DNA polymerase θ-mediated repair of high LET radiation-induced complex DNA double-strand breaks.

DNA polymerase θ (POLQ) is a unique DNA polymerase that is able to perform microhomology-mediated end-joining as well as translesion synthesis (TLS) across an abasic (AP) site and thymine glycol (Tg). However, the biological significance of the TLS activity is currently unknown. Herein we provide evidence that the TLS activity of POLQ plays a critical role in repairing complex DNA double-strand breaks (DSBs) induced by high linear energy transfer (LET) radiation. Radiotherapy with high LET radiation such as carbon ions leads to more deleterious biological effects than corresponding doses of low LET radiation such as X-rays. High LET-induced DSBs are considered to be complex, carrying additional DNA damage such as AP site and Tg in close proximity to the DSB sites. However, it is not clearly understood how complex DSBs are processed in mammalian cells. We demonstrated that genetic disruption of POLQ results in an increase of chromatid breaks and enhanced cellular sensitivity following treatment with high LET radiation. At the biochemical level, POLQ was able to bypass an AP site and Tg during end-joining and was able to anneal two single-stranded DNA tails when DNA lesions were located outside the microhomology. This study offers evidence that POLQ is directly involved in the repair of complex DSBs.

Phenome-wide association study of the major histocompatibility complex region in the Korean population identifies novel association signals.

Human leukocyte antigen (HLA) gene variants in the major histocompatibility complex (MHC) region are associated with numerous complex human diseases and quantitative traits. Previous phenome-wide association studies (PheWAS) for this region demonstrated that HLA association patterns to the phenome have both population-specific and population-shared components. We performed MHC PheWAS in the Korean population by analyzing associations between phenotypes and genetic variants in the MHC region using the Korea Biobank Array project data samples from the Korean Genome and Epidemiology Study cohorts. Using this single-population dataset, we curated and analyzed 82 phenotypes for 125 673 Korean individuals after imputing HLA using CookHLA, a recently developed imputation framework. More than one-third of these phenotypes showed significant associations, confirming 56 known associations and discovering 13 novel association signals that were not reported previously. In addition, we analyzed heritability explained by the variants in the MHC region and genetic correlations among phenotypes based on the MHC variants.

Robot-assisted gastric endoscopic submucosal dissection significantly improves procedure time at challenging dissection locations.

BACKGROUND: Endoscopic submucosal dissection (ESD) is the standard treatment for early malignant stomach lesions. However, this procedure is technically demanding and carries a high complication risk. The level of difficulty in performing ESD is influenced by the location of the lesion. In our study, we aimed to investigate and analyze the effectiveness of robot-assisted ESD for lesions situated in challenging locations within the stomach. METHODS: We developed a gastric simulator that could be used to implement various gastric ESD locations. An EndoGel (Sunarrow, Tokyo, Japan) was attached to the simulator for the dissection procedures. Robot-assisted or conventional ESD was performed at challenging or easy locations by two ESD-trainee endoscopists. RESULTS: The procedure time was remarkably shorter for robotic ESD than conventional dissection at challenging locations (6.2 vs. 10.2 min, P < 0.05), mainly due to faster dissection (220.3 vs. 101.9 mm2/min, P < 0.05). The blind dissection rate was significantly lower with robotic ESD than with the conventional method (17.6 vs. 35.2%, P < 0.05) at challenging locations. CONCLUSION: The procedure time was significantly shortened when robot-assisted gastric ESD procedures were performed at challenging locations. Therefore, our robotic device provides simple, effective, and safe multidirectional traction for endoscopic submucosal dissection at challenging locations, thereby reducing difficulty of the procedure.

MarcoPolo: a method to discover differentially expressed genes in single-cell RNA-seq data without depending on prior clustering.

The standard analysis pipeline for single-cell RNA-seq data consists of sequential steps initiated by clustering the cells. An innate limitation of this pipeline is that an imperfect clustering result can irreversibly affect the succeeding steps. For example, there can be cell types not well distinguished by clustering because they largely share the global structure, such as the anterior primitive streak and mid primitive streak cells. If one searches differentially expressed genes (DEGs) solely based on clustering, marker genes for distinguishing these types will be missed. Moreover, clustering depends on many parameters and can often be subjective to manual decisions. To overcome these limitations, we propose MarcoPolo, a method that identifies informative DEGs independently of prior clustering. MarcoPolo sorts out genes by evaluating if the distributions are bimodal, if similar expression patterns are observed in other genes, and if the expressing cells are proximal in a low-dimensional space. Using real datasets with FACS-purified cell labels, we demonstrate that MarcoPolo recovers marker genes better than competing methods. Notably, MarcoPolo finds key genes that can distinguish cell types that are not distinguishable by the standard clustering. MarcoPolo is built in a convenient software package that provides analysis results in an HTML file.

Impact of Chain Conformation on Structural Heterogeneity in Polymer Network.

Polymer networks generally consist of an ensemble of single chains. However, understanding how chain conformation affects the structure and properties of polymer networks remains a challenge for optimizing their functionality. Here, we present the fabrication and comparative study of a polymer network composed of collapsed self-entangled chains (intrachain entangled network) and a standard polymer network in which random-coil chains are entangled with each other (interchain entangled network). For poly(methyl methacrylate) thin films composed of these networks, we coupled solvent vapor swelling and single-molecule tracking techniques to examine the anomalies in the dynamics of a small-molecular probe included in the system. We demonstrate that when compared to the interchain entangled network the intrachain one exhibits a more substantial structural heterogeneity, particularly under highly crowded conditions. This network also exhibits physical compactness, which keeps the heterogeneous network structure frozen over time and impedes network plasticization through solvent uptake by the film.

Selective production of retinol by engineered Saccharomyces cerevisiae through the expression of retinol dehydrogenase.

Retinol is a fat-soluble vitamin A that is widely used in the food and pharmaceutical industries. Currently, retinol is commercially produced by chemical synthesis. Microbial production of retinol has been alternatively explored but restricted to a mixture of retinoids including retinol, retinal, and retinoic acid. Thus, we introduced heterologous retinol dehydrogenase into retinoids mixture-producing Saccharomyces cerevisiae for the selective production of retinol using xylose. Expression of human RDH10 and Escherichia coli ybbO led to increase in retinol production, but retinal remained as a major product. In contrast, S. cerevisiae harboring human RDH12 produced retinol selectively with negligible production of retinal. The resulting strain (SR8A-RDH12) produced retinol only. However, more glycerol was accumulated due to intracellular redox imbalance. Therefore, Lactococcus lactis noxE coding for H2 O-forming NADH oxidase was additionally introduced to resolve the redox imbalance. The resulting strain produced 52% less glycerol and more retinol with a 30% higher yield than a parental strain. As the produced retinol was not stable, we examined culture and storage conditions including temperature, light, and antioxidants for the optimal production of retinol. In conclusion, we achieved selective production of retinol efficiently from xylose by introducing human RDH12 and NADH oxidase into S. cerevisiae.

Growth and Bone Mineral Density Changes in Ovariectomized Rats Treated with Estrogen Receptor Alpha or Beta Agonists.

BACKGROUND: Estrogen controls the pubertal growth spurt, growth plate closure, and accretion of bone mineral density (BMD) of long bones after biding estrogen receptor (ER). There are two subtypes of ER, ERα and ERß. If each ER subtype has different effects, we may control those actions by manipulating the estrogen binding intensity to each ER subtype and increase the final adult height without markedly reducing BMD or impairing reproductive functions. The purpose of our study was to compare these effects of ERα and ERß on long bones in ovariectomized rats. METHODS: Thirty female rats were ovariectomized and randomly divided into 3 groups. The control, propylpyrazole triol (PPT), and 2,3-bis (4-hydroxyphenyl) propionitrile (DPN) groups were subcutaneously injected for 5 weeks with sesame oil, PPT as an ERα agonist, and DPN as an ERß agonist, respectively. The crown-lump length and body weight were measured weekly. BMD, serum levels of growth hormone (GH) and estradiol were checked before and after 5 weeks of injections. Pituitary GH1 expression levels were determined with quantitative real-time polymerase chain reaction, the proximal tibias were dissected, decalcified and stained with hematoxylin-eosin, and the thicknesses of epiphyseal plates including proliferative and hypertrophic zones were measured in 20-evenly divided sites after 5 weeks of injections. Comparisons for auxological data, serum hormone and pituitary GH1 expression levels, BMD, and epiphyseal plate thicknesses among 3 groups before and after injections were conducted. RESULTS: There was no significant difference in body lengths among 3 groups. The body weights were significantly lower, but, serum GH, pituitary GH1 expression levels, and BMDs were higher in PPT group than the other 2 groups after 5 weeks of injections. There was no significant difference in the thicknesses of the total epiphyseal plate, proliferative, and hypertrophic zone among 3 groups. CONCLUSION: ERα is more involved in pituitary GH secretion and bone mineral deposition than ERß. Weight gain might be prevented with the ERα agonist.

Correlations between Tumor to Background Ratio on Breast-Specific Gamma Imaging and Prognostic Factors in Breast Cancer.

The purpose of this study was to investigate the correlations between tumor-to-background ratio (TBR) obtained from breast-specific gamma imaging (BSGI) and the prognostic factors of breast cancer. Sixty-seven patients with invasive ductal carcinoma who underwent preoperative BSGI were enrolled. The BSGI images were visually scored from 1 to 5 according to a breast imaging reporting and data system (BIRADS). The TBR results obtained from positive BSGI images were compared according to the following prognostic factors: tumor size; axillary lymph node metastasis; nuclear grade (NG); histologic grade (HG); subtype; Ki-67; and the expression profile of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). Among 67 images, 60 were classified as a positive finding (sensitivity 89.6%). A higher TBR value was significantly correlated with tumor size ≥ 2 cm (P = 0.001), axillary lymph node metastasis (P = 0.007), high HG (P = 0.029), negative PR status (P = 0.036), and Ki-67 ≥ 14% (P = 0.007). The TBR showed a significant difference between the luminal A and non-luminal A subtypes (P = 0.007). On multivariate analysis, TBR had a high correlation with tumor size ≥ 2 cm, axillary lymph node metastasis, and negative PR status (P = 0.003, 0.048, and 0.030, respectively). A high TBR on BSGI was significantly correlated with poor prognostic factors of breast cancer. Luminal A subtype, a breast cancer subtype with more favorable prognosis, was associated with a low TBR on BSGI.

Effects of 2'-fucosyllactose on the viability of starter cultures and Bifidobacterium strains of human origin in yogurt during refrigerated storage.

2'-Fucosyllactose (2'-FL) is postulated to provide health benefits and promote the growth of probiotics. This work was undertaken to study the effects of 2'-FL on the viability of starter cultures and Bifidobacterium strains of human origin in yogurt during refrigerated storage. Yogurts were produced containing 2'-FL (0 or 2 g/L) and Bifidobacterium strains of human origin (Bifidobacterium longum subsp. longum BB536 or Bifidobacterium longum subsp. infantis ATCC 15697) at a concentration of at least 109 CFU/mL. All yogurts were stored at 4°C for 5 weeks. Results showed that 2'-FL was stable in yogurts for at least 5 weeks of cold storage, and the addition of 2'-FL did not significantly alter yogurt fermentation parameters, associated metabolites, and the viability of mixed yogurt starter cultures and Bifidobacterium strains (p > 0.05). The addition of bifidobacteria had a negative impact (p < 0.05) on the survival rate of starter cultures, Streptococcus thermophilus and Lactobacillus delbureckii subsp. bulgaricus. Meanwhile, it is difficult to maintain a high survival rate of bifidobacteria in final yogurt products, and the addition of 2'-FL could not enhance the viability of bifidobacteria. B. longum BB536 survived at a level higher than 106 CFU/g for 28 days, while B. infantis ATCC15697 maintained this level for only 7 days. In summary, this study has shown the impact of 2'-FL and bifidobacterial species on yogurt properties, and results suggest that it is promising to use 2'-FL in yogurt products as a prebiotic. PRACTICAL APPLICATION: Yogurt is known for its beneficial effects on human health and nutrition. This study reported the production of symbiotic yogurt containing bifidobacteria and 2'-fucosyllactose (2'-FL) as a functional food for specified health uses. The viability of yogurt starter cultures and probiotic bifidobacterial strains was analyzed in this study. Moreover, this research demonstrated that 2'-FL could be added to yogurt without affecting the characteristics of yogurt significantly.

Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium.

Synthetic microbial communities have emerged as an attractive route for chemical bioprocessing. They are argued to be superior to single strains through microbial division of labor (DOL), but the exact mechanism by which DOL confers advantages remains unclear. Here, we utilize a synthetic Saccharomyces cerevisiae consortium along with mathematical modeling to achieve tunable mixed sugar fermentation to overcome the limitations of single-strain fermentation. The consortium involves two strains with each specializing in glucose or xylose utilization for ethanol production. By controlling initial community composition, DOL allows fine tuning of fermentation dynamics and product generation. By altering inoculation delay, DOL provides additional programmability to parallelly regulate fermentation characteristics and product yield. Mathematical models capture observed experimental findings and further offer guidance for subsequent fermentation optimization. This study demonstrates the functional potential of DOL in bioprocessing and provides insight into the rational design of engineered ecosystems for various applications.

Self-Buffering system for Cost-Effective production of lactic acid from glucose and xylose using Acid-Tolerant Issatchenkia orientalis.

This study presents a cost-effective strategy for producing organic acids from glucose and xylose using the acid-tolerant yeast, Issatchenkia orientalis. I. orientalis was engineered to produce lactic acid from xylose, and the resulting strain, SD108XL, successfully converted sorghum hydrolysates into lactic acid. In order to enable low-pH fermentation, a self-buffering strategy, where the lactic acid generated by the SD108XL strain during fermentation served as a buffer, was developed. As a result, the SD108 strain produced 67 g/L of lactic acid from 73 g/L of glucose and 40 g/L of xylose, simulating a sugar composition of sorghum biomass hydrolysates. Moreover, techno-economic analysis underscored the efficiency of the self-buffering strategy in streamlining the downstream process, thereby reducing production costs. These results demonstrate the potential of I. orientalis as a platform strain for the cost-effective production of organic acids from cellulosic hydrolysates.

Triphenylphosphonium-functionalized dimeric BODIPY-based nanoparticles for mitochondria-targeting photodynamic therapy.

The dimerization of boron dipyrromethene (BODIPY) moieties is an appealing molecular design approach for developing heavy-atom-free triplet photosensitizers (PSs). However, BODIPY dimer-based PSs generally lack target specificity, which limits their clinical use for photodynamic therapy. This study reports the synthesis of two mitochondria-targeting triphenylphosphonium (TPP)-functionalized meso-ß directly linked BODIPY dimers (BTPP and BeTPP). Both BODIPY dimers exhibited solvent-polarity-dependent singlet oxygen (1O2) quantum yields, with maximum values of 0.84 and 0.55 for BTPP and BeTPP, respectively, in tetrahydrofuran. The compact orthogonal geometry of the BODIPY dimers facilitated the generation of triplet excited states via photoinduced charge separation (CS) and subsequent spin-orbit charge-transfer intersystem crossing (SOCT-ISC) processes and their rates were dependent on the energetic configuration between the frontier molecular orbitals of the two BODIPY subunits. The as-synthesized compounds were amphiphilic and hence formed stable nanoparticles (∼36 nm in diameter) in aqueous solutions, with a zeta potential of ∼33 mV beneficial for mitochondrial targeting. In vitro experiments with MCF-7 and HeLa cancer cells indicated the effective localization of BTPP and BeTPP within cancer-cell mitochondria. Under light irradiation, BTPP and BeTPP exhibited robust photo-induced therapeutic effects in both cell lines, with half-maximal inhibitory concentration (IC50) values of ∼30 and ∼55 nM, respectively.

Transparent medical image AI via an image-text foundation model grounded in medical literature.

Building trustworthy and transparent image-based medical artificial intelligence (AI) systems requires the ability to interrogate data and models at all stages of the development pipeline, from training models to post-deployment monitoring. Ideally, the data and associated AI systems could be described using terms already familiar to physicians, but this requires medical datasets densely annotated with semantically meaningful concepts. In the present study, we present a foundation model approach, named MONET (medical concept retriever), which learns how to connect medical images with text and densely scores images on concept presence to enable important tasks in medical AI development and deployment such as data auditing, model auditing and model interpretation. Dermatology provides a demanding use case for the versatility of MONET, due to the heterogeneity in diseases, skin tones and imaging modalities. We trained MONET based on 105,550 dermatological images paired with natural language descriptions from a large collection of medical literature. MONET can accurately annotate concepts across dermatology images as verified by board-certified dermatologists, competitively with supervised models built on previously concept-annotated dermatology datasets of clinical images. We demonstrate how MONET enables AI transparency across the entire AI system development pipeline, from building inherently interpretable models to dataset and model auditing, including a case study dissecting the results of an AI clinical trial.

Red fluorescent BODIPY-based nanoparticles for targeted cancer imaging-guided photodynamic therapy.

Imaging-guided diagnosis and treatment of cancer hold potential to significantly improve therapeutic accuracies and efficacies. Central to this theragnostic approach has been the use of multicomponent-based multimodal nanoparticles (NPs). Apart from this conventional approach, here we propose a design strategy for the simple and straightforward formulation of NPs based on boron dipyrromethene (BODIPY) derivatives, LaB-X (X = H, Et, and Br). Specifically, the conjugation of lactose to the inherently hydrophobic BODIPY promoted the formation of LaB-X NPs in water. Furthermore, the BODIPY backbone was subjected to distyrylation, dibromination, and diethylation to tailor the optical window and the balance between fluorescence and singlet oxygen generation capabilities. We demonstrate that while the photoinduced anticancer activities of LaB-H and LaB-Et NPs were trivial, LaB-Br NPs effectively induced the apoptotic death of hepatocellular carcinoma cells under red light irradiation while allowing fluorescence cell imaging in the phototherapeutic window. This dual fluorescence photosensitizing activity of LaB-Br NPs could be switched off and on, so that both fluorescence and singlet oxygen generation were paused during NP formation in an aqueous solution, while both processes resumed after cellular uptake, likely due to NP disassembly.

A Novel Retractable Robotic Device for Colorectal Endoscopic Submucosal Dissection.

Background/Aims: : Appropriate tissue tension and clear visibility of the dissection area using traction are essential for effective and safe endoscopic submucosal dissection (ESD). In this study, we developed a retractable robot-assisted traction device and evaluated its performance in colorectal ESD. Methods: : An experienced endoscopist performed ESD 18 times on an ex vivo porcine colon using the robot and 18 times using the conventional method. The outcome measures were procedure time, dissection speed, procedure-related adverse events, and blind dissection rate. Results: : Thirty-six colonic lesions were resected from ex vivo porcine colon samples. The total procedure time was significantly shorter in robot-assisted ESD (RESD) than in conventional ESD (CESD) (20.1±4.1 minutes vs 34.3±8.3 minutes, p<0.05). The submucosal dissection speed was significantly faster in the RESD group than in the CESD group (36.8±9.2 mm2/min vs 18.1±4.7 mm2/min, p<0.05). The blind dissection rate was also significantly lower in the RESD group (12.8%±3.4% vs 35.1%±3.9%, p<0.05). In an in vivo porcine feasibility study, the robotic device was attached to a colonoscope and successfully inserted into the proximal colon without damaging the colonic wall, and ESD was successfully performed. Conclusions: : The dissection speed and safety profile improved significantly with the retractable RESD. Thus, our robotic device has the potential to provide simple, effective, and safe multidirectional traction during colonic ESD.

Malignant Transformation of Warthin Tumor in the Cervical Lymph Node.

ABSTRACT: Warthin tumor is the second most common benign tumor of salivary glands. Here we present an interesting case of squamous cell carcinoma arising from the Warthin tumor in the cervical lymph node. The patient had another Warthin tumor in the parotid gland as well. Both the malignant transformation of Warthin tumor and the heterotopic occurrence of Warthin tumor in the cervical lymph node are rare. This exceptionally rare case demonstrates that the 2 rare clinical entities can occur simultaneously and affect clinical decisions.

Concurrent FDG-Avid and Non-FDG-Avid Pleomorphic Adenomas in the Submandibular Gland and Parapharyngeal Space.

ABSTRACT: Pleomorphic adenoma is the most common benign tumor of salivary glands. Here we present an interesting case of concurrent pleomorphic adenomas in the parapharyngeal space and submandibular gland. The tumors showed stark differences in the imaging findings on FDG PET/CT and MRI. Pathology confirmed the diagnosis of pleomorphic adenomas with the different composition of the cellular component and chondromyxoid stroma. This case suggests that the difference in cellularity of pleomorphic adenomas can affect FDG uptake and diffusion-weighted MRI-derived apparent diffusion coefficient values.

Fostering transparent medical image AI via an image-text foundation model grounded in medical literature.

Building trustworthy and transparent image-based medical AI systems requires the ability to interrogate data and models at all stages of the development pipeline: from training models to post-deployment monitoring. Ideally, the data and associated AI systems could be described using terms already familiar to physicians, but this requires medical datasets densely annotated with semantically meaningful concepts. Here, we present a foundation model approach, named MONET (Medical cONcept rETriever), which learns how to connect medical images with text and generates dense concept annotations to enable tasks in AI transparency from model auditing to model interpretation. Dermatology provides a demanding use case for the versatility of MONET, due to the heterogeneity in diseases, skin tones, and imaging modalities. We trained MONET on the basis of 105,550 dermatological images paired with natural language descriptions from a large collection of medical literature. MONET can accurately annotate concepts across dermatology images as verified by board-certified dermatologists, outperforming supervised models built on previously concept-annotated dermatology datasets. We demonstrate how MONET enables AI transparency across the entire AI development pipeline from dataset auditing to model auditing to building inherently interpretable models.