Systematic identification of post-transcriptional regulatory modules.

In our cells, a limited number of RNA binding proteins (RBPs) are responsible for all aspects of RNA metabolism across the entire transcriptome. To accomplish this, RBPs form regulatory units that act on specific target regulons. However, the landscape of RBP combinatorial interactions remains poorly explored. Here, we perform a systematic annotation of RBP combinatorial interactions via multimodal data integration. We build a large-scale map of RBP protein neighborhoods by generating in vivo proximity-dependent biotinylation datasets of 50 human RBPs. In parallel, we use CRISPR interference with single-cell readout to capture transcriptomic changes upon RBP knockdowns. By combining these physical and functional interaction readouts, along with the atlas of RBP mRNA targets from eCLIP assays, we generate an integrated map of functional RBP interactions. We then use this map to match RBPs to their context-specific functions and validate the predicted functions biochemically for four RBPs. This study provides a detailed map of RBP interactions and deconvolves them into distinct regulatory modules with annotated functions and target regulons. This multimodal and integrative framework provides a principled approach for studying post-transcriptional regulatory processes and enriches our understanding of their underlying mechanisms.

Integrative identification of non-coding regulatory regions driving metastatic prostate cancer.

Large-scale sequencing efforts have been undertaken to understand the mutational landscape of the coding genome. However, the vast majority of variants occur within non-coding genomic regions. We designed an integrative computational and experimental framework to identify recurrently mutated non-coding regulatory regions that drive tumor progression. Applying this framework to sequencing data from a large prostate cancer patient cohort revealed a large set of candidate drivers. We used (1) in silico analyses, (2) massively parallel reporter assays, and (3) in vivo CRISPR interference screens to systematically validate metastatic castration-resistant prostate cancer (mCRPC) drivers. One identified enhancer region, GH22I030351, acts on a bidirectional promoter to simultaneously modulate expression of the U2-associated splicing factor SF3A1 and chromosomal protein CCDC157. SF3A1 and CCDC157 promote tumor growth in vivo. We nominated a number of transcription factors, notably SOX6, to regulate expression of SF3A1 and CCDC157. Our integrative approach enables the systematic detection of non-coding regulatory regions that drive human cancers.

Evaluating the Effect of MarginProbe® Use on Re-excisions After Partial Mastectomy: A Single-Institution Analysis.

BACKGROUND: Breast conservation therapy is a widely accepted approach in treating breast cancer, yet the average re-excision rates are approximately 25% despite surgical advancements. The Food and Drug Administration (FDA)-approved MarginProbe® device uses radiofrequency spectroscopy for intraoperative margin assessment, potentially reducing re-excision rates. This study evaluated the effectiveness of MarginProbe® in reducing re-excisions compared with standard of care (SOC). METHODS: A prospective cohort with MarginProbe® usage during partial mastectomies from June 2019 to July 2023 (153 patients) was compared with a retrospective control group without the device from January 2015 to May 2019 (300 patients). Both groups underwent partial mastectomies performed by two breast surgeons. Positive margins were defined as tumor on ink for invasive cancers and within 2 mm for ductal carcinoma in situ. RESULTS: When control was used for patient demographics and tumor characteristics, the findings showed that MarginProbe® significantly decreased the probability of re-excision by 58% (p < 0.001), although it led to a higher shave volume, with an average of 9.8 cc additional tissue removed compared with SOC (p < 0.001). Human epidermal growth factor 2 (HER2) positivity was significantly associated with increased odds of re-excision (p = 0.036). MarginProbe® demonstrated a sensitivity of 70.1% and a specificity of 47.5%. CONCLUSIONS: MarginProbe® is an effective adjunct for intraoperative margin assessment to decrease re-excision rates. However, patient selection is paramount. Given its significant increase in shave volume, women with small breasts may be at higher risk for poor cosmesis. Surgeons should exercise clinical judgement when determining the suitability of MarginProbe® use for patients undergoing breast conservation. Further research is necessary to refine MarginProbe®'s specificity and to optimize its clinical application.

Preliminary isotopic assessment of weaning in bonobos shows evidence for extended nursing, sibling competition and invested first-time mothers.

Although considered a hallmark in early ontogeny, weaning from breastmilk is difficult to monitor in wild primates and weaning ages remain unknown for wild bonobos (Pan Paniscus). Here, we calculated inter-birth intervals from demographic data and measured the isotopic offsets (Δ15N and Δ13C) between mother (n = 17) and offspring (n = 28) fecal sample pairs (n = 131, total n = 246) in the LuiKotale bonobos to assess nutritional weaning for the first time. We tested the effects of infant age, female parity, and sibling competition on Δ15N and Δ13C values. We found bonobo inter-birth intervals ranging from 2.2 to 7.3 years (x̄ = 4.7 ± 1.3 years) at LuiKotale. The Δ15N and Δ13C values suggested nutritional weaning on average by 6.6 and 7.0 years of age respectively, considerably exceeding weaning ages reported for chimpanzees (P. troglodytes) using the same approach. Our Δ13C data suggested that the number of offspring present affected nursing, with first-time mothers nursing more and possibly longer. The Δ15N and Δ13C values decreased with the arrival of the next sibling, suggesting sibling competition reduces milk access. Nevertheless, offspring may continue nursing 2.5-3 years after the birth of the next sibling, corresponding well with observations on low infant mortality. In conclusion, bonobo mothers provide remarkably enduring materna l support in the form of nursing concurrently to several offspring.

Desmoplastic small round cell tumor: from genomics to targets, potential paths to future therapeutics.

Desmoplastic Small Round Cell Tumor (DSRCT) is a highly aggressive pediatric cancer caused by a reciprocal translocation between chromosomes 11 and 22, leading to the formation of the EWSR1::WT1 oncoprotein. DSRCT presents most commonly in the abdominal and pelvic peritoneum and remains refractory to current treatment regimens which include chemotherapy, radiotherapy, and surgery. As a rare cancer, sample and model availability have been a limiting factor to DSRCT research. However, the establishment of rare tumor banks and novel cell lines have recently propelled critical advances in the understanding of DSRCT biology and the identification of potentially promising targeted therapeutics. Here we review model and dataset availability, current understanding of the EWSR1::WT1 oncogenic mechanism, and promising preclinical therapeutics, some of which are now advancing to clinical trials. We discuss efforts to inhibit critical dependencies including NTRK3, EGFR, and CDK4/6 as well as novel immunotherapy strategies targeting surface markers highly expressed in DSRCT such as B7-H3 or neopeptides either derived from or driven by the fusion oncoprotein. Finally, we discuss the prospect of combination therapies and strategies for prioritizing clinical translation.

Risk of Bleeding Versus Venous Thromboembolism After Surgery for Breast Cancer: A National Surgical Quality Improvement Program Analysis.

INTRODUCTION: Patients who undergo surgery for breast cancer are at risk for venous thromboembolism (VTE) and bleeding, which can lead to significant consequences on outcomes. This study examined factors related to VTE and bleeding risk in breast cancer surgery, with and without reconstruction. We also investigated the relationship between operative time and resident involvement on bleeding and VTE risk. METHODS: Using the ACS-NSQIP database, patients who underwent mastectomy, implant, pedicled, or free flap reconstruction from 2005 to 2021 were identified. Resident involvement was available from 2007 to 2010. We fitted two logistic regressions to model the log odds of bleeding occurrence and VTE as linear functions of procedure type, controlling for age, body mass index, and comorbidities. RESULTS: Implant reconstruction had significantly reduced 30-d incidence of bleeding, compared to those who underwent transverse rectus abdominus muscle flap (P < 0.001). Free flap was associated with a significant increase in bleeding but not VTE risk (P < 0.001; P = 0.132). Increase in operative time significantly increased the risk of bleeding and VTE (P < 0.001). For surgeries with resident involvement coded, there was no significantly increased risk of bleeding or VTE (P = 0.600; P = 0.766). CONCLUSIONS: Implant reconstruction remains the procedure with the lowest risk of both bleeding and VTE. Free flap reconstruction did not show a significantly increased risk of VTE, potentially expanding reconstruction options for patients previously excluded from autologous reconstruction. Surgeons should be mindful of operative time, with re-evaluation of risk factors with each additional hour of surgery, irrespective of reconstruction type. Resident involvement in surgeries should continue to be encouraged by faculty.

Trends of female authorship in head and neck surgery publications over the last decade.

BACKGROUND: While other otolaryngology subspecialties have established female authorship trends, there is no comprehensive study within head and neck surgery (HNS). METHODS: Five researchers recorded the gender identity of first and senior authors from HNS subspecialty papers (head and neck oncology, endocrine surgery, salivary gland pathology, and microsurgery) derived from 10 journals in otolaryngology and oncology in the years 2013, 2016, 2019, and 2022. RESULTS: From 3457 articles, 6901 unique author identities were analyzed. Female authors represented 32% (N = 1103) of first authors and 20% (N = 690) of senior authors. Female authors were less likely to publish in microvascular and reconstructive surgery. Senior female authors were more likely to publish in higher impact journals than male senior authors, and first female authors had an increased likelihood of funding compared to their male counterparts. CONCLUSIONS: While female authors remain underrepresented in certain literature, we illustrate promising trends in productivity, funding allocation, and impact.

Enzalutamide induces cytotoxicity in desmoplastic small round cell tumor independent of the androgen receptor.

Desmoplastic Small Round Cell Tumor (DSRCT) is a rare, pediatric cancer caused by the EWSR1::WT1 fusion protein. DSRCT predominantly occurs in males, which comprise 80-90% of the patient population. While the reason for this male predominance remains unknown, one hypothesis is that the androgen receptor (AR) plays a critical role in DSRCT and elevated testosterone levels in males help drive tumor growth. Here, we demonstrate that AR is highly expressed in DSRCT relative to other fusion-driven sarcomas and that the AR antagonists enzalutamide and flutamide reduce DSRCT growth. However, despite these findings, which suggest an important role for AR in DSRCT, we show that DSRCT cell lines form xenografts in female mice at the same rate as male mice and AR depletion does not significantly alter DSRCT growth in vitro. Further, we find that AR antagonists reduce DSRCT growth in cells depleted of AR, establishing an AR-independent mechanism of action. These findings suggest that AR dependence is not the reason for male predominance in DSRCT and that AR-targeted therapies may provide therapeutic benefit primarily through an AR-independent mechanism that requires further elucidation.

Comprehensive Transcriptomic Analysis of EWSR1::WT1 Targets Identifies CDK4/6 Inhibitors as an Effective Therapy for Desmoplastic Small Round Cell Tumors.

Desmoplastic small round cell tumors (DSRCT) are a type of aggressive, pediatric sarcoma characterized by the EWSR1::WT1 fusion oncogene. Targeted therapies for DSRCT have not been developed, and standard multimodal therapy is insufficient, leading to a 5-year survival rate of only 15% to 25%. Here, we depleted EWSR1::WT1 in DSRCT and established its essentiality in vivo. Transcriptomic analysis revealed that EWSR1::WT1 induces unique transcriptional alterations compared with WT1 and other fusion oncoproteins and that EWSR1::WT1 binding directly mediates gene upregulation. The E-KTS isoform of EWSR1::WT1 played a dominant role in transcription, and it bound to the CCND1 promoter and stimulated DSRCT growth through the cyclin D-CDK4/6-RB axis. Treatment with the CDK4/6 inhibitor palbociclib successfully reduced growth in two DSRCT xenograft models. As palbociclib has been approved by the FDA for the treatment of breast cancer, these findings demonstrate the sensitivity of DSRCT to palbociclib and support immediate clinical investigation of palbociclib for treating this aggressive pediatric cancer. SIGNIFICANCE: EWSR1::WT1 is essential for desmoplastic small round cell tumors and upregulates the cyclin D-CDK4/6-RB axis that can be targeted with palbociclib, providing a targeted therapeutic strategy for treating this deadly tumor type.

iPad-Based Neurocognitive Testing (ImPACT-QT) in Acute Adult Mild Traumatic Brain Injury/Concussion: Study on Practicality and Bedside Cognitive Scores in a Level-1 Trauma Center.

BACKGROUND: There lacks rapid standardized bedside testing to screen cognitive deficits following mild traumatic brain injury (mTBI). Immediate Post-Concussion Assessment & Cognitive Testing-Quick Test (ImPACT-QT) is an abbreviated-iPad form of computerized cognitive testing. The aim of this study is to test ImPACT-QT utility in inpatient settings. We hypothesize ImPACT-QT is feasible in the acute trauma setting. METHOD: Trauma patients ages 12-70 were administered ImPACT-QT (09/2022-09/2023). Encephalopathic/medically unstable patients were excluded. Mild traumatic brain injury was defined as documented-head trauma with loss-of-consciousness <30 minutes and arrival Glasgow Coma Scale 13-15. Patients answered Likert-scale surveys. Bivariate analyses compared demographics, attention, motor speed, and memory scores between mTBI and non-TBI controls. Multivariable logistic regression assessed memory score as a predictor of mTBI diagnosis. RESULTS: Of 233 patients evaluated (36 years [IQR 23-50], 71% [166/233] female), 179 (76%) were mTBI patients. For all patients, mean test-time was 9.3 ± 2 minutes with 93% (73/76) finding the test "easy to understand." Mild traumatic brain injury patients than non-TBI control had lower memory scores (25 [IQR 7-100] vs 43 [26-100], P = .001) while attention (5 [1-23] vs 11 [1-32]) and motor score (14 [3-28] vs 13 [4-32]) showed no significant differences. Multivariable-regression (adjustment: age, sex, race, education level, ISS, and time to test) demonstrated memory score predicted mTBI positive status (OR .96, CI .94-.98, P = .004). DISCUSSION: Immediate Post-Concussion Assessment & Cognitive Testing-Quick Test is feasible in trauma patients. Preliminary findings suggest acute mTBIs have lower memory but not attention/motor scores vs non-TBI trauma controls.

Efficacy of cytoreductive radical cystectomy in metastatic urothelial bladder cancer based on site and number of metastases.

BACKGROUND: Recent studies have highlighted the overall survival (OS) benefit of cytoreductive radical cystectomy (CRC) in metastatic bladder cancer (mBCa). Cytoreductive surgery has been established in other urologic cancers. However, the efficacy of CRC and optimal criteria for patient selection in mBCa is unclear. This study investigated the oncologic efficacy of CRC, particularly emphasizing the location and number of metastasis sites as a predictor of survival and treatment response. METHODS: A retrospective analysis of cT2-4N0-3M1 mBCa patients treated with multiagent chemotherapy between 2004 and 2019 was conducted using the National Cancer Database. Patients were classified by additional treatment with CRC or conservative local treatment (CLT), consisting of transurethral resection of bladder tumor, radiation, or no local treatment and propensity score (PS) matched. Kaplan-Meier analysis and multivariate Cox Proportional Hazards model assessed the effect of CRC or CLT on OS within the matched cohort and in four subgroups (1) patients with only distant lymph node (LN) metastasis vs. any organ metastasis, (2) patients with single metastasis vs. multiple metastases. Sensitivity analysis estimated the influence of unmeasured confounders on CRC OS benefit. RESULTS: Propensity matching yielded 247 and 251 patients treated with CRC and CLT, respectively. Median OS in patients who received CRC was greater than that of patients treated with CLT (20.4 months vs. 12.0 months, P < 0.001). CRC was associated with reduced mortality risk in patients with only distant LN metastases (HR = 0.545, P = 0.039), any organ metastasis (HR = 0.421, P < 0.001), and single visceral metastasis (HR = 0.483, P = 0.002). However, CRC did not significantly improve OS in patients with multiple metastases (HR = 0.501, P = 0.064). CONCLUSION: These findings demonstrate an OS benefit of CRC with multiagent chemotherapy and pinpoint multiple visceral metastases as a potential contraindication for CRC. Although limited by the influence of unmeasured confounders, these findings may inform future prospective investigations into CRC.

Flourishing or Frightening? Feelings about Natural and Built Green Spaces in Singapore.

The current study's aim was to better understand people's feelings towards different types of natural and built green space environments in the highly urbanized "garden city" of Singapore. We examined which types of green spaces elicited positive (eudemonic) or negative (apprehensive) affective responses. A total of 288 adult residents of Singapore completed a survey that asked them to report their affective states in response to images of 10 locally different environment types and to complete measures of childhood location, frequency of visiting natural/built environments, nature connectedness, and dispositional anxiety, as well as demographic items on age and gender. The 10 green space environment types were mapped onto an experiential state space representing feelings of apprehension and eudemonia in response to specific types of urban green spaces. In terms of a biophilic response, feelings of eudemonia were no different in natural green spaces compared to built green spaces. A higher frequency of experience in specific environments is associated with enhanced feelings of eudemonia in these environments. The findings indicate that people in Singapore can be apprehensive as much in natural green spaces as in built green spaces, and they can also find eudemonic experiences in built green spaces such as roof-top gardens or town parks.

Streptomyces sungeiensis SD3 as a Microbial Chassis for the Heterologous Production of Secondary Metabolites.

We present the newly isolated Streptomyces sungeiensis SD3 strain as a promising microbial chassis for heterologous production of secondary metabolites. S. sungeiensis SD3 exhibits several advantageous traits as a microbial chassis, including genetic tractability, rapid growth, susceptibility to antibiotics, and metabolic capability supporting secondary metabolism. Genomic and transcriptomic sequencing unveiled the primary metabolic capabilities and secondary biosynthetic pathways of S. sungeiensis SD3, including a previously unknown pathway responsible for the biosynthesis of streptazone B1. The unique placement of S. sungeiensis SD3 in the phylogenetic tree designates it as a type strain, setting it apart from other frequently employed Streptomyces chassis. This distinction makes it the preferred chassis for expressing biosynthetic gene clusters (BGCs) derived from strains within the same phylogenetic or neighboring phylogenetic clade. The successful expression of secondary biosynthetic pathways from a closely related yet slow-growing strain underscores the utility of S. sungeiensis SD3 as a heterologous expression chassis. Validation of CRISPR/Cas9-assisted genetic tools for chromosomal deletion and insertion paved the way for further strain improvement and BGC refactoring through rational genome editing. The addition of S. sungeiensis SD3 to the heterologous chassis toolkit will facilitate the discovery and production of secondary metabolites.

An assessment of the relationship between body mass index and minor complications in percutaneous gastrostomy tubes.

Objectives: The aim of our study was to determine if patients with obesity have different postoperative outcomes than their peers. Material and Methods: A single-center retrospective review of all fluoroscopically-guided percutaneous gastrostomy tube, with 183 patients and 90 patients in the BAG and dilator groups, respectively. Patients were stratified, based on body mass index (BMI) percentile and for age. Demographic information and data on medical comorbidities and post-operative complications were collected. All analyses were conducted using Chi-square or Kruskal-Wallis testing. Results: The median BMI was 26.6 kg/m2 with a standard deviation of 7.7. 106 (38.8%) patients were classified in the normal BMI category, 57 (20.9%) were overweight, and 50 (28.3%) were classified as obese. No major complications were reported in either group. 106 patients (38.8%) reported minor complications. The most common complication observed across both groups was procedural pain, with a higher incidence in the balloon group compared to the dilator group (17.5% vs. 12.2%). Dislodgement emerged as the second most common complication, occurring more frequently in the balloon group (12%) compared to the dilator group (6.7%). When considering weight categories, the overall rate of minor complications was highest among underweight patients (57.6%, P = 0.124). Both underweight and normal BMI patients showed a significantly higher incidence of tube dislodgement compared to other BMI categories (27.2% and 9.4%, respectively, P = 0.015). In a multivariable logistic regression, age was associated with an increased risk of minor complications (odds ratio [OR] 1.03, F [1.01, 1.05], P = 0.002). BAG had a greater OR for minor complication rate compared to dilator-assisted gastrostomy, although the difference was not statistically significant (OR 1.19, 95% confidence interval [0.69, 2.06]). Conclusion: Few studies have identified the relationship between BMI and complications related to gastrostomy tube placement. Our study highlights the importance of individualized care for patients across different BMI classes to minimize complications and improve patient outcomes.