Associations between multiple sleep dimensions and suicide and non-suicidal self-injury: a cross-sectional study of 3828 Chinese young people.

PURPOSE: Suicide and non-suicidal self-injury (NSSI) are preventable concerns in young people. Suicidal ideation (SI), suicidal plans (SP) and suicidal attempt (SA) are closely related to death. Sleep problems are known risk factors for suicide and NSSI. This study aimed to explore the relationship between sleep, suicidality and NSSI. METHODS: Participants were 3,828 middle school and college students aged 11-23 years from urban and rural areas of Henan Province. Sleep, suicidal phenomena and NSSI were assessed by applying self-reported questionnaires. Chi-squared tests were utilized to demonstrate the demographic data and sleep variables. The correlation between sleep, suicidality and NSSI were explored by using binary logistic regression, while adjusting socio-demographic characteristics with multivariate models. RESULTS: Sleep variables except mid-sleep time were related to suicidal phenomena (P < 0.05). Greater social jet lag (SJL) [≥ 2 h (h)] was associated with increased risk of SI [Odds ratios (OR) = 1.72, 95% confidence intervals (CI):1.40-2.11], SP (OR = 2.10, 95%CI:1.59-2.79) and SA (OR = 1.50, 95%CI:1.00-2.26). Non-only child participants with SJL (≥ 2 h) had significantly increased odds of SI (OR = 1.75, 95%CI: 1.41-2.18) and SP (OR = 2.25, 95%CI: 1.66-3.05). Eveningness chronotype had the strongest correlation with SI (OR = 3.87, 95%CI:2.78-5.38), SP (OR = 4.72, 95%CI:2.97-7.50), SA (OR = 6.69, 95%CI:3.08-14.52) and NSSI (OR = 1.39, 95%CI:1.02-1.90). CONCLUSION: Overlong or short sleep duration, SJL, eveningness chronotype and other sleep abnormalities (e.g., daytime dysfunction, low sleep efficiency) were associated with a higher prevalence of SI, SP and SA. Additionally, eveningness was significantly correlated with NSSI among young people. These findings suggested the importance of assessing and intervening in sleep habits to prevent suicide and NSSI in young people.

Associations of multiple sleep dimensions with overall and abdominal obesity among children and adolescents: a population-based cross-sectional study.

BACKGROUND: The relationship of insufficient sleep with the increased risk of obesity has been reported, but less is known about other sleep dimensions in the sleep-obesity associations. OBJECTIVES: To assess the associations of multiple sleep dimensions with overall and abdominal obesity among Chinese students. METHODS: This was a cross-sectional study involving 10,686 Han students aged 9-18 from Chinese National Survey on Students' Constitution and Health (CNSSCH). We collected sex, age, regions, parental educational levels, physical activity duration and sleep-related information by questionnaire survey, and also conducted anthropometric measurements including height, weight and waist circumference (WC). Unadjusted and adjusted binary logistic regression models were used to estimate the associations of sleep-related dimensions with obesity-related indicators. RESULTS: Short sleep duration was associated with higher body mass index (BMI), larger WC and higher waist-to-height ratio (WHtR) in 9-12 and 16-18 age groups, whereas prolonged sleep duration on weekday was associated with higher BMI in 13-15 age group. Non-habitual midday napping and midday napping ≤0.5 h/d (vs 0.5 to 1 h/d) increased the risk of higher BMI in 13-15 age group, and the former was also associated with larger WC in 9-12 age group. Late bedtime was associated with larger WC and higher WHtR in 9-12 age group and with higher BMI and WHtR in 13-15 age group. Students aged 9-12 with social jet lag ≥2 h were found to have greater BMI after adjustment (Odds Ratio: 1.421; 95% confidence interval: 1.066-1.894). CONCLUSIONS: Short or overlong sleep duration, late bedtime and great social jet lag were associated with higher prevalence of overall or abdominal obesity, while moderate midday napping can effectively decrease the risk. Those findings may assist in developing preventive strategies to combat obesity epidemic.

Proteomic Profiling of Gastric Signet Ring Cell Carcinoma Tissues Reveals Characteristic Changes of the Complement Cascade Pathway.

Signet ring cell carcinoma (SRCC) is a histological subtype of gastric cancer with distinct features in multiple aspects compared with adenocarcinomas (ACs). The lack of a systematic molecular overview of this disease has led to slow progress in its clinical practice. In the present proteomics study, gastric tissues were collected from tumors and adjacent tissues, including 14 SRCCs and 34 ACs, and laser capture microdissection (LCM) was employed to eradicate the cellular heterogeneity of the tissues. The proteomes of tissues were profiled by data-independent acquisition (DIA) mass spectrometry (MS). Based on the over 6000 proteins quantified, univariate analysis and pathway enrichment revealed that some proteins and pathways demonstrated differences between SRCC and ACs. Importantly, the upregulation of a majority of complement-related proteins was notable for SRCC but not for ACs. A hypothesis, based on the proteomics evidence, was proposed that the complement cascade was evoked in the SRCC microenvironment upon infiltration, and the SRCC cells survived the complement cytotoxicity by secreting endogenous negative regulators. Moreover, an attempt was made to establish appropriate cell models for gastric SRCC through proteomic comparison of the 15 gastric cell lines and gastric tumors. The predictions of a supervised classifier suggested that none of these gastric cell lines qualified to mimic SRCC. This study discovered that the complement cascade is activated at a higher level in gastric SRCC than in ACs.

Unhealthy lifestyles and clusters status among 3637 adolescents aged 11-23 years: a school-based cross-sectional study in China.

BACKGROUND: Unhealthy lifestyles are risk factors for non-communicable diseases (NCDs) and tend to be clustered, with a trajectory that extends from adolescence to adulthood. This study investigated the association of diets, tobacco, alcohol, physical activity (PA), screen time (ST) and sleep duration (SD) in a total of six lifestyles, separately and as cumulative lifestyle scores, with sociodemographic characteristics among school-aged adolescents in the Chinese city of Zhengzhou. METHODS: In the aggregate, 3,637 adolescents aged 11-23 years were included in the study. The questionnaire collected data on socio-demographic characteristics and lifestyles. Healthy and unhealthy lifestyles were identified and scored, depending on the individual score (0 and 1 for healthy and unhealthy lifestyles respectively), with a total score between 0 and 6. Based on the sum of the dichotomous scores, the number of unhealthy lifestyles was calculated and divided into three clusters (0-1, 2-3, 4-6). Chi-square test was used to analyze the group difference of lifestyles and demographic characteristics, and multivariate logistic regression was used to explore the associations between demographic characteristics and the clustering status of unhealthy lifestyles. RESULTS: Among all participants, the prevalence of unhealthy lifestyles was: 86.4% for diet, 14.5% for alcohol, 6.0% for tobacco, 72.2% for PA, 42.3% for ST and 63.9% for SD. Students who were in university, female, lived in country (OR = 1.725, 95% CI: 1.241-2.398), had low number of close friends (1-2: OR = 2.110, 95% CI: 1.428-3.117; 3-5: OR = 1.601, 95% CI: 1.168-2.195), and had moderate family income (OR = 1.771, 95% CI: 1.208-2.596) were more likely to develop unhealthy lifestyles. In total, unhealthy lifestyles remain highly prevalent among Chinese adolescents. CONCLUSION: In the future, the establishment of an effective public health policy may improve the lifestyle profile of adolescents. Based on the lifestyle characteristics of different populations reported in our findings, lifestyle optimization can be more efficiently integrated into the daily lives of adolescents. Moreover, it is essential to conduct well-designed prospective studies on adolescents.

Temporal trends in physical fitness among Chinese children and adolescents from 2000 to 2019 and analysis of social-ecological factors.

This study aimed to estimate temporal trends in physical fitness (PF) by regions, age groups and nutritional status among Chinese children and adolescents and to longitudinally examine PF determinants based on social-ecological model. Participants (n = 68,265) aged 7-18 were from five successive national surveys (2000 to 2019). Six tested items of PF were calculated as PF indicator (PFI), which was used to divide participants into two categories: low vs. moderate/high. One-way analysis of variance was used to compare difference and change trend of PFI. Linear regression evaluated relationship between PFI and body mass index (BMI), and logistic regression assessed association between PFI and factors of behaviours and lifestyles on individual-, family- and school-level based on the social-ecological model. PFI declined sharply from 2000 to 2010, increased slightly from 2010 to 2014 and then edged down in 2019. Students with moderate BMI and students in urban areas tended to have higher PFI, and larger increase of PFI was found in students aged 7-9 and 13-15 after 2010. Several determinants on individual-, family- and school-level related to PFI. Efforts to develop PF mainly include increasing PA and reducing sedentary behaviours by facilitating home-school collaboration and emphasizing age-, region- and BMI-specific actions.

Multidimensional self-rating biological rhythm disorder and its association with depression and anxiety symptoms among adolescents aged 11-23 years: a school-based cross-sectional study from China.

BACKGROUND: Depression and anxiety are topical concerns worldwide, especially among adolescents. Besides, biological rhythm disorder as a candidate mechanism for mood disorders is highly prevalent, but relevant research among adolescents in China is presently limited. We conducted the present study to investigate the distribution of multi-dimensional self-rating biological rhythm disorder and the association of self-rating biological rhythm disorders with depression and anxiety symptoms among Chinese adolescents in different academic stages. METHODS: In the cross-sectional study, 3693 students aged 11-23 from Zhengzhou City, Henan Province, China were included. The Patient Health Questionnaire (PHQ-9) and General Anxiety Disorder (GAD-7) were used to evaluate symptoms of depression and anxiety, respectively. Additionally, the Self-Rating of Biological Rhythm Disorder for Adolescents (SBRDA) was used to assess status of biological rhythm disorders. Multivariate logistic regression was developed to explore factors potentially associated with symptoms of depression and anxiety stratified by academic stages. RESULTS: Among all participants, 44.14 and 36.15% suffered from depression and anxiety symptoms, respectively. On average, participants scored 74.66 ± 19.37 on the measure of total biological rhythm disorder. Adjusted for demographic confounding factors, the logistic regression analysis showed higher scores of total biological rhythm disorder were associated with more severe depression (OR = 14.38, 95%CI: 11.38-18.16) and anxiety symptoms (OR = 11.63, 95%CI: 9.14-14.81). The similar results were also found in the stratified analysis by academic stages. CONCLUSIONS: Self-rating biological rhythm disorders are significantly associated with depression and anxiety symptoms among adolescents. Discrepancy across academic stages should also be taken into account in establishing public health strategies.

[Development and Application of Medical Device Recall Event Tracking System].

A medical device recall event tracking system was designed, which can enable the users to obtain the recall, early warning and other information related to medical devices in time. The tracking system can timely obtain and release the recall information of medical devices, effectively improve the quality control of hospital medical devices, reduce the use risk of medical devices, and ensure the life safety of patients.

Pathway attenuation of fatty acid beta-oxidation in the skeletal muscle of a type 2 diabetic mouse model.

RATIONALE: Whether catabolic abnormalities of fatty acids exist in the skeletal muscle of type 2 diabetes mellitus (T2DM) has not been determined. In this study, we postulated that a systematic evaluation of the protein abundance and metabolic activity related to fatty acids in the skeletal muscle tissues of a T2DM mouse model was feasible to address this question. METHODS: Mitochondria were extracted from wild-type (WT) and db/db mice followed by quantitative analysis of the proteins involved in mitochondrial fatty acid oxidation (mFAO). The pathway activity of mFAO in skeletal muscle tissues was monitored in vitro using mass spectrometry, and tissue lipidomic analysis was conducted in profiling and target mode to distinguish the levels of long-chain acylcarnitines between WT and db/db mice. RESULTS: Two proteins related to the mFAO pathway were significantly downregulated in the skeletal muscle mitochondria of db/db mice. The measurement of mFAO pathway activity in vitro revealed that the abundance of long-chain acylcarnitines (C14 to C18) in db/db mice was lower than that in WT mice, and the determination of acylcarnitines in skeletal muscle tissues in vivo revealed that most long-chain acylcarnitines were decreased in db/db mice. CONCLUSIONS: The findings of lower abundance of ACAD9 and CPT1B, reduced activity of the mFAO pathway in vitro and decreased acylcarnitines in vivo firmly support that the mFAO pathway in the skeletal muscle of diabetic mice is attenuated, possibly resulting in cell/tissue dysfunction in diabetes.

Lowering Endogenous Cathepsin D Abundance Results in Reactive Oxygen Species Accumulation and Cell Senescence.

Cathepsin D is reportedly to be closely associated with tumor development, migration, and invasion, but its pathological mechanism is not fully elucidated. We aimed to evaluate phenotypic changes and molecular events in response to cathepsin D knockdown. Lowering endogenous cathepsin D abundance (CR) induced senescence in HeLa cells, leading to reduced rate of cell proliferation and impaired tumorigenesis in a mouse model. Quantitative proteomics revealed that compared with control cells (EV), the abundances of several typical lysosomal proteases were decreased in the lysosomal fraction in CR cells. We further showed that cathepsin D knockdown caused increased permeability of lysosomal membrane and reactive oxygen species accumulation in CR cells, and the scavenging of reactive oxygen species by antioxidant was able to rescue cell senescence. Despite the increased reactive oxygen species, the proteomic data suggested a global reduction of redox-related proteins in CR cells. Subsequent analysis indicated that the transcriptional activity of nuclear factor erythroid-related factor 2 (Nrf2), which regulates the expression of groups of antioxidant enzymes, was down-regulated by cathepsin D knockdown. Importantly, Nrf2 overexpression significantly reduced cell senescence. Although transient oxidative stress promoted the accumulation of Nrf2 in the nucleus, we showed that the Nrf2 protein exited nucleus if oxidative stress persisted. In addition, when cathepsin D was transiently knocked down, the cathepsin-related events followed a sequential order, including lysosomal leakage during the early stage, followed by oxidative stress augmentation, and ultimately Nrf2 down-regulation and senescence. Our results suggest the roles of cathepsin D in cancer cells in maintaining lysosomal integrity, redox balance, and Nrf2 activity, thus promoting tumorigenesis. The MS Data are available via ProteomeXchange with identifier PXD002844.

Reagents for Isobaric Labeling Peptides in Quantitative Proteomics.

Currently, the commercial reagents for isobaric peptides labeling (TMT and iTRAQ) have some drawbacks, such as high cost in experiments, especially in quantitation for the modified peptides, and inconvenient handling for variable sizes of samples. Herein, we developed a set of 10-plex isobaric tags (IBT) with high stability and low cost. The labeled peptides were sensitively detected on Orbitrap Q Exactive MS with an MS2 resolution of 35 000 at 30% NCE, while the peptides were efficiently labeled over 97% by IBT at a ratio of 10:1 of reagent/peptide (w/w) in 200 mM TEAB buffer for 2 h. The IBT labeling was demonstrated with a wide dynamic range of 50-fold without obvious matrix effects on quantification. Importantly, there was little quantification bias found among the individual IBT tags, indicating that the peptides labeled by different tags were quantitatively comparable. The IBT 10-plex reagents were applied for dynamically monitoring the quantitative responses of phosphoproteome stimulated by EGF treatment in HeLa cells. In total, 5 361 unique phosphopeptides were identified, which reached a similar conclusion as others reported. The IBT reagents were therefore experimentally proven as a new type of reagents for isobaric peptides labeling and useful in a large quantity peptides of quantitative proteomics.

Peptide Biosynthesis with Stable Isotope Labeling from a Cell-free Expression System for Targeted Proteomics with Absolute Quantification.

Because of its specificity and sensitivity, targeted proteomics using mass spectrometry for multiple reaction monitoring is a powerful tool to detect and quantify pre-selected peptides from a complex background and facilitates the absolute quantification of peptides using isotope-labeled forms as internal standards. How to generate isotope-labeled peptides remains an urgent challenge for accurately quantitative targeted proteomics on a large scale. Herein, we propose that isotope-labeled peptides fused with a quantitative tag could be synthesized through an expression system in vitro, and the homemade peptides could be enriched by magnetic beads with tag-affinity and globally quantified based on the corresponding multiple reaction monitoring signals provided by the fused tag. An Escherichia coli cell-free protein expression system, protein synthesis using recombinant elements, was adopted for the synthesis of isotope-labeled peptides fused with Strep-tag. Through a series of optimizations, we enabled efficient expression of the labeled peptides such that, after Strep-Tactin affinity enrichment, the peptide yield was acceptable in scale for quantification, and the peptides could be completely digested by trypsin to release the Strep-tag for quantification. Moreover, these recombinant peptides could be employed in the same way as synthetic peptides for multiple reaction monitoring applications and are likely more economical and useful in a laboratory for the scale of targeted proteomics. As an application, we synthesized four isotope-labeled glutathione S-transferase (GST) peptides and added them to mouse sera pre-treated with GST affinity resin as internal standards. A quantitative assay of the synthesized GST peptides confirmed the absolute GST quantification in mouse sera to be measurable and reproducible.

Body image as risk factor for emotional and behavioral problems among Chinese adolescents.

BACKGROUND: Being overweight and obesity during adolescence are worldwide public health problems. This study examined the relationship between actual weight, body image, and emotional and behavioral problems among Chinese adolescents. METHODS: A total of 3841 adolescents (age range, 11-16 years) from 5 Chinese cities were included in this cross-sectional study. All of the study participants were asked to complete questionnaires (including demographic features, strengths and difficulties questionnaires, pubertal development scale), and their height and weight were measured at the same time. Body image was measured in two ways: self-perceived weight and body satisfaction. The relationship between weight status and mental health was estimated by multivariate logistic regression for boys and girls. RESULTS: Our study showed a difference by sex for prevalence of being overweight/obesity and body dissatisfaction among Chinese adolescents. Boys were more likely to be overweight or obese than girls (30.4% vs. 21.5%, p < 0.05), but girls were more likely to be dissatisfied with their bodies than boys (41.2% vs. 27.9%, p < 0.05). In the logistic regression, body image, not actually being overweight, was significantly associated with a higher risk of emotional and behavioral problems. Compared to perceived normal weight boys, boys who perceived themselves as underweight had an increased likelihood of emotional problems (adjusted odds ratio [OR] = 1.73; 95% confidence interval (CI), 1.16-2.57), conduct problems (OR = 1.73; 95% CI, 1.20-2.50), and total difficulties (OR = 1.50; 95% CI, 1.09-2.05). Compared to body satisfaction, body dissatisfaction was a risk factor for emotional problems (boys: OR = 2.80; 95% CI, 1.84-4.25; girls: OR = 2.18; 95% CI, 1.42-3.36), conduct problems (boys: OR = 1.87, 95% CI, 1.26-2.76; girls: OR = 2.79; 95% CI, 1.46-5.30), hyperactivity problems (boys: OR = 1.67; 95% CI, 1.09-2.55; girls: OR = 2.04; 95% CI, 1.13-3.69), and total difficulties (boys: OR = 2.03; 95% CI, 1.45-2.84; girls: OR = 2.30; 95% CI, 1.46-3.56). CONCLUSIONS: Being overweight and obese during adolescence are very serious public health problems in China. Body image was a more substantial predictor for adolescent emotional and behavioral problems than actually being overweight/obesity.

Fungal Immunomodulatory Protein from Nectria haematococca Suppresses Growth of Human Lung Adenocarcinoma by Inhibiting the PI3K/Akt Pathway.

Lung cancer is a common disease that is associated with poor prognosis. Fungal immunomodulatory protein from Nectria haematococca (FIP-nha) has potential as a lung cancer therapeutic; as such, illuminating its anti-tumor mechanism is expected to facilitate novel treatment options. Here, we showed that FIP-nha affects lung adenocarcinoma growth ex vivo and in vivo. Comparative quantitative proteomics showed that FIP-nha negatively regulates PI3K/Akt signaling and induces cell cycle arrest, autophagy, and apoptosis. We further demonstrated that FIP-nha suppresses Akt phosphorylation, leading to upregulation of p21 and p27 and downregulation of cyclin B1, cyclin D1, CDK2, and CDK4 expression, ultimately resulting in G1/S and G2/M cell cycle arrest. Meanwhile, FIP-nha-induced PI3K/Akt downregulation promotes A549 apoptosis by increasing the expression ratio of Bax/Bcl-2 and c-PARP and autophagy by decreasing the phosphorylation of mTOR. Thus, we comprehensively revealed the anti-tumor mechanism of FIP-nha, which inhibits tumor growth by modulating PI3K/Akt-regulated cell cycle arrest, autophagy, and apoptosis, and provided the basis for further application of fungal immunomodulatory proteins, especially FIP-nha.

The serum protein responses to treatment with Xiaoke Pill and Glibenclamide in type 2 diabetes patients.

AIM: The Xiaoke Pill containing Chinese herb extracts and Glibenclamide, is used in therapy for type 2 diabetes mellitus (T2DM), and is effective in reducing the risk of hypoglycemia and improving diabetes symptoms compared with Glibenclamide. We describe a quantitative proteomics project to measure the T2DM serum proteome response to the Xiaoke Pill and Glibenclamide. METHODS: Based on a recently conducted 48-week clinical trial comparing the safety and efficacy of Glibenclamide (n = 400) and Xiaoke Pill (n = 400), after matching for age, sex, BMI, drug dose and whether hypoglycemia occurred, 32 patients were selected for the serum based proteomic analysis and divided into four groups (with/without hypoglycemia treated with Xiaoke Pill or Glibenclamide, n = 8 for each group). We screened the differential serum proteins related to treatments and the onset of hypoglycemia using the iTRAQ labeling quantitative proteomics technique. Baseline and follow-up samples were used. RESULTS: The quantitative proteomics experiments demonstrated that 25 and 21 proteins differed upon treatment with the Xiaoke Pill in patients without and with hypoglycemia, respectively, while 24 and 25 proteins differed upon treatment with Glibenclamide in patients without and with hypoglycemia, respectively. The overlap of different proteins between the patients with and without hypoglycemia given the same drug treatment was much greater than between the patients given different drug treatments. CONCLUSIONS: We conclude that the serum proteins response to the two different anti-diabetic drug treatments may serve as a sensitive biomarker for evaluation of the therapeutic effects and continue investigations into the mechanism.

A Comprehensive Investigation toward the Indicative Proteins of Bladder Cancer in Urine: From Surveying Cell Secretomes to Verifying Urine Proteins.

Urine is an ideal material to study the cancer-related protein biomarkers in bladder, whereas exploration to these candidates is confronting technique challenges. Herein, we propose a comprehensive strategy of searching the urine proteins related with bladder cancer. The strategy consists of three core combinations, screening the biomarker candidates in the secreted proteins derived from the bladder cancer cell lines and verifying them in patient urines, defining the differential proteins through two-dimensional electrophoresis (2DE) and isobaric tags for relative and absolute quantitation (iTRAQ) coupled with LC-MS/MS, and implementing quantitative proteomics of profiling and targeting analysis. With proteomic survey, a total of 700 proteins were found with their abundance of secreted proteins in cancer cell lines different from normal, while 87 proteins were identified in the urine samples. The multiple reaction monitoring (MRM)-based quantification was adapted in verifying the bladder cancer related proteins in individual urine samples, resulting in 10 differential urine proteins linked with the cancer. Of these candidates, receiver operating characteristic analysis revealed that the combination of CO3 and LDHB was more sensitive as the cancer indicator than other groups. The discovery of the bladder cancer indicators through our strategy has paved an avenue to further biomarker validation.

A Comprehensive Proteomics Analysis Reveals a Secretory Path- and Status-Dependent Signature of Exosomes Released from Tumor-Associated Macrophages.

Exosomes are 30-120 nm-sized membrane vesicles of endocytic origin that are released into the extracellular environment and play roles in cell-cell communication. Tumor-associated macrophages (TAMs) are important constituents of the tumor microenvironment; thus, it is critical to study the features and complex biological functions of TAM-derived exosomes. Here, we constructed a TAM cell model from a mouse macrophage cell line, Ana-1, and performed comparative proteomics on exosomes, exosome-free media, and cells between TAMs and Ana-1. Proteomic analysis between exosome and exosome-free fractions indicated that the functions of exosome dominant proteins were mainly enriched in RNA processing and proteolysis. TAM status dramatically affected the abundances of 20S proteasome subunits and ribosomal proteins in their exosomes. The 20S proteasome activity assay strongly indicated that TAM exosomes possessed higher proteolytic activity. In addition, Ana-1- and TAM-derived exosomes have different RNA profiles, which may result from differential RNA processing proteins. Taken together, our comprehensive proteomics study provides novel views for understanding the complicated roles of macrophage-derived exosomes in the tumor microenvironment.

Biomarker Discovery and Verification of Esophageal Squamous Cell Carcinoma Using Integration of SWATH/MRM.

We propose an efficient integration of SWATH with MRM for biomarker discovery and verification when the corresponding ion library is well established. We strictly controlled the false positive rate associated with SWATH MS signals and carefully selected the target peptides coupled with SWATH and MRM. We collected 10 samples of esophageal squamous cell carcinoma (ESCC) tissues paired with tumors and adjacent regions and quantified 1758 unique proteins with FDR 1% at protein level using SWATH, in which 467 proteins were abundance-dependent with ESCC. After carefully evaluating the SWATH MS signals of the up-regulated proteins, we selected 120 proteins for MRM verification. MRM analysis of the pooled and individual esophageal tissues resulted in 116 proteins that exhibited similar abundance response modes to ESCC that were acquired with SWATH. Because the ESCC-related proteins consisted of a high percentile of secreted proteins, we conducted the MRM assay on patient sera that were collected from pre- and postoperation. Of the 116 target proteins, 42 were identified in the ESCC sera, including 11 with lowered abundances postoperation. Coupling SWATH and MRM is thus feasible and efficient for the discovery and verification of cancer-related protein biomarkers.

Ubiquitination of inositol-requiring enzyme 1 (IRE1) by the E3 ligase CHIP mediates the IRE1/TRAF2/JNK pathway.

Deciphering the inositol-requiring enzyme 1 (IRE1) signaling pathway is fundamentally important for understanding the unfolded protein response (UPR). The ubiquitination of proteins residing on the endoplasmic reticulum (ER) membrane has been reported to be involved in the UPR, although the mechanism has yet to be fully elucidated. Using immunoprecipitation and mass spectrometry, IRE1 was identified as a substrate of the E3 ligase CHIP (carboxyl terminus of HSC70-interacting protein) in HEK293 cells under geldanamycin-induced ER stress. Two residues of IRE1, Lys(545) and Lys(828), were targeted for Lys(63)-linked ubiquitination. Moreover, in CHIP knockdown cells, IRE1 phosphorylation and the IRE1-TRAF2 interaction were nearly abolished under ER stress, which may be due to lacking ubiquitination of IRE1 on Lys(545) and Lys(828), respectively. The cellular responses were evaluated, and the data indicated that CHIP-regulated IRE1/TRAF2/JNK signaling antagonized the senescence process. Therefore, our findings suggest that CHIP-mediated ubiquitination of IRE1 contributes to the dynamic regulation of the UPR.

MFAP3L activation promotes colorectal cancer cell invasion and metastasis.

An abundance of microfibril-associated glycoprotein 3-like (MFAP3L) significantly correlates with distant metastasis in colorectal cancer (CRC), although the mechanism has yet to be explained. In this study, we observed that MFAP3L knock-down resulted in reduced CRC cell invasion and hepatic metastasis. We evaluated the cellular location and biochemical functions of MFAP3L and found that this protein was primarily localized in the nucleus of CRC cells and acted as a protein kinase. When EGFR translocated into the nucleus upon stimulation with EGF, MFAP3L was phosphorylated at Tyr287 within its SH2 motif, and the activated form of MFAP3L phosphorylated ERK2 at Thr185 and Tyr187. Moreover, the metastatic behavior of CRC cells in vitro and in vivo could be partially explained by activation of the nuclear ERK pathway through MFAP3L phosphorylation. Hence, we experimentally demonstrated for the first time that MFAP3L likely participates in the nuclear signaling of EGFR and ERK2 and acts as a novel nuclear kinase that impacts CRC metastasis.

Omics evidence: single nucleotide variants transmissions on chromosome 20 in liver cancer cell lines.

Cancer genomics unveils many cancer-related mutations, including some chromosome 20 (Chr.20) genes. The mutated messages have been found in the corresponding mRNAs; however, whether they could be translated to proteins still requires more evidence. Herein, we proposed a transomics strategy to profile the expression status of human Chr.20 genes (555 in Ensembl v72). The data of transcriptome and translatome (the mRNAs bound with ribosome, translating mRNAs) revealed that ∼80% of the coding genes on Chr.20 were detected with mRNA signals in three liver cancer cell lines, whereas of the proteome identified, only ∼45% of the Chr.20 coding genes were detected. The high amount of overlapping of identified genes in mRNA and RNC-mRNA (ribosome nascent-chain complex-bound mRNAs, translating mRNAs) and the consistent distribution of the abundance averages of mRNA and RNC-mRNA along the Chr.20 subregions in three liver cancer cell lines indicate that the mRNA information is efficiently transmitted from transcriptional to translational stage, qualitatively and quantitatively. Of the 457 genes identified in mRNAs and RNC-mRNA, 136 were found to contain SNVs with 213 sites, and >40% of these SNVs existed only in metastatic cell lines, suggesting them as the metastasis-related SNVs. Proteomics analysis showed that 16 genes with 20 SNV sites were detected with reliable MS/MS signals, and some SNVs were further validated by the MRM approach. With the integration of the omics data at the three expression phases, therefore, we are able to achieve the overall view of the gene expression of Chr.20, which is constructive in understanding the potential trend of encoding genes in a cell line and exploration of a new type of markers related to cancers.