Combined RAF and MEK Inhibition to Treat Activated Non-V600 BRAF-Altered Advanced Cancers.

BACKGROUND: Cancers with non-V600 BRAF-activating alterations have no matched therapy. Preclinical data suggest that these tumors depend on ERK signaling; however, clinical response to MEK/ERK inhibitors has overall been low. We hypothesized that a narrow therapeutic index, driven by ERK inhibition in healthy (wild-type) tissues, limits the efficacy of these inhibitors. As these mutants signal as activated dimers, we further hypothesized that RAF inhibitors given concurrently would improve the therapeutic index by opposing ERK inhibition in normal tissues and not activate ERK in the already activated tumor. MATERIALS AND METHODS: Using cell lines and patient-derived xenografts, we evaluated the effect of RAF inhibition, alone and in combination with MEK/ERK inhibitors. We then undertook a phase I/II clinical trial of a higher dose of the MEK inhibitor binimetinib combined with the RAF inhibitor encorafenib in patients with advanced cancer with activating non-V600 BRAF alterations. RESULTS: RAF inhibition led to modest inhibition of signaling and growth in activated non-V600 BRAF preclinical models and allowed higher dose of MEK/ERK inhibitors in vivo for more profound tumor regression. Fifteen patients received binimetinib 60 mg twice daily plus encorafenib 450 mg daily (6 gastrointestinal primaries, 6 genitourinary primaries, 3 melanoma, and 2 lung cancer; 7 BRAF mutations and 8 BRAF fusions). Treatment was well tolerated without dose-limiting toxicities. One patient had a confirmed partial response, 8 had stable disease, and 6 had radiographic or clinical progression as best response. On-treatment biopsies revealed incomplete ERK pathway inhibition. CONCLUSION: Combined RAF and MEK inhibition does not sufficiently inhibit activated non-V600 BRAF-mutant tumors in patients.

Exploration of piperidine 3D fragment chemical space: synthesis and 3D shape analysis of fragments derived from 20 regio- and diastereoisomers of methyl substituted pipecolinates.

Fragment-based drug discovery is now widely adopted for lead generation in the pharmaceutical industry. However, fragment screening collections are often predominantly populated with flat, 2D molecules. Herein, we report the synthesis of piperidine-based 3D fragment building blocks - 20 regio- and diastereoisomers of methyl substituted pipecolinates using simple and general synthetic methods. cis-Piperidines, accessed through a pyridine hydrogenation were transformed into their trans-diastereoisomers using conformational control and unified reaction conditions. Additionally, diastereoselective lithiation/trapping was utilised to access trans-piperidines. Analysis of a virtual library of fragments derived from the 20 cis- and trans-disubstituted piperidines showed that it consisted of 3D molecules with suitable molecular properties to be used in fragment-based drug discovery programs.

A Method for Economical Smartphone-Based Clinical 3D Facial Scanning.

PURPOSE: Three-dimensional (3D) facial scanning is an emerging clinical tool to capture external anatomical features for quantitative assessment and treatment in a wide range of clinical settings. MATERIALS AND METHODS: In this study, an economical approach for rapid scanning of faces in the clinic was developed and validated to record valuable 3D patient data using smartphone cameras and photogrammetry software. Five novice operators were recruited to watch an instructional video developed on the technique before scanning 20 healthy adult participants. RESULTS: The smartphone-based photogrammetry approach produced scans with 1.3 mm (±0.3 mm) accuracy in comparison to a metrology-rated gold standard device and were 88% (±14%) complete, with no significant difference observed between operators. A moderate to strong intrarater reliability was determined for all novice operators, suggesting that first-use operators can capture consistent scans based on watching an instructional video. CONCLUSION: Smartphone photogrammetry could provide a rapid, noninvasive and economical method to capture patient morphological data for clinical assessment and personalized device manufacture. Inexperienced operators can quickly learn and utilize smartphone photogrammetry to provide accurate and reliable facial scans, essential for future clinical translation.

Design and Synthesis of 56 Shape-Diverse 3D Fragments.

Fragment-based drug discovery is now widely adopted for lead generation in the pharmaceutical industry. However, fragment screening collections are often predominantly populated with flat, 2D molecules. Herein, we describe a workflow for the design and synthesis of 56 3D disubstituted pyrrolidine and piperidine fragments that occupy under-represented areas of fragment space (as demonstrated by a principal moments of inertia (PMI) analysis). A key, and unique, underpinning design feature of this fragment collection is that assessment of fragment shape and conformational diversity (by considering conformations up to 1.5 kcal mol-1 above the energy of the global minimum energy conformer) is carried out prior to synthesis and is also used to select targets for synthesis. The 3D fragments were designed to contain suitable synthetic handles for future fragment elaboration. Finally, by comparing our 3D fragments with six commercial libraries, it is clear that our collection has high three-dimensionality and shape diversity.

A preclinical large-animal model for the assessment of critical-size load-bearing bone defect reconstruction.

Critical-size bone defects, which require large-volume tissue reconstruction, remain a clinical challenge. Bone engineering has the potential to provide new treatment concepts, yet clinical translation requires anatomically and physiologically relevant preclinical models. The ovine critical-size long-bone defect model has been validated in numerous studies as a preclinical tool for evaluating both conventional and novel bone-engineering concepts. With sufficient training and experience in large-animal studies, it is a technically feasible procedure with a high level of reproducibility when appropriate preoperative and postoperative management protocols are followed. The model can be established by following a procedure that includes the following stages: (i) preoperative planning and preparation, (ii) the surgical approach, (iii) postoperative management, and (iv) postmortem analysis. Using this model, full results for peer-reviewed publication can be attained within 2 years. In this protocol, we comprehensively describe how to establish proficiency using the preclinical model for the evaluation of a range of bone defect reconstruction options.

Histomorphometric Evaluation of Critical-Sized Bone Defects Using Osteomeasure and Aperio Image Analysis Systems.

Most histological evaluations of critical-sized bone defects are limited to the analysis of a few regions of interest at a time. Manual and semiautomated histomorphometric approaches often have intra- and interobserver subjectivity, as well as variability in image analysis methods. Moreover, the production of large image data sets makes histological assessment and histomorphometric analysis labor intensive and time consuming. Herein, we tested and compared two image segmentation methods: thresholding (automated) and region-based (manual) modes, for quantifying complete image sets across entire critical-sized bone defects, using the widely used Osteomeasure system and the freely downloadable Aperio Image Scope software. A comparison of bone histomorphometric data showed strong agreement between the automated segmentation mode of the Osteomeasure software with the manual segmentation mode of Aperio Image Scope analysis (bone formation R2 = 0.9615 and fibrous tissue formation R2 = 0.8734). These results indicate that Aperio is capable of handling large histological images, with excellent speed performance in producing highly consistent histomorphometric evaluations compared with the Osteomeasure image analysis system. The statistical evaluation of these two major bone parameters demonstrated that Aperio Image Scope is as capable as Osteomeasure. This study developed a protocol to improve the quality of results and reduce analysis time, while also promoting the standardization of image analysis protocols for the histomorphometric analysis of critical-sized bone defect samples. Impact Statement Despite bone tissue engineering innovations increasing over the last decade, histomorphometric analysis of large bone defects used to study such approaches continues to pose a challenge for pathological assessment. This is due to the resulting large image data set, and the lack of a gold standard image analysis protocol to quantify histological outcomes. Herein, we present a standardized protocol for the image analysis of critical-sized bone defect samples stained with Goldner's Trichrome using the Osteomeasure and Aperio Image Scope image analysis systems. The results were critically examined to determine their reproducibility and accuracy for analyzing large bone defects.

V211D Mutation in MEK1 Causes Resistance to MEK Inhibitors in Colon Cancer.

We report the emergence of the novel MEK1 V211D gatekeeper mutation in a patient with BRAF K601E colon cancer treated with the allosteric MEK inhibitor binimetinib and the anti-EGFR antibody panitumumab. The MEK1 V211D mutation concurrently occurs in the same cell with BRAF K601E and leads to RAF-independent activity but remains regulated by RAF. The V211D mutation causes resistance to binimetinib by both increasing the catalytic activity of MEK1 and reducing its affinity for the drug. Moreover, the mutant exhibits reduced sensitivity to all the allosteric MEK inhibitors tested. Thus, this mutation serves as a general resistance mutation for current MEK inhibitors; however, it is sensitive to a newly reported ATP-competitive MEK inhibitor, which therefore could be used to overcome drug resistance. SIGNIFICANCE: We report a resistance mechanism to allosteric MEK inhibitors in the clinic. A MEK1 V211D mutation developed in a patient with BRAF K601E colon cancer on MEK and EGFR inhibitors. This mutant increases the catalytic activity of MEK1 and reduces its affinity for binimetinib, but remains sensitive to ATP-competitive MEK inhibitors.This article is highlighted in the In This Issue feature, p. 1143.

Two high-risk susceptibility loci at 6p25.3 and 14q32.13 for Waldenström macroglobulinemia.

Waldenström macroglobulinemia (WM)/lymphoplasmacytic lymphoma (LPL) is a rare, chronic B-cell lymphoma with high heritability. We conduct a two-stage genome-wide association study of WM/LPL in 530 unrelated cases and 4362 controls of European ancestry and identify two high-risk loci associated with WM/LPL at 6p25.3 (rs116446171, near EXOC2 and IRF4; OR = 21.14, 95% CI: 14.40-31.03, P = 1.36 × 10-54) and 14q32.13 (rs117410836, near TCL1; OR = 4.90, 95% CI: 3.45-6.96, P = 8.75 × 10-19). Both risk alleles are observed at a low frequency among controls (~2-3%) and occur in excess in affected cases within families. In silico data suggest that rs116446171 may have functional importance, and in functional studies, we demonstrate increased reporter transcription and proliferation in cells transduced with the 6p25.3 risk allele. Although further studies are needed to fully elucidate underlying biological mechanisms, together these loci explain 4% of the familial risk and provide insights into genetic susceptibility to this malignancy.

Erratum: Author Correction: The contribution of pathogenic variants in breast cancer susceptibility genes to familial breast cancer risk.

[This corrects the article DOI: 10.1038/s41523-017-0024-8.].

Equivalence and Bias in the South African Substance Use Contextual Risk Instrument.

This article forms part of a larger study that sought to develop and validate a scale to measure individual and contextual factors associated with adolescent substance use in low-socio-economic status South African communities. The scale was developed to inform the process of designing preventative interventions in these communities. This study assessed the construct equivalence and item bias across different language versions of the scale. Exploratory factor analysis, equality of reliabilities, and the Tucker's phi coefficient of congruence were employed to assess whether the two language versions were equivalent at a scale level. Differential item functioning analysis was conducted using ordinal logistic regression and the Mantel-Haenszel method at an item level. The findings revealed that there are significant differences between the two groups at a scale level. Items were flagged as presenting with moderate to large differential item functioning. The biased items have to be closely examined in order to decide how to address the bias.

The contribution of pathogenic variants in breast cancer susceptibility genes to familial breast cancer risk.

Understanding the gene-specific risks for development of breast cancer will lead to improved clinical care for those carrying germline mutations in cancer predisposition genes. We sought to detail the spectrum of mutations and refine risk estimates for known and proposed breast cancer susceptibility genes. Targeted massively-parallel sequencing was performed to identify mutations and copy number variants in 26 known or proposed breast cancer susceptibility genes in 2134 BRCA1/2-negative women with familial breast cancer (proband with breast cancer and a family history of breast or ovarian cancer) from a largely European-Caucasian multi-institutional cohort. Case-control analysis was performed comparing the frequency of internally classified mutations identified in familial breast cancer women to Exome Aggregation Consortium controls. Mutations were identified in 8.2% of familial breast cancer women, including mutations in high-risk (odds ratio > 5) (1.4%) and moderate-risk genes (2 < odds ratio < 5) (2.9%). The remaining familial breast cancer women had mutations in proposed breast cancer genes (1.7%), Lynch syndrome genes (0.5%), and six cases had two mutations (0.3%). Case-control analysis demonstrated associations with familial breast cancer for ATM, PALB2, and TP53 mutations (odds ratio > 3.0, p < 10-4), BARD1 mutations (odds ratio = 3.2, p = 0.012), and CHEK2 truncating mutations (odds ratio = 1.6, p = 0.041). Our results demonstrate that approximately 4.7% of BRCA1/2 negative familial breast cancer women have mutations in genes statistically associated with breast cancer. We classified PALB2 and TP53 as high-risk, ATM and BARD1 as moderate risk, and CHEK2 truncating mutations as low risk breast cancer predisposition genes. This study demonstrates that large case-control studies are needed to fully evaluate the breast cancer risks associated with mutations in moderate-risk and proposed susceptibility genes.

A Recurrent ERCC3 Truncating Mutation Confers Moderate Risk for Breast Cancer.

Known gene mutations account for approximately 50% of the hereditary risk for breast cancer. Moderate and low penetrance variants, discovered by genomic approaches, account for an as-yet-unknown proportion of the remaining heritability. A truncating mutation c.325C>T:p.Arg109* (R109X) in the ATP-dependent helicase ERCC3 was observed recurrently among exomes sequenced in BRCA wild-type, breast cancer-affected individuals of Ashkenazi Jewish ancestry. Modeling of the mutation in ERCC3-deficient or CRISPR/Cas9-edited cell lines showed a consistent pattern of reduced expression of the protein and concomitant hypomorphic functionality when challenged with UVC exposure or treatment with the DNA alkylating agent IlludinS. Overexpressing the mutant protein in ERCC3-deficient cells only partially rescued their DNA repair-deficient phenotype. Comparison of frequency of this recurrent mutation in over 6,500 chromosomes of breast cancer cases and 6,800 Ashkenazi controls showed significant association with breast cancer risk (ORBC = 1.53, ORER+ = 1.73), particularly for the estrogen receptor-positive subset (P < 0.007). SIGNIFICANCE: A functionally significant recurrent ERCC3 mutation increased the risk for breast cancer in a genetic isolate. Mutated cell lines showed lower survival after in vitro exposure to DNA-damaging agents. Thus, similar to tumors arising in the background of homologous repair defects, mutations in nucleotide excision repair genes such as ERCC3 could constitute potential therapeutic targets in a subset of hereditary breast cancers. Cancer Discov; 6(11); 1267-75. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 1197.

Germline ETV6 Mutations Confer Susceptibility to Acute Lymphoblastic Leukemia and Thrombocytopenia.

Somatic mutations affecting ETV6 often occur in acute lymphoblastic leukemia (ALL), the most common childhood malignancy. The genetic factors that predispose to ALL remain poorly understood. Here we identify a novel germline ETV6 p. L349P mutation in a kindred affected by thrombocytopenia and ALL. A second ETV6 p. N385fs mutation was identified in an unrelated kindred characterized by thrombocytopenia, ALL and secondary myelodysplasia/acute myeloid leukemia. Leukemic cells from the proband in the second kindred showed deletion of wild type ETV6 with retention of the ETV6 p. N385fs. Enforced expression of the ETV6 mutants revealed normal transcript and protein levels, but impaired nuclear localization. Accordingly, these mutants exhibited significantly reduced ability to regulate the transcription of ETV6 target genes. Our findings highlight a novel role for ETV6 in leukemia predisposition.

A Platform to Build Mobile Health Apps: The Personal Health Intervention Toolkit (PHIT).

Personal Health Intervention Toolkit (PHIT) is an advanced cross-platform software framework targeted at personal self-help research on mobile devices. Following the subjective and objective measurement, assessment, and plan methodology for health assessment and intervention recommendations, the PHIT platform lets researchers quickly build mobile health research Android and iOS apps. They can (1) create complex data-collection instruments using a simple extensible markup language (XML) schema; (2) use Bluetooth wireless sensors; (3) create targeted self-help interventions based on collected data via XML-coded logic; (4) facilitate cross-study reuse from the library of existing instruments and interventions such as stress, anxiety, sleep quality, and substance abuse; and (5) monitor longitudinal intervention studies via daily upload to a Web-based dashboard portal. For physiological data, Bluetooth sensors collect real-time data with on-device processing. For example, using the BinarHeartSensor, the PHIT platform processes the heart rate data into heart rate variability measures, and plots these data as time-series waveforms. Subjective data instruments are user data-entry screens, comprising a series of forms with validation and processing logic. The PHIT instrument library consists of over 70 reusable instruments for various domains including cognitive, environmental, psychiatric, psychosocial, and substance abuse. Many are standardized instruments, such as the Alcohol Use Disorder Identification Test, Patient Health Questionnaire-8, and Post-Traumatic Stress Disorder Checklist. Autonomous instruments such as battery and global positioning system location support continuous background data collection. All data are acquired using a schedule appropriate to the app's deployment. The PHIT intelligent virtual advisor (iVA) is an expert system logic layer, which analyzes the data in real time on the device. This data analysis results in a tailored app of interventions and other data-collection instruments. For example, if a user anxiety score exceeds a threshold, the iVA might add a meditation intervention to the task list in order to teach the user how to relax, and schedule a reassessment using the anxiety instrument 2 weeks later to re-evaluate. If the anxiety score exceeds a higher threshold, then an advisory to seek professional help would be displayed. Using the easy-to-use PHIT scripting language, the researcher can program new instruments, the iVA, and interventions to their domain-specific needs. The iVA, instruments, and interventions are defined via XML files, which facilities rapid app development and deployment. The PHIT Web-based dashboard portal provides the researcher access to all the uploaded data. After a secure login, the data can be filtered by criteria such as study, protocol, domain, and user. Data can also be exported into a comma-delimited file for further processing. The PHIT framework has proven to be an extensible, reconfigurable technology that facilitates mobile data collection and health intervention research. Additional plans include instrument development in other domains, additional health sensors, and a text messaging notification system.

A genome-wide association study of marginal zone lymphoma shows association to the HLA region.

Marginal zone lymphoma (MZL) is the third most common subtype of B-cell non-Hodgkin lymphoma. Here we perform a two-stage GWAS of 1,281 MZL cases and 7,127 controls of European ancestry and identify two independent loci near BTNL2 (rs9461741, P=3.95 × 10(-15)) and HLA-B (rs2922994, P=2.43 × 10(-9)) in the HLA region significantly associated with MZL risk. This is the first evidence that genetic variation in the major histocompatibility complex influences MZL susceptibility.

Estrogen Deficiency-Associated Bone Loss in the Maxilla: A Methodology to Quantify the Changes in the Maxillary Intra-radicular Alveolar Bone in an Ovariectomized Rat Osteoporosis Model.

The effects of estrogen deficiency on bone characteristics are site-dependent, with the most commonly studied sites being appendicular long bones (proximal femur and tibia) and axial bones (vertebra). The effect on the maxillary and mandibular bones is still inconsistent and requires further investigation. This study was designed to evaluate bone quality in the posterior maxilla of ovariectomized rats to validate this site as an appropriate model to study the effect of osteoporotic changes. Forty-eight 3-month-old female Sprague-Dawley rats were randomly divided into two groups: an ovariectomized (OVX) group (n=24) and Sham-operated (SHAM) group (n=24). Six rats were randomly sacrificed from both groups at time points 8, 12, 16, and 20 weeks. The samples from tibia and maxilla were collected for micro computed tomography (µCT) and histological analysis. For the maxilla, the volume of interest area focused on the furcation areas of the first and second molar. Trabecular bone volume fraction (BV/TV, %), trabecular thickness (Tb.Th.), trabecular number (Tb.N.), trabecular separation (Tb.Sp.), and connectivity density (Conn.Dens) were analyzed after Micro CT scanning. At 8 weeks the indices BV/TV, Tb.Sp., Tb.N., and Conn.Dens showed significant differences (p<0.05) between the OVX and SHAM groups in the tibia. Compared with the tibia, the maxilla developed osteoporosis at a later stage, with significant changes in maxillary bone density only occurring after 12 weeks. Compared with the SHAM group, both the first and second molars of the OVX group showed significantly decreased BV/TV values from 12 weeks, and these changes were sustained through 16 and 20 weeks. For Tb.Sp., there were significant increases in bone values for the OVX group compared with the SHAM group at 12, 16, and 20 weeks. Histological changes were highly consistent with Micro CT results. This study established a method to quantify the changes of intra-radicular alveolar bone in the posterior maxilla in an accepted rat osteoporosis model. The degree of the osteoporotic changes to trabecular bone architecture is site-dependent and at least 3 months are required for the osteoporotic effects to be apparent in the posterior maxilla following rat OVX.

Appropriate development of the liver Treg compartment is modulated by the microbiota and requires TGF-ß and MyD88.

Neither the early postnatal development of the liver Treg compartment nor the factors that regulate its development has been characterized. We compared the early developmental patterns of Treg cell accumulation in murine liver, thymus, and spleen. A FoxP3(EGFP) reporter mouse was employed to identify Treg cells. Mononuclear cells were isolated from organs postnatally, stained for CD4, and examined by flow cytometry to enumerate FoxP3(+)CD4(hi) cells. To assess roles for TGF-ß1, MyD88, and TLR2, gene-specific knockout pups were generated from heterozygous breeders. To test the role of commensal bacteria, pregnant dams were administered antibiotics during gestation and after parturition. The pattern of appearance of Treg cells differed in liver, spleen, and thymus. Notably, at 1-2 weeks, the frequency of CD4(hi) FoxP3(+) T cells in liver exceeded that in spleen by 1.5- to 2-fold. The relative increase in liver Treg frequency was transient and was dependent upon TGF-ß1 and MyD88, but not TLR2, and was abrogated by antibiotic treatment. A relative increase in liver Treg frequency occurs approximately 1-2 weeks after parturition that appears to be driven by colonization of the intestine with commensal bacteria and is mediated by a pathway that requires TGF-ß1 and MyD88, but not TLR2.