Synthetic Lethal and Resistance Interactions with BET Bromodomain Inhibitors in Triple-Negative Breast Cancer.

BET bromodomain inhibitors (BBDIs) are candidate therapeutic agents for triple-negative breast cancer (TNBC) and other cancer types, but inherent and acquired resistance to BBDIs limits their potential clinical use. Using CRISPR and small-molecule inhibitor screens combined with comprehensive molecular profiling of BBDI response and resistance, we identified synthetic lethal interactions with BBDIs and genes that, when deleted, confer resistance. We observed synergy with regulators of cell cycle progression, YAP, AXL, and SRC signaling, and chemotherapeutic agents. We also uncovered functional similarities and differences among BRD2, BRD4, and BRD7. Although deletion of BRD2 enhances sensitivity to BBDIs, BRD7 loss leads to gain of TEAD-YAP chromatin binding and luminal features associated with BBDI resistance. Single-cell RNA-seq, ATAC-seq, and cellular barcoding analysis of BBDI responses in sensitive and resistant cell lines highlight significant heterogeneity among samples and demonstrate that BBDI resistance can be pre-existing or acquired.

Breast tumours maintain a reservoir of subclonal diversity during expansion.

Our knowledge of copy number evolution during the expansion of primary breast tumours is limited1,2. Here, to investigate this process, we developed a single-cell, single-molecule DNA-sequencing method and performed copy number analysis of 16,178 single cells from 8 human triple-negative breast cancers and 4 cell lines. The results show that breast tumours and cell lines comprise a large milieu of subclones (7-22) that are organized into a few (3-5) major superclones. Evolutionary analysis suggests that after clonal TP53 mutations, multiple loss-of-heterozygosity events and genome doubling, there was a period of transient genomic instability followed by ongoing copy number evolution during the primary tumour expansion. By subcloning single daughter cells in culture, we show that tumour cells rediversify their genomes and do not retain isogenic properties. These data show that triple-negative breast cancers continue to evolve chromosome aberrations and maintain a reservoir of subclonal diversity during primary tumour growth.

The neuroimmune guidance cue netrin-1 promotes atherosclerosis by inhibiting the emigration of macrophages from plaques.

Atherosclerotic plaque formation is fueled by the persistence of lipid-laden macrophages in the artery wall. The mechanisms by which these cells become trapped, thereby establishing chronic inflammation, remain unknown. Here we found that netrin-1, a neuroimmune guidance cue, was secreted by macrophages in human and mouse atheroma, where it inactivated the migration of macrophages toward chemokines linked to their egress from plaques. Acting via its receptor, UNC5b, netrin-1 inhibited the migration of macrophages directed by the chemokines CCL2 and CCL19, activation of the actin-remodeling GTPase Rac1 and actin polymerization. Targeted deletion of netrin-1 in macrophages resulted in much less atherosclerosis in mice deficient in the receptor for low-density lipoprotein and promoted the emigration of macrophages from plaques. Thus, netrin-1 promoted atherosclerosis by retaining macrophages in the artery wall. Our results establish a causative role for negative regulators of leukocyte migration in chronic inflammation.

Cancer risk associated with soil distribution of polycyclic aromatic hydrocarbons within three environmental justice neighborhoods in Houston, Texas.

Residents and advocacy groups began voicing concerns over the environmental quality located in the neighborhoods of Kashmere Gardens, Fifth Ward, and Denver Harbor in Houston, TX, following the confirmation of a cancer cluster in 2019 and another in 2021. These neighborhoods are in close proximity to a railyard and former wood treatment plant known to have utilized coal tar creosote and contain polycyclic aromatic hydrocarbons (PAHs). This research took core soil samples in September and October 2020 from 46 sites to assess for the presence and concentration of the U.S. Environmental Protection Agency's (USEPA) 7 Carcinogenic PAHs. Results showed the cumulative concentration of these PAHs in each sample was variable with a range of 13,767 ng/g to 328 ng/g and a mean of 2,517.2 ng/g ± 3122. A regional soil screening evaluation revealed that 40 of the 46 soil samples were in excess of the USEPAs most conservative screening levels of 1.0 × 10-6 increased cancer risk, but none exceeding levels considered actionable for remediation. This study is a fundamental first step for quantifying the environmental pollutants in this minority-majority community. Findings revealed a low risk of cancer risk based on current PAH concentrations alone but cannot assess contributions from other contaminants or from past, possibly higher, levels of contamination. Further research is needed to identify the potential casual pathways of the observed cancer cluster and to explore possible remediation needs.

Biosensor applications in contaminated estuaries: Implications for disaster research response.

BACKGROUND: Given the time and monetary costs associated with traditional analytical chemistry, there remains a need to rapidly characterize environmental samples for priority analysis, especially within disaster research response (DR2). As PAHs are both ubiquitous and occur as complex mixtures at many National Priority List sites, these compounds are of interest for post-disaster exposures. OBJECTIVE: This study tests the field application of the KinExA Inline Biosensor in Galveston Bay and the Houston Ship Channel (GB/HSC) and in the Elizabeth River, characterizing the PAH profiles of these region's soils and sediments. To our knowledge, this is the first application of the biosensor to include soils. METHODS: The biosensor enables calculation of total free PAHs in porewater (C free), which is confirmed through gas chromatography-mass spectrometry (GC-MS) analysis. To determine potential risk of the collected soils the United States Environmental Protection (USEPA) Agency's Regional Screening Level (RSL) Calculator is used along with the USEPA Region 4 Ecological Screening Values (R4-ESV) and Refined Screening Values (R4-RSV). RESULTS: Based on GC-MS results, all samples had PAH-related hazard indices below 1, indicating low noncarcinogenic risks, but some samples exceeded screening levels for PAH-associated cancer risks. Combining biosensor-based C free with Total Organic Carbon yields predictions highly correlated (r > 0.5) both with total PAH concentrations as well as with hazard indices and cancer risks. Additionally, several individual parent PAH concentrations in both the GB/HSC and Elizabeth River sediments exceeded the R4- ESV and R4-RSV values, indicating a need for follow-up sediment studies. CONCLUSIONS: The resulting data support the utility of the biosensor for future DR2 efforts to characterize PAH contamination, enabling preliminary PAH exposure risk screening to aid in prioritization of environmental sample analysis.

Characterization of Compositional Variability in Petroleum Substances.

In the process of registration of substances of Unknown or Variable Composition, Complex Reaction Products or Biological Materials (UVCBs), information sufficient to enable substance identification must be provided. Substance identification for UVCBs formed through petroleum refining is particularly challenging due to their chemical complexity, as well as variability in refining process conditions and composition of the feedstocks. This study aimed to characterize compositional variability of petroleum UVCBs both within and across product categories. We utilized ion mobility spectrometry (IMS)-MS as a technique to evaluate detailed chemical composition of independent production cycle-derived samples of 6 petroleum products from 3 manufacturing categories (heavy aromatic, hydrotreated light paraffinic, and hydrotreated heavy paraffinic). Atmospheric pressure photoionization and drift tube IMS-MS were used to identify structurally related compounds and quantified between- and within-product variability. In addition, we determined both individual molecules and hydrocarbon blocks that were most variable in samples from different production cycles. We found that detailed chemical compositional data on petroleum UVCBs obtained from IMS-MS can provide the information necessary for hazard and risk characterization in terms of quantifying the variability of the products in a manufacturing category, as well as in subsequent production cycles of the same product.

Surveys of community garden affiliates and soils in Houston, Texas.

Although urban community food gardens have the capacity to strengthen and support neighborhoods in need, the benefits of such operations must be considered in tandem with the potential risks associated with urban environmental contamination. Therefore, research is needed to characterize existing community gardens in urban areas. In the present study, a survey of Houston, TX, community gardeners (N = 20) was conducted to better understand their risk-based knowledge and perceptions, current gardening practices, and willingness to implement risk mitigation measures. Soil samples collected from the beds (N = 22) and surrounding grounds (N = 24) of existing community garden sites in Houston, TX, were screened for trace and heavy metals using X-ray fluorescence spectrometry. The survey indicated that community gardeners had few concerns with regard to potential soilborne hazards and were generally willing to use diverse strategies to reduce potential hazards related to garden soil contamination. Ground and garden bed soil collected from community gardens were found to have excess concentrations of arsenic compared to federal health screening limits. The information provided here provides insight into possible discordance between community gardening risk perception and contamination risk that could be addressed through outreach, engagement, and remediation approaches.

High-Throughput UHPLC/MS/MS-Based Metabolic Profiling Using a Vacuum Jacketed Column.

In UHPLC, frictional heating from the eluent flowing through the column at pressures of ca. 10-15 Kpsi causes radial diffusion via temperature differences between the center of the column and its walls. Longitudinal dispersion also occurs due to temperature gradients between the inlet and outlet. These effects cause band broadening but can be mitigated via a combination of vacuum jacketed stainless steel tubing, reduced column end nut mass, and a constant temperature in the column from heating the inlet fitting. Here, vacuum jacketed column (VJC) technology, employing a novel column housing located on the source of the mass spectrometer and minimized tubing from the column outlet to the electrospray probe, was applied to profiling metabolites in urine. For a 75 s reversed-phase gradient separation, the average peak widths for endogenous compounds in urine were 1.2 and 0.6 s for conventional LC/MS and VJC systems, respectively. The peak tailing factor was reduced from 1.25 to 1.13 when using the VJC system compared to conventional UHPLC, and the peak capacity increased from 65 to 120, with a 25% increase in features detected in urine. The increased resolving power of the VJC system reduced co-elution, simplifying MS and MS/MS spectra, providing a more confident metabolite identification. The increased LC performance also gave more intense MS peaks, with a 10-120% increase in response, improving the quality of the MS data and detection limits. Reducing the LC gradient duration to 37 s gave peak widths of ca. 0.4 s and a peak capacity of 84.

In vitro and in vivo cardiac toxicity of flavored electronic nicotine delivery systems.

The usage of flavored electronic nicotine delivery systems (ENDS) is popular, specifically in the teen and young adult age-groups. The possible cardiac toxicity of the flavoring aspect of ENDS is largely unknown. Vaping, a form of electronic nicotine delivery, uses "e-liquid" to generate "e-vapor," an aerosolized mixture of nicotine and/or flavors. We report our investigation into the cardiotoxic effects of flavored e-liquids. E-vapors containing flavoring aldehydes such as vanillin and cinnamaldehyde, as indicated by mass spectrometry, were more toxic in HL-1 cardiomyocytes than fruit-flavored e-vapor. Exposure of human induced pluripotent stem cell-derived cardiomyocytes to cinnamaldehyde or vanillin-flavored e-vapor affected the beating frequency and prolonged the field potential duration of these cells more than fruit-flavored e-vapor. In addition, vanillin aldehyde-flavored e-vapor reduced the human ether-à-go-go-related gene (hERG)-encoded potassium current in transfected human embryonic kidney cells. In mice, inhalation exposure to vanillin aldehyde-flavored e-vapor for 10 wk caused increased sympathetic predominance in heart rate variability measurements. In vivo inducible ventricular tachycardia was significantly longer, and in optical mapping, the magnitude of ventricular action potential duration alternans was significantly larger in the vanillin aldehyde-flavored e-vapor-exposed mice than in controls. We conclude that the widely popular flavored ENDS are not harm free, and they have a potential for cardiac harm. More studies are needed to further assess their cardiac safety profile and long-term health effects.NEW & NOTEWORTHY The use of electronic nicotine delivery systems (ENDS) is not harm free. It is not known whether ENDS negatively affect cardiac electrophysiological function. Our study in cell lines and in mice shows that ENDS can compromise cardiac electrophysiology, leading to action potential instability and inducible ventricular arrhythmias. Further investigations are necessary to assess the long-term cardiac safety profile of ENDS products in humans and to better understand how individual components of ENDS affect cardiac toxicity.

Functional testing for variant prioritization in a family with long QT syndrome.

Next-generation sequencing platforms are being increasingly applied in clinical genetic settings for evaluation of families with suspected heritable disease. These platforms potentially improve the diagnostic yield beyond that of disease-specific targeted gene panels, but also increase the number of rare or novel genetic variants that may confound precise diagnostics. Here, we describe a functional testing approach used to interpret the results of whole exome sequencing (WES) in a family presenting with syncope and sudden death. One individual had a prolonged QT interval on electrocardiogram (ECG) and carried a diagnosis of long QT syndrome (LQTS), but a second individual did not meet criteria for LQTS. Filtering WES results for uncommon variants with arrhythmia association identified four for further analyses. In silico analyses indicated that two of these variants, KCNH2 p.(Cys555Arg) and KCNQ1 p.(Arg293Cys), were likely to be causal in this family's LQTS. We subsequently performed functional characterization of these variants in a heterologous expression system. The expression of KCNQ1-Arg293Cys did not show a deleterious phenotype but KCNH2-Cys555Arg demonstrated a loss-of-function phenotype that was partially dominant. Our stepwise approach identified a precise genetic etiology in this family, which resulted in the establishment of a LQTS diagnosis in the second individual as well as an additional asymptomatic family member, enabling personalized clinical management. Given its ability to aid in the diagnosis, the application of functional characterization should be considered as a value adjunct to in silico analyses of WES.

ESTIpop: a computational tool to simulate and estimate parameters for continuous-time Markov branching processes.

SUMMARY: ESTIpop is an R package designed to simulate and estimate parameters for continuous-time Markov branching processes with constant or time-dependent rates, a common model for asexually reproducing cell populations. Analytical approaches to parameter estimation quickly become intractable in complex branching processes. In ESTIpop, parameter estimation is based on a likelihood function with respect to a time series of cell counts, approximated by the Central Limit Theorem for multitype branching processes. Additionally, simulation in ESTIpop via approximation can be performed many times faster than exact simulation methods with similar results. AVAILABILITY AND IMPLEMENTATION: ESTIpop is available as an R package on Github (https://github.com/michorlab/estipop). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Cooperative insertion of CO2 in diamine-appended metal-organic frameworks.

The process of carbon capture and sequestration has been proposed as a method of mitigating the build-up of greenhouse gases in the atmosphere. If implemented, the cost of electricity generated by a fossil fuel-burning power plant would rise substantially, owing to the expense of removing CO2 from the effluent stream. There is therefore an urgent need for more efficient gas separation technologies, such as those potentially offered by advanced solid adsorbents. Here we show that diamine-appended metal-organic frameworks can behave as 'phase-change' adsorbents, with unusual step-shaped CO2 adsorption isotherms that shift markedly with temperature. Results from spectroscopic, diffraction and computational studies show that the origin of the sharp adsorption step is an unprecedented cooperative process in which, above a metal-dependent threshold pressure, CO2 molecules insert into metal-amine bonds, inducing a reorganization of the amines into well-ordered chains of ammonium carbamate. As a consequence, large CO2 separation capacities can be achieved with small temperature swings, and regeneration energies appreciably lower than achievable with state-of-the-art aqueous amine solutions become feasible. The results provide a mechanistic framework for designing highly efficient adsorbents for removing CO2 from various gas mixtures, and yield insights into the conservation of Mg(2+) within the ribulose-1,5-bisphosphate carboxylase/oxygenase family of enzymes.

A Dilute and Shoot Strategy for Determining Alternaria Toxins in Tomato-Based Samples and in Different Flours Using LC-IDMS Separation.

Alternaria toxins are emerging mycotoxins whose regulation and standardization are in progress by the European Commission and the European Committee for Standardization. This paper describes a dilute and shoot approach to determine five Alternaria toxins in selected food samples using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The strategy involves sample extraction with acidified aqueous methanol, followed by a solvent change accomplished via sample evaporation and reconstitution. The quantification is based on isotope dilution, applying all corresponding isotopically labeled internal standards to compensate possible matrix effects of the analysis. The main advantages of the present method over other existing methods includes simple and effective sample preparation, as well as detection with high sensitivity. The five-fold sample dilution can decrease matrix effects, which were evaluated with both external and internal standard methods. The results demonstrated a limit of quantification lower than 1.0 µg/kg for all five analytes for the first time. The newly presented method showed acceptable accuracy (52.7-111%) when analyzing naturally contaminated and spiked standard samples at the described levels. The method was validated for tomato-based and flour samples (wheat, rye, and maize). The absolute recovery ranged from 66.7% to 91.6% (RSD < 10%). The developed method could be an alternative approach for those laboratories that exclude sample cleanup and pre-concentration of state-of-the-art instruments with enhanced sensitivity.

Decreased bioavailability of aminomethylphosphonic acid (AMPA) in genetically modified corn with activated carbon or calcium montmorillonite clay inclusion in soil.

The widespread use of pesticides has resulted in detectable residues throughout the environment, sometimes at concentrations well above regulatory limits. Therefore, the development of safe, effective, field-practical, and economically feasible strategies to mitigate the effects of pesticides is warranted. Glyphosate is an organophosphorus herbicide that is degraded to aminomethylphosphonic acid (AMPA), a toxic and persistent metabolite that can accumulate in soil and sediment and translocate to plants. In this study, we investigated the binding efficacy of activated carbon (AC) and calcium montmorillonite (CM) clay to decrease AMPA bioavailability from soil and AMPA translocation to plants. Adsorption isotherms and thermodynamic studies on AC and CM were conducted and showed tight binding (enthalpy values >-20 kJ/mol) for AMPA with high capacities (0.25 mol/kg and 0.38 mol/kg, respectively), based on derivations from the Langmuir model. A hydra assay was utilized to indicate toxicity of AMPA and the inclusion of 1% AC and CM both resulted in 90% protection of the hydra (**p ≤ 0.01). Further studies in glyphosate-contaminated soil showed that AC and CM significantly reduced AMPA bioavailability by 53% and 44%, respectively. Results in genetically modified (GM) corn showed a conversion of glyphosate to AMPA in roots and sprouts over a 10-day exposure duration. Inclusion of AC and CM reduced AMPA residues in roots and sprouts by 47%-61%. These studies collectively indicate that AC and CM are effective sorbents for AMPA and could be used to reduce AMPA bioavailability from soil and AMPA residues in GM corn plants.

Physical and functional interaction sites in cytoplasmic domains of KCNQ1 and KCNE1 channel subunits.

The cardiac potassium IKs current is carried by a channel complex formed from α-subunits encoded by KCNQ1 and ß-subunits encoded by KCNE1. Deleterious mutations in either gene are associated with hereditary long QT syndrome. Interactions between the transmembrane domains of the α- and ß-subunits determine the activation kinetics of IKs. A physical and functional interaction between COOH termini of the proteins has also been identified that impacts deactivation rate and voltage dependence of activation. We sought to explore the specific physical interactions between the COOH termini of the subunits that confer such control. Hydrogen/deuterium exchange coupled to mass spectrometry narrowed down the region of interaction to KCNQ1 residues 352-374 and KCNE1 residues 70-81, and provided evidence of secondary structure within these segments. Key mutations of residues in these regions tended to shift voltage dependence of activation toward more depolarizing voltages. Double-mutant cycle analysis then revealed energetic coupling between KCNQ1-I368 and KCNE1-D76 during channel activation. Our results suggest that the proximal COOH-terminal regions of KCNQ1 and KCNE1 participate in a physical and functional interaction during channel opening that is sensitive to perturbation and may explain the clustering of long QT mutations in the region.NEW & NOTEWORTHY Interacting ion channel subunits KCNQ1 and KCNE1 have received intense investigation due to their critical importance to human cardiovascular health. This work uses physical (hydrogen/deuterium exchange with mass spectrometry) and functional (double-mutant cycle analyses) studies to elucidate precise and important areas of interaction between the two proteins in an area that has eluded structural definition of the complex. It highlights the importance of pathogenic mutations in these regions.

DIFFpop: a stochastic computational approach to simulate differentiation hierarchies with single cell barcoding.

SUMMARY: DIFFpop is an R package designed to simulate cellular differentiation hierarchies using either exponentially-expanding or fixed population sizes. The software includes functionalities to simulate clonal evolution due to the emergence of driver mutations under the infinite-allele assumption as well as options for simulation and analysis of single cell barcoding and labeling data. The software uses the Gillespie Stochastic Simulation Algorithm and a modification of expanding or fixed-size stochastic process models expanded to a large number of cell types and scenarios. AVAILABILITY AND IMPLEMENTATION: DIFFpop is available as an R-package along with vignettes on Github (https://github.com/ferlicjl/diffpop). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Synonymous nucleotide modification of the KCNH2 gene affects both mRNA characteristics and translation of the encoded hERG ion channel.

Synonymous nucleotide variation is increasingly recognized as a factor than can affect protein expression, but the underlying mechanisms are incompletely understood. Here, we investigated whether synonymous changes could affect expression of the potassium voltage-gated channel subfamily H member 2 (KCNH2) gene, encoding the human ether-a-go-go-related gene (hERG) ion channel, which is linked to hereditary cardiac arrhythmia. We examined a previously described synthetic version (hERG-codon modified (CM)) with synonymous substitutions designed to reduce GC content, rare codons, and mRNA secondary structure relative to the native construct (hERG-NT). hERG-CM exhibited lower protein expression than hERG-NT in HEK293T cells. We found that the steady-state abundance of hERG-NT mRNA was greater than hERG-CM because of an enhanced transcription rate and increased mRNA stability for hERG-NT. Translation of hERG-CM was independently reduced, contributing to the overall greater synthesis of hERG-NT channel protein. This was partially offset, however, by a higher aggregation of a newly synthesized hERG-NT channel, resulting in nonfunctional protein. Regional mRNA analyses of chimeras of hERG-NT and hERG-CM revealed that synonymous changes in the 5' segments of the coding region had the greatest influence on hERG synthesis at both the mRNA and protein levels. Taken together, these results indicate that synonymous nucleotide variations within the coding region, particularly in the 5' region of the hERG mRNA, can affect both transcription and translation. These findings support the notion that greater attention should be given to the effects of synonymous genetic variation when analyzing hERG DNA sequences in the study of hereditary cardiac disease.

The History and Future of the Gene.

This essay reviews three books that trace the development of the contemporary conception of the gene in the early 20th century: The Gene: An Intimate History (2016) by Siddhartha Mukherjee, The Gene: A Historical Perspective (2007) by Ted Everson, and In Pursuit of the Gene: From Darwin to DNA (2008) by James Schwartz. Each of these books is written for the educated lay reader, and each approaches its subject in a different way. Read together, they show how the now-dominant conception of the gene was not the inevitable result of impartial scientific inquiry; rather, it emerged within a particular historical context, and was shaped by specific social and intellectual forces.

SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution.

SUMMARY: SIApopr (Simulating Infinite-Allele populations) is an R package to simulate time-homogeneous and inhomogeneous stochastic branching processes under a very flexible set of assumptions using the speed of C ++. The software simulates clonal evolution with the emergence of driver and passenger mutations under the infinite-allele assumption. The software is an application of the Gillespie Stochastic Simulation Algorithm expanded to a large number of cell types and scenarios, with the intention of allowing users to easily modify existing models or create their own. AVAILABILITY AND IMPLEMENTATION: SIApopr is available as an R library on Github ( https://github.com/olliemcdonald/siapopr ). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: michor@jimmy.harvard.edu.

Creatinine downregulates TNF-α in macrophage and T cell lines.

Creatinine is the breakdown product of creatine, a key participant in the generation of ATP and is traditionally considered to be a biologically inert waste product. Based on our earlier work, we analyzed the effects of creatinine hydrochloride on the expression of tumor necrosis factor-alpha (TNF-α), a pro-inflammatory cytokine, in a human T cell line, as well as human and mouse macrophage cell lines. Exposing cells to creatinine hydrochloride significantly reduced TNF-α mRNA and protein levels compared to control-treated cultures in all cell lines tested. Lipopolysaccharide (LPS), a potent inducer of inflammation, was employed with in mouse macrophage cell lines to induce high levels of TNF-α in order to determine whether creatinine hydrochloride could reduce preexisting inflammation. Cells treated with LPS and creatinine hydrochloride had significantly reduced TNF-α levels compared to cells treated with LPS alone. As the NF-κB signaling pathway represents a major mechanism of TNF-α generation, nuclear extracts were examined for NF-κB pathway activation. Cells exposed to CRN had significantly lower levels of NF-κB in the nucleus compared to control-treated cells. Together, these results support the hypothesis that CRN can alter anti-inflammatory responses by interfering with the activation of the NF-κB pathway.