Faculty Bibliography

A key limitation of the widely used CRISPR enzyme S. pyogenes Cas9 is the strict requirement of an NGG protospacer-adjacent motif (PAM) at the target site. This constraint can be limiting for genome editing applications that require precise Cas9 positioning. Recently, two Cas9 variants with a relaxed PAM requirement (NG) have been developed (xCas9 and Cas9-NG), but their activity has been measured at only a small number of endogenous sites. Here, we devise a high-throughput Cas9 pooled competition screen to compare the performance of Cas9 variants at thousands of genomic loci for gene knockout, transcriptional activation, and inhibition. We show that PAM flexibility comes at a substantial cost of decreased DNA targeting and cleavage. Of the PAM-flexible variants, we find that Cas9-NG outperforms xCas9 regardless of genome engineering modality or PAM. Finally, we combine xCas9 mutations with those of Cas9-NG, creating a stronger transcriptional modulator than existing PAM-flexible Cas9 variants.

A spectroscopic paradigm has been developed that allows the magnetic field emissions generated by the electrical activity in the human body to be imaged in real time. The growing significance of imaging modalities in biology is evident by the almost exponential increase of their use in research, from the molecular to the ecological level. The method of analysis described here allows totally noninvasive imaging of muscular activity (heart, somatic musculature). Such imaging can be obtained without additional methodological steps such as the use of contrast media.

PURPOSE/OBJECTIVE:Biomarkers for disease specific survival (DSS) in early stage melanoma are needed to select patients for adjuvant immunotherapy and accelerate clinical trial design. We present a pathology-based computational method using a deep neural network architecture for DSS prediction. EXPERIMENTAL DESIGN/METHODS:The model was trained on 108 patients from four institutions and tested on 104 patients from Yale School of Medicine (YSM). A receiver operating characteristic (ROC) curve was generated based on vote aggregation of individual image sequences, an optimized cutoff was selected, and the computational model was tested on a third independent population of 51 patients from Geisinger Health Systems (GHS). RESULTS:Area under the curve (AUC) in the YSM patients was 0.905 (p<0.0001). AUC in the GHS patients was 0.880 (p<0.0001). Using the cutoff selected in the YSM cohort, the computational model predicted DSS in the GHS cohort based on Kaplan-Meier (KM) analysis (p<0.0001). CONCLUSIONS:The novel method presented is applicable to digital images, obviating the need for sample shipment and manipulation and representing a practical advance over current genetic and IHC-based methods.

OBJECTIVE:Impaired multisensory integration in autism spectrum disorder (ASD) may arise from functional dysconnectivity among brain systems. Our study examines the functional connectivity integration between primary modal sensory regions and heteromodal processing cortex in ASD, and whether abnormalities in network integration relate to clinical severity. METHOD/METHODS:We studied a sample of 55 high-functioning ASD and 64 healthy controls (HC) male children and adolescents (total n = 119, age range 7-18). Stepwise functional connectivity analysis (SFC) was applied to resting state functional magnetic resonance images (rsfMRI) to characterize the connectivity paths that link primary sensory cortices to higher-order brain cognitive functional circuits and relate alterations in functional connectivity integration with three clinical scales: Social Communication Questionnaire, Social Responsiveness Scale, and Vineland Adaptive Behavior Scales. RESULTS:HC displayed typical functional connectivity transitions from primary sensory systems to association areas, but the ASD group showed altered patterns of multimodal sensory integration to heteromodal systems. Specifically, compared to the HC group, the ASD group showed (1) hyper-connectivity in visual cortex at initial link step distances; (2) hyper-connectivity between sensory unimodal regions and regions of the default mode network; and (3) hypo-connectivity between sensory unimodal regions and areas of the fronto-parietal and attentional networks. These patterns of hyper- and hypo-connectivity were associated with increased clinical severity in ASD. CONCLUSION/CONCLUSIONS:Network-wise reorganization in high-functioning ASD individuals affects strategic regions of unimodal-to-heteromodal cortical integration predicting clinical severity. Additionally, SFC analysis appears to be a promising approach for studying the neural pathophysiology of multisensory integration deficits in ASD.

Oscillatory brain activities support many physiological functions from motor control to cognition. Disruptions of the normal oscillatory brain activities are commonly observed in neurological and psychiatric disorders including epilepsy, Parkinson's disease, Alzheimer's disease, schizophrenia, anxiety/trauma-related disorders, major depressive disorders, and drug addiction. Therefore, these disorders can be considered as common oscillation defects despite having distinct behavioral manifestations and genetic causes. Recent technical advances of neuronal activity recording and analysis have allowed us to study the pathological oscillations of each disorder as a possible biomarker of symptoms. Furthermore, recent advances in brain stimulation technologies enable time- and space-targeted interventions of the pathological oscillations of both neurological disorders and psychiatric disorders as possible targets for regulating their symptoms.

Introduction: Albuminuria is a strong risk factor for kidney disease progression and cardiovascular disease as reflected in the KDIGO categories of urinary ACR <30mg/g, 30-300 and >300 mg/g. The CREDENCE trial recruited participants with substantial levels of albuminuria. We examined the relative and absolute effects of canagliflozin according to baseline albuminuria among people in the CREDENCE trial.
Method(s): The CREDENCE double-blind randomised study of 4401 participants with eGFR 30-<90mL/min/1.73m² and urinary albumin:creatinine ratio [uACR]>300-5000mg/g, demonstrated that canagliflozin significantly reduced renal and cardiovascular outcomes including the primary composite of end-stage kidney disease, doubling serum creatinine, or renal or cardiovascular death. We analysed the effect of canagliflozin on these and renal safety outcomes according to categories of baseline uACR of <=1000, >1000-<3000 and >=3000mg/g.
Result(s): At baseline, 2348 (53.4%), 1547 (35.2%), and 506 (11.5%) participants had uACR <=1000, >1000-<3000, >=3000mg/g, respectively. Higher categories of uACR were associated with higher rates of events (Figure). Canagliflozin reduced renal and cardiovascular endpoints, with no statistical evidence the effect varied in different uACR groups (all p heterogeneity >0.17). Canagliflozin led to a greater absolute reduction in renal events in those with higher grades of uACR (number needed to treat [NTT] to prevent one episode of the primary composite: 22 and 8 for uACR >1000-<3000 and >=3000mg/g, respectively). Rates of renal-related adverse events were lower overall with canagliflozin, with greater relative reduction greater in higher grades of uACR (p heterogeneity=0.003). Canagliflozin had no significant effect on the individual events of acute kidney injury, volume depletion, hyperkalaemia, urinary tract infections or hypoglycaemia, with no differences among grades of uACR (all p heterogeneity >0.12).
Conclusion(s): Albuminuria predicts renal and cardiovascular risk at high levels of albuminuria. Canagliflozin safely reduces renal and cardiovascular events in people with type 2 diabetes and substantial albuminuria, with the greatest absolute renal benefit in those with albuminuria of 3000-5000mg/g. [Formula presented]
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PURPOSE OF REVIEW/OBJECTIVE:Men have more kidney stones compared with women; however, the difference is progressively decreasing. The reasons for higher prevalence of stones in men, as well as increasing prevalence in women, is a subject of ongoing speculation. In this review, we summarize the evidence of differences between men and women and expand on the speculative causes. RECENT FINDINGS/RESULTS:Stone incidence is rising in women and adolescent girls. Stone disease is more heritable among men than women, and women demonstrate greater influence of the unique environment. Women under the age of 50 years who have been pregnant, have more than double the odds of kidney stones compared with those who have never been pregnant. Women are more burdened with obesity, bariatric surgery and dieting, all associated with increased stones. Women have higher urinary pH because of greater absorption of dietary organic anions leading to increased urinary citrate, compared with men, and they differ in tubular calcium handling. SUMMARY/CONCLUSIONS:It is obvious that the cause of stones in men and women is complex and requires further study. Potential clues offered are in the change of the female environment, influencing increasing incidence in stones, particularly of younger women and female adolescents.

BACKGROUND:A scarcity of organs has driven the transplant community to broaden selection criteria for both living and deceased donors. Living donor transplants offer better patient and allograft survival when compared with deceased donor transplants. Many transplant centers now allow complex living donors such as those with nephrolithiasis to undergo nephrectomy. METHODS:We conducted a survey of medical and surgical directors of kidney transplant programs in the United States to shed light on current practices pertaining to medical evaluation of living kidney donors with nephrolithiasis. 353 surveys were e-mailed to medical directors and surgical directors of transplant programs after contacts were obtained from UNOS. RESULTS:49 completed surveys were returned (13.9%). 77.7% (38/49) of survey participants said their centers will consider living kidney donor candidates with a history of symptomatic kidney stones, 69.4% (34/49) said their centers will consider candidates who are incidentally found to have kidney stones and 10.2% (5/49) said their centers decline all potential donors with nephrolithiasis. CONCLUSIONS:Several programs are still reluctant to allow potential donors with nephrolithiasis to donate. There is an unmet need to develop evidence-based guidelines to optimize outcomes in this population of kidney donors with nephrolithiasis and their recipients.

To navigate through the environment, animals rely on visual feedback to control their movements relative to their surroundings. In dipteran flies, visual feedback is provided by the wide-field motion-sensitive neurons in the visual system called lobula plate tangential cells (LPTCs). Understanding the role of LPTCs in fly behaviors can address many fundamental questions on how sensory circuits guide behaviors. The blowfly was estimated to have ~ 60 LPTCs, but only a few have been identified in Drosophila. We conducted a Gal4 driver screen and identified five LPTC subtypes in Drosophila, based on their morphological characteristics: LPTCs have large arborizations in the lobula plate and project to the central brain. We compared their morphologies to the blowfly LPTCs and named them after the most similar blowfly cells: CH, H1, H2, FD1 and FD3, and V1. We further characterized their pre- and post-synaptic organizations, as well as their neurotransmitter profiles. These anatomical features largely agree with the anatomy and function of their likely blowfly counterparts. Nevertheless, several anatomical details indicate the Drosophila LPTCs may have more complex functions. Our characterization of these five LPTCs in Drosophila will facilitate further functional studies to understand their roles in the visual circuits that instruct fly behaviors.