Urine Biopsy as Dynamic Biomarker to Enhance Clinical Staging of Bladder Cancer in Radical Cystectomy Candidates.

PURPOSE: There is significant interest in identifying complete responders to neoadjuvant chemotherapy (NAC) before radical cystectomy (RC) to potentially avoid removal of a pathologically benign bladder. However, clinical restaging after NAC is highly inaccurate. The objective of this study was to develop a next-generation sequencing-based molecular assay using urine to enhance clinical staging of patients with bladder cancer. METHODS: Urine samples from 20 and 44 patients with bladder cancer undergoing RC were prospectively collected for retrospective analysis for molecular correlate analysis from two clinical trials, respectively. The first cohort was used to benchmark the assay, and the second was used to determine the performance characteristics of the test as it correlates to responder status as measured by pathologic examination. RESULTS: First, to benchmark the assay, known mutations identified in the tissue (MT) of patients from the Accelerated Methotrexate, Vinblastine, Doxorubicin, Cisplatin trial (ClinicalTrials.gov identifier: NCT01611662, n = 16) and a cohort from University of California-San Francisco (n = 4) were cross referenced against mutation profiles from urine (MU). We then determined the correlation between MU persistence and residual disease in pre-RC urine samples from a second prospective clinical trial (The pT0 trial; ClinicalTrials.gov identifier: NCT02968732). Residual MU status correlated strongly with residual disease status (pT0 trial; n = 44; P = .0092) when MU from urine supernatant and urine pellet were assessed separately and analyzed in tandem. The sensitivity, specificity, PPV, and NPV were 91%, 50%, 86%, and 63% respectively, with an overall accuracy of 82% for this second cohort. CONCLUSION: MU are representative of MT and thus can be used to enhance clinical staging of urothelial carcinoma. Urine biopsy may be used as a reliable tool that can be further developed to identify complete response to NAC in anticipation of safe RC avoidance.

Post-infarction ventricular septal defect: percutaneous or surgical management in the UK national registry.

AIMS: Post-infarction ventricular septal defect (PIVSD) is a mechanical complication of acute myocardial infarction (AMI) with a poor prognosis. Surgical repair is the mainstay of treatment, although percutaneous closure is increasingly undertaken. METHODS AND RESUTS: Patients treated with surgical or percutaneous repair of PIVSD (2010-2021) were identified at 16 UK centres. Case note review was undertaken. The primary outcome was long-term mortality. Patient groups were allocated based upon initial management (percutaneous or surgical). Three-hundred sixty-two patients received 416 procedures (131 percutaneous, 231 surgery). 16.1% of percutaneous patients subsequently had surgery. 7.8% of surgical patients subsequently had percutaneous treatment. Times from AMI to treatment were similar [percutaneous 9 (6-14) vs. surgical 9 (4-22) days, P = 0.18]. Surgical patients were more likely to have cardiogenic shock (62.8% vs. 51.9%, P = 0.044). Percutaneous patients were substantially older [72 (64-77) vs. 67 (61-73) years, P < 0.001] and more likely to be discussed in a heart team setting. There was no difference in long-term mortality between patients (61.1% vs. 53.7%, P = 0.17). In-hospital mortality was lower in the surgical group (55.0% vs. 44.2%, P = 0.048) with no difference in mortality after hospital discharge (P = 0.65). Cardiogenic shock [adjusted hazard ratio (aHR) 1.97 (95% confidence interval 1.37-2.84), P < 0.001), percutaneous approach [aHR 1.44 (1.01-2.05), P = 0.042], and number of vessels with coronary artery disease [aHR 1.22 (1.01-1.47), P = 0.043] were independently associated with long-term mortality. CONCLUSION: Surgical and percutaneous repair are viable options for management of PIVSD. There was no difference in post-discharge long-term mortality between patients, although in-hospital mortality was lower for surgery.

Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements.

BACKGROUND: Divergence time estimation is fundamental to understanding many aspects of the evolution of organisms, such as character evolution, diversification, and biogeography. With the development of sequence technology, improved analytical methods, and knowledge of fossils for calibration, it is possible to obtain robust molecular dating results. However, while phylogenomic datasets show great promise in phylogenetic estimation, the best ways to leverage the large amounts of data for divergence time estimation has not been well explored. A potential solution is to focus on a subset of data for divergence time estimation, which can significantly reduce the computational burdens and avoid problems with data heterogeneity that may bias results. RESULTS: In this study, we obtained thousands of ultraconserved elements (UCEs) from 130 extant galliform taxa, including representatives of all genera, to determine the divergence times throughout galliform history. We tested the effects of different "gene shopping" schemes on divergence time estimation using a carefully, and previously validated, set of fossils. Our results found commonly used clock-like schemes may not be suitable for UCE dating (or other data types) where some loci have little information. We suggest use of partitioning (e.g., PartitionFinder) and selection of tree-like partitions may be good strategies to select a subset of data for divergence time estimation from UCEs. Our galliform time tree is largely consistent with other molecular clock studies of mitochondrial and nuclear loci. With our increased taxon sampling, a well-resolved topology, carefully vetted fossil calibrations, and suitable molecular dating methods, we obtained a high quality galliform time tree. CONCLUSIONS: We provide a robust galliform backbone time tree that can be combined with more fossil records to further facilitate our understanding of the evolution of Galliformes and can be used as a resource for comparative and biogeographic studies in this group.

The onset of embryo maturation in Arabidopsis is determined by its developmental stage and does not depend on endosperm cellularization.

Seeds are dormant and desiccated structures, filled with storage products to be used after germination. These properties are determined by the maturation program, which starts, in Arabidopsis thaliana, mid-embryogenesis, at about the same time and developmental stage in all the seeds in a fruit. The two factors, chronological and developmental time, are closely entangled during seed development, so their relative contribution to the transition to maturation is not well understood. It is also unclear whether that transition is determined autonomously by each seed or whether it depends on signals from the fruit. The onset of maturation follows the cellularization of the endosperm, and it has been proposed that there exists a causal relationship between both processes. We explored all these issues by analyzing markers for maturation in Arabidopsis mutant seeds that develop at a slower pace, or where endosperm cellularization happens too early, too late, or not at all. Our data show that the developmental stage of the embryo is the key determinant of the initiation of maturation, and that each seed makes that transition autonomously. We also found that, in contrast with previous models, endosperm cellularization is not required for the onset of maturation, suggesting that this transition is independent of the hexose/sucrose ratio in the seed. Our observations indicate that the mechanisms that control endosperm cellularization, embryo growth, and embryo maturation act independently of each other.

Granulocytic Sarcoma of the Orbit Presenting as a Fulminant Orbitopathy in an Adult With Acute Myeloid Leukemia.

A 64-year-old woman with relapsed acute myelogenous leukemia (AML) undergoing salvage chemotherapy developed rapid onset of right-sided ophthalmoplegia, proptosis, optic neuropathy, and vision loss from 20/30 to hand motions over a 3-hour period on day 4 of her treatment. CT scan of her orbits revealed a superolateral orbital mass and periocular edema. She underwent immediate canthotomy and cantholysis, and lateral orbitotomy with debulking of the mass later the same day. The histopathology was consistent with aggregates of myeloid blasts. Her vision recovered to 20/20 on postoperative day 1. Orbital granulocytic sarcoma is a rare condition often concurrent with AML, typically in the pediatric population and rarely in adults. Presentation as a fulminant orbitopathy with rapidly progressive optic neuropathy and vision loss over several hours has not been previously reported.

Limitations on orchid recruitment: not a simple picture.

Mycorrhizal fungi have substantial potential to influence plant distribution, especially in specialized orchids and mycoheterotrophic plants. However, little is known about environmental factors that influence the distribution of mycorrhizal fungi. Previous studies using seed packets have been unable to distinguish whether germination patterns resulted from the distribution of appropriate edaphic conditions or the distribution of host fungi, as these cannot be separated using seed packets alone. We used a combination of organic amendments, seed packets and molecular assessment of soil fungi required by three terrestrial orchid species to separate direct and indirect effects of fungi and environmental conditions on both seed germination and subsequent protocorm development. We found that locations with abundant mycorrhizal fungi were most likely to support seed germination and greater growth for all three orchids. Organic amendments affected germination primarily by affecting the abundance of appropriate mycorrhizal fungi. However, fungi associated with the three orchid species were affected differently by the organic amendments and by forest successional stage. The results of this study help contextualize the importance of fungal distribution and abundance to the population dynamics of plants with specific mycorrhizal requirements. Such phenomena may also be important for plants with more general mycorrhizal associations.

Thapsigargin resistance in human prostate cancer cells.

BACKGROUND: Thapsigargin (TG) is a potent inhibitor of sarcoplasmic/endoplasmic reticulum Ca2+ ATPases (SERCAs). TG-based prodrugs are being developed for the treatment of prostate cancer (PC). To develop optimal TG-based therapeutics it is important to understand the mechanisms of resistance to TG that may potentially occur in cancer cells. METHODS: DU145/TG and PC3/TG cells were derived from human PC DU145 and PC3 cells, respectively, by incremental exposure to TG. Growth assays, Western blot analyses, cDNA microarrays, semiquantitative and real-time polymerase chain reaction (PCR), Northern blot analyses, and immunohistochemistry were used to study these cells. RESULTS: DU145/TG cells are 1100-fold and PC3/TG cells are 1350-fold resistant to TG. Although expression of both SERCA and p-glycoprotein can mediate TG resistance in hamster cells, neither is modulated in DU145/TG cells. In contrast, in PC3/TG cells, SERCA, and not p-glycoprotein, is significantly overexpressed but cannot by itself account for the 1350-fold resistance to TG in these cells. Several genes not previously identified to be altered by TG selection are modulated in DU145/TG and PC3/TG cells. Furthermore, the spectrum of genes modulated in DU145/TG cells are distinct from that in PC3/TG cells, even though both cells are of prostate origin and share the same TG-resistant phenotype. CONCLUSIONS: PC cells can adapt to SERCA inhibition by TG. However, they demonstrate cell type-specific plasticity with respect to gene expression upon TG selection. Further, previously not described mechanisms of resistance appear to be recruited in the TG-resistant PC cells, which provide a novel model to study mechanisms of resistance and adaptation in PC on TG-mediated dysregulation of Ca2+ homeostasis.

Development and validation of a food-frequency questionnaire for the determination of detailed fatty acid intakes.

OBJECTIVE: To validate a fat intake questionnaire (FIQ) developed to assess habitual dietary intake while focusing on the assessment of detailed fatty acid intake including total trans unsaturated fatty acids (TUFA). DESIGN: An 88 food item/food group FIQ was developed using a meal pattern technique. Validation was achieved by comparison with dietary intake assessed by a modified diet history (DH) in a cross-over design. Eighty-four individuals supplied adipose tissue biopsies for linoleic acid and total TUFA analysis as an independent validation of the FIQ and DH. SETTING: Medical Centre, Dublin Airport, Republic of Ireland. SUBJECTS: One hundred and five healthy volunteers (43 females and 62 males aged 23-63 years). RESULTS: Significant correlations (P<0.0005) were achieved for intakes of energy (0.78), total fat (0.77), saturated fat (0.77), monounsaturated fat (0.63), polyunsaturated fat (0.73), TUFA (0.67) and linoleic acid (0.71) assessed by the FIQ compared with the DH. Linoleic acid intake assessed by the FIQ and the DH was significantly correlated with adipose tissue concentrations (r=0.58 and 0.49, respectively; P<0.005); however, total TUFA intake was poorly correlated with adipose tissue concentrations (r=0.17 and 0.10 for FIQ and DH, respectively). CONCLUSIONS: The FIQ compared favourably with the DH in assessing habitual diet, in particular fatty acid intake. In addition, the FIQ was successfully validated against the linoleic acid composition of adipose tissue, an independent biomarker of relative fatty acid status. The FIQ could therefore be used as an alternative to the DH as it is a shorter, less labour-intensive method.

The human LMX1B gene: transcription unit, promoter, and pathogenic mutations.

LMX1B is a LIM-homeodomain transcription factor required for the normal development of dorsal limb structures, the glomerular basement membrane, the anterior segment of the eye, and dopaminergic and serotonergic neurons. Heterozygous loss-of-function mutations in LMX1B cause nail patella syndrome (NPS). To further understand LMX1B gene regulation and to identify pathogenic mutations within the coding region, a detailed analysis of LMX1B gene structure was undertaken. 5' -RACE and primer extension identified a long 5' -untranslated region of 1.3 kb that contains two upstream open-reading frames (uORFs). Transient transfection assays showed that sequences required for basal promoter activity extend no further than 112 bp upstream. An additional 47 mutations have been identified in the coding region, as well as nine deletions of large portions of the gene, but not in the promoter or highly conserved intronic sequences. The range of mutations and the identification of uORFs suggest further complexity in the regulation of LMX1B expression.