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The dispersed sources and inconvenient transportation of rural domestic waste (RDW) lead to difficult centralized treatment. Gasification is suitable for decentralized waste treatment, which can effectively avoid RDW long-distance transportation and reduce dioxin emissions compared with small-scale incineration. Hence, economically-affordable and environmentally-friendly RDW treatment models with different gasification scales are required, and village, town and county models were compared via life cycle assessment (LCA) and life cycle cost (LCC) methods in this study. Furthermore, scenario analysis investigated waste sorting based on two food waste (FW) treatment technologies, different FW separate collection efficiency, and electricity recovery to explore the environmental and economic improvement potentials of three models. LCA results show that electricity consumption and direct emissions are significant contributors to environmental impacts, and the county model outperforms village and town models. Moreover, transportation accounts for 6% of the overall environmental impact in the county model. Scenario analysis reveals that waste sorting and electricity recovery can reduce the overall environmental impact by 29% to 146% for three models. LCC results demonstrate that the town model delivers the lowest economic cost, while the village model is the highest. In scenario analysis, resource utilization of FW and electricity recovery of other waste exhibit promising economic benefits. The findings provide comprehensive references for sustainable RDW treatment.

Ensembl IDs for genes used to predict smoking status.

Supplemental Methods, Tables, and Figures

Purpose: Lung cancer is the leading cause of cancer-related death in the United States. The molecular events preceding the onset of disease are poorly understood, and no effective tools exist to identify smokers with premalignant lesions (PMLs) that will progress to invasive cancer. Prior work identified molecular alterations in the smoke-exposed airway field of injury associated with lung cancer. Here, we focus on an earlier stage in the disease process leveraging the airway field of injury to study PMLs and its utility in lung cancer chemoprevention.Experimental Design: Bronchial epithelial cells from normal appearing bronchial mucosa were profiled by mRNA-Seq from subjects with (n = 50) and without (n = 25) PMLs. Using surrogate variable and gene set enrichment analysis, we identified genes, pathways, and lung cancer–related gene sets differentially expressed between subjects with and without PMLs. A computational pipeline was developed to build and test a chemoprevention-relevant biomarker.Results: We identified 280 genes in the airway field associated with the presence of PMLs. Among the upregulated genes, oxidative phosphorylation was strongly enriched, and IHC and bioenergetics studies confirmed pathway findings in PMLs. The relationship between PMLs and squamous cell carcinomas (SCC) was also confirmed using published lung cancer datasets. The biomarker performed well predicting the presence of PMLs (AUC = 0.92, n = 17), and changes in the biomarker score associated with progression/stability versus regression of PMLs (AUC = 0.75, n = 51).Conclusions: Transcriptomic alterations in the airway field of smokers with PMLs reflect metabolic and early lung SCC alterations and may be leveraged to stratify smokers at high risk for PML progression and monitor outcome in chemoprevention trials. Clin Cancer Res; 23(17); 5091–100. ©2017 AACR.

Results of pathway enrichment using ROAST (FDR

GSEA results detailing lung cancer associated dataset enrichment among genes differentially expressed in the airway field associated with PMLs

Background Chronic tobacco smoke exposure results in a broad range of lung pathologies including emphysema, airway disease and parenchymal fibrosis as well as a multitude of extra-pulmonary comorbidities. Prior work using CT imaging has identified several clinically relevant subgroups of smoking related lung disease, but these investigations have generally lacked organ specific molecular correlates. Research Question Can CT imaging be used to identify clinical phenotypes of smoking related lung disease that have specific bronchial epithelial gene expression patterns to better understand disease pathogenesis? Study Design and Methods Using K-means clustering, we clustered participants from the COPDGene study (n = 5,273) based on CT imaging characteristics and then evaluated their clinical phenotypes. These clusters were replicated in the Detection of Early Lung Cancer Among Military Personnel (DECAMP) cohort (n = 360), and were further characterized using bronchial epithelial gene expression. Results Three clusters (preserved, interstitial predominant and emphysema predominant) were identified. Compared to the preserved cluster, the interstitial and emphysema clusters had worse lung function, exercise capacity and quality of life. In longitudinal follow-up, individuals from the emphysema group had greater declines in exercise capacity and lung function, more emphysema, more exacerbations, and higher mortality. Similarly, genes involved in inflammatory pathways (tumor necrosis factor-α, interferon-β) are more highly expressed in bronchial epithelial cells from individuals in the emphysema cluster, while genes associated with T-cell related biology are decreased in these samples. Samples from individuals in the interstitial cluster generally had intermediate levels of expression of these genes. Interpretation Using quantitative CT imaging, we identified three groups of individuals in older ever-smokers that replicate in two cohorts. Airway gene expression differences between the three groups suggests increased levels of inflammation in the most severe clinical phenotype, possibly mediated by the tumor necrosis factor-α and interferon-β pathways. Clinical Trial Registration COPDGene (NCT00608764), DECAMP-1 (NCT01785342), DECAMP-2 (NCT02504697)

Microscopic vascular invasion (VI) is predictive of recurrence in stage I lung adenocarcinoma (LUAD) but is difficult to assess in resection specimens and cannot be accurately predicted prior to surgery. Thus, new biomarkers are needed to identify this aggressive subset of stage I LUAD tumors. To assess molecular and tumor microenvironment (TME) features associated with angioinvasive LUAD we profiled 171 resected stage I tumors with and without VI by RNA-seq, including 16 tumors by high-resolution spatial transcriptomics (10x Genomics Visium). Visium capture areas were selected by an experienced thoracic pathologist to include invasive foci, tumor regions distal to foci, and tumors without invasive foci. We identified a robust molecular signature of VI from the RNA-seq data containing subclusters of genes involved in hallmark programs of tumor suppression, EMT, angiogenesis, growth and metabolism. This VI-associated signature increases across the spectrum of indolent to aggressive stage I LUAD histopathology and is predictive of recurrence-free survival. Analysis of 43,421 Visium spots across 16 tumors revealed high inter-tumor patient heterogeneity, with most spots clustering by tumor identity, suggesting tumor-intrinsic properties. Scoring the Visium data for VI signature expression revealed spatial variability around VI foci, with distinct spatial distributions of different signature subclusters among tumor and stromal compartments within and adjacent to regions of tumor intravasation. We found increased expression of the bulk VI signature in invasive tumors, regardless of whether the capture area contained the invasive focus. We independently verified this finding by performing laser-capture microdissection and RNA-seq from invaded vessel regions and uninvaded parenchyma of 8 additional tumors with VI and tumor regions of non-VI tumors. Given increased signature expression in regions of invasive tumors at a distance from VI foci, we leveraged our bulk RNA-seq dataset to develop a transcriptomic predictor of VI. We applied a nested cross-validation approach within a training cohort to select a machine learning model. We then evaluated the performance of our model in an independent test set. Finally, we generated over 200 pseudo-bulked in silico biopsies similar in size to standard transthoracic needle biopsies using the spatial data. The scores from these in silico biopsies were similar to predictions from matched bulk RNA-seq data, suggesting robustness to intra-tumor heterogeneity. Our combined bulk and spatial transcriptomics analysis suggests that VI-associated gene expression extends far from the site of intravasation and can be used to predict the presence of VI. This may enable the prediction of angioinvasive LUAD from small biopsy specimens, allowing for more tailored treatment prior to surgery. Citation Format: Dylan Steiner, Lila Sultan, Travis Sullivan, Emily Green, Hanqiao Liu, Xiaohui Xiao, Gang Liu, Avrum Spira, Sarah Mazzilli, Kimberly Rieger-Christ, Eric Burks, Jennifer Beane, Marc Lenburg. Evaluating a novel molecular biomarker of angioinvasive lung adenocarcinoma with spatial transcriptomics. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5632.

Plant cell expands via a tip growth or diffuse growth mode. In plants, RabA is the largest group of Rab GTPases that regulate vesicle trafficking. The functions of RabA protein in modulating polarized expansion in tip growth cells have been demonstrated. However, whether and how RabA protein functions in diffuse growth plant cells have never been explored. Here, we addressed this question by examining the role of GhRabA4c in cotton fibers. GhRabA4c was preferentially expressed in elongating fibers with its protein localized to endoplasmic reticulum and Golgi apparatus. Over- and down-expression of GhRabA4c in cotton lead to longer and shorter fibers, respectively. GhRabA4c interacted with GhACT4 to promote the assembly of actin filament to facilitate vesicle transport for cell wall synthesis. Consistently, GhRabA4c-overexpressed fibers exhibited increased content of wall components and the transcript levels of the genes responsible for the synthesis of cell wall materials. We further identified two MYB proteins that directly regulate the transcription of GhRabA4c. Collectively, our data showed that GhRabA4c promotes diffused cell expansion by supporting vesicle trafficking and cell wall synthesis.

Background: SARS-CoV-2 infection and disease severity are influenced by viral entry (VE) gene expression patterns in airway epithelium. The similarities and differences of VE gene expression (ACE2, TMPRSS2, and CTSL) across nasal and bronchial compartments has not been fully characterized using matched samples from large cohorts. Results: Gene expression data from 793 nasal and 1,673 bronchial brushes obtained from individuals participating in lung cancer screening or diagnostic workup revealed that smoking was the only clinical factor significantly and reproducibly associated with VE gene expression. ACE2 and TMPRSS2 expression were higher in smokers in the bronchus but not in the nose. scRNA-seq of nasal brushings indicated that ACE2 co-expressed genes were highly expressed in club and C15orf48+ secretory cells while TMPRSS2 co-expressed genes were highly expressed in keratinizing epithelial cells. In contrast, these ACE2 and TMPRSS2 modules were highly expressed in goblet cells in scRNA-seq from bronchial brushings. Cell-type deconvolution of the RNA-seq confirmed that smoking increased the abundance of several secretory cell populations in the bronchus, but only goblet cells in the nose. Conclusions: The association of ACE2 and TMPRSS2 with smoking in the bronchus is due to their high expression in goblet cells which increase in abundance in current smoker airways. In contrast, in the nose these genes are not predominantly expressed in cell populations modulated by smoking. Smoking-induced VE gene expression changes in the nose likely has minimal impact on SARS-CoV-2 infection, but in the bronchus, smoking may lead to higher viral loads and more severe disease.

ObjectivesDiscovering airway gene expression alterations associated with radiological bronchiectasis may improve the understanding of the pathobiology of early-stage bronchiectasis.MethodsPresence of radiological bronchiectasis in 173 individuals without a clinical diagnosis of bronchiectasis was evaluated. Bronchial brushings from these individuals were transcriptomically profiled and analysed. Single-cell deconvolution was performed to estimate changes in cellular landscape that may be associated with early disease progression.Results20 participants have widespread radiological bronchiectasis (three or more lobes). Transcriptomic analysis reflects biological processes associated with bronchiectasis including decreased expression of genes involved in cell adhesion and increased expression of genes involved in inflammatory pathways (655 genes, false discovery rate 2fold-change >0.25). Deconvolution analysis suggests that radiological bronchiectasis is associated with an increased proportion of ciliated and deuterosomal cells, and a decreased proportion of basal cells. Gene expression patterns separated participants into three clusters: normal, intermediate and bronchiectatic. The bronchiectatic cluster was enriched by participants with more lobes of radiological bronchiectasis (pConclusionsGenes involved in cell adhesion, Wnt signalling, ciliogenesis and interferon-γ pathways had altered expression in the bronchus of participants with widespread radiological bronchiectasis, possibly associated with decreased basal and increased ciliated cells. This gene expression pattern is not only highly enriched among individuals with radiological bronchiectasis, but also associated with airway-related symptoms in those without discernible radiological bronchiectasis, suggesting that it reflects a bronchiectasis-associated, but non-bronchiectasis-specific lung pathophysiological process.

BACKGROUND: Although e-cigarette (ECIG) use has increased in the United States, their potential health effects remain uncertain. Understanding the effects of tobacco cigarette (TCIG) smoke on bronchial airway epithelial gene expression have previously provided insights into tobacco-related disease pathogenesis. Identifying the impact of ECIGs on airway gene expression could provide insights into their potential long-term health effects. We sought to compare the bronchial airway gene-expression profiles of former TCIG smokers now using ECIGs with the profiles of former and current TCIG smokers. METHODS: We performed gene-expression profiling of bronchial epithelial cells collected from current TCIG smokers (n = 9), current ECIG users who are former TCIG smokers (n = 15), and former TCIG smokers (n = 21). We then compared our findings with previous studies of the effects of TCIG use on bronchial epithelium, as well an in vitro model of ECIG exposure. RESULTS: Among 3,165 genes whose expression varied between the three study groups (q < 0.05), we identified 468 genes altered in ECIG users relative to former smokers (P < .05). Seventy-nine of these genes were up- or down-regulated concordantly among ECIG and TCIG users. We did not detect ECIG-associated gene-expression changes in known pathways associated with TCIG usage. Genes downregulated in ECIG users are enriched among the genes most downregulated by exposure of airway epithelium to ECIG vapor in vitro. CONCLUSIONS: ECIGs induce both distinct and shared patterns of gene expression relative to TCIGs in the bronchial airway epithelium. The concordance of the genes altered in ECIG users and in the in vitro study suggests that genes altered in ECIG users are likely to be changed as the direct effect of ECIG exposure.

Bronchial premalignant lesions (PMLs) are precursors of lung squamous cell carcinoma, but have variable outcome, and we lack tools to identify and treat PMLs at risk for progression to cancer. Here we report the identification of four molecular subtypes of PMLs with distinct differences in epithelial and immune processes based on RNA-Seq profiling of endobronchial biopsies from high-risk smokers. The Proliferative subtype is enriched with bronchial dysplasia and exhibits up-regulation of metabolic and cell cycle pathways. A Proliferative subtype-associated gene signature identifies subjects with Proliferative PMLs from normal-appearing uninvolved large airway brushings with high specificity. In progressive/persistent Proliferative lesions expression of interferon signaling and antigen processing/presentation pathways decrease and immunofluorescence indicates a depletion of innate and adaptive immune cells compared with regressive lesions. Molecular biomarkers measured in PMLs or the uninvolved airway can enhance histopathological grading and suggest immunoprevention strategies for intercepting the progression of PMLs to lung cancer., Bronchial premalignant lesions can potentially progress to lung squamous cell carcinoma. Here, the authors profile bronchial biopsies from high-risk smokers by RNA sequencing and identify four molecular subtypes of premalignant lesions and an immune molecular signature that associates with lesion progression.

The molecular events involved in the development of bronchial premalignant lesions (PMLs), and their progression to lung squamous cell carcinoma, are not well understood. Prior work characterized lung PML molecular subtypes by identifying co-expressed gene modules associated with histologic severity and progression/persistence. The proliferative subtype was enriched for PMLs with dysplasia. Genes related to interferon signaling and antigen processing/presentation (Module 9) were decreased in progressive/persistent lesions within this subtype, suggesting early immune suppression is related to PML progression. However, the mechanisms that drive these alterations are unclear. We investigated the role of microRNAs (miRNAs) in regulating gene expression associated with PML outcomes. mRNA and miRNA were extracted and sequenced from longitudinally collected endobronchial biopsies from patients with PMLs (148 samples, 30 patients). miRNAs targeting each gene co-expression module were identified based on target gene enrichment and the degree of negative correlation between the miRNA expression and its targets. Expression association with outcome within the proliferative subtype was tested with a mixed effects model adjusting for batch and patient as random effect. Cell type specificity of miRNA expression was tested based on cell type specific sequencing data from FANTOM5 and cell type marker correlation analysis. Genes regulated by NLRC5 were identified with ChIPseq data from Ludigs et al. Target gene suppression was confirmed by transfecting SW900 cells with miR-149-5p. miR-149-5p level in PML biopsies was examined by miRNA in situ hybridization (miR-ISH). miR-149-5p is identified as potential regulator of Module 9 gene expression and is significantly up-regulated in progressive/persistent PMLs. Its expression is highly enriched in epithelial cells in FANTOM5 and positively correlates with basal cell markers within PMLs. Predicted targets of miR-149-5p are down-regulated in the progressive PMLs in both our and data from Merrick et al. MHC-I and related gene expressions are down-regulated in progressing/persistent PMLs. These genes are regulated by the transcriptional coactivator NLRC5 which is a predicted target gene of miR-149-5p. We find that overexpressing miR-149-5p in SW900 cells decreases the expression levels of both NLRC5 and NLRC5 regulated genes. Additionally, miR-ISH targeting miR-149-5p in proliferative biopsy samples confirm its expression in epithelium compartment and association with outcome. Our data suggest epithelial miR-149-5p might be a key regulator of gene expression contributing to PML progression. We hypothesize that by suppressing NLRC5, miR-149-5p inhibits MHC-I gene expression of epithelial cells, promoting early immune depletion and lesion progression. miR-149-5p might therefore be a therapeutic target for preventing PML progression. Citation Format: Boting Ning, Roxana M. Pfefferkorn, Gang Liu, Sherry Zhang, Hanqiao Liu, Christopher Stevenson, Sarah A. Mazzilli, Avrum E. Spira, Marc E. Lenburg, Jennifer E. Beane. The role of epithelial miR-149 in immune modulation and progression of bronchial premalignant lesions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1488.

Coronavirus Disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 SARS-CoV-2), which infects host cells with help from the Viral Entry (VE) proteins ACE2, TMPRSS2, and CTSL1–4. Proposed risk factors for viral infection, as well as the rate of disease progression, include age5,6, sex7, chronic obstructive pulmonary disease7,8, cancer9, and cigarette smoking10–13. To investigate whether the proposed risk factors increase viral infection by modulation of the VE genes, we examined gene expression profiles of 796 nasal and 1,673 bronchial samples across four lung cancer screening cohorts containing individuals without COVID-19. Smoking was the only clinical factor reproducibly associated with the expression of any VE gene across cohorts. ACE2 expression was significantly up-regulated with smoking in the bronchus but significantly down-regulated with smoking in the nose. Furthermore, expression of individual VE genes were not correlated between paired nasal and bronchial samples from the same patients. Single-cell RNA-seq of nasal brushings revealed that an ACE2 gene module was detected in a variety of nasal secretory cells with the highest expression in the C15orf48+ secretory cells, while a TMPRSS2 gene module was most highly expressed in nasal keratinizing epithelial cells. In contrast, single-cell RNA-seq of bronchial brushings revealed that ACE2 andTMPRSS2 gene modules were most enriched in MUC5AC+ bronchial goblet cells. The CTSL gene module was highly expressed in immune populations of both nasal and bronchial brushings. Deconvolution of bulk RNA-seq showed that the proportion of MUC5AC+ goblet cells was increased in current smokers in both the nose and bronchus but proportions of nasal keratinizing epithelial cells, C15orf48+ secretory cells, and immune cells were not associated with smoking status. The complex association between VE gene expression and smoking in the nasal and bronchial epithelium revealed by our results may partially explain conflicting reports on the association between smoking and SARS-CoV-2 infection.

ObjectiveThe immune response to invasive carcinoma has been the focus of published work, but little is known about the adaptive immune response to bronchial premalignant lesions (PMLs), precursors of lung squamous cell carcinoma. This study was designed to characterize the T cell receptor (TCR) repertoire in PMLs and its association with clinical, pathological, and molecular features.MethodsEndobronchial biopsies (n=295) and brushings (n=137) from high-risk subjects (n=50), undergoing lung cancer screening at approximately 1-year intervals via autofluorescence bronchoscopy and CT, were profiled by RNA-seq. We applied the TCR Repertoire Utilities for Solid Tissue/Tumor (TRUST) tool to the RNA-seq data to identify TCR CDR3 sequences across all samples. In the biopsies, we measured the correlation of TCR diversity with previously derived immune-associated PML transcriptional signatures and outcome. We also quantified the spatial and temporal distribution of shared and clonally expanded TCRs. Using the biopsies and brushes, the ratio of private (i.e., found in one patient only) and public (i.e., found in two or more patients) TCRs was quantified and the CDR3 sequences were compared to those found in curated databases with known antigen specificities.ResultsWe detected 39,303 unique TCR sequences across all samples. In PML biopsies, TCR diversity was negatively associated with a transcriptional signature of T-cell mediated immune activation (Spearman’s rho −0.34, p < 0.001) associated with PML outcome.Additionally, in lesions of the proliferative molecular subtype, TCR diversity was decreased in regressive versus progressive/persistent PMLs (p=0.045). Within each patient, TCRs were more likely to be shared between biopsies sampled at the same timepoint than biopsies sampled at the same anatomic location at different times. Clonally expanded TCRs, within a biopsied lesion, were more likely to be expanded at future time points than non-expanded clones. The majority of TCR sequences were found in a single sample, with only 3,396 (8.6%) found in more than one sample and 1,057 (2.7%) found in two or more patients (i.e. public), however, when compared to a public database of CDR3 sequences, 4,543 (11.6%) of TCRs were identified as public. TCRs with known antigen specificities were enriched among Public TCRs (p < 0.001).ConclusionsDecreased TCR diversity may reflect nascent immune responses that contribute to PML elimination. Further studies are needed to explore the potential for immunoprevention of PMLs.

Introduction: Although three randomized control trials have proven mortality benefit of CT lung cancer screening (CTLS)

The surge of medical waste (MW) generated during the COVID-19 pandemic has exceeded the disposal capacity of existing facilities. The timely, safe, and efficient emergency disposal of MW is critical to prevent the epidemic spread. Therefore, this review presents the current status of MW generation and disposal in China and analyzes the characteristics and applicability of emergency disposal technologies. The results show that movable disposal facilities can dispose of infectious MW on site, even though most of their disposal capacity is at a low level (, Graphical abstract Unlabelled Image

In this study, dilute nitric acid was selected as the catalyst to pretreat corn stover. The effects of nitric acid pretreatments on the efficiency of acidogenic fermentation and the acidogenic characteristic of prehydrolysates were evaluated. The results showed that about 97% hemicelluloses were recovered at the optimal condition (150 °C, 0.6% HNO3, 2 min). Acidogenic fermentation of prehydrolysate B (the highest yield of total sugar) obtained at the optimal condition proved to be more efficient compared with prehydrolysate A (no inhibitor) and prehydrolysate C (the highest yield of inhibitors), the VFAs concentration can reach the highest level, and the distribution of VFAs exhibited butyric acid type fermentation; this was more suitable for subsequent methanogenic fermentation. This research provided an effective and suitable method for accelerating biogas production from corn stover.

ObjectiveThe immune response to invasive carcinoma has been the focus of published work, but little is known about the adaptive immune response to bronchial premalignant lesions (PMLs), precursors of lung squamous cell carcinoma. This study was designed to characterize the T cell receptor (TCR) repertoire in PMLs and its association with clinical, pathological, and molecular features.MethodsEndobronchial biopsies (n=295) and brushings (n=137) from high-risk subjects (n=50), undergoing lung cancer screening at approximately 1-year intervals via autofluorescence bronchoscopy and CT, were profiled by RNA-seq. We applied the TCR Repertoire Utilities for Solid Tissue/Tumor tool to the RNA-seq data to identify TCR CDR3 sequences across all samples. In the biopsies, we measured the correlation of TCR diversity with previously derived immune-associated PML transcriptional signatures and PML outcome. We also quantified the spatial and temporal distribution of shared and clonally expanded TCRs. Using the biopsies and brushes, the ratio of private (ie, found in one patient only) and public (ie, found in two or more patients) TCRs was quantified, and the CDR3 sequences were compared with those found in curated databases with known antigen specificities.ResultsWe detected 39,303 unique TCR sequences across all samples. In PML biopsies, TCR diversity was negatively associated with a transcriptional signature of T cell mediated immune activation (p=4e-4) associated with PML outcome. Additionally, in lesions of the proliferative molecular subtype, TCR diversity was decreased in regressive versus progressive/persistent PMLs (p=0.045). Within each patient, TCRs were more likely to be shared between biopsies sampled at the same timepoint than biopsies sampled at the same anatomic location at different times. Clonally expanded TCRs, within a biopsied lesion, were more likely to be expanded at future time points than non-expanded clones. The majority of TCR sequences were found in a single sample, with only 3396 (8.6%) found in more than one sample and 1057 (2.7%) found in two or more patients (ie, public); however, when compared with a public database of CDR3 sequences, 4543 (11.6%) of TCRs were identified as public. TCRs with known antigen specificities were enriched among public TCRs (pConclusionsDecreased TCR diversity may reflect nascent immune responses that contribute to PML elimination. Further studies are needed to explore the potential for immunoprevention of PMLs.

Background: Diesel engine exhaust (DEE) is classified as a Group 1 human carcinogen by the International Agency for Research on Cancer because of its carcinogenicity to the lung. However, the underlying molecular mechanisms of DEE carcinogenicity are not well understood. Methods: We previously conducted a cross-sectional molecular epidemiology study of diesel engine factory workers exposed to a wide range of DEE and unexposed comparable controls. Here, we carried out a pilot study of a representative subgroup of 19 exposed workers (total n = 54) and 19 unexposed controls (total n = 55). We measured serum level of 1238 targeted proteins using the SOMAScan assay (SOMALogic, Boulder, CA), which measures protein involved in a wide range of biological processes. We used linear regression to identify proteins associated with DEE (permutation p-value Results: Occupational exposure to DEE was significantly associated with altered levels of 22 serum proteins. Of these, 13 proteins (CXCL11, HAPLN1, FLT4, CD40LG, PES1, IGHE.IGK..IGL, TNFSF9, PGD, NAGK, CCL25, CCL4L1, PDXK, and PLA2G1B) showed a significant exposure-response relationship with EC (p-trend Conclusion: Results from our pilot study suggest that DEE exposure is associated with alteration of multiple proteins in the serum, which play a role in inflammation and immune regulation. Analysis of a larger sample size will be needed to confirm our findings. Citation Format: Mohammad L. Rahman, Yufei Dai, Roel Vermeulen, Wei Hu, Bryan Bassig, Eduard Drizik, Sean Corbett, Dianzhi Ren, Huawei Duan, Yong Niu, Jun Xu, Wei Fu, Kees Meliefste, Baosen Zhou, Xiaohui Zhang, Jufang Yang, Hanqiao Liu, Meng Ye, Gang Liu, Xiaowei Jia, Tao Meng, Ping Bin, Avrum Spira, Marc E. Lenburg, Debra Silverman, Nathaniel Rothman, Yuxin Zheng, Qing Lan. Proteomic analysis of serum in workers exposed to diesel engine exhaust [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 856.

A chemopreventive effect of aspirin (ASA) on lung cancer risk is supported by epidemiologic and preclinical studies. We conducted a randomized, double-blinded study in current heavy smokers to compare modulating effects of intermittent versus continuous low-dose ASA on nasal epithelium gene expression and arachidonic acid (ARA) metabolism. Fifty-four participants were randomized to intermittent (ASA 81 mg daily for one week/placebo for one week) or continuous (ASA 81 mg daily) for 12 weeks. Low-dose ASA suppressed urinary prostaglandin E2 metabolite (PGEM; change of −4.55 ± 11.52 from baseline 15.44 ± 13.79 ng/mg creatinine for arms combined, P = 0.02), a surrogate of COX-mediated ARA metabolism, but had minimal effects on nasal gene expression of nasal or bronchial gene-expression signatures associated with smoking, lung cancer, and chronic obstructive pulmonary disease. Suppression of urinary PGEM correlated with favorable changes in a smoking-associated gene signature (P < 0.01). Gene set enrichment analysis (GSEA) showed that ASA intervention led to 1,079 enriched gene sets from the Canonical Pathways within the Molecular Signatures Database. In conclusion, low-dose ASA had minimal effects on known carcinogenesis gene signatures in nasal epithelium of current smokers but results in wide-ranging genomic changes in the nasal epithelium, demonstrating utility of nasal brushings as a surrogate to measure gene-expression responses to chemoprevention. PGEM may serve as a marker for smoking-associated gene-expression changes and systemic inflammation. Future studies should focus on NSAIDs or agent combinations with broader inhibition of pro-inflammatory ARA metabolism to shift gene signatures in an anti-carcinogenic direction.

NAC protein is a large plant specific transcription factor family, which plays important roles in the response to abiotic stresses. However, the regulation mechanism of most NAC proteins in drought stress remains to be further uncovered. In this study, we elucidated the molecular functions of a NAC protein, GhirNAC2, in response to drought stress in cotton. GhirNAC2 was greatly induced by drought and phytohormone abscisic acid (ABA). Subcellular localization demonstrated that GhirNAC2 was located in the nucleus. Co-suppression of GhirNAC2 in cotton led to larger stomata aperture, elevated water loss and finally reduced transgenic plants tolerance to drought stress. Furthermore, the endogenous ABA content was significantly lower in GhirNAC2-suppressed transgenic plant leaves compared to wild type. in vivo and in vitro studies showed that GhirNAC2 directly binds to the promoter of GhNCED3a/3c, key genes in ABA biosynthesis, which were both down-regulated in GhirNAC2-suppressed transgenic lines. Transient silencing of GhNCED3a/3c also significantly reduced the resistance to drought stress in cotton plants. However, ectopic expression of GhirNAC2 in tobacco significantly enhanced seed germination, root growth and plant survival under drought stress. Taken together, GhirNAC2 plays a positive role in cotton drought tolerance, which functions by modulating ABA biosynthesis and stomata closure via regulating GhNCED3a/3c expression.

Novel microchannel heat sinks (MCHSs) with cavities and fins are put forward for the cooling demand of microelectronic devices with high heat production. The flow and convective heat transfer of the microchannels with isosceles triangular cavities and four different fins, including rectangular fins, streamlined fins, backward drop-shaped fins and forward drop-shaped fins, are studied numerically for Reynolds number (Re) ranging of 173–635, i.e. flow rate (Qv) ranging of 12–54 ml/min. Firstly, the combined effect of the cavities and fins on the thermal and hydraulic characteristics is analyzed. Secondly, the field synergy principle is adopted to explore the synergy between the fluid temperature and velocity fields; the entropy generation is used to investigate the thermodynamic performance and the irreversibility for different MCHSs in terms of second law of thermodynamics. Lastly, the effect of fin shape on the comprehensive performance of the complex MCHSs is evaluated based on thermal resistance and performance evaluation criterion (PEC). Results indicate that the novel designs present conspicuous heat transfer improvement owing to the redevelopment of boundary layer, intensive secondary flow and effective chaotic mixing compared to conventional rectangular microchannel (R). According to the field synergy principle and thermodynamic analysis, the superior thermal performance of the novel MCHSs can be attributed to the improved synergy between the temperature and flow fields, and the reduction of total irreversible loss. But the micro structures lead to the mainstream separation, acceleration and disturbance, which increase the pressure drop and friction loss. Nevertheless, the comprehensive performance of the complex MCHSs has been improved obviously compared to the conventional one. Among the novel heat sinks, the microchannel with isosceles triangular cavities and forward drop-shaped fins acquires the greatest overall performance with PEC = 1.617 at Qv = 36 ml/min, with the advantage of the notably enhanced thermal performance accompanied by the acceptable pressure drop.

Background: Diesel engine exhaust (DEE) exposure causes lung cancer, but the molecular mechanisms by which this occurs are not well understood. Objectives: To assess transcriptomic alterations in nasal epithelium of DEE-exposed factory workers to better understand the cellular and molecular effects of DEE. Methods: Nasal epithelial brushings were obtained from 41 diesel engine factory workers exposed to relatively high levels of DEE (17.2–105.4 μg/m3), and 38 unexposed workers from factories without DEE exposure. mRNA was profiled for gene expression using Affymetrix microarrays. Linear modeling was used to identify differentially expressed genes associated with DEE exposure and interaction effects with current smoking status. Pathway enrichment among differentially expressed genes was assessed using EnrichR. Gene Set Enrichment Analysis (GSEA) was used to compare gene expression patterns between datasets. Results: 225 genes had expression associated with DEE exposure after adjusting for smoking status (FDR q

Hospital solid waste (HSW) incinerator fly ash was designated as a special controlled waste because of its high concentrations of toxic heavy metals, polychlorinated dibenzo-p-dioxins, and dibenzofurans (PCDD/Fs). Most of the PCDD/Fs along with carbon constituents including powder activated carbon and unburned carbon in fly ash could be removed by column flotation on the basis of their hydrophobicity. The feasibility of extracting heavy metals from fly ash by adding a little of hydrochloric acid to the slurry during the flotation process was examined in this paper. The results showed that the acidic pulp could contribute to the high extraction ratio of the heavy metals, but the performance of decarburization and removal of PCDD/Fs was inhibited at very low pH value. Given consideration to the removal of two toxic matter including PCDD/Fs and heavy metals in HSW incinerator fly ash, the appropriate pulp pH value should be controlled at about 5. After flotation, both PCDD/Fs and heavy metals in the tailings...

Production of glass-ceramics by sintering the molten slag obtained from electric arc furnace treatment of fly ash was investigated. The effect of washing pretreatment prior to melting the fly ash on the microstructure and properties of the glass-ceramics was examined. The results show that washing pretreatment of fly ash can decrease alkali metal chloride and increase network former in fly ash, which results in the increase of peak crystallization temperature of parent glass and strengthening of properties of bending strength and chemical stability of the glass-ceramics. The optimal heat treatment temperature for parent glass of washed fly ash is 1 173 K, at which the crystalline phase of glass-ceramics is composed of gelignite (Ca2Al2SiO7) and akermanite (Ca2MgSi2O7). Glass-ceramics produced at optimal heat treatment temperature are excellent in term of the physical and chemical properties and leaching characteristics, indicating attractive potential as substitute of nature materials.

Purpose: Lung cancer is the leading cause of cancer-related death in the United States. The molecular events preceding the onset of disease are poorly understood, and no effective tools exist to identify smokers with premalignant lesions (PMLs) that will progress to invasive cancer. Prior work identified molecular alterations in the smoke-exposed airway field of injury associated with lung cancer. Here, we focus on an earlier stage in the disease process leveraging the airway field of injury to study PMLs and its utility in lung cancer chemoprevention. Experimental Design: Bronchial epithelial cells from normal appearing bronchial mucosa were profiled by mRNA-Seq from subjects with (n = 50) and without (n = 25) PMLs. Using surrogate variable and gene set enrichment analysis, we identified genes, pathways, and lung cancer–related gene sets differentially expressed between subjects with and without PMLs. A computational pipeline was developed to build and test a chemoprevention-relevant biomarker. Results: We identified 280 genes in the airway field associated with the presence of PMLs. Among the upregulated genes, oxidative phosphorylation was strongly enriched, and IHC and bioenergetics studies confirmed pathway findings in PMLs. The relationship between PMLs and squamous cell carcinomas (SCC) was also confirmed using published lung cancer datasets. The biomarker performed well predicting the presence of PMLs (AUC = 0.92, n = 17), and changes in the biomarker score associated with progression/stability versus regression of PMLs (AUC = 0.75, n = 51). Conclusions: Transcriptomic alterations in the airway field of smokers with PMLs reflect metabolic and early lung SCC alterations and may be leveraged to stratify smokers at high risk for PML progression and monitor outcome in chemoprevention trials. Clin Cancer Res; 23(17); 5091–100. ©2017 AACR.

Background: Lung squamous cell carcinoma (SqCC) arises in the epithelial layer of the bronchial airway and is often preceded by the development of premalignant lesions. However, not all premalignant lesions progress to lung SqCC and many will regress spontaneously. Understanding the somatic alterations and molecular subtypes associated with progression will allow us to identify biomarkers for early detection and develop therapeutic strategies for disease prevention and interception. Methods: Biopsies were obtained from high-risk smokers undergoing lung cancer screening by auto-fluorescence bronchoscopy and CT at the Roswell Park Cancer Institute. For each subject, multiple sites were sampled repeatedly over time. One biopsy from each region was sent for pathological review while another biopsy was taken for molecular studies. Whole-exome sequencing (WES) was performed at Uniform Services University to 120x coverage and RNA-seq was performed at Boston University School of Medicine. Results: The median number of somatic mutations across all premalignant lesions that underwent DNA-seq (150 biopsies from 20 subjects) was 0.45 per megabase and displayed a modest association with histological grade (p=0.05). The most frequently mutated known lung cancer genes included NOTCH1 (14%), TP53 (6%), FAT1 (3%), PIK3CA (2%), KRAS ( Citation Format: Joshua D. Campbell, Xijun Zhang, Catalina Perdomo, Sarah Mazzilli, Yaron Geshalter, Samjot S. Dhillon, Gang Liu, Sherry Zhang, Hanqiao Liu, Jessica Vick, Christopher Moy, Stefano Monti, Evan Johnson, Matthew Meyerson, Matthew Wilkerson, Clifton Dalgard, Suso Platero, Chris Stevenson, Marc Lenburg, Mary Reid, Jennifer Beane, Avrum Spira. Genomic characterization of premalignant lung squamous cell carcinoma lesions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3248.

Fibrotic lung diseases are characterized by excess extracellular matrix production, in particular type I collagen. Phenylbutyrate (PB) is a non-toxic pharmacological compound that functions as a weak histone deacetylase inhibitor. In hepatic stellate cells, the synthesis of type I collagen expression is decreased by inhibiting histone acetylation. Our studies examined the regulation of type I collagen by PB in human lung fibroblasts. We found that PB decreases basal and transforming growth factor-beta-stimulated alpha1(I) collagen mRNA and protein levels. Northern blot analyses demonstrated that PB decreases steady-state alpha1(I) collagen mRNA levels by 78% without significantly changing the stability of the mRNA transcript. PB stimulates cAMP production and increases the acetylation of histone H4, but does not affect the activity of two transforming growth factor-beta (TGF-beta)-responsive luciferase reporter constructs. These data suggest that PB regulates type I collagen expression in human lung fibroblasts by mechanisms that include cAMP production and histone acetylation. PB may have therapeutic use in fibrotic lung diseases.

Transforming growth factor-β (TGF-β) and interleukin-4 (IL-4) have fibrogenic properties and induce extracellular matrix production in a variety of lung diseases. Connective tissue growth factor (CTGF) is a matrix signaling molecule stimulated by TGF-β that in part mediates α1(I) collagen mRNA expression. In these studies, the regulation of CTGF expression by IL-4 in human lung fibroblasts was examined. Following 6 h of stimulation with IL-4, basal CTGF mRNA levels were unchanged as assessed by Northern blot analysis. However, IL-4 attenuated the TGF-β-stimulated induction of CTGF mRNA expression by 50%. This effect was selective because IL-4 did not affect fibronectin or α1(I) collagen mRNA expression induced by TGF-β. Experiments employing the transcriptional inhibitor actinomycin D suggest that IL-4 did not affect the stability of the CTGF mRNA. Transient transfection assays with 3TP-Lux, a luciferase gene controlled by a TGF-β inducible promoter, and with a CTGF promoter construct indicate that IL-4 interfered with the TGF-β-induced transcriptional activation of the CTGF gene. J. Cell. Biochem. 85: 496–504, 2002. © 2002 Wiley-Liss, Inc.

Background: Squamous cell carcinoma (SCC) of the lung is a leading cause of cancer mortality in the US due to late stage diagnosis and lack of effective treatments. Lung SCC arises in the epithelial layer of the bronchial airways and is often preceded by the development of premalignant lesions (PMLs). The molecular events involved in the progression of PMLs to lung SCC are not clearly understood, and not all PMLs go on to form carcinoma. By molecularly characterizing PMLs and non-lesion areas in the airway of individuals with PMLs, we hypothesize that we will be able to identify subgroups of PMLs that are more likely to progress. Methods: We used mRNA sequencing to profile biopsies obtained from high-risk smokers undergoing lung cancer screening by auto-fluorescence bronchoscopy and CT at the Roswell Park Cancer Institute in Buffalo, NY. For each subject (n=30), we sampled bronchial biopsies repeatedly over time (394 +/- 170 days) with serial bronchoscopies (6 +/- 5 biopsies/subject) as the biopsied area progressed towards or regressed away from frank malignancy. mRNA-Seq (n=197 biopsies) data was aligned to hg19 using STAR, and gene/transcript levels were summarized using RNA-Seq using RSEM and Ensembl 74 annotation. Immune, stromal, and epithelial cells content were inferred using the ESTIMATE algorithm and pathway activity of in vitro derived oncogenic signatures was estimated using GSVA for each sample. Molecular subtypes were derived using non-negative matrix factorization (NMF) and consensus clustering. Linear modeling was used to associate PML outcome metrics and pathway activity scores with subtype membership. Results: We identified six distinct molecular subtypes of bronchial biopsies using NMF across the 10% most variable genes (n=2,322 gene). One subtype contained samples with stable high-grade histology (p Conclusions: Molecular classification of premalignant lesions may lead to biomarkers of disease progression that could be used to stratify patients into prevention trials and to monitor efficacy of the treatment. Additionally, the results suggest that personalized interventions targeting specific cancer-related pathways or the immune system may be have potential therapeutic benefits. Citation Format: Jennifer E. Beane, Sarah Mazzilli, Joshua Campbell, Christopher Moy, Michael Schaffer, Catalina Perdomo, David Jenkins, Gang Liu, Sherry Zhang, Hanqiao Liu, Jessica Vick, Evan Johnson, Suso Platero, Marc Lenburg, Mary Reid, Samjot S. Dhillon, Avrum Spira. Premalignant squamous cell lung carcinoma lesions have distinct molecular subtypes associated with histologic progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5002. doi:10.1158/1538-7445.AM2017-5002

This study investigated a novel route for fast acidogenic fermentation of corn stover through a two-step method. Corn stover was first hydrolyzed by nitric acid, and the hydrolysate was then used for acidogenic fermentation. The results showed that the yields of soluble xylose, arabinose, and glucose in hydrolysate obtained from HNO3 hydrolysis of corn stover at the optimum condition achieved 96.86% of initial xylose, 98.54% of initial arabinose, and 18.58% of initial glucose, respectively. Acidogenic fermentation of hydrolysate proved to be effective, compared to acidogenic fermentation of raw corn stover; the production of volatile fatty acids (VFAs) increased by 54.8%, fermentation time decreased by 50%, and the distribution of VFAs was more suitable for subsequent methanogenic fermentation. This research provided an effective, suitable, and economical method for biogas production from corn stover.

Introduction We have previously shown that gene expression alterations in the cytologically-normal mainstem bronchus can be leveraged as a biomarker for lung cancer detection (Silvestri et al. NEJM 2015), a test that is now used clinically. Extending this approach, we hypothesized that bronchial microRNA (miRNA) expression is altered in patients with lung cancer and that incorporating miRNA expression into the mRNA classifier may improve its performance. Methods Using bronchial brushes collected prospectively from current and former smokers undergoing bronchoscopy for suspect lung cancer across 28 medical centers as part of the AEGIS 1 and 2 clinical trials, we profiled miRNA expression via small RNA sequencing of 341 patients for which gene expression data was also available on the same bronchial brush sample. Patients were followed for up to one year post-bronchoscopy until a final diagnosis was established. 138 patients from AEGIS 1 (88 cancer-positive and 50 cancer-free) served as a discovery set, while other 203 patients from AEGIS 1 and 2 (103 cancer-positive and 100 cancer-free) were used as an independent test set. First, we identified miRNAs whose expression is associated with cancer by linear modeling in the discovery set. We next explored the relationships between the expression of these miRNAs and their predicted mRNA targets. Lastly, using logistic regression, we incorporated a cancer miRNA feature into our bronchial gene-expression classifier (Silvestri et al., NEJM 2015) and validated its performance in the test set. Results We found that expression profiles of 42 miRNAs were associated with cancer status in the discovery set (p Conclusions We have established that there are alterations in miRNA expression in the cytologically normal mainstem bronchus of smokers with lung cancer. Importantly, we demonstrated the potential of these miRNA alterations to improve the performance of an existing bronchial gene expression biomarker for lung cancer detection. Citation Format: Ana Brandusa Pavel, Joshua Campbell, Gang Liu, Sherry Zhang, Hanqiao Liu, Ji Xiao, Kate Porta, Duncan Whitney, Steven Dubinett, David Elashoff, Marc Lenburg, Avrum Spira. microRNA expression in bronchial epithelium for lung cancer detection. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1954.