Nominating novel proteins for anxiety via integrating human brain proteomes and genome-wide association study.

BACKGROUND: The underlying pathogenesis of anxiety remain elusive, making the pinpointing of potential therapeutic and diagnostic biomarkers for anxiety paramount to its efficient treatment. METHODS: We undertook a proteome-wide association study (PWAS), fusing human brain proteomes from both discovery (ROS/MAP; N = 376) and validation cohorts (Banner; N = 152) with anxiety genome-wide association study (GWAS) summary statistics. Complementing this, we executed transcriptome-wide association studies (TWAS) leveraging human brain transcriptomic data from the Common Mind Consortium (CMC) to discern the confluence of genetic influences spanning both proteomic and transcriptomic levels. We further scrutinized significant genes through a suite of methodologies. RESULTS: We discerned 14 genes instrumental in the genesis of anxiety through their specific cis-regulated brain protein abundance. Out of these, 6 were corroborated in the confirmatory PWAS, with 4 also showing associations with anxiety via their cis-regulated brain mRNA levels. A heightened confidence level was attributed to 5 genes (RAB27B, CCDC92, BTN2A1, TMEM106B, and DOC2A), taking into account corroborative evidence from both the confirmatory PWAS and TWAS, coupled with insights from mendelian randomization analysis and colocalization evaluations. A majority of the identified genes manifest in brain regions intricately linked to anxiety and predominantly partake in lysosomal metabolic processes. LIMITATIONS: The limited scope of the brain proteome reference datasets, stemming from a relatively modest sample size, potentially curtails our grasp on the entire gamut of genetic effects. CONCLUSION: The genes pinpointed in our research present a promising groundwork for crafting therapeutic interventions and diagnostic tools for anxiety.

Nomogram-based prognostic tool for stage IIIB/IV non-small cell lung cancer patients undergoing traditional Chinese medicine treatment.

Objective: Given the significant impact of long-term traditional Chinese medicine (TCM) treatment on the prognosis of patients with non-small cell lung cancer (NSCLC), we aimed to develop nomograms, with or without consideration of TCM treatment duration, to accurately predict the overall survival (OS) of patients with stage IIIB/IV NSCLC treated with TCM. Methods: Nomograms were developed from a training cohort comprised of 292 patients diagnosed with NSCLC, using univariate and multivariate Cox regression analyses to screen for various prognostic factors with and without TCM treatment. The nomograms were evaluated using the concordance index (C-index), calibration curve, and decision curve analysis (DCA), after which they were validated, using the bootstrap self-sampling method for internal validation, and a validation cohort comprised of 175 patients for external validation. Bootstrap validation is a resampling technique that involves randomly selecting and replacing data from the original dataset to make statistical inferences, thereby circumventing the issue of sample reduction that can arise from cross-validation. Results: We identified seven significant prognostic factors for OS. For nomogram A (excluding TCM treatment time), the C-indexes (95 % confidence interval [CI]) were 0.674 (0.635-0.712) and 0.660 (0.596-0.724) for the training and validation cohorts, respectively. For nomogram B (including TCM treatment time), the C-indices (95 % CI) were 0.846 (0.822-0.870) and 0.783 (0.730-0.894), for the training and validation cohorts, respectively, indicating that nomogram B was superior to nomogram A. Both the calibration curves and DCA results exhibited favorable clinical concordance and usefulness. Conclusion: The nomogram B yielded precise prognostic predictions for patients with advanced NSCLC treated with TCM.

SlCRCa is a key D-class gene controlling ovule fate determination in tomato.

Cell fate determination and primordium initiation on the placental surface are two key events for ovule formation in seed plants, which directly affect ovule density and seed yield. Despite ovules form in the marginal meristematic tissues of the carpels, angiosperm carpels evolved after the ovules. It is not clear how the development of the ovules and carpels is coordinated in angiosperms. In this study, we identify the S. lycopersicum CRABS CLAW (CRC) homologue SlCRCa as an essential determinant of ovule fate. We find that SlCRCa is not only expressed in the placental surface and ovule primordia but also functions as a D-class gene to block carpel fate and promote ovule fate in the placental surface. Loss of function of SlCRCa causes homeotic transformation of the ovules to carpels. In addition, we find low levels of the S. lycopersicum AINTEGUMENTA (ANT) homologue (SlANT2) favour the ovule initiation, whereas high levels of SlANT2 promote placental carpelization. SlCRCa forms heterodimer with tomato INNER NO OUTER (INO) and AGAMOUS (AG) orthologues, SlINO and TOMATO AGAMOUS1 (TAG1), to repress SlANT2 expression during the ovule initiation. Our study confirms that angiosperm basal ovule cells indeed retain certain carpel properties and provides mechanistic insights into the ovule initiation.

Artificially sweetened beverages consumption and risk of obesity-related cancers: a wide-angled Mendelian randomization study.

Background: The impact of artificially sweetened beverages (ASBs) consumption on obesity-related cancers (ORCs) risk remains controversial. To address this challenging issue, this study employed wide-angle mendelian randomization (MR) analyses to explore the genetic causality between ASB consumption and the risk of ORCs, thereby effectively minimizing the impact of external confounders. Methods: We conducted a suite of analyses encompassing univariable, multivariable, and two-step MR to evaluate causal associations between ASB consumption (samples = 85,852) and risk of ORCs (total samples = 2,974,770) using summary statistics from genome-wide association studies (GWAS). Total, direct, and intermediary effects were derived by performing inverse-variance weighted (IVW), MR-Egger, weighted mode, weighted median, and lasso method. Additionally, we performed an extensive range of sensitivity analyses to counteract the potential effects of confounders, heterogeneity, and pleiotropy, enhancing the robustness and reliability of the findings. Results: Genetically predicted ASB consumption was positively associated with the risk of colorectal cancer (CRC, p = 0.011; OR: 6.879; 95% CI: 1.551, 30.512 by IVW) and breast cancer (p = 0.022; OR: 3.881; 95% CI: 2.023, 9.776 by IVW). Multivariable analysis yielded similar results. The results of the two-step MR unveiled that body mass index (BMI) assumes a pivotal role in mediating the association between ASB consumption and CRC risk (intermediary effect = 0.068, p = 0.024). Conclusion: No causal connection exists between ASB consumption and the majority of ORCs, in addition to CRC and breast cancer. Additionally, our findings suggest that BMI might be a potential mediator in the association between ASB consumption and CRC.

Heat stress impairs floral meristem termination and fruit development by affecting the BR-SlCRCa cascade in tomato.

Floral meristem termination is a key step leading to carpel initiation and fruit development. The frequent occurrence of heat stress due to global warming often disrupts floral determinacy, resulting in defective fruit formation. However, the detailed mechanism behind this phenomenon is largely unknown. Here, we identify CRABS CLAW a (SlCRCa) as a key regulator of floral meristem termination in tomato. SlCRCa functions as an indispensable floral meristem terminator by suppressing SlWUS activity through the TOMATO AGAMOUS 1 (TAG1)-KNUCKLES (SlKNU)-INHIBITOR OF MERISTEM ACTIVITY (SlIMA) network. A direct binding assay revealed that SlCRCa specifically binds to the promoter and second intron of WUSCHEL (SlWUS). We also demonstrate that SlCRCa expression depends on brassinosteroid homeostasis in the floral meristem, which is repressed by heat stress via the circadian factor EARLY FLOWERING 3 (SlELF3). These results provide new insights into floral meristem termination and the heat stress response in flowers and fruits of tomato and suggest that SlCRCa provides a platform for multiple protein interactions that may epigenetically abrogate stem cell activity at the transition from floral meristem to carpel initiation.

Retracted: Effect of Sham Acupuncture on Chronic Pain: A Bayesian Network Meta-Analysis.

BACKGROUND: Along with increasing research on acupuncture for chronic pain, the validity of sham acupuncture (SA) has also been argued. METHODS: Nine databases were searched for randomized controlled trials (RCTs) from the inception dates of the databases to July 5, 2022. With Markov Chain Monte Carlo methods, a Bayesian multiple-treatment network meta-analysis (NMA) with random-effects model was conducted. RESULTS: A total of 62 RCTs with 6,806 patients and four kinds of treatments (real acupuncture [RA], non-acupuncture [NA], penetrative SA [PSA], and non-penetrative SA [NPSA]) were included. The results indicated that both NPSA and PSA were not superior to NA in improving chronic pain (NPSA: mean difference [MD]= -4.77, 95% confidence interval [CI] -11.09 to 1.52; PSA: MD= -4.96, 95% CI -10.38 to 0.48). After NPSA and PSA were combined into the SA group, the weak trend of pain relief from SA was still not statistically significant (MD= -4.91, 95% CI -9.93 to 0.05). NPSA and PSA had similar effects (MD= 0.18, 95% CI -5.45 to 5.81). RA was significantly associated with pain relief, compared with NPSA and PSA (NPSA: MD= -12.03, 95% CI -16.62 to -7.41; PSA: MD= -11.85, 95% CI -15.48 to -8.23). The results were generally consistent regardless of pain phenotype, frequency, duration, acupuncture methods, analgesic intake, or detection bias. CONCLUSION: These results suggested that acupuncture was significantly associated with reduced chronic pain. The two kinds of placebo acupuncture, NPSA and PSA, have similar effects. Both NPSA and PSA, with a weak but not significant effect, are appropriate to be inert placebo controls in RCTs for chronic pain.

Establishment of an acquired lorlatinib-resistant cell line of non-small cell lung cancer and its mediated resistance mechanism

Although lorlatinib, the third generation of echinoderm microtubule protein 4-anaplastic lymphoma kinase (EML4-ALK) tyrosine kinase inhibitor (TKI), overcame the previous generation ALK-TKIs’ drug resistance problems, but the mechanism of lorlatinib resistance remained unclear. Furthermore, optimal chemotherapy for lorlatinib-resistant non-small cell lung cancer (NSCLC) patients was still unknown.MethodsA lorlatinib-resistant NSCLC cell line SNU-2535LR was generated by gradually increasing dose of lorlatinib to crizotinib-resistant cell line SNU-2535 in vitro. To study the resistance mechanism of SNU-2535LR cells, we applied CCK-8 assay to detect the sensitivity of crizotinib and the reverse effect of APR-246, a p53 activator, on lorlatinib-induced resistance and different chemotherapy drugs to SNU-2535LR cells. We also detected the expressions of EML4-ALK-related proteins of SNU-2535LR cells via western blot.Please confirm that author names have been identified correctly and are presented in the right order. (AU)

Establishment of an acquired lorlatinib-resistant cell line of non-small cell lung cancer and its mediated resistance mechanism.

PURPOSE: Although lorlatinib, the third generation of echinoderm microtubule protein 4-anaplastic lymphoma kinase (EML4-ALK) tyrosine kinase inhibitor (TKI), overcame the previous generation ALK-TKIs' drug resistance problems, but the mechanism of lorlatinib resistance remained unclear. Furthermore, optimal chemotherapy for lorlatinib-resistant non-small cell lung cancer (NSCLC) patients was still unknown. METHODS: A lorlatinib-resistant NSCLC cell line SNU-2535LR was generated by gradually increasing dose of lorlatinib to crizotinib-resistant cell line SNU-2535 in vitro. To study the resistance mechanism of SNU-2535LR cells, we applied CCK-8 assay to detect the sensitivity of crizotinib and the reverse effect of APR-246, a p53 activator, on lorlatinib-induced resistance and different chemotherapy drugs to SNU-2535LR cells. We also detected the expressions of EML4-ALK-related proteins of SNU-2535LR cells via western blot.Please confirm that author names have been identified correctly and are presented in the right order.Dear Editor:     I have carefully confirmed that the author names have been identified correctly and are presented in right order.Thank you very much!                                                                     Your sincerely BoXie RESULTS: The sensitivity of SNU-2535LR cells to lorlatinib was decreased significantly than that of SNU-2535 cells. EML4-ALK fusion was decreased both at protein level and DNA level in SNU-2535LR cells. More interesting, the crizotinib-resistant mutation ALK p.G1269A disappeared, while new TP53 mutation emerged in SNU-2535LR cells. APR-246 can reverse the lorlatinib resistance in SNU-2535LR cells, with a reversal index of 4.768. Compared with SNU-2535 cells, the sensitivity of SNU-2535LR cells to gemcitabine, docetaxel and paclitaxel was significantly increased (P < 0.05), but decreased to cisplatin (P < 0.05). CONCLUSION: This study demonstrated that the combination of p53 protein agonist and lorlatinib may provide a new therapeutic strategy for NSCLC patients with lorlatinib resistance and TP53 mutation. Furthermore, the results also provide guidance for selecting optimal chemo-regimens for NSCLC patients after ALK-TKIs failure.

Dissecting the ferroptosis-related prognostic biomarker and immune microenvironment of driver gene-negative lung cancer.

Despite significant advances in targeted and immune therapy for non-small cell lung cancer (NSCLC), effective therapies for wild-type epidermal growth factor receptor/anaplastic lymphoma kinase (EGFR/ALKWT) with low expression of programmed death ligand-1 (PD-L1) NSCLC remain elusive. Numerous studies have shown that ferroptosis plays an essential role in antitumor activity. To identify the molecular regulation patterns associated with ferroptosis, 351 EGFR/ALKWT NSCLC samples with low-level PD-L1 were extracted from The Cancer Genome Atlas (TCGA) and clustered using the k-means clustering technique. The two clusters associated with ferroptosis showed significantly different prognoses. In total, 169 differential expression genes (DEGs) were identified. Cluster differential analysis revealed that Cluster 1 had a significantly poorer overall survival (OS) and was associated with more negative immune regulation. In addition, TCGA samples were randomly assigned in a 7:3 ratio to a training group or testing group. A signature of eight genes associated with ferroptosis was established in the training cohort using DEGs and validated in the test cohort and three independent cohorts (GSE72049, GSE41271, and GSE50081). The 5-year area under the curve (AUC) was 0.713, which was significantly higher than that of other predictors, including TNM stage and age. Furthermore, the risk score was associated with immune function, immune infiltration, and immunotherapy response, with high-risk patients having a worse prognosis, an immune-suppressing phenotype, and a poor response to immune checkpoint inhibitors. This study aims to contribute to our understanding of the biological role of ferroptosis in EGFR/ALKWT NSCLC with low-level PD-L1, laying the groundwork for the development of novel therapeutic strategies.

Bone metastasis attenuates efficacy of immune checkpoint inhibitors and displays "cold" immune characteristics in Non-small cell lung cancer.

OBJECTIVES: This study aimed to assess the clinical characteristics affecting outcomes after immune checkpoint inhibitors (ICI) therapies in non-small cell lung cancer (NSCLC) patients, and the underlying mechanism in tumor immune micro-environment (TIME). MATERIALS AND METHODS: A total of 144 patients treated with ICI-based strategies were retrospectively analyzed. Expression of 10 immune antibodies in tumor tissues from other 60 untreated NSCLC patients were sequentially tested using multiplexed immunofluorescence (mIF) staining method. Correlation of clinical characteristics with ICI treatment outcomes and TIME characteristics were analyzed. RESULTS: Multivariate logistic and cox regression indicated that BoM negatively affected disease control rate (OR = 0.32, 95%CI: 0.13-0.82, P = 0.018), progression free survival (HR = 3.44, 95% CI:1.97-6.00, P < 0.001) and overall survival (HR = 3.24, 95% CI:1.62-6.50, P = 0.001), irrespective of programmed death-ligand 1 (PD-L1) expression. BoM patients were with significantly lower PD-L1, and this heterogeneity of TIME was then confirmed in the mIF staining, where 36 (61.0%) patients were clustered into immune-subtype A, with low expression of all the detected immune markers, similar to "cold" tumors, and 23 (39.0%) in cluster B with likely "hot" tumors. More patients in immune-subtype A were non-smokers (63.9% vs. 39.1% P = 0.063), with BoM (66.7% vs. 21.7%, P = 0.001), in stage IV(88.9% vs. 65.2%, P = 0.045), and with adenocarcinoma (91.7% vs. 69.6%, P = 0.037). Multivariate logistic regression indicated that BoM was independently associated with the "cold" immune characteristics (OR = 0.19, 95% CI:0.04-0.84, P = 0.028). Combination therapy with chemotherapy /antiangiogenesis or use of bisphosphonate during ICI treatment significantly improved clinical outcomes in BoM patients. CONCLUSIONS: BoM displays adverse impact on clinical outcomes after ICI treatments in NSCLC patients. The "cold" characteristics of TIME may be the underlying mechanism for the attenuated efficacy of ICIs in bone metastatic NSCLC patients.

Lung cancer organoids, a promising model still with long way to go.

Lung cancer organoids (LCOs) have sprung up in more and more researching fields, because of their ability to recapitulate the three-dimensional structure and functions of the in vivo counterpart organs. However, the culture system for LCOs is still immature, resulting in limited success rate and low tumor purity when culturing LCOs. This is mainly due to the deficiency of an optimal formula of culture medium specially for LCOs. Various cytokines and small molecules have been added in the LCOs culturing system. Compound screening, considering both the mechanism of these molecules and the complexity of lung cancer types is warranted to optimize LCOs culture medium. As methods to culture LCOs increase in sophistication, this model will undoubtedly stand its ground in the coming years in every aspect of cancer researches, especially with major advantages in the field of personalized medicine and tumor microenvironment researches.

A Clinical Nomogram for Predicting Cancer-Specific Survival in Pulmonary Large-Cell Neuroendocrine Carcinoma Patients: A Population-Based Study.

PURPOSE: This study was designed to construct and validate a nomogram that was available for predicting cancer-specific survival (CSS) in patients with pulmonary large-cell neuroendocrine carcinoma (LCNEC). PATIENTS AND METHODS: Using the US Surveillance, Epidemiology, and End Results (SEER) database, we identified patients pathologically diagnosed as LCNEC from 1975 to 2016. Univariate and multivariate Cox regression was conducted to assess prognostic factors of CSS. A novel nomogram model was constructed and validated by the concordance index (C-index), calibration curves and decision curve analysis (DCA). RESULTS: A total of 624 LCNEC patients were enrolled. Five prognostic factors for CSS were identified and merged to establish nomograms. In the training and validation cohorts, calibration curves displayed the nomogram predictions are in a good agreement with the actual survival. The C-Index of the training and validation cohorts were both higher than 0.8, and the DCA results showed that the nomogram has clinical validity and utility. CONCLUSION: The proposed nomogram resulted in accurate CSS prognostic prediction for patients with LCNEC.

Comparative efficacy and safety of first-line treatments for advanced non-small cell lung cancer with ALK-rearranged: a meta-analysis of clinical trials.

BACKGROUND: Whereas there are many pharmacological interventions prescribed for patients with advanced anaplastic lymphoma kinase (ALK)- rearranged non-small cell lung cancer (NSCLC), comparative data between novel generation ALK-tyrosine kinase inhibitors (TKIs) remain scant. Here, we indirectly compared the efficacy and safety of first-line systemic therapeutic options used for the treatment of ALK-rearranged NSCLC. METHODS: We included all phase 2 and 3 randomised controlled trials (RCTs) comparing any two or three treatment options. Eligible studies reported at least one of the following outcomes: progression free survival (PFS), overall survival (OS), objective response rate (ORR), or adverse events of grade 3 or higher (Grade ≥ 3 AEs). Subgroup analysis was conducted according to central nervous system (CNS) metastases. RESULTS: A total of 9 RCTs consisting of 2484 patients with 8 treatment options were included in the systematic review. Our analysis showed that alectinib (300 mg and 600 mg), brigatinib, lorlatinib and ensartinib yielded the most favorable PFS. Whereas there was no significant OS or ORR difference among the ALK-TKIs. According to Bayesian ranking profiles, lorlatinib, alectinib 600 mg and alectinib 300 mg had the best PFS (63.7%), OS (35.9%) and ORR (37%), respectively. On the other hand, ceritinib showed the highest rate of severe adverse events (60%). CONCLUSION: Our analysis indicated that alectinib and lorlatinib might be associated with the best therapeutic efficacy in first-line treatment for major population of advanced NSCLC patients with ALK-rearrangement. However, since there is little comparative evidence on the treatment options, there is need for relative trials to fully determine the best treatment options as well as the rapidly evolving treatment landscape.