Biology subjects

Flory, A.

Publications and source records attributed to Flory, A..

5 recordsLinked to original sources

bioRxiv2024

Study Design and Interim Analysis of the Cancer Lifetime Assessment Screening Study in Canines (CLASSiC): The First Prospective Cancer Screening Study in Dogs Using Next-Generation Sequencing-Based Liquid Biopsy

ObjectiveThe Cancer Lifetime Assessment Screening Study in Canines (CLASSiC) is a prospective, longitudinal cancer screening study, in which enrolled dogs are screened for cancer with physical exams and next-generation sequencing-based liquid biopsy testing on a serial basis. The goals of the first interim analysis, presented here, are to assess the benefits of using the OncoK9(R) liquid biopsy test as a cancer screening tool in a prospective clinical setting, and to demonstrate test performance for cancer detection, including preclinical detection. Subjects726 presumably cancer-free client-owned dogs were prospectively enrolled in the study across 24 clinical sites in the US and Canada. Most subjects were at high risk of cancer at the time of enrollment based on age and/or breed. 419 dogs that were enrolled for at least one year and had at least two cancer screening study visits, or that had received a definitive or presumptive diagnosis of cancer up to the time of the interim analysis, were included in the analysis. MethodsClinical data and a blood sample were collected at each study visit (once or twice per year and when cancer was clinically suspected). Cell-free DNA extracted from plasma was tested by OncoK9(R) using next-generation sequencing (NGS) technology. Results417 dogs were eligible for inclusion in the interim analysis and had classifiable outcomes, with a mean on-study duration of 422 days. Of these, 51 dogs were newly diagnosed with cancer (37 definitive, 14 presumptive), translating to a 12% (51/417) observed incidence over the study period; the liver, skin, bone, heart, spleen, lung, and lymph node(s) were the most common anatomic locations for disease. The prospectively observed sensitivity (detection rate) of the test was 56.9% (95% CI: 42.3-70.4%) with a specificity of 98.9% (95% CI: 97.0-99.6%). The prospectively observed positive predictive value was 87.9% (95% CI: 70.9-96.0%) and the negative predictive value was 94.3% (95% CI: 91.3-96.3%). NGS-based liquid biopsy doubled the overall number of cancer cases detected in this study population (from 25 to 51); remarkably, the detection rate for preclinical cancer was increased 4.6-fold from 12% (6/51) by routine care alone to 55% (28/51) by combining routine care with OncoK9(R) testing. Clinical RelevanceCLASSiC is the [fi]rst study to prospectively document the incidence of cancer in a predominantly high-risk canine population, and to prospectively demonstrate that the addition of NGS-based cancer screening to regularly scheduled wellness visits has the potential to substantially increase preclinical cancer detection in this population.

genomics↗

bioRxiv2023

Next-generation sequencing-based liquid biopsy can be used for detection of residual disease and cancer recurrence monitoring in dogs

ObjectiveThe purpose of this study was to evaluate the performance of a next-generation sequencing-based liquid biopsy test for cancer monitoring in dogs. SamplesPre- and post-operative blood samples were collected prospectively from dogs with confirmed cancer diagnoses originally enrolled in the CANcer Detection in Dogs (CANDiD) study. A subset of these dogs also had longitudinal blood samples collected for recurrence monitoring. MethodsAll patients had a pre-operative blood sample collected (after diagnosis but prior to surgical intervention) in which a cancer signal was detected, and had at least one post-operative sample collected. Clinical data were collected for all patients and used to assign a clinical disease status for each follow-up visit. ResultsFollowing excisional surgery, in the absence of clinical residual disease at the post-operative visit, patients with Cancer Signal Detected results at that visit were 1.95-times as likely to have clinical recurrence within 6 months compared to patients with Cancer Signal Not Detected results. In the subset of patients with longitudinal liquid biopsy samples that had clinical recurrence documented during the study period, 73% (8/11; 95% CI: 39 - 93%) of patients had Cancer Signal Detected in blood prior to or concomitant with clinical recurrence; in the 6 patients where molecular recurrence was detected prior to clinical recurrence, the median lead time was 168 days (range: 47 - 238). Clinical RelevanceNext-generation sequencing-based liquid biopsy is a non-invasive tool for cancer monitoring in dogs that can be used as an adjunct to current standard-of-care clinical assessment methods.

genomics↗

bioRxiv2022

Gene regulatory network inference in soybean upon infection by Phytophthora sojae

Phytophthora sojae is a soil-borne oomycete and the causal agent of Phytophthora root and stem rot (PRR) in soybean (Glycine max [L.] Merrill). Yield losses attributed to P. sojae are devastating in disease-conducive environments, with global estimates surpassing 1.1 million tonnes annually. Historically, management of PRR has entailed host genetic resistance (both vertical and horizontal) complemented by disease-suppressive cultural practices (e.g., oomicide application). However, the vast expansion of complex and/or diverse P. sojae pathotypes necessitates developing novel technologies to attenuate PRR in field environments. Therefore, the objective of the present study was to couple high-throughput sequencing data and deep learning to elucidate molecular features in soybean following infection by P. sojae. In doing so, we generated transcriptomes to identify differentially expressed genes (DEGs) during compatible and incompatible interactions with P. sojae and a mock inoculation. The expression data were then used to select two defense-related transcription factors (TFs) belonging to WRKY and RAV families. DNA Affinity Purification and sequencing (DAP-seq) data were obtained for each TF, providing putative DNA binding sites in the soybean genome. These bound sites were used to train Deep Neural Networks with convolutional and recurrent layers to predict new target sites of WRKY and RAV family members in the DEG set. Moreover, we leveraged publicly available Arabidopsis (Arabidopsis thaliana) DAP-seq data for five TF families enriched in our transcriptome analysis to train similar models. These Arabidopsis data-based models were used for cross-species TF binding site prediction on soybean. Finally, we created a gene regulatory network depicting TF-target gene interactions that orchestrate an immune response against P. sojae. Information herein provides novel insight into molecular plant-pathogen interaction and may prove useful in developing soybean cultivars with more durable resistance to P. sojae. Author SummaryGlobal food security is threatened continually by plant pathogens. One approach to circumvent these disease-causing agents entails understanding how hosts balance primary growth and defense upon pathogen perception. Molecular signatures of perception-rendered defense may be leveraged subsequently to develop resistant/tolerant crop plants. Additionally, evidence suggests that the plant immune system is characterized by tuning primary and secondary metabolic activity via transcription factor-mediated transcriptional reprogramming. Therefore, we investigated transcription factor-target gene interactions in soybean upon infection by compatible and incompatible races of Phytophthora sojae. Through transcriptome analysis, we found that the interactions elicited vast, overlapping transcriptional responses and identified overrepresented, defense-related transcription factor families. We then generated/acquired DNA-protein interactome data for the most represented transcription factor families in the transcriptome analysis and trained deep learning-based models to predict novel transcription factor targets. Transcription factor/target gene metrics were used to construct a gene regulatory network with prioritized components. We identified hub transcription factors belonging to WRKY and ERF families, the majority of which function in response to various biotic and abiotic stressors. These findings propose novel regulators in the soybean defense response to Phytophthora sojae and provide an avenue for the investigation of transcription factor-target gene interactions in plants.

plant biology↗

bioRxiv2022

Age at cancer diagnosis by breed, weight, sex, and cancer type in a cohort of over 3,000 dogs: determining the optimal age to initiate cancer screening in canine patients

The goal of cancer screening is to detect disease at an early stage when treatment may be more effective. Until recently, cancer screening in dogs has relied upon annual physical examinations and routine laboratory tests, which are largely inadequate for detecting preclinical disease. With the introduction of non-invasive "liquid biopsy" cancer detection methods, the discussion is shifting from "How to screen dogs for cancer" to "When to screen dogs for cancer". To address this question, data from 3,452 cancer-diagnosed subjects were analyzed to determine the age at which dogs of certain breeds and weights are typically diagnosed with cancer. In the study population, the median age at cancer diagnosis was 8.8 years, with males diagnosed at younger ages than females, and spayed/neutered dogs diagnosed at significantly later ages than intact dogs. Overall, weight was inversely correlated with age at cancer diagnosis, and purebred dogs were diagnosed at significantly younger ages than mixed-breed dogs. For breeds with 10 or more subjects, a breed-based median age at diagnosis was calculated. A weight-based linear regression model was developed to predict the median age at diagnosis for breeds represented by fewer than 10 subjects and for mixed-breed dogs. The study findings support a general recommendation to start cancer screening for all dogs at the age of 7, and as early as 4 years of age for breeds with a lower median age at cancer diagnosis, in order to increase the chances of early detection and treatment.

cancer biology↗

bioRxiv2021

Blood-based liquid biopsy for comprehensive cancer genomic profiling using next-generation sequencing: an emerging paradigm for noninvasive cancer detection and management in dogs

This proof-of-concept study demonstrates that blood-based liquid biopsy using next generation sequencing of cell-free DNA can noninvasively detect multiple classes of genomic alterations in dogs with cancer, including alterations that originate from spatially separated tumor sites. Eleven dogs with a variety of confirmed cancer diagnoses (including localized and disseminated disease) who were scheduled for surgical resection, and 5 presumably cancer-free dogs, were enrolled. Blood was collected from each subject, and multiple spatially separated tumor tissue samples were collected during surgery from 9 of the cancer subjects. All samples were analyzed using an advanced prototype of a novel liquid biopsy test designed to noninvasively interrogate multiple classes of genomic alterations for the detection, characterization, and management of cancer in dogs. In 5 of the 9 cancer patients with matched tumor and plasma samples, pre-surgical liquid biopsy testing identified genomic alterations, including single nucleotide variants and copy number variants, that matched alterations independently detected in corresponding tumor tissue samples. Importantly, the pre-surgical liquid biopsy test detected alterations observed in spatially separated tissue samples from the same subject, demonstrating the potential of blood-based testing for comprehensive genomic profiling of heterogeneous tumors. Among the 3 patients with post-surgical blood samples, genomic alterations remained detectable in one patient with incomplete tumor resection, suggesting utility for noninvasive detection of minimal residual disease following curative-intent treatment. Liquid biopsy allows for noninvasive profiling of cancer-associated genomic alterations with a simple blood draw and has potential to overcome the limitations of tissue-based testing posed by tissue-level genomic heterogeneity.

genomics↗