Identifying gene expression programs in single-cell RNA-seq data using linear correlation explanation.

OBJECTIVE: Gene expression analysis through single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of gene regulation in diverse cell types, tissues, and organisms. While existing methods primarily focus on identifying cell type-specific gene expression programs (GEPs), the characterization of GEPs associated with biological processes and stimuli responses remains limited. In this study, we aim to infer biologically meaningful GEPs that are associated with both cellular phenotypes and activity programs directly from scRNA-seq data. METHODS: We applied linear CorEx, a machine-learning-based approach, to infer GEPs by grouping genes based on total correlation optimization function in simulated and real-world scRNA-seq datasets. Additionally, we utilized a transfer learning approach to project CorEx-inferred GEPs to other scRNA-seq datasets. RESULTS: By leveraging total correlation optimization, linear CorEx groups genes and demonstrates superior performance in identifying cell types and activity programs compared to similar methods using simulated data. Furthermore, we apply this same approach to real-world scRNA-seq data from the mouse dentate gyrus and embryonic colon development, uncovering biologically relevant GEPs related to cell types, developmental ages, and cell cycle programs. We also demonstrate the potential for transfer learning by evaluating similar datasets, showcasing the cross-species sensitivity of linear CorEx. CONCLUSION: Our findings validate linear CorEx as a valuable tool for comprehensively analyzing complex signals in scRNA-seq data, leading to deeper insights into gene expression dynamics, cellular heterogeneity, and regulatory mechanisms.

Assessment of Blood Pressure and Heart Rate Related Variables in Acute Stroke Patients Receiving Intravenous Antihypertensive Medication Infusions.

BACKGROUND: We performed an analysis of a large intensive care unit electronic database to provide preliminary estimates of various blood pressure parameters in patients with acute stroke receiving intravenous (IV) antihypertensive medication and determine the relationship with in-hospital outcomes. METHODS: We identified the relationship between pre-treatment and post-treatment systolic blood pressure (SBP) and heart rate (HR)-related variables and in-hospital mortality and acute kidney injury in patients with acute stroke receiving IV clevidipine, nicardipine, or nitroprusside using data provided in the Medical Information Mart for Intensive Care (MIMIC) IV database. RESULTS: A total of 1830 patients were treated with IV clevidipine (n = 64), nicardipine (n = 1623), or nitroprusside (n = 143). The standard deviations [SDs] of pre-treatment SBP (16.3 vs. 13.7, p ≤ 0.001) and post-treatment SBP (15.4 vs. 14.4, p = 0.004) were higher in patients who died compared with those who survived, particularly in patients with intracerebral hemorrhage (ICH). The mean SBP was significantly lower post treatment compared with pre-treatment values for clevidipine (130.7 mm Hg vs. 142.5 mm Hg, p = 0.006), nicardipine (132.8 mm Hg vs. 141.6 mm Hg, p ≤ 0.001), and nitroprusside (126.2 mm Hg vs. 139.6 mm Hg, p ≤ 0.001). There were no differences in mean SDs post treatment compared with pre-treatment values for clevidipine (14.5 vs. 13.5, p = 0.407), nicardipine (14.2 vs. 14.6, p = 0.142), and nitroprusside (14.8 vs. 14.8, p = 0.997). The SDs of pre-treatment and post-treatment SBP were not significantly different in patients with ischemic stroke treated with IV clevidipine, nicardipine, or nitroprusside or for patients with ICH treated with IV clevidipine or nitroprusside. However, patients with ICH treated with IV nicardipine had a significantly higher SD of post-treatment SBP (13.1 vs. 14.2, p = 0.0032). CONCLUSIONS: We found that SBP fluctuations were associated with in-hospital mortality in patients with acute stroke. IV antihypertensive medication reduced SBP but did not reduce SBP fluctuations in this observational study. Our results highlight the need for optimizing therapeutic interventions to reduce SBP fluctuations in patients with acute stroke.

Identification of Genomic Signatures for Colorectal Cancer Survival Using Exploratory Data Mining.

Clinicopathological presentations are critical for establishing a postoperative treatment regimen in Colorectal Cancer (CRC), although the prognostic value is low in Stage 2 CRC. We implemented a novel exploratory algorithm based on artificial intelligence (explainable artificial intelligence, XAI) that integrates mutational and clinical features to identify genomic signatures by repurposing the FoundationOne Companion Diagnostic (F1CDx) assay. The training data set (n = 378) consisted of subjects with recurrent and non-recurrent Stage 2 or 3 CRC retrieved from TCGA. Genomic signatures were built for identifying subgroups in Stage 2 and 3 CRC patients according to recurrence using genomic parameters and further associations with the clinical presentation. The summarization of the top-performing genomic signatures resulted in a 32-gene genomic signature that could predict tumor recurrence in CRC Stage 2 patients with high precision. The genomic signature was further validated using an independent dataset (n = 149), resulting in high-precision prognosis (AUC: 0.952; PPV = 0.974; NPV = 0.923). We anticipate that our genomic signatures and NCCN guidelines will improve recurrence predictions in CRC molecular stratification.

Targeting AKR1B10 by drug repurposing with epalrestat overcomes chemoresistance in non-small cell lung cancer patient-derived tumor organoids.

PURPOSE: Systemic treatments given to non-small cell lung cancer (NSCLC) patients are often ineffective due to drug resistance. In the present study, we investigated patient-derived tumor organoids (PDTOs) and matched tumor tissues from surgically treated NSCLC patients to identify drug repurposing targets to overcome resistance towards standard-of-care platinum-based doublet chemotherapy. EXPERIMENTAL DESIGN: PDTOs were established from ten prospectively enrolled non-metastatic NSCLC patients from resected tumors. PDTOs were compared with matched tumor tissues by histopathology/immunohistochemistry, whole exome and transcriptome sequencing. PDTO growths and drug responses were determined by measuring 3D tumoroid volumes, cell viability, and proliferation/apoptosis. Differential gene expression analysis identified drug-repurposing targets. Validations were performed with internal/external NSCLC patient data sets. NSCLC cell lines were used for aldo-keto reductase 1B10 (AKR1B10) knockdown studies and xenograft models to determine the intratumoral bioavailability of epalrestat. RESULTS: PDTOs retained histomorphology and pathological biomarker expression, mutational/transcriptomic signatures, and cellular heterogeneity of the matched tumor tissues. Five (50%) PDTOs were chemoresistant towards carboplatin/paclitaxel. Chemoresistant PDTOs and matched tumor tissues demonstrated overexpression of AKR1B10. Epalrestat, an orally available AKR1B10 inhibitor in clinical use for diabetic polyneuropathy, was repurposed to overcome chemoresistance of PDTOs. In vivo efficacy of epalrestat to overcome drug resistance corresponded to intratumoral epalrestat levels. CONCLUSIONS: PDTOs are efficient preclinical models recapitulating the tumor characteristics and are suitable for drug testing. AKR1B10 can be targeted by repurposing epalrestat to overcome chemoresistance in NSCLC. Epalrestat has the potential to advance to clinical trials in drug-resistant NSCLC patients due to favorable toxicity, pharmacological profile, and bioavailability.