ABSTRACT
The liver is the most common site of metastatic disease1. Although this metastatic tropism may reflect the mechanical trapping of circulating tumour cells, liver metastasis is also dependent, at least in part, on the formation of a 'pro-metastatic' niche that supports the spread of tumour cells to the liver2,3. The mechanisms that direct the formation of this niche are poorly understood. Here we show that hepatocytes coordinate myeloid cell accumulation and fibrosis within the liver and, in doing so, increase the susceptibility of the liver to metastatic seeding and outgrowth. During early pancreatic tumorigenesis in mice, hepatocytes show activation of signal transducer and activator of transcription 3 (STAT3) signalling and increased production of serum amyloid A1 and A2 (referred to collectively as SAA). Overexpression of SAA by hepatocytes also occurs in patients with pancreatic and colorectal cancers that have metastasized to the liver, and many patients with locally advanced and metastatic disease show increases in circulating SAA. Activation of STAT3 in hepatocytes and the subsequent production of SAA depend on the release of interleukin 6 (IL-6) into the circulation by non-malignant cells. Genetic ablation or blockade of components of IL-6-STAT3-SAA signalling prevents the establishment of a pro-metastatic niche and inhibits liver metastasis. Our data identify an intercellular network underpinned by hepatocytes that forms the basis of a pro-metastatic niche in the liver, and identify new therapeutic targets.
Subject(s)
Hepatocytes/pathology , Liver Neoplasms/pathology , Liver Neoplasms/secondary , Liver/pathology , Neoplasm Metastasis , Pancreatic Neoplasms/pathology , Tumor Microenvironment , Animals , Carcinoma, Pancreatic Ductal/pathology , Colorectal Neoplasms/pathology , Colorectal Neoplasms/secondary , Female , Interleukin-6/metabolism , Male , Mice , STAT3 Transcription Factor/metabolism , Serum Amyloid A Protein/metabolismABSTRACT
Novel screening techniques for early detection of lung cancer are urgently needed. Profiling circulating tumor cell-free DNA (ctDNA) has emerged as a promising tool for biopsy-free tumor genotyping. However, both the scarcity and short half-life of ctDNA substantially limit the sensitivity and clinical utility of ctDNA detection methodologies. Our discovery that red blood cells (RBCs) sequester mitochondrial DNA opens a new avenue for detecting circulating nucleic acids, as RBCs represent an unrecognized reservoir of circulating nucleic acid. Here, we show that RBCs acquire tumor DNA following coculture with lung cancer cell lines harboring Kirsten rat sarcoma viral oncogene homolog (KRAS) and epidermal growth factor receptor (EGFR) mutations. RBC-bound tumor DNA is detectable in patients with early-stage non-small cell lung cancer (NSCLC) but not in healthy controls by qPCR. Our results collectively uncover a previously unrecognized yet easily accessible reservoir of tumor DNA, offering a promising foundation for future RBC-based tumor diagnostics.NEW & NOTEWORTHY We present a novel method for lung cancer detection by revealing RBCs as a reservoir for tumor DNA, overcoming the limitations of current circulating tumor ctDNA methodologies. By demonstrating that RBCs can capture tumor DNA, including critical mutations found in lung cancer, we provide a promising, biopsy-free avenue for early cancer diagnostics. This discovery opens up exciting possibilities for developing RBC-based diagnostic tools, significantly enhancing the sensitivity and clinical utility of noninvasive cancer detection.
Subject(s)
Carcinoma, Non-Small-Cell Lung , Circulating Tumor DNA , Erythrocytes , Lung Neoplasms , Humans , Lung Neoplasms/genetics , Lung Neoplasms/blood , Lung Neoplasms/pathology , Lung Neoplasms/diagnosis , Erythrocytes/metabolism , Circulating Tumor DNA/genetics , Circulating Tumor DNA/blood , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/blood , Carcinoma, Non-Small-Cell Lung/pathology , Carcinoma, Non-Small-Cell Lung/diagnosis , Mutation , Cell Line, Tumor , ErbB Receptors/genetics , ErbB Receptors/metabolism , DNA, Mitochondrial/genetics , DNA, Mitochondrial/blood , Proto-Oncogene Proteins p21(ras)/genetics , Male , Female , Biomarkers, Tumor/genetics , Biomarkers, Tumor/blood , DNA, Neoplasm/blood , DNA, Neoplasm/geneticsABSTRACT
OBJECTIVES: To evaluate the influences of social determinants of health (SDOH) on perceived health and well-being among African American (AA)/Black and Hispanic ovarian cancer survivors. METHODS: A cross-sectional study was conducted using overall health and SDOH survey data collected by the National Institutes of Health All of Us Research Program from May 2017 to September 2023. RESULTS: While 1250 enrolled participants with ovarian cancer met the inclusion criteria, 414 (33%) completed SDOH surveys: 29 (7%) AA/Black, 33 (8%) Hispanic, and 352 (85%) White. In the ordinal logistic regression models, for every unit increase in the SDOH neighborhood characteristics score, the odds of having a poor perception of general health decreased by 0.96 times. For every unit increase in the SDOH day-to-day discrimination score, the odds of having a poor perception of general health, general mental health, social satisfaction decreased by 0.95, 0.94 and 0.93 times respectively. For every unit increase in the SDOH food and housing security score, the odds of having a poor perception of general health decreased by 0.57 times. Compared to White ovarian cancer survivors, AA/Black and Hispanic ovarian cancer survivors were significantly more likely to have a poor perception of general health, general mental health, and social satisfaction even when adjusting for these SDOH. CONCLUSIONS: Unfavorable SDOH conditions negatively influence the overall perception of health. These findings signal an urgency for healthcare professionals and scientists to partner together with local communities in designing feasible and imaginative interventions to overcome cancer care disparities in an equitable manner.
ABSTRACT
BACKGROUND: The COVID-19 pandemic brought greater focus to the rural mortality penalty in the U.S., which describes the greater mortality rate in rural compared to urban areas. Although it is widely thought that issues such as access to care, age structure of the population, and differences in behavior are likely drivers of the rural mortality penalty, few studies have attempted to tie delayed access to care in rural populations to healthcare outcomes quantitatively. Therefore, it is critical to try and understand these factors to enable more effective public health policy. METHODS: We performed a cross-sectional analysis of a population of patients with COVID-19 who were admitted to hospitals in the United States between 3/1/2020 and 2/26/2023 to better understand factors leading to outcome disparities amongst groups that all had some level of access to hospital care. Nevertheless, it is widely thought that rural populations often experience delayed access to care, due to transportation and other constraints. Therefore, we hypothesized that deteriorated patient condition at admission likely explained some of the observed difference in mortality between rural and urban populations. RESULTS: Our results supported our hypothesis, showing that the rural mortality penalty persists in this population and that by multiple measures, rural patients were likely to be admitted in worse condition, had worse overall health, and were older. CONCLUSIONS: Although the pandemic threw the rural mortality penalty into sharp relief, it is important to remember that it existed prior to the pandemic and will continue to exist until effective interventions are implemented. This study demonstrates the critical need to address the underlying factors that resulted in rural-dwelling patients being admitted to the hospital in worse condition than their urban-dwelling counterparts during the COVID-19 pandemic, which likely affected other healthcare outcomes as well.
Subject(s)
COVID-19 , Health Services Accessibility , Hospital Mortality , Rural Population , SARS-CoV-2 , Humans , COVID-19/mortality , United States/epidemiology , Female , Male , Cross-Sectional Studies , Middle Aged , Aged , Adult , Pandemics , Hospitalization , Aged, 80 and overABSTRACT
BACKGROUND: Molecular interaction networks have become an important tool in providing context to the results of various omics experiments. For example, by integrating transcriptomic data and protein-protein interaction (PPI) networks, one can better understand how the altered expression of several genes are related with one another. The challenge then becomes how to determine, in the context of the interaction network, the subset(s) of genes that best captures the main mechanisms underlying the experimental conditions. Different algorithms have been developed to address this challenge, each with specific biological questions in mind. One emerging area of interest is to determine which genes are equivalently or inversely changed between different experiments. The equivalent change index (ECI) is a recently proposed metric that measures the extent to which a gene is equivalently or inversely regulated between two experiments. The goal of this work is to develop an algorithm that makes use of the ECI and powerful network analysis techniques to identify a connected subset of genes that are highly relevant to the experimental conditions. RESULTS: To address the above goal, we developed a method called Active Module identification using Experimental data and Network Diffusion (AMEND). The AMEND algorithm is designed to find a subset of connected genes in a PPI network that have large experimental values. It makes use of random walk with restart to create gene weights, and a heuristic solution to the Maximum-weight Connected Subgraph problem using these weights. This is performed iteratively until an optimal subnetwork (i.e., active module) is found. AMEND was compared to two current methods, NetCore and DOMINO, using two gene expression datasets. CONCLUSION: The AMEND algorithm is an effective, fast, and easy-to-use method for identifying network-based active modules. It returned connected subnetworks with the largest median ECI by magnitude, capturing distinct but related functional groups of genes. Code is freely available at https://github.com/samboyd0/AMEND .
Subject(s)
Protein Interaction Mapping , Protein Interaction Maps , Protein Interaction Mapping/methods , Algorithms , Gene Expression Profiling/methods , Transcriptome , Gene Regulatory NetworksABSTRACT
The therapeutic landscape for patients with advanced malignancies has changed dramatically over the last twenty years. The growing number of targeted therapies and immunotherapeutic options available have improved response rates and survival for a subset of patients, however determining which patients will experience clinical benefit from these therapies in order to avoid potential toxicities and reduce healthcare costs remains a clinical challenge. Cell-free circulating tumor DNA (ctDNA) is shed by tumor cells into systemic circulation and is already an integral part of routine clinical practice for the non-invasive tumor genotyping in advanced non-small cell lung cancer as well as other malignancies. The short half-life of ctDNA offers a unique opportunity to utilize early on-treatment changes in ctDNA for real-time assessment of therapeutic response and outcome, termed molecular response. Here, we provide a summary and review of the use of molecular response for the prediction of outcomes in patients with advanced cancer, including the current state of science, its application in clinic, and next steps for the development of this predictive tool.
Subject(s)
Carcinoma, Non-Small-Cell Lung , Circulating Tumor DNA , Lung Neoplasms , Humans , Circulating Tumor DNA/genetics , Carcinoma, Non-Small-Cell Lung/drug therapy , Carcinoma, Non-Small-Cell Lung/genetics , Lung Neoplasms/drug therapy , Biomarkers, Tumor/genetics , MutationABSTRACT
PURPOSE: As part of the management of nephrolithiasis, determination of chemical composition of stones is important. Our objective in this study is to assess urologists' accuracy in making visual, intraoperative determinations of stone composition. MATERIALS AND METHODS: We conducted a REDCap survey asking urologists to predict stone composition based on intraoperative images of 10 different pure-composition kidney stones of 7 different types: calcium oxalate monohydrate (COM), calcium oxalate dihydrate (COD), calcium phosphate (CP) apatite, CP brushite, uric acid (UA), struvite (ST) and cystine (CY). To evaluate experience, we examined specific endourologic training, years of experience, and number of ureteroscopy (URS) cases/week. A self-assessment of ability to identify stone composition was also required. RESULTS: With a response rate of 26% (366 completed surveys out of 1,370 deliveries), the overall accuracy of our cohort was 44%. COM, ST, and COD obtained the most successful identification rates (65.9%, 55.7%, and 52.0%, respectively). The most frequent misidentified stones were CP apatite (10.7%) and CY (14.2%). Predictors of increased overall accuracy included self-perceived ability to determine composition and number of ureteroscopies per week, while years of experience did not show a positive correlation. CONCLUSIONS: Although endoscopic stone recognition can be an important tool for surgeons, it is not reliable enough to be utilized as a single method for stone identification, suggesting that urologists need to refine their ability to successfully recognize specific stone compositions intraoperatively.
Subject(s)
Kidney Calculi , Urinary Calculi , Humans , Urologists , Kidney Calculi/surgery , Struvite , Apatites , Calcium Oxalate , Cystine , Urinary Calculi/chemistryABSTRACT
Batch effect Reduction of mIcroarray data with Dependent samples usinG Empirical Bayes (BRIDGE) is a recently developed statistical method to address the issue of batch effect correction in batch-confounded microarray studies with dependent samples. The key component of the BRIDGE methodology is the use of samples run as technical replicates in two or more batches, "bridging samples", to inform batch effect correction/attenuation. While previously published results indicate a relationship between the number of bridging samples, M, and the statistical power of downstream statistical testing on the batch-corrected data, there is of yet no formal statistical framework or user-friendly software, for estimating M to achieve a specific statistical power for hypothesis tests conducted on the batch-corrected data. To fill this gap, we developed pwrBRIDGE, a simulation-based approach to estimate the bridging sample size, M, in batch-confounded longitudinal microarray studies. To illustrate the use of pwrBRIDGE, we consider a hypothetical, longitudinal batch-confounded study whose goal is to identify Alzheimer's disease (AD) progression-associated genes from amnestic mild cognitive impairment (aMCI) to AD in human blood after a 5-year follow-up. pwrBRIDGE helps researchers design and plan batch-confounded microarray studies with dependent samples to avoid over- or under-powered studies.
Subject(s)
Software , Bayes Theorem , Humans , Longitudinal Studies , Microarray Analysis , Sample SizeABSTRACT
OBJECTIVE: To assess healthcare costs and healthcare resource utilization (HCRU) among adult patients who newly initiated erenumab in the United States. METHODS: This retrospective, non-interventional analysis included adult patients (aged ≥18 years) newly initiating erenumab and who had three consecutive monthly claims for erenumab (11/1/2017-9/1/2019) from the Komodo Health database. Outcomes included migraine-related and all-cause costs, use of other preventive/acute migraine medications, and HCRU. All outcomes were compared during the 180-day pre- versus the 180-day post-index periods. Cost outcomes were also assessed for longer periods including post-index Days 91-270 and monthly mean post-index costs for the longest time of continuous insurance enrollment. RESULTS: Overall, 1839 patients with migraine were included for analysis. Compared to the 180-day pre-index period, an increase in total migraine-related costs (+$2639; p < 0.0001), migraine-related prescription costs (+$3435, p < 0.0001), all-cause total costs (+$2977; p < 0.001), and all-cause prescription costs (+$4102; p < 0.0001) were observed during the 180-day post-index period after adjusting for covariates. Conversely, reduction in migraine-related medical costs (-$896; p < 0.0001), and significantly lower odds of migraine-related emergency room visits (odds ratio [OR] 0.60, 95% confidence interval [CI] 0.44-0.82; p = 0.001), migraine-related office visits (OR 0.58, 95% CI 0.53-0.64; p < 0.0001), and migraine-related neurologist visits (OR 0.69, 95% CI 0.63-0.75; p < 0.0001) were observed during the 180-days post-index period. There were significant decreases in the odds of having overall preventive migraine medications (OR 0.81, 95% CI 0.75-0.87; p < 0.0001), acute-migraine medications (OR 0.92, 95% CI 0.85-1.00; p = 0.038), and triptan (OR 0.79, 95% CI 0.73-0.85; p < 0.0001) during the 180-day post-index period. Sensitivity analyses on cost outcomes found no statistically significant differences in pre-index migraine-related costs compared to post-index migraine-related costs when assessing longer post-index follow-up periods. CONCLUSION: Initiation of therapy with a novel treatment is often associated with an increase in overall healthcare costs due to the entrance costs associated with novel therapy. For a chronic condition such as migraine, cost versus health benefits should be evaluated over a long period (e.g., ≥2 years) to better understand the true benefits of therapy. Data from this study suggest that the entrance cost for erenumab, the primary driver of the high post-index prescription costs gets mitigated by reduced medical costs over long-term follow-up. The results indicate better disease management in adult patients with migraine, which should be an important consideration for both patients and payors, as these findings have shown an offset between migraine-related prescription and medical costs.
Subject(s)
Health Care Costs , Migraine Disorders , Adult , Humans , United States , Adolescent , Retrospective Studies , Migraine Disorders/prevention & control , Antibodies, Monoclonal, Humanized/therapeutic useABSTRACT
Due to widespread adoption of screening mammography, there has been a significant increase in new diagnoses of ductal carcinoma in situ (DCIS). However, DCIS prognosis remains unclear. To address this gap, we developed an in vivo model, Mouse-INtraDuctal (MIND), in which patient-derived DCIS epithelial cells are injected intraductally and allowed to progress naturally in mice. Similar to human DCIS, the cancer cells formed in situ lesions inside the mouse mammary ducts and mimicked all histologic subtypes including micropapillary, papillary, cribriform, solid, and comedo. Among 37 patient samples injected into 202 xenografts, at median duration of 9 months, 20 samples (54%) injected into 95 xenografts showed in vivo invasive progression, while 17 (46%) samples injected into 107 xenografts remained non-invasive. Among the 20 samples that showed invasive progression, nine samples injected into 54 xenografts exhibited a mixed pattern in which some xenografts showed invasive progression while others remained non-invasive. Among the clinically relevant biomarkers, only elevated progesterone receptor expression in patient DCIS and the extent of in vivo growth in xenografts predicted an invasive outcome. The Tempus XT assay was used on 16 patient DCIS formalin-fixed, paraffin-embedded sections including eight DCISs that showed invasive progression, five DCISs that remained non-invasive, and three DCISs that showed a mixed pattern in the xenografts. Analysis of the frequency of cancer-related pathogenic mutations among the groups showed no significant differences (KW: p > 0.05). There were also no differences in the frequency of high, moderate, or low severity mutations (KW; p > 0.05). These results suggest that genetic changes in the DCIS are not the primary driver for the development of invasive disease. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Subject(s)
Breast Neoplasms/pathology , Carcinoma, Intraductal, Noninfiltrating/pathology , Epithelial Cells/pathology , Animals , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Carcinoma, Intraductal, Noninfiltrating/genetics , Carcinoma, Intraductal, Noninfiltrating/metabolism , Cell Movement , Cell Proliferation , Disease Progression , Epithelial Cells/metabolism , Epithelial Cells/transplantation , Female , Heterografts , Humans , Mice, Inbred NOD , Mice, SCID , Mutation , Neoplasm Invasiveness , Neoplasm Transplantation , Receptors, Progesterone/metabolism , Time FactorsABSTRACT
BACKGROUND: Invasive fungal infections (IFIs) are a common infectious complication during the treatment of acute myeloid leukemia (AML), high-risk myelodysplastic syndrome (MDS) or post hematopoietic cell transplantation (HCT). For these patients, the National Comprehensive Cancer Network recommends posaconazole or voriconazole for IFI prophylaxis. In clinical practice, however, there has been increased use of isavuconazole due to favorable pharmacokinetic and pharmacodynamic parameters despite limited data for this indication. The comparative prophylactic efficacy of antifungals in this patient population has not been reported, and an analysis is warranted. METHODS: This retrospective, matched cohort, single-center study, included AML, MDS, or HCT patients who began treatment or underwent transplant between January 1, 2015 and July 31, 2021. Isavuconazole patients were matched 1:2 with patients receiving posaconazole or voriconazole prophylaxis. RESULTS: A total of 126 patients were included, 42 received isavuconazole, 81 received posaconazole, and three received voriconazole. The majority of patients were male receiving secondary IFI prophylaxis while receiving steroids for treatment of GVHD. The incidence of possible, probable or proven IFI was 16.7% in the isavuconazole group compared to 10.7% in the posaconazole and voriconazole group (OR 1.28, 95% CI -0.9-1.4; p = .67). Hepatotoxicity occurred in 16 total patients, 14 receiving posaconazole and two receiving isavuconazole. CONCLUSION: Patients who received isavuconazole prophylaxis during AML induction therapy or post-HCT experienced a similar incidence of breakthrough fungal infections compared to those who received posaconazole or voriconazole. These results suggest no difference in antifungal prophylactic efficacy; however larger prospective comparative studies are needed.
Subject(s)
Invasive Fungal Infections , Leukemia, Myeloid, Acute , Mycoses , Humans , Male , Female , Voriconazole/adverse effects , Retrospective Studies , Incidence , Prospective Studies , Mycoses/epidemiology , Mycoses/prevention & control , Mycoses/drug therapy , Antifungal Agents/adverse effects , Invasive Fungal Infections/epidemiology , Invasive Fungal Infections/prevention & control , Invasive Fungal Infections/drug therapy , Leukemia, Myeloid, Acute/therapy , Leukemia, Myeloid, Acute/drug therapyABSTRACT
INTRODUCTION: High-performing biomarkers measuring the vascular contributions to cognitive impairment and dementia are lacking. METHODS: Using a multi-site observational cohort study design, we examined the diagnostic accuracy of plasma placental growth factor (PlGF) within the MarkVCID Consortium (n = 335; CDR 0-1). Subjects underwent clinical evaluation, cognitive testing, MRI, and blood sampling as defined by Consortium protocols. RESULTS: In the prospective population of 335 subjects (72.2 ± 7.8 years of age, 49.3% female), plasma PlGF (pg/mL) shows an ordinal odds ratio (OR) of 1.16 (1.07-1.25; P = .0003) for increasing Fazekas score and ordinal OR of 1.22 (1.14-1.32; P < .0001) for functional cognitive impairment measured by the Clinical Dementia Rating scale. We achieved the primary study outcome of a site-independent association of plasma PlGF (pg/mL) with white matter injury and cognitive impairment in two of three study cohorts. Secondary outcomes using the full MarkVCID cohort demonstrated that plasma PlGF can significantly discriminate individuals with Fazekas ≥ 2 and CDR = 0.5 (area under the curve [AUC] = 0.74) and CDR = 1 (AUC = 0.89) from individuals with CDR = 0. DISCUSSION: Plasma PlGF measured by standardized immunoassay functions as a stable, reliable, diagnostic biomarker for cognitive impairment associated with substantial white matter burden.
Subject(s)
Cognitive Dysfunction , Female , Humans , Male , Middle Aged , Biomarkers , Cognitive Dysfunction/diagnosis , Placenta Growth Factor , Prospective Studies , Aged , Aged, 80 and overABSTRACT
Echinoderms are characterized by a distinctive high-magnesium calcite endoskeleton as adults, but elements of this have been drastically reduced in some groups. Herein, we describe a new pentaradial echinoderm, Yorkicystis haefneri n. gen. n. sp., which provides, to our knowledge, the oldest evidence of secondary non-mineralization of the echinoderm skeleton. This material was collected from the Cambrian Kinzers Formation in York (Pennsylvania, USA) and is dated as ca 510 Ma. Detailed morphological observations demonstrate that the ambulacra (i.e. axial region) are composed of flooring and cover plates, but the rest of the body (i.e. extraxial region) is preserved as a dark film and lacks any evidence of skeletal plating. Moreover, X-ray fluorescence analysis reveals that the axial region is elevated in iron. Based on our morphological and chemical data and on taphonomic comparisons with other fossils from the Kinzers Formation, we infer that the axial region was originally calcified, while the extraxial region was non-mineralized. Phylogenetic analyses recover Yorkicystis as an edrioasteroid, indicating that this partial absence of skeleton resulted from a secondary reduction. We hypothesize that skeletal reduction resulted from lack of expression of the skeletogenic gene regulatory network in the extraxial body wall during development. Secondary reduction of the skeleton in Yorkicystis might have allowed for greater flexibility of the body wall.
Subject(s)
Echinodermata , Fossils , Animals , Biological Evolution , Calcium Carbonate , Echinodermata/anatomy & histology , Phylogeny , Skeleton/anatomy & histologyABSTRACT
Phylogenomic and paleontological data constitute complementary resources for unraveling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthesizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic data set for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic data sets that selects loci with high phylogenetic signal, low systematic biases, and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of undiscovered evolutionary history of the crown group in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two. [Echinoidea; fossils; paleontology; phylogenomics; time calibration; total evidence.].
Subject(s)
Fossils , Paleontology , Animals , Biological Evolution , Phylogeny , Sea UrchinsABSTRACT
PURPOSE: Clinically significant differences in radiation-related bladder tumors are not well-characterized, and survival analyses are needed. In this study, we aimed to utilize a national cancer database to evaluate the effect of prior radiation on tumor characteristics and survival in bladder cancer patients. METHODS: The Surveillance, Epidemiology, and End Results (SEER) 9 database was queried to identify patients diagnosed with bladder cancer as a second malignancy. Patients having undergone radiation prior to developing bladder cancer were selected for comparative analysis. Logistic regression was used to generate odds ratios to evaluate differences in differentiation, stage, grade, and tumor size. Kaplan-Meier analysis and Cox non-proportional hazards regression models were used to assess the association between previous radiation and bladder cancer survival. RESULTS: A total of 25,408 patients were identified, of which 14,570 patients had sufficient data for analysis. Of these, 5968 (41.0%) received radiation for their primary malignancy. Prior radiation conferred a lower risk of developing moderately- or poorly-differentiated bladder tumors and muscle invasive or node-positive disease. An increased risk of squamous cell carcinoma was noted (OR 1.43, CI 1.06-1.93). Prior radiation led to an increased risk of bladder cancer-specific (HR 1.13, CI 1.03-1.24) mortality at 5 years. The greatest effect of prior radiation was an increased risk of bladder cancer-specific mortality for carcinoma in situ at 5 years (OR 2.37, CI 1.45-3.86). CONCLUSION: Prior radiation is associated with lower grade and stage of bladder tumors in addition to worse cancer-specific survival.
Subject(s)
Urinary Bladder Neoplasms , Humans , Kaplan-Meier Estimate , Neoplasm Staging , Proportional Hazards Models , SEER Program , Urinary Bladder/pathologyABSTRACT
Batch-effects present challenges in the analysis of high-throughput molecular data and are particularly problematic in longitudinal studies when interest lies in identifying genes/features whose expression changes over time, but time is confounded with batch. While many methods to correct for batch-effects exist, most assume independence across samples; an assumption that is unlikely to hold in longitudinal microarray studies. We propose Batch effect Reduction of mIcroarray data with Dependent samples usinGEmpirical Bayes (BRIDGE), a three-step parametric empirical Bayes approach that leverages technical replicate samples profiled at multiple timepoints/batches, so-called "bridge samples", to inform batch-effect reduction/attenuation in longitudinal microarray studies. Extensive simulation studies and an analysis of a real biological data set were conducted to benchmark the performance of BRIDGE against both ComBat and longitudinalComBat. Our results demonstrate that while all methods perform well in facilitating accurate estimates of time effects, BRIDGE outperforms both ComBat and longitudinal ComBat in the removal of batch-effects in data sets with bridging samples, and perhaps as a result, was observed to have improved statistical power for detecting genes with a time effect. BRIDGE demonstrated competitive performance in batch effect reduction of confounded longitudinal microarray studies, both in simulated and a real data sets, and may serve as a useful preprocessing method for researchers conducting longitudinal microarray studies that include bridging samples.
Subject(s)
Gene Expression Profiling , Research Design , Bayes Theorem , Gene Expression Profiling/methods , Longitudinal Studies , Microarray Analysis/methodsABSTRACT
Progressive wear of the components of an implant-supported overdenture can lead to loss of denture retention, which affects masticatory function and the patient's quality of life. The primary objective of this in vitro study was to investigate frictional wear in a type of commonly used abutment and thereby estimate the general clinical lifespan of a typical stud abutment and establish a protocol for replacement. Therefore, simulated overdenture insertions and removals equivalent to 2 years of overdenture use were performed to evaluate surface changes in the metal stud abutment component. A digital caliper, scanning electron micrographs taken at ×500 magnification, and profilometer data were used to determine the wear rate and surface roughness. A universal testing machine was used to measure retention load force with 4 clear male nylon inserts (5.0-lb retention) during 2160 insertion and removal cycles. The results showed that with a 6-month replacement program for clear male nylon inserts, the frictional wear on the titanium nitride coating of abutments placed at a 0° position resulted in a decrease of up to 50% in removal forces of the inserts after a simulated 2 years of wear. The combination of wear of the titanium nitride coating and the decrease in retention load values suggests that stud abutments should be replaced after 2 years of use for optimal retention.
Subject(s)
Dental Implants , Denture, Overlay , Dental Abutments , Dental Materials , Dental Prosthesis, Implant-Supported , Dental Stress Analysis , Denture Retention , Humans , Male , Materials Testing , Nylons , Quality of LifeABSTRACT
Cerebrovascular reactivity (CVR), which measures the ability of cerebral blood vessels to dilate or constrict in response to vasoactive stimuli such as CO2 inhalation, is an important index of the brain's vascular health. Quantification of CVR using BOLD MRI with hypercapnia challenge has shown great promises in research and clinical studies. However, in order for it to be used as a potential imaging biomarker in large-scale and multi-site studies, the reliability of CO2-CVR quantification across different MRI acquisition platforms and researchers/raters must be examined. The goal of this report from the MarkVCID small vessel disease biomarkers consortium is to evaluate the reliability of CO2-CVR quantification in three studies. First, the inter-rater reliability of CO2-CVR data processing was evaluated by having raters from 5 MarkVCID sites process the same 30 CVR datasets using a cloud-based CVR data processing pipeline. Second, the inter-scanner reproducibility of CO2-CVR quantification was assessed in 10 young subjects across two scanners of different vendors. Third, test-retest repeatability was evaluated in 20 elderly subjects from 4 sites with a scan interval of less than 2 weeks. In all studies, the CO2 CVR measurements were performed using the fixed inspiration method, where the subjects wore a nose clip and a mouthpiece and breathed room air and 5% CO2 air contained in a Douglas bag alternatively through their mouth. The results showed that the inter-rater CoV of CVR processing was 0.08 ± 0.08% for whole-brain CVR values and ranged from 0.16% to 0.88% in major brain regions, with ICC of absolute agreement above 0.9959 for all brain regions. Inter-scanner CoV was found to be 6.90 ± 5.08% for whole-brain CVR values, and ranged from 4.69% to 12.71% in major brain regions, which are comparable to intra-session CoVs obtained from the same scanners on the same day. ICC of consistency between the two scanners was 0.8498 for whole-brain CVR and ranged from 0.8052 to 0.9185 across major brain regions. In the test-retest evaluation, test-retest CoV across different days was found to be 18.29 ± 17.12% for whole-brain CVR values, and ranged from 16.58% to 19.52% in major brain regions, with ICC of absolute agreement ranged from 0.6480 to 0.7785. These results demonstrated good inter-rater, inter-scanner, and test-retest reliability in healthy volunteers, and suggested that CO2-CVR has suitable instrumental properties for use as an imaging biomarker of cerebrovascular function in multi-site and longitudinal observational studies and clinical trials.
Subject(s)
Cerebrovascular Circulation , Hypercapnia/diagnostic imaging , Administration, Inhalation , Aged , Aging , Brain/diagnostic imaging , Brain Mapping , Carbon Dioxide/pharmacology , Female , Healthy Volunteers , Humans , Hypercapnia/metabolism , Image Processing, Computer-Assisted , Magnetic Resonance Imaging , Male , Middle Aged , Observer Variation , Reproducibility of Results , Young AdultABSTRACT
Plasma cell-free DNA (cfDNA) genotyping is an alternative to tissue genotyping, particularly when tissue specimens are insufficient or unavailable, and provides critical information that can be used to guide treatment decisions in managing patients with non-small cell lung cancer (NSCLC). In this article, we review the evolution of plasma cfDNA genotyping from an emerging concept, through development of analytical methods, to its clinical applications as a standard-of-care tool in NSCLC. The number of driver or resistance mutations recommended for testing in NSCLC continues to increase. Because of the expanding list of therapeutically relevant variants, comprehensive testing to investigate larger regions of multiple genes in a single run is often preferable and saves on time and cost, compared with performing serial single-gene assays. Recent advances in nucleic acid next-generation sequencing have led to a rapid expansion in cfDNA genotyping technologies. Analytic assays that have received regulatory approval are now routinely used as diagnostic companions in the setting of metastatic NSCLC. As the demand for plasma-based technologies increases, more regulatory approvals of cfDNA genotyping assays are expected in the future. Plasma cfDNA genotyping is currently aiding oncologists in the delivery of personalized care by facilitating matching of patients with targeted therapy and monitoring emergence of resistance to therapy in NSCLC. Further advances currently underway to increase assay sensitivity and specificity will potentially expand the use of plasma cfDNA genotyping in early cancer detection, monitoring response to therapy, detection of minimal residual disease, and measurement of tumor mutational burden in NSCLC. IMPLICATIONS FOR PRACTICE: Plasma cell-free DNA (cfDNA) genotyping offers an alternative to tissue genotyping, particularly when tissue specimens are insufficient or unavailable. Advances in cfDNA genotyping technologies have led to analytic assays that are now routinely used to aid oncologists in the delivery of personalized care by facilitating matching of patients with targeted therapy and monitoring emergence of resistance to therapy. Further advances underway to increase assay sensitivity and specificity will potentially expand the use of plasma cfDNA genotyping in early cancer detection, monitoring response to therapy, detection of minimal residual disease, and evaluation of tumor mutational burden in non-small cell lung cancer.
Subject(s)
Carcinoma, Non-Small-Cell Lung , Cell-Free Nucleic Acids , Lung Neoplasms , Biomarkers, Tumor/genetics , Carcinoma, Non-Small-Cell Lung/genetics , Cell-Free Nucleic Acids/genetics , Genotype , Humans , Lung Neoplasms/genetics , MutationABSTRACT
Aim: To describe treatment patterns and patient and provider characteristics associated with the recently introduced biosimilar rituximab-pvvr. Methods: This retrospective analysis included adult patients with one or more claims for rituximab-pvvr, with an index date of 23 January 2020 and a study period covering 1 January 2019-31 July 2020. Results: Of 249 patients included, the most common rituximab-pvvr indications were non-Hodgkin's lymphoma (77.5%) and chronic lymphocytic leukemia (11.2%). Some patients with non-Hodgkin's lymphoma (42.5%) and chronic lymphocytic leukemia (39.3%) switched to rituximab-pvvr from the reference product or another rituximab biosimilar. Most patients were aged ≥65 years (63.5%) and were male (54.6%). Most (59.0%) rituximab-pvvr prescribers practiced in the south of the USA. Conclusion: Utilization occurred in approved and extrapolated indications. These preliminary findings suggest switching between reference product and rituximab biosimilars; rituximab-pvvr combination regimens are being adopted in real-world oncology practice.
Lay abstract A biosimilar is a biological medication that is highly similar in structure and function to a biological medication already approved by the US FDA the 'original biologic'. The first biosimilars approved to treat certain blood cancers have become available in the USA. This study examined how a recently introduced rituximab biosimilar was being utilized, looking at patient and physician characteristics from a medical and prescription insurance claims database. This study did not examine the safety or effectiveness of this medication. While initial data are limited, the biosimilar, rituximab-pvvr, appears to be utilized to treat the same types of cancer as the original biologic, rituximab. The biosimilar was most frequently prescribed for non-Hodgkin's lymphoma and chronic lymphocytic leukemia.