Faculty Bibliography

Computational methods and tools are a powerful complementary approach to experimental work for studying regulatory interactions in living cells and systems. We demonstrate the use of formal reasoning methods as applied to the Caenorhabditis elegans germ line, which is an accessible system for stem cell research. The dynamics of the underlying genetic networks and their potential regulatory interactions are key for understanding mechanisms that control cellular decision-making between stem cells and differentiation. We model the "stem cell fate" versus entry into the "meiotic development" pathway decision circuit in the young adult germ line based on an extensive study of published experimental data and known/hypothesized genetic interactions. We apply a formal reasoning framework to derive predictive networks for control of differentiation. Using this approach we simultaneously specify many possible scenarios and experiments together with potential genetic interactions, and synthesize genetic networks consistent with all encoded experimental observations. In silico analysis of knock-down and overexpression experiments within our model recapitulate published phenotypes of mutant animals and can be applied to make predictions on cellular decision-making. A methodological contribution of this work is demonstrating how to effectively model within a formal reasoning framework a complex genetic network with a wealth of known experimental data and constraints. We provide a summary of the steps we have found useful for the development and analysis of this model and can potentially be applicable to other genetic networks. This work also lays a foundation for developing realistic whole tissue models of the C. elegans germ line where each cell in the model will execute a synthesized genetic network.

The current standard of care for an alveolar cleft defect is an autogenous bone graft, typically from the iliac crest. Given the limitations of alveolar bone graft surgery, such as limited supply, donor site morbidity, graft failure, and need for secondary surgery, there has been growing interest in regenerative medicine strategies to supplement and replace traditional alveolar bone grafts. Though there have been preliminary clinical studies investigating bone tissue engineering methods in human subjects, lack of consistent results as well as limitations in study design make it difficult to determine the efficacy of these interventions. As the field of bone tissue engineering is rapidly advancing, reconstructive surgeons should be aware of the preclinical studies informing these regenerative strategies. We review preclinical studies investigating bone tissue engineering strategies in large animal maxillary or mandibular defects and provide an overview of scaffolds, stem cells, and osteogenic agents applicable to tissue engineering of the alveolar cleft. An electronic search conducted in the PubMed database up to December 2021 resulted in 35 studies for inclusion in our review. Most studies showed increased bone growth with a tissue engineering construct compared to negative control. However, heterogeneity in the length of follow up, method of bone growth analysis, and inconsistent use of positive control groups make comparisons across studies difficult. Future studies should incorporate a pediatric study model specific to alveolar cleft with long-term follow up to fully characterize volumetric defect filling, cellular ingrowth, bone strength, tooth movement, and implant support.

BACKGROUND:Psychological, emotional, and mental distress affects many patients who experience early pregnancy loss (EPL). A common concern is that the patient's actions or choices caused the loss. Understanding the cause of EPL may improve the distress of EPL patients and their partners. Chromosomal abnormalities leading to a significant portion of EPL. Cell-free DNA (cfDNA) testing, a non-invasive test providing high quality information about the chromosomal makeup of a fetus, may offer assurance that a fetal abnormality caused the loss, and provide more certainty or closure in processing EPL. CfDNA may be a useful adjunct to patient-centered care in the setting of EPL. This commentary explores the possibility of cfDNA testing in lessening the emotional distress that often accompanies EPL. METHODS:The peer reviewed literature was explored for manuscripts addressing (1) the potential for cfDNA serum testing for patients experiencing EPL and screening products of conception to determine the cause of EPL; and/or (2) the impact that information might have on the psychological morbidity of EPL for patients and their partners. Themes generated from extracted data were used to generate key questions for future research. RESULTS:Preliminary findings suggest fetal fraction values are instrumental in the success of cfDNA testing, and a successful cfDNA testing experience can have a positive impact on patients. CONCLUSIONS:Ultimately, we conclude cfDNA testing could have a positive impact in patient care and improve the well-being of patients undergoing the emotional toll of EPL by reducing feelings of guilt and providing closure to those who learn the loss was associated with chromosomal abnormality. Further trials and studies that explore the intersection of mental health of EPL on patients should explore the efficacy of cfDNA testing as an adjunct to patient-centered care in these cases.

Dysregulation of cholesterol homeostasis is associated with many diseases such as cardiovascular disease and cancer. Liver X receptors (LXRs) are major upstream regulators of cholesterol homeostasis and are activated by endogenous cholesterol metabolites such as 27-hydroxycholesterol (27HC). LXRs and various LXR ligands such as 27HC have been described to influence several extra-hepatic biological systems. However, disparate reports of LXR function have emerged, especially with respect to immunology and cancer biology. This would suggest that, similar to steroid nuclear receptors, the LXRs can be selectively modulated by different ligands. Here, we use RNA-sequencing of macrophages and single-cell RNA-sequencing of immune cells from metastasis-bearing murine lungs to provide evidence that LXR satisfies the 2 principles of selective nuclear receptor modulation: (1) different LXR ligands result in overlapping but distinct gene expression profiles within the same cell type, and (2) the same LXR ligands differentially regulate gene expression in a highly context-specific manner, depending on the cell or tissue type. The concept that the LXRs can be selectively modulated provides the foundation for developing precision pharmacology LXR ligands that are tailored to promote those activities that are desirable (proimmune), but at the same time minimizing harmful side effects (such as elevated triglyceride levels).

Thoracic aortic aneurysms (TAA) in Marfan syndrome, caused by fibrillin-1 mutations, are characterized by elevated cytokines and fragmentated elastic laminae in the aortic wall. This study explored whether and how specific fibrillin-1-regulated miRNAs mediate inflammatory cytokine expression and elastic laminae degradation in TAA. miRNA expression profiling at early and late TAA stages using a severe Marfan mouse model (Fbn1^mgR/mgR) revealed a spectrum of differentially regulated miRNAs. Bioinformatic analyses predicted the involvement of these miRNAs in inflammatory and extracellular matrix-related pathways. We demonstrate that upregulation of pro-inflammatory cytokines and matrix metalloproteinases is a common characteristic of mouse and human TAA tissues. miR-122, the most downregulated miRNA in the aortae of 10-week-old Fbn1^mgR/mgR mice, post-transcriptionally upregulated CCL2, IL-1β and MMP12. Similar data were obtained at 70 weeks of age using Fbn1^C1041G/+ mice. Deficient fibrillin-1-smooth muscle cell interaction suppressed miR-122 levels. The marker for tissue hypoxia HIF-1α was upregulated in the aortic wall of Fbn1^mgR/mgR mice, and miR-122 was reduced under hypoxic conditions in cell and organ cultures. Reduced miR-122 was partially rescued by HIF-1α inhibitors, digoxin and 2-methoxyestradiol in aortic smooth muscle cells. Digoxin-treated Fbn1^mgR/mgR mice demonstrated elevated miR-122 and suppressed CCL2 and MMP12 levels in the ascending aortae, with reduced elastin fragmentation and aortic dilation. In summary, this study demonstrates that miR-122 in the aortic wall inhibits inflammatory responses and matrix remodeling, which is suppressed by deficient fibrillin-1-cell interaction and hypoxia in TAA.

BACKGROUND: METHODS:Experiments were performed in myocytes from a cardiomyocyte-specific, tamoxifen-activated, PKP2 knockout murine line (PKP2cKO). For training, mice underwent 75 minutes of treadmill running once per day, 5 days each week for 6 weeks. We used multiple approaches including imaging, high-resolution mass spectrometry, electrocardiography, and pharmacological challenges to study the functional properties of cells/hearts in vitro and in vivo. RESULTS: CONCLUSIONS:

BACKGROUND:Potential complications of pelvic flow disruption during aortic aneurysm repair include buttock ischemia and mesenteric ischemia. Unilateral or bilateral hypogastric artery flow interruption, either from atherosclerosis or intentionally to facilitate aneurysm repair, is considered problematic in endovascular repair; however, it has not been well studied in open abdominal aortic aneurysm (AAA) repair (OAR). We sought to examine the effect of interruption of flow to one or both hypogastric arteries on outcomes after OAR. METHODS:The Society for Vascular Surgery Quality Initiative database was queried for all patients undergoing elective open AAA repair between 2003 and 2020. (redundant) Patients with appropriate data on their hypogastric arteries postoperatively were stratified into two groups-patent bilaterally (normal pelvic perfusion, NPP) and unilateral or bilateral occlusion or ligation (compromised pelvic perfusion, CPP). Primary endpoints were 30-day major morbidity (myocardial infarction, respiratory complications, renal injury, and lower extremity or intestinal ischemia) and mortality. RESULTS:During the study period, 9.492 patients underwent elective open AAA repair-860 (9.1%) with compromised pelvic perfusion and 8,632 (90.9%) with patent bilateral hypogastric arteries. The groups had similar cardiac risk factors, including a history of coronary artery disease, prior coronary intervention, and the use of P2Y12 inhibitors and statins. A majority of patients in the CPP cohort had concurrent iliac aneurysms (63.3% vs. 24.8%; P < 0.001). The perioperative mortality was significantly higher in patients with compromised pelvic perfusion (5.5% vs. 3.1%; P < 0.001). Bilateral flow interruption had a trend toward higher perioperative mortality compared to unilateral interruption (7.1% vs. 4.7%; P < 0.147). The CPP group also had increased rates of myocardial injury (6.7% vs. 4.7%; P = 0.012), renal complications (18.9% vs. 15.9%; P = 0.024), leg and bowel ischemia (3.5% vs. 2.1%; P = 0.008; and 5.7% vs. 3.4%; P < 0.001, respectively). On multivariable analysis, CPP was associated with increased perioperative mortality (OR 1.47, CI 1.14-1.88, P = 0.003). On Kaplan-Meier analysis, there was no difference in survival at 2 years postdischarge between the NPP and CPP cohorts (86.1% vs. 87.5%, log-rank P = 0.275). CONCLUSIONS:Compromised pelvic perfusion is associated with increased perioperative complications and higher mortality in patients undergoing OAR. The sequelae of losing pelvic perfusion, in addition to the presence of more complex atherosclerotic and aneurysmal disease resulting in more difficult dissection, likely contribute to these findings. Thus, patients considered for OAR who have occluded hypogastric arteries or aneurysmal involvement of the hypogastric artery preoperatively may be candidates for more conservative management beyond traditional size criteria.

Autophagy is markedly impaired in Alzheimer's disease (AD). Here we reveal unique autophagy dysregulation within neurons in five AD mouse models in vivo and identify its basis using a neuron-specific transgenic mRFP-eGFP-LC3 probe of autophagy and pH, multiplex confocal imaging and correlative light electron microscopy. Autolysosome acidification declines in neurons well before extracellular amyloid deposition, associated with markedly lowered vATPase activity and build-up of Aβ/APP-βCTF selectively within enlarged de-acidified autolysosomes. In more compromised yet still intact neurons, profuse Aβ-positive autophagic vacuoles (AVs) pack into large membrane blebs forming flower-like perikaryal rosettes. This unique pattern, termed PANTHOS (poisonous anthos (flower)), is also present in AD brains. Additional AVs coalesce into peri-nuclear networks of membrane tubules where fibrillar β-amyloid accumulates intraluminally. Lysosomal membrane permeabilization, cathepsin release and lysosomal cell death ensue, accompanied by microglial invasion. Quantitative analyses confirm that individual neurons exhibiting PANTHOS are the principal source of senile plaques in amyloid precursor protein AD models.

Aerobic exercise is associated with decreased cancer incidence and cancer-associated mortality. However, little is known about the effects of exercise on pancreatic ductal adenocarcinoma (PDA), a disease for which current therapeutic options are limited. Herein, we show that aerobic exercise reduces PDA tumor growth, by modulating systemic and intra-tumoral immunity. Mechanistically, exercise promotes immune mobilization and accumulation of tumor-infiltrating IL15Rα⁺ CD8 T cells, which are responsible for the tumor-protective effects. In clinical samples, an exercise-dependent increase of intra-tumoral CD8 T cells is also observed. Underscoring the translational potential of the interleukin (IL)-15/IL-15Rα axis, IL-15 super-agonist (NIZ985) treatment attenuates tumor growth, prolongs survival, and enhances sensitivity to chemotherapy. Finally, exercise or NIZ985 both sensitize pancreatic tumors to αPD-1, with improved anti-tumor and survival benefits. Collectively, our findings highlight the therapeutic potential of an exercise-oncology axis and identify IL-15 activation as a promising treatment strategy for this deadly disease.