Circulating cell-free DNA methylation-based multi-omics analysis allows early diagnosis of pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with a 5-year survival rate of 7.2% in China. However, effective approaches for diagnosis of PDAC are limited. Tumor-originating genomic and epigenomic aberration in circulating free DNA (cfDNA) have potential as liquid biopsy biomarkers for cancer diagnosis. Our study aims to assess the feasibility of cfDNA-based liquid biopsy assay for PDAC diagnosis. In this study, we performed parallel genomic and epigenomic profiling of plasma cfDNA from Chinese PDAC patients and healthy individuals. Diagnostic models were built to distinguish PDAC patients from healthy individuals. Cancer-specific changes in cfDNA methylation landscape were identified, and a diagnostic model based on six methylation markers achieved high sensitivity (88.7% for overall cases and 78.0% for stage I patients) and specificity (96.8%), outperforming the mutation-based model significantly. Moreover, the combination of the methylation-based model with carbohydrate antigen 19-9 (CA19-9) levels further improved the performance (sensitivity: 95.7% for overall cases and 95.5% for stage I patients; specificity: 93.3%). In conclusion, our findings suggest that both methylation-based and integrated liquid biopsy assays hold promise as non-invasive tools for detection of PDAC.

Underestimation of SARS-CoV-2 in wastewater due to single or double mutations in the N1 qPCR probe binding region.

Wastewater surveillance using RT-qPCR has now been widely adopted to track circulating levels of SARS-CoV-2 virus in many sewersheds. The CDC qPCR assays targeting two regions (N1 and N2) within the N gene are commonly used, but a discrepancy between the two biomarkers has been noticed by independent studies using these methods since late 2021. The reason is presumed to be due to mutations in regions targeted by the N1 qPCR probe. In this study, we systematically investigated and unequivocally confirmed that the underlying reason for this discrepancy was mutations in the N1 probe target, and that a single mutation could cause a significant drop in signal. We first confirmed the proportion of related mutations in wastewater samples (Jan 2021-Dec 2022) using nested PCR and LC-MS. Based on relative proportions of N1 alleles, we separated the wastewater data into four time periods corresponding to different variant waves: Period I (Alpha and Delta waves with 0 mutation), Period II (BA.1/BA.2 waves with a single mutation found in all Omicron strains), Period III (BA.5.2* wave with two mutations), and Period IV (BQ.1* wave with two mutations). Significantly lower N1 copies relative to N2 copies in samples from Periods II-IV compared to those from Period I was observed in wastewater. To further pinpoint the extent to which each mutation impacted N1 quantification, we compared the qPCR response among different synthetic oligomers with corresponding mutations. This study highlighted the impact of even just one or two mutations on qPCR-based wastewater surveillance of SARS-CoV-2.

Population-based screening for colorectal cancer in Wuhan, China.

Fecal DNA test has emerged as a non-invasive alternative for colorectal cancer (CRC) screening in average-risk population. However, there is currently insufficient evidence in China to demonstrate the effectiveness of population-based CRC screening using fecal DNA based test. Here, a large-scale real-world study for CRC screening was implemented in Wuhan, Hubei province, China. A total of 98,683 subjects aged between 45 and 60 years were screened by a fecal DNA test (ColoTect®) which detected methylation status of SDC2, ADHFE1, and PPP2R5C. Participants who tested positive were advised to receive diagnostic colonoscopy. 4449 (4.5%) subjects tested positive for fecal DNA test, and 3200 (71.9%) underwent colonoscopy. Among these, 2347 (73.3%) had abnormal colonoscopy findings, of which 1330 (56.7%) subjects received pathological diagnosis. Detection rates for CRC and advanced precancerous lesions were 1.3% and 2.3%, respectively. Detection rates for nonadvanced adenomas and polyps were 14.0% and 21.6%, respectively. 28.0% of all colonoscopies showed colorectal neoplasm but lack pathological diagnosis. 6.1% showed other abnormalities such as enteritis. In conclusion, preliminary real-world evidence suggested that fecal DNA tests had promising diagnostic yield in population-based CRC screening. Clinical trial registration: https://www.chictr.org.cn/showproj.html?proj=192838, identifier ChiCTR2300070520.

Temporal network of experience sampling methodology identifies sleep disturbance as a central symptom in generalized anxiety disorder.

BACKGROUND: A temporal network of generalized anxiety disorder (GAD) symptoms could provide valuable understanding of the occurrence and maintenance of GAD. We aim to obtain an exploratory conceptualization of temporal GAD network and identify the central symptom. METHODS: A sample of participants (n = 115) with elevated GAD-7 scores (Generalized Anxiety Disorder 7-Item Questionnaire [GAD-7] ≥ 10) participated in an online daily diary study in which they reported their GAD symptoms based on DSM-5 diagnostic criteria (eight symptoms in total) for 50 consecutive days. We used a multilevel VAR model to obtain the temporal network. RESULTS: In temporal network, a lot of lagged relationships exist among GAD symptoms and these lagged relationships are all positive. All symptoms have autocorrelations and there are also some interesting feedback loops in temporal network. Sleep disturbance has the highest Out-strength centrality. CONCLUSIONS: This study indicates how GAD symptoms interact with each other and strengthen themselves over time, and particularly highlights the relationships between sleep disturbance and other GAD symptoms. Sleep disturbance may play an important role in the dynamic development and maintenance process of GAD. The present study may develop the knowledge of the theoretical model, diagnosis, prevention and intervention of GAD from a temporal symptoms network perspective.

Integrating single-cell and spatially resolved transcriptomic strategies to survey the astrocyte response to stroke in male mice.

Astrocytes, a type of glial cell in the central nervous system (CNS), adopt diverse states in response to injury that are influenced by their location relative to the insult. Here, we describe a platform for spatially resolved, single-cell transcriptomics and proteomics, called tDISCO (tissue-digital microfluidic isolation of single cells for -Omics). We use tDISCO alongside two high-throughput platforms for spatial (Visium) and single-cell transcriptomics (10X Chromium) to examine the heterogeneity of the astrocyte response to a cortical ischemic stroke in male mice. We show that integration of Visium and 10X Chromium datasets infers two astrocyte populations, proximal or distal to the injury site, while tDISCO determines the spatial boundaries and molecular profiles that define these populations. We find that proximal astrocytes show differences in lipid shuttling, with enriched expression of Apoe and Fabp5. Our datasets provide a resource for understanding the roles of astrocytes in stroke and showcase the utility of tDISCO for hypothesis-driven, spatially resolved single-cell experiments.

Trace Sample Proteome Quantification by Data-Dependent Acquisition without Dynamic Exclusion.

Despite continuous technological improvements in sample preparation, mass-spectrometry-based proteomics for trace samples faces the challenges of sensitivity, quantification accuracy, and reproducibility. Herein, we explored the applicability of turboDDA (a method that uses data-dependent acquisition without dynamic exclusion) for quantitative proteomics of trace samples. After systematic optimization of acquisition parameters, we compared the performance of turboDDA with that of data-dependent acquisition with dynamic exclusion (DEDDA). By benchmarking the analysis of trace unlabeled human cell digests, turboDDA showed substantially better sensitivity in comparison with DEDDA, whether for unfractionated or high pH fractionated samples. Furthermore, through designing an iTRAQ-labeled three-proteome model (i.e., tryptic digest of protein lysates from yeast, human, and E. coli) to document the interference effect, we evaluated the quantification interference, accuracy, reproducibility of iTRAQ labeled trace samples, and the impact of PIF (precursor intensity fraction) cutoff for different approaches (turboDDA and DEDDA). The results showed that improved quantification accuracy and reproducibility could be achieved by turboDDA, while a more stringent PIF cutoff resulted in more accurate quantification but less peptide identification for both approaches. Finally, the turboDDA strategy was applied to the differential analysis of limited amounts of human lung cancer cell samples, showing great promise in trace proteomics sample analysis.

The Interaction Between Measurement and Individual Difference in Ego Depletion: Task Type, Trait Self-Control and Action Orientation.

Previous research found that performing an initial self-control task impairs subsequent self-control performance, which is referred to as ego depletion. However, recent meta-analyses and replication studies have led to controversies over whether the ego depletion effect is as reliable as previously assumed. The present study aimed to shed more light on these controversies by combining depletion measurement task type and personality as moderators. Study 1 investigated trait self-control and action orientation's moderation role for depletion effects on stop-signal task (inhibitory control). Study 2 examined the trait self-control and action orientation's moderation role for depletion effects on a majority congruent Stroop task (goal maintenance). Results showed that trait self-control moderated the ego depletion effect on stop-signal reaction time (SSRT). High trait self-control people were less vulnerable to the ego depletion effect on the reactive inhibitory control task, whereas the moderating role of trait self-control for ego depletion was not found in the goal maintenance task. More particularly, high action-oriented people were less susceptible to the ego depletion effect on the goal maintenance task, but there was no moderation effect of action orientation for ego depletion in the stop-signal task. We discuss types of task for depletion measurement and individual differences in ego depletion, and we suggest possible avenues for future research.

Digital Microfluidics for Microproteomic Analysis of Minute Mammalian Tissue Samples Enabled by a Photocleavable Surfactant.

Proteome profiles of precious tissue samples have great clinical potential for accelerating disease biomarker discovery and promoting novel strategies for early diagnosis and treatment. However, tiny clinical tissue samples are often difficult to handle and analyze with conventional proteomic methods. Automated digital microfluidic (DMF) workflows facilitate the manipulation of size-limited tissue samples. Here, we report the assessment of a DMF microproteomics workflow enabled by a photocleavable surfactant for proteomic analysis of minute tissue samples. The surfactant 4-hexylphenylazosulfonate (Azo) was found to facilitate fast droplet movement on DMF and enhance the proteomics analysis. Comparisons of Azo and n-Dodecyl ß-d-maltoside (DDM) using small samples of HeLa digest standards and MCF-7 cell digests revealed distinct differences at the peptide level despite similar results at the protein level. The DMF microproteomics workflow was applied for the sample preparation of ∼3 µg biopsies from murine brain tissue. A total of 1969 proteins were identified in three samples, including established neural biomarkers and proteins related to synaptic signaling. Going forward, we propose that the Azo-enabled DMF workflow has the potential to advance the practical clinical application of DMF for the analysis of size-limited tissue samples.

Unlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery.

The identification of tumor-specific antigens (TSAs) is critical for developing effective cancer immunotherapies. Mass spectrometry (MS)-based immunopeptidomics has emerged as a powerful tool for identifying TSAs as physical molecules. However, current immunopeptidomics platforms face challenges in measuring low-abundance TSAs in a precise, sensitive, and reproducible manner from small needle-tissue biopsies (<1 mg). Inspired by recent advances in single-cell proteomics, microfluidics technology offers a promising solution to these limitations by providing improved isolation of human leukocyte antigen (HLA)-associated peptides with higher sensitivity. In this context, we highlight the challenges in sample preparation and the rationale for developing microfluidics technology in immunopeptidomics. Additionally, we provide an overview of promising microfluidic methods, including microchip pillar arrays, valved-based systems, droplet microfluidics, and digital microfluidics, and discuss the latest research on their application in MS-based immunopeptidomics and single-cell proteomics.

Effects of dysfunctional beliefs about sleep on sleep quality and mental health among patients with COVID-19 treated in Fangcang shelter hospitals.

Introduction: With the COVID-19 pandemic in China, a large number of mild or ordinary confirmed cases have been sent to Fangcang shelter hospitals for treatment. We aimed to investigate the mental health condition of Fangcang patients 2 years after the pandemic when patients knew more about COVID-19 and the virus was less virulent. We focused on the effect of dysfunctional beliefs and attitudes about sleep on depression, anxiety, and insomnia. Methods: A total of 1,014 patients from two large Fangcang shelter hospitals in Shanghai between 22 April and 8 May 2022 completed a set of questionnaires comprising: the Dysfunctional Beliefs and Attitudes about Sleep scale, the Generalized Anxiety Disorder scale, the Patient Health Questionnaire, and the Insomnia Severity Index scale. Results: Results show that the positive screening rates for anxiety, depression, and insomnia among tested patients were 55.3, 27.0, and 47.8%, respectively. Patients were more likely to report higher anxiety, depression, and insomnia, and to endorse affective and sleep disorders if they were: female, aged 18-40 years, with undergraduate course or above, white-collar employees, or those who thought the pandemic would have severe economic effects. About 51.4% of the participants had dysfunctional beliefs about sleep to varying degrees. Compared with patients who had accurate beliefs about sleep, the ratios of insomnia, anxiety, and depression were significantly higher among patients with dysfunctional beliefs about sleep. Discussion: Attention should be paid to the mental health problems of patients in Fangcang shelter hospitals. The results indicate that dysfunctional beliefs about sleep significantly increased anxiety, depression, and insomnia of Fangcang patients.

All-in-One digital microfluidics pipeline for proteomic sample preparation and analysis.

Highly sensitive and reproducible analysis of samples containing low amounts of protein is restricted by sample loss and the introduction of contaminants during processing. Here, we report an All-in-One digital microfluidic (DMF) pipeline for proteomic sample reduction, alkylation, digestion, isotopic labeling and analysis. The system features end-to-end automation, with integrated thermal control for digestion, optimized droplet additives for sample manipulation and analysis, and an automated interface to liquid chromatography with tandem mass spectrometry (HPLC-MS/MS). Dimethyl labeling was integrated into the pipeline to allow for relative quantification of the trace samples at the nanogram level, and the new pipeline was applied to evaluating cancer cell lines and cancer tissue samples. Several known proteins (including HSP90AB1, HSPB1, LDHA, ENO1, PGK1, KRT18, and AKR1C2) and pathways were observed between model breast cancer cell lines related to hormone response, cell metabolism, and cell morphology. Furthermore, differentially quantified proteins (such as PGS2, UGDH, ASPN, LUM, COEA1, and PRELP) were found in comparisons of healthy and cancer breast tissues, suggesting potential utility of the All-in-One pipeline for the emerging application of proteomic cancer sub-typing. In sum, the All-in-One pipeline represents a powerful new tool for automated proteome processing and analysis, with the potential to be useful for evaluating mass-limited samples for a wide range of applications.

Comparison of Database Searching Programs for the Analysis of Single-Cell Proteomics Data.

Single-cell proteomics is emerging as an important subfield in the proteomics and mass spectrometry communities, with potential to reshape our understanding of cell development, cell differentiation, disease diagnosis, and the development of new therapies. Compared with significant advancements in the "hardware" that is used in single-cell proteomics, there has been little work comparing the effects of using different "software" packages to analyze single-cell proteomics datasets. To this end, seven popular proteomics programs were compared here, applying them to search three single-cell proteomics datasets generated by three different platforms. The results suggest that MSGF+, MSFragger, and Proteome Discoverer are generally more efficient in maximizing protein identifications, that MaxQuant is better suited for the identification of low-abundance proteins, that MSFragger is superior in elucidating peptide modifications, and that Mascot and X!Tandem are better for analyzing long peptides. Furthermore, an experiment with different loading amounts was carried out to investigate changes in identification results and to explore areas in which single-cell proteomics data analysis may be improved in the future. We propose that this comparative study may provide insight for experts and beginners alike operating in the emerging subfield of single-cell proteomics.

The relationship between sleep quality and occupational well-being in employees: The mediating role of occupational self-efficacy.

Objective: This study aimed to examine the impact of sleep quality on occupational well-being in employees by primarily focusing on the mediating role of occupational self-efficacy. Methods: A total of 487 junior staff completed a set of questionnaires comprised Pittsburgh Sleep Quality Index scale, Occupational Self-efficacy Scale, and occupational well-being measurements. Results: The results revealed that both sleep quality and occupational self-efficacy were significantly correlated with occupational well-being. The structural equation modeling analysis and the bootstrap test indicated that occupational self-efficacy partially mediated the effect of poor sleep quality on occupational well-being. Discussion: These findings expand upon existing research on the relationship between sleep quality and well-being among occupational workers, shed light on the correlation of poor sleep quality with occupational well-being, and are valuable in promoting the occupational well-being of employees.

The functional implication of ATF6α in castration-resistant prostate cancer cells.

Stress in the endoplasmic reticulum (ER) may perturb proteostasis and activates the unfolded protein response (UPR). UPR activation is frequently observed in cancer cells and is believed to fuel cancer progression. Here, we report that one of the three UPR sensors, ATF6α, was associated with prostate cancer (PCa) development, while both genetic and pharmacological inhibition of ATF6α impaired the survival of castration-resistance PCa (CRPC) cells. Transcriptomic analyses identified the molecular pathways deregulated upon ATF6α depletion, and also discovered considerable disparity in global gene expression between ATF6α knockdown and Ceapin-A7 treatment. In addition, combined analyses of human CRPC bulk RNA-seq and single-cell RNA-seq (scRNA-seq) public datasets confirmed that CRPC tumors with higher ATF6α activity displayed higher androgen receptor (AR) activity, proliferative and neuroendocrine (NE) like phenotypes, as well as immunosuppressive features. Lastly, we identified a 14-gene set as ATF6α NE gene signature with encouraging prognostic power. In conclusion, our results indicate that ATF6α is correlated with PCa progression and is functionally relevant to CRPC cell survival. Both specificity and efficacy of ATF6α inhibitors require further refinement and evaluation.

Resistance to Sunk Cost Propensity Moderate Relationship between Negative Life Event and Hopelessness.

Previous research has found that a negative life event is a main risk factor for hopelessness, which in turn is considered to be a proximal cause of major depression disorder and a suicide risk factor. Unfortunately, very little attention has been paid to the role of decision-making constructs between negative life events and hopelessness. To fill this gap, the present study aims to test the moderation role of sunk cost propensity in this relationship, which is an over-generalized tendency to persist, based on past investment. A total of 495 university students completed assessment of their resistance to sunk cost propensity, whereas the negative life events, hopelessness, mental health state (depression, anxiety) and big-five personality traits were measured by various questionnaires. Participants' tendency to resist sunk cost propensity moderated the relationship between negative life events and hopelessness. Individuals who tended to resist sunk cost bias are more vulnerable to the adverse effects of negative life events. This effect is still significant, even after controlling for individuals' psychological well-being (depression, anxiety) and big-five personality traits. The current findings provide preliminary evidence that resistance to sunk cost propensity may be an important characteristic associated with an individual's hopelessness when exposed to a negative life event.

IDO promotes the proliferation and invasion of prostate cancer cells through KYNU.

BACKGROUND: Prostate cancer (PCa) is one of the most common malignant tumors in male. OBJECTIVE: To explore the effect of indoleamine-2, 3-dioxygenase (IDO) on the proliferation and invasion of PCa cells and the potential mechanism. METHODS: PCa tissues and normal adjacent tissues were collected from 43 PCa patients. The expression of IDO in PCa tissues and cell lines were detected. The String website was used to search for IDO-related proteins. The GEPIA website was used to analyze the relationship between KYNU and the prognosis of PCa. Cells models of IDO overexpression and/or KYNU silencing were constructed to verify the role of KYNU in regulating PCa. The cell proliferation, apoptosis and invasion ability of PCa cells were detected by CCK-8 assay, Flow cytometry and Transwell assay. RESULTS: The IDO levels in PCa tissues and cells were higher than those in normal tissues and cells, which promoted the proliferation and invasion of LNCaP cells, and inhibited apoptosis. Silencing IDO inhibited the cells proliferation and invasion activities, and promoted the cell apoptosis. The high expression of KYNU was related to the poor disease free survival of PCa patients. Inhibiting KYUN significantly inhibited the promotion of PCa induced by IDO. CONCLUSION: IDO is overexpressed in PCa, which promotes the proliferation and invasion of PCa cells, and the cancer-promoting mechanism may be related to KYNU.

Parental attachment and emotional intelligence mediates the effect of childhood maltreatment on callous-unemotional traits among incarcerated male adolescents.

This study aimed to examine the impact of childhood maltreatment on callous-unemotional (CU) traits among incarcerated male adolescents, focusing primarily on the roles of parental attachment and emotional intelligence. A total of 454 male incarcerated adolescents from two juvenile correctional facilities, ranging in age from 14 to 18 years, completed a set of questionnaires consisting of a childhood trauma questionnaire, parent-attachment scale, emotional intelligence scale, and the Inventory of CU traits. The results revealed that childhood maltreatment, parental attachment, and emotional intelligence were all correlated with CU traits. Structural equation modeling analysis and the bootstrap test indicated that parental attachment and emotional intelligence mediated, in part, the effect of childhood maltreatment on CU traits. These findings expand the outcomes of previous research and shed light on how childhood maltreatment is related to CU traits.

Study on the mechanisms of enhanced biological nitrogen and phosphorus removal by denitrifying phosphorus removal in a Micro-pressure swirl reactor.

To reveal the mechanisms of enhanced biological nitrogen and phosphorus removal by denitrifying phosphorus removal in a Micro-pressure swirl reactor (MPSR), this study used a MPSR to treat municipal wastewater and enriched denitrifying phosphate accumulating organisms (DPAOs) by using its alternating anaerobic-anoxic-aerobic environment. The coupling of denitrification phosphorus removal (DPR) and simultaneous nitrification endogenous denitrification phosphorus removal (SNEDPR) was achieved in MPSR, and the average removal rates of COD, NH4+-N, TN and TP were 91.57%, 98.51%, 85.88%, 96.08% respectively. The results of the batch experiments showed that DPAOs activity in the low dissolved oxygen (DO) and high DO zones were 70.5% and 74.3%. The results of intracellular carbon source conversion patterns, microbial assays and functional gene prediction indicated that Flavobacterium and Dechloromonas dominated the DPR process in the low DO zone. Based on these findings, nutrient removal pathways within the MPSR were integrated.

The commission of crime from the perspective of decision-making differences.

A criminal act can be regarded as an irrational decision-making process. Therefore, understanding differences in the criminal decision-making process would shed light on criminal behavior. We utilized dual processing theory to propose that offenders' differences in decision-making may cause them to adopt non-adaptive behaviors, such as high reference point setting, abnormal reward-punishment sensitivity, delayed discounting rate, and decision-making style. Our study compares differences in these indicators between offenders (n = 518) and non-offenders (n = 636) in a diverse sample of Chinese adults. The results showed that compared with non-offenders, offenders had higher relative deprivation, reward sensitivity, and delayed discounting rates but lower punishment sensitivity and vigilance in decision-making. A logistic regression analysis also shows that the above factors were significant predictive indicators for the commission of crimes.

Corrigendum: TPX2 enhanced the activation of the HGF/ETS-1 pathway and increased the invasion of endocrine-independent prostate carcinoma cells.

[This corrects the article DOI: 10.3389/fonc.2021.618540.].