Faculty Bibliography

BACKGROUND/UNASSIGNED:Conotruncal defects due to developmental abnormalities of the outflow tract (OFT) are an important cause of cyanotic congenital heart disease. Dysregulation of transcriptional programs tuned by NKX2-5 (NK2 homeobox 5), GATA6 (GATA binding protein 6), and TBX1 (T-box transcription factor 1) have been implicated in abnormal OFT morphogenesis. However, there remains no consensus on how these transcriptional programs function in a unified gene regulatory network within the OFT. METHODS/UNASSIGNED: RESULTS/UNASSIGNED: CONCLUSIONS/UNASSIGNED:Our results using human and mouse models reveal an essential gene regulatory network of the OFT that requires an anterior second heart field enhancer to link GATA6 with NKX2-5-dependent rotation and septation gene programs.

Sequencing of genes, such as BRCA1 and BRCA2, is recommended for individuals with a personal or family history of early onset and/or bilateral breast and/or ovarian cancer or a history of male breast cancer. Such sequencing efforts have resulted in the identification of more than 17,000 BRCA2 variants. The functional significance of most variants remains unknown; consequently, they are called variants of uncertain clinical significance (VUSs). We have previously developed mouse embryonic stem cell (mESC)-based assays for functional classification of BRCA2 variants. We now developed a next-generation sequencing (NGS)-based approach for functional evaluation of BRCA2 variants using pools of mESCs expressing 10-25 BRCA2 variants from a given exon. We use this approach for functional evaluation of 223 variants listed in ClinVar. Our functional classification of BRCA2 variants is concordant with the classification reported in ClinVar or those reported by other orthogonal assays.

Pathogenic variants in BRCA2 are known to significantly increase the lifetime risk of developing breast and ovarian cancers. Sequencing-based genetic testing has resulted in the identification of thousands of BRCA2 variants that are considered to be variants of uncertain significance (VUS) because the disease risk associated with them is unknown. One such variant is p.Arg3052Gln, which has conflicting interpretations of pathogenicity in the ClinVar variant database. Arginine at position 3052 in BRCA2 plays an important role in stabilizing its C-terminal DNA binding domain. We have generated a knock-in mouse model expressing this variant to examine its role on growth and survival in vivo. Homozygous as well as hemizygous mutant mice are viable, fertile and exhibit no overt phenotype. While we did not observe any hematopoietic defects in adults, we did observe a marked reduction in the in vitro proliferative ability of fetal liver cells that were also hypersensitive to PARP inhibitor, olaparib. In vitro studies performed on embryonic and adult fibroblasts derived from the mutant mice showed significant reduction in radiation induced RAD51 foci formation as well as increased genomic instability after mitomycin C treatment. We observed mis-localization of a fraction of R3052Q BRCA2 protein to the cytoplasm which may explain the observed in vitro phenotypes. Our findings suggest that BRCA2 R3052Q should be considered as a hypomorphic variant.

Neuropeptides are key signaling molecules in the endocrine and nervous systems that regulate many critical physiological processes. Understanding the functions of neuropeptides in vivo requires the ability to monitor their dynamics with high specificity, sensitivity, and spatiotemporal resolution. However, this has been hindered by the lack of direct, sensitive, and noninvasive tools. We developed a series of GRAB (G protein-coupled receptor activation‒based) sensors for detecting somatostatin (SST), corticotropin-releasing factor (CRF), cholecystokinin (CCK), neuropeptide Y (NPY), neurotensin (NTS), and vasoactive intestinal peptide (VIP). These fluorescent sensors, which enable detection of specific neuropeptide binding at nanomolar concentrations, establish a robust tool kit for studying the release, function, and regulation of neuropeptides under both physiological and pathophysiological conditions.

The development of programmable nucleases to introduce defined alterations in genomic sequences has been a powerful tool for precision medicine. While several nucleases such as zinc-finger nucleases (ZFN), transcriptor activator-like effector nucleases (TALEN), and meganucleases have been explored, the advent of CRISPR/Cas9 technology has revolutionized the field of genome engineering. In addition to disease modeling, the CRISPR/Cas9 technology has contributed to safer and more effective treatment strategies for hematologic diseases and personalized T-cell-based therapies. Here we discuss the applications of the CRISPR technology in the treatment of hematologic diseases, their efficacy, and ongoing clinical trials. We examine the obstacles to their successful use and the approaches investigated to overcome these challenges. Finally, we provide our perspectives to improve this genome editing tool for targeted therapies.

INTRODUCTION/BACKGROUND:The purpose of this study was to determine what effect, if any, concomitant deformity correction has on outcomes following femoral nonunion repair. METHODS:605 consecutive patients who presented to our center with a long bone nonunion treated by one of 3 surgeons was queried. Sixty-two patients (10 %) with complete follow up were treated for a fracture nonunion following a Type 32 femur fracture (subtrochanteric, femoral shaft or distal third metaphysis) over an 11-year period. Twenty of these patients underwent a deformity correction (DC)-angular, rotational, or a combination of both-as part of their femoral reconstruction. Patient demographics and initial injury information was reviewed and compared. Outcomes including radiographic healing, time to union, postoperative complications, patient reported pain scores, and functional outcome scores using the Short Musculoskeletal Functional Assessment (SMFA) were recorded. Patients with and without deformity correction were analyzed and compared using independent T-tests and Chi-Square tests. RESULTS:Compared to the non-deformity correction (NDC) cohort, the DC cohort demonstrated a worse complication profile. Notably, the DC cohort had longer time to union (11.6 ± 7.3 months vs 7.6 ± 8.5 months, P = 0.042), reported significantly higher VAS pain scores at 1-year post-op (4.2 ± 2.8 vs 2.3 ± 2.6, P = 0.007), experienced more complications (25 % vs 4.8 %, P = 0.019), and had a higher rate of secondary procedures (30 % vs 4.8 %, P = 0.006). The DC patients reported less improvement in functional capability as displayed by a smaller average improvement in initial and final SMFA scores (P = 0.042) There was no difference in ultimate bone healing (P = 0.585), baseline SMFA (P = 0.294), and latest SMFA (P = 0.066). CONCLUSION/CONCLUSIONS:Deformity correction, if needed as part of femoral nonunion repair, is associated with an increased time to heal, greater rate of complications and diminished improvement of functionality. Eventual healing and patient reported outcomes were similar whether a deformity correction is necessary or not. LEVEL OF EVIDENCE/METHODS:III.

INTRODUCTION/BACKGROUND:Cervical cancer is the fourth most common malignancy in women and the fourth leading cause of death among women. The main histological types of cervical cancer are squamous cell carcinoma-75% of all cases; adenocarcinoma-10-25%; and all other rare variants including adenosquamous carcinoma and neuroendocrine carcinoma. Squamotransitional cervical cancer is an extremely rare and poorly studied subtype of squamous cell carcinoma. CASE REPORT/METHODS:We present a case of a 64-year-old female patient with early-stage squamotransitional carcinoma. A metastasis was observed in the left ovary and the left fallopian tube and a benign Brenner tumor in the right ovary. DISCUSSION/CONCLUSIONS:Although it is believed that this cervical cancer subtype shares the same risk factors and prognosis as squamous cell carcinoma, it is more likely to metastasize and recur. It is not unusual for spread to exist within nearby structures like the cervix and adnexa. It is impossible to tell which is the predominant focus from the immunoprofile of the lesions. Practically speaking, the best course of action in these situations is to rule out the presence of a primary tumor in the urinary tract before clarifying the condition of the cervix, uterus, and adnexal tissues. The presence of a Brenner tumor raises the possibility of a connection between the tumor's differentiation from a cell population and potential urothelial differentiation. CONCLUSION/CONCLUSIONS:Squamotransitional cervical cancer is a rare tumor with a poorly studied clinical behavior. Despite a shortage of information in the literature, it should be regarded as a more aggressive variety of squamous cell carcinoma and, as such, should be treated and followed up more aggressively. This case is the first described with involvement of the cervix, endometrium, and adnexal structures and a concomitant Brenner tumor.

Rapid and conditional protein depletion is the gold standard genetic tool for deciphering the molecular basis of developmental processes. Previously, we showed that by conditionally expressing the E3 ligase substrate adaptor ZIF-1 in Caenorhabditis elegans somatic cells, proteins tagged with the first CCCH Zn finger 1 (ZF1) domain from the germline regulator PIE-1 degrade rapidly, resulting in loss-of-function phenotypes. The described role of ZIF-1 is to clear PIE-1 and several other CCCH Zn finger proteins from early somatic cells, helping to enrich them in germline precursor cells. Here, we show that proteins tagged with the PIE-1 ZF1 domain are subsequently cleared from primordial germ cells (PGCs) in embryos and from undifferentiated germ cells in larvae and adults by ZIF-1. We harness germline ZIF-1 activity to degrade a ZF1-tagged fusion protein from PGCs and show that its depletion produces phenotypes equivalent to those of a null mutation. Our findings reveal that ZIF-1 transitions from degrading CCCH Zn finger proteins in somatic cells to clearing them from undifferentiated germ cells, and that ZIF-1 activity can be harnessed as a new genetic tool to study the early germline.

We present single-shot high-performance quantitative phase imaging with a physics-inspired plug-and-play denoiser for polarization differential interference contrast (PDIC) microscopy. The quantitative phase is recovered by the alternating direction method of multipliers (ADMM), balancing total variance regularization and a pre-trained dense residual U-net (DRUNet) denoiser. The custom DRUNet uses the Tanh activation function to guarantee the symmetry requirement for phase retrieval. In addition, we introduce an adaptive strategy accelerating convergence and explicitly incorporating measurement noise. After validating this deep denoiser-enhanced PDIC microscopy on simulated data and phantom experiments, we demonstrated high-performance phase imaging of histological tissue sections. The phase retrieval by the denoiser-enhanced PDIC microscopy achieves significantly higher quality and accuracy than the solution based on Fourier transforms or the iterative solution with total variance regularization alone.