Molecular profiling studies have shown that 85% of canine urothelial carcinomas (UC) harbor an activating BRAF V595E mutation, which is orthologous to the V600E variant found in several human cancer ...subtypes. In dogs, this mutation provides both a powerful diagnostic marker and a potential therapeutic target; however, due to their relative infrequency, the remaining 15% of cases remain understudied at the molecular level. We performed whole exome sequencing analysis of 28 canine urine sediments exhibiting the characteristic DNA copy number signatures of canine UC, in which the BRAF V595E mutation was undetected (UDV595E specimens). Among these we identified 13 specimens (46%) harboring short in-frame deletions within either BRAF exon 12 (7/28 cases) or MAP2K1 exons 2 or 3 (6/28 cases). Orthologous variants occur in several human cancer subtypes and confer structural changes to the protein product that are predictive of response to different classes of small molecule MAPK pathway inhibitors. DNA damage response and repair genes, and chromatin modifiers were also recurrently mutated in UDV595E specimens, as were genes that are positive predictors of immunotherapy response in human cancers. Our findings suggest that short in-frame deletions within BRAF exon 12 and MAP2K1 exons 2 and 3 in UDV595E cases are alternative MAPK-pathway activating events that may have significant therapeutic implications for selecting first-line treatment for canine UC. We developed a simple, cost-effective capillary electrophoresis genotyping assay for detection of these deletions in parallel with the BRAF V595E mutation. The identification of these deletion events in dogs offers a compelling cross-species platform in which to study the relationship between somatic alteration, protein conformation, and therapeutic sensitivity.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
2.
BRAF Mutations in Canine Cancers Mochizuki, Hiroyuki; Kennedy, Katherine; Shapiro, Susan G ...
PloS one,
06/2015, Letnik:
10, Številka:
6
Journal Article
Recenzirano
Odprti dostop
Activating mutations of the BRAF gene lead to constitutive activation of the MAPK pathway. Although many human cancers carry the mutated BRAF gene, this mutation has not yet been characterized in ...canine cancers. As human and canine cancers share molecular abnormalities, we hypothesized that BRAF gene mutations also exist in canine cancers. To test this hypothesis, we sequenced the exon 15 of BRAF, mutation hot spot of the gene, in 667 canine primary tumors and 38 control tissues. Sequencing analysis revealed that a single nucleotide T to A transversion at nucleotide 1349 occurred in 64 primary tumors (9.6%), with particularly high frequency in prostatic carcinoma (20/25, 80%) and urothelial carcinoma (30/45, 67%). This mutation results in the amino acid substitution of glutamic acid for valine at codon 450 (V450E) of canine BRAF, corresponding to the most common BRAF mutation in human cancer, V600E. The evolutional conservation of the BRAF V600E mutation highlights the importance of MAPK pathway activation in neoplasia and may offer opportunity for molecular diagnostics and targeted therapeutics for dogs bearing BRAF-mutated cancers.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Urothelial carcinoma (UC) of the lower urinary tract and prostatic carcinoma (PC) are aggressive genitourinary cancers in dogs, characterized by invasion to surrounding tissues and high metastatic ...potential. Current diagnosis of canine UC and PC requires histopathological examination of a biopsy. Such specimens require specialized medical equipment and are invasive procedures, limiting the availability of diagnosis by histopathology for many canine patients. Access to a non-invasive means to confirm diagnosis is currently an unmet need. Recently, the canine BRAF V595E mutation was detected in ~80% of canine UCs and PCs. In this study, we developed a droplet digital PCR (ddPCR) assay for detection of the canine BRAF V595E mutation in canine urogenital tumors. The assay was evaluated in DNA samples prepared from biopsy specimens of UC (n = 48) and PC (n = 27), as well and non-neoplastic bladder epithelium (n = 38). In addition the assay was assessed for use with DNA isolated from free catch urine samples derived from canine patients with UC (n = 23), PC (n = 3), as well as from dogs with cystitis and healthy controls (n = 37). In all cases the sensitivity to detect the mutant allele was compared with conventional Sanger sequencing. ddPCR had superior sensitivity for detection of the V595E mutation: 75% of UC, 85% of PC, and 0% of control samples were mutation positive, respectively, and the V595E mutation was detected at a level as low as just 1 in 10,000 alleles (~0.01%). Furthermore, the ddPCR assay identified the mutation in free catch urine samples from 83% of canine UC and PC patients, demonstrating its utility as a non-invasive means of diagnosis. We have shown that ddPCR is a sensitive molecular technique with the potential to facilitate accurate and non-invasive means of canine UC and PC diagnosis.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Parchment, the skins of animals prepared for use as writing surfaces, offers a valuable source of genetic information. Many have clearly defined provenance, allowing for the genetic findings to be ...evaluated in temporal and spatial context. While these documents can yield evidence of the animal sources, the DNA contained within these aged skins is often damaged and fragmented. Previously, genetic studies targeting parchment have used destructive sampling techniques and so the development and validation of non-destructive sampling methods would expand opportunities and facilitate testing of more precious documents, especially those with historical significance. Here we present genetic data obtained by non-destructive sampling of eight parchments spanning the 15th century to the modern day. We define a workflow for enriching the mitochondrial genome (mtGenome), generating next-generation sequencing reads to permit species identification, and providing interpretation guidance. Using sample replication, comparisons to destructively sampled controls, and by establishing authentication criteria, we were able to confidently assign full/near full mtGenome sequences to 56.3% of non-destructively sampled parchments, each with greater than 90% of the mtGenome reference covered. Six of eight parchments passed all four established thresholds with at least one non-destructive sample, highlighting promise for future studies.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The pathophysiological similarities shared by many forms of human and canine disease, combined with the sophisticated genomic resources now available for the dog, have placed ‘man’s best friend’ in a ...position of high visibility as a model system for a variety of biomedical concerns, including cancer. The importance of nonrandom cytogenetic abnormalities in human leukemia and lymphoma was recognized over 40 years ago, but the mechanisms of genome reorganization remain incompletely understood. The development of molecular cytogenetics, using fluorescence
in situ
hybridization (FISH) technology, has played a significant role in our understanding of cancer biology by providing a means for ‘interrogating’ tumor cells for a variety of gross genetic changes in the form of either numerical or structural chromosome aberrations. Here, we have identified cytogenetic abnormalities in naturally occurring canine hematopoietic tumors that are evolutionarily conserved compared with those that are considered characteristic of the corresponding human condition. These data suggest that humans and dogs share an ancestrally retained pathogenetic basis for cancer and that cytogenetic evaluation of canine tumors may provide greater insight into the biology of tumorigenesis.
We introduce three architecture modifications to enhance the performance of the end-to-end (E2E) variational network (VarNet) for undersampled MRI reconstructions. We first implemented the Feature ...VarNet, which propagates information throughout the cascades of the network in an N-channel feature-space instead of a 2-channel feature-space. Then, we add an attention layer that utilizes the spatial locations of Cartesian undersampling artifacts to further improve performance. Lastly, we combined the Feature and E2E VarNets into the Feature-Image (FI) VarNet, to facilitate cross-domain learning and boost accuracy. Reconstructions were evaluated on the fastMRI dataset using standard metrics and clinical scoring by three neuroradiologists. Feature and FI VarNets outperformed the E2E VarNet for 4
, 5
and 8
Cartesian undersampling in all studied metrics. FI VarNet secured second place in the public fastMRI leaderboard for 4
Cartesian undersampling, outperforming all open-source models in the leaderboard. Radiologists rated FI VarNet brain reconstructions with higher quality and sharpness than the E2E VarNet reconstructions. FI VarNet excelled in preserving anatomical details, including blood vessels, whereas E2E VarNet discarded or blurred them in some cases. The proposed FI VarNet enhances the reconstruction quality of undersampled MRI and could enable clinically acceptable reconstructions at higher acceleration factors than currently possible.
Native Fish Need A Natural Flow Regime Pennock, Casey A.; Budy, Phaedra; Macfarlane, William W. ...
Fisheries,
March 2022, Letnik:
47, Številka:
3
Journal Article
Recenzirano
Water development has threatened the ecological integrity of riverine ecosystems. Increasing water demand, persistent drought, and climate change exacerbate the effects of habitat degradation and ...loss in altered systems such as the Colorado River basin. Today, biologists are challenged to identify management actions that benefit native fishes while not hindering water development or management. Herein, we discuss the importance of the natural flow regime for functioning riverine ecosystems and provide examples from four tributaries to the Green River, a major headwater branch of the Colorado River. These tributaries represent a gradient of impacts ranging from water ion to the point of complete seasonal desiccation to a relatively natural flow regime, and consequently have maintained different levels of instream habitat complexity and native fish persistence. Despite decades of management, endangered species lack self‐sustaining populations and other native species have been extirpated from over half their ranges, which begs the question: can water development and fish conservation be balanced under current water laws and climate change‐driven declines in runoff? Given the continued decline in freshwater biodiversity and abundance occurring across the globe, we contend that immediate designation of rivers with natural flow regimes as freshwater conservation areas will enhance native species recovery.
Objectives/Hypothesis
Description of a novel use of a submandibular gland (SMG) flap pedicled on the facial vessels to restore facial volume after parotidectomy, and comparison of clinical outcomes ...with alternative modes of reconstruction.
Study Design
Retrospective chart review.
Methods
The surgical technique for a SMG flap is described. Retrospective chart review of cases of parotidectomy at a single tertiary medical center was conducted (n = 43). Cases were grouped in three cohorts of consecutive patients depending on reconstruction technique: SMG flap (n = 13), sternocleidomastoid muscle (SCM) flap (n = 15), and no flap (n = 15). Cohort characteristics and complication rates are reported.
Results
The SMG flap was more often used for a malignant pathology (92%) and in conjunction with a neck dissection (100%), compared to the SCM flap (47% and 15%) or no flap (0% and 0%), respectively. The mean House‐Brackmann score in the immediate postoperative period in the SMG‐flap group was slightly elevated compared to the other groups: 1.6 (standard deviation SD ± 0.5) versus 1.1 (SD ± 0.3) and 1.0 (SD ± 0.0). Otherwise, the complication rate was similar across groups.
Conclusions
The SMG flap is a safe and effective option for volume restoration after parotidectomy. It provides durable volume that will not atrophy and is already exposed in the field of dissection for patients undergoing concurrent level I neck dissection.
Level of Evidence
3 Laryngoscope, 130:E155–E162, 2020
Angiosarcoma is a highly aggressive cancer of blood vessel-forming cells with few effective treatment options and high patient mortality. It is both rare and heterogenous, making large, well-powered ...genomic studies nearly impossible. Dogs commonly suffer from a similar cancer, called hemangiosarcoma, with breeds like the golden retriever carrying heritable genetic factors that put them at high risk. If the clinical similarity of canine hemangiosarcoma and human angiosarcoma reflects shared genomic etiology, dogs could be a critically needed model for advancing angiosarcoma research. We assessed the genomic landscape of canine hemangiosarcoma via whole-exome sequencing (47 golden retriever hemangiosarcomas) and RNA sequencing (74 hemangiosarcomas from multiple breeds). Somatic coding mutations occurred most frequently in the tumor suppressor
(59.6% of cases) as well as two genes in the PI3K pathway: the oncogene
(29.8%) and its regulatory subunit
(8.5%). The predominant mutational signature was the age-associated deamination of cytosine to thymine. As reported in human angiosarcoma,
was recurrently deleted and
, and
recurrently gained. We compared the canine data to human data recently released by The Angiosarcoma Project, and found many of the same genes and pathways significantly enriched for somatic mutations, particularly in breast and visceral angiosarcomas. Canine hemangiosarcoma closely models the genomic landscape of human angiosarcoma of the breast and viscera, and is a powerful tool for investigating the pathogenesis of this devastating disease. IMPLICATIONS: We characterize the genomic landscape of canine hemangiosarcoma and demonstrate its similarity to human angiosarcoma.
Dams can be operated to mimic components of the natural flow regime to minimise impacts on downstream ecosystems. However, infrastructure, societal needs, water management, and catchment runoff ...constrain which and when flow regime attributes can be mimicked.
We compared fish assemblage responses, including native and non‐native species, over 2 decades of managed environmental flows to those in a river retaining a relatively unaltered flow regime. Both of these arid‐land rivers are within the overallocated Colorado River basin and have experienced declines in catchment runoff over the past 20 years. We predicted that fish–flow relationships would be conserved across time and between managed and unmanaged rivers.
Declines in flow in both rivers coincided with declines in some native fishes, and more native and non‐native fish species exhibited declines in the managed river than in the unmanaged river. Our ability to detect previously documented native fish–flow relationships diminished in the managed river system because established environmental flow targets were not met due to water management, but we detected these fish–flow relationships in the unmanaged river.
Our results suggest declining catchment runoff and increased consumptive water use could reduce the effectiveness of environmental flows that have lower priority in most years.
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