Discovering cancer-associated transcripts by RNA sequencing

High-throughput sequencing of poly-adenylated RNA (RNA-Seq) in human cancers shows remarkable potential to identify uncharacterized aspects of tumor biology, including gene fusions with therapeutic significance and disease markers such as long non-coding RNA (lncRNA) species. However, the analysis of RNA-Seq data places unprecedented demands upon computational infrastructures and algorithms, requiring novel bioinformatics approaches. To meet these demands, we present two new open-source software packages - ChimeraScan and AssemblyLine - designed to detect gene fusion events and novel lncRNAs, respectively. RNA-Seq studies utilizing ChimeraScan led to discoveries of new families of recurrent gene fusions in breast cancers and solitary fibrous tumors. Further, ChimeraScan was one of the key components of the repertoire of computational tools utilized in data analysis for MI-ONCOSEQ, a clinical sequencing initiative to identify potentially informative and actionable mutations in cancer patients’ tumors. AssemblyLine, by contrast, reassembles RNA sequencing data into full-length transcripts ab initio. In head-to-head analyses AssemblyLine compared favorably to existing ab initio approaches and unveiled abundant novel lncRNAs, including antisense and intronic lncRNAs disregarded by previous studies. Moreover, we used AssemblyLine to define the prostate cancer transcriptome from a large patient cohort and discovered myriad lncRNAs, including 121 prostate cancer-associated transcripts (PCATs) that could potentially serve as novel disease markers. Functional studies of two PCATs - PCAT-1 and SChLAP1 - revealed cancer-promoting roles for these lncRNAs. PCAT1, a lncRNA expressed from chromosome 8q24, promotes cell proliferation and represses the tumor suppressor BRCA2. SChLAP1, located in a chromosome 2q31 ‘gene desert’, independently predicts poor patient outcomes, including metastasis and cancer-specific mortality. Mechanistically, SChLAP1 antagonizes the genome-wide localization and regulatory functions of the SWI/SNF chromatin-modifying complex. Collectively, this work demonstrates the utility of ChimeraScan and AssemblyLine as open-source bioinformatics tools. Our applications of ChimeraScan and AssemblyLine led to the discovery of new classes of recurrent and clinically informative gene fusions, and established a prominent role for lncRNAs in coordinating aggressive prostate cancer, respectively. We expect that the methods and findings described herein will establish a precedent for RNA-Seq-based studies in cancer biology and assist the research community at large in making similar discoveries.PHDBioinformaticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/120814/1/mkiyer_1.pd

One Eye is All You Need: Lightweight Ensembles for Gaze Estimation with Single Encoders

Gaze estimation has grown rapidly in accuracy in recent years. However, these models often fail to take advantage of different computer vision (CV) algorithms and techniques (such as small ResNet and Inception networks and ensemble models) that have been shown to improve results for other CV problems. Additionally, most current gaze estimation models require the use of either both eyes or an entire face, whereas real-world data may not always have both eyes in high resolution. Thus, we propose a gaze estimation model that implements the ResNet and Inception model architectures and makes predictions using only one eye image. Furthermore, we propose an ensemble calibration network that uses the predictions from several individual architectures for subject-specific predictions. With the use of lightweight architectures, we achieve high performance on the GazeCapture dataset with very low model parameter counts. When using two eyes as input, we achieve a prediction error of 1.591 cm on the test set without calibration and 1.439 cm with an ensemble calibration model. With just one eye as input, we still achieve an average prediction error of 2.312 cm on the test set without calibration and 1.951 cm with an ensemble calibration model. We also notice significantly lower errors on the right eye images in the test set, which could be important in the design of future gaze estimation-based tools

A growing field: The regulation of axonal regeneration by Wnt signaling

The canonical Wnt/β-catenin pathway is a highly conserved signaling cascade that plays critical roles during embryogenesis. Wnt ligands regulate axonal extension, growth cone guidance and synaptogenesis throughout the developing central nervous system (CNS). Recently, studies in mammalian and fish model systems have demonstrated that Wnt/β-catenin signaling also promotes axonal regeneration in the adult optic nerve and spinal cord after injury, raising the possibility that Wnt could be developed as a therapeutic strategy. In this review, we summarize experimental evidence that reveals novel roles for Wnt signaling in the injured CNS, and discuss possible mechanisms by which Wnt ligands could overcome molecular barriers inhibiting axonal growth to promote regeneration. A central challenge in the neuroscience field is developing therapeutic strategies that induce robust axonal regeneration. Although adult axons have the capacity to respond to axonal guidance molecules after injury, there are several major obstacles for axonal growth, including extensive neuronal death, glial scars at the injury site, and lack of axonal guidance signals. Research in rodents demonstrated that activation of Wnt/β-catenin signaling in retinal neurons and radial glia induced neuronal survival and axonal growth, but that activation within reactive glia at the injury site promoted proliferation and glial scar formation. Studies in zebrafish spinal cord injury models confirm an axonal regenerative role for Wnt/β-catenin signaling and identified the cell types responsible. Additionally, in vitro and in vivo studies demonstrated that Wnt induces axonal and neurite growth through transcription-dependent effects of its central mediator β-catenin, potentially by inducing regeneration-promoting genes. Canonical Wnt signaling may also function through transcription-independent interactions of β-catenin with cytoskeletal elements, which could stabilize growing axons and control growth cone movement. Therefore, these studies suggest that Wnt-induced pathways responsible for regulating axonal growth during embryogenesis could be repurposed to promote axonal growth after injury

A growing field: The regulation of axonal regeneration by Wnt signaling

The canonical Wnt/β-catenin pathway is a highly conserved signaling cascade that plays critical roles during embryogenesis. Wnt ligands regulate axonal extension, growth cone guidance and synaptogenesis throughout the developing central nervous system (CNS). Recently, studies in mammalian and fish model systems have demonstrated that Wnt/β-catenin signaling also promotes axonal regeneration in the adult optic nerve and spinal cord after injury, raising the possibility that Wnt could be developed as a therapeutic strategy. In this review, we summarize experimental evidence that reveals novel roles for Wnt signaling in the injured CNS, and discuss possible mechanisms by which Wnt ligands could overcome molecular barriers inhibiting axonal growth to promote regeneration. A central challenge in the neuroscience field is developing therapeutic strategies that induce robust axonal regeneration. Although adult axons have the capacity to respond to axonal guidance molecules after injury, there are several major obstacles for axonal growth, including extensive neuronal death, glial scars at the injury site, and lack of axonal guidance signals. Research in rodents demonstrated that activation of Wnt/β-catenin signaling in retinal neurons and radial glia induced neuronal survival and axonal growth, but that activation within reactive glia at the injury site promoted proliferation and glial scar formation. Studies in zebrafish spinal cord injury models confirm an axonal regenerative role for Wnt/β-catenin signaling and identified the cell types responsible. Additionally, in vitro and in vivo studies demonstrated that Wnt induces axonal and neurite growth through transcription-dependent effects of its central mediator β-catenin, potentially by inducing regeneration-promoting genes. Canonical Wnt signaling may also function through transcription-independent interactions of β-catenin with cytoskeletal elements, which could stabilize growing axons and control growth cone movement. Therefore, these studies suggest that Wnt-induced pathways responsible for regulating axonal growth during embryogenesis could be repurposed to promote axonal growth after injury

Assessment of Transport of Lipid Metabolites Within Trabecular Meshwork Cells

Lipids from trabecular meshwork (TM) cells are of particular interest to ophthalmological researchers as a therapeutic target for lowering intraocular pressure (IOP) in glaucomatous eyes. Fluorescence-based lipid transport assays (FBLTA) and immunocytochemistry (ICC) are dynamic fluorescence analysis techniques that allow for quantitative and qualitative comparisons, respectively, between multiple samples. Here we describe methods for FBLTA, ICC, and mass spectroscopy designed to measure the kinetics and localization of lipid metabolites within the trabecular meshwork

Correlation Between Altmetric Attention Scores and Citations for Articles Published in High-Impact Factor Ophthalmology Journals From 2018 to 2019

The Altmetric attention score (AAS) provides new information to gauge the impact of a research article not found through typical metrics, such as impact factor or citation counts. To explore the association between AAS and common impact markers among high-impact ophthalmology journals from 2018 to 2019. All articles published in the American Journal of Ophthalmology (AJO), JAMA Ophthalmology (JAMAO), and Ophthalmology (OPH) from January 1, 2018, to December 31, 2019, were collected for this cross-sectional study. Excluded articles were those missing Altmetric data at the time of data collection. The AAS and associated social media impact for each article were collected with the AAS calculator bookmarklet. Spearman rank correlation analyses and analysis of variance tests were conducted to assess differences in various metrics between AJO, JAMAO, and OPH. The study included articles published of all document types (article, conference paper, editorial, erratum, letter, note, retracted, review, and short survey) and access status (open access and not open access). The correlation between citation counts and Altmetric variables including AAS. A total of 2467 articles were published in the study period. There were 351 articles excluded owing to missing Altmetric data. Of the 2116 articles included in the analysis, 1039 (49.1%) were published in 2018, and 1077 (50.9%) were published in 2019; the mean number of citations was 8.8 (95% CI, 7.9-9.6) for AJO, 6.2 (95% CI, 5.3-7.1) for JAMAO, and 15.1 (95% CI, 13.3-17.0) for OPH. The mean AAS was 4.5 (95% CI, 3.3-5.6) for AJO (723 publications), 27.4 (95% CI, 22.1-32.8) for JAMAO (758 publications), and 15.1 (95% CI, 10.9-19.3) for OPH (635 publications). Citation rate was moderately correlated with AAS across the 3 journals (AJO, ρ = 0.39; P < .001; JAMAO, ρ = 0.41; P < .001; OPH, ρ = 0.40; P < .001), as well as minimally or moderately correlated with engagement or mention by Facebook posts (AJO, ρ = 0.38; P < .001; JAMAO, ρ = 0.24; P < .001; OPH, ρ = 0.20; P < .001), news outlet reporting (AJO, ρ = 0.12; P < .001; JAMAO, ρ = 0.38; P < .001; OPH, ρ = 0.19; P < .001), and Twitter posts (AJO, ρ = 0.40; P < .001; JAMAO, ρ = 0.38; P < .001; OPH, ρ = 0.42; P < .001). Results of this cross-sectional study suggest that citation rate has a moderate positive correlation with online and social media sharing of research in ophthalmology literature. Peer-reviewed journals may increase their reach and impact by sharing their literature through social media and online platforms

Longitudinal Assessment of Ocular Biomarkers in Individuals With Gulf War Illness Symptoms

Gulf War illness (GWI) is characterized by a constellation of symptoms, including, but not limited to, diarrhea, fatigue, and memory problems that affect Gulf War veterans. Currently, there are no objective biomarkers for GWI. Previous studies have identified differences in optical coherence tomography (OCT) metrics between individuals with GWI symptoms and those without. However, there are limited data on how these metrics change over time. Therefore, in this current study, we conducted a prospective case-control investigation to determine if OCT metrics show longitudinal changes in those affected by GWI.INTRODUCTIONGulf War illness (GWI) is characterized by a constellation of symptoms, including, but not limited to, diarrhea, fatigue, and memory problems that affect Gulf War veterans. Currently, there are no objective biomarkers for GWI. Previous studies have identified differences in optical coherence tomography (OCT) metrics between individuals with GWI symptoms and those without. However, there are limited data on how these metrics change over time. Therefore, in this current study, we conducted a prospective case-control investigation to determine if OCT metrics show longitudinal changes in those affected by GWI.We conducted a prospective study with 100 Gulf War-era veterans at the Miami Veterans Affairs Hospital from November 2018 to February 2022. Inclusion criteria required service during 1990-1991, with both deployed and nondeployed veterans included. Exclusions were based on factors like active infection, unmanaged psychotic disorders, significant head injuries, severe neurological disorders, and eye pathologies affecting OCT imaging. All participants provided informed consent, and the study was institutional review board-approved and conducted per the Declaration of Helsinki and Health Insurance Portability and Accountability Act guidelines. GWI symptoms were assessed using the modified Kansas questionnaire, categorizing veterans into groups based on GWI symptoms presence and deployment status. Data on demographics, comorbidities, medications, and medical and ocular diagnoses were collected. Participants underwent OCT imaging at 2 time points, 1 year apart, with macular, retinal nerve fiber layer, and ganglion cell layer-inner plexiform layer (GCL-IPL) thicknesses measured. Additionally, blood samples were collected and cytokine levels measured at baseline. Data analysis involved descriptive statistics, t-tests, and multivariable regression models. Statistical analyses were performed using SPSS 28.0.MATERIAL AND METHODSWe conducted a prospective study with 100 Gulf War-era veterans at the Miami Veterans Affairs Hospital from November 2018 to February 2022. Inclusion criteria required service during 1990-1991, with both deployed and nondeployed veterans included. Exclusions were based on factors like active infection, unmanaged psychotic disorders, significant head injuries, severe neurological disorders, and eye pathologies affecting OCT imaging. All participants provided informed consent, and the study was institutional review board-approved and conducted per the Declaration of Helsinki and Health Insurance Portability and Accountability Act guidelines. GWI symptoms were assessed using the modified Kansas questionnaire, categorizing veterans into groups based on GWI symptoms presence and deployment status. Data on demographics, comorbidities, medications, and medical and ocular diagnoses were collected. Participants underwent OCT imaging at 2 time points, 1 year apart, with macular, retinal nerve fiber layer, and ganglion cell layer-inner plexiform layer (GCL-IPL) thicknesses measured. Additionally, blood samples were collected and cytokine levels measured at baseline. Data analysis involved descriptive statistics, t-tests, and multivariable regression models. Statistical analyses were performed using SPSS 28.0.Logistic regression demonstrated that post-traumatic stress disorder (odds ratio [OR]: 8.18, 95% confidence interval [CI]: 2.327-28.851, P = .001) and a lower baseline macular thickness in the outer nasal segment (OR: 0.959, 95% CI: 0.924-0.994, P = .023) remained significantly associated with GWI symptoms. The model also found that individuals with GWI symptoms were more likely to have an increase in inner temporal GCL-IPL layer thickness over a 1-year period (OR: 1.187, 95% CI: 0.974-1.447, P = .089). When analysis was conducted only among those deployed, only baseline interleukin (IL) 1a (OR = 1.24, CI = 1.019-1.52, P = .03) and interleukin-10 (OR = 0.95, CI = 0.91-0.99, P = .02) levels remained significantly associated with GWI symptoms.RESULTSLogistic regression demonstrated that post-traumatic stress disorder (odds ratio [OR]: 8.18, 95% confidence interval [CI]: 2.327-28.851, P = .001) and a lower baseline macular thickness in the outer nasal segment (OR: 0.959, 95% CI: 0.924-0.994, P = .023) remained significantly associated with GWI symptoms. The model also found that individuals with GWI symptoms were more likely to have an increase in inner temporal GCL-IPL layer thickness over a 1-year period (OR: 1.187, 95% CI: 0.974-1.447, P = .089). When analysis was conducted only among those deployed, only baseline interleukin (IL) 1a (OR = 1.24, CI = 1.019-1.52, P = .03) and interleukin-10 (OR = 0.95, CI = 0.91-0.99, P = .02) levels remained significantly associated with GWI symptoms.Baseline OCT measures, especially a thinner outer nasal macula, were associated with GWI symptoms. Longitudinally, individuals with GWI symptoms had greater thickening of their inferotemporal GCL compared to those without symptoms. When the model was re-examined in deployed veterans, OCT measures (at baseline and longitudinally) no longer remained significantly related with GWI symptoms and instead baseline levels of plasma inflammatory cytokine markers, IL1a and IL10, were most closely related to symptoms. Our longitudinal study builds on our previous retrospective and cross-sectional work on identifying ocular biomarkers in GWI. Across the studies, macular thinning at baseline and inferotemporal GCL-IPL thickening have been noted between cases and controls. Some of these findings share correlates with OCT biomarkers identified in conditions such as Alzheimer's, Parkinson's and Multiple Sclerosis. This is significant as it may help contextualize future research and help us develop better models of GWI.CONCLUSIONSBaseline OCT measures, especially a thinner outer nasal macula, were associated with GWI symptoms. Longitudinally, individuals with GWI symptoms had greater thickening of their inferotemporal GCL compared to those without symptoms. When the model was re-examined in deployed veterans, OCT measures (at baseline and longitudinally) no longer remained significantly related with GWI symptoms and instead baseline levels of plasma inflammatory cytokine markers, IL1a and IL10, were most closely related to symptoms. Our longitudinal study builds on our previous retrospective and cross-sectional work on identifying ocular biomarkers in GWI. Across the studies, macular thinning at baseline and inferotemporal GCL-IPL thickening have been noted between cases and controls. Some of these findings share correlates with OCT biomarkers identified in conditions such as Alzheimer's, Parkinson's and Multiple Sclerosis. This is significant as it may help contextualize future research and help us develop better models of GWI