Natively Unfolded FG Repeats Stabilize the Structure of the Nuclear Pore Complex.

Nuclear pore complexes (NPCs) are ∼100 MDa transport channels assembled from multiple copies of ∼30 nucleoporins (Nups). One-third of these Nups contain phenylalanine-glycine (FG)-rich repeats, forming a diffusion barrier, which is selectively permeable for nuclear transport receptors that interact with these repeats. Here, we identify an additional function of FG repeats in the structure and biogenesis of the yeast NPC. We demonstrate that GLFG-containing FG repeats directly bind to multiple scaffold Nups in vitro and act as NPC-targeting determinants in vivo. Furthermore, we show that the GLFG repeats of Nup116 function in a redundant manner with Nup188, a nonessential scaffold Nup, to stabilize critical interactions within the NPC scaffold needed for late steps of NPC assembly. Our results reveal a previously unanticipated structural role for natively unfolded GLFG repeats as Velcro to link NPC subcomplexes and thus add a new layer of connections to current models of the NPC architecture.

ß-Oxidation and autophagy are critical energy providers during acute glucose depletion in Saccharomyces cerevisiae.

The ability to tolerate and thrive in diverse environments is paramount to all living organisms, and many organisms spend a large part of their lifetime in starvation. Upon acute glucose starvation, yeast cells undergo drastic physiological and metabolic changes and reestablish a constant-although lower-level of energy production within minutes. The molecules that are rapidly metabolized to fuel energy production under these conditions are unknown. Here, we combine metabolomics and genetics to characterize the cells' response to acute glucose depletion and identify pathways that ensure survival during starvation. We show that the ability to respire is essential for maintaining the energy status and to ensure viability during starvation. Measuring the cells' immediate metabolic response, we find that central metabolites drastically deplete and that the intracellular AMP-to-ATP ratio strongly increases within 20 to 30 s. Furthermore, we detect changes in both amino acid and lipid metabolite levels. Consistent with this, both bulk autophagy, a process that frees amino acids, and lipid degradation via ß-oxidation contribute in parallel to energy maintenance upon acute starvation. In addition, both these pathways ensure long-term survival during starvation. Thus, our results identify bulk autophagy and ß-oxidation as important energy providers during acute glucose starvation.

The double-hit signature identifies double-hit diffuse large B-cell lymphoma with genetic events cryptic to FISH.

High-grade B-cell lymphomas with MYC and BCL2 and/or BCL6 rearrangements (HGBL-DH/THs) include a group of diffuse large B-cell lymphomas (DLBCLs) with inferior outcomes after standard chemoimmunotherapy. We recently described a gene expression signature that identifies 27% of germinal center B-cell DLBCLs (GCB-DLBCLs) as having a double-hit-like expression pattern (DHITsig) and inferior outcomes; however, only half of these cases have both MYC and BCL2 translocations identifiable using standard breakapart fluorescence in situ hybridization (FISH). Here, 20 DHITsig+ GCB-DLBCLs apparently lacking MYC and/or BCL2 rearrangements underwent whole-genome sequencing. This revealed 6 tumors with MYC or BCL2 rearrangements that were cryptic to breakapart FISH. Copy-number analysis identified 3 tumors with MYC and 6 tumors with MIR17HG gains or amplifications, both of which may contribute to dysregulation of MYC and its downstream pathways. Focal deletions of the PVT1 promoter were observed exclusively among DHITsig+ tumors lacking MYC translocations; this may also contribute to MYC overexpression. These results highlight that FISH fails to identify all HGBL-DH/THs, while revealing a range of other genetic mechanisms potentially underlying MYC dysregulation in DHITsig+ DLBCL, suggesting that gene expression profiling is more sensitive for identifying the biology underlying poor outcomes in GCB-DLBCL.

Collaborative intra-tumor heterogeneity detection.

MOTIVATION: Despite the remarkable advances in sequencing and computational techniques, noise in the data and complexity of the underlying biological mechanisms render deconvolution of the phylogenetic relationships between cancer mutations difficult. Besides that, the majority of the existing datasets consist of bulk sequencing data of single tumor sample of an individual. Accurate inference of the phylogenetic order of mutations is particularly challenging in these cases and the existing methods are faced with several theoretical limitations. To overcome these limitations, new methods are required for integrating and harnessing the full potential of the existing data. RESULTS: We introduce a method called Hintra for intra-tumor heterogeneity detection. Hintra integrates sequencing data for a cohort of tumors and infers tumor phylogeny for each individual based on the evolutionary information shared between different tumors. Through an iterative process, Hintra learns the repeating evolutionary patterns and uses this information for resolving the phylogenetic ambiguities of individual tumors. The results of synthetic experiments show an improved performance compared to two state-of-the-art methods. The experimental results with a recent Breast Cancer dataset are consistent with the existing knowledge and provide potentially interesting findings. AVAILABILITY AND IMPLEMENTATION: The source code for Hintra is available at https://github.com/sahandk/HINTRA.

Integration of genomics and metabolomics for prioritization of rare disease variants: a 2018 literature review.

Many inborn errors of metabolism (IEMs) are amenable to treatment; therefore, early diagnosis and treatment is imperative. Despite recent advances, the genetic basis of many metabolic phenotypes remains unknown. For discovery purposes, whole exome sequencing (WES) variant prioritization coupled with clinical and bioinformatics expertise is the primary method used to identify novel disease-causing variants; however, causation is often difficult to establish due to the number of plausible variants. Integrated analysis of untargeted metabolomics (UM) and WES or whole genome sequencing (WGS) data is a promising systematic approach for identifying disease-causing variants. In this review, we provide a literature-based overview of UM methods utilizing liquid chromatography mass spectrometry (LC-MS), and assess approaches to integrating WES/WGS and LC-MS UM data for the discovery and prioritization of variants causing IEMs. To embed this integrated -omics approach in the clinic, expansion of gene-metabolite annotations and metabolomic feature-to-metabolite mapping methods are needed.

Is previous exposure to hepatitis B a risk factor for pancreatic cancer or hepatocellular carcinoma?

GOALS: We evaluated whether prior infection with the hepatitis B virus (HBV) influences the development of pancreatic cancer or hepatocellular carcinoma (HCC). BACKGROUND: Prior infection with HBV may predispose patients to developing pancreatic cancer or HCC. STUDY: We conducted a retrospective cohort study using administrative data from an integrated health care system. We identified all patients who had HBV testing over a 13-year period. These patients were divided into 1 of 3 cohorts based on HBV status: negative infection (n=28,719), previous exposure (n=5141), or active infection (n=404). Pancreatic cancer and HCC data were obtained from pathology reports in the health system's cancer registry. RESULTS: In a multivariable model, age [hazards ratio (HR), 1.08; confidence interval (CI), 1.06-1.09; P<0.001)] and presence of diabetes (HR, 1.88; CI, 1.27-2.80; P=0.002) were identified to have significant influence on pancreatic cancer development, whereas previous HBV exposure did not have a significant influence (HR, 1.41; CI, 0.88-2.27; P=0.16). In a separate multivariable model, male sex (HR, 2.05; CI, 1.35-3.11; P<0.001), age (HR, 1.08; CI, 1.06-1.09; P<0.001), being hepatitis C positive (HR, 5.40; CI, 3.51-8.33; P<0.001), and presence of cirrhosis (HR, 27.84; CI, 17.43-44.46, P<0.001) were all significant predictors of HCC. However, previous HBV exposure was not associated with HCC development (HR, 1.03; CI, 0.68-1.56; P=0.88). CONCLUSIONS: Data from this study indicate that previous HBV exposure is not a risk factor for the development of either pancreatic cancer or HCC.

Barriers and facilitators to implementation of evidence-based task-sharing mental health interventions in low- and middle-income countries: a systematic review using implementation science frameworks.

BACKGROUND: Task-sharing is a promising strategy to expand mental healthcare in low-resource settings, especially in low- and middle-income countries (LMICs). Research on how to best implement task-sharing mental health interventions, however, is hampered by an incomplete understanding of the barriers and facilitators to their implementation. This review aims to systematically identify implementation barriers and facilitators in evidence-based task-sharing mental health interventions using an implementation science lens, organizing factors across a novel, integrated implementation science framework. METHODS: PubMed, PsychINFO, CINAHL, and Embase were used to identify English-language, peer-reviewed studies using search terms for three categories: "mental health," "task-sharing," and "LMIC." Articles were included if they: focused on mental disorders as the main outcome(s); included a task-sharing intervention using or based on an evidence-based practice; were implemented in an LMIC setting; and included assessment or data-supported analysis of barriers and facilitators. An initial conceptual model and coding framework derived from the Consolidated Framework for Implementation Research and the Theoretical Domains Framework was developed and iteratively refined to create an integrated conceptual framework, the Barriers and Facilitators in Implementation of Task-Sharing Mental Health Interventions (BeFITS-MH), which specifies 37 constructs across eight domains: (I) client characteristics, (II) provider characteristics, (III) family and community factors, (IV) organizational characteristics, (V) societal factors, (VI) mental health system factors, (VII) intervention characteristics, and (VIII) stigma. RESULTS: Of the 26,935 articles screened (title and abstract), 192 articles underwent full-text review, yielding 37 articles representing 28 unique intervention studies that met the inclusion criteria. The most prevalent facilitators occur in domains that are more amenable to adaptation (i.e., the intervention and provider characteristics domains), while salient barriers occur in domains that are more challenging to modulate or intervene on-these include constructs in the client characteristics as well as the broader societal and structural levels of influence (i.e., the organizational, mental health system domains). Other notable trends include constructs in the family and community domains occurring as barriers and as facilitators roughly equally, and stigma constructs acting exclusively as barriers. CONCLUSIONS: Using the BeFITS-MH model we developed based on implementation science frameworks, this systematic review provides a comprehensive identification and organization of barriers and facilitators to evidence-based task-sharing mental health interventions in LMICs. These findings have important implications for ongoing and future implementation of this critically needed intervention strategy, including the promise of leveraging task-sharing intervention characteristics as sites of continued innovation, the importance of but relative lack of engagement with constructs in macro-level domains (e.g., organizational characteristics, stigma), and the need for more delineation of strategies for task-sharing mental health interventions that researchers and implementers can employ to enhance implementation in and across levels. TRIAL REGISTRATION: PROSPERO CRD42020161357.

Implementation factors for patient navigation program success: a qualitative study.

BACKGROUND: Patient navigation (PN) is an evidence-based practice that involves assessing and addressing individual barriers to care for patients. While PN has shown effectiveness in numerous studies, designing successful, sustainable PN programs has remained challenging for many healthcare organizations. The purpose of the present study was to examine implementation factors for successful PN programs to optimize the sustainability of PN services across cancer care settings in the USA. METHODS: Data were collected via semi-structured interviews with PN stakeholders (n=17) from diverse cancer care settings. Thematic content analysis was conducted by deductively coding major themes based on constructs from the Exploration-Preparation-Implementation-Sustainability framework and by inductively coding emergent themes. RESULTS: Facilitators in the outer context included payer guidelines, accreditation requirements, community partnerships, and demonstrated need and demand for services. Inner context factors such as alignment with organizational and leadership priorities, appropriate staff support and workloads, and relative advantage were important to program success. Innovation characteristics such as the presence of innovation champions, clear role and scope of practice, clear protocols, strong communication channels, and innovation fit were facilitators of program success. Community-Academic partnerships and funding stability also emerged as facilitators for program sustainability. CONCLUSION: Our qualitative analysis from a diverse sample of PN stakeholders and programs across the USA supports intentional use of implementation theory to design PN programs to optimize implementation success.

Mesalamine protects against colorectal cancer in inflammatory bowel disease.

BACKGROUND: Individuals with inflammatory bowel disease (IBD) are at increased risk of developing colorectal cancer (CRC) compared with the general population. Previous studies show this risk is strongly associated with dysplasia, extent of disease, duration of disease, and degree of inflammation, while chemoprevention of CRC has less support. AIM: Evaluate factors influencing risk of colorectal cancer development in inflammatory bowel disease patients. METHODS: IBD patients with CRC were matched to controls by IBD type, age at diagnosis, sex, race, extent of disease, and disease duration. We compared body mass index, family history of IBD, family history of CRC, tobacco use, and cumulative and daily use of aminosalicylates, immunomodulators, folic acid, steroids, and nonsteroidal anti-inflammatory drugs. Statistical analysis was performed with logistic regression and receiver operating characteristic (ROC) curves. RESULTS: Of 1,594 IBD patients, 30 CRC patients were identified. Of these, 18 CRC patients were matched to 30 controls. More control patients used a cumulative aminosalicylate dose of >or=4,500 g (46.6% versus 5.6%; P = 0.047), folic acid (40.0% versus 16.7%; P = 0.002), cumulative folic acid dose of >or=1,400 mg (30.0% versus 11.1%; P = 0.014), and average daily folic acid dose of >or=1 mg (30.0% versus 16.7%; P = 0.002) compared with CRC patients. Multivariate analysis showed that a cumulative aminosalicylate dose of >or=4,500 g reduced the risk of CRC by 97.6% (P = 0.047). Folic acid reduced CRC risk by 89% (P = 0.002). CONCLUSIONS: Aminosalicylate and folic acid use may decrease the risk of CRC among IBD patients.

PRPS-ST: A protocol-agnostic self-training method for gene expression-based classification of blood cancers.

Gene expression classifiers are gaining increasing popularity for stratifying tumors into subgroups with distinct biological features. A fundamental limitation shared by current classifiers is the requirement for comparable training and testing data sets. Here, we describe a self-training implementation of our probability ratio-based classification prediction score method (PRPS-ST), which facilitates the porting of existing classification models to other gene expression data sets. In comparison to gold standards, we demonstrate favorable performance of PRPS-ST in gene expression-based classification of DLBCL and B-ALL using a diverse variety of gene expression data types and pre-processing methods, including in classifications with a high degree of class imbalance. Tumors classified by our method were significantly enriched for prototypical genetic features of their respective subgroups. Interestingly, this included cases that were unclassifiable by established methods, implying the potential enhanced sensitivity of PRPS-ST.

A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications.

The development of precision medicine approaches for diffuse large B cell lymphoma (DLBCL) is confounded by its pronounced genetic, phenotypic, and clinical heterogeneity. Recent multiplatform genomic studies revealed the existence of genetic subtypes of DLBCL using clustering methodologies. Here, we describe an algorithm that determines the probability that a patient's lymphoma belongs to one of seven genetic subtypes based on its genetic features. This classification reveals genetic similarities between these DLBCL subtypes and various indolent and extranodal lymphoma types, suggesting a shared pathogenesis. These genetic subtypes also have distinct gene expression profiles, immune microenvironments, and outcomes following immunochemotherapy. Functional analysis of genetic subtype models highlights distinct vulnerabilities to targeted therapy, supporting the use of this classification in precision medicine trials.

Validation in a multiple urology practice cohort of the Prostate Cancer Prevention Trial calculator for predicting prostate cancer detection.

PURPOSE: The Prostate Cancer Prevention Trial prostate cancer risk calculator was developed in a clinical trial cohort that does not represent men routinely referred for prostate biopsy. We assessed the generalizability of the Prostate Cancer Prevention Trial calculator in a cohort more representative of patients referred for consideration of prostate biopsy in American urology practice. MATERIALS AND METHODS: Patients undergoing prostate biopsy by 12 urologists at 5 sites were enrolled in an Early Detection Research Network cohort. The Prostate Cancer Prevention Trial risk calculator was validated by examining area underneath the receiver operating characteristic curve, sensitivity, specificity and calibration comparing observed vs predicted risk of prostate cancer detection. RESULTS: Cancer incidence was greater (43% vs 22%, p = 0.001) in the Early Detection Research Network validation cohort (645) compared to the Prostate Cancer Prevention Trial group (5,519). Early Detection Research Network participants were younger and more racially diverse, and had more abnormal digital rectal examinations and higher prostate specific antigen than Prostate Cancer Prevention Trial participants (all p <0.001). Cancer severity was worse in the Early Detection Research Network cohort than in the Prostate Cancer Prevention Trial (Gleason 7 or higher 60% vs 21%, p <0.001). Nevertheless, the Prostate Cancer Prevention Trial risk calculator was superior to prostate specific antigen alone for predicting cancer in the Early Detection Research Network (AUC 0.691 vs 0.655, p = 0.009) and calibration confirmed that the Prostate Cancer Prevention Trial risk score accurately predicted individual risks in the Early Detection Research Network cohort. CONCLUSIONS: Differences between the Early Detection Research Network validation cohort and the Prostate Cancer Prevention Trial cohort underscore the importance of validating calculator performance in the multicenter urology practice setting. Our findings extend the applicability of the Prostate Cancer Prevention Trial calculator for measuring the risk of prostate cancer detection on biopsy to the routine American urology practice setting.

Renal insufficiency after liver transplantation in the MELD era compared to the pre-MELD era.

Because the model for end-stage liver disease (MELD) system for liver allocation gives priority to patients with a higher creatinine, and because pre-transplant renal function is one determinant of post-transplant renal function, this study compares the burden of renal insufficiency in the pre-MELD and MELD eras. Two hundred and eleven patients, at our institution, transplanted in the pre-MELD era, were compared to 143 in the MELD era. The GFR (mL/min/1.73 m2) was significantly higher in the MELD cohort than the pre-MELD cohort at time of transplant, discharge, and 12 months post-transplant (95.5 vs. 85.3, p = 0.039; 90.4 vs. 77.4, p = 0.002; 66.8 vs. 60.3, p = 0.026). There was no difference between the two groups in time to renal failure. There was a higher rate of sirolimus use in the MELD era (27% vs. 18%: p = 0.042) and a slightly higher use of kidney-liver transplant in the MELD era (p = 0.056). We did not identify greater renal insufficiency in the MELD era. There was greater renal function in the MELD era at time of transplant, discharge and month 12. Potential explanations include: absence of an increase in renal insufficiency prior to transplant in the MELD era, greater use of renal sparing immunotherapy and growing use of kidney-liver transplant.

Relationship between thiazolidinedione use and cardiovascular outcomes and all-cause mortality among patients with diabetes: a time-updated propensity analysis.

PURPOSE: To investigate the association of the thiazolidinediones (TZDs), rosiglitazone, and pioglitazone, together and individually on the risk of cardiovascular outcomes and all-cause mortality, using time-updated propensity score adjusted analysis. METHODS: We conducted a retrospective cohort study in a large vertically integrated health system in southeast Michigan. Cohort inclusion criteria included adult patients with diabetes treated with oral medications and followed longitudinally within the health system between 1 January 2000 and 1 December 2006. The primary outcome was fatal and non-fatal acute myocardial infarction (AMI). Secondary outcomes included hospitalizations for congestive heart failure (CHF), fatal, and non-fatal cerebrovascular accidents (CVA) and transient ischemic attacks (TIA), combined coronary heart disease (CHD) events, and all-cause mortality. RESULTS: 19,171 patients were included in this study. Use of TZDs (adjusted hazard ratio (aHR) with propensity adjustment (PA), 0.92; 95% confidence interval (CI) 0.73-1.17), rosiglitazone (aHR with PA, 1.06; 95%CI 0.66-1.70), and pioglitazone (aHR with PA, 0.91; 95%CI 0.69-1.21) was not associated with a higher risk of AMI. However, pioglitazone use was associated with a reduction in all-cause mortality (aHR with PA, 0.60; 95%CI 0.42-0.96). Compared with rosiglitazone, pioglitazone use was associated with a lower risk of all outcomes assessed, particularly CHF (p = 0.013) and combined CHD events (p = 0.048). CONCLUSIONS: Our findings suggest that pioglitazone may have a more favorable risk profile when compared to rosiglitazone, arguing against a singular effect for TZDs on cardiovascular outcomes.

Double-Hit Gene Expression Signature Defines a Distinct Subgroup of Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma.

PURPOSE: High-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements (HGBL-DH/TH) has a poor outcome after standard chemoimmunotherapy. We sought to understand the biologic underpinnings of HGBL-DH/TH with BCL2 rearrangements (HGBL-DH/TH- BCL2) and diffuse large B-cell lymphoma (DLBCL) morphology through examination of gene expression. PATIENTS AND METHODS: We analyzed RNA sequencing data from 157 de novo germinal center B-cell-like (GCB)-DLBCLs, including 25 with HGBL-DH/TH- BCL2, to define a gene expression signature that distinguishes HGBL-DH/TH- BCL2 from other GCB-DLBCLs. To assess the genetic, molecular, and phenotypic features associated with this signature, we analyzed targeted resequencing, whole-exome sequencing, RNA sequencing, and immunohistochemistry data. RESULTS: We developed a 104-gene double-hit signature (DHITsig) that assigned 27% of GCB-DLBCLs to the DHITsig-positive group, with only one half harboring MYC and BCL2 rearrangements (HGBL-DH/TH- BCL2). DHITsig-positive patients had inferior outcomes after rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone immunochemotherapy compared with DHITsig-negative patients (5-year time to progression rate, 57% and 81%, respectively; P < .001), irrespective of HGBL-DH/TH- BCL2 status. The prognostic value of DHITsig was confirmed in an independent validation cohort. DHITsig-positive tumors are biologically characterized by a putative non-light zone germinal center cell of origin and a distinct mutational landscape that comprises genes associated with chromatin modification. A new NanoString assay (DLBCL90) recapitulated the prognostic significance and RNA sequencing assignments. Validating the association with HGBL-DH/TH- BCL2, 11 of 25 DHITsig-positive-transformed follicular lymphomas were classified as HGBL-DH/TH- BCL2 compared with zero of 50 in the DHITsig-negative group. Furthermore, the DHITsig was shared with the majority of B-cell lymphomas with high-grade morphology tested. CONCLUSION: We have defined a clinically and biologically distinct subgroup of tumors within GCB-DLBCL characterized by a gene expression signature of HGBL-DH/TH- BCL2. This knowledge has been translated into an assay applicable to routinely available biopsy samples, which enables exploration of its utility to guide patient management.

Differential Antibody Responses to Conserved HIV-1 Neutralizing Epitopes in the Context of Multivalent Scaffolds and Native-Like gp140 Trimers.

Broadly neutralizing antibodies (bNAbs) have provided valuable insights into the humoral immune response to HIV-1. While rationally designed epitope scaffolds and well-folded gp140 trimers have been proposed as vaccine antigens, a comparative understanding of their antibody responses has not yet been established. In this study, we probed antibody responses to the N332 supersite and the membrane-proximal external region (MPER) in the context of heterologous protein scaffolds and native-like gp140 trimers. Ferritin nanoparticles and fragment crystallizable (Fc) regions were utilized as multivalent carriers to display scaffold antigens with grafted N332 and MPER epitopes, respectively. Trimeric scaffolds were also identified to stabilize the MPER-containing BG505 gp140.681 trimer in a native-like conformation. Following structural and antigenic evaluation, a subset of scaffold and trimer antigens was selected for immunization in BALB/c mice. Serum binding revealed distinct patterns of antibody responses to these two bNAb targets presented in different structural contexts. For example, the N332 nanoparticles elicited glycan epitope-specific antibody responses that could also recognize the native trimer, while a scaffolded BG505 gp140.681 trimer generated a stronger and more rapid antibody response to the trimer apex than its parent gp140.664 trimer. Furthermore, next-generation sequencing (NGS) of mouse splenic B cells revealed expansion of antibody lineages with long heavy-chain complementarity-determining region 3 (HCDR3) loops upon activation by MPER scaffolds, in contrast to the steady repertoires primed by N332 nanoparticles and a soluble gp140.664 trimer. These findings will facilitate the future development of a coherent vaccination strategy that combines both epitope-focused and trimer-based approaches.IMPORTANCE Both epitope-focused and trimer-based strategies are currently being explored in HIV-1 vaccine development, which aims to elicit broadly neutralizing antibodies (bNAbs) targeting conserved epitopes on the viral envelope (Env). However, little is known about the differences in antibody response to these bNAb targets presented by foreign scaffolds and native Env. In this study, a systematic effort was undertaken to design multivalent epitope scaffolds and soluble gp140.681 trimers with a complete antigenic surface, and to comparatively analyze the antibody responses elicited by these antigens to the N332 supersite and MPER in a mouse model. This study will inform both epitope-focused and trimer-based vaccine design and will facilitate integration of the two vaccine strategies.

A glucose-starvation response regulates the diffusion of macromolecules.

The organization and biophysical properties of the cytosol implicitly govern molecular interactions within cells. However, little is known about mechanisms by which cells regulate cytosolic properties and intracellular diffusion rates. Here, we demonstrate that the intracellular environment of budding yeast undertakes a startling transition upon glucose starvation in which macromolecular mobility is dramatically restricted, reducing the movement of both chromatin in the nucleus and mRNPs in the cytoplasm. This confinement cannot be explained by an ATP decrease or the physiological drop in intracellular pH. Rather, our results suggest that the regulation of diffusional mobility is induced by a reduction in cell volume and subsequent increase in molecular crowding which severely alters the biophysical properties of the intracellular environment. A similar response can be observed in fission yeast and bacteria. This reveals a novel mechanism by which cells globally alter their properties to establish a unique homeostasis during starvation.

Importin-ß modulates the permeability of the nuclear pore complex in a Ran-dependent manner.

Soluble karyopherins of the importin-ß (impß) family use RanGTP to transport cargos directionally through the nuclear pore complex (NPC). Whether impß or RanGTP regulate the permeability of the NPC itself has been unknown. In this study, we identify a stable pool of impß at the NPC. A subpopulation of this pool is rapidly turned-over by RanGTP, likely at Nup153. Impß, but not transportin-1 (TRN1), alters the pore's permeability in a Ran-dependent manner, suggesting that impß is a functional component of the NPC. Upon reduction of Nup153 levels, inert cargos more readily equilibrate across the NPC yet active transport is impaired. When purified impß or TRN1 are mixed with Nup153 in vitro, higher-order, multivalent complexes form. RanGTP dissolves the impß•Nup153 complexes but not those of TRN1•Nup153. We propose that impß and Nup153 interact at the NPC's nuclear face to form a Ran-regulated mesh that modulates NPC permeability.

Scaffold nucleoporins Nup188 and Nup192 share structural and functional properties with nuclear transport receptors.

Nucleocytoplasmic transport is mediated by nuclear pore complexes (NPCs) embedded in the nuclear envelope. About 30 different proteins (nucleoporins, nups) arrange around a central eightfold rotational axis to build the modular NPC. Nup188 and Nup192 are related and evolutionary conserved, large nucleoporins that are part of the NPC scaffold. Here we determine the structure of Nup188. The protein folds into an extended stack of helices where an N-terminal 130 kDa segment forms an intricate closed ring, while the C-terminal region is a more regular, superhelical structure. Overall, the structure has distant similarity with flexible S-shaped nuclear transport receptors (NTRs). Intriguingly, like NTRs, both Nup188 and Nup192 specifically bind FG-repeats and are able to translocate through NPCs by facilitated diffusion. This blurs the existing dogma of a clear distinction between stationary nups and soluble NTRs and suggests an evolutionary relationship between the NPC and the soluble nuclear transport machinery. DOI:http://dx.doi.org/10.7554/eLife.00745.001.

Prevalence of TMPRSS2-ERG fusion prostate cancer among men undergoing prostate biopsy in the United States.

PURPOSE: Fusion of the TMPRSS2 prostate-specific gene with the ERG transcription factor is a putatively oncogenic gene rearrangement that is commonly found in prostate cancer tissue from men undergoing prostatectomy. However, the prevalence of the fusion was less common in samples of transurethral resection of the prostate from a Swedish cohort of patients with incidental prostate cancer followed by watchful waiting, raising the question as to whether the high prevalence in prostatectomy specimens reflects selection bias. We sought to determine the prevalence of TMPRSS2-ERG gene fusion among prostate-specific antigen-screened men undergoing prostate biopsy in the United States. EXPERIMENTAL DESIGN: We studied 140 prostate biopsies from the same number of patients for TMPRSS2-ERG fusion status with a fluorescent in situ hybridization assay. One hundred and thirty-four samples (100 cancer and 34 benign) were assessable. RESULTS: ERG gene rearrangement was detected in 46% of prostate biopsies that were found to have prostate cancer and in 0% of benign prostate biopsies (P < 0.0001). Evaluation of morphologic features showed that cribriform growth, blue-tinged mucin, macronucleoli, and collagenous micronodules were significantly more frequent in TMPRSS2-ERG fusion-positive prostate cancer biopsies than gene fusion-negative prostate cancer biopsies (P < or = 0.04). No significant association with Gleason score was detected. In addition, non-Caucasian patients were less likely to have positive fusion status (P = 0.02). CONCLUSIONS: This is the first prospective North American multicenter study to characterize TMPRSS2-ERG prostate cancer prevalence in a cohort of patients undergoing needle biopsy irrespective of whether or not they subsequently undergo prostatectomy. Our results show that this gene rearrangement is common among North American men who have prostate cancer on biopsy, is absent in benign prostate biopsy, and is associated with specific morphologic features. These findings indicate a need for prospective studies to evaluate the relationship of TMPRSS2-ERG rearrangement with clinical course of screening-detected prostate cancer in North American men, and a need for the development of noninvasive screening tests to detect TMPRSS2-ERG rearrangement.