models due to excessive hormone exposure, highlighting the need to improve methods for the establishment and testing of ER+ breast models.

We have developed an alternative method of hormone supplementation in ER+ breast cancer models and optimized this method for testing of endocrine therapies. Using two cell-based breast models, we demonstrated improved breast tumor take and time to tumor volume endpoint while reducing animal toxicity and mortality associated with standard hormone supplementation. Subsequent studies identified the lowest effective dose (LED) of supplement for hormone dependent model growth with a preclinically relevant time to tumor volume endpoint. Activity of endocrine therapies including tamoxifen, letrozole, fulvestrant and exemestane were compared at the standard and LED hormone concentrations. In these studies tamoxifen treatment resulted in tumor regressions which was not appreciably improved using the LED dose of supplement. However letrozole activity was improved in the LED study suggesting hormone supplementation can impact activity of some agents. Using this process we also generated a panel of ER+ patient-derived xenograft (PDX) models, including two novel hormone therapy responsive models from chemo-naïve or hormone therapy pretreated patients, designated ST986 and ST2177, respectively.

This improved method of hormone supplementation diminishes the adverse effects of standard hormone supplementation and provides utility for development of anticancer therapies in ER+ breast models.

Citation Format: Wick MJ, Vaught T, Meade J, Gamez L, Farley M, Tolcher AW, Rasco D, Patnaik A, Drengler RL, Rosenthal A, Papadopoulos KP. Establishment and evaluation of ER+ breast cancer models using an optimized methodology for exogenous hormone delivery. [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 P3-03-05.