Analytical Validation of an Early Detection Pancreatic Cancer Test Using 5-Hydroxymethylation Signatures.

Early detection of pancreatic cancer has been shown to improve patient survival rates. However, effective early detection tools to detect pancreatic cancer do not currently exist. The Avantect Pancreatic Cancer Test, leveraging the 5-hydroxymethylation [5-hydroxymethylcytosine (5hmC)] signatures in cell-free DNA, was developed and analytically validated to address this unmet need. We report a comprehensive analytical validation study encompassing precision, sample stability, limit of detection, interfering substance studies, and a comparison with an alternative method. The assay performance on an independent case-control patient cohort was previously reported with a sensitivity for early-stage (stage I/II) pancreatic cancer of 68.3% (95% CI, 51.9%-81.9%) and an overall specificity of 96.9% (95% CI, 96.1%-97.7%). Precision studies showed a cancer classification of 100% concordance in biological replicates. The sample stability studies revealed stable assay performance for up to 7 days after blood collection. The limit of detection studies revealed equal results between early- and late-stage cancer samples, emphasizing strong early-stage performance characteristics. Comparisons of concordance of the Avantect assay with the enzymatic methyl sequencing (EM-Seq) method, which measures both methylation (5-methylcytosine) and 5hmC, were >95% for all samples tested. The Avantect Pancreatic Cancer Test showed strong analytical validation in multiple validation studies required for laboratory-developed test accreditation. The comparison of 5hmC versus EM-Seq further validated the 5hmC approach as a robust and reproducible assay.

Correction to Brown Carbon from Photo-Oxidation of Glyoxal and SO2 in Aqueous Aerosol.

[This corrects the article DOI: 10.1021/acsearthspacechem.3c00035.].

Brown Carbon from Photo-Oxidation of Glyoxal and SO2 in Aqueous Aerosol.

Aqueous-phase dark reactions during the co-oxidation of glyoxal and S(IV) were recently identified as a potential source of brown carbon (BrC). Here, we explore the effects of sunlight and oxidants on aqueous solutions of glyoxal and S(IV), and on aqueous aerosol exposed to glyoxal and SO2. We find that BrC is able to form in sunlit, bulk-phase, sulfite-containing solutions, albeit more slowly than in the dark. In more atmospherically relevant chamber experiments where suspended aqueous aerosol particles are exposed to gas-phase glyoxal and SO2, the formation of detectable amounts of BrC requires an OH radical source and occurs most rapidly after a cloud event. From these observations we infer that this photobrowning is caused by radical-initiated reactions as evaporation concentrates aqueous-phase reactants and aerosol viscosity increases. Positive-mode electrospray ionization mass spectrometric analysis of aerosol-phase products reveals a large number of CxHyOz oligomers that are reduced rather than oxidized (relative to glyoxal), with the degree of reduction increasing in the presence of OH radicals. This again suggests a radical-initiated redox mechanism where photolytically produced aqueous radical species trigger S(IV)-O2 auto-oxidation chain reactions, and glyoxal-S(IV) redox reactions especially if aerosol-phase O2 is depleted. This process may contribute to daytime BrC production and aqueous-phase sulfur oxidation in the atmosphere. The BrC produced, however, is about an order of magnitude less light-absorbing than wood smoke BrC at 365 nm.

Epigenomic Blood-Based Early Detection of Pancreatic Cancer Employing Cell-Free DNA.

BACKGROUND & AIMS: Early detection of pancreatic cancer (PaC) can drastically improve survival rates. Approximately 25% of subjects with PaC have type 2 diabetes diagnosed within 3 years prior to the PaC diagnosis, suggesting that subjects with type 2 diabetes are at high risk of occult PaC. We have developed an early-detection PaC test, based on changes in 5-hydroxymethylcytosine (5hmC) signals in cell-free DNA from plasma. METHODS: Blood was collected from 132 subjects with PaC and 528 noncancer subjects to generate epigenomic and genomic feature sets yielding a predictive PaC signal algorithm. The algorithm was validated in a blinded cohort composed of 102 subjects with PaC, 2048 noncancer subjects, and 1524 subjects with non-PaCs. RESULTS: 5hmC differential profiling and additional genomic features enabled the development of a machine learning algorithm capable of distinguishing subjects with PaC from noncancer subjects with high specificity and sensitivity. The algorithm was validated with a sensitivity for early-stage (stage I/II) PaC of 68.3% (95% confidence interval [CI], 51.9%-81.9%) and an overall specificity of 96.9% (95% CI, 96.1%-97.7%). CONCLUSIONS: The PaC detection test showed robust early-stage detection of PaC signal in the studied cohorts with varying type 2 diabetes status. This assay merits further clinical validation for the early detection of PaC in high-risk individuals.

Identifying a sublingual triangle as the ideal site for assessment of sublingual microcirculation.

The sublingual mucosa is a commonly used intraoral location for identifying microcirculatory alterations using handheld vital microscopes (HVMs). The anatomic description of the sublingual cave and its related training have not been adequately introduced. The aim of this study was to introduce anatomy guided sublingual microcirculatory assessment. Measurements were acquired from the floor of the mouth using incident dark-field (IDF) imaging before (T0) and after (T1) sublingual cave anatomy instructed training. Instructions consists of examining a specific region of interested identified through observable anatomical structures adjacent and bilaterally to the lingual frenulum which is next to the sublingual papilla. The anatomical location called the sublingual triangle, was identified as stationed between the lingual frenulum, the sublingual fold and ventrally to the tongue. Small, large, and total vessel density datasets (SVD, LVD and TVD respectively) obtained by non-instructed and instructed measurements (NIN (T0) and IM (T1) respectively) were compared. Microvascular structures were analyzed, and the presence of salivary duct-related microcirculation was identified. A total of 72 video clips were used for analysis in which TVD, but not LVD and SVD, was higher in IM compared to NIM (NIM vs. IM, 25 ± 2 vs. 27 ± 3 mm/mm2 (p = 0.044), LVD NIM vs. IM: 7 ± 1 vs. 8 ± 1mm/mm2 (p = 0.092), SVD NIM vs. IM: 18 ± 2 vs. 20 ± 3 mm/mm2 (p = 0.103)). IM resulted in microcirculatory assessments which included morphological properties such as capillaries, venules and arterioles, without salivary duct-associated microcirculation. The sublingual triangle identified in this study showed consistent network-based microcirculation, without interference from microcirculation associated with specialized anatomic structures. These findings suggest that the sublingual triangle, an anatomy guided location, yielded sublingual based measurements that conforms with international guidelines. IM showed higher TVD values, and future studies are needed with larger sample sizes to prove differences in microcirculatory parameters.

Kinetics, Products, and Brown Carbon Formation by Aqueous-Phase Reactions of Glycolaldehyde with Atmospheric Amines and Ammonium Sulfate.

Glycolaldehyde (GAld) is a C2 water-soluble aldehyde produced during the atmospheric oxidation of isoprene and many other species and is commonly found in cloudwater. Previous work has established that glycolaldehyde evaporates more readily from drying aerosol droplets containing ammonium sulfate (AS) than does glyoxal, methylglyoxal, or hydroxyacetone, which implies that it does not oligomerize as quickly as these other species. Here, we report NMR measurements of glycolaldehyde's aqueous-phase reactions with AS, methylamine, and glycine. Reaction rate constants are smaller than those of respective glyoxal and methylglyoxal reactions in the pH range of 3-6. In follow-up cloud chamber experiments, deliquesced glycine and AS seed particles were found to take up glycolaldehyde and methylamine and form brown carbon. At very high relative humidity, these changes were more than 2 orders of magnitude faster than predicted by our bulk liquid NMR kinetics measurements, suggesting that reactions involving surface-active species at crowded air-water interfaces may play an important role. The high-resolution liquid chromatography-electrospray ionization-mass spectrometric analysis of filter extracts of unprocessed AS + GAld seed particles identified sugar-like C6 and C12 GAld oligomers, including proposed product 3-deoxyglucosone, with and without modification by reactions with ammonia to diimine and imidazole forms. Chamber exposure to methylamine gas, cloud processing, and simulated sunlight increased the incorporation of both ammonia and methylamine into oligomers. Many C4-C16 imidazole derivatives were detected in an extract of chamber-exposed aerosol along with a predominance of N-derivatized C6 and C12 glycolaldehyde oligomers, suggesting that GAld is capable of forming brown carbon SOA.

eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants.

While advancements in genome sequencing have identified millions of somatic mutations in cancer, their functional impact is poorly understood. We previously developed the expression-based variant impact phenotyping (eVIP) method to use gene expression data to characterize the function of gene variants. The eVIP method uses a decision tree-based algorithm to predict the functional impact of somatic variants by comparing gene expression signatures induced by introduction of wild-type (WT) versus mutant cDNAs in cell lines. The method distinguishes between variants that are gain-of-function, loss-of-function, change-of-function, or neutral. We present eVIP2, software that allows for pathway analysis (eVIP Pathways) and usage with RNA-seq data. To demonstrate the eVIP2 software and approach, we characterized two recurrent frameshift variants in RNF43, a negative regulator of Wnt signaling, frequently mutated in colorectal, gastric, and endometrial cancer. RNF43 WT, RNF43 R117fs, RNF43 G659fs, or GFP control cDNA were overexpressed in HEK293T cells. Analysis with eVIP2 predicted that the frameshift at position 117 was a loss-of-function mutation, as expected. The second frameshift at position 659 has been previously described as a passenger mutation that maintains the RNF43 WT function as a negative regulator of Wnt. Surprisingly, eVIP2 predicted G659fs to be a change-of-function mutation. Additional eVIP Pathways analysis of RNF43 G659fs predicted 10 pathways to be significantly altered, including TNF-α via NFκB signaling, KRAS signaling, and hypoxia, highlighting the benefit of a more comprehensive approach when determining the impact of gene variant function. To validate these predictions, we performed reporter assays and found that each pathway activated by expression of RNF43 G659fs, but not expression of RNF43 WT, was identified as impacted by eVIP2, supporting that RNF43 G659fs is a change-of-function mutation and its effect on the identified pathways. Pathway activation was further validated by Western blot analysis. Lastly, we show primary colon adenocarcinoma patient samples with R117fs and G659fs variants have transcriptional profiles similar to BRAF missense mutations with activated RAS/MAPK signaling, consistent with KRAS signaling pathways being GOF in both variants. The eVIP2 method is an important step towards overcoming the current challenge of variant interpretation in the implementation of precision medicine. eVIP2 is available at https://github.com/BrooksLabUCSC/eVIP2.

A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery.

The accurate identification and quantitation of RNA isoforms present in the cancer transcriptome is key for analyses ranging from the inference of the impacts of somatic variants to pathway analysis to biomarker development and subtype discovery. The ICGC-TCGA DREAM Somatic Mutation Calling in RNA (SMC-RNA) challenge was a crowd-sourced effort to benchmark methods for RNA isoform quantification and fusion detection from bulk cancer RNA sequencing (RNA-seq) data. It concluded in 2018 with a comparison of 77 fusion detection entries and 65 isoform quantification entries on 51 synthetic tumors and 32 cell lines with spiked-in fusion constructs. We report the entries used to build this benchmark, the leaderboard results, and the experimental features associated with the accurate prediction of RNA species. This challenge required submissions to be in the form of containerized workflows, meaning each of the entries described is easily reusable through CWL and Docker containers at https://github.com/SMC-RNA-challenge. A record of this paper's transparent peer review process is included in the supplemental information.

Elucidating an Atmospheric Brown Carbon Species-Toward Supplanting Chemical Intuition with Exhaustive Enumeration and Machine Learning.

Brown carbon (BrC) is involved in atmospheric light absorption and climate forcing and can cause adverse health effects. Understanding the formation mechanisms and molecular structure of BrC is of key importance in developing strategies to control its environment and health impact. Structure determination of BrC is challenging, due to the lack of experiments providing molecular fingerprints and the sheer number of molecular candidates with identical mass. Suggestions based on chemical intuition are prone to errors due to the inherent bias. We present an unbiased algorithm, using graph-based molecule generation and machine learning, which can identify all molecular structures of compounds involved in biomass burning and the composition of BrC. We apply this algorithm to C12H12O7, a light-absorbing "test case" molecule identified in chamber experiments on the aqueous photo-oxidation of syringol, a prevalent marker in wood smoke. Of the 260 million molecular graphs, the algorithm leaves only 36,518 (0.01%) as viable candidates matching the spectrum. Although no unique molecular structure is obtained from only a chemical formula and a UV/vis absorption spectrum, we discuss further reduction strategies and their efficacy. With additional data, the method can potentially more rapidly identify isomers extracted from lab and field aerosol particles without introducing human bias.

Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway.

RTK/RAS/RAF pathway alterations (RPAs) are a hallmark of lung adenocarcinoma (LUAD). In this study, we use whole-genome sequencing (WGS) of 85 cases found to be RPA(-) by previous studies from The Cancer Genome Atlas (TCGA) to characterize the minority of LUADs lacking apparent alterations in this pathway. We show that WGS analysis uncovers RPA(+) in 28 (33%) of the 85 samples. Among the remaining 57 cases, we observe focal deletions targeting the promoter or transcription start site of STK11 (n = 7) or KEAP1 (n = 3), and promoter mutations associated with the increased expression of ILF2 (n = 6). We also identify complex structural variations associated with high-level copy number amplifications. Moreover, an enrichment of focal deletions is found in TP53 mutant cases. Our results indicate that RPA(-) cases demonstrate tumor suppressor deletions and genome instability, but lack unique or recurrent genetic lesions compensating for the lack of RPAs. Larger WGS studies of RPA(-) cases are required to understand this important LUAD subset.

Brown Carbon Production by Aqueous-Phase Interactions of Glyoxal and SO2.

Oxalic acid and sulfate salts are major components of aerosol particles. Here, we explore the potential for their respective precursor species, glyoxal and SO2, to form atmospheric brown carbon via aqueous-phase reactions in a series of bulk aqueous and flow chamber aerosol experiments. In bulk aqueous solutions, UV- and visible-light-absorbing products are observed at pH 3-4 and 5-6, respectively, with small but detectable yields of hydroxyquinone and polyketone products formed, especially at pH 6. Hydroxymethanesulfonate (HMS), C2, and C3 sulfonates are major products detected by electrospray ionization mass spectrometry (ESI-MS) at pH 5. Past studies have assumed that the reaction of formaldehyde and sulfite was the only atmospheric source of HMS. In flow chamber experiments involving sulfite aerosol and gas-phase glyoxal with only 1 min residence times, significant aerosol growth is observed. Rapid brown carbon formation is seen with aqueous aerosol particles at >80% relative humidity (RH). Brown carbon formation slows at 50-60% RH and when the aerosol particles are acidified with sulfuric acid but stops entirely only under dry conditions. This chemistry may therefore contribute to brown carbon production in cloud-processed pollution plumes as oxidizing volatile organic compounds (VOCs) interact with SO2 and water.

Pathway and network analysis of more than 2500 whole cancer genomes.

The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.

Using Transcriptional Signatures to Find Cancer Drivers with LURE.

Cancer genome projects have produced multidimensional datasets on thousands of samples. Yet, depending on the tumor type, 5-50% of samples have no known driving event. We introduce a semi-supervised method called Learning UnRealized Events (LURE) that uses a progressive label learning framework and minimum spanning analysis to predict cancer drivers based on their altered samples sharing a gene expression signature with the samples of a known event. We demonstrate the utility of the method on the TCGA Pan-Cancer Atlas dataset for which it produced a high-confidence result relating 59 new connections to 18 known mutation events including alterations in the same gene, family, and pathway. We give examples of predicted drivers involved in TP53, telomere maintenance, and MAPK/RTK signaling pathways. LURE identifies connections between genes with no known prior relationship, some of which may offer clues for targeting specific forms of cancer. Code and Supplemental Material are available on the LURE website: https://sysbiowiki.soe.ucsc.edu/lure.

Methylglyoxal Uptake Coefficients on Aqueous Aerosol Surfaces.

In order to predict the amount of secondary organic aerosol formed by heterogeneous processing of methylglyoxal, uptake coefficients (γ) and estimates of uptake reversibility are needed. Here, uptake coefficients are extracted from chamber studies involving ammonium sulfate and glycine seed aerosol at high relative humidity (RH ≥ 72%). Methylglyoxal uptake coefficients on prereacted glycine aerosol particles had a strong dependence on RH, increasing from γ = 0.4 × 10-3 to 5.7 × 10-3 between 72 and 99% RH. Continuous methylglyoxal losses were also observed in the presence of aqueous ammonium sulfate at 95% RH (γAS,wet = 3.7 ± 0.8 × 10-3). Methylglyoxal uptake coefficients measured at ≥95% RH are larger than those reported for glyoxal on nonacidified, aqueous aerosol surfaces at 90% RH. Slight curvature in first-order uptake plots suggests that methylglyoxal uptake onto aqueous aerosol surfaces is not entirely irreversible after 20 min. Methylglyoxal uptake by cloud droplets was rapid and largely reversible, approaching equilibrium within the 1 min mixing time of the chamber. PTR-MS measurements showed that each cloud event extracted 3 to 8% of aerosol-phase methylglyoxal and returned it to the gas phase, likely by an oligomer hydrolysis mechanism.

Nitrogen-Containing, Light-Absorbing Oligomers Produced in Aerosol Particles Exposed to Methylglyoxal, Photolysis, and Cloud Cycling.

Aqueous methylglyoxal chemistry has often been implicated as an important source of oligomers in atmospheric aerosol. Here we report on chemical analysis of brown carbon aerosol particles collected from cloud cycling/photolysis chamber experiments, where gaseous methylglyoxal and methylamine interacted with glycine, ammonium, or methylammonium sulfate seed particles. Eighteen N-containing oligomers were identified in the particulate phase by liquid chromatography/diode array detection/electrospray ionization high-resolution quadrupole time-of-flight mass spectrometry. Chemical formulas were determined and, for 6 major oligomer products, MS2 fragmentation spectra were used to propose tentative structures and mechanisms. Electronic absorption spectra were calculated for six tentative product structures by an ab initio second order algebraic-diagrammatic-construction/density functional theory approach. For five structures, matching calculated and measured absorption spectra suggest that they are dominant light-absorbing species at their chromatographic retention times. Detected oligomers incorporated methylglyoxal and amines, as expected, but also pyruvic acid, hydroxyacetone, and significant quantities of acetaldehyde. The finding that ∼80% (by mass) of detected oligomers contained acetaldehyde, a methylglyoxal photolysis product, suggests that daytime methylglyoxal oligomer formation is dominated by radical addition mechanisms involving CH3CO*. These mechanisms are evidently responsible for enhanced browning observed during photolytic cloud events.

Brown Carbon Production in Ammonium- or Amine-Containing Aerosol Particles by Reactive Uptake of Methylglyoxal and Photolytic Cloud Cycling.

The effects of methylglyoxal uptake on the physical and optical properties of aerosol containing amines or ammonium sulfate were determined before and after cloud processing in a temperature- and RH-controlled chamber. The formation of brown carbon was observed upon methylglyoxal addition, detected as an increase in water-soluble organic carbon mass absorption coefficients below 370 nm and as a drop in single-scattering albedo at 450 nm. The imaginary refractive index component k450 reached a maximum value of 0.03 ± 0.009 with aqueous glycine aerosol particles. Browning of solid particles occurred at rates limited by chamber mixing (<1 min), and in liquid particles occurred more gradually, but in all cases occurred much more rapidly than in bulk aqueous studies. Further browning in AS and methylammonium sulfate seeds was triggered by cloud events with chamber lights on, suggesting photosensitized brown carbon formation. Despite these changes in optical aerosol characteristics, increases in dried aerosol mass were rarely observed (<1 µg/m3 in all cases), consistent with previous experiments on methylglyoxal. Under dry, particle-free conditions, methylglyoxal reacted (presumably on chamber walls) with methylamine with a rate constant k = (9 ± 2) × 10-17 cm3 molecule-1 s-1 at 294 K and activation energy Ea = 64 ± 37 kJ/mol.

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling.

The American alligator, Alligator mississippiensis, like all crocodilians, has temperature-dependent sex determination, in which the sex of an embryo is determined by the incubation temperature of the egg during a critical period of development. The lack of genetic differences between male and female alligators leaves open the question of how the genes responsible for sex determination and differentiation are regulated. Insight into this question comes from the fact that exposing an embryo incubated at male-producing temperature to estrogen causes it to develop ovaries. Because estrogen response elements are known to regulate genes over long distances, a contiguous genome assembly is crucial for predicting and understanding their impact. We present an improved assembly of the American alligator genome, scaffolded with in vitro proximity ligation (Chicago) data. We use this assembly to scaffold two other crocodilian genomes based on synteny. We perform RNA sequencing of tissues from American alligator embryos to find genes that are differentially expressed between embryos incubated at male- versus female-producing temperature. Finally, we use the improved contiguity of our assembly along with the current model of CTCF-mediated chromatin looping to predict regions of the genome likely to contain estrogen-responsive genes. We find that these regions are significantly enriched for genes with female-biased expression in developing gonads after the critical period during which sex is determined by incubation temperature. We thus conclude that estrogen signaling is a major driver of female-biased gene expression in the post-temperature sensitive period gonads.

Maillard Chemistry in Clouds and Aqueous Aerosol As a Source of Atmospheric Humic-Like Substances.

The reported optical, physical, and chemical properties of aqueous Maillard reaction mixtures of small aldehydes (glyoxal, methylglyoxal, and glycolaldehyde) with ammonium sulfate and amines are compared with those of aqueous extracts of ambient aerosol (water-soluble organic carbon, WSOC) and the humic-like substances (HULIS) fraction of WSOC. Using a combination of new and previously published measurements, we examine fluorescence, X-ray absorbance, UV/vis, and IR spectra, complex refractive indices, (1)H and (13)C NMR spectra, thermograms, aerosol and electrospray ionization mass spectra, surface activity, and hygroscopicity. Atmospheric WSOC and HULIS encompass a range of properties, but in almost every case aqueous aldehyde-amine reaction mixtures are squarely within this range. Notable exceptions are the higher UV/visible absorbance wavelength dependence (Angström coefficients) observed for methylglyoxal reaction mixtures, the lack of surface activity of glyoxal reaction mixtures, and the higher N/C ratios of aldehyde-amine reaction products relative to atmospheric WSOC and HULIS extracts. The overall optical, physical, and chemical similarities are consistent with, but not demonstrative of, Maillard chemistry being a significant secondary source of atmospheric HULIS. However, the higher N/C ratios of aldehyde-amine reaction products limits the source strength to ≤50% of atmospheric HULIS, assuming that other sources of HULIS incorporate only negligible quantities of nitrogen.