Overcoming Barriers to Tobacco Cessation and Lung Cancer Screening among Racial and Ethnic Minority Groups and Underserved Patients in Academic Centers and Community Network Sites: The City of Hope Experience

BACKGROUND

Tobacco control is important for cancer patient health, but delivering effective low-dose CT (LDCT) screening and tobacco cessation is more difficult in underserved and patients from racial and ethnic minority groups. At City of Hope (COH), we have developed strategies to overcome barriers to the delivery of LDCT and tobacco cessation.

METHODS

We performed a needs assessment. New tobacco control program services were implemented focusing on patients from racial and ethnic minority groups. Innovations included Whole Person Care with motivational counseling, placing clinician and nurse champions at points of care, training module and leadership newsletters, and a patient-centric personalized medicine Personalized Pathways to Success (PPS) program.

RESULTS

Emphasis on patients from racial and ethnic minority groups was implemented by training cessation personnel and lung cancer control champions. LDCT increased. Tobacco use assessment increased and abstinence was 27.2%. The PPS pilot program achieved 47% engagement in cessation, with self-reported abstinence at 3 months of 38%, with both results slightly higher in patients from racial and ethnic minority groups than in Caucasian patients.

CONCLUSIONS

Tobacco cessation barrier-focused innovations can result in increased lung cancer screening and tobacco cessation reach and effectiveness, especially among patients from racial and ethnic minority groups. The PPS program is promising as a personalized medicine patient-centric approach to cessation and lung cancer screening.

Recent Progress in Plasmonic based Electrochemiluminescence Biosensors: A Review

Electrochemiluminescence (ECL) analysis has become a powerful tool in recent biomarker detection and clinic diagnosis due to its high sensitivity and broad linear range. To improve the analytical performance of ECL biosensors, various advanced nanomaterials have been introduced to regulate the ECL signal such as graphene, gold nanomaterials, and quantum dots. Among these nanomaterials, some plasmonic nanostructures play important roles in the fabrication of ECL biosensors. The plasmon effect for the ECL signal includes ECL quenching by resonant energy transfer, ECL enhancement by surface plasmon resonance enhancement, and a change in the polarized angle of ECL emission. The influence can be regulated by the distance between ECL emitters and plasmonic materials, and the characteristics of polarization angle-dependent surface plasmon coupling. This paper outlines the recent advances of plasmonic based ECL biosensors involving various plasmonic materials including noble metals and semiconductor nanomaterials. The detection targets in these biosensors range from small molecules, proteins, nucleic acids, and cells thanks to the plasmonic effect. In addition to ECL biosensors, ECL microscopy analysis with plasmonic materials is also highlighted because of the enhanced ECL image quality by the plasmonic effect. Finally, the future opportunities and challenges are discussed if more plasmonic effects are introduced into the ECL realm.

Case report: Abolishing primary resistance to PD-1 blockade by short-term treatment of lenvatinib in a patient with advanced metastatic renal cell carcinoma

Anti-PD-1 immunotherapy has been extensively used in treatment of patients with advanced metastatic renal cell carcinoma (mRCC). Several prospective clinical trials showed that the combined treatment of anti-PD-1 antibody plus lenvatinib, a potent receptor tyrosine kinase inhibitor (TKI), exhibited high response rate compared with single-agent sunitinib. However, whether the patients with primary resistance to PD-1 blockade could benefit from the addition of lenvatinib is still unclear. Herein, we reported a patient with mRCC who was primary resistant to pembrolizumab and achieved a durable complete response after a short-term treatment with lenvatinib. This case report indicates that the patients with primary resistance to anti-PD-1 therapy could benefit from the short-term lenvatinib in combination with anti-PD-1 therapy, and provides a useful paradigm worthy of establishing a clinical trial for mRCC patients with primary resistance to anti-PD-1 therapy.

HOXB13 facilitates hepatocellular carcinoma progression by activating AKT/mTOR signaling pathway

INTRODUCTION AND OBJECTIVES

Hepatocellular carcinoma (HCC) is one of the sixth most common malignancies worldwide and is accompanied by high mortality. Homeobox B13 (HOXB13) has been shown to be involved in the development of various cancers. This study aimed to investigate the role of HOXB13 in HCC progression.

MATERIALS AND METHODS

The expression of HOXB13 in HCC tumor tissues was analyzed using qRT-PCR and immunohistochemical staining . After overexpression or downregulation of HOXB13 in HCC cell lines, cell proliferation was detected by CCK8 assay and Ki67 staining and cell invasion ability were tested by transwell assay. Western blot assay was applied to analyze the effect of HOXB13 on related signaling pathways. In addition, the role of HOXB13 on HCC in vivo was explored using a HCC mouse model. IF and WB were performed to detect cell proliferation, apoptosis and related protein expression in mice tumor tissues.

RESULTS

The results showed that the expression of HOXB13 was significantly increased in HCC tissues compared with adjacent tissues and positively correlated with the tumor stage and survival of HCC patients. Overexpression of HOXB13 promoted the proliferation and invasion of HCC cells and up-regulated the protein expression of AKT, mTOR and MMP2. In contrast, the downregulation of HOXB13 resulted in the opposite results. In vivo experiments, HOXB13 significantly promoted tumor growth in mice bearing HCC by promoting cell proliferation and inhibiting cell apoptosis.

CONCLUSIONS

This study suggested that HOXB13 can facilitate HCC progression by activation of the AKT/mTOR signaling pathway. HOXB13 may be a novel target for HCC therapy.

Paeoniflorin protects NOD mice from T1D through regulating gut microbiota and TLR4 mediated myD88/TRIF pathway

This study aimed to explore the effect of PF in regulating the progression of T1D through regulating gut microbiota and inhibiting TLR4-myD88/TRIF pathway. T1D mouse models were established and received PF treatment through intraperitoneal injection. The glucose, sugar tolerance, the incidence of T1D and H&E staining were detected to verify the effect of PF on T1D. Meanwhile, the changes of gut microbiota and the permeability of intestines in mice were also measured. On parallel, the number and function of immune cells were detected by Flow Cytometry. The expressions of ZO-1, ZO-2 and TLR4-myD88/TRIF pathway related proteins were detected by western blotting. Mice received PF treatment had decreased incidence of T1D and inflammatory infiltration in islet tissues compared with those received PBS treatment. In addition to that, PF treated mice had increased Sutterella species and decreased intestinal permeability, in which the decreased ratio of Th1/Th17 and increased Treg cells were also identified. The expression of TLR4-myD88/TRIF pathway was also suppressed in response to PF treatment. Moreover, further treatment with TLR4 agonist, LPS, could reverse the effect of PF on T1D mice. PF can suppress the TLR4 mediated myD88/TRIF pathway to change the distribution of gut microbiota, so as to protect NOD mice from T1D.

[Effect analysis of myectomy guided by personalized three-dimensional reconstruction and printing in the treatment of obstructive hypertrophic cardiomyopathy]

Objective: To examine the clinical efficacy of myectomy guided by personalized three-dimensional reconstruction and printing for patients with obstructive hypertrophic cardiomyopathy. Methods: The clinical data of 28 patients with obstructive hypertrophic cardiomyopathy, who underwent septal myectomy guided by personalized three-dimensional reconstruction and printing in the Department of Cardiaovascular Surgery, Guangdong Provincial People's Hospital from May 2020 to December 2021, were retrospectively analyzed. There were 14 males and 14 females, aging (51.1±14.0) years (range: 18 to 72 years). Enhanced cardiac computed tomography images were imported into Mimics software for preoperative three-dimensional reconstruction. The direction of the short axial plane of each segment was marked perpendicularly to the interventricular septum on the long axial plane of the digital cardiac model, then the thickness was measured on each short axial plane. A figurative digital model was used to determine the extent of resection and to visualize mitral valve and papillary muscle abnormalities. Correlation between the length, width, thickness, and volume of the predicted resected myocardium and those of the surgically resected myocardium was assessed by Pearson correlation analysis or Spearman correlation analysis. The accuracy of detecting mitral valve and papillary muscle abnormalities of transthoracic echocardiography and three-dimensional reconstruction was also compared. Results: There was no death or serious complications like permanent pacemaker implantation, re-sternotomy for bleeding, low cardiac output syndrome, stroke, or multiple organ dysfunction syndromes in the whole group. Namely, the obstruction of the left ventricular outflow tract was effectively relieved. The systolic anterior motion of the anterior mitral valve leaflet was absent in all patients after myectomy. The length, width, and thickness of the predicted resected myocardium by three-dimensional reconstruction were significantly positively correlated with the length (R=0.65, 95%CI: 0.37 to 0.82, P<0.01), width (R=0.39, 95%CI: 0.02 to 0.67, P<0.01), and thickness (R=0.82, 95%CI: 0.65 to 0.92, P<0.01) of the surgically resected myocardium, while the relation of the volume of the predicted resected myocardium and the volume of the surgically resected myocardium was a strong positive correlation (R=0.88, 95%CI: 0.76 to 0.94, P<0.01). Importantly, the interventricular septal myocardial thickness measured by preoperative transthoracic echocardiography showed a moderate positive correlation with the volume of surgically resected myocardium (R=0.52, 95%CI: 0.19 to 0.75, P<0.01). During a follow-up of (14.4±6.8) months (range: 3 to 22 months), no death occurred, and 1 patient was readmitted for endocardial radiofrequency ablation due to atrial fibrillation. Conclusion: Personalized three-dimensional reconstruction and printing can not only visualize the intracardiac structure but also guide septal myectomy by predicting the thickness, volume, and extent of resected myocardium to achieve ideal resection.

A novel multi-view X-ray digital imaging stitching algorithm

BACKGROUND

In fan beam X-ray imaging applications, several X-ray images sometimes need to be stitched together into a panoramic image because of the size limitations of the detector.

OBJECTIVE

This study aims to propose a novel multi-view X-ray digital imaging stitching algorithm (MVS) based on the CdZnTe photon counting linear array detectors to solve the problem of fan beam X-ray stitching deformation.

METHODS

The panoramic image is generated in four steps including (1) multi-view projection data acquisition, (2) overlapping positioning, (3) weighted fusion and (4) projected pixel value calculation. Images of a globe and foot are scanned by fan beam X-rays and a CdZnTe detector. The proposed method is applied to stitch together the scanned images of the globe. Three other methods are also used for comparison. Finally, this MVS algorithm is also used in the stitching of scanned images of the foot.

RESULTS

Compared with the 50% stitching accuracy of other methods, the new MVS algorithm reached a stitching accuracy of 94.4%. Image distortion on the globe and feet is also eliminated and thus image quality is significantly improved.

CONCLUSIONS

This study proposes a new multi-view X-ray digital imaging stitching algorithm. Study results demonstrate the superiority of this new algorithm and its feasibility in practical applications.

COVIDpro: Database for mining protein dysregulation in patients with COVID-19

Background

The ongoing pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) still has limited treatment options partially due to our incomplete understanding of the molecular dysregulations of the COVID-19 patients. We aimed to generate a repository and data analysis tools to examine the modulated proteins underlying COVID-19 patients for the discovery of potential therapeutic targets and diagnostic biomarkers.

Methods

We built a web server containing proteomic expression data from COVID-19 patients with a toolset for user-friendly data analysis and visualization. The web resource covers expert-curated proteomic data from COVID-19 patients published before May 2022. The data were collected from ProteomeXchange and from select publications via PubMed searches and aggregated into a comprehensive dataset. Protein expression by disease subgroups across projects was compared by examining differentially expressed proteins. We also visualize differentially expressed pathways and proteins. Moreover, circulating proteins that differentiated severe cases were nominated as predictive biomarkers.

Findings

We built and maintain a web server COVIDpro ( https://www.guomics.com/covidPro/ ) containing proteomics data generated by 41 original studies from 32 hospitals worldwide, with data from 3077 patients covering 19 types of clinical specimens, the majority from plasma and sera. 53 protein expression matrices were collected, for a total of 5434 samples and 14,403 unique proteins. Our analyses showed that the lipopolysaccharide-binding protein, as identified in the majority of the studies, was highly expressed in the blood samples of patients with severe disease. A panel of significantly dysregulated proteins was identified to separate patients with severe disease from non-severe disease. Classification of severe disease based on these proteomic signatures on five test sets reached a mean AUC of 0.87 and ACC of 0.80.

Interpretation

COVIDpro is an online database with an integrated analysis toolkit. It is a unique and valuable resource for testing hypotheses and identifying proteins or pathways that could be targeted by new treatments of COVID-19 patients.

Funding

National Key R&D Program of China: Key PDPM technologies (2021YFA1301602, 2021YFA1301601, 2021YFA1301603), Zhejiang Provincial Natural Science Foundation for Distinguished Young Scholars (LR19C050001), Hangzhou Agriculture and Society Advancement Program (20190101A04), National Natural Science Foundation of China (81972492) and National Science Fund for Young Scholars (21904107), National Resource for Network Biology (NRNB) from the National Institute of General Medical Sciences (NIGMS-P41 GM103504).

Research in context

Evidence before this study: Although an increasing number of therapies against COVID-19 are being developed, they are still insufficient, especially with the rise of new variants of concern. This is partially due to our incomplete understanding of the disease’s mechanisms. As data have been collected worldwide, several questions are now worth addressing via meta-analyses. Most COVID-19 drugs function by targeting or affecting proteins. Effectiveness and resistance to therapeutics can be effectively assessed via protein measurements. Empowered by mass spectrometry-based proteomics, protein expression has been characterized in a variety of patient specimens, including body fluids (e.g., serum, plasma, urea) and tissue (i.e., formalin-fixed and paraffin-embedded (FFPE)). We expert-curated proteomic expression data from COVID-19 patients published before May 2022, from the largest proteomic data repository ProteomeXhange as well as from literature search engines. Using this resource, a COVID-19 proteome meta-analysis could provide useful insights into the mechanisms of the disease and identify new potential drug targets.Added value of this study: We integrated many published datasets from patients with COVID-19 from 11 nations, with over 3000 patients and more than 5434 proteome measurements. We collected these datasets in an online database, and generated a toolbox to easily explore, analyze, and visualize the data. Next, we used the database and its associated toolbox to identify new proteins of diagnostic and therapeutic value for COVID-19 treatment. In particular, we identified a set of significantly dysregulated proteins for distinguishing severe from non-severe patients using serum samples.Implications of all the available evidence: COVIDpro will support the navigation and analysis of patterns of dysregulated proteins in various COVID-19 clinical specimens for identification and verification of protein biomarkers and potential therapeutic targets.

Metal-Free and Open-Air Arylation Reactions of Diaryliodonium Salts for DNA-Encoded Library Synthesis

A successful DNA-encoded library (DEL) will consist of diverse skeletons and cover chemical space as comprehensive as possible to fully realize its potential in drug discovery and chemical biology. However, the lack of versatile on-DNA arylation methods for phenols that are less nucleophilic and reactive poses a great hurdle for DEL to include diaryl ether, a privileged chemotype in pharmaceuticals and natural products. This work describes the use of "substrate activation" approach to address the arylation of DNA-conjugated phenols. Diaryliodonium salt, a highly electrophilic and reactive arylation reagent, is employed as Ar⁺ sources to ensure highly selective on-DNA arylation of phenols and oximes with both high yields and DNA fidelity. Notably, the new on-DNA arylation reaction can be applied to the late-stage modification of peptides containing tyrosine side-chain and to synthesize DNA-tagged analogues of existing drug molecules such as sorafenib, a known pan-kinase inhibitor. The new on-DNA diaryliodonium salts chemistry affords a greater flexibility in DEL design and synthesis.

Variable frequencies of peripheral T-lymphocyte subsets in the diabetes spectrum from type 1 diabetes through latent autoimmune diabetes in adults (LADA) to type 2 diabetes

T lymphocytes are key players in the pathogenesis of autoimmune diabetes. We recruited subjects with T1D (n=81), LADA (n=82), T2D (n=95) and NGT (n=218) and analyzed the percentages of T-lymphocyte subsets, including T helper 1 (Th1), T helper 2 (Th2), T helper 17 (Th17), T cytotoxic 1 (Tc1), regulatory T cells (Tregs), effector T (Teff), naïve T, central memory T (Tcm), and effector memory T (Tem) cells by flow cytometry. LADA patients possessed similar frequencies of IFN-γ⁺CD4⁺ T (Th1), IFN-γ⁺CD8⁺ T and CD4⁺ Teff cells compared with T1D patients, but much lower than those of NGT subjects. Like T2D patients, LADA patients had increased frequencies of CD4⁺ Tem and CD8⁺ Tem cells with respect to T1D and NGT subjects. In LADA patients, Th2 cells were decreased while CD4⁺ Tcm cells were increased compared with NGT subjects. Notably, we observed significant negative correlations between the CD4⁺ Tcm cell frequency and C-peptide in LADA subjects. These data demonstrates that LADA patients possess T-cell subset changes resembling both T1D and T2D and represent the middle of the diabetes spectrum between T1D and T2D. Based on these T-cell subset alterations, we speculate that autoimmunity-induced β-cell destruction and inflammation-induced insulin resistance might both be involved in the pathogenesis of LADA.

O102 We know about left gastric artery embolisation and will embio provide the next solution to treat obesity?

Introduction

Left gastric artery embolisation (LGAE) is a minimally invasive procedure which has shown promising results for weight loss in recent studies and could play a key role as a treatment option in-between our current tier-3 and tier-4 services. Imperial College NHS Trust will sponsor the EMBIO trial, the first multi-centre double blinded randomised controlled trial comparing LGAE vs Placebo procedure to evaluate its efficacy on weight loss and obesity related comorbidities over a 12 month follow up period. Here, we perform a systematic review of the existing literature.

Methods

9 studies were reviewed. Studies which investigated weight loss as a % +- Ghrelin % change at 3,6 and 12 months were included as these pre-defined time points correlate with the EMBIO protocol. 6 studies met our inclusion criteria, 5 single arm studies and 1 single blinded RCT.

Results

N=62 patients were included in our analysis. Mean weight loss reported was 8.5%, 8.8% and 10% at 3, 6 and 12 months respectively post LGAE. Ghrelin levels reduced by 36%, 16.2% and 16.5% at 3, 6 and 12 months respectively post LGAE. To date, the only reported adverse events recorded include superficial gastric erosions healed on endoscopy by day 90 and one case of subclinical pancreatitis.

Conclusion

LGAE potentially offers a day case procedure under local anaesthesia and sedation to treat obesity and its metabolic complications. The EMBIO trial will provide level 1 evidence to confirm if LGAE is a viable intervention for obesity and evaluate its safety profile.

Take-home message

Left gastric artery embolisation could be the perfect solution to treat obesity in between existing tier-3 and tier-4 treatments.

SlJAZ10 and SlJAZ11 mediate dark-induced leaf senescence and regeneration

During evolutionary adaptation, the mechanisms for self-regulation are established between the normal growth and development of plants and environmental stress. The phytohormone jasmonate (JA) is a key tie of plant defence and development, and JASMONATE-ZIM DOMAIN (JAZ) repressor proteins are key components in JA signalling pathways. Here, we show that JAZ expression was affected by leaf senescence from the transcriptomic data. Further investigation revealed that SlJAZ10 and SlJAZ11 positively regulate leaf senescence and that SlJAZ11 can also promote plant regeneration. Moreover, we reveal that the SlJAV1-SlWRKY51 (JW) complex could suppress JA biosynthesis under normal growth conditions. Immediately after injury, SlJAZ10 and SlJAZ11 can regulate the activity of the JW complex through the effects of electrical signals and Ca²⁺ waves, which in turn affect JA biosynthesis, causing a difference in the regeneration phenotype between SlJAZ10-OE and SlJAZ11-OE transgenic plants. In addition, SlRbcs-3B could maintain the protein stability of SlJAZ11 to protect it from degradation. Together, SlJAZ10 and SlJAZ11 not only act as repressors of JA signalling to leaf senescence, but also regulate plant regeneration through coordinated electrical signals, Ca²⁺ waves, hormones and transcriptional regulation. Our study provides critical insights into the mechanisms by which SlJAZ11 can induce regeneration.

In plants, senescence is the final stage of development, but regeneration can help them beyond the stage. Plants regeneration is essential for propagation, and in cultivated crops to maintain excellent traits as close as possible. JA signaling can sense environmental signals and integrate various regulatory mechanisms to ensure plants regeneration occurs under optimal conditions. In this work, the JAZ-JAV1-WRKY51 complexes with reported was further optimized, the function of SlJAZ10 and SlJAZ11 was identified to promote inhibitory activity of SlJAV1-SlWRKY51 complex which negatively regulated JA biosynthesis by direct binding of the W-box of the SlAOC promoter. The results of further investigation suggest that the differences in regulation of electrical signals, Ca²⁺ waves, hormones and transcriptional regulation are responsible for the regeneration between SlJAZ10 and SlJAZ11. In addition, we have found that SlRbcs-3B could maintain the protein stability of SlJAZ11 to protect it from degradation. In summary, despite both SlJAZ10 and SlJAZ11 can function as senescence, only SlJAZ11 has an important promoting function for regeneration.

Knockout of SlALKBH2 weakens the DNA damage repair ability of tomato

During the growth and evolution of plants, genomic DNA is subject to constant assault from endogenous and environmental DNA damage compounds, which will result in mutagenic or genotoxic covalent adducts. Whether for prokaryotes, eukaryotes or even viruses, maintaining genome integrity is critical for the continuation of life. Escherichia coli and mammals have evolved the AlkB family of Fe(II)/alpha-ketoglutarate-dependent dioxygenases that repair DNA alkylation damage. We identified a functional homologue with EsAlkB and HsALKBH2 in tomatoes, and named it SlALKBH2. In our study, the SlALKBH2 knockout mutant showed hypersensitivity to the DNA mutagen MMS and displayed more severe growth abnormalities than wild-type plants under mutagen treatment, such as slow growth, leaf deformation and early senescence. Additionally, genes with high transcriptional activity, such as rDNA, have increased methylation under MMS treatment. In conclusion, this study shows that the tomato SlALKBH2 gene may play an important role in ensuring the integrity of the genome.

Damage-Free and Time-Saving Platform Integrated by a Flow Membrane Separation Device and a Dual-Target Biofuel Cell-Based Biosensor for Continuous Sorting and Detection of Exosomes and Host Cells in Human Serum

The growth relationship between exosomes (EXOs) and the host cells is highly desired for tumor evaluations, which puts forward high demand on the accurate and convenient acquisition of their individual quantitative information. However, the tedious and destructive separation process and the requirement of dual-channel detection make it become an extremely challenging task. Herein, we integrated an enzymatic biofuel cell (EBFC)-powered biosensor with a flow cell-supported membrane separation device (FMSC) to develop a continuous separation and detection platform for EXOs and host cancer cells in human serum. The FMSC equipped with an aluminum oxide membrane served as a size-dependent sorting unit to nondestructively extract EXOs from human serum within 5 min, representing a 99.3% reduction in isolating time compared to ultracentrifugation. The EBFC-powered biosensors modified with different aptamers on anodes and cathodes were used as a dual-channel sensing unit. By regulating the controlling valves of different fluid passages, the extracted EXOs and residual host cells could be successively inputted into EBFC-powered biosensors, which generated a segmental degradation in output performance due to the EXO-and host cell-caused increase in the steric hindrance of anodes and cathodes, respectively. Based on these degradations, we obtained the quantitative information of EXOs and host cells with a record-breaking sensitivity (EXOs: 5.59 × 10³ particles/mL and host cells: 25 cells/mL). Moreover, the growth relationship between EXOs and host cells was also built, which would be beneficial for the disclosure of the growth state or even more detailed biology information of tumor.

Multi-Omics Analysis Reveals That SlERF.D6 Synergistically Regulates SGAs and Fruit Development

Steroidal glycoalkaloids (SGAs) are cholesterol-derived molecules that contribute to the pathogen defense in tomato but are toxic and considered to be antinutritional compounds to humans. APETALA2/Ethylene Responsive Factor (AP2/ERF) family transcription factors (TFs) play an indispensable role in various biological processes, such as plant growth and development, fruit ripening, biotic and abiotic stresses responses, and SGA biosynthesis. In this study, we identified 176 AP2/ERF genes that were domesticated or improved SlAP2/ERF in the tomato variome (Solanum lycopersicum) within either domestication or improvement sweeps, respectively. According to the RNA-sequencing data, 93 of the ERF genes with high transcriptional level (Transcripts Per Million, TPM > 1) belong to six clusters. Weighted gene co-expression network analysis (WGCNA) and metabolite-based genome-wide association study (mGWAS) analyses revealed that the expression level of the Solyc04g071770 (SlERF.D6) gene in the cluster six gradually increased as the fruit matured. Transient transformation verified that the overexpression of SlERF.D6 significantly promoted fruit ripening and regulated the expression of multiple genes in the SGA synthesis pathway, thereby affecting the SGA content of the fruit. Virus-induced gene silencing (VIGS) showed that the silencing of SlERF.D6 delayed fruit ripening and influenced the content of SGAs. Our data provide new insights into AP2/ERF TFs in tomato, offer a candidate TF for fruit development and steroidal glycoalkaloids, and provide new resources for tomato breeding and improvement.

Combination of spontaneous regional brain activity and HTR1A/1B DNA methylation to predict early responses to antidepressant treatments in MDD

BACKGROUND

Antidepressant medications are suggested as the first-line treatment in patients with major depressive disorder (MDD). However, the drug therapy outcomes vary from person to person. The functional activity of the brain and DNA methylation levels correlate with the antidepressant efficacy. To predict the early antidepressant responses in MDD and establish the prediction framework, we aimed to apply multidimensional data based on the resting-state activity of the brain and HTR1A/1B methylation.

METHODS

The values of Amplitude of Low-Frequency Fluctuations (ALFF) and regional homogeneity (ReHo) were measured as variables in 116 brain regions along with 181 CpG sites in the promoter region of HTR1A/1B and 11 clinical characteristics. After performing the feature reduction step using the least absolute shrinkage and selection operator (LASSO) method, the selected variables were put into Support Vector Machines (SVM), Random Forest (RF), Naïve Bayes (NB), and logistic regression (LR), consecutively, to construct the prediction models. The models' performance was evaluated by the Leave-One-Out Cross-Validation.

RESULTS

The LR model composed of the selected multidimensional features reached a maximum performance of 78.57% accuracy and 0.8340 area under the ROC curve (AUC). The prediction accuracies based on multidimensional datasets were found to be higher than those obtained from the data based only on fMRI or methylation.

LIMITATIONS

A relatively small sample size potentially restricted the usage of our prediction framework in clinical applications.

CONCLUSION

Our study revealed that combining the data of brain imaging and DNA methylation could provide a complementary effect in predicting early-stage antidepressant outcomes.

Influence and interaction of resting state functional magnetic resonance and tryptophan hydroxylase-2 methylation on short-term antidepressant drug response

BACKGROUND

Most antidepressants have been developed on the basis of the monoamine deficiency hypothesis of depression, in which neuronal serotonin (5-HT) plays a key role. 5-HT biosynthesis is regulated by the rate-limiting enzyme tryptophan hydroxylase-2 (TPH2). TPH2 methylation is correlated with antidepressant effects. Resting-state functional MRI (rs-fMRI) is applied for detecting abnormal brain functional activity in patients with different antidepressant effects. We will investigate the effect of the interaction between rs-fMRI and TPH2 DNA methylation on the early antidepressant effects.

METHODS

A total of 300 patients with major depressive disorder (MDD) and 100 healthy controls (HCs) were enrolled, of which 60 patients with MDD were subjected to rs-fMRI. Antidepressant responses was assessed by a 50% reduction in 17-item Hamilton Rating Scale for Depression (HAMD-17) scores at baseline and after two weeks of medication. The RESTPlus software in MATLAB was used to analyze the rs-fMRI data. The amplitude of low-frequency fluctuation (ALFF), regional homogeneity (ReHo), fractional ALFF (fALFF), and functional connectivity (FC) were used, and the above results were used as regions of interest (ROIs) to extract the average value of brain ROIs regions in the RESTPlus software. Generalized linear model analysis was performed to analyze the association between abnormal activity found in rs-fMRI and the effect of TPH2 DNA methylation on antidepressant responses.

RESULTS

Two hundred ninety-one patients with MDD and 100 HCs were included in the methylation statistical analysis, of which 57 patients were included in the further rs-fMRI analysis (3 patients were excluded due to excessive head movement). 57 patients were divided into the responder group (n = 36) and the non-responder group (n = 21). Rs-fMRI results showed that the ALFF of the left inferior frontal gyrus (IFG) was significantly different between the two groups. The results showed that TPH2-1-43 methylation interacted with ALFF of left IFG to affect the antidepressant responses (p = 0.041, false discovery rate (FDR) corrected p = 0.149).

CONCLUSIONS

Our study demonstrated that the differences in the ALFF of left IFG between the two groups and its association with TPH2 methylation affect short-term antidepressant drug responses.

The impact of HTR1A and HTR1B methylation combined with stress/genotype on early antidepressant efficacy

AIMS

Antidepressants are effective in the treatment of major depressive disorder (MDD), while many patients fail to respond to antidepressants. Both 5-HT1A (HTR1A) and 5-HT1B (HTR1B) receptors play an important role in antidepressant activity. Meanwhile, DNA methylation is associated with MDD and antidepressant efficacy. In this study we investigate the influence of HTR1A and HTR1B methylation combined with stress/genotype on antidepressant efficacy.

METHODS

A total of 291 MDD patients and 100 healthy controls received the Life Events Scale (LES) and the Childhood Trauma Questionnaire (CTQ) as stress assessment. Eight single nucleotide polymorphisms (SNPs) of HTR1A and HTR1B involved in antidepressant mechanisms were tested. Methylation status in 181 cytosine-phosphate-guanine (CpG) sites of HTR1A and HTR1B were assessed. All MDD patients were divided into response (RES) and non-response (NRES) after 2 weeks of antidepressant treatment. Logistic regression was conducted for interactions between methylation, NLES/CTQ score and genotype.

RESULTS

Low HTR1A-2-143 methylation is connected with better antidepressant efficacy in subgroup. Low HTR1A-2-143 methylation combined with low CTQ score is related to better antidepressant efficacy. The interaction between high HTR1B methylation with the rs6298 AA/AG genotype affects better antidepressant efficacy.

CONCLUSIONS

HTR1A and HTR1B methylation combined with stress/genotype is associated with antidepressant efficacy.

Development of a widely targeted volatilomics method for profiling volatilomes in plants

Volatile organic compounds play essential roles in plant environment interactions as well as determining the fragrance of plants. Although gas chromatography-mass spectrometry-based untargeted metabolomics is commonly used to assess plant volatiles, it suffers from high spectral convolution, low detection sensitivity, a limited number of annotated metabolites, and relatively poor reproducibility. Here, we report a widely targeted volatilomics (WTV) method that involves using a "targeted spectra extraction" algorithm to address spectral convolution, constructing a high-coverage MS² spectral tag library to expand volatile annotation, adapting a multiple reaction monitoring mode to improve sensitivity, and using regression models to adjust for signal drift. The newly developed method was used to profile the volatilome of rice grains. Compared with the untargeted method, the newly developed WTV method shows higher sensitivity (for example, the signal-to-noise ratio of guaicol increased from 4.1 to 18.8), high annotation coverage (the number of annotated volatiles increased from 43 to 132), and better reproducibility (the number of volatiles in quality control samples with relative standard deviation value below 30.0% increased from 14 to 92 after normalization). Using the WTV method, we studied the metabolic responses of tomato to environmental stimuli and profiled the volatilomes of different rice accessions. The results identified benzothiazole as a potential airborne signal priming tomato plants for enhanced defense and 2-nonanone and 2-heptanone as novel aromatic compounds contributing to rice fragrance. These case studies suggest that the widely targeted volatilomics method is more efficient than those currently used and may considerably promote plant volatilomics studies.