Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin.

Recent genomic analyses of pathologically defined tumor types identify "within-a-tissue" disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head and neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multiplatform classification, while correlated with tissue-of-origin, provides independent information for predicting clinical outcomes. All data sets are available for data-mining from a unified resource to support further biological discoveries and insights into novel therapeutic strategies.

Clinical Risk Factors of Perioperative Pressure Injury in Older Adult Patients with a Hip Fracture.

OBJECTIVE: To examine the clinical risk factors of perioperative pressure injury (PrI) in older adults with a hip fracture, including preoperative chronic comorbidities and postoperative complications. METHODS: In this retrospective study, the authors queried the PearlDiver Patient Records database between January 2011 and January 2020. Data from 54,194 patients without preexisting PrI were included for analyses. Patients were separated into two groups: (1) one or more perioperative PrI and (2) no PrI. Clinical factors as outcome variables include 21 comorbidities and 10 complications. RESULTS: Univariate analyses were computed to compare the variables between groups, and two logistic regression models were developed to find comorbidity predictors and complication predictors. Of all patients, 1,362 (2.5%) developed one or more perioperative PrI. Patients with perioperative PrIs were more likely to be older men. One-year mortality for patients with perioperative PrI was 2.5 times that of patients without PrI. The regression models showed that predictors of perioperative PrI are malnutrition, hypoalbuminemia, frailty, peripheral vascular disease, dementia, urinary tract infection, perioperative red blood cell transfusion, and atrial fibrillation. CONCLUSIONS: Screening for these comorbidities and complications may assist in determining the risk of PrI in older adults undergoing hip fracture surgery. Determining PrI risk enables the appropriate prevention strategies to be applied perioperatively.

Arginine: What You Need to Know for Pressure Injury Healing.

GENERAL PURPOSE: To provide information about arginine, its metabolism, and its role in acute and chronic wound healing, to assist providers in understanding the recommendations for arginine supplementation. TARGET AUDIENCE: This continuing education activity is intended for physicians, physician assistants, nurse practitioners, and nurses with an interest in skin and wound care. LEARNING OBJECTIVES/OUTCOMES: After participating in this educational activity, the participant will:1. Describe the characteristics of arginine.2. Choose the metabolic processes that define arginine's role in wound healing.3. Identify the average daily intake of arginine in an American diet.4. Select the evidence that demonstrates the effectiveness of arginine supplementation for wound healing. ABSTRACT: Nutrition has an important and integral role in wound healing. Arginine, a type of indispensable amino acid, has long been thought to have wound healing properties. The 2019 international guideline by the European Pressure Ulcer Advisory Panel, National Pressure Injury Advisory Panel, and Pan Pacific Pressure Injury Alliance recommends use of a high-protein, high-calorie oral nutrition supplement fortified with arginine and other antioxidants to treat adults with stage 2 or greater pressure injury and who are malnourished or at risk of malnutrition to foster healing. This article provides necessary background on this conditionally indispensable amino acid, its metabolism, and its role in acute and chronic wound healing to assist providers in understanding the recommendation for arginine supplementation.

Acute Skin Failure in the Critical Care Patient.

OBJECTIVE: The purpose of this research was to build on previous work regarding predictive factors of acute skin failure (ASF) in the critically ill population. METHODS: Researchers conducted a retrospective case-control study with a main and validation analysis. Data were extracted from the New York Statewide Planning and Research Cooperative System. For the main analysis, there were 415 cases with a hospital-acquired pressure injury (HAPI) and 194,872 controls without. Researchers then randomly selected 100 cases with a HAPIs and 300 controls without for the validation analysis. A step-up logistic regression model was used. Researchers generated receiver operating characteristic curves for both the main and validation analyses, assessing the overall utility of the regression model. RESULTS: Eleven variables were significantly and independently related to ASF: renal failure (odds ratio [OR], 1.4, P = .003), respiratory failure (OR, 2.2; P = < .001), arterial disease (OR, 2.4; P = .001), impaired nutrition (OR, 2.3; P = < .001), sepsis (OR, 2.2; P = < .001), septic shock (OR, 2.3; P = < .001), mechanical ventilation (OR, 2.5; P = < .001), vascular surgery (OR, 2.2; P = .02), orthopedic surgery (OR, 3.4; P = < .001), peripheral necrosis (OR, 2.5; P = .003), and general surgery (OR, 3.8; P = < .001). The areas under the curve for the main and validation analyses were 0.864 and 0.861, respectively. CONCLUSIONS: The final model supports previous work and is consistent with the current definition of ASF in the setting of critical illness.

Nutrient Deficiency-Related Dermatoses after Bariatric Surgery.

GENERAL PURPOSE: To provide information on obesity, bariatric surgery, and the nutrient deficiency-related dermatoses that may result from these surgeries. TARGET AUDIENCE: This continuing education activity is intended for physicians, physician assistants, NPs, and nurses with an interest in skin and wound care. LEARNING OBJECTIVES/OUTCOMES: After participating in this educational activity, the participant should be better able to:1. Examine issues related to obesity and bariatric surgery.2. Identify the sources and role of specific nutrients.3. Recognize the clinical signs and symptoms of nutrient deficiency following bariatric surgery. ABSTRACT: Obesity is a global epidemic that increases the risk of weight-related comorbidities in modern society. It is complex, multifactorial, and largely preventable. Noninvasive treatments for obesity include diet, exercise, and medication. However, bariatric surgeries are becoming popular procedures for those who do not achieve success with noninvasive weight management treatment. Bariatric surgeries often result in dietary restriction and/or malabsorption, which lead to drastic weight loss. Individuals who had bariatric surgeries need lifelong follow-up and monitoring to ensure adequate intake of nutrients. Nutrient deficiencies can ensue when long-term vitamin and mineral supplementation is not followed. Severe nutrient deficiencies may lead to dermatoses that can be corrected by nutrient repletion and careful monitoring. A case report of nutrient deficiency-related dermatoses is followed by a review of obesity and its treatments with a focus on bariatric surgeries.

Refining Heel Pressure Injury Risk Factors in the Hospitalized Patient.

OBJECTIVE: To replicate previous research that found four independent and significant predictors of heel pressure injuries (HPIs) in hospitalized patients using a larger and more diverse patient population. METHODS: Researchers conducted a retrospective, case-control study with a main and a validation analysis (N = 1,937). The main analysis had 1,697 patients: 323 patients who had HPIs and 1,374 who did not. The validation analysis had 240 patients: 80 patients who developed HPIs and 160 who did not. Researchers used a series of diagnosis codes to define variables associated with an HPI. Data were extracted from the New York Statewide Planning and Research Cooperative System for January 2014 to June 2015. Study authors conducted a series of forward stepwise logistic regression analyses for both samples to select the variables that were significantly and independently associated with the development of an HPI in a multivariable setting. Researchers generated a receiver operating characteristic curve using the final model to assess the regression model's ability to predict HPI development. RESULTS: Seven variables were significant and independent predictors associated with HPIs: diabetes mellitus, vascular disease, perfusion issues, impaired nutrition, age, mechanical ventilation, and surgery. The receiver operating characteristic curve demonstrated predictive accuracy of the model. CONCLUSIONS: Beyond a risk assessment scale, providers should consider other factors, such as comorbidities, which can predispose patients to HPI development.

Subgroup-specific structural variation across 1,000 medulloblastoma genomes.

Medulloblastoma, the most common malignant paediatric brain tumour, is currently treated with nonspecific cytotoxic therapies including surgery, whole-brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, previous attempts to identify targets for therapy have been underpowered because of small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1,087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup-enriched. The most common region of focal copy number gain is a tandem duplication of SNCAIP, a gene associated with Parkinson's disease, which is exquisitely restricted to Group 4α. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1, that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGF-ß signalling in Group 3, and NF-κB signalling in Group 4, suggest future avenues for rational, targeted therapy.

Large-scale profiling of microRNAs for The Cancer Genome Atlas.

The comprehensive multiplatform genomics data generated by The Cancer Genome Atlas (TCGA) Research Network is an enabling resource for cancer research. It includes an unprecedented amount of microRNA sequence data: ~11 000 libraries across 33 cancer types. Combined with initiatives like the National Cancer Institute Genomics Cloud Pilots, such data resources will make intensive analysis of large-scale cancer genomics data widely accessible. To support such initiatives, and to enable comparison of TCGA microRNA data to data from other projects, we describe the process that we developed and used to generate the microRNA sequence data, from library construction through to submission of data to repositories. In the context of this process, we describe the computational pipeline that we used to characterize microRNA expression across large patient cohorts.

Reducing Postsurgical Wound Complications: A Critical Review.

GENERAL PURPOSE: To provide information on risk factors for surgical site infections (SSIs) and actions to mitigate that risk. TARGET AUDIENCE: This continuing education activity is intended for surgeons, surgical teams, physicians, physician assistants, nurse practitioners, and nurses with an interest in skin and wound care. LEARNING OBJECTIVES/OUTCOMES: After participating in this educational activity, the participant should be better able to:1. Identify modifiable risk factors associated with the development of SSIs.2. Select steps to mitigate the risks for and morbidity from SSIs. ABSTRACT: Given the current reimbursement structure, the avoidance of a surgical site infection (SSI) is crucial. Although many risk factors are associated with the formation of an SSI, a proactive and interprofessional approach can help modify some factors. Postoperative strategies also can be applied to help prevent an SSI. If an SSI becomes a chronic wound, there are recommended guidelines and strategies that can foster healing.

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.

BACKGROUND: Many mutations that contribute to the pathogenesis of acute myeloid leukemia (AML) are undefined. The relationships between patterns of mutations and epigenetic phenotypes are not yet clear. METHODS: We analyzed the genomes of 200 clinically annotated adult cases of de novo AML, using either whole-genome sequencing (50 cases) or whole-exome sequencing (150 cases), along with RNA and microRNA sequencing and DNA-methylation analysis. RESULTS: AML genomes have fewer mutations than most other adult cancers, with an average of only 13 mutations found in genes. Of these, an average of 5 are in genes that are recurrently mutated in AML. A total of 23 genes were significantly mutated, and another 237 were mutated in two or more samples. Nearly all samples had at least 1 nonsynonymous mutation in one of nine categories of genes that are almost certainly relevant for pathogenesis, including transcription-factor fusions (18% of cases), the gene encoding nucleophosmin (NPM1) (27%), tumor-suppressor genes (16%), DNA-methylation-related genes (44%), signaling genes (59%), chromatin-modifying genes (30%), myeloid transcription-factor genes (22%), cohesin-complex genes (13%), and spliceosome-complex genes (14%). Patterns of cooperation and mutual exclusivity suggested strong biologic relationships among several of the genes and categories. CONCLUSIONS: We identified at least one potential driver mutation in nearly all AML samples and found that a complex interplay of genetic events contributes to AML pathogenesis in individual patients. The databases from this study are widely available to serve as a foundation for further investigations of AML pathogenesis, classification, and risk stratification. (Funded by the National Institutes of Health.).

The expression level of small non-coding RNAs derived from the first exon of protein-coding genes is predictive of cancer status.

Small non-coding RNAs (smRNAs) are known to be significantly enriched near the transcriptional start sites of genes. However, the functional relevance of these smRNAs remains unclear, and they have not been associated with human disease. Within the cancer genome atlas project (TCGA), we have generated small RNA datasets for many tumor types. In prior cancer studies, these RNAs have been regarded as transcriptional "noise," due to their apparent chaotic distribution. In contrast, we demonstrate their striking potential to distinguish efficiently between cancer and normal tissues and classify patients with cancer to subgroups of distinct survival outcomes. This potential to predict cancer status is restricted to a subset of these smRNAs, which is encoded within the first exon of genes, highly enriched within CpG islands and negatively correlated with DNA methylation levels. Thus, our data show that genome-wide changes in the expression levels of small non-coding RNAs within first exons are associated with cancer.

Validation and calibration of next-generation sequencing to identify Epstein-Barr virus-positive gastric cancer in The Cancer Genome Atlas.

The Epstein-Barr virus (EBV)-positive subtype of gastric adenocarcinoma is conventionally identified by in situ hybridization (ISH) for viral nucleic acids, but next-generation sequencing represents a potential alternative. We therefore determined normalized EBV read counts by whole-genome, whole-exome, mRNA and miRNA sequencing for 295 fresh-frozen gastric tumor samples. Formalin-fixed, paraffin-embedded tissue sections were retrieved for ISH confirmation of 13 high-EBV and 11 low-EBV cases. In pairwise comparisons, individual samples were either concordantly high or concordantly low by all genomic methods for which data were available. Empiric cutoffs of sequencing counts identified 26 (9 %) tumors as EBV positive. EBV positivity or negativity by molecular testing was confirmed by EBER-ISH in all but one tumor evaluated by both approaches (kappa = 0.91). EBV-positive gastric tumors can be accurately identified by quantifying viral sequences in genomic data. Simultaneous analyses of human and viral DNA, mRNA and miRNA could streamline tumor profiling for clinical care and research.

Differentiating a Pressure Ulcer from Acute Skin Failure in the Adult Critical Care Patient.

PURPOSE: The purpose of this learning activity is to provide information regarding the differentiation between pressure ulcers and acute skin failure (ASF) in critically ill patients. TARGET AUDIENCE: This continuing education activity is intended for physicians and nurses with an interest in skin and wound care. OBJECTIVES: After participating in this educational activity, the participant should be better able to:1. Describe the purpose, methodology and impact of this research.2. Differentiate the pathophysiology of pressure ulcers and ASF.3. Identify risk factors and diagnostic criteria for ASF. ABSTRACT: To develop a statistical model to predict the development of acute skin failure in patients admitted to the intensive care unit (ICU) and to validate this model.Retrospective case-control, logistic regression modeling552 ICU patientsIntensive care unit patients with and without pressure ulcers (PrUs) were studied and compared on key variables sorted into the following categories: (1) disease status, (2) physical conditions, and (3) conditions of hospitalization.The variables, peripheral arterial disease (odds ratio [OR], 3.8; P = .002), mechanical ventilation greater than 72 hours (OR, 3.0; P < .001), respiratory failure (OR, 3.2; P < .001), liver failure (OR, 2.9; P = .04), and severe sepsis/septic shock (OR, 1.9; P = .02), were found to be statistically significant and independent predictors of acute skin failure in ICU patients. These variables created a predictor model for acute skin failure in the ICU.Lack of objective criteria to define acute skin failure presents a clinical conundrum for practitioners-the acknowledgment that skin failure exists, but no clear-cut diagnostic criteria in which to support its existence as a result of a paucity of empirical evidence. In certain populations, such as the critically ill patient, the phenomenon of acute skin failure may be occurring, and with the current level of evidence, these ulcers may be incorrectly identified as PrUs. Accurately distinguishing risk factors that lead to a PrU from factors that result in a lesion due to acute skin failure is crucial in the quest to provide evidence-based practice to patients.

Genome-wide microRNA and messenger RNA profiling in rodent liver development implicates mir302b and mir20a in repressing transforming growth factor-beta signaling.

MicroRNAs (miRNAs) are recently discovered small RNA molecules that regulate developmental processes, such as proliferation, differentiation, and apoptosis; however, the identity of miRNAs and their functions during liver development are largely unknown. Here we investigated the miRNA and gene expression profiles for embryonic day (E)8.5 endoderm, E14.5 Dlk1(+) liver cells (hepatoblasts), and adult liver by employing Illumina sequencing. We found that miRNAs were abundantly expressed at all three stages. Using K-means clustering analysis, 13 miRNA clusters with distinct temporal expression patterns were identified. mir302b, an endoderm-enriched miRNA, was identified as an miRNA whose predicted targets are expressed highly in E14.5 hepatoblasts but low in the endoderm. We validated the expression of mir302b in the endoderm by whole-mount in situ hybridization. Interestingly, mir20a, the most highly expressed miRNA in the endoderm library, was also predicted to regulate some of the same targets as mir302b. We found that through targeting Tgfbr2, mir302b and mir20a are able to regulate transforming growth factor beta (TGFß) signal transduction. Moreover, mir302b can repress liver markers in an embryonic stem cell differentiation model. Collectively, we uncovered dynamic patterns of individual miRNAs during liver development, as well as miRNA networks that could be essential for the specification and differentiation of liver progenitors. (HEPATOLOGY 2013).

A novel control scheme for inducing angiostatin-human IgG fusion protein production using recombinant CHO cells in a oscillating bioreactor.

In this study, a novel control scheme for inducing protein production using a recombinant CHO cell line in a BelloCell bioreactor was developed. This control scheme was applied in a simple regular semi-batch process. Production of angiostatin-human IgG fusion protein in a suspension recombinant CHO cell culture and a protein-free medium was used for this study. The bottom holding time (BH) was the sole operating variable to control the exposure time of the cells immobilized on the carriers to the air and allow the nutrient remained on the liquid film of the carriers to be consumed to a threshold level so that the cells can be arrested and promoted for protein production. In the cell cultures with various BH (1.5-90 min), final cell densities of 1.6-4.0 x 10(9) have been obtained in 20 days while total angiostatin-human IgG production of 228-388 mg have been harvested. In general, low BH will minimize the nutrient limitation and favor the cell growth, while high BH will restrict the nutrient and promote the production in this type of non-growth associated production systems. It was found that specific production rate was generally inversely proportional to the specific growth rate. In this case of study, BH of 30 and 60 min were found to be about 72% better than BH of 1.5 min and 35% better than BH of 9 and 90 min in term of the total angiostatin-human IgG production. In comparison to a conventional spinner flask study, a 3.8-fold increase of the total angiostatin-human IgG production was realized in a 35-day culture. This study illustrated that a simple method of using BH in a semi-batch process can effectively control the apparent nutrient concentration to the cells, and thus regulate the cell growth and protein production in a novel oscillating bioreactor.

miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer.

Ovarian cancer presents as an aggressive, advanced stage cancer with widespread metastases that depend primarily on multicellular spheroids in the peritoneal fluid. To identify new druggable pathways related to metastatic progression and spheroid formation, we integrated microRNA and mRNA sequencing data from 293 tumors from The Cancer Genome Atlas (TCGA) ovarian cancer cohort. We identified miR-509-3p as a clinically significant microRNA that is more abundant in patients with favorable survival in both the TCGA cohort (P = 2.3E-3), and, by in situ hybridization (ISH), in an independent cohort of 157 tumors (P < 1.0E-3). We found that miR-509-3p attenuated migration and disrupted multi-cellular spheroids in HEYA8, OVCAR8, SKOV3, OVCAR3, OVCAR4 and OVCAR5 cell lines. Consistent with disrupted spheroid formation, in TCGA data miR-509-3p's most strongly anti-correlated predicted targets were enriched in components of the extracellular matrix (ECM). We validated the Hippo pathway effector YAP1 as a direct miR-509-3p target. We showed that siRNA to YAP1 replicated 90% of miR-509-3p-mediated migration attenuation in OVCAR8, which contained high levels of YAP1 protein, but not in the other cell lines, in which levels of this protein were moderate to low. Our data suggest that the miR-509-3p/YAP1 axis may be a new druggable target in cancers with high YAP1, and we propose that therapeutically targeting the miR-509-3p/YAP1/ECM axis may disrupt early steps in multi-cellular spheroid formation, and so inhibit metastasis in epithelial ovarian cancer and potentially in other cancers.

Comprehensive miRNA sequence analysis reveals survival differences in diffuse large B-cell lymphoma patients.

BACKGROUND: Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease, with 30% to 40% of patients failing to be cured with available primary therapy. microRNAs (miRNAs) are RNA molecules that attenuate expression of their mRNA targets. To characterize the DLBCL miRNome, we sequenced miRNAs from 92 DLBCL and 15 benign centroblast fresh frozen samples and from 140 DLBCL formalin-fixed, paraffin-embedded tissue samples for validation. RESULTS: We identify known and candidate novel miRNAs, 25 of which are associated with survival independently of cell-of-origin and International Prognostic Index scores, which are established indicators of outcome. Of these 25 miRNAs, six miRNAs are significantly associated with survival in our validation cohort. Abundant expression of miR-28-5p, miR-214-5p, miR-339-3p, and miR-5586-5p is associated with superior outcome, while abundant expression of miR-324-5p and NOVELM00203M is associated with inferior outcome. Comparison of DLBCL miRNA-seq expression profiles with those from other cancer types identifies miRNAs that were more abundant in B-cell contexts. Unsupervised clustering of miRNAs identifies two clusters of patients that have distinct differences in their outcomes. Our integrative miRNA and mRNA expression analyses reveal that miRNAs increased in abundance in DLBCL appear to regulate the expression of genes involved in metabolism, cell cycle, and protein modification. Additionally, these miRNAs, including one candidate novel miRNA, miR-10393-3p, appear to target chromatin modification genes that are frequent targets of somatic mutation in non-Hodgkin lymphomas. CONCLUSIONS: Our comprehensive sequence analysis of the DLBCL miRNome identifies candidate novel miRNAs and miRNAs associated with survival, reinforces results from previous mutational analyses, and reveals regulatory networks of significance for lymphomagenesis.

Epigenetic and transcriptional determinants of the human breast.

While significant effort has been dedicated to the characterization of epigenetic changes associated with prenatal differentiation, relatively little is known about the epigenetic changes that accompany post-natal differentiation where fully functional differentiated cell types with limited lifespans arise. Here we sought to address this gap by generating epigenomic and transcriptional profiles from primary human breast cell types isolated from disease-free human subjects. From these data we define a comprehensive human breast transcriptional network, including a set of myoepithelial- and luminal epithelial-specific intronic retention events. Intersection of epigenetic states with RNA expression from distinct breast epithelium lineages demonstrates that mCpG provides a stable record of exonic and intronic usage, whereas H3K36me3 is dynamic. We find a striking asymmetry in epigenomic reprogramming between luminal and myoepithelial cell types, with the genomes of luminal cells harbouring more than twice the number of hypomethylated enhancer elements compared with myoepithelial cells.

The somatic genomic landscape of chromophobe renal cell carcinoma.

We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs) on the basis of multidimensional and comprehensive characterization, including mtDNA and whole-genome sequencing. The result is consistent that ChRCC originates from the distal nephron compared with other kidney cancers with more proximal origins. Combined mtDNA and gene expression analysis implicates changes in mitochondrial function as a component of the disease biology, while suggesting alternative roles for mtDNA mutations in cancers relying on oxidative phosphorylation. Genomic rearrangements lead to recurrent structural breakpoints within TERT promoter region, which correlates with highly elevated TERT expression and manifestation of kataegis, representing a mechanism of TERT upregulation in cancer distinct from previously observed amplifications and point mutations.