DigitalCommons@The Texas Medical Center
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Allosteric Targeted Drug Delivery for Enhanced Blood-Brain Barrier Penetration via Mimicking Transmembrane Domain Interactions
No full textCurrent strategies for active targeting in the brain are entirely based on the effective interaction of the ligand with the orthosteric sites of specific receptors on the blood-brain barrier (BBB), which is highly susceptible to various pathophysiological factors and limits the efficacy of drug delivery. Here, we propose an allosteric targeted drug delivery strategy that targets classical BBB transmembrane receptors by designing peptide ligands that specifically bind to their transmembrane domains. This strategy prevents competitive interference from endogenous ligands and antibodies by using the insulin receptor and integrin
Functional Characterization of QT Interval Associated SCN5A Enhancer Variants Identify Combined Additive Effects
No full textSeveral empirical and theoretical studies suggest the presence of multiple enhancers per gene that collectively regulate gene expression, and that common sequence variation impacting on the activities of these enhancers is a major source of inter-individual gene expression variability. However, for the vast majority of genes, enhancers and the underlying regulatory variation remains unknown. Even for the genes with well-characterized enhancers, the nature of the combined effects from multiple enhancers and their variants, when known, on gene expression regulation remains unexplored. Here, we have evaluated the combined effects from five SCN5A enhancers and their regulatory variants that are known to collectively correlate with SCN5A cardiac expression and underlie QT interval association in the general population. Using small deletions centered at the regulatory variants in episomal reporter assays in a mouse cardiomyocyte cell line, we demonstrate that the variants and their flanking sequences play critical role in individual enhancer activities, likely being a transcription factor (TF) binding site. By oligonucleotide-based pulldown assays on predicted TFs, we identify the TFs likely driving allele-specific enhancer activities. Using all 32 possible allelic synthetic constructs in reporter assays, representing the five bi-allelic enhancers, we demonstrate combined additive effects on overall enhancer activities. Using transient enhancer assays in zebrafish embryos we demonstrate that four elements act as enhancers in vivo. Together, these studies uncover the TFs driving the enhancer activities of QT interval associated SCN5A regulatory variants, reveal the additive effects from allelic combinations of these regulatory variants, and prove their potential to act as enhancers in vivo
Comprehensive Assessment of Initial Adaptation of Extended-Spectrum β-Lactamase-Positive ST131 Escherichia coli to Carbapenem Exposure
No full textBackground: It remains unclear how high-risk Escherichia coli lineages, like sequence type (ST) 131, initially adapt to carbapenem exposure in their progression to carbapenem resistance.
Methods: Carbapenem mutation frequency was measured in multiple subclades of extended-spectrum β-lactamase (ESBL)-positive ST131 clinical isolates using a fluctuation assay followed by whole genome sequencing (WGS) characterization. Genomic, transcriptomic, and porin analyses of the ST131 C2/H30Rx isolate MB1860, under prolonged, increasing carbapenem exposure was performed using 2 experimental evolutionary platforms to measure fast versus slow adaptation.
Results: All 13 ESBL-positive ST131 strains selected from a diverse (n = 184) ST131 bacteremia cohort had detectable ertapenem (ETP) mutational frequencies, with a positive correlation between initial ESBL gene copy number and mutation frequency (r = 0.87, P \u3c 1e-5). WGS analysis of mutants showed that initial response to ETP exposure resulted in significant increases in ESBL gene copy numbers or mutations in Omp genes in the absence of ESBL gene amplification with subclade-specific associations. In both experimental evolutionary platforms, MB1860 responded to initial ETP exposure by increasing blaCTX-M-15 copy numbers via modular, IS26-mediated pseudocompound transposons (PCTns). Increased transcript level of genes present within the PCTn was a conserved expression signal in both experimental evolutionary platforms. Stable mutations in Omp encoding genes were detected only after prolonged increasing carbapenem exposure, consistent with clinical observations.
Conclusions: ESBL gene amplification is a conserved response to initial carbapenem exposure, especially within the high-risk ST131 C2/H30Rx subclade. Targeting such amplification could assist with mitigating carbapenem resistance development
High-Grade Astrocytoma With Piloid Features: A Single-Institution Case Series and Literature Review
No full textHigh-grade astrocytoma with piloid features (HGAP) is a recently described primary brain tumor and the first requiring a specific methylation pattern for diagnosis, as its histologic features are often compatible with other tumors such as glioblastoma (GBM). Characterized by molecular alterations in CDKN2A/B, NF1, BRAF, FGFR1, and ATRX, they may be located anywhere in the CNS but show a predilection for the posterior fossa. Reports are limited to retrospective case series, and the standard of care is not yet established. We performed a retrospective review of electronic medical records of all patients with HGAP at our institution. Records were queried for demographic, radiographic, clinical, surgical, pathologic, and outcome data. Eighteen patients were included with a median 17.1 months follow-up. Of these, 12 (63.2%) were women with a mean age of 43 years (range 24-67). The most common tumor locations were the cerebellum (8 patients, 42.1%) and thalamus (6 patients, 31.6%). On imaging, tumors were most commonly homogeneously contrast-enhancing (10 patients, 52.6%) or rim enhancing with central necrosis (5 patients, 26.3%). Ten patients (52.6%) underwent biopsy, while nine (47.4%) underwent resection, of which four (44.4%) underwent gross total resection. Adjuvant therapy included radiation in 16 patients (88.9%) and systemic treatment in 16 patients (88.9%). The initial systemic treatment was temozolomide in 14 patients (77.8%). One patient received upfront trametinib (a MEK1 inhibitor), and one patient received upfront dabrafenib (a BRAF inhibitor). At last follow up, 11 patients (57.9%) had progressive disease. Median progression-free survival (PFS) was 5.4 months (range 1.6-28.2 months), and median overall survival (OS) had not been reached. HGAP is a newly described rare glial tumor without an established standard of care. Its aggressive behavior and targetable mutations warrant further investigation regarding predictors of outcome for this entity
Outcomes of Patients Treated With Chemotherapy for Breast Cancer During Pregnancy Compared With Nonpregnant Breast Cancer Patients Treated With Systemic Therapy
No full textIntroduction: Prior studies of patients treated for breast cancer during pregnancy (PrBC) report mixed outcomes and are limited by substandard treatment, small cohorts, and short follow-up. This study compared survival outcomes of PrBC patients treated with chemotherapy during pregnancy with nonpregnant patients matched by age, year of diagnosis, stage, and subtype.
Methods: PrBC patients treated from 1989 to 2022 on prospective institutional protocols were eligible. Disease-free survival (DFS), overall survival (OS), and progression-free survival (PFS) were estimated using the Kaplan-Meier method and multivariable Cox proportional hazards regression.
Results: Among 143 PrBC and 285 nonpregnant patients, median follow-up was 11.4 years. Survival differences were statistically significant, with median DFS and OS not attained for PrBC patients versus 5.6 years (95% confidence interval [CI], 3.6-15.4; p = .0001) and 19.3 years (95% CI, 14.1-not estimated; p = .0262) for nonpregnant patients, respectively. Median PFS was 24.1 years (95% CI, 15.8-not estimated) for PrBC patients versus 8.4 years (95% CI, 6.4-10.9) for the nonpregnant cohort (p = .0008). Study cohort was associated with DFS, PFS, and OS in multivariable analyses, with the nonpregnant cohort having increased risks of disease recurrence (hazard ratio [HR], 1.91; 95% CI, 1.33-2.76; p = .0005) and disease progression or death (HR, 1.68; 95% CI, 1.19-2.39; p = .0035), and shorter OS (HR, 1.52; 95% CI, 1.01-2.29; p = .0442).
Conclusion: These data suggest that PrBC patients treated with chemotherapy during pregnancy have at least comparable, if not superior, outcomes than nonpregnant patients with similar age, cancer stage, and subtype. Analyses excluding patients with postpartum breast cancer were unable to be performed and are a priority for future confirmatory studies
Therapeutic Targeting of the Janus Kinase/Signal Transducer and Activator of Transcription Pathway in Cutaneous T-Cell Lymphoma
Full text linkBackground/Objectives: Cutaneous T-cell lymphoma (CTCL) is a rare group of non-Hodgkin lymphomas characterized by the clonal expansion of malignant T cells. While current treatments can alleviate symptoms and significant progress has been made in treating leukemic CTCL, a definitive cure remains elusive. Dysregulation of the Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathway is a key driver of CTCL pathogenesis. As a result, therapeutic strategies targeting JAK/STAT signaling have gained momentum, with the increasing use of JAK inhibitors and other agents that effectively suppress this pathway. These immune-modulating therapies have broad effects on physiological processes, inflammation, and the pathological changes associated with both inflammatory diseases and cancers. Several JAK inhibitors, originally FDA-approved for inflammatory conditions, are now being investigated for cancer treatment.
Methods: In this paper, a brief review of the literature on JAK/STAT pathway dysregulation in CTCL is provided, highlighting both clinical and preclinical studies involving JAK inhibitors and other agents that target this pathway.
Results: Specifically, we focus on six JAK inhibitors currently under clinical investigation-golidocitinib, ruxolitinib, cerdulatinib, tofacitinib, upadacitinib, and abrocitinib. Additionally, we discuss preclinical studies that explore the mechanisms underlying JAK/STAT pathway inhibition in CTCL. Furthermore, we review reported cases in which CTCL relapsed or emerged following JAK inhibitor treatment.
Conclusions: Collectively, these findings support the potential clinical utility of targeting the JAK/STAT pathway in CTCL. However, further research is needed to evaluate safety risks, minimize adverse effects, and optimize these therapeutic strategies
MRI-Based Digital Twins to Improve Treatment Response of Breast Cancer by Optimizing Neoadjuvant Chemotherapy Regimens
No full textWe developed a practical framework to construct digital twins for predicting and optimizing triple-negative breast cancer (TNBC) response to neoadjuvant chemotherapy (NAC). This study employed 105 TNBC patients from the ARTEMIS trial (NCT02276443, registered on 10/21/2014) who received Adriamycin/Cytoxan (A/C)-Taxol (T). Digital twins were established by calibrating a biology-based mathematical model to patient-specific MRI data, which accurately predicted pathological complete response (pCR) with an AUC of 0.82. We then used each patient\u27s twin to theoretically optimize outcome by identifying their optimal A/C-T schedule from 128 options. The patient-specifically optimized treatment yielded a significant improvement in pCR rate of 20.95-24.76%. Retrospective validation was conducted by virtually treating the twins with AC-T schedules from historical trials and obtaining identical observations on outcomes: bi-weekly A/C-T outperforms tri-weekly A/C-T, and weekly/bi-weekly T outperforms tri-weekly T. This proof-of-principle study demonstrates that our digital twin framework provides a practical methodology to identify patient-specific TNBC treatment schedules
Lung Cancer Risk Prediction in Patients with Persistent Pulmonary Nodules Using the Brock Model and Sybil Model
No full textBackground/objectives: Persistent pulmonary nodules are at higher risk of developing into lung cancers. Assessing their future cancer risk is essential for successful interception. We evaluated the performance of two risk prediction models for persistent nodules in hospital-based cohorts: the Brock model, based on clinical and radiological characteristics, and the Sybil model, a novel deep learning model for lung cancer risk prediction.
Methods: Patients with persistent pulmonary nodules-defined as nodules detected on at least two computed tomography (CT) scans, three months apart, without evidence of shrinkage-were included in the retrospective (n = 130) and prospective (n = 301) cohorts. We analyzed the correlations between demographic factors, nodule characteristics, and Brock scores and assessed the performance of both models. We also built machine learning models to refine the risk assessment for our cohort.
Results: In the retrospective cohort, Brock scores ranged from 0% to 85.82%. In the prospective cohort, 62 of 301 patients were diagnosed with lung cancer, displaying higher median Brock scores than those without lung cancer diagnosis (18.65% vs. 4.95%, p \u3c 0.001). Family history, nodule size ≥10 mm, part-solid nodule types, and spiculation were associated with the risks of lung cancer. The Brock model had an AUC of 0.679, and Sybil\u27s AUC was 0.678. We tested five machine learning models, and the logistic regression model achieved the highest AUC at 0.729.
Conclusions: For patients with persistent pulmonary nodules in real-world cancer hospital-based cohorts, both the Brock and Sybil models had values and limitations for lung cancer risk prediction. Optimizing predictive models in this population is crucial for improving early lung cancer detection and interception
Optimized Methods to Quantify Tumor Treating Fields (TTFields)-Induced Permeabilization of Glioblastoma Cell Membranes
No full textGlioblastoma (GBM) is a lethal primary brain cancer with a 5.6% five-year survival rate. Tumor treating fields (TTFields) are alternating low-intensity electric fields that have demonstrated a GBM patient survival benefit. We previously reported that 0.5-24 h of TTFields exposure resulted in an increased uptake of FITC-dextran fluorescent probes (4-20 kDa) in human GBM cells. However, this approach, in which a fluorescence plate-based detector is used to evaluate cells attached to glass coverslips, cannot distinguish FITC-dextran uptake in live vs. dead cells. The goal of the study was to report the optimization and validation of two independent methods to quantify human GBM cell membrane permeabilization induced by TTFields exposure. First, we optimized flow cytometry by measuring mean fluorescence intensity at 72 h for 4 kDa (TTFields 6726 ± 958.0 vs. no-TTFields 5093 ± 239.7
Humanized Saccharomyces cerevisiae Provides a Facile and Effective Tool to Identify Damaging Human Variants That Cause Exosomopathies
No full textThe RNA exosome is an evolutionarily conserved, multiprotein complex that is the major RNase in 3\u27 processing and degradation of a wide range of RNAs in eukaryotes. Single amino acid changes in RNA exosome subunits cause rare genetic diseases collectively called exosomopathies. However, distinguishing disease-causing variants from nonpathogenic ones remains challenging, and the mechanism by which these variants cause disease is largely unknown. Previous studies have employed a budding yeast model of RNA exosome-linked diseases that relies on mutating the orthologous yeast genes. Here, we develop a humanized yeast model of exosomopathies that allows us to unambiguously assess damaging effects of the exact patient variant in budding yeast. Individual replacement of the yeast subunits with corresponding mammalian orthologs identified 6 out of 9 noncatalytic core subunits of the budding yeast RNA exosome that can be replaced by a mammalian subunit, with 3 of the replacements supporting close to normal growth. Further analysis of the disease-associated variants utilizing the hybrid yeast/mammalian RNA exosome revealed functional defects caused by both previously characterized and uncharacterized variants of EXOSC2, EXOSC4, EXOSC7, and EXOSC9. Analysis of the protein levels of these variants indicates that a subset of the patient-derived variants causes reduced protein levels, while other variants are defective but are expressed as well as the reference allele, suggesting a more direct contribution of these residues to RNA exosome function. This humanized yeast model of exosomopathies provides a convenient and sensitive genetic tool to help distinguish damaging RNA exosome variants from benign variants. This disease model can be further exploited to uncover the underpinning mechanism of RNA exosome defects