Sarcopenia Definition Outcome Consortium - defined Weakness and Risk of Falls: The National Health and Aging Trends Survey.

AIM: The prevalence of obesity continues to rise, as does that of weakness. However, it is unclear how this impacts the risk of falling. We aimed to ascertain the risk of falls using new definitions of clinically defined weakness. METHODS: We applied clinically defined weakness definitions to the National Health and Aging Trends Survey using the Sarcopenia Definitions Outcomes Consortium cutpoints. Three exposure variables were created: grip-strength-defined weakness and body mass index [GS/BMI]-defined obesity; weakness and obesity, weakness and waist circumference-derived obesity (GS/WC); and weakness defined by a ratio of GS÷BMI. Proportional hazards modeled incident falls as a function of weakness with/without obesity (hazard ratio [HR] [95% confidence intervals]). RESULTS: Of 4906 respondents aged ≥ 65 years (54.5% female), the mean ± SD grip strength, BMI, and WC were 26.7 ± 10.6 kg, 27.4 ± 5.4 kg/m2 , and 99.5 ± 16.3 cm, respectively. Using the neither weakness/obesity as the referent, weakness was associated with incident falls across all definitions (GS/BMI: HR 1.19 [1.07, 1.33]; GS/WC: HR 1.39 [1.19, 1.62]; GS ÷ BMI: HR 1.16 [1.05, 1.28]). Weakness with obesity was associated with falls using GS/WC (HR 1.28 [1.11, 1.48]). Obesity status was associated with falls in both the BMI and the WC definition (1.17 [1.02-1.35], 1.16 [1.05-1.28]). CONCLUSION: Our findings further evaluate the definitions of clinically defined weakness with and without obesity in older adults. As falls are an important patient outcome, establishing this relationship is critical for both clinicians and researchers. Future study should identify high-risk individuals in order to direct specific interventions to them. Geriatr Gerontol Int 2023; 23: 213-220.

Obesity, multiple chronic conditions, and the relationship with physical function: Data from the national health and aging trends survey.

BACKGROUND: The population of older adults living with multiple chronic conditions (MCC) continues to grow. MCC is independently associated with functional limitation and obesity. The aim of our study was to evaluate the association between obesity and MCC, and secondarily, the combined presence of obesity and functional limitations with MCC. METHODS: We analyzed cross-sectional survey data from the National Health and Aging Trends Survey (NHATS) 2011 baseline data, a nationally representative Medicare beneficiary cohort of adults in the United States. We evaluated the coexistent prevalence of obesity and MCC overall, and by standard body mass index (BMI) categories. We then evaluated the prevalence of functional limitations (mobility, self-care, and household activities) and Fried-defined frailty status in persons with a BMI ≥ 30 kg/m2. Logistic regression was used to measure the association between MCC and BMI, and functional limitations and MCC among those with obesity. RESULTS: In the 6,600 participants, the prevalence of concurrent obesity and MCC was 30.4%. Of those with obesity, the prevalence of MCC was 84.0%, and were more likely to have MCC (adjusted OR: 2.17, 95% CI 1.86, 2.54) compared to a normal BMI. Obesity and functional limitations or frailty were more likely have MCC than individuals with obesity alone. CONCLUSIONS: We found that individuals with obesity is strongly associated with MCC and that functional limitations and frailty status have a greater association with having MCC than individuals with obesity without MCC. Future longitudinal analyses are needed to ascertain this relationship.

The Essentials of Multiomics.

Within the last decade, the science of molecular testing has evolved from single gene and single protein analysis to broad molecular profiling as a standard of care, quickly transitioning from research to practice. Terms such as genomics, transcriptomics, proteomics, circulating omics, and artificial intelligence are now commonplace, and this rapid evolution has left us with a significant knowledge gap within the medical community. In this paper, we attempt to bridge that gap and prepare the physician in oncology for multiomics, a group of technologies that have gone from looming on the horizon to become a clinical reality. The era of multiomics is here, and we must prepare ourselves for this exciting new age of cancer medicine.

Comparison of Machine-Learning Algorithms for the Prediction of Current Procedural Terminology (CPT) Codes from Pathology Reports.

BACKGROUND: Pathology reports serve as an auditable trial of a patient's clinical narrative, containing text pertaining to diagnosis, prognosis, and specimen processing. Recent works have utilized natural language processing (NLP) pipelines, which include rule-based or machine-learning analytics, to uncover textual patterns that inform clinical endpoints and biomarker information. Although deep learning methods have come to the forefront of NLP, there have been limited comparisons with the performance of other machine-learning methods in extracting key insights for the prediction of medical procedure information, which is used to inform reimbursement for pathology departments. In addition, the utility of combining and ranking information from multiple report subfields as compared with exclusively using the diagnostic field for the prediction of Current Procedural Terminology (CPT) codes and signing pathologists remains unclear. METHODS: After preprocessing pathology reports, we utilized advanced topic modeling to identify topics that characterize a cohort of 93,039 pathology reports at the Dartmouth-Hitchcock Department of Pathology and Laboratory Medicine (DPLM). We separately compared XGBoost, SVM, and BERT (Bidirectional Encoder Representation from Transformers) methodologies for the prediction of primary CPT codes (CPT 88302, 88304, 88305, 88307, 88309) as well as 38 ancillary CPT codes, using both the diagnostic text alone and text from all subfields. We performed similar analyses for characterizing text from a group of the 20 pathologists with the most pathology report sign-outs. Finally, we uncovered important report subcomponents by using model explanation techniques. RESULTS: We identified 20 topics that pertained to diagnostic and procedural information. Operating on diagnostic text alone, BERT outperformed XGBoost for the prediction of primary CPT codes. When utilizing all report subfields, XGBoost outperformed BERT for the prediction of primary CPT codes. Utilizing additional subfields of the pathology report increased prediction accuracy across ancillary CPT codes, and performance gains for using additional report subfields were high for the XGBoost model for primary CPT codes. Misclassifications of CPT codes were between codes of a similar complexity, and misclassifications between pathologists were subspecialty related. CONCLUSIONS: Our approach generated CPT code predictions with an accuracy that was higher than previously reported. Although diagnostic text is an important source of information, additional insights may be extracted from other report subfields. Although BERT approaches performed comparably to the XGBoost approaches, they may lend valuable information to pipelines that combine image, text, and -omics information. Future resource-saving opportunities exist to help hospitals detect mis-billing, standardize report text, and estimate productivity metrics that pertain to pathologist compensation (RVUs).

Incident Impaired Cognitive Function in Sarcopenic Obesity: Data From the National Health and Aging Trends Survey.

Objectives: The prevalence of obesity with sarcopenia is increasing in adults aged ≥65 years. This geriatric syndrome places individuals at risk for synergistic complications that leads to long-term functional decline. We ascertained the relationship between sarcopenic obesity and incident long-term impaired global cognitive function in a representative US population. Design: A longitudinal, secondary data set analysis using the National Health and Aging Trends Survey. Setting: Community-based older adults in the United States. Participants: Participants without baseline impaired cognitive function aged ≥65 years with grip strength and body mass index measures. Methods: Sarcopenia was defined using the Foundation for the National Institutes of Health Sarcopenia Project grip strength cut points (men <35.5 kg; women <20 kg), and obesity was defined using standard body mass index (BMI) categories. Impaired global cognition was identified as impairment in the Alzheimer's Disease-8 score or immediate/delayed recall, orientation, clock-draw test, date/person recall. Proportional hazard models ascertained the risk of impaired cognitive function over 8 years (referent = neither obesity or sarcopenia). Results: Of the 5822 participants (55.7% women), median age category was 75 to 80, and mean grip strength and BMI were 26.4 kg and 27.5 kg/m2, respectively. Baseline prevalence of sarcopenic obesity was 12.9%, with an observed subset of 21.2% participants having impaired cognitive function at follow-up. Compared with those without sarcopenia or obesity, the risk of impaired cognitive function was no different in obesity alone [hazard ratio (HR) 0.98; 95% confidence interval (CI) 0.82-1.16]), but was significantly higher in sarcopenia (HR 1.60; 95% CI 1.42-1.80) and sarcopenic obesity (HR 1.20; 95% CI 1.03-1.40). There was no significant interaction term between sarcopenia and obesity. Conclusions: Both sarcopenia and sarcopenic obesity are associated with an increased long-term risk of impaired cognitive function in older adults.

Topological Feature Extraction and Visualization of Whole Slide Images using Graph Neural Networks.

Whole-slide images (WSI) are digitized representations of thin sections of stained tissue from various patient sources (biopsy, resection, exfoliation, fluid) and often exceed 100,000 pixels in any given spatial dimension. Deep learning approaches to digital pathology typically extract information from sub-images (patches) and treat the sub-images as independent entities, ignoring contributing information from vital large-scale architectural relationships. Modeling approaches that can capture higher-order dependencies between neighborhoods of tissue patches have demonstrated the potential to improve predictive accuracy while capturing the most essential slide-level information for prognosis, diagnosis and integration with other omics modalities. Here, we review two promising methods for capturing macro and micro architecture of histology images, Graph Neural Networks, which contextualize patch level information from their neighbors through message passing, and Topological Data Analysis, which distills contextual information into its essential components. We introduce a modeling framework, WSI-GTFE that integrates these two approaches in order to identify and quantify key pathogenic information pathways. To demonstrate a simple use case, we utilize these topological methods to develop a tumor invasion score to stage colon cancer.

Modified STEADI Fall Risk Categories Predict Incident Cognitive Impairment.

BACKGROUND/OBJECTIVES: It is unknown whether older adults at high risk of falls but without cognitive impairment have higher rates of subsequent cognitive impairment. DESIGN: This was an analysis of cross-sectional and longitudinal data from National Health and Aging Trends Study (NHATS). SETTING: NHATS, secondary analysis of data from 2011 to 2019. PARTICIPANTS: Community dwelling adults aged 65 and older without cognitive impairment. MEASUREMENTS: Participants were classified at baseline in three categories of fall risk (low, moderate, severe) using a modified algorithm from the Center for Disease Control's STEADI (Stop Elderly Accidents, Deaths, and Injuries) and fall risk from data from the longitudinal NHATS. Impaired global cognition was defined as NHATS-derived impairment in either the Alzheimer's Disease-8 score, immediate/delayed recall, orientation, clock-drawing test, or date/person recall. The primary outcome was the first incident of cognitive impairment in an 8 year follow-up period. Cox-proportional hazard models ascertained time to onset of cognitive impairment (referent = low modified STEADI incidence). RESULTS: Of the 7,146 participants (57.8% female), the median age category was 75 to 80 years. Prevalence of baseline fall modified STEADI risk categories in participants was low (51.6%), medium (38.5%), and high (9.9%). In our fully adjusted model, the risk of developing cognitive impairment was hazard ratio (HR) 1.18 [95% CI = 1.08, 1.29] in the moderate risk category, and HR 1.74 [95% CI = 1.53, 1.98] in the high-risk category. CONCLUSION: Older, cognitively intact adults at high fall risk at baseline had nearly twice the risk of cognitive decline at 8 year follow-up.

High prevalence of focal and multi-focal somatic genetic variants in the human brain.

Somatic mutations during stem cell division are responsible for several cancers. In principle, a similar process could occur during the intense cell proliferation accompanying human brain development, leading to the accumulation of regionally distributed foci of mutations. Using dual platform >5000-fold depth sequencing of 102 genes in 173 adult human brain samples, we detect and validate somatic mutations in 27 of 54 brains. Using a mathematical model of neurodevelopment and approximate Bayesian inference, we predict that macroscopic islands of pathologically mutated neurons are likely to be common in the general population. The detected mutation spectrum also includes DNMT3A and TET2 which are likely to have originated from blood cell lineages. Together, these findings establish developmental mutagenesis as a potential mechanism for neurodegenerative disorders, and provide a novel mechanism for the regional onset and focal pathology in sporadic cases.

Lethal CD4 T Cell Responses Induced by Vaccination Against Staphylococcus aureus Bacteremia.

Multiple candidate vaccines against Staphylococcus aureus infections have failed in clinical trials. Analysis of a recent prematurely halted vaccine trial revealed increased mortality rates among vaccine recipients in whom postsurgical S. aureus infection developed, emphasizing the potential for induction of detrimental immune responses and the need to better understand the requirements for protective immunity against S. aureus. These failures of single-antigen vaccines have prompted ongoing development of multicomponent vaccines to target the multitude of S. aureus virulence factors. In the current study, we used lethally irradiated S. aureus as a model multicomponent vaccine and showed that vaccination of mice decreased survival in a bacteremia challenge model. These deleterious effects were due to a CD4 T-cell-dependent interferon γ response and could be prevented by inhibiting development of this response during vaccination. Our results identify the potential for vaccination to induce pathological immune responses, and they have implications for recent vaccine failures and the design of future staphylococcal vaccines.

Genome evolution in the allotetraploid frog Xenopus laevis.

To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.

Mitosis in circulating tumor cells stratifies highly aggressive breast carcinomas.

BACKGROUND: Enumeration of circulating tumor cells (CTCs) isolated from the peripheral blood of breast cancer patients holds promise as a clinically relevant, minimally invasive diagnostic test. However, CTC utility has been limited as a prognostic indicator of survival by the inability to stratify patients beyond general enumeration. In comparison, histological biopsy examinations remain the standard method for confirming malignancy and grading malignant cells, allowing for cancer identification and then assessing patient cohorts for prognostic and predictive value. Typically, CTC identification relies on immunofluorescent staining assessed as absent/present, which is somewhat subjective and limited in its ability to characterize these cells. In contrast, the physical features used in histological cytology comprise the gold standard method used to identify and preliminarily characterize the cancer cells. Here, we superimpose the methods, cytologically subtyping CTCs labeled with immunohistochemical fluorescence stains to improve their prognostic value in relation to survival. METHODS: In this single-blind prospective pilot study, we tracked 36 patients with late-stage breast cancer over 24 months to compare overall survival between simple CTC enumeration and subtyping mitotic CTCs. A power analysis (1-ß = 0. 9, α = 0.05) determined that a pilot size of 30 patients was sufficient to stratify this patient cohort; 36 in total were enrolled. RESULTS: Our results confirmed that CTC number is a prognostic indicator of patient survival, with a hazard ratio 5.2, p = 0.005 (95 % CI 1.6-16.5). However, by simply subtyping the same population based on CTCs in cytological mitosis, the hazard ratio increased dramatically to 11.1, p < 0.001 (95 % CI 3.1-39.7). CONCLUSIONS: Our data suggest that (1) mitotic CTCs are relativity common in aggressive late-stage breast cancer, (2) mitotic CTCs may significantly correlate with shortened overall survival, and (3) larger and more defined patient cohort studies are clearly called for based on this initial pilot study.

Development of a novel multiplex electrochemiluminescent-based immunoassay for quantification of human serum IgG against 10 Staphylococcus aureus toxins.

An electrochemiluminescent (ECL)-based multiplex immunoassay using Meso-Scale Discovery (MSD) technology was developed for detecting antibody response toward 10 Staphylococcus aureus (S. aureus) exotoxins. These 10 antigens included three different groups of toxins: 1) single component pore-forming toxins such as alpha- and delta-hemolysins, 2) the bicomponent pore-forming toxin Panton-Valentine leukocidin (PVL), comprised of LukS-PV and LukF-PV subunits, and 3) enterotoxin/superantigens - Staphylococcal enterotoxins A (SEA), B (SEB), C1 (SEC1), D (SED), K (SEK) and Toxic shock syndrome toxin-1 (TSST-1). Assay development included optimization steps with a conventional SEB ELISA-based serological assay and then optimized parameters were transferred and re-optimized in a singleplex ECL format. Finally, two pentaplex solid-phase ECL formats were developed. As proof of concept, one set of pentaplex ECL data was compared with conventional ELISA results. During the assay development controls were screened and developed for both the singleplex and multiplex assays. ECL-based multiplex assays were more sensitive with a wide dynamic range and proved more time-efficient than conventional ELISAs. Using the newly developed ECL method we showed, for the first time, that delta-hemolysin toxin can induce an immune response as antibody titers could be detected.

Achieving high-sensitivity for clinical applications using augmented exome sequencing.

BACKGROUND: Whole exome sequencing is increasingly used for the clinical evaluation of genetic disease, yet the variation of coverage and sensitivity over medically relevant parts of the genome remains poorly understood. Several sequencing-based assays continue to provide coverage that is inadequate for clinical assessment. METHODS: Using sequence data obtained from the NA12878 reference sample and pre-defined lists of medically-relevant protein-coding and noncoding sequences, we compared the breadth and depth of coverage obtained among four commercial exome capture platforms and whole genome sequencing. In addition, we evaluated the performance of an augmented exome strategy, ACE, that extends coverage in medically relevant regions and enhances coverage in areas that are challenging to sequence. Leveraging reference call-sets, we also examined the effects of improved coverage on variant detection sensitivity. RESULTS: We observed coverage shortfalls with each of the conventional exome-capture and whole-genome platforms across several medically interpretable genes. These gaps included areas of the genome required for reporting recently established secondary findings (ACMG) and known disease-associated loci. The augmented exome strategy recovered many of these gaps, resulting in improved coverage in these areas. At clinically-relevant coverage levels (100 % bases covered at ≥20×), ACE improved coverage among genes in the medically interpretable genome (>90 % covered relative to 10-78 % with other platforms), the set of ACMG secondary finding genes (91 % covered relative to 4-75 % with other platforms) and a subset of variants known to be associated with human disease (99 % covered relative to 52-95 % with other platforms). Improved coverage translated into improvements in sensitivity, with ACE variant detection sensitivities (>97.5 % SNVs, >92.5 % InDels) exceeding that observed with conventional whole-exome and whole-genome platforms. CONCLUSIONS: Clinicians should consider analytical performance when making clinical assessments, given that even a few missed variants can lead to reporting false negative results. An augmented exome strategy provides a level of coverage not achievable with other platforms, thus addressing concerns regarding the lack of sensitivity in clinically important regions. In clinical applications where comprehensive coverage of medically interpretable areas of the genome requires higher localized sequencing depth, an augmented exome approach offers both cost and performance advantages over other sequencing-based tests.

Cytometric characterization of circulating tumor cells captured by microfiltration and their correlation to the CellSearch(®) CTC test.

Recent studies reporting hundreds, to thousands, of circulating tumor cells (CTCs) in the blood of cancer patients have raised questions regarding the prevalence of CTCs, as enumerated by the CellSearch(®) CTC Test. Although CellSearch has been shown to consistently detect clinically relevant CTCs; the ability to only capture EpCAM positive cells has led to speculation that it captures limited subsets of CTCs. In contrast, alternative approaches to CTC isolation are often cited as capturing large numbers of CTCs from patient blood. Not surprisingly the number of cells isolated by alternative approaches show poor correlations when compared to CellSearch, even when accounting for EpCAM presence or absence. In an effort to address this discrepancy, we ran an exploratory method comparison study to characterize and compare the CTC subgroups captured from duplicate blood samples from 30 breast and prostate cancer patients using a microfiltration system (CellSieve™) and CellSearch. We then categorized the CellSieve Cytokeratin(CK)+/CD45-/DAPI+ cells into five morphologically distinct subpopulations for correlative analysis. Like other filtration techniques, CellSieve isolated greater numbers of CK+/CD45- cells than CellSearch. Furthermore, analysis showed low correlation between the total CK+/CD45- cells captured by these two assays, regardless of EpCAM presence. However, subgrouping of CK+/CD45-/DAPI+ cells based on distinct cytokeratin staining patterns and nuclear morphologies elucidated a subpopulation correlative to CellSearch. Using method comparison analyses, we identified a specific CTC morphology which is highly correlative between two distinct capture methods. These data suggests that although various morphologic CTCs with similar phenotypic expressions are present in the blood of cancer patients, the clinically relevant cells isolated by CellSearch can potentially be identified using non-EpCAM dependent isolation. © 2014 The Authors. Published by Wiley Periodicals, Inc.

Characterization of the Asian Citrus Psyllid Transcriptome.

The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is a vector for the causative agents of Huanglongbing, which threatens citrus production worldwide. This study reports and discusses the first D. citri transcriptomes, encompassing the three main life stages of D. citri, egg, nymph and adult. The transcriptomes were annotated using Gene Ontology (GO) and insecticide-related genes within each life stage were identified to aid the development of future D. citri insecticides. Transcriptome assemblies and other sequence data are available for download at the International Asian Citrus Psyllid Genome Consortium website [http://psyllid.org/download] and at NCBI [http://www.ncbi.nlm.nih.gov/bioproject/29447].

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals.

Understanding the consequences of regulatory variation in the human genome remains a major challenge, with important implications for understanding gene regulation and interpreting the many disease-risk variants that fall outside of protein-coding regions. Here, we provide a direct window into the regulatory consequences of genetic variation by sequencing RNA from 922 genotyped individuals. We present a comprehensive description of the distribution of regulatory variation--by the specific expression phenotypes altered, the properties of affected genes, and the genomic characteristics of regulatory variants. We detect variants influencing expression of over ten thousand genes, and through the enhanced resolution offered by RNA-sequencing, for the first time we identify thousands of variants associated with specific phenotypes including splicing and allelic expression. Evaluating the effects of both long-range intra-chromosomal and trans (cross-chromosomal) regulation, we observe modularity in the regulatory network, with three-dimensional chromosomal configuration playing a particular role in regulatory modules within each chromosome. We also observe a significant depletion of regulatory variants affecting central and critical genes, along with a trend of reduced effect sizes as variant frequency increases, providing evidence that purifying selection and buffering have limited the deleterious impact of regulatory variation on the cell. Further, generalizing beyond observed variants, we have analyzed the genomic properties of variants associated with expression and splicing and developed a Bayesian model to predict regulatory consequences of genetic variants, applicable to the interpretation of individual genomes and disease studies. Together, these results represent a critical step toward characterizing the complete landscape of human regulatory variation.

Structurally designed attenuated subunit vaccines for S. aureus LukS-PV and LukF-PV confer protection in a mouse bacteremia model.

Previous efforts towards S. aureus vaccine development have largely focused on cell surface antigens to induce opsonophagocytic killing aimed at providing sterile immunity, a concept successfully applied to other Gram-positive pathogens such as Streptococcus pneumoniae. However, these approaches have largely failed, possibly in part due to the remarkable diversity of the staphylococcal virulence factors such as secreted immunosuppressive and tissue destructive toxins. S. aureus produces several pore-forming toxins including the single subunit alpha hemolysin as well as bicomponent leukotoxins such as Panton-Valentine leukocidin (PVL), gamma hemolysins (Hlg), and LukED. Here we report the generation of highly attenuated mutants of PVL subunits LukS-PV and LukF-PV that were rationally designed, based on an octameric structural model of the toxin, to be deficient in oligomerization. The attenuated subunit vaccines were highly immunogenic and showed significant protection in a mouse model of S. aureus USA300 sepsis. Protection against sepsis was also demonstrated by passive transfer of rabbit immunoglobulin raised against LukS-PV. Antibodies to LukS-PV inhibited the homologous oligomerization of LukS-PV with LukF-PV as well heterologous oligomerization with HlgB. Importantly, immune sera from mice vaccinated with the LukS mutant not only inhibited the PMN lytic activity produced by the PVL-positive USA300 but also blocked PMN lysis induced by supernatants of PVL-negative strains suggesting a broad protective activity towards other bicomponent toxins. These findings strongly support the novel concept of an anti-virulence, toxin-based vaccine intended for prevention of clinical S. aureus invasive disease, rather than achieving sterile immunity. Such a multivalent vaccine may include attenuated leukotoxins, alpha hemolysin, and superantigens.

BAP1 loss defines a new class of renal cell carcinoma.

The molecular pathogenesis of renal cell carcinoma (RCC) is poorly understood. Whole-genome and exome sequencing followed by innovative tumorgraft analyses (to accurately determine mutant allele ratios) identified several putative two-hit tumor suppressor genes, including BAP1. The BAP1 protein, a nuclear deubiquitinase, is inactivated in 15% of clear cell RCCs. BAP1 cofractionates with and binds to HCF-1 in tumorgrafts. Mutations disrupting the HCF-1 binding motif impair BAP1-mediated suppression of cell proliferation but not deubiquitination of monoubiquitinated histone 2A lysine 119 (H2AK119ub1). BAP1 loss sensitizes RCC cells in vitro to genotoxic stress. Notably, mutations in BAP1 and PBRM1 anticorrelate in tumors (P = 3 × 10(-5)), [corrected] and combined loss of BAP1 and PBRM1 in a few RCCs was associated with rhabdoid features (q = 0.0007). BAP1 and PBRM1 regulate seemingly different gene expression programs, and BAP1 loss was associated with high tumor grade (q = 0.0005). Our results establish the foundation for an integrated pathological and molecular genetic classification of RCC, paving the way for subtype-specific treatments exploiting genetic vulnerabilities.

An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation.

BACKGROUND: A comprehensive transcriptome survey, or gene atlas, provides information essential for a complete understanding of the genomic biology of an organism. We present an atlas of RNA abundance for 92 adult, juvenile and fetal cattle tissues and three cattle cell lines. RESULTS: The Bovine Gene Atlas was generated from 7.2 million unique digital gene expression tag sequences (300.2 million total raw tag sequences), from which 1.59 million unique tag sequences were identified that mapped to the draft bovine genome accounting for 85% of the total raw tag abundance. Filtering these tags yielded 87,764 unique tag sequences that unambiguously mapped to 16,517 annotated protein-coding loci in the draft genome accounting for 45% of the total raw tag abundance. Clustering of tissues based on tag abundance profiles generally confirmed ontology classification based on anatomy. There were 5,429 constitutively expressed loci and 3,445 constitutively expressed unique tag sequences mapping outside annotated gene boundaries that represent a resource for enhancing current gene models. Physical measures such as inferred transcript length or antisense tag abundance identified tissues with atypical transcriptional tag profiles. We report for the first time the tissue-specific variation in the proportion of mitochondrial transcriptional tag abundance. CONCLUSIONS: The Bovine Gene Atlas is the deepest and broadest transcriptome survey of any livestock genome to date. Commonalities and variation in sense and antisense transcript tag profiles identified in different tissues facilitate the examination of the relationship between gene expression, tissue, and gene function.

A comprehensive catalogue of somatic mutations from a human cancer genome.

All cancers carry somatic mutations. A subset of these somatic alterations, termed driver mutations, confer selective growth advantage and are implicated in cancer development, whereas the remainder are passengers. Here we have sequenced the genomes of a malignant melanoma and a lymphoblastoid cell line from the same person, providing the first comprehensive catalogue of somatic mutations from an individual cancer. The catalogue provides remarkable insights into the forces that have shaped this cancer genome. The dominant mutational signature reflects DNA damage due to ultraviolet light exposure, a known risk factor for malignant melanoma, whereas the uneven distribution of mutations across the genome, with a lower prevalence in gene footprints, indicates that DNA repair has been preferentially deployed towards transcribed regions. The results illustrate the power of a cancer genome sequence to reveal traces of the DNA damage, repair, mutation and selection processes that were operative years before the cancer became symptomatic.