Unprocessed genomic uracil as a source of DNA replication stress in cancer cells.

Alterations of bases in DNA constitute a major source of genomic instability. It is believed that base alterations trigger base excision repair (BER), generating DNA repair intermediates interfering with DNA replication. Here, we show that genomic uracil, a common type of base alteration, induces DNA replication stress (RS) without being processed by BER. In the absence of uracil DNA glycosylase (UNG), genomic uracil accumulates to high levels, DNA replication forks slow down, and PrimPol-mediated repriming is enhanced, generating single-stranded gaps in nascent DNA. ATR inhibition in UNG-deficient cells blocks the repair of uracil-induced gaps, increasing replication fork collapse and cell death. Notably, a subset of cancer cells upregulates UNG2 to suppress genomic uracil and limit RS, and these cancer cells are hypersensitive to co-treatment with ATR inhibitors and drugs increasing genomic uracil. These results reveal unprocessed genomic uracil as an unexpected source of RS and a targetable vulnerability of cancer cells.

Novel Approaches with HIF-2α Targeted Therapies in Metastatic Renal Cell Carcinoma.

Germline inactivation of the Von Hippel-Lindau (VHL) tumor suppressor is the defining hallmark in hereditary VHL disease and VHL-associated renal cell carcinoma (RCC). However, somatic VHL mutations are also observed in patients with sporadic RCC. Loss of function VHL mutations result in constitutive activation of hypoxia-inducible factor-2 alpha (HIF-2α), which leads to increased expression of HIF target genes that promote angiogenesis and tumor growth. As of 2023, belzutifan is currently the only approved HIF-2α inhibitor for both VHL-associated and sporadic metastatic RCC (mRCC). However, there is potential for resistance with HIF-2α inhibitors which warrants novel HIF-2α-targeting strategies. In this review, we discuss the potential resistance mechanisms with belzutifan and current clinical trials evaluating novel combinations of belzutifan with other targeted therapies and immune checkpoint inhibitors which may enhance the efficacy of HIF-2α targeting. Lastly, we also discuss newer generation HIF-2α inhibitors that are currently under early investigation and outline future directions and challenges with HIF-2α inhibitors for mRCC.

Parathyroid gland detection using an intraoperative autofluorescence handheld imager - early feasibility study.

Introduction: Parathyroid glands may be compromised during thyroid surgery which can lead to hypoparathyroidism and hypocalcemia. Identifying the parathyroid glands relies on the surgeon's experience and the only way to confirm their presence was through tissue biopsy. Near infrared autofluorescence technology offers an opportunity for real-time, non-invasive identification of the parathyroid glands. Methods: We used a new research prototype (hANDY-I) developed by Optosurgical, LLC. It offers coaxial excitation light and a dual-Red Green Blue/Near Infrared sensor that guides anatomical landmarks and can aid in identification of parathyroid glands by showing a combined autofluorescence and colored image simultaneously. Results: We tested the imager during 23 thyroid surgery cases, where initial clinical feasibility data showed that out of 75 parathyroid glands inspected, 71 showed strong autofluorescence signal and were correctly identified (95% accuracy) by the imager. Conclusions: The hANDY-I prototype demonstrated promising results in this feasibility study by aiding in real-time visualization of the parathyroid glands. However, further testing by conducting randomized clinical trials with a bigger sample size is required to study the effect on levels of hypoparathyroidism and hypocalcemia.

Integrative analysis of scRNA-seq and scATAC-seq revealed transit-amplifying thymic epithelial cells expressing autoimmune regulator.

Medullary thymic epithelial cells (mTECs) are critical for self-tolerance induction in T cells via promiscuous expression of tissue-specific antigens (TSAs), which are controlled by the transcriptional regulator, AIRE. Whereas AIRE-expressing (Aire+) mTECs undergo constant turnover in the adult thymus, mechanisms underlying differentiation of postnatal mTECs remain to be discovered. Integrative analysis of single-cell assays for transposase-accessible chromatin (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) suggested the presence of proliferating mTECs with a specific chromatin structure, which express high levels of Aire and co-stimulatory molecules, CD80 (Aire+CD80hi). Proliferating Aire+CD80hi mTECs detected using Fucci technology express a minimal number of Aire-dependent TSAs and are converted into quiescent Aire+CD80hi mTECs expressing high levels of TSAs after a transit amplification. These data provide evidence for the existence of transit-amplifying Aire+mTEC precursors during the Aire+mTEC differentiation process of the postnatal thymus.

Determination of Acyl-, O-, and N-Glucuronide Using Chemical Derivatization Coupled with Liquid Chromatography-High-Resolution Mass Spectrometry.

Glucuronidation is the most common phase II metabolic pathway to eliminate small molecule drugs from the body. However, determination of glucuronide structure is quite challenging by mass spectrometry due to its inability to generate structure-informative fragments about the site of glucuronidation. In this article, we describe a simple method to differentiate acyl-, O-, and N-glucuronides using chemical derivatization. The idea is that derivatization of acyl-, O-, or N-glucuronides of a molecule results in predictable and different numbers of derivatized functional groups, which can be determined by the mass shift using mass spectrometry. The following two reactions were applied to specifically derivatize carboxyl and hydroxyl groups that are present on the aglycone and its glucuronide metabolite: Carboxyl groups were activated by thionyl chloride followed by esterification with ethanol. Hydroxyl groups were derivatized via silylation by 1-(trimethylsilyl)imidazole. The mass shift per derivatized carboxyl and hydroxyl group was +28.031 Da and +72.040 Da, respectively. This approach was successfully validated using commercial glucuronide standards, including benazepril acyl-glucuronides, raloxifene O-glucuronide, and silodosin O-glucuronide. In addition, this approach was applied to determine the type of glucuronide metabolites that were isolated from liver microsomal incubation, where alvimopan and diclofenac acyl-glucuronides; darunavir, haloperidol, and propranolol O-glucuronides; and darunavir N-glucuronide were identified. Lastly, this approach was successfully used to elucidate the definitive structure of a clinically observed metabolite, soticlestat O-glucuronide. In conclusion, a novel, efficient, and cost-effective approach was developed to determine acyl-, O-, and N-glucuronides using chemical derivatization coupled with liquid chromatography-high resolution mass spectrometry. SIGNIFICANCE STATEMENT: The method described in this study can differentiate acyl-, O-, and N-glucuronides and allow for elucidation of glucuronide structures when multiple glucuronidation possibilities exist. The type of glucuronidation information is particularly useful for a drug candidate containing carboxyl groups, which can form reactive acyl-glucuronides. Additionally, the method can potentially be used for definitive structure elucidation for a glucuronide with its aglycone containing a single carboxyl, hydroxyl, or amino group even when multiple types of functional groups are present for glucuronidation.

A coaxial excitation, dual-red-green-blue/near-infrared paired imaging system toward computer-aided detection of parathyroid glands in situ and ex vivo.

Early and precise detection of parathyroid glands (PGs) is a challenging problem in thyroidectomy due to their small size and similar appearance to surrounding tissues. Near-infrared autofluorescence (NIRAF) has stimulated interest as a method to localize PGs. However, high incidence of false positives for PGs has been reported with this technique. We introduce a prototype equipped with a coaxial excitation light (785 nm) and a dual-sensor to address the issue of false positives with the NIRAF technique. We test the clinical feasibility of our prototype in situ and ex vivo using sterile drapes on 10 human subjects. Video data (1287 images) of detected PGs were collected to train, validate and compare the performance for PG detection. We achieved a mean average precision of 94.7% and a 19.5-millisecond processing time/detection. This feasibility study supports the effectiveness of the optical design and may open new doors for a deep learning-based PG detection method.

A pilot feasibility study to assess vascularity and perfusion of parathyroid glands using a portable hand-held imager.

OBJECTIVES: Intraoperative localization and preservation of parathyroid glands (PGs) are challenging during thyroid surgery. A new noninvasive technique of combined near-infrared PG autofluorescence detection and dye-free imaging angiography that allows intraoperative feedback has recently been introduced. The objective of this study was to evaluate this technique in real-time. MATERIALS AND METHODS: A pilot feasibility study of a portable imaging device in four patients who underwent either thyroid lobectomy or total thyroidectomy is presented. PG autofluorescence and vascularity/tissue perfusion were monitored using a real-time screen display during the surgical procedure. RESULTS: Three lobectomies and one total thyroidectomy were performed. Among the nine PGs identified by the operating surgeon, eight PGs were confirmed using the autofluorescence device. Each PG was successfully determined to be either well-perfused or devascularized, and devascularized PGs were autotransplanted. CONCLUSIONS: The preliminary results suggest that the combination of PG autofluorescence detection and dye-free angiography can potentially be used to assess PG function. With further validation studies, the effectiveness of this technique in clinical practice can be further delineated.

Laparoscopic cholecystectomy in a swine model using a novel near-infrared fluorescent IV dye (BL-760).

BACKGROUND AND OBJECTIVES: Bile duct injury during laparoscopic cholecystectomy has an incidence rate of 1%-2% and commonly appears under conditions of severe inflammation, adhesion, or unexpected anatomical variations. Despite the difficulties and rising concerns of identifying bile duct during surgeries, surgeons do not have a specific modality to identify bile duct except intraoperative cholangiography. While no biliary-specific fluorescent dye exists for clinical use, our team has previously described the development of a preclinical biliary-specific dye, BL-760. Here, we present our study of laparoscopic cholecystectomy using the fluorescent dye in a swine model. STUDY DESIGN/MATERIALS AND METHODS: With an approval from Institutional Animal Care and Use Committee, two 20-25 kg swine underwent laparoscopic abdominal surgery using a Food and Drug Administration-cleared fluorescent laparoscopic system. Images of the liver and gallbladder were taken both before and after intravenous injection of the novel fluorescent dye. The dye was dosed at 60 µg/kg and injected via the ear vein. The amount of time taken to visualize fluorescence in the biliary tract was measured. Fluorescent signal was observed after injection, and target-to-background ratio (TBR) of the biliary tract to surrounding cystic artery and liver parenchyma was measured. RESULTS: Biliary tract visualization under fluorescent laparoscopy was achieved within 5 min after the dye injection without any adverse effects. Cystic duct and extrahepatic duct were clearly visualized and identified with TBR values of 2.19 and 2.32, respectively, whereas no fluorescent signal was detected in liver. Cystic duct and artery were successfully ligated by an endoscopic clip applier with the visual assistance of highlighted biliary tract images. Laparoscopic cholecystectomy was completed within 30 min in each case without any complications. CONCLUSIONS: BL-760 is a novel preclinical fluorescent dye useful for intraoperative identification and visualization of biliary tract. Such fluorescent dye that is exclusively metabolized by liver and rapidly excreted into biliary tract would be beneficial for all types of hepato-biliary surgeries. With the validation of additional preclinical data, this novel dye has potential to be a valuable tool to prevent any iatrogenic biliary injuries and/or bile leaks during laparoscopic abdominal and liver surgeries.

Development of a non-invasive, dual-sensor handheld imager for intraoperative preservation of parathyroid glands.

Intraoperative localization and preservation of parathyroid glands (PTGs) are challenging during thyroid surgery. Using a technique of combined near-infrared PTG autofluorescence detection and dye-free imaging angiography, this study developed a portable device for localization of PTGs and assessment of viability by confirming tissue perfusion. The imager's performance was evaluated through a pilot clinical study (N=10).

Monitoring Bacterial Translation Rates Genome-Wide.

Modern DNA sequencing technologies have allowed for the sequencing of tens of thousands of bacterial genomes. While this explosion of information has brought about new insights into the diversity of the prokaryotic world, much less is known of the identity of proteins encoded within these genomes, as well as their rates of production. The advent of ribosome profiling, or the deep sequencing of ribosome-protected footprints, has recently enabled the systematic evaluation of every protein-coding region in a given experimental condition, the rates of protein production for each gene, and the variability in translation rates across each message. Here, I provide an update to the bacterial ribosome profiling approach, with a particular emphasis on a simplified strategy to reduce cloning time.

Gene expression and cell identity controlled by anaphase-promoting complex.

Metazoan development requires the robust proliferation of progenitor cells, the identities of which are established by tightly controlled transcriptional networks1. As gene expression is globally inhibited during mitosis, the transcriptional programs that define cell identity must be restarted in each cell cycle2-5 but how this is accomplished is poorly understood. Here we identify a ubiquitin-dependent mechanism that integrates gene expression with cell division to preserve cell identity. We found that WDR5 and TBP, which bind active interphase promoters6,7, recruit the anaphase-promoting complex (APC/C) to specific transcription start sites during mitosis. This allows APC/C to decorate histones with ubiquitin chains branched at Lys11 and Lys48 (K11/K48-branched ubiquitin chains) that recruit p97 (also known as VCP) and the proteasome, which ensures the rapid expression of pluripotency genes in the next cell cycle. Mitotic exit and the re-initiation of transcription are thus controlled by a single regulator (APC/C), which provides a robust mechanism for maintaining cell identity throughout cell division.

Super-Strong Carbon Nanotube Fibers Achieved by Engineering Gas Flow and Postsynthesis Treatment.

Carbon nanotube fibers (CNTFs) are directly spun from a floating-catalyst chemical vapor deposition apparatus using gas-phase carbon and an iron nanocatalyst. The essential synthesis and post-treatment factors that affect the strength of CNTFs are investigated to obtain CNTFs with greater strength than those of any previously reported high-performance fibers. The key factors optimized included the degree of rotational flow inside the reactor, the ratio of the starting materials, and the postsynthesis treatment conditions. The formation of rotational gas flow inside the reactor was confirmed by computational fluid dynamics simulations, and the feed ratio of the starting materials was optimized through response surface methodology. In addition, a reproducible and highly efficient postsynthesis treatment method was established. Pristine CNTFs with a high specific strength (SS) (average 2.2 N/tex, max. 2.3 N/tex) were synthesized through decreased rotational flow and optimization of the CNTF synthesis conditions. To improve the SS of the CNTFs further, we adopted an acid wet-stretching method that included washing and heat treatment. This drastically increased the SS of the CNTFs (average 5.5 N/tex, max. 6.4 N/tex) because of the decrease in the volume of the pores between the CNT bundles.

Identifying alcohol problems among suicide attempters visiting the emergency department.

BACKGROUND: Many suicide attempters brought to our emergency department (ED) have been found to have alcohol problems, and this should be taken serious consideration because alcohol use disorder is a risk factor for suicide reattempt. In this study, we aimed to estimate the effectiveness of alcohol-related biochemical markers and Alcohol Use Disorder Identification Test Consumption (AUDIT-C) in suicide attempters who visited our ED based on the gold standard for clinical diagnosis used by psychiatrists for alcohol use disorder. Moreover, we aimed to search for a significant standard when clinicians make correct predictions about alcohol use disorder using these markers. METHODS: Among the subjects who visited ED following a suicide attempt, a total of 203 subjects were selected. Following a psychiatric interview, the subjects who met the criteria for alcohol abuse or alcohol dependence according to DSM-IV-TR in the past year were defined as the "alcohol use disorder" group. Although some subjects did not meet these criteria, men with a weekly alcohol intake of ≥14 drinks and women with a weekly alcohol intake of ≥7 drinks were classified as the "risky drinking" group. AUDIT-C was used as a self-report; further, aspartate aminotransferase, gamma-glutamyltransferase (GGT), and carbohydrate-deficient transferrin (CDT) were assayed using standard methods, and GGT-CDT was calculated using this formula: 0.8 × ln(GGT) + 1.3 × ln(%CDT). RESULTS: In total, 88 subjects met the criteria for alcohol use disorder and 115 were included in the reference group. In the screening for alcohol use disorder, the AUC of AUDIT-C was 0.89 for men and 0.87 for women. In the screening for risky drinking, the AUC of AUDIT-C was 0.99 for men and 0.93 for women. Compared with other biochemical markers, AUDIT-C showed the highest AUC value for screening for both alcohol use disorder and risky drinking, with the trend being more prominent in men. CONCLUSIONS: Among the biochemical markers, AUDIT-C yielded the highest sensitivity, specificity, and accuracy in diagnosing alcohol use disorder among suicide attempters in ED. Comparison of results revealed that the use of AUDIT-C with biochemical markers or its use alone can help screen for alcohol use disorder or risky drinking in clinical settings.

Noncoding dsRNA induces retinoic acid synthesis to stimulate hair follicle regeneration via TLR3.

How developmental programs reactivate in regeneration is a fundamental question in biology. We addressed this question through the study of Wound Induced Hair follicle Neogenesis (WIHN), an adult organogenesis model where stem cells regenerate de novo hair follicles following deep wounding. The exact mechanism is uncertain. Here we show that self-noncoding dsRNA activates the anti-viral receptor toll like receptor 3 (TLR3) to induce intrinsic retinoic acid (RA) synthesis in a pattern that predicts new hair follicle formation after wounding in mice. Additionally, in humans, rejuvenation lasers induce gene expression signatures for dsRNA and RA, with measurable increases in intrinsic RA synthesis. These results demonstrate a potent stimulus for RA synthesis by non-coding dsRNA, relevant to their broad functions in development and immunity.

Principles of Ubiquitin-Dependent Signaling.

Ubiquitylation is an essential posttranslational modification that controls cell division, differentiation, and survival in all eukaryotes. By combining multiple E3 ligases (writers), ubiquitin-binding effectors (readers), and de-ubiquitylases (erasers) with functionally distinct ubiquitylation tags, the ubiquitin system constitutes a powerful signaling network that is employed in similar ways from yeast to humans. Here, we discuss conserved principles of ubiquitin-dependent signaling that illustrate how this posttranslational modification shapes intracellular signaling networks to establish robust development and homeostasis throughout the eukaryotic kingdom.

Real-time, label-free, intraoperative visualization of peripheral nerves and micro-vasculatures using multimodal optical imaging techniques.

Accurate, real-time identification and display of critical anatomic structures, such as the nerve and vasculature structures, are critical for reducing complications and improving surgical outcomes. Human vision is frequently limited in clearly distinguishing and contrasting these structures. We present a novel imaging system, which enables noninvasive visualization of critical anatomic structures during surgical dissection. Peripheral nerves are visualized by a snapshot polarimetry that calculates the anisotropic optical properties. Vascular structures, both venous and arterial, are identified and monitored in real-time using a near-infrared laser-speckle-contrast imaging. We evaluate the system by performing in vivo animal studies with qualitative comparison by contrast-agent-aided fluorescence imaging.

Crowdsourcing as a Novel Method to Evaluate Aesthetic Outcomes of Treatment for Unilateral Cleft Lip.

BACKGROUND: Lack of convenient and reliable methods to grade aesthetic outcomes limits the ability to study results and optimize treatment of unilateral cleft lip. Crowdsourcing methods solicit contributions from a large group to achieve a greater task. The authors hypothesized that crowdsourcing could be used to reliably grade aesthetic outcomes of unilateral cleft lip. METHODS: Fifty deidentified photographs of 8- to 10-year-old subjects (46 with unilateral cleft lip and four controls) were assembled. Outcomes were assessed using multiple pairwise comparisons that produced a rank order (Elo rank) of nasal appearance and, on a separate survey, by Asher-McDade ratings. Both surveys were repeated to assess reliability. A group of expert surgeons repeated the same tasks on a smaller subset of photographs. RESULTS: The authors obtained 2500 and 1900 anonymous, layperson evaluations by means of crowdsourcing on each Elo rank and Asher-McDade survey, respectively. Elo rank and Asher-McDade scores were highly reproducible (correlation coefficients, 0.87 and 0.98), and crowd evaluations agreed with those by expert surgeons (0.980 and 0.96 for Elo rank and Asher-McDade score, respectively). Crowdsourcing surveys were completed within 9 hours, whereas the expert surgeons required 3 months. On further analysis of their cleft subject sample set, the authors found that greater initial cleft severity was associated with worse aesthetic outcome. CONCLUSIONS: Outcomes assessed by crowds were reliable and correlated well with expert assessments. Crowdsourcing allows acquisition of massive numbers of layperson assessments on an unprecedented scale, and is a convenient, rapid, and reliable means of assessing aesthetic outcome of treatment for unilateral cleft lip. CLINICAL QUESTION/LEVEL OF EVIDENCE: Diagnostic, IV.