Structure learning for gene regulatory networks.

Inference of biological network structures is often performed on high-dimensional data, yet is hindered by the limited sample size of high throughput "omics" data typically available. To overcome this challenge, often referred to as the "small n, large p problem," we exploit known organizing principles of biological networks that are sparse, modular, and likely share a large portion of their underlying architecture. We present SHINE-Structure Learning for Hierarchical Networks-a framework for defining data-driven structural constraints and incorporating a shared learning paradigm for efficiently learning multiple Markov networks from high-dimensional data at large p/n ratios not previously feasible. We evaluated SHINE on Pan-Cancer data comprising 23 tumor types, and found that learned tumor-specific networks exhibit expected graph properties of real biological networks, recapture previously validated interactions, and recapitulate findings in literature. Application of SHINE to the analysis of subtype-specific breast cancer networks identified key genes and biological processes for tumor maintenance and survival as well as potential therapeutic targets for modulating known breast cancer disease genes.

Photoplethysmography-new applications for an old technology: a sleep technology review.

Education is integral to the American Academy of Sleep Medicine (AASM) mission. The AASM Emerging Technology Committee identified an important and evolving piece of technology that is present in many of the consumer and clinical technologies that we review on the AASM #SleepTechnology (https://aasm.org/consumer-clinical-sleep-technology/) resource-photoplethysmography. As more patients with sleep tracking devices ask clinicians to view their data, it is important for sleep providers to have a general understanding of the technology, its sensors, how it works, targeted users, evidence for the claimed uses, and its strengths and weaknesses. The focus in this review is photoplethysmography-a sensor type used in the familiar pulse oximeter that is being developed for additional utilities and data outputs in both consumer and clinical sleep technologies. CITATION: Ryals S, Chang A, Schutte-Rodin S, et al. Photoplethysmography-new applications for an old technology: a sleep technology review. J Clin Sleep Med. 2023;19(1):189-195.

Inactivation of LATS1/2 drives luminal-basal plasticity to initiate basal-like mammary carcinomas.

Basal-like breast cancers, an aggressive breast cancer subtype that has poor treatment options, are thought to arise from luminal mammary epithelial cells that undergo basal plasticity through poorly understood mechanisms. Using genetic mouse models and ex vivo primary organoid cultures, we show that conditional co-deletion of the LATS1 and LATS2 kinases, key effectors of Hippo pathway signaling, in mature mammary luminal epithelial cells promotes the development of Krt14 and Sox9-expressing basal-like carcinomas that metastasize over time. Genetic co-deletion experiments revealed that phenotypes resulting from the loss of LATS1/2 activity are dependent on the transcriptional regulators YAP/TAZ. Gene expression analyses of LATS1/2-deleted mammary epithelial cells notably revealed a transcriptional program that associates with human basal-like breast cancers. Our study demonstrates in vivo roles for the LATS1/2 kinases in mammary epithelial homeostasis and luminal-basal fate control and implicates signaling networks induced upon the loss of LATS1/2 activity in the development of basal-like breast cancer.

Solvent selection for polymers enabled by generalized chemical fingerprinting and machine learning.

We present machine learning models trained on experimental data to predict room-temperature solubility for any polymer-solvent pair. The new models are a significant advancement over past data-driven work, in terms of protocol, validity, and versatility. A generalizable fingerprinting method is used for the polymers and solvents, making it possible, in principle, to handle any polymer-solvent combination. Our data-driven approach achieves high accuracy when either both the polymer and solvent or just the polymer has been seen during the training phase. Model performance is modest though when a solvent (in a newly queried polymer-solvent pair) is not part of the training set. This is likely because the number of unique solvents in our data set is small (much smaller than the number of polymers). Nevertheless, as the data set increases in size, especially as the solvent set becomes more diverse, the overall predictive performance is expected to improve.

The Transulnar Approach to Coronary Angiography and Intervention: Assessing the Anatomy of the Ulnar Artery Using Angiography.

BACKGROUND: The transulnar approach (TUA) has been proposed as a safe alternative to the more established transradial approach (TRA) for cardiac catheterization. However, no study has assessed the anatomy and variability of the ulnar artery using angiography. METHODS: A retrospective analysis of patients who underwent transradial cardiac catheterization during routine clinical care was conducted. Both quantitative and qualitative measurements of artery diameter were collected. RESULTS: Among 700 consecutive patients, mean distal ulnar artery diameter (UAD) was larger in men (3.2 ± 0.9 mm) compared with women (2.7 ± 0.7 mm; P<.001). UAD was larger than radial artery diameter (RAD) at all measured sites (distal ulnar, 3.0 ± 0.8 mm; distal radial, 2.9 ± 0.7 mm; P=.046). Compared with the radial artery, the ulnar artery had more atresia (4.3% ulnar vs 0% radial; P<.001), fewer loops (0.6% ulnar vs 2.4% radial; P<.01), and less spasm (2.7% ulnar vs 23.4% radial; P<.001). UAD had more variability (distal variance, 0.68) as compared with the RAD (distal variance, 0.53; P<.001). CONCLUSION: We found that the ulnar artery has a larger diameter, fewer loops, and less spasm, but more variance than the radial artery. Additionally, males have larger ulnar arteries than women. These findings have implications on the application of TUA either as an alternative to TRA or as the primary point of access.

Left Ventricular Pressure Ratio Predicts In-Hospital Outcomes in Hospitalized Heart Failure With Reduced Ejection Fraction.

BACKGROUND: Given the risk of hemodynamic compromise in heart failure with reduced ejection fraction (HFrEF) patients undergoing left heart catheterization (LHC), there is a need for a simple parameter that can predict clinical outcomes. We hypothesize that left ventricular pressure ratio (LVPR), calculated as left ventricle systolic/left ventricle end-diastolic pressure, is a strong predictor of hemodynamic collapse in these patients. METHODS: Retrospective analysis of consecutive hospitalized HFrEF patients undergoing combined LHC and right heart catheterization (RHC) at a single institution from 2015-2017 was performed. LVPR was compared with standard RHC hemodynamic variables. The primary outcome was in-hospital escalation of therapy, defined as ≥40 mm Hg drop in systolic blood pressure (SBP), SBP ≤90 mm Hg for ≥15 minutes, start or escalation of vasoactive medications, cardiopulmonary resuscitation, or in-hospital death. Receiver-operating characteristic (ROC) analysis and Kaplan-Meier survival analysis were performed for prediction of the primary outcome. RESULTS: A total of 176 patients were included in this study. ROC analysis determined an optimal cut-off value of ≤3.96, which correlated with an area under the curve (AUC) of 0.65 (sensitivity, 45.9%; specificity, 83.2%; correctly classified, 64.9%). AUC was similar to other variables obtained using RHC. In-hospital survival free of escalation of therapy was lower in the low LVPR group vs the high LVPR group (0% vs 33%, respectively; P<.01). CONCLUSION: LVPR is an easily measured index obtained during LHC that can risk stratify hospitalized patients with HFrEF at the time of LHC.

Aberrant epithelial polarity cues drive the development of precancerous airway lesions.

Molecular events that drive the development of precancerous lesions in the bronchial epithelium, which are precursors of lung squamous cell carcinoma (LUSC), are poorly understood. We demonstrate that disruption of epithelial cellular polarity, via the conditional deletion of the apical determinant Crumbs3 (Crb3), initiates and sustains precancerous airway pathology. The loss of Crb3 in adult luminal airway epithelium promotes the uncontrolled activation of the transcriptional regulators YAP and TAZ, which stimulate intrinsic signals that promote epithelial cell plasticity and paracrine signals that induce basal-like cell growth. We show that aberrant polarity and YAP/TAZ-regulated gene expression associates with human bronchial precancer pathology and disease progression. Analyses of YAP/TAZ-regulated genes further identified the ERBB receptor ligand Neuregulin-1 (NRG1) as a key transcriptional target and therapeutic targeting of ERBB receptors as a means of preventing and treating precancerous cell growth. Our observations offer important molecular insight into the etiology of LUSC and provides directions for potential interception strategies of lung cancer.

The Tumor Suppressor CYLD Inhibits Mammary Epithelial to Mesenchymal Transition by the Coordinated Inhibition of YAP/TAZ and TGF Signaling.

Downregulation of the cylindromatosis (CYLD) tumor suppressor has been associated with breast cancer development and progression. Here, we report a critical role for CYLD in maintaining the phenotype of mammary epithelial cells in vitro and in vivo. CYLD downregulation or inactivation induced an epithelial to mesenchymal transition of mammary epithelial cells that was dependent on the concomitant activation of the transcription factors Yes-associated protein (YAP)/transcriptional coactivator with PDZ-binding motif (TAZ) and transforming growth factor beta (TGF)signaling. CYLD inactivation enhanced the nuclear localization of YAP/TAZ and the phosphorylation of Small Mothers Against Decapentaplegic (SMAD)2/3 proteins in confluent cell culture conditions. Consistent with these findings were the hyperplastic alterations of CYLD-deficient mouse mammary epithelia, which were associated with enhanced nuclear expression of the YAP/TAZ transcription factors. Furthermore, in human breast cancer samples, downregulation of CYLD expression correlates with enhanced YAP/TAZ-regulated target gene expression. Our results identify CYLD as a critical regulator of a signaling node that prevents the coordinated activation of YAP/TAZ and the TGF pathway in mammary epithelial cells, in order to maintain their phenotypic identity and homeostasis. Consequently, they provide a novel conceptual framework that supports and explains a causal implication of deficient CYLD expression in aggressive human breast cancers.

Use of Prospective Radiobrachial Angiography in Transradial Cardiac Catheterization and Intervention.

OBJECTIVES: This study examined the utility of prospective radiobrachial angiography (pRBA) in transradial coronary angiography and intervention as a method for reducing procedural complications. BACKGROUND: A growing body of evidence has supported the transradial approach (TRA) as superior to the transfemoral approach (TFA) due to advantages such as reduced bleeding and improved outcomes in high-risk patients. However, TRA has a higher failure rate than TFA, and has seen slow rates of adoption among United States operators. METHODS: This was a retrospective, single center, case-control analysis of coronary angiography procedures, performed by two experienced operators at the University of Chicago Medical Center between October 28, 2015 and July 21, 2017. Operator 1 began using pRBA during the study, whereas Operator 2 used pRBA in all TRA procedures. There were 567 patients stratified into three groups based on operator and pRBA use. Comparisons of procedural outcomes for Operator 1 before and after adoption of pRBA, and of outcomes between Operator 1 and Operator 2 were made. RESULTS: Use of pRBA was associated with reduced overall procedural complication rates (2.5% versus 10.4%, p = 0.004), driven primarily by reflexive radiobrachial angiography (rRBA) after resistance or pain was encountered (8.6% versus 0.0%, p = 0.0001) for Operator 1. A slight reduction in contrast associated with pRBA for Operator 1 was noted, but no difference in procedural time, radiation dose, or additional equipment used across groups was found. No significant difference in adverse procedural outcomes between the pRBA groups of Operator 1 and Operator 2 were observed. In patients with radiobrachial variants in anatomy, use of pRBA was associated with shorter times to cross anatomic lesions, shorter procedure times, reduced use of extra catheters, and less perforations and crossovers compared to patients requiring rRBA. Lack of pRBA was associated with higher procedural complications (hazard ratio 1.08, 95% CI, 1.03-1.13, p = 0.004). CONCLUSION: pRBA may be a useful tool for mitigating procedural complications, reducing time needed to cross difficult radiobrachial anatomy, and reducing the need to utilize additional equipment in TRA. pRBA may offer operators a tool to improve outcomes and increase adoption of this approach.

TAZ Forces Lateral Inhibition.

New mechanisms by which cells communicate to specify cell fate during animal development are continuously being discovered. In a recently published article in Cell, Xia et al. (2019) identify the transcriptional regulator TAZ as a novel mediator of lateral inhibition in zebrafish oogenesis that directs cell fate through mechanical cues.

CaDrA: A Computational Framework for Performing Candidate Driver Analyses Using Genomic Features.

The identification of genetic alteration combinations as drivers of a given phenotypic outcome, such as drug sensitivity, gene or protein expression, and pathway activity, is a challenging task that is essential to gaining new biological insights and to discovering therapeutic targets. Existing methods designed to predict complementary drivers of such outcomes lack analytical flexibility, including the support for joint analyses of multiple genomic alteration types, such as somatic mutations and copy number alterations, multiple scoring functions, and rigorous significance and reproducibility testing procedures. To address these limitations, we developed Candidate Driver Analysis or CaDrA, an integrative framework that implements a step-wise heuristic search approach to identify functionally relevant subsets of genomic features that, together, are maximally associated with a specific outcome of interest. We show CaDrA's overall high sensitivity and specificity for typically sized multi-omic datasets using simulated data, and demonstrate CaDrA's ability to identify known mutations linked with sensitivity of cancer cells to drug treatment using data from the Cancer Cell Line Encyclopedia (CCLE). We further apply CaDrA to identify novel regulators of oncogenic activity mediated by Hippo signaling pathway effectors YAP and TAZ in primary breast cancer tumors using data from The Cancer Genome Atlas (TCGA), which we functionally validate in vitro. Finally, we use pan-cancer TCGA protein expression data to show the high reproducibility of CaDrA's search procedure. Collectively, this work demonstrates the utility of our framework for supporting the fast querying of large, publicly available multi-omics datasets, including but not limited to TCGA and CCLE, for potential drivers of a given target profile of interest.

Clinical determinants of radial artery caliber assessed at the time of transradial cardiac catheterization using routine prospective radiobrachial angiography.

BACKGROUND: Transradial coronary angiography/intervention (TRA/TRI) is associated with reduced rates of bleeding, vascular complications, and major adverse cardiovascular events as compared to the transfemoral approach, but remains underutilized in the United States (U.S.). Small radial caliber is often cited as a technical impediment, however radial artery diameter (RAD) has not yet been systematically studied in the U.S. population using routine, prospective radiobrachial angiography. METHODS: Consecutive patients (pts) with radiobrachial angiography acquired during TRA/TRI from September 2015 to August 2016 were retrospectively analyzed. Quantitative angiography (QA) was performed on digital subtraction angiograms. RAD measurements at distal (dRAD), mid (mRAD), and proximal (pRAD) segments, as well as minimum (minRAD) and maximum (maxRAD) diameters were indexed to radial arterial sheath size and tabulated. RAD measurements were adjudicated by 2 expert operators. Descriptive statistics and regression analyses were performed using STATA (College Station, TX). RESULTS: Of 175 radiobrachial angiograms, 2 were excluded due to uninterpretable QA. Woman had smaller RAD versus men: pRAD (3.11 vs 3.33 mm, p = 0.021), minRAD (2.36 vs 2.59 mm, p = 0.006), and maxRAD (3.32 vs 3.53 mm, p = 0.0195). Univariate analysis showed correlation between minRAD and gender (p = 0.012), age (p = 0.019), and weight (p = 0.008). However, after multivariate analysis, only gender was associated with minRAD (p = 0.05). CONCLUSION: This is the first study to describe the clinical determinants of RAD using prospective post-vasodilator, radiobrachial angiography in a U.S. POPULATION: Women had significantly smaller RAD across proximal, minimum, and maximum segments. Sex was the only multivariate predictor of minRAD.

Pharmacogenetic Manipulation of the Nucleus Accumbens Alters Binge-Like Alcohol Drinking in Mice.

BACKGROUND: Chronic alcohol intake leads to long-lasting changes in reward- and stress-related neuronal circuitry. The nucleus accumbens (NAc) is an integral component of this circuitry. Here, we investigate the effects of DREADDs (Designer Receptors Exclusively Activated by Designer Drugs) on neuronal activity in the NAc and binge-like drinking. METHODS: C57BL/6J mice were stereotaxically injected with AAV2 hSyn-HA hM3Dq, -hM4Di, or -eGFP bilaterally into NAc [core + shell, core or shell]. We measured clozapine-n-oxide (CNO)-induced changes in NAc activity and assessed binge-like ethanol (EtOH) or tastant/fluid intake in a limited access Drinking in the Dark (DID) schedule. RESULTS: We found that CNO increased NAc firing in hM3Dq positive cells and decreased firing in hM4Di cells, confirming the efficacy of these channels to alter neuronal activity both spatially and temporally. Increasing NAc core + shell activity decreased binge-like drinking without altering intake of other tastants. Increasing activity specifically in the NAc core reduced binge-like drinking, and decreasing activity in the NAc core increased drinking. Manipulation of NAc shell activity did not alter DID. Thus, we find that increasing activity in the entire NAc, or just the NAc core is sufficient to decrease binge drinking. CONCLUSIONS: We conclude that the reduction in EtOH drinking is not due to general malaise, altered perception of taste, or reduced calorie-seeking. Furthermore, we provide the first evidence for bidirectional control of NAc core and binge-like drinking. These findings could have promising implications for treatment.

The emerging role and targetability of the TCA cycle in cancer metabolism.

The tricarboxylic acid (TCA) cycle is a central route for oxidative phosphorylation in cells, and fulfills their bioenergetic, biosynthetic, and redox balance requirements. Despite early dogma that cancer cells bypass the TCA cycle and primarily utilize aerobic glycolysis, emerging evidence demonstrates that certain cancer cells, especially those with deregulated oncogene and tumor suppressor expression, rely heavily on the TCA cycle for energy production and macromolecule synthesis. As the field progresses, the importance of aberrant TCA cycle function in tumorigenesis and the potentials of applying small molecule inhibitors to perturb the enhanced cycle function for cancer treatment start to evolve. In this review, we summarize current knowledge about the fuels feeding the cycle, effects of oncogenes and tumor suppressors on fuel and cycle usage, common genetic alterations and deregulation of cycle enzymes, and potential therapeutic opportunities for targeting the TCA cycle in cancer cells. With the application of advanced technology and in vivo model organism studies, it is our hope that studies of this previously overlooked biochemical hub will provide fresh insights into cancer metabolism and tumorigenesis, subsequently revealing vulnerabilities for therapeutic interventions in various cancer types.

NPAS2 Regulation of Anxiety-Like Behavior and GABAA Receptors.

Abnormal circadian rhythms and circadian genes are strongly associated with several psychiatric disorders. Neuronal PAS Domain Protein 2 (NPAS2) is a core component of the molecular clock that acts as a transcription factor and is highly expressed in reward- and stress-related brain regions such as the striatum. However, the mechanism by which NPAS2 is involved in mood-related behaviors is still unclear. We measured anxiety-like behaviors in mice with a global null mutation in Npas2 (Npas2 null mutant mice) and found that Npas2 null mutant mice exhibit less anxiety-like behavior than their wild-type (WT) littermates (in elevated plus maze, light/dark box and open field assay). We assessed the effects of acute or chronic stress on striatal Npas2 expression, and found that both stressors increased levels of Npas2. Moreover, knockdown of Npas2 in the ventral striatum resulted in a similar reduction of anxiety-like behaviors as seen in the Npas2 null mutant mouse. Additionally, we identified Gabra genes as transcriptional targets of NPAS2, found that Npas2 null mutant mice exhibit reduced sensitivity to the GABAa positive allosteric modulator, diazepam and that knockdown of Npas2 reduced Gabra1 expression and response to diazepam in the ventral striatum. These results: (1) implicate Npas2 in the response to stress and the development of anxiety; and (2) provide functional evidence for the regulation of GABAergic neurotransmission by NPAS2 in the ventral striatum.

Transcriptional-mediated effects of radiation on the expression of immune susceptibility markers in melanoma.

BACKGROUND AND PURPOSE: We recently reported a time-sensitive, cooperative, anti-tumor effect elicited by radiation (RT) and intra-tumoral-immunocytokine injection in vivo. We hypothesized that RT triggers transcriptional-mediated changes in tumor expression of immune susceptibility markers at delayed time points, which may explain these previously observed time-dependent effects. MATERIALS AND METHODS: We examined the time course of changes in expression of immune susceptibility markers following in vitro or in vivo RT in B78 murine melanoma and A375 human melanoma using flow cytometry, immunoblotting, and qPCR. RESULTS: Flow cytometry and immunoblot revealed time-dependent increases in expression of death receptors and T cell co-stimulatory/co-inhibitory ligands following RT in murine and human melanoma. Using high-throughput qPCR, we observed comparable time courses of RT-induced transcriptional upregulation for multiple immune susceptibility markers. We confirmed analogous changes in B78 tumors irradiated in vivo. We observed upregulated expression of DNA damage response markers days prior to changes in immune markers, whereas phosphorylation of the STAT1 transcription factor occurred concurrently with changes following RT. CONCLUSION: This study highlights time-dependent, transcription-mediated changes in tumor immune susceptibility marker expression following RT. These findings may help in the design of strategies to optimize sequencing of RT and immunotherapy in translational and clinical studies.

Effect of paliperidone and risperidone on extracellular glutamate in the prefrontal cortex of rats exposed to prenatal immune activation or MK-801.

The NMDA glutamate hypofunction model of schizophrenia is based in part upon acute effects of NMDA receptor blockade in humans and rodents. Several laboratories have reported glutamate system abnormalities following prenatal exposure to immune challenge, a known environmental risk factor for schizophrenia. Here we report indices of NMDA glutamate receptor hypofunction following prenatal immune activation, as well as the effects of treatment during periadolescence with the atypical antipsychotic medications risperidone and paliperidone. Pregnant Sprague-Dawley rats were injected with polyinosinic:polycytidylic acid (poly I:C) or saline on gestational day 14. Male offspring were treated orally via drinking water with vehicle, risperidone (0.01mg/kg/day), or paliperidone (0.01mg/kg/day) between postnatal days 35 and 56 (periadolescence) and extracellular glutamate levels in the prefrontal cortex were determined by microdialysis at PD 56. Consistent with decreased NMDA receptor function, MK-801-induced increases in extracellular glutamate concentration were markedly blunted following prenatal immune activation. Further suggesting NMDA receptor hypofunction, prefrontal cortex basal extracellular glutamate was significantly elevated (p<0.05) in offspring of poly I:C treated dams. Pretreatment with low dose paliperidone or risperidone (0.01mg/kg/day postnatal days 35-56) normalized prefrontal cortical basal extracellular glutamate (p<0.05 vs. poly I:C vehicle-treatment). Pretreatment with paliperidone and risperidone also prevented the acute MK-801-induced increase in extracellular glutamate. These observations demonstrate decreased NMDA receptor function and elevated extracellular glutamate, two key features of the NMDA glutamate receptor hypofunction model of schizophrenia, during periadolescence following prenatal immune activation. Treatment with the atypical antipsychotic medications paliperidone and risperidone normalized basal extracellular glutamate. Demonstration of glutamatergic abnormalities consistent with the NMDA glutamate receptor hypofunction model of schizophrenia as an early developmental consequence of prenatal immune action provides a model to identify novel early interventions targeting glutamatergic systems which play an important role in both positive and negative symptoms of schizophrenia.

Individual differences in maternal response to immune challenge predict offspring behavior: contribution of environmental factors.

Maternal infection during pregnancy elevates risk for schizophrenia and related disorders in offspring. Converging evidence suggests the maternal inflammatory response mediates the interaction between maternal infection, altered brain development, and behavioral outcome. The extent to which individual differences in the maternal response to immune challenge influence the development of these abnormalities is unknown. The present study investigated the impact of individual differences in maternal response to the viral mimic polyinosinic:polycytidylic acid (poly I:C) on offspring behavior. We observed significant variability in body weight alterations of pregnant rats induced by administration of poly I:C on gestational day 14. Furthermore, the presence or absence of maternal weight loss predicted MK-801 and amphetamine stimulated locomotor abnormalities in offspring. MK-801 stimulated locomotion was altered in offspring of all poly I:C treated dams; however, the presence or absence of maternal weight loss resulted in decreased and modestly increased locomotion, respectively. Adult offspring of poly I:C treated dams that lost weight exhibited significantly decreased amphetamine stimulated locomotion, while offspring of poly I:C treated dams without weight loss performed similarly to vehicle controls. Social isolation and increased maternal age predicted weight loss in response to poly I:C but not vehicle injection. In combination, these data identify environmental factors associated with the maternal response to immune challenge and functional outcome of offspring exposed to maternal immune activation.