Multi-Omics Analysis for Transcriptional Regulation of Immune-Related Targets Using Epigenetic Data: A New Research Direction

BackgroundCurrently, a comprehensive method for exploration of transcriptional regulation has not been well established. We explored a novel pipeline to analyze transcriptional regulation using co-analysis of RNA sequencing (RNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq).MethodsThe G protein-coupled receptors (GPCRs) possibly associated with macrophages were further filtered using a reduced-Cox regression model. ATAC-seq profiles were used to map the chromatin accessibility of the GPRC5B promoter region. Pearson analysis was performed to identify the transcription factor (TF) whose expression was correlated with open chromatin regions of GPRC5B promoter. ChIP-seq profiles were obtained to confirm the physical binding of GATA4 and its predicted binding regions. For verification, quantitative polymerase chain reaction (qPCR) and multidimensional database validations were performed.ResultsThe reduced-Cox regression model revealed the prognostic value of GPRC5B. A novel pipeline for TF exploration was proposed. With our novel pipeline, we first identified chr16:19884686-19885185 as a reproducible open chromatin region in the GPRC5B promoter. Thereafter, we confirmed the correlation between GATA4 expression and the accessibility of this region, confirmed its physical binding, and proved in vitro how its overexpression could regulate GPRC5B. GPRC5B was significantly downregulated in colon adenocarcinoma (COAD) as seen in 28 patient samples. The correlation between GPRC5B and macrophages in COAD was validated using multiple databases.ConclusionGPRC5B, correlated with macrophages, was a key GPCR affecting COAD prognosis. Further, with our novel pipeline, TF GATA4 was identified as a direct upstream of GPRC5B. This study proposed a novel pipeline for TF exploration and provided a theoretical basis for COAD therapy.

First and second waves among hospitalised patients with COVID-19 with severe pneumonia: a comparison of 28-day mortality over the 1-year pandemic in a tertiary university hospital in Italy

ObjectiveThe first COVID-19–19 epidemic wave was over the period of February–May 2020. Since 1 October 2020, Italy, as many other European countries, faced a second wave. The aim of this analysis was to compare the 28-day mortality between the two waves among COVID-19 hospitalised patients.DesignObservational cohort study. Standard survival analysis was performed to compare all-cause mortality within 28 days after hospital admission in the two waves. Kaplan-Meier curves as well as Cox regression model analysis were used. The effect of wave on risk of death was shown by means of HRs with 95% CIs. A sensitivity analysis around the impact of the circulating variant as a potential unmeasured confounder was performed.SettingUniversity Hospital of Modena, Italy. Patients admitted to the hospital for severe COVID-19 pneumonia during the first (22 February–31 May 2020) and second (1 October–31 December 2020) waves were included.ResultsDuring the two study periods, a total of 1472 patients with severe COVID-19 pneumonia were admitted to our hospital, 449 during the first wave and 1023 during the second. Median age was 70 years (IQR 56–80), 37% women, 49% with PaO2/FiO2 <250 mm Hg, 82% with ≥1 comorbidity, median duration of symptoms was 6 days. 28-day mortality rate was 20.0% (95% CI 16.3 to 23.7) during the first wave vs 14.2% (95% CI 12.0 to 16.3) in the second (log-rank test p value=0.03). After including key predictors of death in the multivariable Cox regression model, the data still strongly suggested a lower 28-day mortality rate in the second wave (aHR=0.64, 95% CI 0.45 to 0.90, p value=0.01).ConclusionsIn our hospitalised patients with COVID-19 with severe pneumonia, the 28-day mortality appeared to be reduced by 36% during the second as compared with the first wave. Further studies are needed to identify factors that may have contributed to this improved survival.

Impact of asymmetric tethering on outcomes after edge-to-edge mitral valve repair for secondary mitral regurgitation

Background The impact of postero-anterior and medio-lateral mitral valve (MV) tethering patterns on outcomes in patients undergoing transcatheter edge-to-edge repair (M-TEER) for secondary mitral regurgitation (SMR) is unknown. Methods The ratio of the posterior to anterior MV leaflet angle (PLA/ALA) in MV segment 2 was defined as postero-anterior tethering asymmetry. Medio-lateral tethering asymmetry was assessed as the ratio of the medial (segment 3) to lateral (segment 1) MV tenting area. We used receiver-operating characteristics and a Cox regression model to identify cut-off values of asymmetric anteroposterior and medio-lateral tethering for prediction of 2 year all-cause mortality after TMVR. Results Among 178 SMR patients, postero-anterior tethering was asymmetric in 67 patients (37.9%, PLA/ALA ratio > 1.54). Asymmetric medio-lateral tethering (tenting area ratio > 1.49) was observed in 49 patients (27.5%). M-TEER reduced MR to ≤ 2 + in 92.1% of patients; MR reduction was less effective in the presence of asymmetric postero-anterior tethering (p = 0.02). A multivariable Cox regression model identified both types of asymmetric MV tethering to be associated with increased all-cause 2-year mortality (postero-anterior tethering asymmetry: HR = 2.77, CI 1.43–5.38; medio-lateral tethering asymmetry: HR = 2.90, CI 1.54–5.45; p < 0.01). Conclusions Asymmetric postero-anterior and medio-lateral MV tethering patterns are associated with increased 2-year mortality in patients undergoing M-TEER for SMR. A detailed echocardiographic analysis of MV anatomy may help to identify patients who profit most from M-TEER. Graphical abstract

Quiescin Sulfhydryl Oxidase 2 Overexpression Predicts Poor Prognosis and Tumor Progression in Patients With Colorectal Cancer: A Study Based on Data Mining and Clinical Verification

Background: As a member of the atypical thiol oxidase family, quiescin sulfhydryl oxidase 2 (QSOX2) has been reported to play an important role in several biological processes, but the expression and function of QSOX2 in colorectal cancer (CRC) remains elusive.Methods: The difference of QSOX2 expression, and its relationship with clinicopathological features and prognosis in CRC, was analyzed by bioinformatic analysis and validated by clinical CRC specimen cohort. The functional characterization of QSOX2 was detected via in vitro and vivo experiments in CRC cell lines, while the potential signaling pathways were predicted by Gene Set Enrichment Analysis (GSEA).Results: Our data based on bioinformatical analysis and clinical validation demonstrated that the expression of QSOX2 in CRC tissues was significantly upregulated. Additionally, the chi-square test, logistic regression analysis, and Fisher’s exact test showed that QSOX2 overexpression was significantly correlated with advanced clinicopathological parameters, such as pathological stage and lymph node metastasis. The Kaplan–Meier curves and univariate Cox regression model showed that QSOX2 overexpression predicts poor overall survival (OS) and disease-free survival (DFS) in CRC patients. More importantly, multivariate Cox regression model showed that QSOX2 overexpression could serve as an independent factor for CRC patients. In vitro and vivo data showed that the proliferation and metastasis ability of CRC cells were suppressed on condition of QSOX2 inhibition. In addition, GSEA showed that the QSOX2 high expression phenotype has enriched multiple potential cancer-related signaling pathways.Conclusion: QSOX2 overexpression is strongly associated with malignant progression and poor oncological outcomes in CRC. QSOX2 might act as a novel biomarker for prognosis prediction and a new target for biotherapy in CRC.

Maintenance Therapy in Patients with FLT3-ITD-Mutation-Positive Acute Myeloid Leukemia after Allogeneic Hematopoietic Cell Transplantation: Real-World Survival

Background: Patients with FLT3-mutation-positive (FLT3mut+) acute myeloid leukemia (AML) have a poor prognosis, particularly those with a high allelic burden of FLT3-ITD mutations (FLT3-ITD mut+). Further, patients with FLT3-ITD mut+ who have relapsed after allogeneic hematopoietic stem cell transplantation (HSCT) have a 1-year overall survival (OS) rate of less than 20%. While treatment guidelines vary in their recommendations for maintenance therapy after HSCT to prevent relapse, data are emerging on the potential benefits of maintenance therapy for patients with FLT3mut+ AML. Aim/Objective: To examine real-world survival outcomes in adult patients with FLT3-ITD mut+ AML who received maintenance therapy versus those who did not receive maintenance therapy after allogeneic HSCT, including a qualitative comparison with real-world survival outcomes in adults with FLT3mut+ AML. Methods: This was a retrospective chart review wherein hematologists and oncologists from North America, Europe, and Japan extracted data from the medical charts of patients with FLT3mut+ AML who underwent HSCT after achieving complete remission with first-line chemotherapy within the prior 3 years. The index date was the date of HSCT and the study period was from the index date to the date of the last follow-up or death. All patients were grouped into two cohorts based on post-HSCT therapy received (no maintenance therapy or maintenance therapy). In an analysis of a subgroup of patients typically considered to be at high risk of relapse, patients who had both received an allogeneic HSCT and had a high allelic burden of FLT3-ITD mut+ were analyzed; patients with FLT3-ITD and FLT3-TKD co-mutations were also included in this subgroup. Overall survival during the study period was assessed for each cohort in the overall population of patients and in the subgroup. Kaplan-Meier analyses and Cox regression models, including unadjusted models and models with adjustments for baseline covariates, were used to describe and evaluate cross-cohort comparisons of survival. Covariates in the adjusted Cox models were Eastern Cooperative Oncology Group status, risk status, measurable residual disease status, age at index date, sex, extramedullary involvement, race, BMI, time from diagnosis to index month, HSCT type, and country. Results: A total of 1,208 AML patients with FLT3mut+ who received HSCT were included in the general study population; 765 (63.3%) patients received no maintenance therapy and 443 (36.7%) patients received maintenance therapy (including FLT3 inhibitors, hypomethylating agents, cytotoxic chemotherapy, and other targeted therapies). In Kaplan-Meier analyses, OS was longer in patients who received maintenance therapy compared with those who did not receive maintenance therapy (log-rank P&lt;0.001; Figure A). Similar results were seen between maintenance therapy versus no maintenance therapy in an unadjusted Cox regression model (HR 0.52 [95% CI 0.35, 0.76], P&lt;0.001) and adjusted Cox regression model (HR 0.48 [95% CI 0.30, 0.77], P&lt;0.01). In an analysis of the subgroup, data from the charts of 745 patients with FLT3-ITD mut+ who received allogeneic HSCT were reviewed. The mean age at HSCT was 53.2 years; 39.9% and 38.4% of patients had intermediate and poor risk status, respectively. Of this subgroup, 473 (63.5%) patients received no maintenance therapy and 272 (36.5%) patients received maintenance therapy. Kaplan-Meier analyses show that OS was longer in patients receiving maintenance therapy versus no maintenance therapy (log-rank P&lt;0.001; Figure B); the risk of death appeared to plateau after approximately 2 years in patients receiving maintenance treatments. Similar results were seen between maintenance therapy versus no maintenance therapy in an unadjusted Cox regression model (HR 0.39 [95% CI 0.23, 0.65], P&lt;0.001) and adjusted Cox regression model (HR 0.38 [95% CI 0.20, 0.72], P&lt;0.01). Conclusions: In patients with FLT3-ITD mut+ AML, OS was improved in patients that received any type of maintenance therapy compared with patients that received no maintenance therapy after allogeneic HSCT. These improved clinical outcomes in a high-risk subgroup receiving maintenance treatments are consistent with findings in the general population of patients with FLT3mut+ AML. Additional analyses are warranted to statistically verify these results. Figure 1 Figure 1. Disclosures Yang: Astellas Pharma, Inc.: Consultancy. Song: Astellas Pharma, Inc.: Consultancy. Griffin: Astellas Pharma, Inc.: Consultancy; Novartis: Patents & Royalties: Post marketing royalties from midostaurin. Shah: Astellas Pharma, Inc.: Current Employment; University of Michigan School of Public Health Department of Health Management and Policy Alumni Board: Other: Chair-Elect. Freimark: Astellas Pharma, Inc.: Consultancy. Chilelli: Astellas Pharma, Inc.: Current Employment.

551. Remdesivir and Tocilizumab for the Treatment of Severe COVID-19 in a Community Hospital: A Retrospective Cohort Study

Background Growing evidence supports the use of remdesivir and tocilizumab for the treatment of hospitalized patients with severe COVID-19. The purpose of this study was to evaluate the use of remdesivir and tocilizumab for the treatment of severe COVID-19 in a community hospital setting. Methods We used a de-identified dataset of hospitalized adults with severe COVID-19 according to the National Institutes of Health definition (SpO2 &lt; 94% on room air, a PaO2/FiO2 &lt; 300 mm Hg, respiratory frequency &gt; 30/min, or lung infiltrates &gt; 50%) admitted to our community hospital located in Evanston Illinois, between March 1, 2020, and March 1, 2021. We performed a Cox proportional hazards regression model to examine the relationship between the use of remdesivir and tocilizumab and inpatient mortality. To minimize confounders, we adjusted for age, qSOFA score, noninvasive positive-pressure ventilation, invasive mechanical ventilation, and steroids, forcing these variables into the model. We implemented a sensitivity analysis calculating the E-value (with the lower confidence limit) for the obtained point estimates to assess the potential effect of unmeasured confounding. Figure 1. Kaplan–Meier survival curves for in-hospital death among patients treated with and without steroids The hazard ratio was derived from a bivariable Cox regression model. The survival curves were compared with a log-rank test, where a two-sided P value of less than 0.05 was considered statistically significant. Figure 2. Kaplan–Meier survival curves for in-hospital death among patients treated with and without remdesivir The hazard ratio was derived from a bivariable Cox regression model. The survival curves were compared with a log-rank test, where a two-sided P value of less than 0.05 was considered statistically significant. Results A total of 549 patients were included. The median age was 69 years (interquartile range, 59 – 80 years), 333 (59.6%) were male, 231 were White (41.3%), and 235 (42%) were admitted from long-term care facilities. 394 (70.5%) received steroids, 192 (34.3%) received remdesivir, and 49 (8.8%) received tocilizumab. By the cutoff date for data analysis, 389 (69.6%) patients survived, and 170 (30.4%) had died. The bivariable Cox regression models showed decreased hazard of in-hospital death associated with the administration of steroids (Figure 1), remdesivir (Figure 2), and tocilizumab (Figure 3). This association persisted in the multivariable Cox regression controlling for other predictors (Figure 4). The E value for the multivariable Cox regression point estimates and the lower confidence intervals are shown in Table 1. Figure 3. Kaplan–Meier survival curves for in-hospital death among patients treated with and without tocilizumab The hazard ratio was derived from a bivariable Cox regression model. The survival curves were compared with a log-rank test, where a two-sided P value of less than 0.05 was considered statistically significant. Figure 4. Forest plot on effect estimates and confidence intervals for treatments The hazard ratios were derived from a multivariable Cox regression model adjusting for age as a continuous variable, qSOFA score, noninvasive positive-pressure ventilation, and invasive mechanical ventilation. Table 1. Sensitivity analysis of unmeasured confounding using E-values CI, confidence interval. Point estimate from multivariable Cox regression model. The E value is defined as the minimum strength of association on the risk ratio scale that an unmeasured confounder would need to have with both the exposure and the outcome, conditional on the measured covariates, to explain away a specific exposure-outcome association fully: i.e., a confounder not included in the multivariable Cox regression model associated with remdesivir or tocilizumab use and in-hospital death in patients with severe COVID-19 by a hazard ratio of 1.64-fold or 1.54-fold each, respectively, could explain away the lower confidence limit, but weaker confounding could not. Conclusion For patients with severe COVID-19 admitted to our community hospital, the use of steroids, remdesivir, and tocilizumab were significantly associated with a slower progression to in-hospital death while controlling for other predictors included in the models. Disclosures All Authors: No reported disclosures

The significance of maternal asymptomatic bacteriuria during pregnancy on long-term offspring infectious hospitalizations

Asymptomatic bacteriuria (ASB) is a well-acknowledged infectious entity during pregnancy; yet its long-term implications are not well investigated. The present study aimed to test the association between maternal ASB during pregnancy and long-term offspring infectious hospitalizations. A population-based cohort analysis was conducted, comparing the incidence of long-term infectious-related hospitalizations of offspring born to mothers who were diagnosed with ASB during pregnancy, and those who did not have ASB. The study was conducted at a tertiary medical center and included all singleton deliveries between the years 1991 and 2014. Infectious morbidities were based on a predefined set of International Classification of Disease-9 codes. A Kaplan−Meier survival curve compared cumulative infectious hospitalization incidence between the groups, and a Cox regression model was used to adjust for confounding variables. During the study period, 212,984 deliveries met inclusion criteria. Of them, 5378 (2.5%) were diagnosed with ASB. As compared to offspring of non-ASB mothers, total long-term infectious hospitalizations were significantly higher among children to mothers who were diagnosed with ASB (13.1% vs. 11.1%, OR = 1.2, 95% CI 1.11–1.30, P ≤ 0.001). Likewise, a Kaplan−Meier curve demonstrated higher cumulative incidence of infectious hospitalizations among children born to mothers with ASB (log rank, P = 0.006). In the Cox regression model, while controlling for maternal age, diabetes mellitus, ethnicity, hypertensive disorders, and gestational age, maternal ASB was noted as an independent risk factor for long-term infectious morbidity in the offspring (adjusted HR = 1.1, 95% CI 1.01–1.17, P = 0.042). ASB during pregnancy increases offspring susceptibility to long-term infectious hospitalizations.