Abstract 1371: Assessing the utility of cell-free DNA in identifying prostate cancer and characterizing tumor heterogeneity via whole exome and whole genome, multi-region sequencing

Early cancer diagnosis, especially while the disease is still localized and before symptoms appear, results in significantly higher survival rates compared to late-stage diagnosis. At the time of diagnosis, it is also common to find multiple foci within a single prostate gland in men with localized disease. Cell-free DNA (cfDNA) may not only reflect underlying disease biology, but also simultaneously allow for the identification of genetically distinct tumor subclones. The objectives of this study are to determine if 1) cfDNA levels are able to distinguish between healthy individuals from patients with localized or metastatic castration-resistant prostate cancer (mCRPC), and 2) if somatic mutations identified in tumor tissue are detectable in cfDNA and representative of the distribution observed in tumor tissue.

This study includes samples from 130 individuals at UCSF: 21 healthy donors, 100 patients with localized prostate cancer who underwent radical prostatectomy (RP), and 9 mCRPC patients. Blood samples and matched tissue from adjacent normal seminal vesicles and multiple tumor regions (1-9 samples per patient) were collected from patients undergoing radical prostatectomy. CfDNA was extracted from plasma, and the concentration and fragment length distribution were measured with a Bioanalyzer 2100. Comparisons of cfDNA levels between groups were assessed with a Welch’s t-test due to the potential for unequal variances. Fifty-seven samples from nine patients have been subjected to whole exome sequencing, and 22 samples from five patients have been subjected to whole genome sequencing at ~40x coverage. Somatic variant calling was performed with Broad Institute’s Firecloud platform (GATK4/MuTect2) for tumor tissue and with the Curio platform for cfDNA to build consensus sequences leveraging unique molecular tags.

CfDNA levels are able to distinguish between healthy and localized (p = 0.005), as well as healthy and metastatic groups (p = 0.043). Tumor foci within a patient’s prostate gland are genetically heterogeneous, with the majority of somatic mutations private to tumor regions and a subset of mutations at the intersection of these regions. Preliminary analyses result in an average of 72 somatic SNVs and indels per tumor tissue region, with ~10% overlap between regions in the same patient. Additional mCRPC and follow-up blood samples are being collected from all patients. The association between cfDNA levels prior to RP surgery and biochemical recurrence will be investigated when follow-up collection concludes. Further analysis of mutational concordance, clonality, and copy number variation between tumor tissue DNA and cfDNA, along with clinical data, will be performed.

Citation Format: Emmalyn Chen, Clinton Cario, Lancelote Leong, Karen Lopez, Patricia Li, Erica Oropeza, Imelda Tenggara, Janet Cowan, Jeffry Simko, Daniel Wells, Robin Kageyama, June Chan, Terence Friedlander, Pamela Paris, Peter Carroll, John Witte. Assessing the utility of cell-free DNA in identifying prostate cancer and characterizing tumor heterogeneity via whole exome and whole genome, multi-region sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1371.

Discovery of Adults Linked to Cloning Oceanic Starfish Larvae (Oreaster, Asteroidea: Echinodermata)

Two juvenile specimens of a new species of Oreaster were collected at Parque Nacional Arrecife Alacranes and Triángulos Oeste in the southern Gulf of Mexico. DNA of mitochondrial loci identifies them as members of the same clade as cloning larvae of Oreaster found abundantly in waters of the Florida Current-Gulf Stream system, and distinct from Oreaster clavatus and Oreaster reticulatus, the two known Oreasteridae species in the North Atlantic. Larvae from the new species of Oreaster persist as clones but also metamorphose and settle to the benthos with typical asteroid morphology.

Sustained rescue of prefrontal circuit dysfunction by antidepressant-induced spine formation

The neurobiological mechanisms underlying the induction and remission of depressive episodes over time are not well understood. Through repeated longitudinal imaging of medial prefrontal microcircuits in the living brain, we found that prefrontal spinogenesis plays a critical role in sustaining specific antidepressant behavioral effects and maintaining long-term behavioral remission. Depression-related behavior was associated with targeted, branch-specific elimination of postsynaptic dendritic spines on prefrontal projection neurons. Antidepressant-dose ketamine reversed these effects by selectively rescuing eliminated spines and restoring coordinated activity in multicellular ensembles that predict motivated escape behavior. Prefrontal spinogenesis was required for the long-term maintenance of antidepressant effects on motivated escape behavior but not for their initial induction.

Sequence-based identification of Anopheles species in eastern Ethiopia

BACKGROUND

The recent finding of a typically non-African Anopheles species in eastern Ethiopia emphasizes the need for detailed species identification and characterization for effective malaria vector surveillance. Molecular approaches increase the accuracy and interoperability of vector surveillance data. To develop effective molecular assays for Anopheles identification, it is important to evaluate different genetic loci for the ability to characterize species and population level variation. Here the utility of the internal transcribed spacer 2 (ITS2) and cytochrome oxidase I (COI) loci for detection of Anopheles species from understudied regions of eastern Ethiopia was investigated.

METHODS

Adult mosquitoes were collected from the Harewe locality (east) and Meki (east central) Ethiopia. PCR and Sanger sequencing were performed for portions of the ITS2 and COI loci. Both NCBI's Basic Local Alignment Search tool (BLAST) and phylogenetic analysis using a maximum-likelihood approach were performed to identify species of Anopheles specimens.

RESULTS

Two species from the east Ethiopian collection, Anopheles arabiensis and Anopheles pretoriensis were identified. Analyses of ITS2 locus resulted in delineation of both species. In contrast, analysis of COI locus could not be used to delineate An. arabiensis from other taxa in Anopheles gambiae complex, but could distinguish An. pretoriensis sequences from sister taxa.

CONCLUSION

The lack of clarity from COI sequence analysis highlights potential challenges of species identification within species complexes. These results provide supporting data for the development of molecular assays for delineation of Anopheles in east Ethiopia.

Abstract 3669: Assessing the genetic heterogeneity of localized, multifocal prostate cancer via cell-free DNA

At the time of diagnosis, it is common to find multiple spatially distinct foci within a single prostate gland in men with prostate cancer. Recent studies evaluating the genetic heterogeneity of localized, multifocal prostate cancers through whole-genome sequencing and whole-exome sequencing have only recently been described. These tumors were highly heterogeneous for single-nucleotide variants, copy number alterations, and genomic rearrangements. One exciting use of cfDNA is its potential ability to simultaneously capture all genetically distinct tumor subclones. Currently, the degree to which a cfDNA sample is representative of the entire genetic landscape of localized prostate cancer is unknown. The objective of this study is to determine if somatic mutations identified in tumor tissue are detectable in cfDNA. Tumor tissue and blood samples have been collected from twenty-nine patients undergoing radical prostatectomy. Samples from fourteen patients have already been subjected to whole-exome sequencing with a target sequencing depth of 200X (HiSeq 4000). Preliminary analyses indicate that tumor foci within a single prostate gland in an individual are genetically heterogeneous. Further analysis of mutational concordance between tumor tissue DNA and cfDNA along with clinical data will be performed.

Citation Format: Emmalyn Chen, Clinton L. Cario, Lancelote Leong, Karen Lopez, Jeffry P. Simko, Peter R. Carroll, Caroline Tai, John S. Witte. Assessing the genetic heterogeneity of localized, multifocal prostate cancer via cell-free DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3669.

Glucose-6-Phosphate Dehydrogenase Deficiency Genetic Variants in Malaria Patients in Southwestern Ethiopia

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an X-linked erythrocyte enzyme disorder with relevance to malaria treatment policy. Treatment with the antimalarial primaquine can result in hemolytic anemia in G6PD-deficient patients. With increased interest in primaquine use, it is important to identify G6PD variants in Ethiopia to inform malaria treatment policy. In the present study, mutations in the G6PD gene are identified in a sample of patients with malaria in Jimma town in southwest Ethiopia. Plasmodium species of infection were confirmed using polymerase chain reaction (PCR) and gel electrophoresis. PCR and Sanger sequencing were performed to observe a portion of the G6PD gene where the common G6PD mutations (A376G, G202A, and C563T) are found. Molecular analysis revealed that most of the samples were single Plasmodium vivax infections (83.7%). For G6PD genotyping, A376G was detected in 23.26% of individuals, whereas G202A and C563T were absent. Three other uncommon mutations were identified: rs782669677 (535G→A), rs370658483, (485 + 37 G→T), and a new mutation at chrX:154535443(C→T). Bioinformatic analysis of these mutations' potential functional impact suggests minimal effect on protein function. The discovery of both common and uncommon G6PD mutations contributes to the discussion on G6PD deficiency and appropriate primaquine treatment in Ethiopia.

Summarizing US Wildlife Trade with an Eye Toward Assessing the Risk of Infectious Disease Introduction

The aim of this study was to characterize the role of the USA in the global exchange of wildlife and describe high volume trade with an eye toward prioritizing health risk assessment questions for further analysis. Here we summarize nearly 14 years (2000-2013) of the most comprehensive data available (USFWS LEMIS system), involving 11 billion individual specimens and an additional 977 million kilograms of wildlife. The majority of shipments contained mammals (27%), while the majority of specimens imported were shells (57%) and tropical fish (25%). Most imports were facilitated by the aquatic and pet industry, resulting in one-third of all shipments containing live animals. The importer reported origin of wildlife was 77.7% wild-caught and 17.7% captive-reared. Indonesia was the leading exporter of legal shipments, while Mexico was the leading source reported for illegal shipments. At the specimen level, China was the leading exporter of legal and illegal wildlife imports. The number of annual declared shipments doubled during the period examined, illustrating continually increasing demand, which reinforces the need to scale up capacity for border inspections, risk management protocols and disease surveillance. Most regulatory oversight of wildlife trade is aimed at conservation, rather than prevention of disease introduction.

Influenza-like illness surveillance on the California-Mexico border, 2004-2009

BACKGROUND

Since 2004, the Naval Health Research Center, with San Diego and Imperial counties, has collaborated with the US Centers for Disease Control and Prevention to conduct respiratory disease surveillance in the US-Mexico border region. In 2007, the Secretariat of Health, Mexico and the Institute of Public Health of Baja California joined the collaboration.

OBJECTIVES

The identification of circulating respiratory pathogens in respiratory specimens from patients with influenza-like illness (ILI).

METHODS

Demographic, symptom information and respiratory swabs were collected from enrollees who met the case definition for ILI. Specimens underwent PCR testing and culture in virology and bacteriology.

RESULTS

From 2004 through 2009, 1855 persons were sampled. Overall, 36% of the participants had a pathogen identified. The most frequent pathogen was influenza (25%), with those aged 6-15 years the most frequently affected. In April 2009, a young female participant from Imperial County, California, was among the first documented cases of 2009 H1N1. Additional pathogens included influenza B, adenovirus, parainfluenza virus, respiratory syncytial virus, enterovirus, herpes simplex virus, Streptococcus pneumoniae, and Streptococcus pyogenes.

CONCLUSIONS

The US-Mexico border is one of the busiest in the world, with a large number of daily crossings. Due to its traffic, this area is an ideal location for surveillance sites. We identified a pathogen in 36% of the specimens tested, with influenza A the most common pathogen. A number of other viral and bacterial respiratory pathogens were identified. An understanding of the incidence of respiratory pathogens in border populations is useful for development of regional vaccination and disease prevention responses.

Platelet dysfunction in myelodysplastic syndromes: a clinicopathological study

Forty-eight patients with myelodysplastic syndromes and a platelet count greater than 80 x 10(9)/L were the subjects of a study of platelet function. A whole-blood platelet lumi-aggregometer was used for simultaneous measurement of platelet aggregation by the impedance method and of adenosine triphosphate-dense granule release. The results were correlated with skin bleeding time and episodes of clinical bleeding or thrombosis. Thirty-five patients had at least 1 abnormal result indicating platelet hypoactivity; 7 patients had mixed platelet hypoactivity and hyperactivity; and 4 patients had platelet hyperactivity. Only 2 patients had normal results. There was good correlation between platelet hypoactivity and prolonged skin bleeding time (P = .005); however, several patients with platelet hypoactivity had normal skin bleeding times. This finding suggested that whole-blood platelet aggregation studies may be more sensitive than bleeding time in identification of patients at risk of bleeding. Clinical hemorrhage was frequent (32 patients) in this cohort despite platelet counts greater than 100 x 10(9)/L. This finding indicated platelet hypofunction was clinically important. In contrast, only 2 of the 13 patients with thrombotic events had evidence of platelet hyperactivity, suggesting that other clinical factors are probably more important determinants of thrombosis. These observations confirm that platelet dysfunction is common in patients with myelodysplastic syndromes and suggest a useful role for routine whole-blood platelet aggregation studies to identify patients at risk of bleeding.

Cranial neural crest cells contribute to connective tissue in cranial muscles in the anuran amphibian, Bombina orientalis

The contribution of cranial neural crest cells to the development and patterning of cranial muscles in amphibians was investigated in the phylogenetically basal and morphologically generalized frog, Bombina orientalis. Experimental methods included fluorescent marking of premigratory cranial neural crest and extirpation of individual migratory streams. Neural crest cells contributed to the connective tissue component, but not the myofibers, of many larval muscles within the first two branchial arches (mandibular and hyoid), and complex changes in muscle patterning followed neural crest extirpation. Connective tissue components of individual muscles of either arch originate from the particular crest migratory stream that is associated with that arch, and this relationship is maintained regardless of the segmental identity-or embryonic derivation-of associated skeletal components. These developmental relations define a pattern of segmentation in the head of larval anurans that is similar to that previously described in the domestic chicken, the only vertebrate that has been thoroughly investigated in this respect. The fundamental role of the neural crest in patterning skeleton and musculature may represent a primitive feature of cranial development in vertebrates. Moreover, the corresponding developmental processes and cell fates appear to be conserved even when major evolutionary innovations-such as the novel cartilages and muscles of anuran larvae-result in major differences in cranial form.

Thrombosis and bleeding in myeloproliferative disorders: identification of at-risk patients with whole blood platelet aggregation studies

Seventy-five patients with chronic myeloproliferative disorders were studied to investigate platelet function by simultaneous measurement of platelet aggregation by the impedance method and ATP dense granule release using a whole blood platelet lumi-aggregometer, in an attempt to identify patients at risk for thrombosis and bleeding. Thirty-nine patients had at least one abnormal result indicating platelet hyperactivity (i.e. impedance or release with one agonist being above the reference range); 16 patients had platelet hypoactivity (i.e. at least one result was below the reference range), whilst 14 had co-existence of hyper- and hypoactivity. Six patients had normal results. 20/53 patients with platelet hyperactivity (alone or mixed) had a positive history of venous and/or arterial thrombosis; in comparison, only two of the other 22 patients had a positive history. During a median follow-up of 33 months, nine patients with and one patient without platelet hyperactivity respectively developed new thrombotic events before the addition of specific therapy. A total of 50 patients with and eight patients without platelet hyperactivity respectively received specific treatment including aspirin and/or cytotoxic therapy. All but one elderly patient with platelet hyperactivity have remained free of new thrombotic events on specific therapy. Two of the 17 patients with platelet hypoactivity had major clinical bleeding. These observations highlight the need to test platelets for hyper- as well as hypo-function and suggest a useful role for routine whole blood platelet aggregation studies to identify the patients at risk for thrombosis or bleeding.

Bispecific monoclonal antibody complexes bound to primate erythrocyte complement receptor 1 facilitate virus clearance in a monkey model

We investigated the feasibility of using bispecific mAb complexes to redirect and improve the efficiency of the primate E complement receptor 1-based clearance reaction to remove a virus from the circulation. As an initial approach, we used bacteriophage phiX174 as an immunologic model for mammalian viruses. Bispecific complexes were prepared by chemically cross-linking a mAb specific for complement receptor 1 with a mAb specific for the bacteriophage phiX174. In a monkey model these complexes facilitate rapid and quantitative binding of the target bacteriophage to E in vitro and in vivo. Moreover, after in vivo binding to E, the complexes containing mAb and prototype virus are rapidly cleared from the circulation of rhesus and cynomolgus monkeys without loss of E. Our findings suggest that bispecific mAb complexes, in concert with primate E complement receptor 1, may have therapeutic utility in the treatment of diseases associated with blood-borne pathogens.

Bispecific monoclonal antibody complexes bound to primate erythrocyte complement receptor 1 facilitate virus clearance in a monkey model

We investigated the feasibility of using bispecific mAb complexes to redirect and improve the efficiency of the primate E complement receptor 1-based clearance reaction to remove a virus from the circulation. As an initial approach, we used bacteriophage phiX174 as an immunologic model for mammalian viruses. Bispecific complexes were prepared by chemically cross-linking a mAb specific for complement receptor 1 with a mAb specific for the bacteriophage phiX174. In a monkey model these complexes facilitate rapid and quantitative binding of the target bacteriophage to E in vitro and in vivo. Moreover, after in vivo binding to E, the complexes containing mAb and prototype virus are rapidly cleared from the circulation of rhesus and cynomolgus monkeys without loss of E. Our findings suggest that bispecific mAb complexes, in concert with primate E complement receptor 1, may have therapeutic utility in the treatment of diseases associated with blood-borne pathogens.

Effectiveness of a consultation intervention to promote tobacco control policies in Northwest Indian tribes: integrating experimental evaluation and service delivery

A quasi-experimental replication of an intervention for promoting tobacco control policies in Northwest Indian tribes is described and the process of intervention including issues of collaboration among research institutions and Indian organizations is discussed. The policy intervention was evaluated using a pretest-posttest design wherein 20 tribes that had served as wait-list controls now received the intervention. The intervention comprised a tribal representative attending a kickoff orientation; follow-up visits to the tribes; distribution of tobacco policy workbooks; and phone call consultations. Policy status and stringency were assessed by means of telephone interviews with two key contacts per tribe, and by a count of enacted policies. There were significant pre-post changes in the primary outcome measure, a composite summary score of tobacco policy stringency, and changes were also reflected in enacted policies. The intervention effects observed were similar to those found in the prior randomized trial and suggest a robust, disseminable intervention. Much of the success achieved was attributed to the role of an Indian organization in planning the project and implementing the intervention and evaluation protocols.