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Abstract De novo transcriptome assembly from billions of RNA-seq reads is very challenging due to alternative splicing and various levels of expression, which often leads to incorrect, mis-assembled transcripts. BayesDenovo addresses this problem by using both a read-guided strategy to accurately reconstruct splicing graphs from the RNA-seq data and a Bayesian strategy to estimate, from these graphs, the probability of transcript expression without penalizing poorly expressed transcripts. Simulation and cell line benchmark studies demonstrate that BayesDenovo is very effective in reducing false positives and achieves much higher accuracy than other assemblers, especially for alternatively spliced genes and for highly or poorly expressed transcripts. Moreover, BayesDenovo is more robust on multiple replicates by assembling a larger portion of common transcripts. When applied to breast cancer data, BayesDenovo identifies phenotype-specific transcripts associated with breast cancer recurrence.

Abstract Background ChIP-seq combines chromatin immunoprecipitation assays with sequencing and identifies genome-wide binding sites for DNA binding proteins. While many binding sites have strong ChIP-seq ‘peak’ observations and are well captured, there are still regions bound by proteins weakly, with a relatively low ChIP-seq signal enrichment. These weak binding sites, especially those at promoters and enhancers, are functionally important because they also regulate nearby gene expression. Yet, it remains a challenge to accurately identify weak binding sites in ChIP-seq data due to the ambiguity in differentiating these weak binding sites from the amplified background DNAs. Results ChIP-BIT2 ( http://sourceforge.net/projects/chipbitc/ ) is a software package for ChIP-seq peak detection. ChIP-BIT2 employs a mixture model integrating protein and control ChIP-seq data and predicts strong or weak protein binding sites at promoters, enhancers, or other genomic locations. For binding sites at gene promoters, ChIP-BIT2 simultaneously predicts their target genes. ChIP-BIT2 has been validated on benchmark regions and tested using large-scale ENCODE ChIP-seq data, demonstrating its high accuracy and wide applicability. Conclusion ChIP-BIT2 is an efficient ChIP-seq peak caller. It provides a better lens to examine weak binding sites and can refine or extend the existing binding site collection, providing additional regulatory regions for decoding the mechanism of gene expression regulation.

Abstract Exploring complex modularization of intracellular signal transduction pathways is critical to understanding aberrant cellular responses during disease development and drug treatment. IMPALA (Inferred Modularization of PAthway LAndscapes) integrates information from high throughput gene expression experiments and genome-scale knowledge databases to identify aberrant pathway modules, thereby providing a powerful sampling strategy to reconstruct and explore pathway landscapes. Here IMPALA identifies pathway modules associated with breast cancer recurrence and Tamoxifen resistance. Focusing on estrogen-receptor (ER) signaling, IMPALA identifies alternative pathways from gene expression data of Tamoxifen treated ER positive breast cancer patient samples. These pathways were often interconnected through cytoplasmic genes such as IRS1/2, JAK1, YWHAZ, CSNK2A1, MAPK1 and HSP90AA1 and significantly enriched with ErbB, MAPK, and JAK-STAT signaling components. Characterization of the pathway landscape revealed key modules associated with ER signaling and with cell cycle and apoptosis signaling. We validated IMPALA-identified pathway modules using data from four different breast cancer cell lines including sensitive and resistant models to Tamoxifen. Results showed that a majority of genes in cell cycle/apoptosis modules that were up-regulated in breast cancer patients with short survivals (

ARID1A, which is often mutated in human endometrial cancer, is a component of the SWI/SNF chromatin remodelling complex. Here, the authors show that Arid1a mutations in the mouse endometrium and primary human endometrial epithelial cells cause widespread reprogramming of gene transcription and result in a loss of response to TGFβ.

Transcription factors (TFs) often function as a module including both master factors and mediators binding at cis-regulatory regions to modulate nearby gene transcription. ChIP-seq profiling of multiple TFs makes it feasible to infer functional TF modules. However, when inferring TF modules based on co-localization of ChIP-seq peaks, often many weak binding events are missed, especially for mediators, resulting in incomplete identification of modules. To address this problem, we develop a ChIP-seq data-driven Gibbs Sampler to infer Modules (ChIP-GSM) using a Bayesian framework that integrates ChIP-seq profiles of multiple TFs. ChIP-GSM samples read counts of module TFs iteratively to estimate the binding potential of a module to each region and, across all regions, estimates the module abundance. Using inferred module-region probabilistic bindings as feature units, ChIP-GSM then employs logistic regression to predict active regulatory elements. Validation of ChIP-GSM predicted regulatory regions on multiple independent datasets sharing the same context confirms the advantage of using TF modules for predicting regulatory activity. In a case study of K562 cells, we demonstrate that the ChIP-GSM inferred modules form as groups, activate gene expression at different time points, and mediate diverse functional cellular processes. Hence, ChIP-GSM infers biologically meaningful TF modules and improves the prediction accuracy of regulatory region activities.

Background: Spleen tyrosine kinase (SYK) is frequently upregulated in recurrent ovarian carcinomas, for which effective therapy is urgently needed. SYK phosphorylates several substrates, but their translational implications remain unclear. Here, we show that SYK interacts with EGFR and ERBB2, and directly enhances their phosphorylation. Methods: We used immunohistochemistry and immunoblotting to assess SYK and EGFR phosphorylation in ovarian serous carcinomas. Association with survival was determined by Kaplan-Meier analysis and the log-rank test. To study its role in EGFR signaling, SYK activity was modulated using a small molecule inhibitor, a syngeneic knockout, and an active kinase inducible system. We applied RNA-seq and phosphoproteomic mass spectrometry to investigate the SYK-regulated EGF-induced transcriptome and downstream substrates. Findings: Induced expression of constitutively active SYK130E reduced cellular response to EGFR/ERBB2 inhibitor, lapatinib. Expression of EGFRWT, but not SYK non-phosphorylatable EGFR3F mutant, resulted in paclitaxel resistance, a phenotype characteristic to SYK active ovarian cancers. In tumor xenografts, SYK inhibitor reduces phosphorylation of EGFR substrates. Compared to SYKWT cells, SYKKO cells have an attenuated EGFR/ERBB2-transcriptional activity and responsiveness to EGF-induced transcription. In ovarian cancer tissues, pSYK (Y525/526) levels showed a positive correlation with pEGFR (Y1187). Intense immunoreactivity of pSYK (Y525/526) correlated with poor overall survival in ovarian cancer patients. Interpretation: These findings indicate that SYK activity positively modulates the EGFR pathway, providing a biological foundation for co-targeting SYK and EGFR. Fund: Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, NIH/NCI, Ovarian Cancer Research Foundation Alliance, HERA Women's Cancer Foundation and Roseman Foundation. Funders had no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript and eventually in the decision to submit the manuscript.

Abstract Background Maternal and paternal high-fat (HF) diet intake before and/or during pregnancy increases mammary cancer risk in several preclinical models. We studied if maternal consumption of a HF diet that began at a time when the fetal primordial germ cells travel to the genital ridge and start differentiating into germ cells would result in a transgenerational inheritance of increased mammary cancer risk. Methods Pregnant C57BL/6NTac mouse dams were fed either a control AIN93G or isocaloric HF diet composed of corn oil high in n-6 polyunsaturated fatty acids between gestational days 10 and 20. Offspring in subsequent F1–F3 generations were fed only the control diet. Results Mammary tumor incidence induced by 7,12-dimethylbenz[a]anthracene was significantly higher in F1 (p

One of the important tasks in cancer research is to identify biomarkers and build classification models for clinical outcome prediction. In this paper, we develop a CyNetSVM software package, implemented in Java and integrated with Cytoscape as an app, to identify network biomarkers using network-constrained support vector machines (NetSVM). The Cytoscape app of NetSVM is specifically designed to improve the usability of NetSVM with the following enhancements: (1) user-friendly graphical user interface (GUI), (2) computationally efficient core program and (3) convenient network visualization capability. The CyNetSVM app has been used to analyze breast cancer data to identify network genes associated with breast cancer recurrence. The biological function of these network genes is enriched in signaling pathways associated with breast cancer progression, showing the effectiveness of CyNetSVM for cancer biomarker identification. The CyNetSVM package is available at Cytoscape App Store and http://sourceforge.net/projects/netsvmjava; a sample data set is also provided at sourceforge.net.

Precise regulation of the cell cycle is crucial to the growth and development of all organisms. Understanding the regulatory mechanism of the cell cycle is crucial to unraveling many complicated diseases, most notably cancer. Multiple sources of biological data are available to study the dynamic interactions among many genes that are related to the cancer cell cycle. Integrating these informative and complementary data sources can help to infer a mutually consistent gene transcriptional regulatory network with strong similarity to the underlying gene regulatory relationships in cancer cells.We propose an integrative framework that infers gene regulatory modules from the cell cycle of cancer cells by incorporating multiple sources of biological data, including gene expression profiles, gene ontology, and molecular interaction. Among 846 human genes with putative roles in cell cycle regulation, we identified 46 transcription factors and 39 gene ontology groups. We reconstructed regulatory modules to infer the underlying regulatory relationships. Four regulatory network motifs were identified from the interaction network. The relationship between each transcription factor and predicted target gene groups was examined by training a recurrent neural network whose topology mimics the network motif(s) to which the transcription factor was assigned. Inferred network motifs related to eight well-known cell cycle genes were confirmed by gene set enrichment analysis, binding site enrichment analysis, and comparison with previously published experimental results.We established a robust method that can accurately infer underlying relationships between a given transcription factor and its downstream target genes by integrating different layers of biological data. Our method could also be beneficial to biologists for predicting the components of regulatory modules in which any candidate gene is involved. Such predictions can then be used to design a more streamlined experimental approach for biological validation. Understanding the dynamics of these modules will shed light on the processes that occur in cancer cells resulting from errors in cell cycle regulation.

In recent years, there has been an increasing interest in studying the propagation of polarized light in biological cells and tissues. This paper presents a novel approach to cell or tissue imaging using a full Stokes imaging system with advanced polarization image analysis algorithms for improved diagnostics. The key component of the Stokes imaging system is the electrically tunable retarder, enabling high-speed operation of the system to acquire four intensity images sequentially. From the acquired intensity images, four Stokes vector images can be computed to obtain complete polarization information. Polarization image analysis algorithms are then developed to analyze Stokes polarization images for cell or tissue classification. Specifically, wavelet transforms are first applied to the Stokes components for initial feature analysis and extraction. Artificial neural networks (ANNs) are then used to extract diagnostic features for improved classification and prediction. In this study, phantom experiments have been conducted using a prototyped Stokes polarization imaging device. In particular, several types of phantoms, consisting of polystyrene latex spheres in various diameters, were prepared to simulate different conditions of epidermal layer of skin. The experimental results from phantom studies and a plant cell study show that the classification performance using Stokes images is significantly improved over that using the intensity image only.

Image-based change quantitation has been recognized as a promising tool for accurate assessment of tumor's early response to chemoprevention in cancer research. For example, various changes on breast density and vascularity in glandular tissue are the indicators of early response to treatment. Accurate extraction of glandular tissue from pre- and postcontrast magnetic resonance (MR) images requires a nonrigid registration of sequential MR images embedded with local deformations. This paper reports a newly developed registration method that aligns MR breast images using finite-element deformable sheet-curve models. Specifically, deformable curves are constructed to match the boundaries dynamically, while a deformable sheet of thin-plate splines is designed to model complex local deformations. The experimental results on both digital phantoms and real MR breast images using the new method have been compared to point-based thin-plate-spline (TPS) approach, and have demonstrated a significant and robust improvement in both boundary alignment and local deformation recovery.

Functional medical imaging promises powerful tools for the visualization and elucidation of important disease-causing biological processes in living tissue. Recent research aims to dissect the distribution or expression of multiple biomarkers associated with disease progression or response, where the signals often represent a composite of more than one distinct source independent of spatial resolution. Formulating the task as a blind source separation or composite signal factorization problem, we report here a statistically principled method for modeling and reconstruction of mixed functional or molecular patterns. The computational algorithm is based on a latent variable model whose parameters are estimated using clustered component analysis. We demonstrate the principle and performance of the approaches on the breast cancer data sets acquired by dynamic contrast-enhanced magnetic resonance imaging.

Accurate pig body weight (BW) measurement is essential for producers as it is related to pig growth, health, and marketing, yet conventional manual weighing methods are time-consuming and may cause potential stress to the animals. Although there is a growing trend towards the adoption of three-dimensional cameras coupled with computer vision techniques for pig BW estimation, their validation using industry-scale data are still limited. Among the prevailing methodologies, semantic segmentation and supervised pre-training regression are prominent models currently used. Therefore, the objectives of this study were: 1) to estimate pig BW from repeatedly measured video data obtained from a commercial setting, 2) to compare the performance of the two image analysis methods: thresholding segmentation and deep regression approaches, and 3) to evaluate the predictive ability of BW estimation models. An Intel RealSense D435 camera was installed in the commercial farm to collect top-view videos of 540 pigs biweekly at five different time points over three months. At the same time, manually measured BW records were collected using a digital weighing system. We used an automated video conversion pipeline and fine-tuned YOLOv8 to pre-process the raw depth videos. Subsequently, we acquired a total of 151,756 depth images and depth map files. Adaptive thresholding was applied to segment the pig body from the background. Four image-derived biometric features, including dorsal length, abdominal width, height, and volume, were estimated from the segmented images and fitted using ordinary least squares and random forest models. We applied transfer learning by initializing the weights of five deep learning models, including ResNet50, Xception, EfficientNetV2S, ConvNeXtBase, and Vision Transformer, with pretrained weights from ImageNet. We then fine-tuned these models on the pig depth images. The last layer of each model was adapted to linear regression, enabling direct estimation of BW for each image without the need for additional image pre-processing steps. We employed random repeated subsampling crossvalidation, dividing 80% of the pigs for training and 20% for testing, to evaluate prediction performance at each time point. The best prediction coefficients of determination and mean absolute percentage error for each time point were 0.76, 0.86, 0.90, 0.83, 0.90, and 4.57%, 3.76%, 3.01%, 3.41%, 4.84%, respectively. On average, the Xception model resulted in the best prediction coefficient of determination and mean absolute percentage error of 0.90 and 3.01%. Our results suggest that deep learning-based supervised learning models improve the prediction performance of pig BW from industry-scale depth video data. [ABSTRACT FROM AUTHOR]