Gene-specific ACMG/AMP classification criteria for germline APC variants: Recommendations from the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel

PURPOSE

The Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP) was established by the International Society for Gastrointestinal Hereditary Tumours and the Clinical Genome Resource, who set out to develop recommendations for the interpretation of germline APC variants underlying Familial Adenomatous Polyposis, the most frequent hereditary polyposis syndrome.

METHODS

Through a rigorous process of database analysis, literature review, and expert elicitation, the APC VCEP derived gene-specific modifications to the ACMG/AMP (American College of Medical Genetics and Genomics and Association for Molecular Pathology) variant classification guidelines and validated such criteria through the pilot classification of 58 variants.

RESULTS

The APC-specific criteria represented gene- and disease-informed specifications, including a quantitative approach to allele frequency thresholds, a stepwise decision tool for truncating variants, and semiquantitative evaluations of experimental and clinical data. Using the APC-specific criteria, 47% (27/58) of pilot variants were reclassified including 14 previous variants of uncertain significance (VUS).

CONCLUSION

The APC-specific ACMG/AMP criteria preserved the classification of well-characterized variants on ClinVar while substantially reducing the number of VUS by 56% (14/25). Moving forward, the APC VCEP will continue to interpret prioritized lists of VUS, the results of which will represent the most authoritative variant classification for widespread clinical use.

Macrocephaly and developmental delay caused by missense variants in RAB5C

Rab GTPases are important regulators of intracellular vesicular trafficking. RAB5C is a member of the Rab GTPase family that plays an important role in the endocytic pathway, membrane protein recycling and signaling. Here we report on 12 individuals with nine different heterozygous de novo variants in RAB5C. All but one patient with missense variants (n = 9) exhibited macrocephaly, combined with mild-to-moderate developmental delay. Patients with loss of function variants (n = 2) had an apparently more severe clinical phenotype with refractory epilepsy and intellectual disability but a normal head circumference. Four missense variants were investigated experimentally. In vitro biochemical studies revealed that all four variants were damaging, resulting in increased nucleotide exchange rate, attenuated responsivity to guanine exchange factors and heterogeneous effects on interactions with effector proteins. Studies in C. elegans confirmed that all four variants were damaging in vivo and showed defects in endocytic pathway function. The variant heterozygotes displayed phenotypes that were not observed in null heterozygotes, with two shown to be through a dominant negative mechanism. Expression of the human RAB5C variants in zebrafish embryos resulted in defective development, further underscoring the damaging effects of the RAB5C variants. Our combined bioinformatic, in vitro and in vivo experimental studies and clinical data support the association of RAB5C missense variants with a neurodevelopmental disorder characterized by macrocephaly and mild-to-moderate developmental delay through disruption of the endocytic pathway.

Specifications of the ACMG/AMP Variant Classification Guidelines for Germline DICER1 Variant Curation

Germline pathogenic variants in DICER1 predispose individuals to develop a variety of benign and malignant tumors. Accurate variant curation and classification is essential for reliable diagnosis of DICER1-related tumor predisposition and identification of individuals who may benefit from surveillance. Since 2015, most labs have followed the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) sequence variant classification guidelines for DICER1 germline variant curation. However, these general guidelines lack gene-specific nuances and leave room for subjectivity. Consequently, a group of DICER1 experts joined ClinGen to form the DICER1 and miRNA-Processing Genes Variant Curation Expert Panel (VCEP), to create DICER1- specific ACMG/AMP guidelines for germline variant curation. The VCEP followed the FDA-approved ClinGen protocol for adapting and piloting these guidelines. A diverse set of 40 DICER1 variants were selected for piloting, including 14 known Pathogenic/Likely Pathogenic (P/LP) variants, 12 known Benign/Likely Benign (B/LB) variants, and 14 variants classified as variants of uncertain significance (VUS) or with conflicting interpretations in ClinVar. Clinically meaningful classifications (i.e., P, LP, LB, or B) were achieved for 82.5% (33/40) of the pilot variants, with 100% concordance among the known P/LP and known B/LB variants. Half of the VUS or conflicting variants were resolved with four variants classified as LB and three as LP. These results demonstrate that the DICER1-specific guidelines for germline variant curation effectively classify known pathogenic and benign variants while reducing the frequency of uncertain classifications. Individuals and labs curating DICER1 variants should consider adopting this classification framework to encourage consistency and improve objectivity.

Finerenone reduces renal RORgt gd T-Cells and protects against cardiorenal damage

 

Chronic activation of the mineralocorticoid receptor (MR) through the agonist aldosterone leads to pathological processes like inflammation, fibrosis, and increased blood pressure. Therefore, MR antagonists (MRA) belong to guideline-based therapy for hypertension and heart failure with reduced ejection fraction. The nonsteroidal, selective MRA finerenone (FIN) induces distinct pharmacological actions when compared to steroidal MRAs including less adverse effects and improved efficacy (e.g. anti-fibrosis). In this study, we investigated the effects of FIN in a deoxycorticosterone acetate (DOCA)-salt model which induces an increase of blood pressure and end organ damage including hypertrophy, fibrosis, and inflammatory cell infiltration in heart and kidney.

Male C57BL6/J mice were either uni-nephrectomized in addition to DOCA-pellet application (2.4mg/d) and 0.9% NaCl in the drinking water (DOCA/UNX) or received a sham operation. One week prior to the surgery, oral treatment with FIN (10mg/kg/d) or vehicle (VEH) started and lasted throughout the experiment. Five weeks after the procedure, final examinations including blood pressure (BP) measurement, urine analysis, speckle-tracking echocardiography (STE), and FACS analysis of the heart and kidney were performed.

BP was significantly reduced by FIN treatment. FACS analysis revealed a notable immune response due to DOCA/ UNX exposure. Especially infiltrating renal RORγt γδ T-Cells were upregulated, which was significantly ameliorated by the FIN-treatment. This was accompanied by an improvement of kidney function shown by a reduction of the urinary albumin/creatinine ratio in FIN-treated mice. In the heart, FIN reduced DOCA/ UNX-induced cardiac hypertrophy, cardiac fibrosis and led to an improvement of the global longitudinal strain (GLS) in the STE-analysis. Cardiac actions of FIN were not associated with a regulation of cardiac RORγt γδ T-Cells.

The present study shows cardiac and renal protective effects of FIN in a DOCA/UNX model. The cardiorenal protection was accompanied by a reduction of renal RORγt γδ T-Cells. Anti-inflammatory actions of FIN may provide a potential mechanism of its clinical efficacy recently observed in clinical trials.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): Bayer AG

Abstract 210: Advancing knowledgebase representation of pediatric cancer variants through ClinGen/CIViC collaboration

Childhood cancers are driven by unique profiles of somatic genetic alterations, with a significant contribution from predisposing germline variants. Understanding the genomic landscape of pediatric cancers is complicated by their rarity, the heterogeneity of variation within a given disease, and the complex forms of structural variation they contain. Variants in childhood disease may differ from those in adult versions of the same cancer type, or may have different clinical significance. Currently, pediatric variants are underrepresented in cancer variant databases, and an urgent need exists for their publicly available expert curation. To address this, the Pediatric Cancer Taskforce (PCT) was formed within the Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group (CDWG) (https://www.clinicalgenome.org/working-groups/somatic/). The PCT is a multi-institutional group of 39 members with broad experience in childhood cancer and variant curation, whose work consists of standardization and classification of genetic variants in pediatric cancers. The CIViC knowledgebase (www.civicdb.org) is a freely available resource for Clinical Interpretation of Variants in Cancer, which leverages public curation and expert moderation to address the problem of annotating the large volume of clinically actionable cancer variants. PCT curators work together with PCT expert members and the CIViC team on variant curation, and have submitted over 230 Evidence Items and over 10 Assertions to CIViC. To further address issues specific to pediatric curation, the PCT is working with CIViC to develop new pediatric-specific CIViC features and modifications of the data model that will aid in pediatric curation. A pediatric user interface, as well as representation of large scale structural and copy number variation are being developed for version two of CIViC, expected to be released in 1-2 years, which will enable curation of a new class of structural variants often encountered in pediatric cancer. A novel standard operating procedure for childhood cancer curation in CIViC is being developed by PCT experts, curators and the CIViC team. This SOP will cover topics including curation of structural variants, as well as pediatric-specific variant tiering guidelines which take into account the sparse nature of evidence in pediatric cases. A companion resource, CIViCmine (http://bionlp.bcgsc.ca/civicmine/), will be further developed to incorporate pediatric data. These and other joint efforts of the PCT and CIViC will significantly enhance pediatric variant representation for public use, to support the care of children with cancer.

Citation Format: Arpad Danos, Wan-Hsin Lin, Jason Saliba, Angshumoy Roy, Alanna J. Church, Shruti Rao, Deborah Ritter, Kilannin Krysiak, Alex Wagner, Erica Barnell, Lana Sheta, Adam Coffman, Susanna Kiwala, Joshua F. McMichael, Laura Corson, Kevin Fisher, Heather E. Williams, Matthew Hiemenz, Katherine A. Janeway, Jianling Ji, Kesserwan A. Chimene, Laura Fuqua, Lisa Dyer, Huiling Xu, Jeffrey Jean, Laveniya Satgunaseelan, Liying Zhang, Ted W. Laetsch, Donald W. Parsons, Ryan Schmidt, Lynn M. Schriml, Kristen L. Sund, Shashikant Kulkarni, Subha Madhavan, Xinjie Xu, Rashmi Kanagal-Shamana, Marian Harris, Yasmine Akkari, Nurit Paz Yacov, Panieh Terraf, Malachi Griffith, Obi L. Griffith, Gordana Raca. Advancing knowledgebase representation of pediatric cancer variants through ClinGen/CIViC collaboration [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 210.

Abstract 3215: ClinGen somatic cancer working group: Disseminating standardized cancer molecular diagnostic data and evidence through global collaboration and expert curation

The Clinical Genome (ClinGen) Resource is a US National Human Genome Research Institute (NHGRI)-funded program dedicated to building an expert curated and freely available central resource that defines the clinical relevance of genes and variants for use in precision medicine. Teams of experts in various clinical domains come together as working groups within ClinGen to facilitate the interpretation, annotation and utilization of genes-variants for clinical application. Somatic Cancer is one such ClinGen Clinical Domain Working Group (CDWG) that consists of over 90 members worldwide, including clinicians, clinical laboratory diagnosticians, genomic scientists and bioinformaticians. Members of this CDWG identify high priority somatic variants in different cancer types that require expert curation and consensus in their clinical interpretation. In order to accurately implement practice guidelines/standards for variant interpretation, the Somatic Cancer CDWG recently established a somatic Variant Curation Expert Panel (VCEP) approval process. Based on their interest and clinical domain expertise, a subset of the CDWG members formed somatic VCEPs to perform authoritative curation on the shortlisted genes-somatic variants within the context of a disease, therapeutic indication or biological pathway. Expert curation within these VCEPs is performed by utilizing guidelines such as those recommended by AMP/ASCO/CAP (Li et al. 2017) and the Somatic Cancer CDWG (Ritter et al. 2016). Wherever necessary, the somatic VCEPs will develop: 1) gene- and disease-specific modifications to address gaps in existing variant assessment guidelines, 2) quantitative approaches for variant interpretation, and 3) implement standardized protocols for annotating somatic variants in genes for a specific disease, drug or biological pathway. Furthermore, ClinGen recently formed the Cancer Variant Interpretation (CVI) committee to provide support, review and feedback on the provisional somatic variant interpretation proposals developed by the VCEPs. The CVI provides somatic VCEPs with a preliminary approval before the final approval by the ClinGen CDWG oversight committee and ultimately ‘expert panel' status in ClinVar, an NCBI-maintained database of clinically relevant gene variants. NTRK fusions in cancer is the first Somatic VCEP going through the ClinGen Somatic Expert Panel approval process. Alterations in the FGFR pathway in GU cancers is the second somatic VCEP under consideration. The Somatic CDWG uses the CIViC (Clinical Interpretation of Variants in Cancer) platform for curation of somatic variants. To date, the CDWG has curated 268 evidence items relating to cancer variants in CIViC, 6 assertions, and 33 evidence source suggestions. The ultimate goal of the Somatic CDWG is to enhance the usability, dissemination and implementation of cancer somatic changes in the ClinGen resource and other cancer variant knowledgebases.

Citation Format: Shruti Rao, Deborah Ritter, Arpad Danos, Gordana Raca, Angshumoy Roy, Kilannin Krysiak, Wan-Hsin Lin, Erica Barnell, Matthew McCoy, Beth Pitel, Dmitriy Sonkin, Jue Wang, Seyed Ali Hosseini, Shamini Selvarajah, Ian King, Rashmi Kanagal-Shamana, Xinjie Xu, Jeremy L. Warner, Funda Meric-Bernstam, Jason D. Merker, Marilyn Li, Alex H. Wagner, Malachi Griffith, Obi L. Griffith, Shashikant Kulkarni, Subha Madhavan. ClinGen somatic cancer working group: Disseminating standardized cancer molecular diagnostic data and evidence through global collaboration and expert curation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3215.

Abstract 1096: Harmonization standards from the Variant Interpretation for Cancer Consortium

The use of clinical gene sequencing is now commonplace, and genome analysts and molecular pathologists are often tasked with the labor-intensive process of interpreting the clinical significance of large numbers of tumor variants. Numerous independent knowledgebases have been constructed to alleviate this manual burden, however these knowledgebases are non-interoperable. As a result, the analyst is left with a difficult tradeoff: for each knowledgebase used the analyst must understand the nuances particular to that resource and integrate its evidence accordingly when generating the clinical report, but for each knowledgebase omitted there is increased potential for missed findings of clinical significance.The Variant Interpretation for Cancer Consortium (VICC; cancervariants.org) was formed as a driver project of the Global Alliance for Genomics and Health (GA4GH; ga4gh.org) to address this concern. VICC members include representatives from several major somatic interpretation knowledgebases including CIViC, OncoKB, Jax-CKB, the Weill Cornell PMKB, the IRB-Barcelona Cancer Biomarkers Database, and others. Previously, the VICC built and reported on a harmonized meta-knowledgebase of 19,551 biomarker associations of harmonized variants, diseases, drugs, and evidence across the constituent resources.In that study, we analyzed the frequency with which the tumor samples from the AACR Project GENIE cohort would match to harmonized associations. Variant matches increased dramatically from 57% to 86% when broader matching to regions describing categorical variants were allowed. Unlike precise sequence variants with specified alternate alleles, categorical variants describe a collection of potential variants with a common feature, such as “V600” (non-valine alleles at the 600 residue), “Exon 20 mutations” (all non-silent mutations in exon 20), or “Gain-of-function” (hypermorphic alterations that activate or amplify gene activity). However, matching observed sequence variants to categorical variants is challenging, as the latter are typically only described as unstructured text. Here we describe the expressive and computational GA4GH Variation Representation specification (vr-spec.readthedocs.io), which we co-developed as members of the GA4GH Genomic Knowledge Standards work stream. This specification provides a schema for common, precise forms of variation (e.g. SNVs and Indels) and the method for computing identifiers from these objects. We highlight key aspects of the specification and our work to apply it to the characterization of categorical variation, showcasing the variant terminology and classification tools developed by the VICC to support this effort. These standards and tools are free, open-source, and extensible, overcoming barriers to standardized variant knowledge sharing and search.

Citation Format: Alex H. Wagner, Reece K. Hart, Larry Babb, Robert R. Freimuth, Adam Coffman, Yonghao Liang, Beth Pitel, Angshumoy Roy, Matthew Brush, Jennifer Lee, Anna Lu, Thomas Coard, Shruti Rao, Deborah Ritter, Brian Walsh, Susan Mockus, Peter Horak, Ian King, Dmitriy Sonkin, Subha Madhavan, Gordana Raca, Debyani Chakravarty, Malachi Griffith, Obi L. Griffith. Harmonization standards from the Variant Interpretation for Cancer Consortium [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1096.

Abstract A58: Curation of pediatric cancer variants within the Clinical Genome Resource (ClinGen)

Introduction: The Clinical Genome Resource (ClinGen) Somatic Working Group (sWG) is a multi-institution team engaged in developing processes, resources, and standards to support accurate classification of somatic variants in cancer. Existing decision support resources in cancer knowledgebases are heavily skewed towards genes and variants relevant in adult cancers; however, information to support variant interpretation in childhood cancers is limited. Here we report on the goals and progress of the Pediatric Cancer Taskforce, created within the ClinGen sWG, to lead curation efforts of actionable alterations in childhood cancers.

Methods: The ClinGen sWG Pediatric Cancer Taskforce (PCT) consists of a core group of twelve members comprising geneticists, pathologists, and oncologists with expertise in different pediatric cancers and with representation from 9 leading pediatric institutions. The taskforce has a total of 35 members including volunteer-curators who work under guidance of the expert members. Curation of childhood cancer variants is conducted in collaboration with the Clinical Interpretation of Variants in Cancer (CIViC) team at Washington University in Saint Louis, using the CIViC knowledgebase (civicdb.org) and the ClinVar database as open-access curation and data-sharing platforms. Diagnostic, prognostic, and therapeutic evidence is tiered according to the AMP/ASCO/CAP guidelines for the clinical interpretation of somatic variants. PCT members are assigned specific genetic variant-tumor type associations for curation, which are then reviewed in monthly conferences to finalize assertions in CIViC.

Results: The PCT has prioritized 40 genetic alterations relevant to pediatric cancer for curation based on their clinical relevance and the lack of sufficient existing curated evidence in clinical knowledgebases. To date, 4 assertions have been created and added to the database: HEY1-NCOA2 fusion in mesenchymal chondrosarcoma, KIAA1549-BRAF fusion and ACVR1 p.G328V variant in pediatric glioma, and EBF1-PDGFRB fusion in pediatric B-cell precursor acute lymphoblastic leukemia. Active curation has been initiated for NTRK fusions agnostic of tissue histology, targetable kinase fusions in Ph-like B-lymphoblastic leukemia, and common variants in selected pediatric sarcomas and brain tumors, focusing heavily on driver gene fusions in childhood cancers. 119 evidence items have been created in CIViC by the members. The PCT also works to implement more standardized and accurate classification of pediatric cancers in CIViC and other cancer resources, and to enhance search for pediatric-specific data through appropriate tagging of evidence using ontology terms.

Conclusions: As molecular alterations are increasingly relevant to the care of children with cancer, the ClinGen PCT will work to develop standards, processes, and resources for efficient and accurate determination of clinical relevance of pediatric cancer variants.

Citation Format: Alanna J. Church, Shruti Rao, Deborah Ritter, Arpad Danos, Kilann Krysiak, Laura B. Corson, Kevin E. Fisher, Matthew Hiemenz, Katherine A. Janeway, Jianling Ji, Chimene A. Kesserwan, Theodore W. Laetsch, Donald W. Parsons, Ryan J. Schmidt, Kristen L. Sund, Wan-Hsin Lin, Malachi Griffith, Obi L. Griffith, Shashikant Kulkarni, Subha Madhavan, Angshumoy Roy, Gordana Raca. Curation of pediatric cancer variants within the Clinical Genome Resource (ClinGen) [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A58.

Viable Eimeria oocysts in poultry house litter at the time of chick placement

The purpose of this study was to determine if Eimeria oocysts recovered from litter at the time of chick placement in commercial broiler houses contained oocysts that were infectious for chickens. Over 100 litter samples were collected from 30 poultry farms representing a total of 60 different broiler houses with 9 houses sampled more than once over 1.5 yr. The samples were collected just before the placement of newly hatched chicks and after an anticoccidial drug (ACD) or Eimeria vaccine (VAC) program, and processed for counting oocysts followed by Eimeria species determination using ITS1 PCR. Broiler chicks were inoculated with recovered Eimeria oocysts to determine if the litter oocysts were viable and capable of causing patent infection. At placement, E. maxima (Emax) oocysts were detected in 70 of 75 houses after ACD program and 46 of 47 houses after VAC program. Eimeria acervulina, E. praecox, and/or E. tenella (Eapt) were detected in 75 of 75 houses after ACD program and 47 of 47 houses after VAC program. Viability testing revealed that 33.0% of broiler houses contained viable Emax oocysts, while 46.9% contained viable Eapt oocysts. During VAC programs, the concentration of Emax oocysts at placement and the total number of Emax oocysts shed by chickens in viability studies showed a very strong correlation (r = 0.83). Likewise, during ACD programs, the concentration of Eapt oocysts at placement and the total number of Eapt oocysts shed by chickens in the viability study showed a strong correlation (r = 0.62). In general, Eimeria oocyst levels at placement and number of viable oocysts shed by chickens in the viability study were similar among houses on the same farm. However, the number of Eimeria oocysts shed in the viability studies was considerably less than expected based on the number of oocysts given. These data suggest that nearly 100% of all poultry houses contain Emax and Eapt oocysts at placement with 30 to 50% of the houses containing viable Eimeria oocysts, thus possibly representing a source of the protozoa to newly hatched chicks.

Standardizing And Democratizing Access To Cancer Molecular Diagnostic Test Data From Patients To Drive Translational Research

In the last 3-5 years, there has been a rapid increase in clinical use of next generation sequencing (NGS) based cancer molecular diagnostic (MolDx) testing to develop better treatment plans with targeted therapies. To truly achieve precision oncology, it is critical to catalog cancer sequence variants from MolDx testing for their clinical relevance along with treatment information and patient outcomes, and to do so in a way that supports large-scale data aggregation and new hypothesis generation. Through the NIH-funded Clinical Genome Resource (ClinGen), in collaboration with NLM's ClinVar database and >50 academic and industry based cancer research organizations, a Minimal Variant Level Data (MVLD) framework to standardize reporting and interpretation of drug associated alterations was developed. Methodological and technology development to standardize and map MolDx data to the MVLD standard are presented here. Also described is a novel community engagement effort through disease-focused taskforces to provide usecases for technology development.

ClinGen Cancer Somatic Working Group - standardizing and democratizing access to cancer molecular diagnostic data to drive translational research

A growing number of academic and community clinics are conducting genomic testing to inform treatment decisions for cancer patients (1). In the last 3-5 years, there has been a rapid increase in clinical use of next generation sequencing (NGS) based cancer molecular diagnostic (MolDx) testing (2). The increasing availability and decreasing cost of tumor genomic profiling means that physicians can now make treatment decisions armed with patient-specific genetic information. Accumulating research in the cancer biology field indicates that there is significant potential to improve cancer patient outcomes by effectively leveraging this rich source of genomic data in treatment planning (3). To achieve truly personalized medicine in oncology, it is critical to catalog cancer sequence variants from MolDx testing for their clinical relevance along with treatment information and patient outcomes, and to do so in a way that supports large-scale data aggregation and new hypothesis generation. One critical challenge to encoding variant data is adopting a standard of annotation of those variants that are clinically actionable. Through the NIH-funded Clinical Genome Resource (ClinGen) (4), in collaboration with NLM's ClinVar database and >50 academic and industry based cancer research organizations, we developed the Minimal Variant Level Data (MVLD) framework to standardize reporting and interpretation of drug associated alterations (5). We are currently involved in collaborative efforts to align the MVLD framework with parallel, complementary sequence variants interpretation clinical guidelines from the Association of Molecular Pathologists (AMP) for clinical labs (6). In order to truly democratize access to MolDx data for care and research needs, these standards must be harmonized to support sharing of clinical cancer variants. Here we describe the processes and methods developed within the ClinGen's Somatic WG in collaboration with over 60 cancer care and research organizations as well as CLIA-certified, CAP-accredited clinical testing labs to develop standards for cancer variant interpretation and sharing.

Viral oncoprotein antibodies as a marker for recurrence of Merkel cell carcinoma: A prospective validation study

BACKGROUND

Merkel cell carcinoma (MCC) is an aggressive skin cancer with a recurrence rate of >40%. Of the 2000 MCC cases per year in the United States, most are caused by the Merkel cell polyomavirus (MCPyV). Antibodies to MCPyV oncoprotein (T-antigens) have been correlated with MCC tumor burden. The present study assesses the clinical utility of MCPyV-oncoprotein antibody titers for MCC prognostication and surveillance.

METHODS

MCPyV-oncoprotein antibody detection was optimized in a clinical laboratory. A cohort of 219 patients with newly diagnosed MCC were followed prospectively (median follow-up, 1.9 years). Among the seropositive patients, antibody titer and disease status were serially tracked.

RESULTS

Antibodies to MCPyV oncoproteins were rare among healthy individuals (1%) but were present in most patients with MCC (114 of 219 patients [52%]; P < .01). Seropositivity at diagnosis independently predicted decreased recurrence risk (hazard ratio, 0.58; P = .04) in multivariate analyses adjusted for age, sex, stage, and immunosuppression. After initial treatment, seropositive patients whose disease did not recur had rapidly falling titers that became negative by a median of 8.4 months. Among seropositive patients who underwent serial evaluation (71 patients; 282 time points), an increasing oncoprotein titer had a positive predictive value of 66% for clinically evident recurrence, whereas a decreasing titer had a negative predictive value of 97%.

CONCLUSIONS

Determination of oncoprotein antibody titer assists in the clinical management of patients with newly diagnosed MCC by stratifying them into a higher risk seronegative cohort, in which radiologic imaging may play a more prominent role, and into a lower risk seropositive cohort, in which disease status can be tracked in part by oncoprotein antibody titer. Cancer 2017;123:1464-1474. © 2016 American Cancer Society.

Detection of the insulating gap and conductive filament growth direction in resistive memories

Filament growth is a key aspect in the operation of bipolar resistive random access memory (RRAM) devices, yet there are conflicting reports in the literature on the direction of growth of conductive filaments in valence change RRAM devices. We report here that an insulating gap between the filament and the semiconductor electrode can be detected by the metal-insulator-semiconductor bipolar transistor structure, and thus provide information on the filament growth direction. Using this technique, we show how voltage polarity and electrode chemistry control the filament growth direction during electro-forming. The experimental results and the nature of a gap between the filament and an electrode are discussed in light of possible models of filament formation.

A randomized, placebo-controlled phase III trial of masitinib plus gemcitabine in the treatment of advanced pancreatic cancer

BACKGROUND

Masitinib is a selective oral tyrosine-kinase inhibitor. The efficacy and safety of masitinib combined with gemcitabine was compared against single-agent gemcitabine in patients with advanced pancreatic ductal adenocarcinoma (PDAC).

PATIENTS AND METHODS

Patients with inoperable, chemotherapy-naïve, PDAC were randomized (1 : 1) to receive gemcitabine (1000 mg/m(2)) in combination with either masitinib (9 mg/kg/day) or a placebo. The primary endpoint was overall survival (OS) in the modified intent-to-treat population. Secondary OS analyses aimed to characterize subgroups with poor survival while receiving single-agent gemcitabine with subsequent evaluation of masitinib therapeutic benefit. These prospectively declared subgroups were based on pharmacogenomic data or a baseline characteristic.

RESULTS

Three hundred and fifty-three patients were randomly assigned to receive either masitinib plus gemcitabine (N = 175) or placebo plus gemcitabine (N = 178). Median OS was similar between treatment-arms for the overall population, at respectively, 7.7 and 7.1 months, with a hazard ratio (HR) of 0.89 (95% CI [0.70; 1.13]. Secondary analyses identified two subgroups having a significantly poor survival rate when receiving single-agent gemcitabine; one defined by an overexpression of acyl-CoA oxidase-1 (ACOX1) in blood, and another via a baseline pain intensity threshold (VAS > 20 mm). These subgroups represent a critical unmet medical need as evidenced from median OS of 5.5 months in patients receiving single-agent gemcitabine, and comprise an estimated 63% of patients. A significant treatment effect was observed in these subgroups for masitinib with median OS of 11.7 months in the 'ACOX1' subgroup [HR = 0.23 (0.10; 0.51), P = 0.001], and 8.0 months in the 'pain' subgroup [HR = 0.62 (0.43; 0.89), P = 0.012]. Despite an increased toxicity of the combination as compared with single-agent gemcitabine, side-effects remained manageable.

CONCLUSIONS

The present data warrant initiation of a confirmatory study that may support the use of masitinib plus gemcitabine for treatment of PDAC patients with overexpression of ACOX1 or baseline pain (VAS > 20mm). Masitinib's effect in these subgroups is also supported by biological plausibility and evidence of internal clinical validation.

TRIAL REGISTRATION

ClinicalTrials.gov:NCT00789633.

Control of morphology and crystal purity of InP nanowires by variation of phosphine flux during selective area MOMBE

We present experimental results showing how the growth rate, morphology and crystal structure of Au-catalyzed InP nanowires (NWs) fabricated by selective area metal organic molecular beam epitaxy can be tuned by the growth parameters: temperature and phosphine flux. The InP NWs with 20-65 nm diameters are grown at temperatures of 420 and 480 °C with the PH3 flow varying from 1 to 9 sccm. The NW tapering is suppressed at a higher temperature, while pure wurtzite crystal structure is preferred at higher phosphine flows. Therefore, by combining high temperature and high phosphine flux, we are able to fabricate non-tapered and stacking fault-free InP NWs with the quality that other methods rarely achieve. We also develop a model for NW growth and crystal structure which explains fairly well the observed experimental tendencies.

Abstract 01: Genetic variation within genes related to telomere maintenance and DNA repair in a cohort of pediatric acute myeloid leukemia (AML) subjects

Introduction: Short telomeres characterize a spectrum of disorders related to defects in telomere maintenance. The prototypic telomere biology disorder is dyskeratosis congenita (DC), a syndrome associated with specific mucocutaneous features in combination with a markedly increased risk for bone marrow failure, myelodysplastic syndrome (MDS), and acute myeloid leukemia (AML), among other cancers. Germline defects in a subset of telomere maintenance genes have been observed in cohorts of subjects with various hematologic malignancies, including AML. In the setting of defects in DNA repair, critical telomere shortening may result in genomic instability and subsequent malignant transformation. However, a more extensive evaluation of telomere biology and DNA repair genes in childhood AML has not been performed. We hypothesized that variants resulting in premature truncation or rare missense mutations would be identified in a pediatric AML cohort.

Methods: Our patient population included 82 subjects diagnosed with AML or MDS at the Texas Children's Cancer Center, all between the ages of 0 and 18. DNA samples included 61 that were from initial AML diagnosis, 18 that were in AML remission, and 3 from individuals with MDS. The specimens were analyzed using a custom Ampliseq Ion Torrent platform comprised of 43 genes related to telomere maintenance and DNA repair.

Results: Our preliminary analysis focused on 13 genes with the strongest association to a DC or AML/MDS clinical phenotype, including the nine genes currently recognized as DC-associated genes. In addition, for the purposes of this initial analysis we included only variants categorized as stoploss/stopgain mutations or frameshift insertions/deletions. After excluding variants found in HapMap controls, those with a MAF ≥ 1% as reported in dbSNP or ARIC, and those with unacceptably low coverage or quality reads, 87 variants remained of which 33 were unique. Sequence reads for all 87 underwent two distinct and independent reviews for verification, using Integrated Genomics Viewer (IGV), with discordant variants undergoing re-review. After eliminating those variants with consensus from both reviewers to be false positives, 33 samples from all three patient subpopulations demonstrated a total of 14 unique variants resulting in a stoploss/stopgain or frameshift mutation in the following genes: CTC1, RTEL1, RUNX1, TEP1, TERC, TERT, TINF2, and WRAP53. Three of the variants were described in dbSNP and the remaining 11 variants were novel. None of the variants were previously associated with DC-spectrum, AML, or MDS phenotype.

Conclusions: Preliminary analysis indicates that a proportion of this pediatric AML/MDS cohort demonstrates rare and potentially deleterious stoploss/stopgain or frameshift mutations within a set of genes related to telomere maintenance and DNA repair. Further analysis of this data, including variants resulting in missense changes, may provide additional evidence supporting the utility of this platform in better understanding factors contributing to the development of AML and MDS.

Citation Format: Maria Gramatges, Ninad Oak, David Wheeler, Deborah Ritter, Donna Muzny, Sharon Plon. Genetic variation within genes related to telomere maintenance and DNA repair in a cohort of pediatric acute myeloid leukemia (AML) subjects. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Susceptibility and Cancer Susceptibility Syndromes; Jan 29-Feb 1, 2014; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(23 Suppl):Abstract nr 01. doi:10.1158/1538-7445.CANSUSC14-01

Abstract A8: Functional analysis of genomic variants identified through whole exome sequencing of pediatric lymphocytic leukemia kindreds

The underlying genetic basis of many childhood cancers remains largely unknown, which places a significant focus on the discovery and understanding of cancer susceptibility genes. Even genetic predisposition of the most common childhood cancer, acute lymphocytic leukemia (ALL), remains poorly understood. Our research focuses on the identification of novel high risk cancer susceptibility genes through the use of next generation sequencing methods, bioinformatics tools, and functional assays. We are analyzing a small cohort of ethnically diverse families with at least two first-degree relatives with childhood ALL or lymphoma transmitting in an autosomal dominant manner. Whole exome sequencing was performed on affected individuals' normal lymphoblasts and tumor samples when available. In one particular Hispanic kindred, sequencing generated a list of over 1500 heterozygous missense variants shared among three affected individuals. Filtering out common variants found in databases such as dbSNP, reduced this list by 95% and filtering variants seen in a whole exome sequenced intrafamilial control narrowed down the list to 33 potential rare heterozygous cancer susceptibility variants. In order to select which rare variants to analyze by functional methods, various bioinformatics tools were utilized. Variants leading to the change of a conserved amino acid were given a higher priority. In addition, variants had to be predicted to be damaging or deleterious to protein structure or function by 3 out of 4 algorithms. These bioinformatics analyses left us with 8 candidate variant genes (PIK3R4, SUPT3H, NT5C1A, TRPM4, PRKAG3, C6orf136, GLT25D1, and LPIN2). All of these rare variants were retained in tumors from affected family members, but there was no evidence for second hits. RNA-seq data assessing expression in hematopoietic cell populations from murine bone marrow has been a valuable tool to select genes from this variant list for further analysis. Variants that are potential inactivating mutations in genes robustly expressed in murine bone marrow, such as PIK3R4, are prioritized for knock down in murine bone marrow transplantation studies. The p.M239V variant is located in the serine/threonine kinase domain of PIK3R4. PIK3R4 is needed to regulate and activate PIK3C3, which is involved in vesicle trafficking, autophagy, and nutrient sensing. We are currently developing a novel murine model in which we harvest the bone marrow from 5-FU treated CD45.2 mice. Harvested bone marrow is then transduced with murine stem cell virus (MSCV) retroviral vectors expressing GFP and miRNAi to target the knock down of our gene of interest (GOI). The transduced bone marrow is then transplanted into CD45.1 recipient mice that have had their bone marrow ablated by radiation. These mice are then observed for signs of leukemia and their blood is collected at different time points to detect any alterations in hematopoiesis caused by the knockdown of the GOI. Alternatively, if an activating mutation is predicted of a candidate gene, we can use the MSCV retroviral system to overexpress the mutant cDNA in donor bone marrow transplanted into a recipient mouse. Within our larger cohort of ALL kindreds, none of these 8 variants are present, which demonstrates genetic heterogeneity of familial childhood leukemia. Determining the underlying genetic cause of childhood cancers will require collaborative studies across many cancer centers along with multiple model systems for functional analysis.

Citation Format: Jason Saliba, Ryan Zabriskie, Bradford Powell, Stephanie Hicks, Marek Kimmel, Hannah Cheung, Deborah Ritter, Donna M. Muzny, Jeffrey G. Reid, David A. Wheeler, Richard A. Gibbs, Sharon E. Plon. Functional analysis of genomic variants identified through whole exome sequencing of pediatric lymphocytic leukemia kindreds. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A8.

Shadowing and mask opening effects during selective-area vapor-liquid-solid growth of InP nanowires by metalorganic molecular beam epitaxy

Indium phosphide nanowires were grown by metalorganic molecular beam epitaxy using the selective-area vapor-liquid-solid method. We show experimentally and theoretically that the size of the annular opening around the nanowire has a major impact on nanowire growth rate. In addition, we observed a considerable reduction of the growth rate in dense two-dimensional arrays, in agreement with a calculation of the shadowing of the scattered precursors. Due to the impact of these effects on growth, they should be considered during selective-area vapor-liquid-solid nanowire epitaxy.

Whole genome sequencing of sporadic Burkitt lymphoma in HIV-infected and uninfected patients

8577

Background: Burkitt Lymphoma is defined by canonical translocations between MYC and immunoglobulin IgH, IgK or IgL (8:14, 8:2, 8:22, respectively), and is commonly associated with HIV. The identification of HIV from sequenced samples is critical to understanding HIV-associated Burkitt Lymphoma. While recent novel gene mutations (ID3 and TCF3) have been implicated in functional roles, concomitant genomic structural variants and the interaction of HIV with structural variation is less well defined. Methods: We sequenced the whole genomes of 15 patients with 100bp paired-end reads on Illumina Hi-Seq platform, resulting in an average insert size of 278 (+/- 63) and coverage of 60X tumor and 30X normal. We included 7 HIV-negative, and 8 HIV-positive subjects. Sequencing reads were mapped to the reference genome using BWA. Large-scale structural variation was detected by the BreakDancer and Crest programs. Functional annotation was used to prioritize structural variants for validation. Single nucleotide variants and small insertions and deletions were detected by CARNAC, a somatic variation discovery pipeline. The subset of WGS reads that failed to align to the human reference genome were tested for the presence of HIV sequences by comparing the unmapped reads to a database of viral DNA sequences which included the common subtypes of HIV defined by Los Alamos. Reads matching HIV or EBV with an expectation value of <10-4 were analyzed to determine virus coverage and viral integration sites. Results: Canonical MYC-IgH translocations were identified in 9/15 (60%) tumor samples, with 2 additional subjects harboring either a deletion or an inversion near exon1 of MYC; 4 had no MYC rearrangement. MYC translocations occurred equally in both groups. TP53 and SMARC4 point mutations were observed recurrently in the HIV uninfected group but not in the HIV infected patients. Variable levels of HIV DNA sequence were observed in normal tissue of all HIV infected patients. Conclusions: Whole genome sequencing has identified known somatic variants in HIV infected and uninfected patients. Two genes, TP53 and SMARC4, appear to be differentially mutated, but additional samples are needed to achieve statistical significance.

Determination of genotoxicity by the Comet assay applied to murine precision-cut lung slices

Precision-cut lung slices (PCLSs) are an organotypic lung model that is widely used in pharmacological, physiological, and toxicological studies. Genotoxicity testing, as a pivotal part of early risk assessment, is currently established in vivo in various organs including lung, brain, or liver, and in vitro in cell lines or primary cells. The aim of the present study was to provide the three-dimensional organ culture PCLS as a new ex vivo model for determination of genotoxicity using the Comet assay. Murine PCLS were exposed to increasing concentrations of ethyl methane sulfonate 'EMS' (0.03-0.4%) and formalin (0.5-5mM). Tissue was subsequently dissociated, and DNA single-strand breaks were quantified using the Comet assay. Number of viable dissociated lung cells was between 4×10(5) and 6.7×10(5)cells/slice. Even treatment with EMS did not induce toxicity compared to untreated tissue control. As expected, DNA single-strand breaks were increased dose-dependently and significantly after exposure to EMS. Here, tail length rose from 24μm to 75μm. In contrast, formalin resulted in a significant induction of DNA cross-links. The effects induced by EMS and formalin demonstrate the usefulness of PCLS as a new ex vivo lung model for genotoxicity testing in the early risk assessment of airborne substances in the future.

Evaluation of the local temperature of conductive filaments in resistive switching materials

The resistive switching effect in metal oxides and other dielectric materials is among the leading future non-volatile memory technologies. Resistive switching is widely ascribed to the formation and rupture of conductive filaments in the oxide, which are generated by temperature-enhanced nano-scale ion migration or other thermal effects. In spite of the central role of the local filament temperature on the switching effect, as well as on the conduction and reliability physics, no measurement methods of the filament temperature are yet available. In this work, we report on a method for evaluating the conducting filament temperature, using a metal-insulator-semiconductor bipolar transistor structure. The filament temperature is obtained by analyzing the thermal excitation rate of electrons from the filament Fermi level into the conduction band of a p-type semiconductor electrode. Measurements were carried out to obtain the conductive filament temperature in hafnia at varying ambient temperatures in the range of 3-300 K. Significant Joule heating of the filament was observed across the entire measured ambient temperature range. The extracted temperatures provide physical insight into the resistive switching effect.

No correlation between lithium serum levels and psychopathological features during the euthymic interval of patients with recurrent affective disorder

INTRODUCTION

The aim of this prospective study was to investigate the influence of lithium serum levels on subclinical psychopathological features during the euthymic interval in patients with an affective disorder.

METHODS

The study included 54 patients with a recurrent affective disorder undergoing a continuous prophylactic lithium treatment (31 unipolar, 23 bipolar). The observation period lasted for 2 years and included 332 visits. Visits consisted of a detailed interview, a continuous measurement of lithium levels and the collection of validated scales including HAMD, YMRS, CGI, VAMS and the SCL-90R. Several correlations between lithium serum levels and different psychopathological features during the euthymic interval were calculated on an individual patient basis and on a group basis to reveal generally occurring correlations.

RESULTS

No generally occurring significant correlations between lithium serum levels and specific psychopathological features were found. Only on a single patient level, 32 significant correlations between lithium level and specific psychopathological features were found, partly indicating a negative and partly indicating a positive influence of higher lithium levels on psychopathological symptoms. Nevertheless, in the group analyses no significant correlations were found.

DISCUSSION

Higher lithium levels were not associated with an improved psychopathological status, but they were not associated with a worse status (due to a higher burden of side effects) either. According to the literature there is currently no strong evidence to treat patients with a higher lithium level. It is recommended to start with a lower level and to continue with individual adjustments in accordance to prophylactic efficacy and tolerability.

Effects of lithium on the HPA axis in patients with unipolar major depression

Background

(I)

Design and methods

Three 4-week studies with each 30 acutely depressed patients (unipolar, SCID I confirmed) were conducted. In study 1, patients refractory to a treatment trial with an antidepressant of at least four weeks were treated with lithium augmentation. In study 2 and 3, drug free patients were treated with lithium monotherapy or citalopram monotherapy respectively. Weekly HAM-D ratings were performed. In each study, the DEX/CRH test was conducted right before and four weeks after initiation of the pharmacotherapy.

Results

All three pharmacological strategies showed good antidepressive efficacy. Both lithium monotherapy and lithium augmentation led to a (for most parameters significant) increase in the HPA axis activity. In contrast, citalopram monotherapy resulted in a decrease of the hormone response to the DEX/CRH test.

Mechanisms Causing Capacity Loss on Long Term Storage in NiMH System

Capacity recovery after long term storage and loaded storage is a critical issue with the NiMH system since its inception. A measurable loss in capacity is observed when cells are stored for long periods of time or discharged deeply to zero volts. The different mechanisms that are known to cause self discharge and capacity loss after storage and loaded storage will be the focus of this paper. Capacity loss after long term storage involves two main events. One is self discharge which causes the open circuit voltage(OCV) of the cell to drop. Self discharge is caused by decomposition of NiOOH, migration of metal ions and possible degradation of separator. Self discharge can be prevented by using separators which are stable at high temperatures and pH and have good ion trapping capability. Various separator types and treatments can play an important role in inhibiting metal ions from migrating thus reducing self discharge. Self discharge during storage causes a severe suppression in the voltage of the foam positive electrode. This drop in voltage causes a breakdown of the cobalt conductive network in the nickel positive electrode. Reduction of high valence cobalt(III) which forms the electrode's conductive network takes place at these low voltages. A permanent breakdown in the conductive network results in low efficiency of the cell on consecutive charge and discharge cycles. In addition, the cobalt in its lower valence states can migrate away from the electrode into the separator causing shorts. These events effect the charge and discharge efficiency of these cells thereby resulting in capacity loss. Various mechanisms causing self discharge which affect capacity recovery after long term storage and loaded storage are discussed in this paper.

Comparison of Eimeria species distribution and salinomycin resistance in commercial broiler operations utilizing different coccidiosis control strategies

The purpose of the present study was to evaluate the species composition and salinomycin sensitivity of Eimeria oocysts isolated from commercial broiler farms that differed by means of coccidiosis control (anticoccidial drugs [ACD] vs. live oocyst vaccines [VAC]). A comparison of Eimeria species composition and salinomycin sensitivity was also made before and after a producer switched from salinomycin to live oocyst vaccines. In general, no significant difference was observed in the concentration of Eimeria spp. oocysts in litter from VAC-utilizing farms compared to litter from ACD-utilizing farms. Application of PCR-based methods to detect coccidia found that Eimeria species distribution in litter from VAC operations more closely resembled the species composition in the live oocyst vaccines. Drug sensitivity testing found that Eimeria oocysts from VAC operations displayed greater salinomycin sensitivity as measured by weight gain and feed conversion efficiency compared to oocysts from ACD farms. These findings provide additional evidence for the usefulness of live oocyst vaccines to restore ionophore sensitivity in poultry operations that contain an ionophore-resistant population of Eimeria spp. oocysts.

Novel approaches for studying pulmonary toxicity in vitro

The in vitro study of adverse cellular effects induced by inhaled pollutants poses a special problem due to the difficulties of exposing cultured cells of the respiratory tract directly to test atmospheres that can include complex gaseous and particulate mixtures. In general, there is no widely accepted in vitro exposure system. However, in vitro methods offer the unique possibility for use of human cells, developed and validated cell culture and exposure device (CULTEX(1)) using the principle of the air/liquid exposure technique. Cells of the respiratory tract are grown on porous membranes in transwell inserts. After removal of the medium, the cells can be treated on their superficial surfaces with the test atmosphere, and at the same time they are supplied with nutrients through the membrane below. In comparison with other experimental approaches, the goal of our studies is to analyze the biological effects of test atmospheres under environmental conditions, i.e. without humidifying the atmosphere or adding additional CO(2). The system used is small and flexible enough independent of a cultivation chamber and thus offers the opportunity for onsite study of indoor and outdoor atmospheres in the field. The efficacy of the exposure device has already been demonstrated in the analysis of dose-dependent cytotoxic and genotoxic effects of exposure of epithelial lung cells to complex mixtures such as native diesel exhaust and side-stream smoke.

Exposure of human lung cells to native diesel motor exhaust--development of an optimized in vitro test strategy

To investigate the effects of native diesel motor exhaust on human lung cells in vitro, a new experimental concept was developed using an exposure device on the base of the cell cultivation system CULTEX (Patent No. DE19801763.PCT/EP99/00295) to handle the cells during a 1-h exposure period independent of an incubator and next to an engine test rig. The final experimental set-up allows the investigation of native (chemically and physically unmodified) diesel exhaust using short distances for the transportation of the gas to the target cells. The analysis of several atmospheric compounds as well as the particle concentration of the exhaust was performed by online monitoring in parallel. To validate the complete system we concentrated on the measurement of two distinct viability parameters after exposure to air and undiluted, diluted and filtered diesel motor exhaust generated under different engine operating conditions. Cell viability was not influenced by the exposure to clean air, whereas dose-dependent cytotoxicity was found contingent on the dosage of exhaust. Additionally, the quality of exhaust, represented by two engine operating conditions (idling, higher load), also showed well-distinguishable cytotoxicity. In summary, the experimental set-up allows research on biological effects of native engine emissions using short exposure times.