SOCS3 regulates pathological retinal angiogenesis through modulating SPP1 expression in microglia and macrophages

Pathological ocular angiogenesis has long been associated with myeloid cell activation. However, the precise cellular and molecular mechanisms governing the intricate crosstalk between the immune system and vascular changes during ocular neovascularization formation remain elusive. In this study, we demonstrated that the absence of the suppressor of cytokine signaling 3 (SOCS3) in myeloid cells led to a substantial accumulation of microglia and macrophage subsets during the neovascularization process. Our single-cell RNA sequencing data analysis revealed a remarkable increase in the expression of the secreted phosphoprotein 1 (Spp1) gene within these microglia and macrophages, identifying subsets of Spp1-expressing microglia and macrophages during neovascularization formation in angiogenesis mouse models. Notably, the number of Spp1-expressing microglia and macrophages exhibited further elevation during neovascularization in mice lacking myeloid SOCS3. Moreover, our investigation unveiled the Spp1 gene as a direct transcriptional target gene of signal transducer and activator of transcription 3. Importantly, pharmaceutical activation of SOCS3 or blocking of SPP1 resulted in a significant reduction in pathological neovascularization. In conclusion, our study highlights the pivotal role of the SOCS3/STAT3/SPP1 axis in the regulation of pathological retinal angiogenesis.

Short-Term Dietary Restriction Potentiates an Anti-Inflammatory Circulating Mucosal-Associated Invariant T-Cell Response

Short-term protein-calorie dietary restriction (StDR) is a promising preoperative strategy for modulating postoperative inflammation. We have previously shown marked gut microbial activity during StDR, but relationships between StDR, the gut microbiome, and systemic immunity remain poorly understood. Mucosal-associated invariant T-cells (MAITs) are enriched on mucosal surfaces and in circulation, bridge innate and adaptive immunity, are sensitive to gut microbial changes, and may mediate systemic responses to StDR. Herein, we characterized the MAIT transcriptomic response to StDR using single-cell RNA sequencing of human PBMCs and evaluated gut microbial species-level changes through sequencing of stool samples. Healthy volunteers underwent 4 days of DR during which blood and stool samples were collected before, during, and after DR. MAITs composed 2.4% of PBMCs. More MAIT genes were differentially downregulated during DR, particularly genes associated with MAIT activation (CD69), regulation of pro-inflammatory signaling (IL1, IL6, IL10, TNFα), and T-cell co-stimulation (CD40/CD40L, CD28), whereas genes associated with anti-inflammatory IL10 signaling were upregulated. Stool analysis showed a decreased abundance of multiple MAIT-stimulating Bacteroides species during DR. The analyses suggest that StDR potentiates an anti-inflammatory MAIT immunophenotype through modulation of TCR-dependent signaling, potentially secondary to gut microbial species-level changes.

OSCAA: A two-dimensional Gaussian mixture model for copy number variation association analysis

Copy number variants (CNVs) are prevalent in the human genome and are found to have a profound effect on genomic organization and human diseases. Discovering disease-associated CNVs is critical for understanding the pathogenesis of diseases and aiding their diagnosis and treatment. However, traditional methods for assessing the association between CNVs and disease risks adopt a two-stage strategy conducting quantitative CNV measurements first and then testing for association, which may lead to biased association estimation and low statistical power, serving as a major barrier in routine genome-wide assessment of such variation. In this article, we developed One-Stage CNV-disease Association Analysis (OSCAA), a flexible algorithm to discover disease-associated CNVs for both quantitative and qualitative traits. OSCAA employs a two-dimensional Gaussian mixture model that is built upon the PCs from copy number intensities, accounting for technical biases in CNV detection while simultaneously testing for their effect on outcome traits. In OSCAA, CNVs are identified and their associations with disease risk are evaluated simultaneously in a single step, taking into account the uncertainty of CNV identification in the statistical model. Our simulations demonstrated that OSCAA outperformed the existing one-stage method and traditional two-stage methods by yielding a more accurate estimate of the CNV-disease association, especially for short CNVs or CNVs with weak signals. In conclusion, OSCAA is a powerful and flexible approach for CNV association testing with high sensitivity and specificity, which can be easily applied to different traits and clinical risk predictions.

CYP2A6 Activity and Cigarette Consumption Interact in Smoking-Related Lung Cancer Susceptibility

Cigarette smoke, containing both nicotine and carcinogens, causes lung cancer. However, not all smokers develop lung cancer, highlighting the importance of the interaction between host susceptibility and environmental exposure in tumorigenesis. Here, we aimed to delineate the interaction between metabolizing ability of tobacco carcinogens and smoking intensity in mediating genetic susceptibility to smoking-related lung tumorigenesis. Single-variant and gene-based associations of 43 tobacco carcinogen-metabolizing genes with lung cancer were analyzed using summary statistics and individual-level genetic data, followed by causal inference of Mendelian randomization, mediation analysis, and structural equation modeling. Cigarette smoke-exposed cell models were used to detect gene expression patterns in relation to specific alleles. Data from the International Lung Cancer Consortium (29,266 cases and 56,450 controls) and UK Biobank (2,155 cases and 376,329 controls) indicated that the genetic variant rs56113850 C>T located in intron 4 of CYP2A6 was significantly associated with decreased lung cancer risk among smokers (OR = 0.88, 95% confidence interval = 0.85-0.91, P = 2.18 × 10-16), which might interact (Pinteraction = 0.028) with and partially be mediated (ORindirect = 0.987) by smoking status. Smoking intensity accounted for 82.3% of the effect of CYP2A6 activity on lung cancer risk but entirely mediated the genetic effect of rs56113850. Mechanistically, the rs56113850 T allele rescued the downregulation of CYP2A6 caused by cigarette smoke exposure, potentially through preferential recruitment of transcription factor helicase-like transcription factor. Together, this study provides additional insights into the interplay between host susceptibility and carcinogen exposure in smoking-related lung tumorigenesis.

SIGNIFICANCE

The causal pathway connecting CYP2A6 genetic variability and activity, cigarette consumption, and lung cancer susceptibility in smokers highlights the need for behavior modification interventions based on host susceptibility for cancer prevention.

A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data

The availability of single-cell sequencing (SCS) enables us to assess intra-tumor heterogeneity and identify cellular subclones without the confounding effect of mixed cells. Copy number aberrations (CNAs) have been commonly used to identify subclones in SCS data using various clustering methods, as cells comprising a subpopulation are found to share a genetic profile. However, currently available methods may generate spurious results (e.g., falsely identified variants) in the procedure of CNA detection, thereby diminishing the accuracy of subclone identification within a large, complex cell population. In this study, we developed a subclone clustering method based on a fused lasso model, referred to as FLCNA, which can simultaneously detect CNAs in single-cell DNA sequencing (scDNA-seq) data. Spike-in simulations were conducted to evaluate the clustering and CNA detection performance of FLCNA, benchmarking it against existing copy number estimation methods (SCOPE, HMMcopy) in combination with commonly used clustering methods. Application of FLCNA to a scDNA-seq data set of breast cancer revealed different genomic variation patterns in neoadjuvant chemotherapy-treated samples and pretreated samples. We show that FLCNA is a practical and powerful method for subclone identification and CNA detection with scDNA-seq data.

New olive-pomace fertilizer tested with a 2-tiers approach: Biomarkers on Eisenia fetida, physiochemical effects on Solanum lycopersicum and Olea europaea

Every year, the olive oil industry generates a substantial amount of pomace, a semi-solid residue made up of skin, pulp, pit, and kernel fragments. Rather than being disposed of, the pomace can be dried and transported to an extraction facility where pomace oil can be extracted. Utilizing its high thermal capacity, the extracted pomace can be used as a supplementary fuel in the drying process, resulting in the production of ashes. In this study, the effect of pomace waste applied to the soil was investigated by testing two mixtures with different proportions of de-oiled pomace flour and kernel ash (50:50 and 70:30, respectively) in powder and pellet form. We used a dual approach, evaluating the effects of the mixtures on both soil communities and plant physiology and productivity, to assess the actual usability of the fertilizer in agriculture. The biomarker approach was valuable in assessing the sublethal effects of the two mixtures in powder form in soil. After 30 days of exposure, the bioindicator organism Eisena fetida showed lipid peroxidation, glutathione S-transferase and lactate dehydrogenase levels similar to the control, while lysozyme activity was reduced in all treatments. The powder mixture was lethal to the tomato plants, while there was no evidence of any damage to the olive trees. During 60 days of monitoring, both mixtures in pellet form showed a slight increase in physiological parameters, suggesting a benefit to the photosynthetic system. The improved carbon assimilation in tomato plants treated with the mixtures results in increased plant productivity, both in terms of number and weight of fruits, while maintaining the antioxidant content. This study paves the way for the use of the pomace mixture as a soil improver, thus increasing the value of this waste product.

MerTK-dependent efferocytosis by monocytic-MDSCs mediates resolution of post-lung transplant injury

Rationale

Patients with end stage lung diseases require lung transplantation (LTx) that can be impeded by ischemia-reperfusion injury (IRI) leading to subsequent chronic lung allograft dysfunction (CLAD) and inadequate outcomes.

Objectives

We examined the undefined role of MerTK (receptor Mer tyrosine kinase) on monocytic myeloid-derived suppressor cells (M-MDSCs) in efferocytosis (phagocytosis of apoptotic cells) to facilitate resolution of lung IRI.

Methods

Single-cell RNA sequencing of lung tissue and BAL from post-LTx patients was analyzed. Murine lung hilar ligation and allogeneic orthotopic LTx models of IRI were used with Balb/c (WT), cebpb -/- (MDSC-deficient), Mertk -/- or MerTK-CR (cleavage resistant) mice. Lung function, IRI (inflammatory cytokine and myeloperoxidase expression, immunohistology for neutrophil infiltration), and flow cytometry of lung tissue for efferocytosis of apoptotic neutrophils were assessed in mice.

Measurements and Main Results

A significant downregulation in MerTK-related efferocytosis genes in M-MDSC populations of CLAD patients compared to healthy subjects was observed. In the murine IRI model, significant increase in M-MDSCs, MerTK expression and efferocytosis was observed in WT mice during resolution phase that was absent in cebpb -/- Land Mertk -/- mice. Adoptive transfer of M-MDSCs in cebpb -/- mice significantly attenuated lung dysfunction, and inflammation leading to resolution of IRI. Additionally, in a preclinical murine orthotopic LTx model, increases in M-MDSCs were associated with resolution of lung IRI in the transplant recipients. In vitro studies demonstrated the ability of M-MDSCs to efferocytose apoptotic neutrophils in a MerTK-dependent manner.

Conclusions

Our results suggest that MerTK-dependent efferocytosis by M-MDSCs can significantly contribute to the resolution of post-LTx IRI.

The Effect of Different Diluents and Curing Agents on the Performance of Epoxy Resin-Based Intumescent Flame-Retardant Coatings

The epoxy resin-based (ESB) intumescent flame-retardant coatings were modified with 1,4-butanediol diglycidyl ether (14BDDE) and butyl glycidyl ether (BGE) as diluents and T403 and 4,4'-diaminodiphenylmethane (DDM) as curing agents, respectively. The effects of different diluents and curing agents on the flame-retardant and mechanical properties, as well as the composition evolution of the coatings, were investigated by using large-plate combustion, the limiting oxygen index (LOI), vertical combustion, a cone calorimeter, X-ray diffraction, FTIR analysis, a N2 adsorption and desorption test, a scanning electron microscope (SEM), a tensile strength test, and a viscosity test. The results showed that the addition of 14BBDE and T403 promoted the oxidation of B4C and the formation of boron-containing glass or ceramics, increased the residual mass of char, densified the surface char layer, and increased the specific surface area of porous residual char. When their dosage was 30%, ESB-1T-3 coating exhibited the most excellent flame-retardant properties. During the 2 h large-plate combustion test, the backside temperature was only 138.72 °C, without any melting pits. In addition, the peak heat release rate (PHRR), total heat release rate (THR), total smoke production (TSP), and peak smoke production (PSPR) were reduced by 13.15%, 13.9%, 5.48%, and 17.45%, respectively, compared to the blank ESB coating. The LOI value reached 33.4%, and the vertical combustion grade was V-0. In addition, the tensile strength of the ESB-1T-3 sample was increased by 10.94% compared to ESB. In contrast, the addition of BGE and DDM promoted the combustion of the coating, affected the ceramic process of the coating, seriously affected the formation of borosilicate glass, and exhibited poor flame retardancy. The backside temperature reached 190.93 °C after 2 h combustion. A unified rule is that as the amount of diluent and curing agent increases, the flame retardancy improves while the mechanical properties decrease. This work provides data support for the preparation and process optimization of resin-based coatings.

The global burden of lymphoma: estimates from the Global Burden of Disease 2019 study

OBJECTIVES

The aim of this study was to describe the global trends in the burden of lymphoma from 1990 to 2019.

STUDY DESIGN

The data used in this study were from the Global Burden of Disease 2019 study.

METHODS

This study described the age-standardised rates of incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life years (DALYs) of lymphoma (non-Hodgkin and Hodgkin's lymphoma, NHL and HL, respectively) annually from 1990 to 2019, stratified by sociodemographic index (SDI) and 21 world regions. The estimated annual percentage changes in these indexes were calculated.

RESULTS

In 2019, the age-standardised rates of HL per 100,000 population were lower than those of NHL in terms of incidence (1.1 vs 6.7 per 100,000 person-years, respectively) and prevalence (0.3 vs 5.7 per 100,000 person-years, respectively) but not mortality (21.6 vs 3.2 per 100,000 person-years, respectively). From 1999 to 2019, the global incidence of HL decreased and the incidence of NHL increased, and the prevalence of both HL and NHL increased, but the mortality rates decreased. When stratified by SDI, the incidence of HL decreased in all but middle-SDI regions, the mortality rate of HL decreased in all regions, and both the incidence and mortality rate of NHL increased in all but high-SDI regions. The prevalence of HL and NHL increased in all SDI regions, especially in middle-SDI regions. YLLs and DALYs of HL in all SDI regions and those of NHL in high-SDI regions decreased. YLDs slightly increased in middle- to high-SDI regions.

CONCLUSIONS

Lymphoma remains a major public health issue, and better prevention, precise identification, and promising treatments are vitally important.

Migraine and major depression: localizing shared genetic susceptibility in different cell types of the nervous systems

Background

There is a bidirectional relationship between migraine and major depression disorder (MDD). They likely share important risk genes associated with different cell types in the central nervous system (CNS) and peripheral nervous system (PNS). Profiling the expression of these genes in specific cell types is critical in understanding the pathophysiology of the relationship between migraine and MDD.

Methods

Associated genes shared by migraine and MDD were identified by consolidating multiple curations of human disease-gene associations. Subsequently, the expression of overlapping genes was profiled and compared across the different cell types in CNS, PNS and neurovascular cells using eight single cell RNA sequencing datasets, including two human CNS datasets, two mouse CNS datasets, one human PNS dataset and three mouse PNS datasets.

Results

45 shared genes between migraine and MDD were identified. Consistently found in all eight datasets, dopaminergic and serotonergic neurotransmitters were broadly expressed in CNS and PNS cell types. Glutamatergic and endocannabinoid genes were specifically expressed in CNS neurons and astrocytes. Synthesis and/or Release and Binding of Neuropeptides were specifically expressed in PNS peptidergic nociceptor (PEP). Genes related to inflammatory factors and immune responses were specifically expressed in CNS microglia. Among which, IL1B and COMT were highly expressed in CNS microglia cells.

Conclusion

Single cell RNA sequencing of the CNS and PNS helps to identify the shared genes between migraine and MDD that are enriched in specific cell types. The findings provide new insight in understanding the underlying mechanism of action for the bidirectional co-morbidity between migraine and MDD.

Vibrio parahaemolyticus and Vibrio vulnificus in vitro biofilm dispersal from microplastics influenced by simulated human environment

Growing concerns exist regarding human ingestion of contaminated seafood that contains Vibrio biofilms on microplastics (MPs). One of the mechanisms enhancing biofilm related infections in humans is due to biofilm dispersion, a process that triggers release of bacteria from biofilms into the surrounding environment, such as the gastrointestinal tract of human hosts. Dispersal of cells from biofilms can occur in response to environmental conditions such as sudden changes in temperature, pH and nutrient conditions, as the bacteria leave the biofilm to find a more stable environment to colonize. This study evaluated how brief exposures to nutrient starvation, elevated temperature, different pH levels and simulated human media affect Vibrio parahaemolyticus and Vibrio vulnificus biofilm dispersal and processes on and from low-density polyethylene (LDPE), polypropylene (PP), and polystyrene (PS) MPs. Both species were able to adequately disperse from all types of plastics under most exposure conditions. V. parahaemolyticus was able to tolerate and survive the low pH that resembles the gastric environment compared to V. vulnificus. pH had a significantly (p ≤ 0.05) positive effect on overall V. parahaemolyticus biofilm biomass in microplates and cell colonization from PP and PS. pH also had a positive effect on V. vulnificus cell colonization from LDPE and PP. However, most biofilm biomass, biofilm cell and dispersal cell densities of both species greatly varied after exposure to elevated temperature, pH, and nutrient starvation. It was also found that certain exposures to simulated human media affected both V. parahaemolyticus and V. vulnificus biofilm biomass and biofilm cell densities on LDPE, PP and PS compared to exposure to traditional media of similar pH. Cyclic-di-GMP was higher in biofilm cells compared to dispersal cells, but exposure to more stressful conditions significantly increased signal concentrations in both biofilm and dispersal states. Taken together, this study suggests that human pathogenic strains of V. parahaemolyticus and V. vulnificus can rapidly disperse with high cell densities from different plastic types in vitro. However, the biofilm dispersal process is highly variable, species specific and dependent on plastic type, especially under different human body related environmental exposures.

Prognostic and Predictive Significance of Tumor Immune Microenvironment in Breast Ductal Carcinoma In Situ

PURPOSE/OBJECTIVE(S)

This study aims to identify the role of different subtypes of tumor infiltrating lymphocytes (TILs) in ductal carcinoma in situ (DCIS) in predicting risk of recurrence and benefit of whole breast irradiation (WBI).

MATERIALS/METHODS

Immunohistochemical stain for CD3, CD4, CD8, FOXP3 and CD20 were carried in a well characterized DCIS cohort who received breast-conserving surgery (BCS) from Jan 2009 to Dec 2018. All the TILs subtypes were evaluated by the average numbers of touching-TILs which defined as TILs touching or within one lymphocyte cell thickness from the malignant ducts' basement membrane. The optimal cut-off values of TILs subtypes were selected by the X-tile.

RESULTS

In total, 167 patients were enrolled in this analysis with 114 patients received WBI. After a median follow-up of 67 months, 15 IBTR events occurred with 6 invasive-IBTRs. Nine out of 15 IBTRs occurred outside of the original quadrant (elsewhere failure event, EFE). CD3+ lymphocytes were the predominant cell subtype while Treg showed the lowest levels. High abundance of TILs subtypes was associated with high tumor grade, presence of microinvasion, high Ki67 index, ER negativity and HER2 positivity. For various TILs subtypes, the multivariate analyses showed that dense CD4+ TILs (HR = 9.84, 95% CI 2.43-39.91, p<0.01) and dense Treg (HR = 4.22, 95% CI 1.24-14.36, p = 0.02) were independent prognostic factors for higher IBTR. As the infiltration of TIL subsets was correlated with one another, we also analyzed the relationship between IBTR and the ratios of different TILs subtypes. By adjusted by clinicopathological parameters, high ratios of CD4+/CD8+, Treg/CD4+ and Treg/CD8+ were found to be independent prognostic factors for higher IBTR (HR = 11.31, 95% CI 3.14-40.76, p<0.01; HR = 3.09, 95% CI 1.05-9.11, p = 0.04; HR = 7.14, 95% CI 1.98-25.73, p<0.01). Consistent with the results of IBTR, the 5-y rate of invasive-IBTR and EFE was both significantly associated with the high CD4+/CD8+, Treg/CD4+ and Treg/CD8+ TILs ratios (all p<0.01). WBI reduced the rate of 5y-IBTR risk from 8.4% to 1.3% (p = 0.02) in the low Treg/CD8+ group, but there was no benefit of WBI in the high group. With respect to EFE, WBI significantly reduced the rate from 2.8% to 0.0% (p = 0.03) in the low Treg/CD8+ group while not in the high group. The benefits of WBI in reducing IBTR and EFE were not significant difference between different CD4+/CD8+ and Treg/CD4+ groups.

CONCLUSION

Assessment of overall TILs provides a tool for comprehensive evaluation of the DCIS immune microenvironment. Patients with pro-tumoral immune infiltrate (high Treg, high ratios of CD4+/CD8+, Treg/CD4+ and Treg/CD8+) in tumor microenvironment show an increased risk of IBTR and less benefit from breast radiotherapy.

TFAM Modulates Cardiomyocytes Pyroptosis Induced by Ionizing Radiation through mtDNA/TLR9/NF-kB Pathway

PURPOSE/OBJECTIVE(S)

Mitochondrial transcription factor A (TFAM) is a pivotal factor for regulating mitochondrial DNA (mtDNA) replication, transcription and biogenesis. Previous studies have reported that cytosolic mtDNA stress can lead to cardiomyocytes pyroptosis, which is characterized by inflammasome formation. In this study, we attempted to investigate the mechanism of TFAM regulate cardiomyocytes pyroptosis induced by ionizing radiation.

MATERIALS/METHODS

The peripheral blood serum of patients with esophageal cancer before and after definitive chemoradiotherapy was collected for Luminex multiplex cytokine assays. C57BL/6 mice were irradiated with the whole heart using small animal radiation research platform (SARRP) to construct a radiation-induced myocardial damage (RIMD) mouse model, and the ventricular function was evaluated using 9.4T Bruker magnetic resonance (MR) scanner. The function changes of cardiomyocytes exposed to radiation were observed in vitro and in vivo after knocking out GSDMD. Furthermore, the changes of mitochondrial function, the levels of cytosolic mtDNA, and the protein levels of NF-kB and pyroptosis pathway in irradiated cardiomyocytes were analyzed by knockdown and overexpression of TFAM in vitro and in vivo.

RESULTS

By multifactor cytokine assays we found that pyroptosis related IL-1β and IL-18 were significantly increased in patients with high mean heart dose (MHD) after radiotherapy, while those with low MHD were not significantly increased after radiotherapy. Next, we successfully constructed the RIMD mouse model using a single heart irradiation of 20 Gy. We found that the gene expression of pyroptosis pathway was significantly up-regulated after cardiac irradiation by myocardial tissue transcriptomic sequencing. Compared with wild-type (WT) mice, cardiac systolic function of Gsdmd-/- mice was significantly improved at 1, 2, 6, 12, and 24 weeks after heart irradiation. In vitro, we also demonstrated increased viability of irradiated cardiomyocytes by knocking out GSDMD. In vitro and in vivo experiments confirmed the expression of TFAM decreased after radiation. By overexpression of TFAM, we found that irradiated cardiomyocytes showed improved mitochondrial function, decreased release of mtDNA into cytoplasm through mitochondrial permeability transition pores (mPTPs), decreased binding of cytosolic mtDNA to TLR9, and decreased expression of NF-kB and pyroptosis pathway proteins. Dual luciferase gene reporter assays and Chromatin immunoprecipitation (CHIP) assay confirmed that p65 could bind the NLRP3 promoter region. In addition, we found that ventricular function deteriorated and improved in mice with knockdown and overexpression of TFAM through adeno-associated virus serotype 9 (AAV9), respectively.

CONCLUSION

Our study indicated that TFAM regulate irradiated cardiomyocytes pyroptosis through mtDNA/TLR9/NF-kB pathway. We provide a novel mechanism of RIMD, revealing an underappreciated intervention target for RIMD.

Quality Assurance of Protocol Compliance in a Multicenter Randomized Trial Investigating the Role of Hypofractionated Comprehensive Reginal Nodal Irradiation in Node-Positive Breast Cancer (HARVEST)

PURPOSE/OBJECTIVE(S)

The HARVEST trial (NCT03829553) is a phase III, multicenter, randomized clinical trial to explore efficacy and safety of hypofractionated irradiation (HFI) involving regional nodal irradiation (RNI, including internal mammary nodes, IMN) in N+ breast cancer patients treated with mastectomy or breast conserving surgery (BCS). Current study aims to analyze the dosimetric quality assurance so as to evaluate the compliance to the trial protocol.

MATERIALS/METHODS

Eligible patients were randomly assigned (1:1) to receive conventional fractionated irradiation (CFI: 50 Gy/25Fx) or HFI (40.05 Gy/15Fx), which is delivered to ipsilateral chest wall or whole breast (CW/WB) with tumor bed boost (HFI: 10.68 Gy/4Fx; CFI: 10 Gy/5Fx) and comprehensive RNI (supra/infraclavicular nodes and IMN in each patient, lower axilla if indicated) by using IMRT technique. The plan quality was evaluated based on dose distribution, dose volume histogram (DVH) and field parameters. The target coverage, including planning target volume of CW/WB (PTV1) and tumor bed (PTV2) and doses of the organs at risk (OARs) were evaluated. The LQ model was used to convert doses of OARs in HFI group using α/β = 3 Gy (EQD23) for comparison.

RESULTS

Between Feb 21, 2019 and Feb 14, 2022, 801 patients were enrolled at 8 centers with 401 and 400 in CFI and HFI group, respectively. There were 182 patients received BCS and 387 patients were with more than three positive lymph nodes. In the CFI group, the D90 and V45 of PTV1 reached the prescribed dose in 70.6% and 96.0% of the patients, respectively. In the HFI group, the D90 and V36 of PTV1 reached the prescribed dose in 87.8% and 95.5% of the patients, respectively. When the tumor bed was irradiated, the D90 of PTV2 reached the prescribed dose in 95.6% in the CFI group and 100% in the HFI group, respectively. The mean D90 of PTV1 and PTV2 were 50.09±0.65 Gy and 60.63±0.91 Gy in CFI group while 40.11±0.56 Gy and 50.79±2.03 Gy in HFI group. For OARs constraints, protocol compliance was all above 95% (heart: 95.3%; ipsilateral lung: 95.5%; contralateral lung: 97.1%; humeral head: 98.2% and spinal cord: 100%) with no significant difference between CFI and HFI groups. For patients with left-sided breast cancer, the Dmean of the heart was 5.10±1.75 Gy vs. 4.59±1.86 Gy (EQD23) in CFI and HFI groups (p = 0.51), respectively. No significant differences in Dmean of the heart (1.45±0.71 Gy vs. 1.33±0.77 Gy (EQD23), p = 0.40) was found either between two groups in right-sided patients. The differences were significant in the Dmean of the ipsilateral lung (13.37±1.99 Gy vs. 11.17±3.50 Gy (EQD23), p<0.01), contralateral lung (0.88±0.73 Gy vs. 0.74±0.61 Gy (EQD23), p<0.01) and the ipsilateral humeral head (15.27±7.62 Gy vs. 13.05±6.19 Gy (EQD23), p<0.01) and the Dmax of spinal cord (21.40±8.82 Gy vs. 19.47±7.99 Gy (EQD23), p = 0.05) between CFI and HFI groups.

CONCLUSION

A high degree of compliance with protocol dose constraints was found for treatment plans in the HARVEST trial and doses to the most of OARs decreased in HFI group.

The Predictive Value of Changes in Basal Myocardial F-18 Fluorodeoxyglucose Uptake for Cardiotoxicity in Locally Advanced Esophageal Cancer Patients Receiving Definitive Radiotherapy

PURPOSE/OBJECTIVE(S)

To investigate the predictive value of changes in myocardial 18F-FDG uptake for major adverse cardiac events (MACEs) in locally advanced esophageal cancer patients receiving definitive radiotherapy.

MATERIALS/METHODS

Between August 2012 and January 2018, 400 patients with stage II-III esophageal cancer receiving definitive radiotherapy at two institutions were divided into the training (n = 240) and external validation cohorts (n = 160). All patients underwent FDG-PET imaging within 1 week before treatment and 3 months after treatment. Myocardium delineation was performed by Carimas software (version 2.10) based on the AHA 17-segment model. When contouring the left ventricle, the myocardium was automatically divided into basal (segments 1-6), middle (segments 7-12), and apical (segments 13-16) regions, and the mean dose and FDG uptake parameters of each region were obtained by Carimas. Our primary endpoint was MACEs. Patient clinicopathologic factors, dosimetric parameters for the whole heart and cardiac substructures, and myocardial changes within the three regions on 18F-FDG PET were utilized to seek the best predictive models for cardiotoxicity. To avoid multicollinearity between dose-volume histogram (DVH) parameters, we selected the variables with the lowest Akaike Information Criterion (AIC) value from the DVH parameters of the same cardiac structure for the actual modeling procedure. Competing risk analysis and Cox regressions analysis were performed. The predictive performance of the models was evaluated using the area under the receiver operating characteristic curve (AUC) and Brier score.

RESULTS

At a median follow-up interval of 78 months, 28 patients (11.7%) developed MACEs. The basal region of the myocardium received the highest radiation dose, followed by the middle and the apex region. The basal myocardial SUVmax and SUVmean significantly increased after radiotherapy while the apical and middle myocardial SUVmax and SUVmean not significantly increased. In univariate analysis, age, pre-existing cardiac disease, changes in pre- and post-treatment basal myocardial SUVmax and SUVmean (∆SUVmax and ∆SUVmean), and dosimetric parameters for MHD, mean LCX, mean LAD, and mean LV dose were associated with an increased hazard of MACEs. Multivariate analysis showed that basal ∆SUVmean retained significance after adjusting for age, pre-existing cardiac disease, and dosimetric parameters for whole heart and cardiac substructures. The AUCs and Brier scores demonstrated favorable predictive accuracies of the model's integrating variables with significant difference in multivariate analysis when predicting MACEs in the training and validation cohorts.

CONCLUSION

∆SUVmean was an independent indicator of MACE in locally advanced esophageal cancer patients receiving definitive radiotherapy. Changes in basal myocardial FDG uptake is a promising biomaker for predicting radiation-induced cardiotoxicity.

Establishing a Risk Stratification Model to Identify Clinically High-Risk N0 Breast Cancer Who Could Benefit from Regional Nodal Irradiation: A Single Institute Analysis

PURPOSE/OBJECTIVE(S)

The adverse clinical features for pN0 BC patients significantly varies and there is no established clinical risk stratification system to identify those "high-risk" pN0 BC patients who might benefit from RNI. The purpose of this real-world study was to investigate the risk factors for developing recurrence among patients with pathological T1-3N0 breast cancer (BC) treated with breast-conserving surgery (BCS) followed by whole breast irradiation alone (WBI) and identify those clinically high-risk BCs who could benefit from regional nodal irradiation (RNI).

MATERIALS/METHODS

Female BC patients treated from 2009 to 2016 were retrospectively reviewed. The disease-free survival (DFS) and overall survival (OS) were estimated by the Kaplan-Meier method, and survival differences were compared with the log-rank test. Univariate and multivariate analysis was performed using Cox logistic regression analysis. An external validation was conducted by using SEER database.

RESULTS

A total of 622 BC patients treated with BCS+WBI alone were included. With a median follow-up of 82 months, the 7-year OS and DFS for the entire cohort was 97% and 91%, respectively. Multivariable Cox analysis indicated that tumor size (p = 0.006), tumor location (p = 0.033), lymphovascular invasion (LVI) status (p = 0.0028) and Ki-67 index (p = 0.051) were independent risk factors for DFS, while only tumor size was the only independent risk factors for OS (p = 0.029). A scoring system was developed using these four factors and the 7-year DFS and OS were 97% and 96% for patients with 0-1 risk factors, 95% and 82% for patients with ≥2 risk factors (p<0.0001 for DFS, and p = 0.0063 for OS). Based on tumor size and tumor location, an external validation by demonstrated that the 7-year OS was 90% and 88% for patients with 0-1 risk factor, which was significantly better than those defined as high-risk BC patients (82%, p<0.0001).

CONCLUSION

By using our institute database, we establish a risk stratification system for identifying sub-group of pN0 BC patients, who are at high risk for developing recurrence. The results of our study support tailored RT decision-making according to individual risks, which needed to be confirmed in further studies.

Treatment Outcomes and Prognostic Factors of Chemotherapy Combined with Radiotherapy for Patients with Stage I-II Nasal-Type Natural Killer/T-Cell Lymphoma

PURPOSE/OBJECTIVE(S)

The purpose of this study was to assess the treatment outcome and the potential prognostic factors for patients with stage I-II nasal ENKTL treated with radiotherapy (RT) combined chemotherapy (CT).

MATERIALS/METHODS

From July, 2005 to January, 2019, 118 eligible patients were retrospective included in the study. Among the 118 patients, 84 were male and 34 were female. The median age was 45 years (range: 14-77 years). According to the Ann Arbor staging system, 66 patients had stage I disease (Primary tumor invasion (PTI) was present in 29 patients), and 52 patients had stage II disease. B symptoms were observed in 61 patients. The Eastern Cooperative Oncology Group (ECOG) performance score was 0 to 1 in 88 patients. Cervical lymph node involvement was observed in 51 patients. The primary lesions were located in the nasal cavity in 92 cases and in the Waldeyer ring in 26 cases. Five patients had received RT followed by CT (RT + CT), 20 patients had received CT followed by RT (CT + RT), 90 patients had received CT followed by RT, again followed by CT (CT+RT+CT), and 3 patients had received concurrent chemoradiotherapy (CRT) (1 patient received CRT + CT, other 2 patients received CT+CRT+CT). Patients were irradiated with a median dose of 50 Gy (range, 24-61.2). All patients received chemotherapy, 91 received non-anthracycline-based chemotherapy, whereas 27 patients received anthracycline-based chemotherapy. The median number of courses of chemotherapy was four (range: 1-10). Patients were scored as having low-risk disease (n = 50), intermediate-risk disease (n = 60) or high-risk disease (n = 8) according to the prognostic index of natural killer cell lymphoma (PINK).

RESULTS

Among the 118 patients, after initial therapy, the complete response (CR) rate was 82.2% (n = 97), and the partial response (PR) rate was 11.0% (n = 13). The stable disease (SD) rate was 2.5% (n = 3), and the progressive disease (PD) rate was 4.2% (n = 5). With a median follow-up of 43 months (range, 4-201) after irradiation, the 3-year PFS and OS were 76.9% and 82.9%, respectively. The 3-year OS rate was 75.0% for RT + CT, 70.0% for CT + RT, 87.1% for CT + RT+ CT, and 50.0% for CRT (P = 0.052). Three-year OS and PFS were 88.6% and 83.4%, respectively, for non-anthracycline-based chemotherapy regimen compared to 61.6% (P = 0.001) and 58.4% (P = 0.003), respectively, for the anthracycline-based chemotherapy regimen. Three-year OS and PFS were 84.0% and 79.0%, respectively, for patients receiving high-dose RT (≥50 Gy, n = 111) compared to 71.4% (P = 0.076) and 71.4% (P = 0.228), respectively, for low-dose RT (<50 Gy, n = 7). In multivariate analysis, adverse factors associated with OS in our study were chemotherapy regimen and response to RT and CT (P = 0.047, <0.001).

CONCLUSION

Radiotherapy combined with chemotherapy reported promising response rate and a favorable survival for patients with stage I-II nasal ENKTL. Anthracycline-based chemotherapy regimen and no remission after RT and CT were adverse factors of OS.

Nodal Response to Neo-Adjuvant Systemic Therapy Predicts Prognosis of cN3c Breast Cancer Patients Receiving Multidisciplinary Therapy

PURPOSE/OBJECTIVE(S)

cN3c breast cancer with ipsilateral supraclavicular (SCV) lymph nodal (SCLN) metastasis has a dismal prognosis. We investigated the survival outcomes, patterns and risks of recurrence in those patients after multidisciplinary therapy, as well as the predictors of candidates for SCV area boosting.

MATERIALS/METHODS

Consecutive cN3c breast cancer patients without distant metastases from January 2009 to December 2020 in our institution were retrospectively reviewed. Based on nodal response to neoadjuvant therapy (NAT), patients were categorized into three groups: clinical complete response (cCR) not achieved in SCLN (Group A, n = 66), SCLN cCR but axillary node (ALN) did not achieve pathological complete response (pCR, Group B, n = 34), cCR in SCLN and pCR in ALN (Group C, n = 13).

RESULTS

The median follow-up time was 32.7 months (range, 21.9-53.3months). The 5-year overall survival (OS) and recurrence-free survival (RFS) rates were 64.6% and 43.7% respectively. Multivariate analysis showed cumulative SCV dose and ypT stage, ALN response and SCV response to NAT were significantly associated with OS and RFS respectively. The 3-year for patients receiving the cumulative SCV dose of ≥60 Gy versus <60 Gy was 81.3% versus 69.0% (P = 0.042). Compared with Group A or B, Group C showed significantly improved RFS (3y-RFS: 53.8% vs 73.6% vs 100%, p = 0.003) and a numerically longer OS (3y-OS: 73.4% vs 86.7% vs 100%, p = 0.089). Meanwhile, Group C showed the lowest rate of DM as first failure (37.9 % vs 23.5% vs 0 in group A, B and C, respectively, p = 0.010). In patients of Group A, the 3-year OS rates for patients receiving the cumulative SCV dose of ≥60 Gy versus <60 Gy was 78.0% versus 57.3% (p = 0.029).

CONCLUSION

Nodal response to NAT is an independent prognostic factor for survival and pattern of failure. cN3c breast cancer patients with SCLN cCR and ALN pCR after NAT are potentially curable. A cumulative SCV dose of ≥60 Gy is positively associated with improved OS, especially in patients of SCLN without achieving cCR. Our data supports the perspective of optimizing radiotherapeutic strategy based on nodal response.

OSCAA: A Two-Dimensional Gaussian Mixture Model for Copy Number Variation Association Analysis

Copy number variants (CNVs) are prevalent in the human genome which provide profound effect on genomic organization and human diseases. Discovering disease associated CNVs is critical for understanding the pathogenesis of diseases and aiding their diagnosis and treatment. However, traditional methods for assessing the association between CNVs and disease risks adopt a two-stage strategy conducting quantitative CNV measurements first and then testing for association, which may lead to biased association estimation and low statistical power, serving as a major barrier in routine genome wide assessment of such variation. In this article, we developed OSCAA, a flexible algorithm to discover disease associated CNVs for both quantitative and qualitative traits. OSCAA employs a two-dimensional Gaussian mixture model that is built upon the principal components from copy number intensities, accounting for technical biases in CNV detection while simultaneously testing for their effect on outcome traits. In OSCAA, CNVs are identified and their associations with disease risk are evaluated simultaneously in a single step, taking into account the uncertainty of CNV identification in the statistical model. Our simulations demonstrated that OSCAA outperformed the existing one-stage method and traditional two-stage methods by yielding a more accurate estimate of the CNV-disease association, especially for short CNVs or CNVs with weak signal. In conclusion, OSCAA is a powerful and flexible approach for CNV association testing with high sensitivity and specificity, which can be easily applied to different traits and clinical risk predictions.

CDK8 and CDK19: positive regulators of signal-induced transcription and negative regulators of Mediator complex proteins

We have conducted a detailed transcriptomic, proteomic and phosphoproteomic analysis of CDK8 and its paralog CDK19, alternative enzymatic components of the kinase module associated with transcriptional Mediator complex and implicated in development and diseases. This analysis was performed using genetic modifications of CDK8 and CDK19, selective CDK8/19 small molecule kinase inhibitors and a potent CDK8/19 PROTAC degrader. CDK8/19 inhibition in cells exposed to serum or to agonists of NFκB or protein kinase C (PKC) reduced the induction of signal-responsive genes, indicating a pleiotropic role of Mediator kinases in signal-induced transcriptional reprogramming. CDK8/19 inhibition under basal conditions initially downregulated a small group of genes, most of which were inducible by serum or PKC stimulation. Prolonged CDK8/19 inhibition or mutagenesis upregulated a larger gene set, along with a post-transcriptional increase in the proteins comprising the core Mediator complex and its kinase module. Regulation of both RNA and protein expression required CDK8/19 kinase activities but both enzymes protected their binding partner cyclin C from proteolytic degradation in a kinase-independent manner. Analysis of isogenic cell populations expressing CDK8, CDK19 or their kinase-inactive mutants revealed that CDK8 and CDK19 have the same qualitative effects on protein phosphorylation and gene expression at the RNA and protein levels, whereas differential effects of CDK8 versus CDK19 knockouts were attributable to quantitative differences in their expression and activity rather than different functions.

A Novel Inorganic Aluminum Phosphate-Based Flame Retardant and Thermal Insulation Coating and Performance Analysis

Currently, most thin-layer expandable coatings are polymer-based, with very few inorganic expandable coatings. Due to the high environmental friendliness of inorganic coatings, studying new types of inorganic coatings is of great significance. A novel amorphous aluminum phosphate-based flame-retardant coating was prepared by modifying it with nano-silica, hollow silica beads, hollow glass microspheres, and boron carbide. A comprehensive study was conducted on the flame retardancy and thermal insulation performance, composition and structural evolution under flame and physical and chemical properties, and the mechanisms of flame retardancy and thermal insulation were elucidated. Large-plate combustion testing, bonding strength testing, XRD, IR, TG-DSC, and SEM testing were all applied in this work. The synergistic effect of the four fillers was very obvious, and a series of AP22XY (nano-silica/silica beads/hollow glass microspheres/boron carbide = 2:2:0:4, 2:2:1:3, 2:2:2:2, 2:2:3:1, 2:2:4:0) coatings were prepared. The change in the ratio of glass microspheres to boron carbide had a significant impact on the composition and structural evolution of the coating, thus reflecting its effectiveness as a flame retardant and thermal insulation. Although decreasing the ratio would promote the formation of borosilicate glass and Al₁₈B₄O₃₃ and improve the thermal stability of coatings, the structure inside of the coating, especially the skeleton, would be dense, which is not conducive to thermal insulation. When the ratio of glass microspheres to boron carbide is 3:1, AP2231 shows the best fire resistance. Under the combustion of butane flame at about 1200-1300 °C, the backside temperature reaches a maximum of 226 °C at 10 min, and then the temperature gradually decreases to 175 °C at 60 min. This excellent performance is mainly attributed to three aspects: (1) the foaming and expandability of coatings when exposed to fire, (2) the multiple endothermic reactions the coating undergoes, and (3) the improvement effect of boron carbide. Additionally, AP2231 shows the best bonding performance with a strength of close to 4.5 MPa after combustion, because of the appropriate content matching between borosilicate glass, Al₁₈B₄O₃₃, and hollow glass microspheres. The coating has potential application prospects in the construction and transportation fields, such as the protection of structural steel, fire prevention in subways and tunnels, and the prevention of lithium battery fires.

A pilot randomized controlled trial evaluating outdoor community walking for knee osteoarthritis: walk

OBJECTIVES

To determine the feasibility of a randomized controlled trial (RCT) examining outdoor walking on knee osteoarthritis (KOA) clinical outcomes and magnetic resonance imaging (MRI) structural changes.

METHOD

This was a 24-week parallel two-arm pilot RCT in Tasmania, Australia. KOA participants were randomized to either a walking plus usual care group or a usual care control group. The walking group trained 3 days/week. The primary outcome was feasibility assessed by changes being required to the study design, recruitment, randomization, program adherence, safety, and retention. Exploratory outcomes were changes in symptoms, physical performance/activity, and MRI measures.

RESULTS

Forty participants (mean age 66 years (SD 1.4) and 60% female) were randomized to walking (n = 24) or usual care (n = 16). Simple randomization resulted in a difference in numbers randomized to the two groups. During the study, class sizes were reduced from 10 to 8 participants to improve supervision, and exclusion criteria were added to facilitate program adherence. In the walking group, total program adherence was 70.0% and retention 70.8% at 24 weeks. The walking group had a higher number of mild adverse events and experienced clinically important improvements in symptoms (e.g., visual analogue scale (VAS) knee pain change in the walking group: - 38.7 mm [95% CI - 47.1 to - 30.3] versus usual care group: 4.3 mm [- 4.9 to 13.4]).

CONCLUSIONS

This study supports the feasibility of a full-scale RCT given acceptable adherence, retention, randomization, and safety, and recruitment challenges have been identified. Large symptomatic benefits support the clinical usefulness of a subsequent trial.

TRIAL REGISTRATION NUMBER

12618001097235. Key Points • This pilot study is the first to investigate the effects of an outdoor walking program on knee osteoarthritis clinical outcomes and MRI joint structure, and it indicates that a full-scale RCT is feasible. • The outdoor walking program (plus usual care) resulted in large improvements in self-reported knee osteoarthritis symptoms compared to usual care alone. • The study identified recruitment challenges, and the manuscript explores these in more details and provides recommendations for future studies.

A statistical learning method for simultaneous copy number estimation and subclone clustering with single cell sequencing data

The availability of single cell sequencing (SCS) enables us to assess intra-tumor heterogeneity and identify cellular subclones without the confounding effect of mixed cells. Copy number aberrations (CNAs) have been commonly used to identify subclones in SCS data using various clustering methods, since cells comprising a subpopulation are found to share genetic profile. However, currently available methods may generate spurious results (e.g., falsely identified CNAs) in the procedure of CNA detection, hence diminishing the accuracy of subclone identification from a large complex cell population. In this study, we developed a CNA detection method based on a fused lasso model, referred to as FLCNA, which can simultaneously identify subclones in single cell DNA sequencing (scDNA-seq) data. Spike-in simulations were conducted to evaluate the clustering and CNA detection performance of FLCNA benchmarking to existing copy number estimation methods (SCOPE, HMMcopy) in combination with the existing and commonly used clustering methods. Interestingly, application of FLCNA to a real scDNA-seq dataset of breast cancer revealed remarkably different genomic variation patterns in neoadjuvant chemotherapy treated samples and pre-treated samples. We show that FLCNA is a practical and powerful method in subclone identification and CNA detection with scDNA-seq data.

Abstract 4286: A statistical learning method for simultaneous copy number estimation and subclone clustering with single cell sequencing data

The availability of single cell sequencing (SCS) enables us to assess intra-tumor heterogeneity and identify cellular subclones without the confounding effect from mixed cells. Copy number aberrations (CNAs) have been commonly used to identify subclones in SCS data since cells comprising a subpopulation are found to share genetic profile. However, currently available methods may generate spurious results (e.g., falsely identified CNAs) in the procedure of CNA detection, hence diminishing the accuracy of subclones identification from a large complex cell population. In this study, we developed a CNA detection method based on a fused lasso model, referred to as FLCNA, which can simultaneously identify subclones in single cell DNA sequencing (scDNA-seq) data. Spike-in simulations were conducted to evaluate the clustering and CNA detection performance of FLCNA benchmarking to existing copy number estimation methods (SCOPE, HMMcopy) in combination with commonly used clustering methods. FLCNA was also applied to a real scDNA-seq dataset with breast cancer and clusters identified using FLCNA showed clearly different genomic variation patterns. In conclusion, FLCNA provided superior performance in subclone identification and CNA detection with scDNA-seq data.

Citation Format: Feifei Xiao, Fei Qin, Guoshuai Cai. A statistical learning method for simultaneous copy number estimation and subclone clustering with single cell sequencing data. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4286.

Integrated multi-omics approach to distinct molecular characterization and classification of early-onset colorectal cancer

Incidence of early-onset colorectal cancer (EOCRC), defined by a diagnosed age under 50 years, is increasing, but its heterogeneous etiologies that differ from general CRC remain undetermined. We initially characterize the genome, epigenome, transcriptome, and proteome of tumors from 79 patients in a Chinese CRC cohort. Data for an additional 126 EOCRC subjects are obtained from the International Cancer Genome Consortium Chinese cohort and The Cancer Genome Atlas European cohort. We observe that early-onset tumors have a high tumor mutation burden; increased DNA repair features by mutational signature 3 and multi-layer pathway enrichments; strong perturbations at effects of DNA methylation and somatic copy-number alteration on gene expression; and upregulated immune infiltration as hot tumors underlying immunophenotypes. Notably, LMTK3 exhibits ancestral mutation disparity, potentially being a functional modulator and biomarker that drives molecular alterations in EOCRC development and immunotherapies. This integrative omics study provides valuable knowledge for precision oncology of CRC.

Vibrio parahaemolyticus and Vibrio vulnificus in vitro colonization on plastics influenced by temperature and strain variability

Marine bacteria often exist in biofilms as communities attached to surfaces, like plastic. Growing concerns exist regarding marine plastics acting as potential vectors of pathogenic Vibrio, especially in a changing climate. It has been generalized that Vibrio vulnificus and Vibrio parahaemolyticus often attach to plastic surfaces. Different strains of these Vibrios exist having different growth and biofilm-forming properties. This study evaluated how temperature and strain variability affect V. parahaemolyticus and V. vulnificus biofilm formation and characteristics on glass (GL), low-density polyethylene (LDPE), polypropylene (PP), and polystyrene (PS). All strains of both species attached to GL and all plastics at 25, 30, and 35°C. As a species, V. vulnificus produced more biofilm on PS (p ≤ 0.05) compared to GL, and biofilm biomass was enhanced at 25°C compared to 30° (p ≤ 0.01) and 35°C (p ≤ 0.01). However, all individual strains' biofilm biomass and cell densities varied greatly at all temperatures tested. Comparisons of biofilm-forming strains for each species revealed a positive correlation (r = 0.58) between their dry biomass weight and OD₅₇₀ values from crystal violet staining, and total dry biofilm biomass for both species was greater (p ≤ 0.01) on plastics compared to GL. It was also found that extracellular polymeric substance (EPS) chemical characteristics were similar on all plastics of both species, with extracellular proteins mainly contributing to the composition of EPS. All strains were hydrophobic at 25, 30, and 35°C, further illustrating both species' affinity for potential attachment to plastics. Taken together, this study suggests that different strains of V. parahaemolyticus and V. vulnificus can rapidly form biofilms with high cell densities on different plastic types in vitro. However, the biofilm process is highly variable and is species-, strain-specific, and dependent on plastic type, especially under different temperatures.

Risks of suicide in migraine, non-migraine headache, back, and neck pain: a systematic review and meta-analysis

Objective

To conduct a systematic review and meta-analysis on suicidal ideation, attempts, and death in patients with head, neck, and back pain.

Method

Search was performed using PubMed, Embase, and Web of Science from the date of the first available article through September 31, 2021. A random effects model was used to estimate the pooled odds ratios (ORs) and 95% confidence intervals (95% CI) for the association between suicidal ideation and/or attempt and head, back/neck pain conditions. Articles describing non-migraine headache disorders and death by suicide were also reviewed but not included in the meta-analysis due to an insufficient number of studies.

Results

A total of 20 studies met criteria for systemic review. A total of 186,123 migraine patients and 135,790 of neck/back pain patients from 11 studies were included in the meta-analysis. The meta-analysis showed that the estimated risk of combined suicidal ideation and attempt in migraine [OR 2.49; 95% CI: 2.15-2.89] is greater than that in back/neck pain pain [OR 2.00; 95% CI: 1.63-2.45] compared to non-pain control groups. Risk of suicide ideation/planning is 2 folds higher [OR: 2.03; 95% CI: 1.92-2.16] and risk of suicide attempt is more than 3 folds higher [OR: 3.47; 95% CI: 2.68-4.49] in migraine as compared to healthy controls.

Conclusion

There is an elevated risk of suicidal ideation and attempt in both migraine and neck/back pain patients in comparison to healthy controls, and this risk is particularly higher among migraine patients. This study underscores the critical need for suicide prevention in migraine patients.

A pilot study that provides evidence of epigenetic changes among mother-child pairs living proximal to mining in the US

Environmental exposures to chemicals can disrupt gene expression, and the effects could be mediated by methylation. This investigation focused on methylation of genes associated with exposure to metals. Mother-child pairs from three locations in Montana were recruited, and buccal cells were collected for genome-wide methylation assay. Four pairs were from Butte, where there is mining and a Superfund site, four pairs were from Anaconda with a Superfund site, and four pairs were from Missoula with neither a mine nor a Superfund site. Principal component analysis, linear mixed models, hierarchical clustering and heatmap, and gene set enrichment analysis were used to visualize the profiles, identify the top associated methylation loci, and investigate the involved pathways. Distinctly higher or lower methylation in samples from Butte were found at the top differentially methylated loci. The 200 genes harboring the most hypermethylated loci were significantly enriched in genes involved in actin cytoskeleton regulation, ABC transporters, leukocyte transendothelial migration, focal adhesion, and adherens junction, which plays a role in pathogenesis of disease, including autism spectrum disorders. This study lays a foundation for inquiry about genetic changes associated with environmental exposure to metals for people living in proximity to Superfund and open pit mining.

BMI-CNV: a Bayesian framework for multiple genotyping platforms detection of copy number variants

Whole-exome sequencing (WES) enables the detection of copy number variants (CNVs) with high resolution in protein-coding regions. However, variants in the intergenic or intragenic regions are excluded from studies. Fortunately, many of these samples have been previously sequenced by other genotyping platforms which are sparse but cover a wide range of genomic regions, such as SNP array. Moreover, conventional single sample-based methods suffer from a high false discovery rate due to prominent data noise. Therefore, methods for integrating multiple genotyping platforms and multiple samples are highly demanded for improved copy number variant detection. We developed BMI-CNV, a Bayesian Multisample and Integrative CNV (BMI-CNV) profiling method with data sequenced by both whole-exome sequencing and microarray. For the multisample integration, we identify the shared copy number variants regions across samples using a Bayesian probit stick-breaking process model coupled with a Gaussian Mixture model estimation. With extensive simulations, BMI-copy number variant outperformed existing methods with improved accuracy. In the matched data from the 1000 Genomes Project and HapMap project data, BMI-CNV also accurately detected common variants and significantly enlarged the detection spectrum of whole-exome sequencing. Further application to the data from The Research of International Cancer of Lung consortium (TRICL) identified lung cancer risk variant candidates in 17q11.2, 1p36.12, 8q23.1, and 5q22.2 regions.

BISC: accurate inference of transcriptional bursting kinetics from single-cell transcriptomic data

Gene expression in mammalian cells is inherently stochastic and mRNAs are synthesized in discrete bursts. Single-cell transcriptomics provides an unprecedented opportunity to explore the transcriptome-wide kinetics of transcriptional bursting. However, current analysis methods provide limited accuracy in bursting inference due to substantial noise inherent to single-cell transcriptomic data. In this study, we developed BISC, a Bayesian method for inferring bursting parameters from single cell transcriptomic data. Based on a beta-gamma-Poisson model, BISC modeled the mean-variance dependency to achieve accurate estimation of bursting parameters from noisy data. Evaluation based on both simulation and real intron sequential RNA fluorescence in situ hybridization data showed improved accuracy and reliability of BISC over existing methods, especially for genes with low expression values. Further application of BISC found bursting frequency but not bursting size was strongly associated with gene expression regulation. Moreover, our analysis provided new mechanistic insights into the functional role of enhancer and superenhancer by modulating both bursting frequency and size. BISC also formulated a downstream framework to identify differential bursting (in frequency and size separately) genes in samples under different conditions. Applying to multiple datasets (a mouse embryonic cell and fibroblast dataset, a human immune cell dataset and a human pancreatic cell dataset), BISC identified known cell-type signature genes that were missed by differential expression analysis, providing additional insights in understanding the cell-specific stochastic gene transcription. Applying to datasets of human lung and colon cancers, BISC successfully detected tumor signature genes based on alterations in bursting kinetics, which illustrates its value in understanding disease development regarding transcriptional bursting. Collectively, BISC provides a new tool for accurately inferring bursting kinetics and detecting differential bursting genes. This study also produced new insights in the role of transcriptional bursting in regulating gene expression, cell identity and tumor progression.

Fire Extinguishing Performance of Chemically Bonded Struvite Ceramic Powder with High Heat-Absorbing and Flame Retardant Properties

Struvite is a chemically bonded ceramic product in the pipeline of a sewage treatment plant. In order to explore the fire extinguishing potential of struvite, a new type of struvite ultrafine dry powder with excellent performance was prepared by a simple process, and its fire extinguishing performance and mechanism were analyzed in depth. Under the same process conditions, the refinement degree (D50 = 5.132 μm) and the specific surface area (BET = 25.72 m²/g) of ultrafine struvite were larger than those of NH₄H₂PO₄ (D50 = 8.961 μm, BET = 13.64 m²/g), making struvite more suitable for fire extinguishing. Besides, the pyrolysis process of struvite was relatively concentrated and absorbed more heat in a short time. Its heat absorption (458.4 J/mg) was higher than that of NH₄H₂PO₄ (156.4 J/mg). Water, ammonia, and PO· were released during the pyrolysis of struvite, which effectively reduced fire temperature, diluted oxygen concentrations and captured free radicals. At the same time, the final products were magnesium orthophosphate and magnesium pyrophosphate, which formed a dense flame-retardant ceramic layer with good thermal insulation and environmental protection functions. In these cases, the fire extinguishing mechanism of struvite was determined to have three stages: the cooling effect, the asphyxiation effect, and the chemical effect. Correspondingly, the fire extinguishing time of struvite was three seconds faster than that of ammonium phosphate under 0.2 MPa based on the local oil basin test.

Breast cancer cell-derived microRNA-155 suppresses tumor progression via enhancing immune cell recruitment and anti-tumor function

Evidence suggests that increased microRNA-155 (miR-155) expression in immune cells enhances anti-tumor immune responses. However, given the reported association of miR-155 to tumorigenesis in various cancers, a debate is provoked on whether miR-155 is oncogenic or tumor suppressive. We aimed to interrogate the impact of tumor miR-155 expression, particularly cancer cell-derived miR-155, on anti-tumor immunity in breast cancer. We performed bioinformatic analysis of human breast cancer databases, murine experiments, and human specimen examination. We revealed that higher tumor miR-155 levels correlate with a favorable anti-tumor immune profile and better patient outcomes. Murine experiments demonstrated that miR-155 overexpression in breast cancer cells enhanced T cell influx, delayed tumor growth, and sensitized the tumors to immune checkpoint blockade (ICB) therapy. Mechanistically, miR-155 overexpression in breast cancer cells upregulated their CXCL9/10/11 production, which was mediated by SOCS1 inhibition and increased pSTAT1/pSTAT3 ratio. We further found that serum miR-155 levels in breast cancer patients correlate with tumor miR-155 levels and tumor immune status. Our findings suggest that high serum and tumor miR-155 levels may be a favorable prognostic marker for breast cancer patients, and therapeutic elevation of miR-155 in breast tumors may improve the efficacy of ICB therapy via remodeling the anti-tumor immune landscape.

Relationship Between Headache Characteristics and a Remote History of TBI in Veterans: A 10-Year Retrospective Chart Review

BACKGROUND AND OBJECTIVES

The objective of this work was to examine the association between deployment-related traumatic brain injury (TBI) severity, frequency, and other injury characteristics with headache outcomes in veterans evaluated at a Veterans Administration (VA) polytrauma support clinic.

METHODS

We conducted a retrospective chart review of 594 comprehensive TBI evaluations between 2011 and 2021. Diagnostic criteria were based on the Department of Defense/VA Consensus-Based Classification of Closed TBI. Adjusted odds ratios (AORs) and 95% CIs were estimated for headache prevalence (logistic), headache severity (ordinal), and prevalence of migraine-like features (logistic) with multiple regression analysis. Regression models were adjusted for age, sex, race/ethnicity, time since injury, and mental health diagnoses.

RESULTS

TBI severity groups were classified as sub concussive exposure (n = 189) and mild (n = 377), moderate (n = 28), and severe TBI (n = 0). Increased headache severity was reported in veterans with mild TBI (AOR 1.72 [95% CI 1.15, 2.57]) and moderate TBI (AOR 3.89 [1.64, 9.15]) compared to those with subconcussive exposure. A history of multiple mild TBIs was associated with more severe headache (AOR 2.47 [1.34, 4.59]) and migraine-like features (AOR 5.95 [2.55, 13.77]). No differences were observed between blast and nonblast injuries; however, greater headache severity was reported in veterans with both primary and tertiary blast effects (AOR 2.56 [1.47, 4.49]). Alteration of consciousness (AOC) and posttraumatic amnesia (PTA) >30 minutes were associated with more severe headache (AOR 3.37 [1.26, 9.17] and 5.40 [2.21, 13.42], respectively). The length of time between the onset of last TBI and the TBI evaluation was associated with headache severity (AOR 1.09 [1.02, 1.17]) and prevalence of migraine-like features (AOR 1.27 [1.15, 1.40]). Last, helmet use was associated with less severe headache (AOR 0.42 [0.23, 0.75]) and lower odds of migraine-like features (AOR 0.45 [0.21, 0.98]).

DISCUSSION

Our data support the notion of a dose-response relationship between TBI severity and headache outcomes. A history of multiple mild TBIs and longer duration of AOC and PTA are unique risk factors for poor headache outcomes in veterans. Furthermore, this study sheds light on the poor headache outcomes associated with subconcussive exposure. Past TBI characteristics should be considered when developing headache management plans for veterans.

AB0994 Exploring knee osteoarthritis pain trajectories and movement-evoked pain changes during a 24-week outdoor walking program (WALK)

Background

Exercise therapy is recommended as first line treatment for knee osteoarthritis (OA), but it remains to be sub-optimally applied (1). Movement-evoked pain is a potential barrier to exercise adherence, but recent evidence suggests that such pain can be improved by training (2). Walking programs are low-cost, easily adopted and can be performed outdoors which can minimize the risk of SARS-CoV-2 transmission when in a group (3).

Objectives

To explore the acute pain trajectories of individuals with knee OA during a 24-week outdoor walking intervention. In addition, to explore the effect of pain trajectories and/or baseline characteristics on retention and adherence.

Methods

Individuals with clinical knee OA and bone marrow lesions (BMLs) on magnetic resonance imaging (MRI) were asked to follow a 24-week walking program. Every week consisted of two one hour supervised group sessions at various outdoor locations and one unsupervised session. At the start and end of every supervised group walk, knee pain was self-reported by participants to their trainer using a numerical rating scale (NRS) (0-10). The difference between the NRS pain values was considered as an acute pain change evoked by that walk. At baseline, the most affected knee of each participant was assessed using the Visual Analogue Scale (VAS) pain, the Western Ontario and McMasters Universities Osteoarthritis Index (WOMAC) pain, stiffness and function, wellbeing (3 questionnaires) and the Osteoarthritis Research Society International (OARSI) recommended strength and performance measures.

Results

In total, N = 24 participants started the program of whom N = 7 (29%) withdrew. Pain at the start of each walk decreased from NRS 2.5 (SD 1.6) at the first walk (N = 24) to NRS 0.9 (SD 0.8) at the final walk (N = 17). This pain was estimated to decrease on NRS by -0.04 (95% CI -0.05 to -0.02) per supervised session, p < 0.001 during the first 12 weeks and -0.01 (95% CI -0.02 to -0.004), p = 0.004 during the second twelve weeks of the program. The number (%) of participants who experienced an acute increase in pain decreased from 11 (45.8%) at the first walk to 4 (23.5%) at the last walk.

At baseline, non-adherent participants (<70% of group sessions) (N = 11) had lower physical performance scores, including the 30s Chair Stand Test (mean 10 (SD 1.7) stands versus mean 12.0 (SD 1.7) stands, p = 0.011), Fast Past Walk Test (1.23 (SD 0.14) meter per seconds (m/s) vs 1.50 (SD 0.20) m/s, p = 0.001), Six Minute Walk Test (418.8 (SD 75.9) m vs 529 (SD 72.6) m, p = 0.002), compared to adherent participants (N = 13). Non-adherent participants also had less severe self-reported symptoms including WOMAC stiffness (90.7 (SD 44.5) mm vs 121.5 (SD 17.0) mm, p = 0.031), compared to adherent participants. During the first two weeks of walking, acute increases in pain on average (mean ≥0.5 NRS) were reported by a greater number of non-adherent (N = 5 (45.5%)) than adherent participants (n = 4 (30.8%)).

Conclusion

This was an exploratory study and results need to be interpreted with caution due to the small sample size. The walking program resulted in clinically important improvements (MCIIs) (≥ 1 on NRS) (4) in start pain and acute pain changes. Improvements in start pain during the first 12-weeks were comparable to improvements measured in the NEMEX program (2) and may suggest that 12 weeks of exercise is sufficient to achieve MCIIs in pain. Improvements in acute changes in pain were smaller, which may have been related to a floor effect (5). Lower physical performance scores at baseline and more acute increases in pain during the first two weeks was associated with non-adherence. Participants with these characteristics may benefit from a lighter introduction to exercise.

References

[1]Bennell KL, et al. The Lancet Regional Health-Western Pacific. 2021;12:100187.

[2]Sandal LF, et al. Osteoarthritis and cartilage. 2016;24(4):589-92.

[3]Bulfone TC, et al. The Journal of infectious diseases. 2021;223(4):550-61.

[4]Perrot S, et al. Pain. 2013;154(2):248-56.

[5]McHorney CA, et al. Quality of life research. 1995;4(4):293-307.

Acknowledgements

We thank the participants who made this study possible. We would like to acknowledge the research staff, Kate Probert, Lizzy Reid, Simone Fitzgerald, Claire Roberts, Jasmin Ritchie, Dawn Simpson, and Tim Albion. We also thank Hamish Newsham-West for his contribution to the study design.

Disclosure of Interests

Stan Drummen: None declared, Saliu Balogun: None declared, Lieke Scheepers Grant/research support from: Competitive Grant Program Inflammation ASPIRE 2020 Rheumatology International Developed Markets from Pfizer, Employee of: previously worked as an Associate Director Epidemiology at the Medical Evidence Observational Research Department at AstraZeneca., Ishanka Munugoda: None declared, aroub lahham: None declared, Kim Bennell: None declared, Rana Hinman: None declared, Michele Callisaya: None declared, Guoqi Cai: None declared, Petr Otahal: None declared, Tania Winzenberg Consultant of: received payment to create educational material by AMGEN, Zhiqiang Wang: None declared, Benny Antony: None declared, Johanne Martel-Pelletier Shareholder of: ArthroLab Inc., Jean-Pierre Pelletier Shareholder of: ArthroLab Inc., François Abram Consultant of: ArthroLab Inc., Employee of: Arthrolab Inc., Graeme Jones Speakers bureau: received payment for a speakers bureau from Novartis, Dawn Aitken: None declared

Knee symptom but not radiographic knee osteoarthritis increases the risk of falls and fractures: results from the Osteoarthritis Initiative

OBJECTIVE

To describe the effect of knee symptoms and radiographic osteoarthritis (ROA) on the risk of falls, recurrent falls, and fractures.

DESIGN

Participants from the Osteoarthritis Initiative were classified as having 'no', 'unilateral' or 'bilateral' knee symptoms (≥19 on a 0-96 Western Ontario and McMaster Universities Osteoarthritis Index) and ROA (Kellgren-Lawrence grade ≥2) for each visit. Self-reported falls and fractures in the past 12 months were extracted at baseline and follow-up visits until month 96. Recurrent falls were defined as having ≥2 falls in the past 12 months. Hazard ratios (HR) with 95% confidence intervals (CI) were estimated using mixed-effects complementary log-log regression.

RESULTS

Of 4465 participants, 3145 (70%), 1681 (38%), and 806 (18%) experienced at least one fall, recurrent fall, and fracture, respectively, over 96 months. Compared to participants without symptomatic knee, unilateral and bilateral knee symptoms were associated with a 17% increased risk of falls and a 36-46% increased risk of recurrent falls, and bilateral knee symptoms increased the risk of fractures (HR 1.45, 95%CI 1.17 to 1.81). Compared to participants with no ROA in either knee, bilateral ROA was associated with a reduced risk of falls (HR 0.87, 95%CI 0.77 to 0.99) and fractures (HR 0.78, 95%CI 0.64 to 0.96). No statistically significant interactions between knee symptoms and ROA were observed.

CONCLUSIONS

This large population-based study showed that knee symptoms but not ROA increased the risk of falls, recurrent falls, and fractures, and that adults with bilateral ROA may have a lower risk of falls and fractures.

SCRIP: an accurate simulator for single-cell RNA sequencing data

MOTIVATION

Recent advancements in single-cell RNA sequencing (scRNA-seq) have enabled time-efficient transcriptome profiling in individual cells. To optimize sequencing protocols and develop reliable analysis methods for various application scenarios, solid simulation methods for scRNA-seq data are required. However, due to the noisy nature of scRNA-seq data, currently available simulation methods cannot sufficiently capture and simulate important properties of real data, especially the biological variation. In this study, we developed scRNA-seq information producer (SCRIP), a novel simulator for scRNA-seq that is accurate and enables simulation of bursting kinetics.

RESULTS

Compared to existing simulators, SCRIP showed a significantly higher accuracy of stimulating key data features, including mean-variance dependency in all experiments. SCRIP also outperformed other methods in recovering cell-cell distances. The application of SCRIP in evaluating differential expression analysis methods showed that edgeR outperformed other examined methods in differential expression analyses, and ZINB-WaVE improved the AUC at high dropout rates. Collectively, this study provides the research community with a rigorous tool for scRNA-seq data simulation.

AVAILABILITY AND IMPLEMENTATION

https://CRAN.R-project.org/package=SCRIP.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data

In recent years, efficient scRNA-seq methods have been developed, enabling the transcriptome profiling of single cells massively in parallel. Meanwhile, its high dimensionality and complexity bring challenges to the data analysis and require extensive collaborations between biologists and bioinformaticians and/or biostatisticians. The communication between these two units demands a platform for easy data sharing and exploration. Here we developed Single-Cell Transcriptomics Annotated Viewer (SCANNER), as a public web resource for the scientific community, for sharing and analyzing scRNA-seq data in a collaborative manner. It is easy-to-use without requiring special software or extensive coding skills. Moreover, it equipped a real-time database for secure data management and enables an efficient investigation of the activation of gene sets on a single-cell basis. Currently, SCANNER hosts a database of 19 types of cancers and COVID-19, as well as healthy samples from lungs of smokers and non-smokers, human brain cells and peripheral blood mononuclear cells (PBMC). The database will be frequently updated with datasets from new studies. Using SCANNER, we identified a larger proportion of cancer-associated fibroblasts cells and more active fibroblast growth-related genes in melanoma tissues in female patients compared to male patients. Moreover, we found ACE2 is mainly expressed in lung pneumocytes, secretory cells and ciliated cells and differentially expressed in lungs of smokers and never smokers.