Leukemic mutation FLT3-ITD is retained in dendritic cells and disrupts their homeostasis leading to expanded Th17 frequency

Dendritic cells (DC) are mediators between innate and adaptive immune responses to pathogens and tumors. DC development is determined by signaling through the receptor tyrosine kinase Fms-like tyrosine kinase 3 (FLT3) in bone marrow myeloid progenitors. Recently the naming conventions for DC phenotypes have been updated to distinguish between "Conventional" DCs (cDCs) and plasmacytoid DCs (pDCs). Activating mutations of FLT3, including Internal Tandem Duplication (FLT3-ITD), are associated with poor prognosis for acute myeloid leukemia (AML) patients. Having a shared myeloid lineage it can be difficult to distinguish bone fide DCs from AML tumor cells. To date, there is little information on the effects of FLT3-ITD in DC biology. To further elucidate this relationship we utilized CITE-seq technology in combination with flow cytometry and multiplex immunoassays to measure changes to DCs in human and mouse tissues. We examined the cDC phenotype and frequency in bone marrow aspirates from patients with AML to understand the changes to cDCs associated with FLT3-ITD. When compared to healthy donor (HD) we found that a subset of FLT3-ITD+ AML patient samples have overrepresented populations of cDCs and disrupted phenotypes. Using a mouse model of FLT3-ITD+ AML, we found that cDCs were increased in percentage and number compared to control wild-type (WT) mice. Single cell RNA-seq identified FLT3-ITD+ cDCs as skewed towards a cDC2 T-bet- phenotype, previously shown to promote Th17 T cells. We assessed the phenotypes of CD4+ T cells in the AML mice and found significant enrichment of both Treg and Th17 CD4+ T cells in the bone marrow and spleen compartments. Ex vivo stimulation of CD4+ T cells also showed increased Th17 phenotype in AML mice. Moreover, co-culture of AML mouse-derived DCs and naïve OT-II cells preferentially skewed T cells into a Th17 phenotype. Together, our data suggests that FLT3-ITD+ leukemia-associated cDCs polarize CD4+ T cells into Th17 subsets, a population that has been shown to be negatively associated with survival in solid tumor contexts. This illustrates the complex tumor microenvironment of AML and highlights the need for further investigation into the effects of FLT3-ITD mutations on DC phenotypes and their downstream effects on Th polarization.

Mapping the proteogenomic landscape enables prediction of drug response in acute myeloid leukemia

Acute myeloid leukemia is a poor-prognosis cancer commonly stratified by genetic aberrations, but these mutations are often heterogeneous and fail to consistently predict therapeutic response. Here, we combine transcriptomic, proteomic, and phosphoproteomic datasets with ex vivo drug sensitivity data to help understand the underlying pathophysiology of AML beyond mutations. We measure the proteome and phosphoproteome of 210 patients and combine them with genomic and transcriptomic measurements to identify four proteogenomic subtypes that complement existing genetic subtypes. We build a predictor to classify samples into subtypes and map them to a "landscape" that identifies specific drug response patterns. We then build a drug response prediction model to identify drugs that target distinct subtypes and validate our findings on cell lines representing various stages of quizartinib resistance. Our results show how multiomics data together with drug sensitivity data can inform therapy stratification and drug combinations in AML.

Synthesis and evaluation of druglike parameters via in silico techniques for a series of heterocyclic monosquarate-amide derivatives as potential carboxylic acid bioisosteres

Herein, we present a synthetic compound library comprising of 13 structurally diverse heterocyclic monosquarate-amide derivatives. The compounds featured in this library were designed as potential bioisosteric replacements carboxylic acid moiety's. A good selection of the compounds presented exhibit unique molecular architecture and have shown promising results following in silico evaluation of 'druglike properties' using Swiss ADME. The research presented in this work focuses on the preparation of derivatives of 3,4-dihydroxycyclobut-3-ene-1,2-dione, a known carboxylic acid bioisostere.

Clinical Correlates of Venetoclax-Based Combination Sensitivities to Augment Acute Myeloid Leukemia Therapy

The BCL2 inhibitor venetoclax combined with the hypomethylating agent azacytidine shows significant clinical benefit in a subset of patients with acute myeloid leukemia (AML); however, resistance limits response and durability. We prospectively profiled the ex vivo activity of 25 venetoclax-inclusive combinations on primary AML patient samples to identify those with improved potency and synergy compared with venetoclax + azacytidine (Ven + azacytidine). Combination sensitivities correlated with tumor cell state to discern three patterns: primitive selectivity resembling Ven + azacytidine, monocytic selectivity, and broad efficacy independent of cell state. Incorporation of immunophenotype, mutation, and cytogenetic features further stratified combination sensitivity for distinct patient subtypes. We dissect the biology underlying the broad, cell state-independent efficacy for the combination of venetoclax plus the JAK1/2 inhibitor ruxolitinib. Together, these findings support opportunities for expanding the impact of venetoclax-based drug combinations in AML by leveraging clinical and molecular biomarkers associated with ex vivo responses.

SIGNIFICANCE

By mapping drug sensitivity data to clinical features and tumor cell state, we identify novel venetoclax combinations targeting patient subtypes who lack sensitivity to Ven + azacytidine. This provides a framework for a taxonomy of AML informed by readily available sets of clinical and genetic features obtained as part of standard care. See related commentary by Becker, p. 437 . This article is featured in Selected Articles from This Issue, p. 419.

Influence of marker weights optimization on scapular kinematics estimated with a multibody kinematic optimization

Scapular kinematic estimates are altered by soft tissue artefacts, therefore experimental and numerical methods should be developed to improve their accuracy. This study aimed to assess the influence of weights applied to the scapula markers within a closed-loop multibody kinematic optimization on scapular kinematic estimates. Fifteen healthy volunteers performed static postures mimicking analytical, daily living and sport movements. Scapulo-thoracic angles were computed either from a scapula locator as the reference, or from a closed-loop multibody-kinematic optimization (MKO) including a participant-specific point-on-ellipsoid scapulothoracic joint. Weights applied to scapula markers in the MKO were optimized to minimize the difference in scapular orientation from the reference. Optimizing weighting sets significantly (p < 0.0001) improved scapular orientation from 0.9° to 12.1° in comparison to scapular kinematics estimated with non-optimized weighting sets. The mean optimized weighting set contained no neglectable weight for all markers from the acromion to the medial border of the scapular spine but showed no significant difference (p = 0.547) compared to homogeneous weights. Optimized weighting sets were participant- and movement- specific. To conclude, homogenous weights applied on redundant markers located from acromion to scapular medial border spine are recommended when estimating scapular kinematics in upper limb MKO.

Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Mutations in Fms-like tyrosine kinase 3 (FLT3) are common drivers in acute myeloid leukemia (AML) yet FLT3 inhibitors only provide modest clinical benefit. Prior work has shown that inhibitors of lysine-specific demethylase 1 (LSD1) enhance kinase inhibitor activity in AML. Here we show that combined LSD1 and FLT3 inhibition induces synergistic cell death in FLT3-mutant AML. Multi-omic profiling revealed that the drug combination disrupts STAT5, LSD1, and GFI1 binding at the MYC blood superenhancer, suppressing superenhancer accessibility as well as MYC expression and activity. The drug combination simultaneously results in the accumulation of repressive H3K9me1 methylation, an LSD1 substrate, at MYC target genes. We validated these findings in 72 primary AML samples with the nearly every sample demonstrating synergistic responses to the drug combination. Collectively, these studies reveal how epigenetic therapies augment the activity of kinase inhibitors in FLT3-ITD (internal tandem duplication) AML.

IMPLICATIONS

This work establishes the synergistic efficacy of combined FLT3 and LSD1 inhibition in FLT3-ITD AML by disrupting STAT5 and GFI1 binding at the MYC blood-specific superenhancer complex.

Immune cell proportions correlate with clinicogenomic features and ex vivo drug responses in acute myeloid leukemia

Introduction

The implementation of small-molecule and immunotherapies in acute myeloid leukemia (AML) has been challenging due to genetic and epigenetic variability amongst patients. There are many potential mechanisms by which immune cells could influence small-molecule or immunotherapy responses, yet, this area remains understudied.

Methods

Here we performed cell type enrichment analysis from over 560 AML patient bone marrow and peripheral blood samples from the Beat AML dataset to describe the functional immune landscape of AML.

Results

We identify multiple cell types that significantly correlate with AML clinical and genetic features, and we also observe significant correlations of immune cell proportions with ex vivo small-molecule and immunotherapy responses. Additionally, we generated a signature of terminally exhausted T cells (Tex) and identified AML with high monocytic proportions as strongly correlating with increased proportions of these immunosuppressive T cells.

Discussion

Our work, which is accessible through a new "Cell Type" module in our visualization platform (Vizome; http://vizome.org/), can be leveraged to investigate potential contributions of different immune cells on many facets of the biology of AML.

NGS-defined measurable residual disease (MRD) after initial chemotherapy as a prognostic biomarker for acute myeloid leukemia

Treated AML patients often have measurable residual disease (MRD) due to persisting low-level clones. This study assessed whether residual post-treatment somatic mutations, detected by NGS, were significantly prognostic for subsequent clinical outcomes. AML patients (n = 128) underwent both pre-and post-treatment testing with the same 42-gene MRD-validated NGS assay. After induction, 59 (46%) patients were mutation-negative (0.0024 VAF detection limit) and 69 (54%) had ≥1 persisting NGS-detectable mutation. Compared with NGS-negative patients, NGS-positive patients had shorter overall survival (17 months versus median not reached; P = 0.004; hazard ratio = 2.2 [95% CI: 1.3-3.7]) and a shorter time to relapse (14 months versus median not reached; P = 0.014; HR = 1.9 [95% CI: 1.1-3.1]). Among 95 patients with a complete morphologic remission (CR), 43 (45%) were MRD-positive by NGS and 52 (55%) were MRD-negative. These MRD-positive CR patients had a shorter overall survival (16.8 months versus median not reached; P = 0.013; HR = 2.1 [95% CI: 1.2-3.9]) than did the MRD-negative CR patients. Post-treatment persisting MRD positivity, defined by the same NGS-based test used at diagnosis, is thus a more sensitive biomarker for low-level leukemic clones compared to traditional non-molecular methods and is prognostic of subsequent relapse and death.

Integrative analysis of drug response and clinical outcome in acute myeloid leukemia

Acute myeloid leukemia (AML) is a cancer of myeloid-lineage cells with limited therapeutic options. We previously combined ex vivo drug sensitivity with genomic, transcriptomic, and clinical annotations for a large cohort of AML patients, which facilitated discovery of functional genomic correlates. Here, we present a dataset that has been harmonized with our initial report to yield a cumulative cohort of 805 patients (942 specimens). We show strong cross-cohort concordance and identify features of drug response. Further, deconvoluting transcriptomic data shows that drug sensitivity is governed broadly by AML cell differentiation state, sometimes conditionally affecting other correlates of response. Finally, modeling of clinical outcome reveals a single gene, PEAR1, to be among the strongest predictors of patient survival, especially for young patients. Collectively, this report expands a large functional genomic resource, offers avenues for mechanistic exploration and drug development, and reveals tools for predicting outcome in AML.

Identification and prioritization of myeloid malignancy germline variants in a large cohort of adult patients with AML

Inherited predisposition to myeloid malignancies is more common than previously appreciated. We analyzed the whole-exome sequencing data of paired leukemia and skin biopsy samples from 391 adult patients from the Beat AML 1.0 consortium. Using the 2015 American College of Medical Genetics and Genomics (ACMG) guidelines for variant interpretation, we curated 1547 unique variants from 228 genes. The pathogenic/likely pathogenic (P/LP) germline variants were identified in 53 acute myeloid leukemia (AML) patients (13.6%) in 34 genes, including 6.39% (25/391) of patients harboring P/LP variants in genes considered clinically actionable (tier 1). 41.5% of the 53 patients with P/LP variants were in genes associated with the DNA damage response. The most frequently mutated genes were CHEK2 (8 patients) and DDX41 (7 patients). Pathogenic germline variants were also found in new candidate genes (DNAH5, DNAH9, DNMT3A, and SUZ12). No strong correlation was found between the germline mutational rate and age of AML onset. Among 49 patients who have a reported history of at least one family member affected with hematological malignancies, 6 patients harbored known P/LP germline variants and the remaining patients had at least one variant of uncertain significance, suggesting a need for further functional validation studies. Using CHEK2 as an example, we show that three-dimensional protein modeling can be one of the effective methodologies to prioritize variants of unknown significance for functional studies. Further, we evaluated an in silico approach that applies ACMG curation in an automated manner using the tool for assessment and (TAPES) prioritization in exome studies, which can minimize manual curation time for variants. Overall, our findings suggest a need to comprehensively understand the predisposition potential of many germline variants in order to enable closer monitoring for disease management and treatment interventions for affected patients and families.

Correlation study between the magnetic resonance imaging features of breast cancer and expression of immune molecular subtypes

OBJECTIVE

To investigate the correlation between breast cancer magnetic resonance imaging features and immune molecular subtypes.

PATIENTS AND METHODS

A total of 129 breast cancer patients were selected as the research object. All the patients were diagnosed by histopathology. All of them had breast magnetic resonance imaging and examination data of immunohistochemical (IHC) ER, PR, HER-2, and Ki-67. The correlation of breast cancer magnetic resonance imaging features with different immune molecular subtypes was retrospectively analyzed.

RESULTS

Breast cancer is divided into different molecular subtypes. There were 72 cases with Luminal A type (55.81%), 20 cases with Luminal B type (15.50%), 14 cases with HER-2+ type (HER-2 type for over-expression) (10.85%), 23 cases with TNBC type (ER, PR and HER-2 were negative) (17.84%). The magnetic resonance imaging features of breast cancer were included, the post-enhanced morphology, margins, internal enhancement features, time-signal intensity curve (TIC) and molecular subtype expression of lesions were significantly correlated with the immune molecular subtypes (C=0.602, 0.439, 0.350 and 0.407, p=0.000, 0.000, 0.006 and 0.000). Lesion morphology: Luminal A type was mainly oval, accounting for 76.39% (55/76). Luminal B type and HER-2+ type was mainly irregular, accounting for 75.00% (15/20) and 64.29% (9/14) respectively. TNBC type was mainly shown as lobulation, accounting for 60.87% (14/23). Margin of the lesion: Luminal A type was mainly smooth margin, accounting for 73.61% (53/72). Luminal B type and TNBC type were mainly irregular margin, accounting for 70.00% (14/20) and 56.52% (13/23) respectively. The margin of HER-2+ type was mainly spiculation, accounting for 64.29% (9/14). The internal enhancement features: Luminal A type was mainly even enhancement, accounting for 62.50% (45/72). Luminal B type and HER-2+ type were mainly heterogeneous enhancement, accounting for 65.00% (13/20) and 64.29% (9/14) respectively. TNBC type was mainly annular enhancement, accounting for 73.91% (17/23). TIC type: Luminal A type was mainly Type II, accounting for 66.67% (48/72). Luminal B, HER-2+ type and TNBC type was mainly Type III, accounting for 70.00% (14/20), 64.29% (9/14) and 60.87% (14/23) respectively. The clinical signs include painless breast lumps, bloody breast discharge, and orange peel-like skin changes, nipple retraction and nipple elevation. There is no significant correlation between the above signs and the expression of molecular subtypes (C=0.014, 0.129, 0.154, 0.097 and 0.057, p=0.999, 0.533, 0.447, 0.747 and 0.935 respectively), the difference is not statistically significant (p>0.05).

CONCLUSIONS

The characteristics of breast cancer magnetic resonance imaging was certainly correlated with the expression of immune molecular subtypes. The breast cancer molecular subtypes can be predicted by the imaging signs, which can provide valuable information for preoperative neoadjuvant treatment of breast cancer.

The correlation of 18F-FDG PET/CT metabolic parameters, clinicopathological factors, and prognosis in breast cancer

PURPOSE

To study the imaging parameters of ¹⁸F-fluorodeoxy glucose (¹⁸F-FDG) in breast cancer on positron emission tomography/computed tomography (PET/CT)-the correlation of clinical pathological factors and prognosis among the maximum standardized uptake value (SUVmax), metabolic tumor volume (MTV), and total lesion glycolysis (TLG) of lesions for patients.

METHODS

From January 2012 to December 2014, a total of 125 female patients were treated in our hospital for the first time and were diagnosed as breast cancer by histopathology. They were selected as the research subjects. All of them had complete ¹⁸F-FDG PET/CT examination data before surgery, the postoperative clinicopathological information, and follow-up data. They were divided into the event group (38 cases) and the event-free group (87 cases) according to whether local recurrence or distant metastasis occurred after the follow-up, with the follow-up time 4-60 months. The correlation on ¹⁸F-FDG PET/CT metabolic parameters of breast cancer with clinicopathological factors and prognosis was retrospectively evaluated.

RESULTS

The primary lesions of 125 cases with breast cancers all had higher ¹⁸F-FDG uptake, and the SUVmax, MTV, and TLG of the primary tumors in the event group were significantly higher than those in the event-free group (t = 2.645, 2.782, 15.263, p = 0.011, 0.008, 0.000), p < 0.05; SUVmax, MTV, and TLG of primary breast cancer have no correlation with age and tumor site of patient (p > 0.05); there were statistically significant differences in the SUVmax, MTV, and TLG of primary tumor in the comparison of different tumor size, T stage, N stage, and histological grades (p < 0.05); all of SUVmax, MTV, and TLG in the estrogen receptor (ER) and/or progesterone receptor (PR) positive groups were lower than those in the negative group, with statistically significant difference (p < 0.05); the SUVmax, MTV, and TLG of human epidermal growth factor receptor 2 (HER2) positive group, proliferating cell nuclear antigen (Ki-67) high expression group were higher than those in the negative group and low expression group, with statistically significant difference (p < 0.05). There were 38 recurrence and metastasis cases within 125 cases with breast cancer in 5 years after operation, with the total recurrence and metastasis rate as 30.40% (38/125). The event-free survival rate in the SUVmax ≥ 8.64 group was significantly lower than that in the SUVmax < 8.64 group (p < 0.01).

CONCLUSIONS

The metabolic parameters of ¹⁸F-FDG PET/CT in breast cancer can reflect the biological behavior of the tumor indirectly; therefore, it was studied on the related correlation to provide the guidance of clinical individualized comprehensive treatment and prognostic judgment.

Simultaneous kinase inhibition with ibrutinib and BCL2 inhibition with venetoclax offers a therapeutic strategy for acute myeloid leukemia

Acute myeloid leukemia (AML) results from the enhanced proliferation and impaired differentiation of hematopoietic stem and progenitor cells. Using an ex vivo functional screening assay, we identified that the combination of the BTK inhibitor ibrutinib and BCL2 inhibitor venetoclax (IBR + VEN), currently in clinical trials for chronic lymphocytic leukemia (CLL), demonstrated enhanced efficacy on primary AML patient specimens, AML cell lines, and in a mouse xenograft model of AML. Expanded analyses among a large cohort of hematologic malignancies (n = 651 patients) revealed that IBR + VEN sensitivity associated with selected genetic and phenotypic features in both CLL and AML specimens. Among AML samples, 11q23 MLL rearrangements were highly sensitive to IBR + VEN. Analysis of differentially expressed genes with respect to IBR + VEN sensitivity indicated pathways preferentially enriched in patient samples with reduced ex vivo sensitivity, including IL-10 signaling. These findings suggest that IBR + VEN may represent an effective therapeutic option for patients with AML.

Genomic landscape of neutrophilic leukemias of ambiguous diagnosis

Chronic neutrophilic leukemia (CNL), atypical chronic myeloid leukemia (aCML), and myelodysplastic/myeloproliferative neoplasms, unclassifiable (MDS/MPN-U) are a group of rare and heterogeneous myeloid disorders. There is strong morphologic resemblance among these distinct diagnostic entities as well as a lack of specific molecular markers and limited understanding of disease pathogenesis, which has made diagnosis challenging in certain cases. The treatment has remained empirical, resulting in dismal outcomes. We, therefore, performed whole-exome and RNA sequencing of these rare hematologic malignancies and present the most complete survey of the genomic landscape of these diseases to date. We observed a diversity of combinatorial mutational patterns that generally do not cluster within any one diagnosis. Gene expression analysis reveals enrichment, but not cosegregation, of clinical and genetic disease features with transcriptional clusters. In conclusion, these groups of diseases represent a continuum of related diseases rather than discrete diagnostic entities.

CSF1R inhibitors exhibit antitumor activity in acute myeloid leukemia by blocking paracrine signals from support cells

To identify new therapeutic targets in acute myeloid leukemia (AML), we performed small-molecule and small-interfering RNA (siRNA) screens of primary AML patient samples. In 23% of samples, we found sensitivity to inhibition of colony-stimulating factor 1 (CSF1) receptor (CSF1R), a receptor tyrosine kinase responsible for survival, proliferation, and differentiation of myeloid-lineage cells. Sensitivity to CSF1R inhibitor GW-2580 was found preferentially in de novo and favorable-risk patients, and resistance to GW-2580 was associated with reduced overall survival. Using flow cytometry, we discovered that CSF1R is not expressed on the majority of leukemic blasts but instead on a subpopulation of supportive cells. Comparison of CSF1R-expressing cells in AML vs healthy donors by mass cytometry revealed expression of unique cell-surface markers. The quantity of CSF1R-expressing cells correlated with GW-2580 sensitivity. Exposure of primary AML patient samples to a panel of recombinant cytokines revealed that CSF1R inhibitor sensitivity correlated with a growth response to CSF1R ligand, CSF1, and other cytokines, including hepatocyte growth factor (HGF). The addition of CSF1 increased the secretion of HGF and other cytokines in conditioned media from AML patient samples, whereas adding GW-2580 reduced their secretion. In untreated cells, HGF levels correlated significantly with GW-2580 sensitivity. Finally, recombinant HGF and HS-5-conditioned media rescued cell viability after GW-2580 treatment in AML patient samples. Our results suggest that CSF1R-expressing cells support the bulk leukemia population through the secretion of HGF and other cytokines. This study identifies CSF1R as a novel therapeutic target of AML and provides a mechanism of paracrine cytokine/growth factor signaling in this disease.

Two myeloid leukemia cases with rare FLT3 fusions

Genetic rearrangements involving FLT3 are rare and only recently have been detected in myeloid/lymphoid neoplasms associated with eosinophilia (MLN-eos) and chronic myeloproliferative disorders. Here we report two cases with FLT3 fusions in patients demonstrating mixed features of myelodysplastic/myeloproliferative neoplasms. In the first case, FLT3 was fused with a new fusion partner MYO18A in a patient with marrow features most consistent with atypical chronic myeloid leukemia; the second case involving ETV6-FLT3 fusion was observed in a case with bone marrow features most consistent with chronic myelomonocytic leukemia. Notably, we observed that samples from both patients demonstrated FLT3 inhibitor (quizartinib and sorafenib) sensitivity in ex vivo drug screening assay.

Functional genomic landscape of acute myeloid leukaemia

The implementation of targeted therapies for acute myeloid leukaemia (AML) has been challenging because of the complex mutational patterns within and across patients as well as a dearth of pharmacologic agents for most mutational events. Here we report initial findings from the Beat AML programme on a cohort of 672 tumour specimens collected from 562 patients. We assessed these specimens using whole-exome sequencing, RNA sequencing and analyses of ex vivo drug sensitivity. Our data reveal mutational events that have not previously been detected in AML. We show that the response to drugs is associated with mutational status, including instances of drug sensitivity that are specific to combinatorial mutational events. Integration with RNA sequencing also revealed gene expression signatures, which predict a role for specific gene networks in the drug response. Collectively, we have generated a dataset-accessible through the Beat AML data viewer (Vizome)-that can be leveraged to address clinical, genomic, transcriptomic and functional analyses of the biology of AML.

Negative association of antibiotics on clinical activity of immune checkpoint inhibitors in patients with advanced renal cell and non-small-cell lung cancer

Background

The composition of gut microbiota affects antitumor immune responses, preclinical and clinical outcome following immune checkpoint inhibitors (ICI) in cancer. Antibiotics (ATB) alter gut microbiota diversity and composition leading to dysbiosis, which may affect effectiveness of ICI.

Patients and methods

We examined patients with advanced renal cell carcinoma (RCC) and non-small-cell lung cancer (NSCLC) treated with anti-programmed cell death ligand-1 mAb monotherapy or combination at two academic institutions. Those receiving ATB within 30 days of beginning ICI were compared with those who did not. Objective response, progression-free survival (PFS) determined by RECIST1.1 and overall survival (OS) were assessed.

Results

Sixteen of 121 (13%) RCC patients and 48 of 239 (20%) NSCLC patients received ATB. The most common ATB were β-lactam or quinolones for pneumonia or urinary tract infections. In RCC patients, ATB compared with no ATB was associated with increased risk of primary progressive disease (PD) (75% versus 22%, P < 0.01), shorter PFS [median 1.9 versus 7.4 months, hazard ratio (HR) 3.1, 95% confidence interval (CI) 1.4-6.9, P < 0.01], and shorter OS (median 17.3 versus 30.6 months, HR 3.5, 95% CI 1.1-10.8, P = 0.03). In NSCLC patients, ATB was associated with similar rates of primary PD (52% versus 43%, P = 0.26) but decreased PFS (median 1.9 versus 3.8 months, HR 1.5, 95% CI 1.0-2.2, P = 0.03) and OS (median 7.9 versus 24.6 months, HR 4.4, 95% CI 2.6-7.7, P < 0.01). In multivariate analyses, the impact of ATB remained significant for PFS in RCC and for OS in NSCLC.

Conclusion

ATB were associated with reduced clinical benefit from ICI in RCC and NSCLC. Modulatation of ATB-related dysbiosis and gut microbiota composition may be a strategy to improve clinical outcomes with ICI.

Not your average birth: considering the possibility of denied or concealed pregnancy

A 23-year-old woman presented to the emergency department (ED) with a 3-day history of lower back pain. She had seen her general practitioner 2 days previously who prescribed trimethoprim for a confirmed urinary tract infection. Routine admission observations showed she was tachycardic, tachypnoeic and slightly hypotensive but non-feverish with normal oxygen saturations. Her urine sample revealed that she was pregnant but was otherwise negative. The patient maintained that she was unaware she was pregnant. She was reviewed by an ED staff grade who was suspicious of a ruptured ectopic pregnancy. She was subsequently referred to the obstetrics and gynaecology registrar who on examination found she had a gravid uterus and vaginal examination revealed that her cervix was 8 cm dilated. The patient was very promptly admitted onto the labour ward for further assessment. She gave birth to a live male infant in the early hours of the next morning.

Genomic-enabled prediction with classification algorithms

Pearson's correlation coefficient (ρ) is the most commonly reported metric of the success of prediction in genomic selection (GS). However, in real breeding ρ may not be very useful for assessing the quality of the regression in the tails of the distribution, where individuals are chosen for selection. This research used 14 maize and 16 wheat data sets with different trait–environment combinations. Six different models were evaluated by means of a cross-validation scheme (50 random partitions each, with 90% of the individuals in the training set and 10% in the testing set). The predictive accuracy of these algorithms for selecting individuals belonging to the best α=10, 15, 20, 25, 30, 35, 40% of the distribution was estimated using Cohen's kappa coefficient (κ) and an ad hoc measure, which we call relative efficiency (RE), which indicates the expected genetic gain due to selection when individuals are selected based on GS exclusively. We put special emphasis on the analysis for α=15%, because it is a percentile commonly used in plant breeding programmes (for example, at CIMMYT). We also used ρ as a criterion for overall success. The algorithms used were: Bayesian LASSO (BL), Ridge Regression (RR), Reproducing Kernel Hilbert Spaces (RHKS), Random Forest Regression (RFR), and Support Vector Regression (SVR) with linear (lin) and Gaussian kernels (rbf). The performance of regression methods for selecting the best individuals was compared with that of three supervised classification algorithms: Random Forest Classification (RFC) and Support Vector Classification (SVC) with linear (lin) and Gaussian (rbf) kernels. Classification methods were evaluated using the same cross-validation scheme but with the response vector of the original training sets dichotomised using a given threshold. For α=15%, SVC-lin presented the highest κ coefficients in 13 of the 14 maize data sets, with best values ranging from 0.131 to 0.722 (statistically significant in 9 data sets) and the best RE in the same 13 data sets, with values ranging from 0.393 to 0.948 (statistically significant in 12 data sets). RR produced the best mean for both κ and RE in one data set (0.148 and 0.381, respectively). Regarding the wheat data sets, SVC-lin presented the best κ in 12 of the 16 data sets, with outcomes ranging from 0.280 to 0.580 (statistically significant in 4 data sets) and the best RE in 9 data sets ranging from 0.484 to 0.821 (statistically significant in 5 data sets). SVC-rbf (0.235), RR (0.265) and RHKS (0.422) gave the best κ in one data set each, while RHKS and BL tied for the last one (0.234). Finally, BL presented the best RE in two data sets (0.738 and 0.750), RFR (0.636) and SVC-rbf (0.617) in one and RHKS in the remaining three (0.502, 0.458 and 0.586). The difference between the performance of SVC-lin and that of the rest of the models was not so pronounced at higher percentiles of the distribution. The behaviour of regression and classification algorithms varied markedly when selection was done at different thresholds, that is, κ and RE for each algorithm depended strongly on the selection percentile. Based on the results, we propose classification method as a promising alternative for GS in plant breeding.

Anatomical characterisation of the cricothyroid membrane in females of childbearing age using computed tomography

BACKGROUND

In the event of failure to secure the airway by conventional means, it may be necessary to perform invasive airway access via the cricothyroid membrane. No studies have addressed anatomy of this structure in the obstetric population. We aimed to review the anatomical variation of this structure in a population of childbearing age.

METHODS

We searched the radiology database for computed tomography studies of the neck performed in a 13-month period in consecutive patients aged 15-55 years. Studies on 18 females and 22 males were reviewed. Male patients were included for comparison. Data were reconstructed using a high spatial frequency algorithm to optimise spatial resolution. Five parameters were measured: distance from the skin to the membrane, maximum midline height of the membrane in the vertical plane, maximum transverse diameter of the membrane, neck diameter and cartilaginous calcification.

RESULTS

The distance (mean range) from skin to the membrane was similar in females and males (16.2 [3-33] vs. 13.9 [3-37] mm, P = 0.42). The vertical height (9.9 [7-17] vs. 11.4 [8-15] mm, P = 0.04) and maximum width of the membrane (14.5 [10-17] mm vs. 12.5 [10-15] mm, P < 0.01) were greater in males. Cartilaginous calcification was low and did not differ between genders.

CONCLUSIONS

The cricothyroid membrane is not necessarily a superficial structure and consequently may be difficult to palpate. The smallest dimensions of the membrane indicate that smaller than recommended cricothyroidotomy devices may be required in some patients as the external diameter of commercial trocar devices and tracheal tubes may exceed 7 mm.

Comparison of selective genotyping strategies for prediction of breeding values in a population undergoing selection

Genomewide marker information can improve the reliability of breeding value predictions for young selection candidates in genomic selection. However, the cost of genotyping limits its use to elite animals, and how such selective genotyping affects predictive ability of genomic selection models is an open question. We performed a simulation study to evaluate the quality of breeding value predictions for selection candidates based on different selective genotyping strategies in a population undergoing selection. The genome consisted of 10 chromosomes of 100 cM each. After 5,000 generations of random mating with a population size of 100 (50 males and 50 females), generation G(0) (reference population) was produced via a full factorial mating between the 50 males and 50 females from generation 5,000. Different levels of selection intensities (animals with the largest yield deviation value) in G(0) or random sampling (no selection) were used to produce offspring of G(0) generation (G(1)). Five genotyping strategies were used to choose 500 animals in G(0) to be genotyped: 1) Random: randomly selected animals, 2) Top: animals with largest yield deviation values, 3) Bottom: animals with lowest yield deviations values, 4) Extreme: animals with the 250 largest and the 250 lowest yield deviations values, and 5) Less Related: less genetically related animals. The number of individuals in G(0) and G(1) was fixed at 2,500 each, and different levels of heritability were considered (0.10, 0.25, and 0.50). Additionally, all 5 selective genotyping strategies (Random, Top, Bottom, Extreme, and Less Related) were applied to an indicator trait in generation G(0,) and the results were evaluated for the target trait in generation G(1), with the genetic correlation between the 2 traits set to 0.50. The 5 genotyping strategies applied to individuals in G(0) (reference population) were compared in terms of their ability to predict the genetic values of the animals in G(1) (selection candidates). Lower correlations between genomic-based estimates of breeding values (GEBV) and true breeding values (TBV) were obtained when using the Bottom strategy. For Random, Extreme, and Less Related strategies, the correlation between GEBV and TBV became slightly larger as selection intensity decreased and was largest when no selection occurred. These 3 strategies were better than the Top approach. In addition, the Extreme, Random, and Less Related strategies had smaller predictive mean squared errors (PMSE) followed by the Top and Bottom methods. Overall, the Extreme genotyping strategy led to the best predictive ability of breeding values, indicating that animals with extreme yield deviations values in a reference population are the most informative when training genomic selection models.

Association of cigarette smoking with drug use and risk taking behaviour in Irish teenagers

BACKGROUND

Cigarette smoking has been shown to act as a 'gateway' to cannabis use and further risk taking behaviours. This study aims to (1) establish the prevalence of cigarette smoking and cannabis use in Irish teenagers, (2) to quantify the strength and significance of the association of cigarette smoking and cannabis use and other high risk behaviours and (3) examine whether the above associations are independent of the extent of social networking.

METHODS

Adolescent students across five urban, non-fee paying schools completed an abridged European schools survey project on alcohol and other drugs (ESPAD) questionnaire.

RESULTS

370/417 (88.7%) students completed the questionnaire. 228 (61.6%) were female, 349 (94.3%) were aged 15-16 years. 48.4% of those surveyed had smoked tobacco at some stage in their lifetime, 18.1% in the last 30 days. 15.1% have used cannabis with 5.7% using it in the last 30 days. 29.6% of cigarette smokers have used cannabis in comparison to 1.6% of non-smokers. On multivariate analysis lifetime cigarette smoking status was independently associated with hard drug use, adjusted OR=6.0, p<0.01; soft drug use, adjusted OR=4.6, p<0.01 and high risk sex practises, adjusted OR=10.6, p<0.05.

CONCLUSIONS

Cigarette smoking prevalence remains high in Irish teenagers and is significantly associated with drug use and other risk taking behaviours. Specific teenage smoking cessation strategies need to be developed targeting these combined high risk health behaviours.

Predictive ability of direct genomic values for lifetime net merit of Holstein sires using selected subsets of single nucleotide polymorphism markers

The objective of the present study was to assess the predictive ability of subsets of single nucleotide polymorphism (SNP) markers for development of low-cost, low-density genotyping assays in dairy cattle. Dense SNP genotypes of 4,703 Holstein bulls were provided by the USDA Agricultural Research Service. A subset of 3,305 bulls born from 1952 to 1998 was used to fit various models (training set), and a subset of 1,398 bulls born from 1999 to 2002 was used to evaluate their predictive ability (testing set). After editing, data included genotypes for 32,518 SNP and August 2003 and April 2008 predicted transmitting abilities (PTA) for lifetime net merit (LNM$), the latter resulting from progeny testing. The Bayesian least absolute shrinkage and selection operator method was used to regress August 2003 PTA on marker covariates in the training set to arrive at estimates of marker effects and direct genomic PTA. The coefficient of determination (R(2)) from regressing the April 2008 progeny test PTA of bulls in the testing set on their August 2003 direct genomic PTA was 0.375. Subsets of 300, 500, 750, 1,000, 1,250, 1,500, and 2,000 SNP were created by choosing equally spaced and highly ranked SNP, with the latter based on the absolute value of their estimated effects obtained from the training set. The SNP effects were re-estimated from the training set for each subset of SNP, and the 2008 progeny test PTA of bulls in the testing set were regressed on corresponding direct genomic PTA. The R(2) values for subsets of 300, 500, 750, 1,000, 1,250, 1,500, and 2,000 SNP with largest effects (evenly spaced SNP) were 0.184 (0.064), 0.236 (0.111), 0.269 (0.190), 0.289 (0.179), 0.307 (0.228), 0.313 (0.268), and 0.322 (0.291), respectively. These results indicate that a low-density assay comprising selected SNP could be a cost-effective alternative for selection decisions and that significant gains in predictive ability may be achieved by increasing the number of SNP allocated to such an assay from 300 or fewer to 1,000 or more.

Machine learning classification procedure for selecting SNPs in genomic selection: application to early mortality in broilers

Genome-wide association studies using single nucleotide polymorphisms (SNPs) can identify genetic variants related to complex traits. Typically thousands of SNPs are genotyped, whereas the number of phenotypes for which there is genomic information may be smaller. When predicting phenotypes, options for statistical model building range from incorporating all possible markers into the specification to including only sets of relevant SNPs (features). In the latter case, an efficient method of selecting influential features is required. A two-step feature selection method for binary traits was developed, which consisted of filtering (using information gain), and wrapping (using naïve Bayesian classification). The filter reduces the large number of SNPs to a much smaller size, to facilitate the wrapper step. As the procedure is tailored for discrete outcomes, an approach based on discretization of phenotypic values was developed, to enable feature selection in a classification framework. The method was applied to chick mortality rates (0-14 days of age) on progeny from 201 sires in a commercial broiler line, with the goal of identifying SNPs (over 5000) related to progeny mortality. To mimic a case-control study, sires were clustered into two groups, low and high, according to two arbitrarily chosen mortality rate cut points. By varying these thresholds, 11 different 'case-control' samples were formed, and the SNP selection procedure was applied to each sample. To compare the 11 sets of chosen SNPs, predicted residual sum of squares (PRESS) from a linear model was used. The two-step method improved naïve Bayesian classification accuracy over the case without feature selection (from around 50 to above 90% without and with feature selection in each case-control sample). The best case-control group (63 sires above or below the thresholds) had the smallest PRESS statistic among groups with model p-values below 0.003. The 17 SNPs selected using this group accounted for 31% of the variation in raw mortality rates between sire families.

Machine learning classification procedure for selecting SNPs in genomic selection: application to early mortality in broilers

In genome-wide association studies using single nucleotide polymorphisms (SNPs), typically thousands of SNPs are genotyped, whereas the number of phenotypes for which there is genomic information may be smaller. Atwo-step SNP (feature) selection method was developed, which consisted of filtering (using information gain), and wrapping (using naïve Bayesian classification). This was based on discretization of the continuous phenotypic values. The method was applied to chick early mortality rates (0-14 days of age) on progeny from 201 sires in a commercial broiler line, with the goal of identifying SNPs (over 5000) related to progeny mortality. Sires were clustered into two groups, low and high, according to two arbitrarily chosen mortality rate thresholds. By varying these thresholds, 11 different "case-control" samples were formed, and the SNP selection procedure was applied to each sample. To compare the 11 sets of chosen SNPs, predicted residual sum of squares (PRESS)from a linear model was used. Naive Bayesian classification accuracy was improved over the case without feature selection (from 50% to 90%). Seventeen SNPs in the best case-control group (with smallest PRESS) accounted for 31% of the variance among sire family mortality rates.

Relationship of pediatric overall performance category and pediatric cerebral performance category scores at pediatric intensive care unit discharge with outcome measures collected at hospital discharge and 1- and 6-month follow-up assessments

OBJECTIVE

Given the current focus on outcomes, there is a crucial need for easily utilized measures that can effectively quantify morbidity or disability after a child's critical illness or injury. The purpose of this study is to significantly extend the research on two such promising measures: the Pediatric Overall Performance Category (POPC) and the Pediatric Cerebral Performance Category (PCPC).

DESIGN

Cross-sectional analysis of a sample of pediatric intensive care unit (PICU) discharges and a prospective follow-up of this cohort of children.

SETTING

Arkansas Children's Hospital.

PATIENTS

Two hundred children (ranging in age from birth to 21 yrs) discharged from a PICU.

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

Data were collected at PICU discharge, hospital discharge, and 1- and 6-month follow-up assessments after hospital discharge. Measures utilized included the POPC (at PICU discharge), PCPC (at PICU discharge), Stanford-Binet Intelligence Scale, fourth edition (at hospital discharge), Bayley Scales of Infant Development, second edition (at hospital discharge), and the Vineland Adaptive Behavior Scales (at 1 and 6 months after discharge). Stanford-Binet Intelligence Quotients and Bayley Mental Developmental Index scores were significantly different across PCPC categories (p < .0001). Bayley Psychomotor Developmental Index scores and Vineland Adaptive Behavior Scales scores varied significantly across POPC categories (p < .0001). The test for linear trend was also significant for each of the comparisons.

CONCLUSIONS

The results of this study offer additional support for the use of the PCPC and POPC. These brief and easily completed measures can provide useful information regarding probable outcomes for pediatric intensive care patients when more extensive psychometric testing is not feasible or desirable.

Strong-willed children: a challenge to parents and pediatric dentists

Uncooperative behavior that is associated with a child being strong-willed is responsive to specific behavioral intervention strategies that have been extensively studied. These strategies are ones which are likely to be effective in the pediatric dental setting. We propose that these strategies are most effective when an integrative approach to strong-willed behavior is adopted by the pediatric dentist. Utilization of such an approach will reduce difficult child behavior, increase positive interactions between the dentist and child, and reduce parent frustration and concern.

Posttraumatic stress disorder and interpersonal functioning in Vietnam War veterans: a mediational model

This study examines the association between posttraumatic stress disorder (PTSD) and interpersonal functioning in a New Zealand community sample of 756 Vietnam War veterans. The results support previous research findings showing that PTSD adversely affects veterans' interpersonal relationships, family functioning, and marital/dyadic adjustment and show that the effects of PTSD on family functioning and dyadic adjustment are mediated by severity of interpersonal problems. It is suggested that higher levels of PTSD affect the ability of veterans to initiate and maintain interpersonal relationships and that these interpersonal problems are evident in poorer levels of family functioning and poorer dyadic adjustment.

Dose-rate effects of ethylene oxide exposure on developmental toxicity

In risk assessment, evaluating a health effect at a duration of exposure that is untested involves assuming that equivalent multiples of concentration (C) and duration (T) of exposure have the same effect. The limitations of this approach (attributed to F. Haber, Zur Geschichte des Gaskrieges [On the history of gas warfare], in Funf Vortrage aus den Jahren 1920-1923 [Five lectures from the years 1920-1923], 1924, Springer, Berlin, pp. 76-92), have been noted in several studies. The study presented in this paper was designed to specifically look at dose-rate (C x T) effects, and it forms an ideal case study to implement statistical models and to examine the statistical issues in risk assessment. Pregnant female C57BL/6J mice were exposed, on gestational day 7, to ethylene oxide (EtO) via inhalation for 1.5, 3, or 6 h at exposures that result in C x T multiples of 2100 or 2700 ppm-h. EtO was selected because of its short half-life, documented developmental toxicity, and relevance to exposures that occur in occupational settings. Concurrent experiments were run with animals exposed to air for similar periods. Statistical analysis using models developed to assess dose-rate effects revealed significant effects with respect to fetal death and resorptions, malformations, crown-to-rump length, and fetal weight. Animals exposed to short, high exposures of EtO on day 7 of gestation were found to have more adverse effects than animals exposed to the same C x T multiple but at longer, lower exposures. The implication for risk assessment is that applying Haber's Law could potentially lead to an underestimation of risk at a shorter duration of exposure and an overestimation of risk at a longer duration of exposure. Further research, toxicological and statistical, are required to understand the mechanism of the dose-rate effects, and how to incorporate the mechanistic information into the risk assessment decision process.

Gradual painless visual loss: chronic optic neuropathies

The clinician must be the ultimate medical detective when dealing with chronic optic neuropathies. History taking is crucial. Clinical examination may require supplementation with visual field testing, fluorescein angiography, ocular and orbital ultrasound imaging, CT and MR imaging, blood test data, and cerebrospinal fluid or tissue biopsy data to determine the specific diagnosis. This supplementation is labor-intensive and time-consuming; the visual loss usually will progress throughout the process, frustrating and frightening the patient and physician. The final common pathway is gradual optic atrophy; the appearance of the optic nerve is rarely adequate to determine the cause of the visual loss. This article includes tables that review diagnostic aids and therapies, and lists the frequency with which several disease entities were encountered over 15 years in one tertiary care neuro-ophthalmic practice. If a specific cause is discernible, then a specific therapy may be available. This approach has the best chance of saving the patient's vision with the least toxicity caused by erroneous trials. By necessity, the work-up for these patients is expensive, but the cost of not pursuing the cause is irrevocable, permanent blindness.

Mental health, physical health, and stressors reported by New Zealand Defence Force peacekeepers: a longitudinal study

The psychological effect of peacekeeping duties on 277 New Zealand Defence Force personnel was investigated using a longitudinal, cross-sectional study. Self-report data were collected in five stages from before deployment to approximately 6 months after return. Multiple measures of mental health, physical health, and stressors were used. Results revealed that the most stressful periods of the deployment, and those with the greatest effect on overall health and well-being, appear to be the predeployment and follow-up stages. These findings demonstrate the need for effective predeployment training and postdeployment debriefing and support.

Group hydrotherapy versus group land-based treatment for chronic low back pain

Sixty subjects with chronic low back pain (LBP) were sequentially allocated to either hydrotherapy treatment or land treatment groups in order of presentation. Subjects acted as their own controls for a period of three weeks, after which they attended their respective group sessions twice weekly for six weeks. Twenty-eight subjects from each group attended all treatment and assessment sessions. Results indicated that both groups improved significantly in functional ability and in decreasing pain levels. Thoracolumbar mobility did not improve significantly in either group. Overall there was no significant difference found between the two types of treatment, although results should be viewed as encouraging for the advocates of both hydrotherapy and land-based exercise as a treatment for chronic LBP.