Faculty Bibliography

Thiouracil (TU)-tagging is an intersectional method for covalently labeling newly transcribed RNAs within specific cell types. Cell type specificity is generated through targeted transgenic expression of the enzyme uracil phosphoribosyl transferase (UPRT); temporal specificity is generated through a pulse of the modified uracil analog 4TU. This technique has been applied in mouse using a Cre-dependent UPRT transgene, CA>GFPstop>HA-UPRT, to profile RNAs in endothelial cells, but it remained untested whether 4TU can cross the blood-brain barrier (BBB) or whether this transgene can be used to purify neuronal RNAs. Here, we crossed the CA>GFPstop>HA-UPRT transgenic mouse to a Sepw1-cre line to express UPRT in layer 2/3 of visual cortex or to an Nr5a1-cre line to express UPRT in layer 4 of visual cortex. We purified thiol-tagged mRNA from both genotypes at postnatal day (P)12, as well as from wild-type (WT) mice not expressing UPRT (background control). We found that a comparison of Sepw1-purified RNA to WT or Nr5a1-purified RNA allowed us to identify genes enriched in layer 2/3 of visual cortex. Here, we show that Cre-dependent UPRT expression can be used to purify cell type-specific mRNA from the intact mouse brain and provide the first evidence that 4TU can cross the BBB to label RNA in vivo.

Identification of biomarkers for early detection of lung cancer (LC) is important, in turn leading to more effective treatment and reduction of mortality. Serological proteome analysis (SERPA) was used to identify proteins around 34 kD as ECH1 and HNRNPA2B1, which had been recognized by serum autoantibody from 25 LC patients. In the validation study, including 90 sera from LC patients and 89 sera from normal individuals, autoantibody to ECH1 achieved an area under the curve (AUC) of 0.799 with sensitivity of 62.2% and specificity of 95.5% in discriminating LC from normal individuals, and showed negative correlation with tumor size (rs = -0.256, p = 0.023). Autoantibody to HNRNPA2B1 performed an AUC of 0.874 with sensitivity of 72.2% and specificity of 95.5%, and showed negative correlation with lymph node metastasis (rs = -0.279, p = 0.012). By using longitudinal preclinical samples, autoantibody to ECH1 showed an AUC of 0.763 with sensitivity of 60.0% and specificity of 89.3% in distinguishing early stage LC from matched normal controls, and elevated autoantibody levels could be detected greater than 2 y before LC diagnosis. ECH1 and HNRNPA2B1 are autoantigens that elicit autoimmune responses in LC and their autoantibody can be the potential biomarkers for the early detection of LC.

BACKGROUND: The epidemiological and programmatic implications of inclusivity of HIV-positive males in voluntary medical male circumcision (VMMC) programs are uncertain. We modeled these implications using Zambia as an illustrative example. METHODS AND FINDINGS: We used the Age-Structured Mathematical (ASM) model to evaluate, over an intermediate horizon (2010-2025), the effectiveness (number of VMMCs needed to avert one HIV infection) of VMMC scale-up scenarios with varying proportions of HIV-positive males. The model was calibrated by fitting to HIV prevalence time trend data from 1990 to 2014. We assumed that inclusivity of HIV positive males may benefit VMMC programs by increasing VMMC uptake among higher risk males, or by circumcision reducing HIV male-to-female transmission risk. All analyses were generated assuming no further antiretroviral therapy (ART) scale-up. The number of VMMCs needed to avert one HIV infection was projected to increase from 12.2 VMMCs per HIV infection averted, in a program that circumcises only HIV-negative males, to 14.0, in a program that includes HIV-positive males. The proportion of HIV-positive males was based on their representation in the population (e.g. 12.6% of those circumcised in 2010 would be HIV-positive based on HIV prevalence among males of 12.6% in 2010). However, if a program that only reaches out to HIV-negative males is associated with 20% lower uptake among higher-risk males, the effectiveness would be 13.2 VMMCs per infection averted. If improved inclusivity of HIV-positive males is associated with 20% higher uptake among higher-risk males, the effectiveness would be 12.4. As the assumed VMMC efficacy against male-to-female HIV transmission was increased from 0% to 20% and 46%, the effectiveness of circumcising regardless of HIV status improved from 14.0 to 11.5 and 9.1, respectively. The reduction in the HIV incidence rate among females increased accordingly, from 24.7% to 34.8% and 50.4%, respectively. CONCLUSION: Improving inclusivity of males in VMMC programs regardless of HIV status increases VMMC effectiveness, if there is moderate increase in VMMC uptake among higher-risk males and/or if there is moderate efficacy for VMMC against male-to-female transmission. In these circumstances, VMMC programs can reduce the HIV incidence rate in males by nearly as much as expected by some ART programs, and additionally, females can benefit from the intervention nearly as much as males.

Background: Arrhythmogenic cardiomyopathy (also known as "ARVC") is an inherited disease characterized by fibrous or fibrofatty infiltration of the heart muscle, commonly of right ventricular (RV) predominance, ventricular arrhythmias, and high propensity for sudden death. Sudden cardiac arrest frequently associates with exercise and most often occurs in early adulthood during the subclinical ("concealed") phase of the disease. Understanding electrical remodeling in the early stage of the disease is paramount to understand sudden death mechanisms. Methods: We generated a cardiomyocyte-specif-ic, tamoxifen-activated, PKP2 knockout murine line (alphaMHC-Cre-ERT2/PKP2 fl/fl) which allowed us to control the onset of PKP2 loss of expression, limit it to adult cardiomyocytes, and establish a time line for progression of molecular and functional events. Results: The first consequence of PKP2 loss was RV mechanical dysfunction (14 days post-tamoxifen injection, 14 dpi), followed by fibrosis of RV predominance and RV dilation (21 dpi), then biventricular dilated cardiomyopa-thy and left ventricular (LV) failure (28 dpi and beyond). End-stage failure and death occurred between 30 and 49 dpi. Isoproterenol (ISO)-induced ventricular arrhythmias were first detected prior to LV dysfunction (17/17 mice), and ISO-induced fatal ventricular fibrillation was observed only at 16 dpi, i.e., during the concealed stage (3/9). Differential tran-scriptome analysis at 21 dpi revealed reduced transcript levels for a gene network involved in intracellular calcium ([Ca²⁺]i) cycling, most critically genes encoding Ca²⁺ channel proteins (RyR2 and CaV1.2) and structural molecules that scaffold the dyad (ankyrin-B and triadin). Nanoscale imaging (3D super-resolution microscopy, SICM, and FIB-SEM) showed preservation of T-tubular structure, reduced size and increased separation of CaV1.2 clusters, and displacement of functional CaV1.2 channels from the T-tubular domain. Calcium imaging showed disruption of [Ca²⁺]i homeostasis, potentially causative of ventricular arrhythmias. Flecainide i.p. prevented ISO-induced arrhythmias in all animals. Retrospective analysis of clinical cases showed instances of sudden cardiac arrest without structural disease and suspect diagnosis of catechol-aminergic polymorphic ventricular tachycardia (CPVT) later revealed to foster PKP2 nonsense mutations. Conclusions: Our data provide the first evidence that PKP2 deficiency in adult ventricular myocytes is sufficient to cause an arrhythmo-genic cardiomyopathy of RV predominance. Adrenergic-induced arrhythmias and sudden death occur before the onset of overt structural disease and can mimic a CPVT phenotype. Our data also document a transcript-based [Ca²⁺]i dysfunction as a new key mechanism of arrhythmias in PKP2-deficient hearts and suggest flecainide as potential effective antiarrhyth-mic treatment

Uroplakins are a widespread group of vertebrate integral membrane proteins that belong to two different families: UPK1a and UPK1b belong to the large tetraspanin (TSPAN) gene family, and UPK3a, UPK3b, UPK3c, UPK3d, UPK2a and UPK2b form a family of their own, the UPK2/3 tetraspanin-associated family. In a previous study, we reported that uroplakins first appeared in vertebrates, and that uroplakin tetraspanins (UPK1a and UPK1b) should have originated by duplication of an ancestor tetraspanin gene. However, the evolutionary origin of the UPK2/3 family remains unclear. In this study, we provide evidence that the UPK2/3 family originated by gene duplication and domain loss from a protoPTPRQ-like basal deuterostome gene. PTPRQs are members of the subtype R3 tyrosine phosphatase receptor (R3 PTPR) family, which are characterized by having a unique modular composition of extracellular fibronectin (FN3) repeats, a transmembrane helix, and a single intra-cytoplasmic phosphotyrosine phophatase (PTP) domain. Our assumption of a deuterostome protoPTPRQ-like gene as an ancestor of the UPK2/3 family by gene duplication and loss of its PTP and fibronectin (FN3) domains, excluding the one closest to the transmembrane helix, is based on the following: (i) phylogenetic analyses, (ii) the existence of an identical intron/exon gene pattern between UPK2/3 and the corresponding genetic region in R3 PTPRs, (iii) the conservation of cysteine patterns and protein motifs between UPK2/3 and PTPRQ proteins and, (iv) the existence in tunicates, the closest organisms to vertebrates, of two sequences related to PTPRQ; one with the full subtype R3 modular characteristic and another without the PTP domain but with a short cytoplasmic tail with some sequence similarity to that of UPK3a. This finding will facilitate further studies on the structure and function of these important proteins with implications in human diseases.

Human brown and white preadipocytes offer unique cell models to study human adipogenesis and thermogenesis. Here, we describe the detailed procedures for isolation of human brown and white predipocytes from deep and superficial neck fat. To grow these cells in vitro for a prolonged period of time, they should be immortalized following the procedure discussed here. We also provide the protocol for expansion, cryopreservation, and adipogenic differentiation of cells.

With recent advances in stem cell technology, it is becoming efficient to differentiate human pluripotent stem cells (hPSCs) into cardiomyocytes, which can subsequently be used for myriad purposes, ranging from interrogating mechanisms of cardiovascular disease, developing novel cellular therapeutic approaches, as well as assessing the cardiac safety profile of compounds. However, the relative inability to acquire abundant pure and mature cardiomyocytes still hinders these applications. Recently, it was reported that glucose-depleted culture medium supplemented with lactate can facilitate purification of hPSC-derived cardiomyocytes. Here, we report that fatty acid as a lactate replacement has not only a similar purification effect but also improves the electrophysiological characteristics of hPSC-derived cardiomyocytes. Glucose-depleted culture medium supplemented with fatty acid and 3,3',5-Triiodo-l-thyronine (T3) was used during enrichment of hPSC-derived cardiomyocytes. Compared to untreated control cells, the treated cardiomyocytes exhibited enhanced action potential (AP) maximum upstroke velocity (as shown by a significant increase in dV/dtmax), action potential amplitude, as well as AP duration at 50% (APD50) and 90% (APD90) of repolarization. The treated cardiomyocytes displayed higher sensitivity to isoproterenol, more organized sarcomeric structures, and lower proliferative activity. Expression profiling showed that various ion channel and cardiac-specific genes were elevated as well. Our results suggest that the use of fatty acid and T3 can facilitate purification and maturation of hPSC-derived cardiomyocytes.

Effective anti-rat sarcoma viral oncogene (RAS) therapies have remained the holy grail of cancer treatment. Mutant Kirsten rat sarcoma viral oncogene homolog (KRAS) sustains tumorigenesis when linked to the plasma membrane (PM). The G protein-coupled receptor 31 (GPR31) is now identified to mediate KRAS membrane association and is crucial for proliferation, survival and macropinocytosis of KRAS-dependent cancer cells, suggesting that GPR31 is a druggable target for anti-RAS therapy.